UKPMC:_a_full_text_article_resource_for_th.pdf.

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<article>
  <front>
    <journal-meta />
    <article-meta>
      <title-group>
        <article-title>UKPMC: a full text article resource for the life sciences</article-title>
      </title-group>
      <article-id pub-id-type="doi">10.1093/nar/gkq1063</article-id>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Johanna R. McEntyre</string-name>
          <email>mcentyre@ebi.ac.uk</email>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Sophia Ananiadou</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Stephen Andrews</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>William J. Black</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Richard Boulderstone</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Paula Buttery</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>David Chaplin</string-name>
          <xref ref-type="aff" rid="4">4</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Sandeepreddy Chevuru</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Norman Cobley</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Lee-Ann Coleman</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Paul Davey</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Bharti Gupta</string-name>
          <xref ref-type="aff" rid="4">4</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Lesley Haji-Gholam</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Craig Hawkins</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Alan Horne</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Simon J. Hubbard</string-name>
          <xref ref-type="aff" rid="3">3</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jee-Hyub Kim</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Ian Lewin</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Vic Lyte</string-name>
          <xref ref-type="aff" rid="4">4</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Ross MacIntyre</string-name>
          <xref ref-type="aff" rid="4">4</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Sami Mansoor</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Linda Mason</string-name>
          <xref ref-type="aff" rid="4">4</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>John McNaught</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Elizabeth Newbold</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Chikashi Nobata</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Ernest Ong</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Sharmila Pillai</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Dietrich Rebholz-Schuhmann</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Heather Rosie</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Rob Rowbotham</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>C. J. Rupp</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Peter Stoehr</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Philip Vaughan</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <aff id="0">
          <label>0</label>
          <institution>The British Library</institution>
          ,
          <addr-line>96 Euston Road, London, NW1 2DB</addr-line>
        </aff>
        <aff id="1">
          <label>1</label>
          <institution>National Centre for Text Mining, School of Computer Science, University of Manchester</institution>
          ,
          <addr-line>131 Princess Street, Manchester, M1 7DN</addr-line>
        </aff>
        <aff id="2">
          <label>2</label>
          <institution>EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus</institution>
          ,
          <addr-line>Hinxton, Cambridge, CB10 1SD</addr-line>
        </aff>
        <aff id="3">
          <label>3</label>
          <institution>Faculty of Life Sciences, University of Manchester</institution>
          ,
          <addr-line>M13 9PT</addr-line>
          ,
          <country country="UK">UK</country>
        </aff>
        <aff id="4">
          <label>4</label>
          <institution>Mimas</institution>
          ,
          <addr-line>Roscoe Building</addr-line>
          ,
          <institution>The University of Manchester</institution>
          ,
          <addr-line>Oxford Road, Manchester, M13 9PL</addr-line>
        </aff>
      </contrib-group>
      <abstract>
        <p>historical context and future directions, 10 years on from when PMC was first launched.</p>
      </abstract>
      <volume>39</volume>
      <pub-date>
        <year>2007</year>
      </pub-date>
      <history>
        <date date-type="accepted">
          <day>13</day>
          <month>10</month>
          <year>2010</year>
        </date>
        <date date-type="received">
          <day>29</day>
          <month>9</month>
          <year>2010</year>
        </date>
        <date date-type="revised">
          <day>12</day>
          <month>10</month>
          <year>2010</year>
        </date>
      </history>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>BACKGROUND</title>
      <p>
        UK PubMed Central (UKPMC) is a free digital
repository of biomedical and life sciences journal literature
(http://ukpmc.ac.uk). It is based on PubMed Central
(PMC), developed at the NCBI in the USA (
        <xref ref-type="bibr" rid="1">1</xref>
        ) and is
part of a network of PMC International (PMCI)
repositories that now also includes PMC Canada.
      </p>
      <p>
        In 2006, the Wellcome Trust announced that research
papers that had been funded by them must be made freely
available via UKPMC no later than 6 months after
publication (
        <xref ref-type="bibr" rid="2">2</xref>
        ). Working with other major funders of UK
biomedical research, UKPMC was launched in January 2007
as a mirror of PMC (Figure 1). The funding agencies that
support UKPMC are: Arthritis Research UK, BBSRC,
British Heart Foundation, Cancer Research UK, Chief
Scientist Office (Scotland), the MRC, National Institute
for Health Research and the Wellcome Trust. Each of
these funding bodies have a public access policy that
states how publications arising from the research they
fund have to be made publicly available in UKPMC. A
list of websites listing each organizations? public access
policy can be seen here: http://ukpmc.ac.uk/Funders.
      </p>
      <p>The mission of UKPMC is to become the information
resource of choice for the UK?s life science and health
research communities. To this end, it supports UK
researchers in article deposition and grant reporting and
provides access to the articles based on publicly funded
research through a comprehensive electronic archive of
the peer-reviewed literature relevant to the life sciences.
The partner organizations charged with these tasks for
UKPMC are the University of Manchester [Mimas and
the National Centre for Text Mining (NaCTeM)], the
European Bioinformatics Institute (EBI) and the British
Library.</p>
      <p>Since inception, UKPMC has developed tools for both
researchers and funders that meet the specific
requirements of the UK research community; these will be
described later in this article. In terms of the archive
itself, UKPMC is a ?mirror? of PMC USA, hosting the
same content (with a few exceptions, see below),
transferred daily from PMC in the USA to the PMCI
nodes in the UK and Canada. Until recently, the article
search and browse mechanisms used at all three sites were
identical, supported by the software distributed as a
component of the PMCI package. However, in January 2010,
UKPMC launched a new interface that introduces novel
features for navigating and searching the content. These
include, for example, the ability to search biomedical
abstracts and full-text articles from the same search box,
the provision of different subsets of records such as
patents and theses and the incorporation of citation data
and text-mining-based applications. The new website and
the related developments specific to UKPMC are the focus
of this article; however we will set these developments
within the broader context of PMCI (Figure 2).</p>
    </sec>
    <sec id="2">
      <title>THE RELATIONSHIP BETWEEN UKPMC AND PMC</title>
      <p>
        PMCI is a collaborative effort between the NCBI
(National Library of Medicine, National Institutes of
Health, USA), PMCI nodes (UKPMC and PMC
Canada) and the publishers whose journal content is
archived in PMC. The vision of PMCI is to create a
network of digital archives that share content in a
manner analogous to the International Nucleotide
Sequence Database Collaboration (GenBank/EMBL/
DDBJ) model for data archiving and exchange across
the globe (
        <xref ref-type="bibr" rid="5 4">3?5</xref>
        ). In this model, repositories in the network
accept deposition of content locally, which is then
distributed to the other repositories on a daily basis, as
appropriate. This has the advantage of maintaining data
integrity and the viability of the archive through
replication across several different global sites. Furthermore, the
ability for all sites to ingest content engages the local user
community and allows location-specific requirements to
be addressed. This model also encourages innovation:
using the same base set of data, novel access methods or
uses of the data can be developed.
      </p>
      <p>To date, all the content in UKPMC is routed via PMC,
even manuscripts submitted locally via the UKPMC
Manuscript Submission System (see below). Once added
to PMC, new content is pushed to UKPMC daily, from
where articles are displayed using the PMCI software
supplied as a bundle with the PMC database. Using the
same rendering engine to display articles ensures that
article content is faithfully displayed at all sites, having
undergone rigorous quality assurance and sign-off by a
combination of PMC in-house staff, authors and/or the
publishers that supplied the article. Therefore if you
compare the same article displayed in both PMC and
UKPMC, the websites look different and offer different
functionality, but the core of the article is exactly the
same.</p>
    </sec>
    <sec id="3">
      <title>CONTENT GROWTH</title>
      <p>
        When PubMed Central was first launched in 2000 (
        <xref ref-type="bibr" rid="1">1</xref>
        ), it
was with a nucleus of only a few participating journals
such as the ?Proceedings of the National Academy of
Sciences USA? and ?Molecular Biology of the Cell?. Over
the past 10 years, these few pioneers have grown to a list
of over 2000 titles whose content is represented in the
archive. At the time of writing, there are over two
million articles available in PMC, about 1.8 million of
which are distributed to UKPMC and PMC Canada.
      </p>
      <sec id="3-1">
        <title>How does content get into UKPMC?</title>
        <p>
          With the growing content base there has been an increased
variety of ways in which content gets deposited. These are
described below:
(
          <xref ref-type="bibr" rid="1">1</xref>
          ) The journal makes 100% of its content available in
the archive
. at the time of publication; these are usually Open
        </p>
        <p>Access journals, but not always.
. with a specified time delay after the publication
date. The time delay is stipulated by the publisher
and does not necessarily coincide with the time
delay specified by funder public access policies.</p>
        <p>
          These are usually Free Access articles.
(
          <xref ref-type="bibr" rid="2">2</xref>
          ) The journal deposits content on an article-by-article
basis
. because an author has chosen an open access track
publishing option, (for example as a result of a
funder?s requirement for public access); Open
Access tracks are now offered by a number of
journals.
. the journal has agreed to deposit?for no fee?the
final published article on behalf of an author
funded by one of the UKPMC funders, NIH or
HHMI. In such cases, articles are typically
embargoed and are not included in the Open Access
subset.
        </p>
        <p>
          In all of the above scenarios, the journal handles the
logistics of depositing the article in PMC on behalf of
the authors.
(
          <xref ref-type="bibr" rid="3">3</xref>
          ) The final, accepted manuscript (not the published
PDF) of an article is deposited via the Manuscript
Submission System by the author (?self-archiving?).
This occurs when a researcher has to deposit an
article as a condition of being funded by an agency
with a public access policy and the journal agrees to
that requirement, but the journal does not have an
in-house publication option to deposit the article on
the author?s behalf.
(
          <xref ref-type="bibr" rid="4">4</xref>
          ) The article is available as a part of the PMC Back
Issue Digitization Project. In this project, journals
that joined PMC prior to 2008 had the opportunity
to have back-copy paper-based content scanned. This
was a joint project between NLM, the Wellcome
Trust and the UK Joint Information Systems
Committee (JISC) and has resulted in 1.2 million
articles in the archive, although some of these are not
available in UKPMC.
        </p>
      </sec>
      <sec id="3-2">
        <title>Are all the articles in UKPMC open access?</title>
        <p>All of the articles in UKPMC are ?Free Access? which
means that they are free for anyone to search, view, read
and download in PDF form, if available. However these
articles are still protected by publisher copyright and
cannot be reused in any way for research (e.g. text
mining) or commercial purposes without the explicit
permission of the copyright holder. For these reasons,
UKPMC content cannot be redistributed and the
display of articles is tightly regulated.</p>
        <p>About 10% (over 190 000) of all the articles are ?Open
Access?, which means that they can be used in any way
(e.g. for text mining) as long as the original authors and
journal source are acknowledged (Figure 3). (Although,
some open access licenses contain some restriction, for
example to non-commercial use). These articles,
complete with associated graphics files, are available for
FTP download from here: http://www.ncbi.nlm.nih.gov/
pmc/about/ftp.html</p>
        <p>An XML files-only download of Open Access articles
is also available from here: http://ukpmc.ac.uk/ftp/oa</p>
      </sec>
      <sec id="3-3">
        <title>Differences between PMC and UKPMC content</title>
        <p>As described earlier, not all content available in PMC is
made available to UKPMC and PMC Canada (Figure 3).
Since July 2006, all PMC Participation Agreements have
included permission to make a participating journal?s
PMC content available at UKPMC and since June 2009,
to PMC Canada also. However, while most publishers
participating in PMC prior to July 2006 agreed to
deposit their content in UKPMC, some did not. This
means that some 250 000 articles are not part of the PMCI
Agreement, the vast majority of which, about 190 000, are
articles from the Back Issue Digitization Project. Content
not currently available in UKPMC is listed here: http://
ukpmc.ac.uk/ppmc-localhtml/not_in_ukpmc.html</p>
      </sec>
    </sec>
    <sec id="4">
      <title>THE UKPMC WEBSITE AND SERVICES</title>
      <p>The partner organizations responsible for UKPMC
hosting and development are the University of
Manchester (Mimas and NaCTeM), the EBI and the
British Library. In close collaboration with the NCBI,
these partners have developed the website, the search
and retrieval system, integrated text-mining-based
features, manuscript submission and grant reporting
tools. All these tools and features are available from:
http://ukpmc.ac.uk.</p>
      <p>The UKPMC archive is supplemented by the
CiteXplore citations database (http://www.ebi.ac.uk/
citexplore) and both can be searched directly from the
homepage. Further links to UKPMC+ (manuscript
submission and grant reporting), FAQs and information
about the project are also provided.</p>
      <sec id="4-1">
        <title>User-centered development</title>
        <p>To inform the development of services, UKPMC
conducted a user survey in 2008 to review user attitudes and
requirements. The feedback highlighted several key areas
where enhancements to the service were desirable:
. Improving information retrieval and knowledge
discovery through the development of text and
data-mining solutions;
. Identifying and providing access to additional
non-journal content; and
. Creating tools to enable users to track research grants
and the research papers associated with them.
The results of the survey and a follow-up workshop have
translated into some of the new developments now
available at the UKPMC website.</p>
        <p>UKPMC has undertaken a public engagement
campaign to present emerging developments to focus
groups of life science researchers, promote the use of the
service within UK Higher Education Institutions and
encourage article deposition by researchers. Along with
directives and feedback from the UKPMC Advisory Board,
these activities have been critical to ensure the continued
relevance of UKPMC to its core constituency.</p>
      </sec>
      <sec id="4-2">
        <title>Additional content available at the UKPMC website</title>
        <p>The UKPMC website enables single-point access for the
search and retrieval of both the full text content of
UKPMC and the content of CiteXplore, the citations
database developed at the EBI. CiteXplore contains
metadata only and includes all of PubMed?s 20 million
and more abstracts, around 0.5 million records from
Agricola and 3.4 million records from the European
Patent Office. Further content has also been added to
CiteXplore in response to user feedback, which requested
that other relevant non-journal content be made available.
This additional content includes over 40 000 theses and
2700 clinical guideline documents that have full-text
links, sourced from the UK National Health Service
(NHS). Furthermore, CiteXplore also contains the
metadata for about 400 000 UKPMC full text records
that are not represented in PubMed.</p>
      </sec>
      <sec id="4-3">
        <title>Using UKPMC</title>
        <p>Core search and retrieval. When a search term is typed
into the search box on the homepage, both the UKPMC
full text archive and the CiteXplore citations database are
automatically searched. The default view shows the results
found from the citations search (indicated by ?All
Citations? and the number of results in red) in publication
date order. The results from the full text UKPMC search
can be viewed by clicking on the ?Full text articles? link,
which also displays the count of results. Popular content
subsets are highlighted on the right hand side of the
page; these include, for the citations search: reviews,
clinical trials, systematic reviews, patents, theses and the
NHS clinical guideline documents mentioned previously.
Any citation for which there is full text in UKPMC is
highlighted by the UKPMC logo.</p>
        <p>All results lists can be toggled for browsing purposes;
furthermore, the default sort order of publication date can
be changed to ?relevance? sort, which is based on the
frequency of the term appearing in the document, compared
with the corpus as a whole. This relevancy ranking is a
core function of Lucene, the open source software on
which the search index is based. We have further
extended the basic Lucene query handling and logic to
incorporate:
. use of the usual terminology for Boolean (AND,</p>
        <p>NOT, OR), phrase (????) and wildcard (*) searching;
. stemming of search terms in the title, abstract and
keyword fields only;
. a query expansion function that expands your search
terms to its known synonyms in MeSH and UniProt
gene symbols (switched on by default in UKPMC
searches); and
. special handling of author name searches that gives
additional weight to terms found in the author field,
promoting them to the top of the search results
The abstract for any citation or full text article can be
viewed either by clicking ?More? at the end of each result
or by clicking on the title of the article. Clicking on an
author name or journal title will elicit searches for or
refine the current search on those entities.</p>
        <p>In a given session of searching and browsing, previous
searches and article views can be revisited using the
Recent Activity function, found on the top right of
every search page. Clicking on this icon pops up a list of
all searches and pages viewed in the past 24 h, providing a
useful overview of the navigation history across search
sessions.</p>
        <p>The Clipboard, located next to the Recent Activity,
used in conjunction with the red Clipboard icons next to
each result returned, allows the user to collect citations
and export them in the Research Information Systems
(RIS) format widely used by reference managers including
EndNote, Mendeley and ProCite. In addition to citations,
the Clipboard can also be used to collect search queries,
?Cited By? citations, text-mined biological terms
(Bioentities) and Related Articles (see below). Snapshots
of the Clipboard can be exported as HTML either to file
or email. These exported Clipboard snapshots contain a
link that enables the user to resume their previous
Clipboard session at a later date, even from a different
computer.</p>
        <p>Viewing abstracts and full text articles. Having clicked on
an article title from the search results, the complete
citation record is viewed (Figure 4). Each citation is
displayed with:
. links to the full-text article in UKPMC or on the
publisher?s website, where available;
. a Citations Tab, containing information on the
references listed in the article and a list of articles citing the
current one, along with counts, where available;
. a Bioentities Tab, containing a summary of terms
text-mined from the full text article, linked to as well
as links to databases such as UniProt, PDB and
Entrez Gene;
. Related Articles Tab, populated via NCBI eUtilties.
(These are the same related articles as seen in
PubMed.);
. a ?Highlight Terms? function on the abstract. This
function uses the same back-end processes as used to
generate the text-mined terms list in the Bioentities
Tab, with links to similar databases. The terms are
colour-coded by entity type (listed below); and
. a list of subject terms based on MeSH terms (when
available) that can be used to initiate new searches or
refine your current search. In the case of a full-text
article view, this MeSH-based list is replaced with an
abbreviated form of the text-mined terms list displayed
in the Bioentities Tab.</p>
        <p>All these features, in concert with the Clipboard and
Recent Activity facilities, offer alternative ways to
browse and search the content, providing integrated
scientific context as well as complementary means to assess
the relevance of an article for your needs.</p>
        <p>The application of text mining in UKPMC. The text-mined
terms lists located in the Bioentities Tab and the term
highlighting function in abstracts are based on the
application of text mining to the CiteXplore and UKPMC
collections, thanks to expertise supplied by the collaborative
efforts of the EBI and NaCTeM.</p>
        <p>Several broad categories of terms have been extracted
by means of Named Entity Recognition algorithms that
leverage a variety of vocabularies to identify those terms
in full text articles. At the time of writing, these are:
. genes/proteins;
. organisms;
. Gene Ontology (GO) terms;
. diseases;
. Accession numbers; and
. chemicals.</p>
        <p>The mined terms are made available as summary tables, as
described above, with the genes/proteins, organisms and
GO terms linked to UniProt; Accession numbers linked to
the EMBL Nucleotide Archive, UniProt or PDB;
chemicals linked to ChEMBL; and disease terms reissuing a
literature search. The text-mined term summary tables
also shows a count of the frequency of occurrence of the
category as a whole as well as a count of how often
individual terms appear in the article. These same terms are
also indexed, allowing a user to limit keyword searches to
the specific mined-term fields. As of July 2010, there are
over 40 million text-mined annotations in UKPMC
full-text articles, covering over half a million unique terms.
Citation information. The Citations Tab contains two
article lists: ?Cited By?, articles that have cited the
current article and ?Cites the Following?, articles in the
reference list of the current article. The construction of
the ?Cited By? list requires access to article reference
lists, plus the ability to resolve those references to an
unequivocal source (for example a PubMed ID). In this way,
reference lists from articles published subsequent to the
current one can be processed to provide a list of ?Cited
By? articles and thereby one indication of the impact of the
article.</p>
        <p>The number of ?Cited By? articles listed is to some
extent a factor of the total number of articles in the data
set used to calculate it. The UKPMC citation network is
calculated from the UKPMC content, supplemented with
metadata supplied by CrossRef (http://www.crossref.org).
While it is the largest citation network available in the
public domain, the amount of content available to
UKPMC is less than that used in commercially available
services. The citation counts displayed on the UKPMC
website are therefore often lower than those from
commercial products; for comparative purposes, counts from
Thompson-Reuters? Web of Science are listed alongside
the UKPMC counts.</p>
      </sec>
      <sec id="4-4">
        <title>UKPMC+: tools for UK funded researchers</title>
        <p>While most of the UKPMC website is open for anyone to
use, some features are restricted to the funding agencies
that support UKPMC and the Principal Investigator (PI)
on grants awarded by those funders. These services relate
to manuscript submission and grant reporting (Figure 5).
The exception to this is the ?Grant Lookup? facility,
available on the main UKPMC website. Here, anyone can
search and retrieve information on grants awarded by
the UKPMC Funders. However, the remainder of the
tools described in this section are available only to
researchers funded by supporting funding bodies via
UKPMC+, at http://ukpmc.ac.uk/ukpmcplus.</p>
      </sec>
      <sec id="4-5">
        <title>Manuscript submission service</title>
        <p>UKPMC+ provides a manuscript submission service to
support authors depositing articles in order to comply
with the UKPMC Funders public access policies. It
extends software distributed via PMCI, originally
developed for the NIH Manuscript System and allows
users to deposit and manage their final, peer-reviewed
manuscripts, in line with journal policy. Manuscripts in
a wide range of electronic formats can be submitted along
with figures, tables or supplementary data.</p>
        <p>A username and password is required to access the
service. These login details are provided to PIs
automatically, by Email, once their grant has been awarded. Other
users, such as administrators, can use the system to create
their own accounts and submit on behalf of PIs. Papers
submitted through UKPMC+ are made accessible
through all PMCI nodes. The UKPMC+ manuscript
submission service also allows users to attach their grants to
existing PubMed and PubMed Central papers via the
?Grant Reporting? facility and is integrated with
MyNCBI.</p>
        <p>The UKPMC+ submission service is supported by a
dedicated Helpdesk Team who manage each submission,
from deposit through to publication on UKPMC. The
Helpdesk is also there to provide support on the full
range of UKPMC services. (Contact the Helpdesk at
ukpmc@bl.uk or on +44 [0]1937 546699.)</p>
      </sec>
      <sec id="4-6">
        <title>Grant reporting tools</title>
        <p>Within UKPMC+, the existing MyNCBI function has
been supplemented by My UKPMC, which offers
reporting for individual authors, including unique reports that
link the PIs portfolio of grants with the associated
research articles and those that report the impact of
those articles (Figure 5):
. ?My Grants? shows a PI?s known grants and the
associated publications, which link to the full-text
articles in UKPMC. A grant report can be ?published?,
i.e. made available at a persistent URL, suitable for
inclusion in an end-of-grant report.
. ?My Impact? shows the impact of a PI?s research as a
list of the reported published articles along with
citation counts from Web of Science and Scopus and
a count of article downloads from the UKPMC
website. The citation counts are calculated daily and
link through to the relevant pages in Web of Science
and Scopus. This too can be ?published? as a static web
page for inclusion on author?s personal web site, for
example.</p>
      </sec>
    </sec>
    <sec id="5">
      <title>FUTURE DIRECTIONS</title>
      <p>In the tradition of UKPMC?s commitment to
community engagement, we invite you to explore the UKPMC
website and welcome feedback on all aspects of the
project.</p>
    </sec>
    <sec id="6">
      <title>ACKNOWLEDGEMENTS</title>
      <p>The authors would like to thank the UKPMC Board
Members, 2006?2011: Michael Ashburner University of
Cambridge (until 2008), Casey Bergman University of
Manchester; Anne De Roeck Open University; Alison
Henning Wellcome Trust; Colin Hopkins Imperial
College (until 2008); Tim Hubbard Wellcome Trust
Sanger Institute; David Ingram (Chair) University
College London; Douglas Kell BBSRC (until 2008);
Robert Kiley Wellcome Trust; Peter Murray-Rust
University of Cambridge; Tony Peatfield Medical
Research Council; Philippa Saunders MRC Human
Reproductive Sciences Unit; Lynne Roberts Warwick
University (until 2008); Frank Uhlmann Cancer
Research UK.</p>
    </sec>
    <sec id="7">
      <title>FUNDING</title>
      <p>Funding for open access charge: UKPMC Funders (led by
Wellcome Trust).</p>
      <p>Conflict of interest statement. None declared.</p>
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Intraspecies_sequence_comparisons_for_anno.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>Downloaded from genome.cshlp.org on January</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>Intraspecies sequence comparisons for annotating genomes</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Dario Boffelli</string-name>
          <xref ref-type="aff" rid="1">1</xref>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Claire V. Weer</string-name>
          <xref ref-type="aff" rid="1">1</xref>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Li Weng</string-name>
          <xref ref-type="aff" rid="1">1</xref>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Keith D. Lewis</string-name>
          <xref ref-type="aff" rid="1">1</xref>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Malak I. Shoukry</string-name>
          <xref ref-type="aff" rid="1">1</xref>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Lior Pachter</string-name>
          <xref ref-type="aff" rid="0">0</xref>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>David N. Keys</string-name>
          <xref ref-type="aff" rid="1">1</xref>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Edward M. Rubin</string-name>
          <xref ref-type="aff" rid="1">1</xref>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <aff id="0">
          <label>0</label>
          <institution>Department of Mathematics, University of California, Berkeley</institution>
          ,
          <addr-line>Berkeley, California 94720</addr-line>
          ,
          <country country="US">USA</country>
        </aff>
        <aff id="1">
          <label>1</label>
          <institution>Genomics Division, Lawrence Berkeley National Laboratory</institution>
          ,
          <addr-line>Berkeley, California 94720</addr-line>
          ,
          <country country="US">USA</country>
        </aff>
        <aff id="2">
          <label>2</label>
          <institution>US Dept. of Energy Joint Genome Institute</institution>
          ,
          <addr-line>Walnut Creek, California 94598</addr-line>
          ,
          <country country="US">USA</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intraspecies sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents, and a set of genomic intervals were amplified, resequenced, and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C. intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom. It also raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species.</p>
      </abstract>
      <volume>15</volume>
      <issue>2016</issue>
      <fpage>2406</fpage>
      <lpage>2412</lpage>
      <pub-date>
        <year>2016</year>
      </pub-date>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>-</title>
      <p>[Supplemental material is available online at www.genome.org. The sequence data from this study were submitted to
GenBank under accession nos. AY667278?AY667407. The following individuals kindly provided reagents, samples,
or unpublished information as indicated in the paper: S. Fujiwara, A. Gittenberger, K. Heasman, H. Huelvan, D.</p>
    </sec>
    <sec id="2">
      <title>Jiang, S. Kano, A. Phillippi, A. Sexton, and S. Shimeld.]</title>
      <p>Sequence comparisons between the genomes of organisms
separated by a varying degree of evolutionary distances currently
serve as an essential means to identify genes as well as gene
regulatory elements (Ansari-Lari et al. 1998; Nobrega et al. 2003;
Thomas et al. 2003). These comparisons are based on the well
established molecular evolution principle that negative selection
reduces the accumulation of sequence differences in functional
sequences of related species (Hartl and Clark 1997; Hardison
2003). An important limitation of interspecies comparisons is
that they can only be used to identify sequences underlying
biological traits shared by the species examined. Although recently
described approaches, leveraging the sequences of many closely
related species to increase the total evolutionary branch length of
the comparisons, have begun to address this issue (Boffelli et al.
2003), they are nevertheless ill-suited to uncover species-specific
features. Intraspecies comparisons of the genomes of numerous
members of the same species offer a theoretical strategy to tackle
this problem. Although this approach is clearly expected to
require the sequences of a very large number of individuals of the
same species, the progressive lowering of the barrier to large-scale
resequencing made possible by advances in sequencing
technology now provides the opportunity to determine whether the
theoretical advantages of intraspecies comparisons for genome
annotation can be supported by experimental data.</p>
      <p>The sequencing of the ascidian Ciona intestinalis (sea squirt)
genome recently revealed this organism to be a particularly
attractive candidate target for testing the feasibility of
resequencing for annotating genomes. An important attribute is its very
high allelic polymorphism, with an average 1.2% of the
nucleotides differing between chromosome pairs of a single individual
(Dehal et al. 2002). This high degree of allelic variation, more
than 15-fold that noted in humans, is probably a consequence of
the large effective population size of C. intestinalis. In addition,
the genetic manipulability of the sea squirts offers a rigorous in
vivo experimental system to test the functional activity of
identified candidate regulatory elements (Satoh 2003).</p>
      <p>In this study, we determined the extent of sequence
polymorphism in several C. intestinalis subpopulations collected at
multiple locations worldwide. We exploited sequence variation
within C. intestinalis to computationally identify regions
subjected to fast and slow rates of evolution, and we experimentally
characterized their functional roles. These studies illustrate that
slowly evolving regions correspond to protein-coding or
enhancer regions, indicating the feasibility of using intraspecies
polymorphism to annotate a species? genome.</p>
      <sec id="2-1">
        <title>Results</title>
      </sec>
    </sec>
    <sec id="3">
      <title>Amplification of genomic targets and phylogenetic analysis</title>
      <p>C. intestinalis specimens were collected from several coastal
locations in North America, Europe, Eastern Asia, and Oceania.</p>
      <p>14:2406?2411 ©2004 by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/04; www.genome.org
I n t r a s p e c i e s c o m p a r a t i v e g e n o m i c s
Samples were defined as C. intestinalis based on characteristic
morphological features supported by sequence analysis.
Although the formal proof that all the samples analyzed are
members of the same species would require successful sexual mating,
the sequence difference among the samples examined indicated
that they are several-fold more similar to each other than to their
closest intra-genus relative, C. savignyi. Any two pairs of C.
intestinalis analyzed in this study were at least 85% identical, a value
within the range of allelic polymorphism reported for a single C.
intestinalis individual (Dehal et al. 2002). Conversely, BLAST
comparisons between C. intestinalis and C. savignyi, carried out at
the relaxed threshold of e = 1, revealed sequence alignments
for less than 10% of the sequences. Four genomic intervals, each
?4 kb long, were chosen for analysis in this study based on
previous knowledge of genes and gene regulatory elements located
within these intervals. Target regions included exons 18?25 of
patched homolog, exons 1?4 of col5a1, and the 5 sequences of
forkhead and snail. The targeted coding regions all had strong
gene structure predictions supported by EST sequences, while
several 5 tissue-specific enhancers for forkhead and the promoter
of snail had been previously defined and characterized (Erives et
al. 1998; Di Gregorio et al. 2001).</p>
      <p>Using the consensus sequence of an individual collected
from a West Coast location for PCR primer design, amplification
was attempted for each of the four genomic target regions from
140 animals. Successful PCR reactions yielded unique bands in
most cases. When two bands were obtained, they were both
sequenced independently and in all instances resulted in
heterozygous allelic variants due to insertion/deletion events. Even
though all four target regions were unique in the current C.
intestinalis assembly, its draft status raises the possibility that
amplicons from different individuals represent paralogous, rather
than allelic, copies. This is unlikely, since all the sequences for
the same target locus had stretches of perfect identity longer than
100 base pairs, which are not normally observed between
paralogous loci.</p>
      <p>We were able to obtain amplified genomic targets from
?50% of the individuals collected from West Coast locations,
20% of the individuals from New Zealand and Japan, and less
than 20% of the individuals collected from coastal locations on
the Atlantic Ocean or the Mediterranean Sea (Table 1). The
difficulty in amplifying C. intestinalis genomic samples, explained
by the high levels of polymorphism of this species, suggests that
only a reduced subset of the polymorphism present in C.
intestinalis was likely captured by this study.</p>
      <p>Successfully amplified target regions were fully sequenced
using custom primers designed ?every 250 bp on each strand, for
a total of 40 sequencing reads for each amplified target region.</p>
      <p>This level of coverage ensured that each base was read at least
four times. Analysis of the sequences revealed that specimens
from the same collection location clustered nearly exclusively
close to each other as estimated by their degree of sequence
similarity, supporting the conjecture that they are members of largely
isolated subpopulations (Fig. 1). Surprisingly, individuals from
Mediterranean locations appeared more related to individuals
collected from the Pacific rather than Atlantic Ocean. In
addition, subpopulations collected from locations on the Atlantic
Ocean showed much higher heterozygosity than subpopulations
from locations on the Pacific Ocean, as reflected by the size of the
circles in Figure 1. C. intestinalis is an invasive species reported to
be spread in ship bilges along shipping routes. This is supported
by the clustering of samples from the Pacific Ocean, reflecting
the greater shipping activity between California, Japan, and New
Zealand ports. The lower heterozygosity among those samples
also suggests that the Pacific Ocean was colonized after the
Atlantic Ocean.</p>
      <p>The phylogenetic tree of the individuals sequenced in each
genomic interval was obtained in two steps. First, phylogenetic
relationships between subpopulations were calculated from the
consensus sequences for each subpopulation, defined by their
collection locations (see legend, Table 1). Phylogenetic
relationships for individuals from the same subpopulation were then
estimated from the average distance of all members of that
subpopulation, since the degree of sequence similarity among
individuals from the same subpopulation did not allow the
computation of statistically significant trees within subpopulations. The
resulting composite trees were used to calculate the likelihood
that each nucleotide site in the multiple sequence alignment is
mutating at a high or at a low rate (Boffelli et al. 2003). Variation
profiles of the genomic intervals analyzed were displayed
through likelihood ratio curves to identify regions undergoing
the slowest mutation rates relative to the rate of their
surrounding regions.</p>
    </sec>
    <sec id="4">
      <title>Identification of regulatory elements of forkhead and snail</title>
      <p>The identification of gene regulatory elements in the proximity
of two early-development genes, forkhead and snail, was sought
using C. intestinalis sequence comparisons. Both genes are
expressed in the larval stage of C. intestinalis development and are
therefore amenable to in vivo assessments in transgenic C.
intestinalis tadpoles. The mutation rate ratio plot for the forkhead 5
regulatory region revealed five distinct minima representing the
sequences likely under the strongest selective constraints (Fig.
2A, regions 1, 2, 4, 5, and 7). We explored the ability of these five
regions to function as enhancers in vivo using reporter
constructs assayed in transgenic C. intestinalis tadpoles. Constructs
which reproducibly drove expression in a tissue-specific manner
included that for region 1 in the notochord and endoderm,
region 4 in the notochord, endoderm, and neural tube, region 5 in
the notochord, and region 7 in the neural tube, endoderm, and
notochord (Fig. 2B). These patterns are consistent with the
endogenous forkhead expression characteristics (Corbo et al.
1997a). As putative negative controls, we examined two regions
with high mutation rates (regions 3 and 6, Fig. 2A). Consistent
with the expectation that fast-evolving regions likely lack gene
regulatory activity, these two regions failed to drive gene
expression in this assay (data not shown).</p>
      <p>While the slow-evolving region 2 failed to show
tissuespecific expression in this assay, a previous study, analyzing a
reporter construct containing the forkhead 5 region through
sequential deletions, had shown that removal of a segment
containing region 2 abolished neural tube expression in the C.
intestinalis tadpole (Di Gregorio et al. 2001). This suggests that this
functional element might require interactions with nearby
enhancers for driving gene expression in the neural tube. The same
previous study also demonstrated that deletions corresponding
to regions 1 and 3 resulted in a loss of neural tube, endoderm,
and notochord expression, in a manner consistent with our
results.</p>
      <p>We applied a similar analysis to the genomic interval
containing snail?s 5 region. One 5 noncoding region characterized
by a mutation rate similar to that of forkhead enhancers was
also investigated using the transgenic C. intestinalis tadpole assay
(region 2, Fig. 3). The reporter construct for this region drove
expression in the neuronal lineage (inset, Fig. 3). The other
5 noncoding region showing a similarly low variation rate
(region 1, Fig. 3) corresponded exactly to the previously described
minimal promoter/mesodermal enhancer
of snail (Erives et al. 1998). The mutation
rate ratio plot for this interval also correctly
identified the first exon of snail (region E,
Fig. 3).</p>
    </sec>
    <sec id="5">
      <title>Identification of coding exons of col5a1</title>
      <p>and patched
To further test our ability to predict the
location of exonic sequences through
intraspecies sequence comparisons, we
investigated two genomic intervals containing
several exons of the col5a1 and patched
genes. Both intervals revealed a similarly
uneven distribution of mutation rates, with
several regions characterized by a low rate
interspersed among high mutation rate
regions (Fig. 4). Of the six regions with low
mutation in the col5a1 interval, four
corresponded to the exon-coding regions
annotated by gene prediction programs and EST
sequences available for this interval (1?4,
Fig. 4A). The two additional regions of very
low mutation rate revealed by the variation
plot were not functionally investigated in
this study but could represent additional
col5a1 regulatory elements. Consistent with
the results for the col5a1 interval, the
position of the eight patched exons were all
coincident with regions of low mutation
rate (Fig. 4B). Overall sequence diversity was
very low in the patched interval (total
tree length = 0.10 substitutions per site),
likely due to the successful amplification
of DNA from only 20 individuals
exclusively from California or Japanese
locations, but was nevertheless sufficient to
identify regions encompassing the exon
locations.</p>
      <sec id="5-1">
        <title>Discussion</title>
        <p>In contrast to all previous comparative genomic studies, which
used evolutionarily fixed sequence differences between two or
more species to estimate mutation rates, we are here able to show
that intraspecies sequence polymorphism can be effectively used
to identify gene regulatory elements and exons through a
combination of phylogenetic analysis and polymorphism diversity.
Intraspecies sequence polymorphism has been extensively used
by population geneticists to study the action of selection on
protein coding sequences and by biologists to detect linkage
disequilibrium and associate deleterious allelic variants with disease.
Our results extend the interest in using polymorphism beyond
those applications and suggest that intraspecies sequence
comparisons may be useful for identifying functional regions in a genome.</p>
        <p>Intraspecies comparisons fill several important niches in the
comparative genomics analysis of sequenced genomes. First, they
have the potential to identify sequences underlying biological
traits unique to a single species. They are also useful when a
species under investigation is too far away from its nearest
evolutionary neighbor for useful pair-wise comparisons. For
example, C. intestinalis shared a last common ancestor with its sister
species, C. savignyi, ?100 million years ago. Consequently, these
two species show limited sequence similarity that, while often
sufficient to identify many highly constrained sequences, might
lead to failure in identifying many other functional sequences,
which can otherwise be detected by the approach described here.
Finally, intraspecies comparisons suggest a path for the
annotation of organisms occupying previously uncharacterized
phylogenetic branches of the animal kingdom, including the green
alga C. reinhardtii, the diatom T. pseudonana, and human malaria
parasite P. falciparum, whose sequences are now becoming
available.</p>
        <p>Because of the high rate of allelic polymorphism of C.
intestinalis, the sequences from as few as 30 individuals were required
to achieve sufficient total sequence variation to identify intervals
evolving significantly more slowly than their surrounding
regions. Applying the same intraspecies approach to human is
made more difficult by its low rate of polymorphism
(Sachidanandam et al. 2001). The complexity of human population
dynamics and haplotype structure complicates estimating the
number of individuals required for such a study. Nonetheless, making
several simplifications and assumptions, extrapolation of the
data from Yu et al. (2002) suggests that sequencing of a few
thousand individuals would yield 0.3 single nucleotide
polymorphism (SNP)/site, a number comparable to the total tree length of
the sequences used in the analysis of forkhead 5 region in this
study. Irregardless of the exact number of humans required for
such a study, with the increase in human genome resequencing
predicted for the near future (Collins et al. 2003; Shendure et al.
2004), intra-Homo sapiens comparisons exploiting the
approaches described here for C. intestinalis may prove fruitful for
the identification of functional sequences shared with other
species as well as human-specific ones.</p>
      </sec>
      <sec id="5-2">
        <title>Methods</title>
      </sec>
    </sec>
    <sec id="6">
      <title>Collection of C. intestinalis specimens</title>
      <p>Specimens were collected from the following coastal locations:
South San Francisco, California; Half-Moon Bay, California;
Santa Barbara, California; Cobscook Bay, Maine; Darling Marine
Center, Maine; Woods Hole, Massachussetts; Kobe, Japan; Kochi,
Japan; Marlborough Sounds, New Zealand; Reading, England;
Roscoff, France; Grevelingen, Netherlands; Den Hosse,
Netherlands; Viaggio Coppola, Italy; Fusaro, Italy.</p>
    </sec>
    <sec id="7">
      <title>Direct resequencing of target regions</title>
      <p>Genomic DNA was isolated from C. intestinalis muscle tissue
using the Puregene kit (Gentra Systems). Target regions were
amplified by PCR using the Elongase systems (Invitrogen) following
the manufacturer?s recommendations, with primers described in
the Supplemental information. Single-band PCR products were
gel-purified (SNAP UV-free Gel purification Kit, Invitrogen) and
subjected to direct microsequencing using custom primers
designed every 250 bp on each strand. Fluorescence automated
DNA sequencing was carried out using BygDye chemistry in an
ABI3700 Sequencer (Applied Biosystems). Both the (+) and ( )
strands were sequenced at least twice. Base calling, quality
assessment, and assembly were carried out using the phred, Phrap,
Consed software suite developed by Phil Green (www.phrap.org).
All the sequences generated in this study have been submitted to
GenBank.</p>
    </sec>
    <sec id="8">
      <title>Data analysis</title>
      <p>Sequences were aligned using MAVID (Bray and Pachter 2003)
(baboon.math.berkeley.edu/mavid) or ClustalW (www.ebi.ac.
uk/clustalw/index.html) and the alignments were manually
verified. Consensus sequences for individuals collected from
California, Japan, New Zealand, East Coast, and Europe were derived
from the multiple alignment. Maximum likelihood phylogenetic
trees for the consensus sequences were reconstructed using
FastDNAml. In order to identify conserved sequences, a
likelihood ratio (conserved vs. nonconserved) was calculated for
each position in the multiple alignment of the individuals
(McAuliffe et al. 2004) (http://bonaire.lbl.gov/newshadower/).
To explicitly account for both the phylogenetic relationships
between the consensus sequences, as well as the polymorphic
diversity between individuals from the same subpopulation, a
phylogenetic likelihood computation was coupled with a
nucleotide diversity calculation for both fast and slow rates (Pamilo
et al. 1987). Although nucleotide diversity is typically computed
with a Jukes-Cantor correction, it can be viewed as a
phylogenetic likelihood computation on a star tree and can be based on
any evolutionary model. We matched the model to that used for
the phylogenetic computations on the consensus sequences
(Boffelli et al. 2003), and by conditioning on the consensus
sequences we obtain a probabilistic model for modeling
phylogenetic relationships between groups as well as polymorphic
differences among same-population individuals. The rates for
the slow (conserved) and fast (nonconserved) computations
were based on previous estimates. Regions characterized by
the slowest rates were defined relative to the rates of their
surroundings, implicitly accounting for the local rate of
mutation.</p>
    </sec>
    <sec id="9">
      <title>Maintenance of C. intestinalis colony</title>
      <p>Adult C. intestinalis were collected from several locations in
Northern California, purchased from Woods Hole,
Massachusetts, and Long Beach, Southern California. The animals were
kept at 18°C in recirculating artificial seawater.</p>
    </sec>
    <sec id="10">
      <title>Construction of plasmids and electroporation</title>
      <p>All constructs were made with the pCES (plasmid Ciona
enhancer screen) vector previously reported (Harafuji et al. 2002).
Different fragments from the Ci-fkh 5 and Ci-snail 5 flanking
regions were amplified by PCR using the Ciona genomic DNA
isolated from Northern California animals, with primers
described in the Supplemental information. The DNA
fragments were then ligated into the BamHI site of the pCES
vector. Electroporations, fixation, and staining reactions were
done as described by Corbo et al. (1997b). Aliquots containing
100 µg of purified plasmid were used in each
electroporation. Each transgene was tested at least twice. The number of
positive embryos scored in each experiment ranged ?between 70
and 200.</p>
    </sec>
    <sec id="11">
      <title>GenBank accession numbers</title>
      <p>Forkhead region: AY667314?AY667347. Snail region: AY667371?
AY667407. Col5a1 region: AY667278?AY667313. Patched region:
AY667348?AY667370.</p>
      <sec id="11-1">
        <title>Acknowledgments</title>
        <p>We thank Shigeki Fujiwara, Arjan Gittenberger, Kevin
Heasman, Helene Huelvan, Di Jiang, Shungo Kano, Aimee Phillippi,
Andy Sexton, and Seb Shimeld for providing C. intestinalis
samples. Research was conducted at the E.O. Lawrence Berkeley
National Laboratory and at the Joint Genome Institute, with
support by grants from the Programs for Genomic
Application, NHLBI (E.M.R.) and NIH (L.P.), and performed under
Dept. of Energy Contract DE-AC0378SF00098, Univ. of
California.
I n t r a s p e c i e s c o m p a r a t i v e g e n o m i c s</p>
      </sec>
      <sec id="11-2">
        <title>Web site references</title>
        <p>http://bonaire.lbl.gov/newshadower/; phylogenetic shadowing.
www.phrap.org; consed suite.
www.ebi.ac.uk/clustalw/index.html; multiple sequence alignment.
baboon.math.berkeley.edu/mavid; multiple sequence alignment.</p>
        <p>Received May 18, 2004; accepted in revised form October 5, 2004.
Intraspecies sequence comparisons for annotating genomes
 
Dario Boffelli, Claire V. Weer, Li Weng, et al.
 
Genome Res. 2004 14: 2406-2411
Access the most recent version at doi:10.1101/gr.3199704</p>
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          <title>Service</title>
          <p>This article cites 18 articles, 9 of which can be accessed free at:
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12e6028fd3092a2395cb9ccae211a414.pdf.

Cermine / Crossref / Grobid

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<?xml version="1.0"?>
<pdf>
  <title line_height="8.78" font="Times-Roman">Your use of the JSTOR
archive indicates your acceptance of the Terms &amp; Conditions of Use,
available at http://www.jstor.org/page/
info/about/policies/terms.jsp</title>
  <reference>tthhee hheeaaddwwoorrdd rreeaaddeerrssnn oott OOlldd
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''ppiippee'' oonnllyy DDiivvyyaavvaaddaannaa)),, UUyygghhuurr,,
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wwoorrdd bbuutt aallssoo ttoo aanndd TToocchhaarriiaannAA ..
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</reference>
  <reference>CCrreeee vveerrbb sstteemmss tthhaattdd eessccrriibbeecc
eerreemmoonniiaallaa ccttiioonnss oonnee ooff AAllll tthheessee aarree
nnoott eexxaacctt ttrraannssllaattiioonnss ccoommppoossiittiioonnss
ttaakkee aa oorr aass wweellll aass ttoo nnoouunn ooff tthhee ttrraaddii--
wwoorrkkbb uutt rraatthheerrss iimmiillaarrvv eerrssiioonnss tthhee
ssaammee uussiinngg </reference>
  <reference>mmaayy ppiippee ppiippeesstteemm,, ffoorr wwoorrddss aarree
ttoo </reference>
  <reference>sstteemmss tthhaatt rreellaatteedd tthhaatt ddee-- ttiioonn
ooff tthhee nnuummeerroouuss ppiippee cceerreemmoonnyy
MMaaiittrreeyyaavvyyaakkaarraannaa </reference>
  <reference>rriitteess.. WWhheerree ootthheerr rreecceenntt CCrreeee
ddiiccttiioonnaarriieess ooff tthhee ffuuttuurree BBuuddddhhaa.. TThhee
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ddrraammaattiiccww oorrkk lliikkee ((ee..gg.. ppaarrlliiaammeenntt,,
tthhaatt,, MMaaiittrreeyyaassaammiittiinnaattaakkaa tthhiiss iiss ffoorr
tthhee vvaalluuaabbllee 2266,,000000 </reference>
  <reference>sscchhoooollbbuuss)),, ooff tthhee tthhee ootthheerr
ddiiccttiioonnaarryy ccoommiinngg pprreeddiiccttss
MMaaiittrreeyyaavvyyaakkaarraannaa,, ooff ooff PPllaaiinnss CCrreeee
bbeeccaauussee iittss ffooccuuss oonn tthhee </reference>
  <reference>ssppeeaakkeerrss OOnnee"" TToocchhaarriiaann tthhee
""MMeerrcciiffuull ((SSaannsskkrriitt MMaaiittrreeyyaa,, ooff CCrreeee
ttrraaddiittiioonnssaa nndd cceerreemmoonniieess.. </reference>
  <reference>llaanngguuaaggee AA MMeettrraakk)).. IIttss eennttrriieess
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XXiiaannlliinn,, </reference>
  <reference>ffoorrmm ooff tthhee TThhiiss ddooeess nnoott
ddiiccttiioonnaarryy ggiivvee llaanngguuaaggee.. ooff tthhee 4444 aanndd
ooffffeerrss aann eeddiittiioonn PPiinnaauulltt,, GGeeoorrggeess--JJeeaann
ddaattaa ffrroomm ootthheerr PPllaaiinnss CCrreeee ssoouurrcceess,,
</reference>
  <reference>ccoommppaarraattiivvee ccoonnttaaiinn-- ooff tthhee
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</reference>
  <reference>ootthheerr CCrreeee oorr ootthheerr ddiiaalleeccttss,,
llaanngguuaaggeess.. AAllggoonnqquuiiaann AA ooff tthhee tthhee
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llooaannwwoorrddss ffrroomm FFrreenncchh aanndd tthhaatt </reference>
  <reference>HHoowweevveerr,, EEnngglliisshh iinn iinn ddiissttrriicctt
ooff tthhee ttaakkaa ffoouunndd 11997733 tthhee YYaannqqii </reference>
  <reference>hhaavvee ssoo bbeeeenn aass ttoo hhaavvee CCrreeee
ssuuffffiicciieennttllyy iinntteeggrraatteedd CChhiinnaa.. AA sshhoorrttii
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</reference>
  <reference>ffoorrmmss aarree iinncclluuddeedd NNoo CCrreeee ((vviiii))..
ssyyllllaabbiicc oorrtthhooggrraa-- oonn aa rreeccoonn-- ffooccuusseedd
dduuccttiioonn ((11--1199)),, mmoossttllyy ggiivviinngg iinn iiss uusseedd
tthhiiss </reference>
  <reference>pphhyy ddiiccttiioonnaarryy.. oonn tthhee ssttrruuccttiioonnoo
ff tthhee bbaasseedd CChhiinneessee TTrriippiittaakkaa,, ssttoorryy IInn
tthhee CCrreeee--EEnngglliisshh sseeccttiioonn ((11--220033)),, tthhee
aauutthhoorrss ttrraannsslliitteerraattiioonnaa nndd
ttrraannssllaattiioonnoo ff tthhiiss iiss ffoolllloowweedd aa bbyy iinn
ooff </reference>
  <reference>lliisstt nnoouunnss aanndd vveerrbbss sstteemm ffoorrmm
iinnsstteeaadd ffuullllyy-- ffiirree ddaamm-- tteexxtt
ffrraaggmmeennttaarryy ((2211--2211 11)).. UUnnffoorrttuunnaatteellyy,,
</reference>
  <reference>iinnfflleecctteedd wwoorrddss.. nnoouunn sstteemmss aarree
lliisstteedd aass DDeeppeennddeenntt ooff aanndd tthhee lleefftt mmaarr--
tthhee lleefftt ssiiddee tthhee aaggeedd mmaannuussccrriipptt,, ooff tthhee
</reference>
  <reference>aa ddiissccrreettee aatt tthhee ggrroouupp bbeeggiinnnniinngg
ddiiccttiioonnaarryy.. oonn aarree lloosstt TThhee aanndd ccoorrnneerrss
ggiinn eennttiirreellyy eevveerryy ppaaggee.. tteerrmm''ss </reference>
  <reference>EEaacchh CCrreeee iiddeennttiiffiieess tthhee eennttrryy
ggrraammmmaattiiccaall tthhee tteexxtt aarree eeddiittoorr''ss nnootteess
ttoo ssccaannttyy aalltthhoouugghhpp rreecciissee aanndd aann
PPaarreenntthheettiiccaall </reference>
  <reference>ccaatteeggoorryy ggiivveess EEnngglliisshh gglloossss.. ooff
TThhee rroollee ssoommee aannnnoottaa-- aanndd iinnffoorrmmaattiivvee..
ppoossssiibbllee </reference>
  <reference>nnootteess iinnfflleecctteedd oorr uunnuu-- eexxppllaaiinn
ffiigguurraattiivveeuu ssaaggee,, ffuullllyy iiss aa ddeettaaiilleedd
iinnddeexx ttiioonnss ppaarrttiiaallllyy rreeppllaacceedd bbyy vveerryy
eettcc.. </reference>
  <reference>ssuuaall ffoorr ffoorrmmss,, eettyymmoollooggiieess
ppllaaccee--nnaammeess,, aann ooff vveerrbbaall ffoorrmmss vveerrbboorruumm
iinnddeexx ((221133--6688)),, IInnsstteeaaddoo ff aann tthhee
EEnngglliisshh--CCrreeeess eeccttiioonn,, ddiiccttiioonnaarryy aa ooff
ffoorrmmss aanndd nnoonnvveerrbbaall ((226699--7799)),, gglloossssaarryy
iinn wwhhiicchh </reference>
  <reference>uusseess aann iinnddeexx EEnngglliisshh ((220055--442255))
EEnngglliisshh tthhee iiss tthhee ooff tthhiiss vvoolluummee
((228800--330011)).. PPrroobbaabbllyy jjeewweell aa ooff sstteemmss aanndd
</reference>
  <reference>hheeaaddwwoorrddssaa rree ffoolllloowweedd lliisstt CCrreeee
bbyy iinn wwrriitttteenn CCeennttrraall AAssiiaann BBrraahhmmii
mmaannuussccrriippttii ttsseellff,, ooff ooff tthhee </reference>
  <reference>wwoorrddss tthhaatttt rraannssllaatteevv aarriioouussss
hhaaddeess mmeeaanniinngg aanndd iinn tthhee cclleeaarreessttaa nndd
mmoosstt ssccrriipptt rreepprroodduucceedd ssuuppeerrbb TThhee iinn
</reference>
  <reference>hheeaaddwwoorrdd.. CCrreeee eennttrriieessaa rree lliisstteedd
aallpphhaabbeettiiccaall ccoouulldd aasskk ffoorr sscchhoollaarrss
pphhoottooggrraapphhss ((330044--9911)).. wwiitthh nnoo ttoo tthheemm
</reference>
  <reference>oorrddeerr,, aatttteemmpptt ggrroouupp
sseemmaannttiiccaallllyy.. ccoouulldd hhaavvee TThhiiss iiss aa
ffaabbuulloouuss aanndd oonnee eeddiittiioonn,, oonnllyy iinn iinnddeexx
tthhee </reference>
  <reference>EEaacchh CCrreeee tthhee eennttrryy EEnngglliisshh ggiivveess
sstteemm,, ddeettaaiilleedd ddiissccuussssiioonn ooff tthhee ccoomm--
wwiisshheedd ttoo sseeee aa mmoorree aanndd sshhoorrtt oonnee mmuusstt
ccoonnssuulltt </reference>
  <reference>sstteemm--ccllaassss aa ccooddee,, gglloossss;; tthhee
ddiiff-- aanndd rreeddaaccttiioonnaallii ssssuueess ppoossiittiioonnaall
ccoonncceerrnniinngg WW ffuullll iiss ccaarree-- </reference>
  <reference>tthhee sseeccttiioonn ffoorr tthhee CCrreeee--EEnngglliisshh
gglloossss.. tthhiiss FFoorr aaccttuuaall ffeerreenntt vveerrssiioonnss
ooff tthhee ssttoorryy.. iinnssttaannccee,, iiss </reference>
  <reference>ffuull ttoo oouutt tthhaatt tthhee iinnddeexx aa
sseelleeccttiivvee ppooiinntt gguuiiddee,, tthhee ddiiffffeerreenntt
vveerrssiioonnss hhiissttoorriiccaall rreellaattiioonn bbeettwweeeenn
aallll tthhee ooff aa </reference>
  <reference>nnoott EEnngglliisshh--CCrreeee ppaarrtt bbiilliinngguuaall
ddiiccttiioonnaarryy iiss ooff ssaammee nnaarrrraattiivvee nnoott
cclleeaarr.. EEttiieennnnee LLaammoottttee tthhee </reference>
  <reference>((vv)).. IInnddiiaann LLoouuvvaaiinn--LLaa--NNeeuuvvee::
((HHiissttoorryy ooff BBuuddddhhiissmm,, TThhiiss iiss aa vvaalluuaabbllee
ccaarreeffuullllyy pprreeppaarreedddd iiccttiioonnaarryy ttoo tthhee
IInnssttiittuutt OOrriieennttaalliissttee,,11 998888,, pp.. 770022))
ppooiinnttss ppoossssii-- IIttss ffooccuuss </reference>
  <reference>rreeffeerreenncceeff oorr ssttuuddeennttss PPllaaiinnss
CCrreeee.. lleeaarrnniinngg ooff aann IInnddiiaann mmooddeell ffoorr tthhee
TToocchhaarriiaann bbllee eexxiisstteennccee iitt tthhee ooff aann
</reference>
  <reference>oonn llaanngguuaaggee ssppiirriittuuaalliittyygg iivveess
aaddvvaannttaaggee bbuutt tthhee ttrraaddiittiioonnaallaa
ttttrriibbuuttiioonnoo ff ccoommppoossiittiioonn aacccceeppttss
</reference>
  <reference>oovveerr aallll ootthheerr PPllaaiinnss CCrreeee
ddiiccttiioonnaarriieess.. [[DDAAVVEE ttoo VVaaiibbhhaassiikkaa tthhee
MMaaiittrreeyyaassaammiittiinnaattaakkaa AArryyaaccaannddrraa </reference>
  <reference>PPRRUUEETTrr,, TTeexxaass AA&amp;&amp;MM
UUnniivveerrssiittyy..]] ooff ooff aacctt NNaakkrriiddiiss ((sseeee
ccoolloopphhoonn II,, ffrraaggmmeennttaarriillyypp rree-- 11..11 BB.. NN..
oonn 11//22 vveerrssoo bb sseerrvveedd YYQQ 55)).. MMoorreeoovveerr,,
BBaa-- PPuurrii iinn DDeellhhii:: MMoottiillaall ((BBuuddddhhiissmm
CCeennttrraall AAssiiaa,, ttaakkeess ffoorr tthhaatt nnaarrssiiddaassss,,
11998877,, pppp.. 221122--1133)) ggrraanntteedd AA ooff tthhee
TToocchhaarriiaann </reference>
  <reference>FFrraaggmmeennttss ooff oouurr TToocchhaarriiaannww oorrkk
iiss aa ttrraannssllaattiioonn aa MMaa-- mmeerreellyy ooff tthhee
MMaaiittrreeyyaassaammiittii--NNaattaakkaa XXiinnjjii-- BBuuddddhhiisstt
SSaannsskkrriitttt eexxtt.. hhaayyaannaa ssoommee ooff tthhee
AAlltthhoouugghh ffrraaggmmeennttss MMaaiittrreeyyaassaammiittii-- JJii
CChhiinnaa.. aanngg MMuusseeuumm,, BByy XXIIAANNLLIINN,, AAllbbeerrtt
aanndd wweerree ddiissccoovveerreedd GGrruunnwweeddeell nnaattaakkaa bbyy
WWEERRNNEERR WWIINNTTEERR,, PPIINNAAUULLTT..BB eerrlliinn:: MMoouuttoonn
ddee GGrruuyytteerr,, 11999988.. 339922.. PPpp.. TThhee
MMaaiittrreeyyaassaammiittiinnaattaakkaa((
MMaaiittrreeyyaassaammiittiinnaattddkk iiss </reference>
  <reference>iinn ooff tthhee ccaannoonniiccaall TToocchhaarriiaann AA))
ppaarrtt MMaahhaayyaannaa ooff BBuuddddhhiisstt tteexxttss.. TThheerree
eexxiisstt ccoomm-- SSaannsskkrriitt </reference>
  <reference>ccoorrppuuss llaann-- oorr iinn sseevveerraalldd
iiffffeerreenntt </reference>
  <reference>pplleettee ffrraaggmmeennttaarryypp aarraalllleellss iinn
tthhee </reference>
  <reference>gguuaaggeess:: SSaannsskkrriitt
((MMaaiittrreeyyaavvaaddaaddnnaavvyyaaddkkllrraannaa aanndd
GGEEOORRGGEESS--JJEEAANN iinn iinn aanndd ssuubbssee-- vvoonn LLee 11990066
AAllbbeerrtt CCooqq XXiinnjjiiaanngg EEmmiill aanndd WWiillhheellmm
qquueennttllyy ppuubblliisshheedd bbyy SSiieegg SSiieegg-- &amp;&amp; iinn
tthheeiirr TToocchhaarriisscchhee lliinngg SSpprraacchhtteexxttee
((BBeerrlliinn ooff ddee tthhee eeddiittiioonn tthhiiss WWaalltteerr
LLeeiippzziigg:: GGrruuyytteerr,,11 992211)),, iinn tthhee
ccoonnssttiittuutteessaa eevveenntt mmaannuussccrriipptt mmaajjoorr
ddeevveelloopp-- iinn oouurr uunn-- mmeenntt ooff TToocchhaarriiaannss
ttuuddiieess aanndd,, hhooppeeffuullllyy,, tthhee tthhee ccaannoonn.. ooff
ffoorrmmaattiioonnoo ff ddeerrssttaannddiinngg MMaahhaayyaannaa
[[GGOONNZZAALLRROOUU BBIIOO,, TThhee OOhhiioo SSttaattee
UUnniivveerrssiittyy..]] </reference>
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Evaluation_of_16S_rRNA_Gene_PCR_Sensitivit.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>October</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>Evaluation of 16S rRNA Gene PCR Sensitivity and Specificity for Diagnosis of Prosthetic Joint Infection: a Prospective Multicenter Cross-Sectional Study</article-title>
      </title-group>
      <contrib-group>
        <aff id="0">
          <label>0</label>
          <institution>; CHU Angers</institution>
          ,
          <addr-line>Angers</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="1">
          <label>1</label>
          <institution>CHU Nantes, Laboratoire de Bacte?riologie</institution>
          ,
          <addr-line>Nantes</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="2">
          <label>2</label>
          <institution>; CHU Tours, Laboratoire de Bacte?riologie</institution>
          ,
          <addr-line>Tours</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="3">
          <label>3</label>
          <institution>Pascale Be?mer</institution>
        </aff>
        <aff id="4">
          <label>4</label>
          <institution>; CHU Rennes, Laboratoire de Bacte?riologie</institution>
          ,
          <addr-line>Rennes</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="5">
          <label>5</label>
          <institution>; CHU Brest, Laboratoire de Bacte?riologie</institution>
          ,
          <addr-line>Brest</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="6">
          <label>6</label>
          <institution>; INSERM</institution>
          ,
          <addr-line>CIC 1415, Tours</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="7">
          <label>7</label>
          <institution>; CHU Poitiers, Laboratoire de Bacte?riologie</institution>
          ,
          <addr-line>Poitiers</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>There is no standard method for the diagnosis of prosthetic joint infection (PJI). The contribution of 16S rRNA gene PCR sequencing on a routine basis remains to be defined. We performed a prospective multicenter study to assess the contributions of 16S rRNA gene assays in PJI diagnosis. Over a 2-year period, all patients suspected to have PJIs and a few uninfected patients undergoing primary arthroplasty (control group) were included. Five perioperative samples per patient were collected for culture and 16S rRNA gene PCR sequencing and one for histological examination. Three multicenter quality control assays were performed with both DNA extracts and crushed samples. The diagnosis of PJI was based on clinical, bacteriological, and histological criteria, according to Infectious Diseases Society of America guidelines. A molecular diagnosis was modeled on the bacteriological criterion (&gt;1 positive sample for strict pathogens and &gt;2 for commensal skin flora). Molecular data were analyzed according to the diagnosis of PJI. Between December 2010 and March 2012, 264 suspected cases of PJI and 35 control cases were included. PJI was confirmed in 215/264 suspected cases, 192 (89%) with a bacteriological criterion. The PJIs were monomicrobial (163 cases [85%]; staphylococci, n 108; streptococci, n 22; Gram-negative bacilli, n 16; anaerobes, n 13; others, n 4) or polymicrobial (29 cases [15%]). The molecular diagnosis was positive in 151/215 confirmed cases of PJI (143 cases with bacteriological PJI documentation and 8 treated cases without bacteriological documentation) and in 2/49 cases without confirmed PJI (sensitivity, 73.3%; specificity, 95.5%). The 16S rRNA gene PCR assay showed a lack of sensitivity in the diagnosis of PJI on a multicenter routine basis.</p>
      </abstract>
      <volume>52</volume>
      <issue>10</issue>
      <fpage>3583</fpage>
      <lpage>3589</lpage>
      <pub-date>
        <year>2014</year>
      </pub-date>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>-</title>
      <p>
        Pplications of orthopedic surgery, increasing the risk of
morrosthetic joint infection (PJI) is one of the most serious
combidity and death for this very frequent operation. The infection
rates are estimated to be about 1% for hip or shoulder replacement
and about 2% for knee prosthesis (
        <xref ref-type="bibr" rid="1">1</xref>
        ). Despite the lack of a
standard definition of PJI, bacterial documentation remains the
cornerstone of diagnosis.
      </p>
      <p>
        Bacterial adherence to biomaterials and tissues adjacent to
prostheses is essential for the development of PJI (
        <xref ref-type="bibr" rid="1">1</xref>
        ).
Bacteriological diagnosis requires the extraction of bacteria from a
periprosthetic tissue biofilm. Culture of prosthetic sonicate fluid was more
sensitive than traditional tissue culture when antibiotic treatment
was stopped within 14 days before surgery (75% versus 45%; P
0.001) (
        <xref ref-type="bibr" rid="2">2</xref>
        ). Nevertheless, the conventional bacteriological method
used, in comparison with sonication, was simple homogenization
of tissue specimens before culture (
        <xref ref-type="bibr" rid="2">2</xref>
        ). Recently, bacterial
extraction using bead mill processing of specimens improved
bacteriological diagnosis of PJI (
        <xref ref-type="bibr" rid="3">3</xref>
        ).
      </p>
      <p>
        Histological examination of periprosthetic tissue is
recommended if there is any suspicion of PJI (
        <xref ref-type="bibr" rid="4 5">4, 5</xref>
        ). The standard method is
based on counts of polymorphonuclear neutrophils (PMN) per
highpower field (HPF). The cutoff point (number of neutrophils per
field) to affirm infection differed among authors, but the criterion of
5 PMN/HPF described by Mirra et al. and adapted by Feldman et al.
remains the most commonly used (
        <xref ref-type="bibr" rid="8 6">6?8</xref>
        ).
      </p>
      <p>
        Broad-range 16S rRNA gene PCR analysis has already been
evaluated for the diagnosis of PJI; 16S rRNA gene PCR assays of
periprosthetic tissue or periprosthetic sonicate fluid samples
showed a wide range of sensitivity and specificity values, from 50
to 92% and from 65 to 94%, respectively (
        <xref ref-type="bibr" rid="13 14 12 9">9?15</xref>
        ). Compared with
conventional culture, the sensitivity of 16S rRNA gene PCR
analysis was higher, lower, or equivalent, sometimes to the detriment
of specificity (
        <xref ref-type="bibr" rid="13 14 12 9">9?15</xref>
        ). More-recent studies on 16S rRNA gene PCR
assays of periprosthetic sonicate fluids have also shown
contradictory results. In one study, 16S rRNA gene PCR analysis and culture
of sonicate fluid were shown to have equivalent performance
results for PJI diagnosis (
        <xref ref-type="bibr" rid="16">16</xref>
        ). In another study, 16S rRNA gene PCR
assays of periprosthetic tissue or sonicate fluid samples did not
diagnose more PJI cases than did culture of adequate
periprosthetic tissue samples (
        <xref ref-type="bibr" rid="17">17</xref>
        ). Finally, a recent study found greater
sensitivity with a multiplex PCR panel, including anaerobic
bacteria, applied to implant-derived sonicate fluid samples (
        <xref ref-type="bibr" rid="18">18</xref>
        ).
These contradictory results may be due to different pretreatment
procedures applied to samples before DNA extraction, different
numbers of samples per patient, and use of the largest panel of
bacteria, especially anaerobes (such as Propionibacterium acnes,
which is often missed by 16S rRNA gene PCR assays). The wide
range of PCR assay performance in different single-center studies
underlines the interest in multicenter protocols for evaluation of
16S rRNA gene PCR analysis.
      </p>
      <p>
        The Infectious Diseases Society of America (IDSA) provided
recent guidelines assessing definitive evidence of PJI when
perioperative surgical features of infection were observed, with multiple
tissue specimens found to be positive in culture (
        <xref ref-type="bibr" rid="4">4</xref>
        ). At the end of
the IDSA guidelines, gaps in information were identified, such as
the role of PCR assays and bead mill processing in the diagnosis of
PJI on a routine basis (
        <xref ref-type="bibr" rid="4">4</xref>
        ).
      </p>
      <p>The main objective of our study was to assess the contributions
of 16S rRNA gene PCR assays to PJI diagnosis. Our network
organization for the multidisciplinary diagnosis and treatment of
bone and joint infections in seven referral centers was used to
achieve the first prospective multicenter study related to the
molecular diagnosis of PJI.</p>
    </sec>
    <sec id="2">
      <title>MATERIALS AND METHODS</title>
      <p>Study design. This study was designed as a multicenter, prospective,
observational, cross-sectional study of adult patients suspected to have PJIs.
The study protocol was approved by the institutional review board or
ethics committee at every site. Informed consent was obtained from each
patient before inclusion.</p>
      <p>Study population. Consecutive patients with clinical signs suggesting
acute or chronic PJI in 7 French university hospitals between December
2010 and March 2012 were included. Five patients per center who were
undergoing primary total arthroplasty, with no history of joint surgery,
during the same study period were also included, and their tissue samples
were processed as negative controls for the PCR and culture procedures.
Six tissue samples were collected during surgery, i.e., five samples for
culture and PCR and one periprosthetic membrane sample for
histological analysis. Case report forms were created for collection of the following
data for each patient: patient characteristics, arthroplasty localization,
presentation of infection, and antibiotic treatment in the 15 days before
surgery.</p>
      <p>
        Definition of PJI. Acute PJI was suspected for patients with pain,
disunion, necrosis, or inflammation of the scar in the months following
prosthesis implantation. Chronic infection was suspected in the presence
of chronic pain without systemic symptoms, as well as a loosened
prosthesis (
        <xref ref-type="bibr" rid="4 5">4, 5</xref>
        ). According to the IDSA guidelines, PJI was diagnosed when at
least one of the following criteria was positive: (i) clinical evidence with
the presence of a sinus tract communicating with the prosthesis and/or
purulence around the prosthesis, (ii) histological results positive for
infection (as specified above), and/or (iii) bacteriological evidence of
infection (as specified below).
      </p>
      <p>
        Microbiological methods. Cultures of periprosthetic tissue samples
were performed in each center following a standardized protocol. For
each patient, 5 perioperative specimens were collected in sterile vials with
different surgical instruments. After the addition of 10 ml sterile water and
10 sterile stainless steel beads (4-mm diameter), the vials were shaken on
a Retsch MM401 bead mill for 2.5 min, at 30 Hz. Two aliquots of each of
the 5 bead-milled suspensions were collected for molecular assays.
Aliquots (2 ml) were inoculated into a blood culture bottle and Schaedler
anaerobic liquid broth, and both were incubated at 37°C. Three additional
50- l aliquots were spread on a blood agar plate and a Polyvitex chocolate
agar plate, both of which were incubated for 7 days at 37°C in 5% CO2, and
3584 jcm.asm.org
a blood agar plate, which was incubated for 5 days at 37°C in an anaerobic
atmosphere. The Schaedler anaerobic liquid broth was subcultured for 72
h on blood agar plates in an anaerobic atmosphere if cloudy (or
systematically at the 14th day). Isolated bacteria were identified according to
standard laboratory procedures. Antibiotic susceptibility testing was
performed as recommended (http://eucast.org/clinical_breakpoints). The
bacteriological results were considered positive if at least one culture
yielded a strict pathogen (Staphylococcus aureus, Pseudomonas aeruginosa,
Enterobacteriaceae, or anaerobes) or two cultures yielded a pathogen that
was a skin commensal (such as coagulase-negative staphylococci [CoNS]
or Propionibacterium acnes) (
        <xref ref-type="bibr" rid="4">4</xref>
        ).
      </p>
      <p>
        Histological analysis. The periprosthetic membrane samples were
fixed in buffered formalin, and paraffin block sections were stained with
hematoxylin and eosin. Using the criteria described by Feldman et al.
(adapted from the criteria described by Mirra et al.), the histological
results were considered positive for infection when at least 5 neutrophils per
high-power field (magnification, 400) were found with examination of
at least five separate microscopic fields (
        <xref ref-type="bibr" rid="7 6">6, 7</xref>
        ). The specimens were
examined by pathologists who were blinded to the presence of infection and the
results of the cultures.
      </p>
      <p>Molecular methods. PCR assays of periprosthetic tissue specimens
were performed in a highly standardized manner with the 5 patient
samples. All PCRs were performed in parallel with cultures from the same
bead-milled suspension. A 200- l aliquot of each bead-milled suspension
was treated with proteinase K (2 g/liter) for 3 h at 65°C. Then, DNA
extraction was performed using Qiagen manual extraction (4
laboratories) or automated extraction (3 laboratories, using MagNA Pure
[Roche], EasyMag [bioMérieux], and iPrep [Invitrogen] systems).
Realtime PCR was performed with Sybr green to target the 5= part of the 16S
rRNA gene (forward primer 27F, 5=-AGA GTT TGA TCM TGG CTC
AG-3=; reverse primer 685R3, 5=-TCT RCG CAT TYC ACC GCT AC-3=;
658-bp amplification product; GenBank accession number NR_024570).
The corresponding amplicons were sequenced in both strands and
assembled, and the consensus sequences were compared with those in the
Bioinformatics Bacteria Identification (BIBI) and BLAST databases. The rates
of concordance between 16S rRNA gene PCR and bacteriological results
were based on results at the genus ( 96% similarity) and species ( 98%
similarity) levels. A negative control and a positive control with
Roseomonas DNA were assayed in parallel with each series of 5 samples per patient.
A fragment of the human beta-globin gene was amplified for each negative
sample, to control for DNA extraction and to confirm the absence of PCR
inhibitors. All specimens for which inhibition was observed were diluted
1:10 and retested. Patients with inhibitors in at least two specimens were
excluded from analysis. The criterion for molecular diagnosis was
modeled on the bacteriological criterion ( 1 positive sample for strict
pathogens and 2 positive samples for commensal skin flora). Molecular data
were analyzed according to the diagnosis of PJI.</p>
      <p>A multicenter external quality control (MEQC) assay was set up to
validate the 16S rRNA gene PCR results obtained with the diverse
molecular laboratory equipment. Three sets of samples, including 4 bacterial
DNA extracts and 4 bead-milled osteoarticular tissue specimens, were
sent to each laboratory, in November 2010, June 2011, and March 2012.</p>
      <p>Statistical analysis. Categorical data were expressed as numbers and
percentages, and continuous variables were reported as medians with
interquartile ranges. Molecular data were analyzed using numbers and
percentages according to the number of confirmed PJIs or unconfirmed PJIs.
The sensitivity and specificity of the 16S rRNA gene PCR were estimated
with 95% exact confidence intervals.</p>
    </sec>
    <sec id="3">
      <title>RESULTS</title>
      <p>Patient characteristics. Three hundred five patients were
included and 6 were excluded, yielding 299 patients for analysis
(Table 1). There were 264 suspected cases of PJI and 35 controls.</p>
      <p>Of the suspected cases of PJI, 127 (48%) occurred in male patients,
and the median age at the time of diagnosis was 73 years. The
6 patients excluded from the study
299 patients analysed
suspected cases of PJI included 165 hip arthroplasty infections
(63%) and 88 knee arthroplasty infections (33%). The patients
presented with symptoms of acute infection in 19% of cases and
chronic infection in 81% of cases. Seventy-six patients (29%; 19
with acute PJIs and 57 with chronic PJIs) received antibiotics for 2
weeks before surgery.</p>
      <p>Diagnosis of infection. After analysis of clinical,
bacteriological, and histological findings, a definitive diagnosis of infection
was confirmed in 215 of 264 suspected cases of PJI (Fig. 1). Of the
215 patients with confirmed PJIs, 192 (89%) had positive
bacteriological findings, monomicrobial in 163 cases (85%; 35 acute and
128 chronic infections) and polymicrobial in 29 cases (15%; 10
acute and 19 chronic infections) (Table 2). Of the monomicrobial
infections, staphylococci were isolated in 108 cases (66%),
streptococci and enterococci in 22 cases (13.5%), Gram-negative bacilli
in 16 cases (10%), anaerobes in 13 cases (8%), and other bacteria
in 4 cases (2.5%) (Table 2). The 29 polymicrobial infections were
caused by 2 bacterial species in 22 cases and 3 or 4 species in the
remaining 7 cases (Table 3). Cultures remained sterile for 23
confirmed cases of PJI, including 16 patients (70%) being treated with
antibiotics at the time of surgery (Fig. 2). Forty-nine patients
35 patients as a control group
undergoing total primary hip
arthroplasty</p>
      <p>264 patients with suspected PJI
49 unconfirmed PJI</p>
      <p>215 confirmed PJI
192 confirmed PJI with positive
microbiological culture
23 confirmed PJI with negative</p>
      <p>microbiological culture
163 with monomicrobial PJI</p>
      <p>29 with polymicrobial PJI
FIG 1 Flow chart of enrolled patients. Six patients were excluded for the following reasons: inclusion criteria not met (n 4), microbiological protocol not
respected (n 1), and patient included twice (n 1). The 35 control patients had negative culture results. The 49 unconfirmed cases of PJI had no clinical,
bacteriological, or histological evidence.
Microbiologically
documented PJI</p>
      <p>Available PCR Positive PCR
results results
showed no clinical, bacteriological, or histological evidence of
infection. The diagnosis of PJI could not be confirmed
postoperatively in those cases, which were considered aseptic failures.</p>
      <p>Analysis of 16S rRNA gene PCR assay results. Of the 192
confirmed PJIs with bacteriological documentation, the molecular
diagnosis was positive for 143 PJIs (121 monomicrobial and 22
polymicrobial infections), negative for 40 PJIs, and
uninterpretable for 9 PJIs, owing to the presence of PCR inhibition (Fig. 2).</p>
      <p>Of the 40 bacteriologically documented PJIs with negative
molecular diagnoses, 33 were monomicrobial infections with
Staphylococcus epidermidis (n 10), Staphylococcus lugdunensis (n 4), P.
acnes (n 7), S. aureus (n 6), Enterobacter cloacae (n 1),
Klebsiella oxytoca (n 1), Proteus mirabilis (n 1), P. aeruginosa
(n 1), Enterococcus faecalis (n 1), or Corynebacterium
amycolatum (n 1); among them, 8 patients had a single specimen
positive for the same bacterium in the PCR assay as in culture (S.
epidermidis, n 4; S. lugdunensis, n 2; P. acnes, n 2); the
remaining 7 bacteriologically documented PJIs with negative
molecular diagnoses were polymicrobial infections. Regarding
polymicrobial infections with positive molecular diagnoses,
sequencing of 16S rRNA gene PCR products found one bacterium in 19
cases, 2 bacteria in 1 case, and uninterpretable results due to
unreadable sequences in 2 cases (Table 3).</p>
      <p>Of the 23 confirmed PJIs that remained negative in culture, the
molecular diagnoses were positive for 8 of 16 patients treated with
antibiotics at the time of surgery and negative for 7 patients who
did not receive antibiotics (Fig. 2). Of the 49 patients without
confirmed diagnoses of PJI, the molecular diagnoses were positive
in 2 cases, negative for 42 PJIs, and uninterpretable for 5 PJIs
owing to PCR inhibitors (Fig. 2). The patients with positive PCR
results for Listeria monocytogenes and S. aureus had been treated
with antibiotics several months earlier for previous PJIs due to
these bacteria; they were not treated after the current operations.
3586 jcm.asm.org</p>
      <p>In 3 of 49 unconfirmed PJIs, 1 of 5 samples was PCR positive for
Acinetobacter johnsonii, Corynebacterium lipophiloflavum, or P.
acnes. The sensitivity and specificity of the 16S rRNA gene PCR
assay according to the diagnosis of PJI were 73.3% (95%
confidence interval, 66.7 to 79.2%) and 95.5% (95% confidence
interval, 84.5 to 99.4%), respectively.</p>
      <p>In the external quality control assay, 160/168 quality controls
(one laboratory did not participate in the first quality control
series) could be analyzed, including 80 DNA extracts and 80 crushed
samples. The overall rate of correct answers was 93.8% (150/160
samples), with the same proportions for bacterial DNA extracts
and crushed samples. Our results showed that manual and
automated extraction methods had similar performance results for
osteoarticular specimens, whatever equipment was used for the
16S rRNA gene PCR assays.</p>
      <p>Control patient analysis. All 35 control patients were found to
be negative by culture. Among them, the molecular diagnoses
were negative for 33 patients and uninterpretable for 2 patients
owing to the presence of PCR inhibitors.</p>
    </sec>
    <sec id="4">
      <title>DISCUSSION</title>
      <p>
        Our study is the first prospective multicenter study to explore the
performance of 16S rRNA gene PCR assays for a large number of
PJIs. Clinical, bacteriological, and histological criteria were
chosen according to the latest IDSA guidelines on prosthetic joint
infections (
        <xref ref-type="bibr" rid="4">4</xref>
        ). Molecular biology results were validated through a
multicenter external quality control study, which will soon be
submitted for publication. The correct results obtained uniformly
showed that 16S rRNA gene PCR assays may be used with different
types of laboratory equipment for molecular diagnosis of bone
and joint infections. DNA samples were extracted from the same
bead-milled suspensions used for the cultures. The PCR assays
and cultures were performed with the five periprosthetic tissue
samples collected for each patient included in the study. The
criterion for molecular diagnosis was adapted from the
bacteriological one, depending on whether the bacteria belonged to skin flora
or were strict pathogens (
        <xref ref-type="bibr" rid="19 4">4, 19</xref>
        ).
      </p>
      <p>One of the main findings from our study is the excellent
spec215 confirmed PJI
192 confirmed PJI with
positive culture
23 confirmed PJI with</p>
      <p>negative culture
163 with
monomicrobial PJI
16 treated patients
7 untreated patients
8 with a positive
molecular diagnosis
8 with a negative
molecular diagnosis
7 with a negative
molecular diagnosis
264 patients with
suspected PJI
Negative molecular
diagnosis n=42
Positive molecular
diagnosis n=2
PCR-inhibitors n=5
29 with polymicrobial</p>
      <p>
        PJI
121 with a positive
molecular diagnosis
33 with a negative
molecular diagnosis
9 with PCR-inhibitors
22 with a positive
molecular diagnosis
7 with a negative
molecular diagnosis
0 with PCR-inhibitors
FIG 2 Molecular results. The 49 unconfirmed cases of PJI had no clinical, bacteriological, or histological evidence. Two patients with positive PCR results for
Listeria monocytogenes or Staphylococcus aureus had been treated with antibiotics several months previously for PJIs caused by these bacteria. The diagnosis of 215
cases of PJI was confirmed according to guidelines.
ificity of our 16S rRNA gene PCR results. PCR results that were
positive for environmental or skin bacteria and negative when
assays were performed with the second DNA extract allowed us to
eliminate rare cases of contamination. Samples that tested positive
for S. aureus and L. monocytogenes using PCR were from two
patients who had been treated for PJIs caused by these bacteria
several months earlier. The persistence of DNA from nonviable
bacteria several months after clinical cure has already been
reported for infective endocarditis and is shown here for the
first time for PJIs (
        <xref ref-type="bibr" rid="20">20</xref>
        ). The excellent specificity of broad-range
PCR assays, when standard recommendations are followed to
prevent contamination, was already reported in many other
studies (
        <xref ref-type="bibr" rid="13 14 15">11, 13?15</xref>
        ).
      </p>
      <p>A lack of sensitivity of broad-range PCR assays was observed in
our multicenter study of a large number of patients with PJIs.</p>
      <p>
        Indeed, 16S rRNA gene PCR results were not contributory in the
diagnosis of 64 confirmed cases of PJI (30%), including 40 cases
with positive culture results. A number of cases (n 8) had
positive 16S rRNA gene PCR results for S. epidermidis, S. lugdunensis,
or P. acnes for a single sample, which can be explained by the low
bacterial inocula in chronic infections and thus the small amount
of bacterial DNA in the extracts. One question that remains
unresolved is whether the bacterium identified by the 16S rRNA gene
PCR assay in a single sample is responsible for the infection. The
lack of sensitivity of broad-range PCR assays was already shown in
two previous studies, including 13 and 18 PJIs (
        <xref ref-type="bibr" rid="11 17">11, 17</xref>
        ), despite the
use of pretreatment with lytic enzymes (proteinase K, lysozyme,
lysostaphin, and mutanolysin) to ensure optimal lysis of bacteria
(17).
      </p>
      <p>Conversely, the PCR results became positive after DNA
dilution for five patients with positive culture results, which
highlighted the risk of PCR inhibition caused by excessively high DNA
concentrations and the need to test diluted and undiluted DNA
when performing PCR assays. Finally, of 16 patients who were
receiving antibiotics at the time of surgery and had negative
culture results, 8 also had negative PCR results, highlighting the lack
of sensitivity of the 16S rRNA gene PCR system. Concerning
polymicrobial infections, one potential benefit of 16S rRNA gene PCR
assays may be the identification of all bacteria involved, which is
time-consuming using traditional cultures. However, cloning of
PCR products is often needed to analyze mixed sequence results,
which is impossible to perform on a routine basis. Unfortunately,
in our study, almost one-quarter of the polymicrobial PJIs yielded
negative PCR results, and 66% tested positive for only one species.</p>
      <p>
        Our study is the first multicenter study that proposes a
multicenter homogenization of culture techniques. We chose a uniform
number of samples, with many being collected at the
bone-prosthesis interface. Using a bead mill provides better bacterial
extraction from the tissue matrix. The bead-milled suspensions can be
used to seed solid and culture media, and portions of the samples
can be frozen for molecular tests. This approach enabled us to
document the infection in 89% of cases, compared with 61% or
70% in other reported studies, and for 96% of patients who were
not receiving antibiotics at the time of surgery (
        <xref ref-type="bibr" rid="2 18">2, 18</xref>
        ).
      </p>
      <p>
        Concerning the distribution of bacteria in PJIs, our study
confirms the predominance of staphylococci, which accounted for
56% of infections, and the same representations of Gram-negative
bacilli (8%) and polymicrobial infections (15%) over the decades
(
        <xref ref-type="bibr" rid="1 21 23">1, 21?24</xref>
        ). There was an almost-equal distribution between S.
aureus and CoNS. Of the CoNS, S. lugdunensis was the second
most frequently isolated species after S. epidermidis, confirming its
strong virulence, as reported previously (
        <xref ref-type="bibr" rid="25">25</xref>
        ). Concerning
streptococcal infections, our study confirms the importance of
Streptococcus agalactiae and shows the existence of true PJIs caused by
the Streptococcus mitis and Streptococcus milleri groups (
        <xref ref-type="bibr" rid="26">26</xref>
        ). P.
acnes infections represented 7% of monomicrobial anaerobic PJIs,
which highlights its role in the pathogenicity of
implant-associated infections (
        <xref ref-type="bibr" rid="27">27</xref>
        ). Considering the performance of the 16S
rRNA gene PCR assay according to the different bacteria,
sensitivity was excellent for S. aureus and streptococci, poorer for CoNS,
and bad for P. acnes, as only 11% of P. acnes and 72% of CoNS
infections were detected by PCR, compared with 92% and 100%
of S. aureus and streptococci, respectively.
      </p>
      <p>
        In conclusion, our prospective study demonstrated the
reliability of routine 16S rRNA gene PCR assays through the use of
multicenter quality control. However, its lack of sensitivity even in
treated patients did not allow us to recommend the systematic use
of the 16S rRNA gene PCR assay for optimal detection of
microorganisms causing monomicrobial or polymicrobial PJIs. Finally,
the use of other techniques in addition to cultures, such as
multiplex PCR or pathogen-specific PCR assays, should be considered
for infections that remain negative in culture (
        <xref ref-type="bibr" rid="28 18">18, 28</xref>
        ).
      </p>
    </sec>
    <sec id="5">
      <title>ACKNOWLEDGMENTS</title>
      <p>This study was supported by a grant from the French Ministry of Health
(Programme Hospitalier de Recherche Clinique Interrégionale grant API/
N/041) and a grant from the Centre de Référence des Infections
Ostéoarticulaires du Grand Ouest (CRIOGO).</p>
      <p>We gratefully acknowledge Karine Fèvre and Line Happi for their help
with the study and technical assistance. We are indebted to Jane Cottin
(deceased) for her enthusiasm until the end. We are also very grateful to all
members of the CRIOGO for their continuing support.
3588 jcm.asm.org
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Spectroscopic_evidence_of_thermally_induce.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>Phys. Chem. Chem. Phys.</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>Spectroscopic evidence of thermally induced metamorphosis in ethenylene-bridged periodic mesoporous organosilicasw</article-title>
      </title-group>
      <article-id pub-id-type="doi">10.1039/b808630n</article-id>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Carl Vercaemst</string-name>
          <email>carl.vercaemst@Ugent.be</email>
          <xref ref-type="aff" rid="3">3</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>James T. A. Jones</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Yaroslav Z. Khimyak</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jos e´ C. Martins</string-name>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Francis Verpoort</string-name>
          <xref ref-type="aff" rid="3">3</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Pascal Van Der Voort</string-name>
          <xref ref-type="aff" rid="3">3</xref>
        </contrib>
        <aff id="0">
          <label>0</label>
          <institution>H MAS NMR. See DOI: 10.1039/b808630n</institution>
        </aff>
        <aff id="1">
          <label>1</label>
          <institution>Department of Chemistry, University of Liverpool</institution>
          ,
          <addr-line>Crown Street, Liverpool</addr-line>
          ,
          <country country="UK">United Kingdom</country>
          <addr-line>L69 72D</addr-line>
        </aff>
        <aff id="2">
          <label>2</label>
          <institution>Department of Organic Chemistry, University of Ghent</institution>
          ,
          <addr-line>Krijgslaan 281, building S4, 9000 Ghent, Belgium w Electronic supplementary information (ESI) available:</addr-line>
        </aff>
        <aff id="3">
          <label>3</label>
          <institution>Department of Inorganic and Physical Chemistry, Centre for Ordered Materials</institution>
          ,
          <addr-line>Organometallics and Catalysis (COMOC)</addr-line>
          ,
          <institution>University of Ghent</institution>
          ,
          <addr-line>Krijgslaan 281, building S3, 9000 Ghent</addr-line>
          ,
          <country country="BE">Belgium</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Spectroscopic evidence of the thermally induced generation of multifunctional mesoporous materials through metamorphism within the pore walls of ethenylene-bridged PMOs is presented.</p>
      </abstract>
      <volume>10</volume>
      <fpage>5349</fpage>
      <lpage>5352</lpage>
      <pub-date>
        <year>2008</year>
      </pub-date>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>-</title>
      <p>Since their introduction in 1992,1 materials with
welldefined mesopores continue to attract a great deal of attention
of scientists from various research fields, ranging from
catalysis,2 adsorption chemistry3 and environmental technology4
to sensing,5 microelectronics6 and drug delivery.7 In
particular, functionalized, ordered mesoporous materials with tuned
physical and chemical properties have proven to be very
interesting. With the discovery of periodic mesoporous
organosilicas (PMOs) in 1999, a novel method to obtain
organic?inorganic hybrid materials with high organic content was
introduced.8 These materials are prepared via the direct
condensation of bridged organosilanes, most commonly
(EtO)3Si?R?Si(OEt)3, in the presence of a liquid crystal template.8?10
This way the obtained PMO materials combine both the
structural rigidity of the siloxane bridges and the chemical
functionality of the organic groups. In contrast to mesoporous
materials functionalized via post-modification, these organic
entities are an intrinsic part of the hybrid framework. This
unique feature not only offers the possibility of modifying the
chemical and physical properties of the framework by
adjusting the organic functionality, but also permits one to study the
occurrence of intermolecular interactions in the PMO pore
walls. In the case of methylene-bridged PMOs, it has been
reported that the bridging methylene groups can transform
into terminal methyl groups.9 In this report, clear
spectroscopic evidence is given of a thermally induced metamorphosis
in the pore walls of diastereoisomerically pure
ethenylenebridged PMOsz (B100% trans), that were recently reported
upon for the first time by our group.11</p>
      <p>This contribution is mainly focused on the generation of
multifunctional PMOsz through transformation of bridging
ethenylene groups into pendant vinyl and aliphatic groups and
on the elucidation of the mechanism whereby this process
occurs. In particular, the thermal properties of these materials
are investigated by means of DRIFT, FT-Raman and
solidstate NMR spectroscopy.</p>
      <p>In Fig. 1 the N2-isotherms and X-ray diffraction patterns
(XRD-patterns) of the diastereoisomerically pure
?CHQCH?PMO, (a) before and (b) after thermal treatment,
are given. The XRD-patterns (a) and (b) reveal intense peaks
with d100 spacings of 9.10 and 7.95 nm respectively. The two
smaller, but well-resolved peaks, can be ascribed to the (110)
and (200) reflections. These assignments are consistent with a
hexagonally well-ordered PMO material with a P6mm space
group. From Table 1 it is evident that the thermal treatment
results in a decrease of the surface area and overall porosity of
the PMO material. Furthermore, some shrinkage of the pores
is visible. FT-Raman and 1H?29Si CP/MAS (cross
polarization/magic angle spinning) NMR spectroscopic data confirm
that no cleavage of the carbon?silicon bond occurs during the
synthesis or extraction of the PMOs.</p>
      <p>In Fig. 2 the DRIFT-spectra are given of a
?CHQCH?PMO, before and after thermal treatment. As a
reference, the DRIFT-spectrum of pure vinylsilica is also
illustrated. The thermally treated PMO exhibits four
additional peaks at 3067, 3026, 1602 and 1411 cm 1. When
compared to the DRIFT-spectrum of vinylsilica, these peaks
can be assigned to the anti-symmetric and symmetric C?H
stretch, the CQC stretch and the QCH2 deformation of the
.
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thermally generated vinyl groups respectively. The thermally
treated PMO also exhibits a band at 2890 cm 1. The presence
of this band is unexpected, as it cannot be assigned to
thermally generated vinyl groups. Moreover, the frequency
of the band is typical for a C?H stretch of an alkane, implying
the formation of an aliphatic group.</p>
      <p>In Fig. 3 the FT-Raman spectra of the ?CHQCH?PMO, (a)
before and (b) after thermal treatment are presented. Here
also, the spectrum of pure vinylsilica is given for reference
purposes. FT-Raman spectrum (a) reveals three intense peaks
at 2961, 1572 and 1302 cm 1. These peaks can be assigned to
the C?H stretch, CQC stretch and in-plane C-H deformation
of the ethenylene bridges respectively. Besides the typical
Raman frequencies of the ethenylene bridges, the FT-Raman
spectrum (b), of the thermally treated PMO, exhibits
additional well-resolved peaks at 3068, 1603 and 1412 cm 1. These
peaks, when compared to spectrum (c), can be assigned to the
anti-symmetric C?H stretch, the CQC stretch and the
symmetric QCH2 deformation of the thermally generated vinyl
groups. FT-Raman spectrum (b) also reveals two shoulder
peaks at 2986 and 1279 cm 1 which can be assigned to the
C?H stretch and the in-plane C?H deformation of the vinyl
groups, respectively. These Raman results confirm the
thermally induced generation of vinyl groups. Spectrum (b) in
Fig. 3 reveals an intense peak at 2908 cm 1. This peak, which
is typical for the C?H stretch of an aliphatic group, further
suggests that the thermal treatment also induces the formation
of a saturated C?C bond.</p>
      <p>Fig. 4 illustrates the 1H?13C CP/MAS NMR spectra of the
CHQCH?PMO both before and after thermal treatment and
of pure vinylsilica. The 1H?13C CP/MAS NMR spectrum of
the template extracted ?CHQCH?PMO shows a single
resonance at ca. 146.4 ppm corresponding to the ?CHQCH?
bridging organic groups. The thermal treatment resulted in
appearance of additional resonances at 6.1, 18.9, 129.6 and
136.4 ppm. The resonances at 129.6 and 136.4 ppm can be
assigned to terminal vinyl groups, as confirmed by the 1H?13C
CP/MAS NMR spectrum of the pure vinylsilica. This is
.
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      <p>Scheme 1 Schematic representation of the silanol?ethene interaction and the cleavage of the Si?C bond of the ethenylene-bridge, leading to the
formation of a pendant vinyl group and a siloxane bridge.
consistent with the results of DRIFT and FT-Raman
measurements (Fig. 2 and 3 respectively). The resonances at 6.1
and 18.9 ppm are somewhat unexpected. The line at 6.1 ppm is
typical of an aliphatic O3Si?CH2CH2?SiO3 bridging group, in
agreement with the observation of an aliphatic C?H stretch in
the DRIFT and FT-Raman spectra. The broad resonance at
18.9 ppm suggests the formation of terminal RSi?CH2CH3
functionalities with a broad line at ca. 19 ppm resulting from
the ?CH2? groups and the resonance at 6.1 ppm resulting from
the terminal ?CH3.</p>
      <p>1H?29Si CP/MAS NMR is indicative of the degree of
condensation of pore walls and integrity of the framework
upon synthesis, template extraction and thermal treatment.</p>
      <p>The three resonances in the 1H?29Si CP/MAS NMR spectrum
of the ?CHQCH?PMO, illustrated in Fig. 5, can be assigned
as follows: T1 (R?Si(OSi)(OH)2) sites at 64.2 ppm; T2
(R?Si(OSi)2(OH)) sites at 73.6 ppm and fully condensed T3
(R?Si(OSi)3) sites at 82.9 ppm. The absence of Qn silicon
species in the region of 90 to 120 ppm confirms that no
Si?C bond cleavage occurred during synthesis or template
extraction.</p>
      <p>The 1H?29Si CP/MAS NMR spectrum of the
?CHQCH?PMO after thermal treatment (Fig. 5b) shows
the same three major resonances although broadening of the
peaks is observed. An increased intensity of the resonance at</p>
      <p>65.7 ppm suggests the presence of ?CH2CH2? and ?CH2CH3
T3 sites along with ?CHQCH? T1 sites. A shoulder line at</p>
      <p>58.6 ppm is a result of T2 resonance representing silicon sites
bound to the aliphatic carbon, also consistent with the
DRIFT, FT-Raman and 1H?13C CP/MAS NMR data. The
low intensity line at ca. 100 ppm is a silicon Qn site, a direct
result of Si?C bond cleavage during thermal treatment. The
29Si{1H} MAS NMR spectrum (see ESIw) confirms the variety
of chemical environment of 29Si in these materials.</p>
      <p>Consistent with the DRIFT, FT-Raman and NMR data,
revealing both a decrease in RSi?OH and ?CHQCH? species
and an increase in RSi?O?SiR and ?CHQCH2 species, we
propose a mechanism which is depicted in Scheme 1. Herein,
by means of elevating the temperature, terminal vinyl groups
and siloxane bridges are generated via proton transfer from
silanol groups to ethenylene bridging groups. The absence of
any surfactant in the pores excludes the possibility that the
proton transfer arises from the surfactant template.</p>
      <p>In conclusion, we have developed a multifunctional PMO
material with stereochemical environment. Clear
spectroscopic evidence of thermally induced metamorphosis in the
pore walls of these ethenylene-bridged PMOs is given for the
first time. The transformation occurs via proton transfer from
silanol groups to ethenylene bridging groups, resulting in
terminal vinyl groups and siloxane bridges.</p>
      <p>Acknowledgements
The authors are indebted to the FWO-Vlaanderen (Fund for
Scientific Research Flanders) and the University of Ghent for
financial support. The FWO Scientific Research Network on
Magnetic Resonance is thanked for facilitating scientific
exchanges.
z The ethenylene-bridged PMOs were synthesized using a procedure
very similar to that recently reported by our group.11 In a typical
synthesis 1.00 g of Pluronic P123 was diluted in an acidified solution
containing 47.80 ml of distilled H2O, 3.42 ml of concentrated HCl and
2.45 ml of BuOH. The solution was stirred at room temperature
for 1.5 h upon which 1.86 ml of trans-1,2-bis(triethoxysilyl)ethene
(E-BTSE) was added. The final reactant molar composition was
P123 : E-BTSE : HCl : H2O : BuOH = 1 : 29.3 : 238 : 16 097 : 155. This
solution was stirred for 4 h at 35 1C, after which 18 ml of BuOH
was added. The precipitated PMO was successively aged for an
additional 16 h at 90 1C under static conditions. The template was
removed by means of soxhlet extraction using acetone over a period of
5 h. Prior to the thermal treatment the PMOs were dried under
vacuum at 120 1C and analyzed by N2-physisorption, PXRD,
solidstate NMR, DRIFT and FT-Raman spectroscopy. The PMOs were
then thermally treated at 380 1C for 10 h under vacuum.
1 C. T. Kresge, M. E. Leonowicz, W. J. Roth, J. C. Vartuli and J. S.</p>
      <p>Beck, Nature, 1992, 359, 710.
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TFIID_TAF6-TAF9_Complex_Formation_Involves.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>Received for publication, May</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>TFIID TAF6-TAF9 Complex Formation Involves the HEAT Repeat-containing C-terminal Domain of TAF6 and Is Modulated by TAF5 Protein*</article-title>
      </title-group>
      <article-id pub-id-type="doi">10.1074/jbc.M112.379206</article-id>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Elisabeth Scheer</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Frédéric Delbac</string-name>
          <xref ref-type="aff" rid="0">0</xref>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Laszlo Tora</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Dino Moras</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Christophe Romier</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>From the</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Département de Biologie Intégrative</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Département de Génomique Fonctionnelle et Cancer</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Institut de Génétique et</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <aff id="0">
          <label>0</label>
          <institution>Biologie Mole?culaire et Cellulaire (IGBMC), Universite? de Strasbourg (UDS)</institution>
          ,
          <addr-line>CNRS, INSERM, 1 rue Laurent Fries, B.P. 10142, 67404 Illkirch Cedex and the</addr-line>
        </aff>
        <aff id="1">
          <label>1</label>
          <institution>Laboratoire Microorganismes: Ge?nome et Environnement, Clermont Universite?, Universite? Blaise Pascal</institution>
          ,
          <addr-line>B.P. 10448, 63000 Clermont-Ferrand</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Background: TFIID/SAGA histone fold-containing subunits contain conserved additional domains of unknown function. Results: The large TAF6 conserved C-terminal domain contains HEAT repeats and influences TAF6-TAF9 complex formation. Conclusion: TAF6 C-terminal domain is important for TFIID assembly and may trigger signals from transcriptional effectors. Significance: The noncanonical nature of TFIID/SAGA histone fold-containing subunits appears essential for assembly of these complexes.</p>
      </abstract>
      <volume>7</volume>
      <issue>2012</issue>
      <fpage>27580</fpage>
      <lpage>27592</lpage>
      <pub-date>
        <year>2012</year>
      </pub-date>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>-</title>
      <p>The general transcription factor TFIID recognizes specifically
the core promoter of genes transcribed by eukaryotic RNA
polymerase II, nucleating the assembly of the preinitiation
complex at the transcription start site. However, the understanding
in molecular terms of TFIID assembly and function remains
poorly understood. Histone fold motifs have been shown to be
extremely important for the heterodimerization of many TFIID
subunits. However, these subunits display several evolutionary
conserved noncanonical features when compared with histones,
including additional regions whose role is unknown. Here we
show that the conserved additional C-terminal region of TFIID
subunit TAF6 can be divided into two domains: a small middle
domain (TAF6M) and a large C-terminal domain (TAF6C). Our
crystal structure of the TAF6C domain from Antonospora
locustae at 1.9 Å resolution reveals the presence of five conserved
HEAT repeats. Based on these data, we designed several
mutants that were introduced into full-length human TAF6.
Surprisingly, the mutants affect the interaction between TAF6
and TAF9, suggesting that the formation of the complex
between these two TFIID subunits do not only depend on their
histone fold motifs. In addition, the same mutants affect even
more strongly the interaction between TAF6 and TAF9 in the
context of a TAF5-TAF6-TAF9 complex. Expression of these
mutants in HeLa cells reveals that most of them are unstable,
suggesting their poor incorporation within endogenous TFIID.
* This work was supported by institutional funds from the CNRS, the INSERM,
and the Université de Strasbourg. Further funding was provided by the
European Commission SPINE2-Complexes project (Contract
LSHG-CT2006-031220) (to C. R. and D. M.) and by grants from the Agence Nationale
de la Recherche (ANR) (ANR-09-BLAN-0052) and the European Union (EU)
(EUTRACC, LSHG-CT-2007-037445) (to L. T.).</p>
      <p>The atomic coordinates and structure factors (code 4ATG) have been deposited in
the Protein Data Bank, Research Collaboratory for Structural Bioinformatics,
Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).
1 To whom correspondence should be addressed. Tel.: 33-3-88-65-57-98; Fax:
33-3-88-65-32-79; E-mail: romier@igbmc.fr.
Taken together, our results suggest that the conserved
additional domains in histone fold-containing subunits of TFIID
and of co-activator SAGA are important for the assembly of
these complexes.</p>
      <p>
        Transcription initiation by eukaryotic RNA polymerase II
requires the binding at the core promoters of several general
transcription factors (TFIIA,2 -B, -D, -E, -F, -H) that correctly
position RNA polymerase II at the transcription start site and
subsequently initiate promoter clearance (
        <xref ref-type="bibr" rid="1 2">1, 2</xref>
        ). TFIID, a large
multiprotein complex composed of 15 well conserved subunits
(the TATA box-binding protein (TBP) and 14 TBP-associated
factors, TAF1 to TAF14), binds specifically to core promoters
and initiates the recruitment of the other general transcription
factors and RNA polymerase II over the transcription start site
(
        <xref ref-type="bibr" rid="3 4">2? 4</xref>
        ).
      </p>
      <p>
        Recruitment of TFIID is carried out by interaction of its
subunits with transcriptional activators as well as its specific
recognition of promoter elements such as the TATA box (TBP),
the initiator (TAF1 and TAF2), as well as the downstream
promoter element and the mutation ten element (TAF6 and TAF9)
(
        <xref ref-type="bibr" rid="5 4">4, 5</xref>
        ). In metazoans, recognition of the doubly acetylated H4
histone tail by the tandem bromodomains of TAF1 and the
trimethylated lysine 4 of histone H3 (H3K4me3) by TAF3 PHD
(plant homeo domain) domain also contributes to TFIID
recruitment at promoters (
        <xref ref-type="bibr" rid="6">6, 7</xref>
        ).
      </p>
      <p>
        Recently, electron microscopy (EM) studies at 20 Å
resolution have shed light on the TFIID mechanism (
        <xref ref-type="bibr" rid="8">8</xref>
        ). Upon
recruitment by the Rap1 transcriptional activator, and in the presence
2 The abbreviations used are: TFII, general transcription factor II; TBP, TATA
box-binding protein; TAF, TBP-associated factor; HFT, histone
fold-containing TAF; CHES, N-cyclohexyl-2-aminoethane-sulfonic acid; WCE, whole
cell extract; SAGA, Spt-Ada-Gcn5 acetyltransferase.
of TFIIA, TFIID binds to a TATA box-containing promoter by
inducing the formation of a DNA loop. This process appears to
lock TFIID onto promoter DNA, suggesting the first steps of
the assembly of the transcription preinitiation complex.
However, despite these first results, the mode of action of TFIID at
the molecular level still remains poorly understood. Notably,
high resolution structural data on the whole complex are still
crucially missing, such data being difficult to obtain due to the
large size and the intrinsic flexibility of this complex.
      </p>
      <p>
        Nevertheless, many biochemical and structural studies have
provided information on the structure of submodules of TFIID
as well as on TFIID assembly. Notably, the histone fold motif
has been shown to play an essential role for the dimerization
of several TAFs, and five different histone-like pairs
(TAF4TAF12, TAF6-TAF9, TAF10-TAF3, TAF10-TAF8, and
TAF11TAF13) have been characterized so far (
        <xref ref-type="bibr" rid="15 16 14 12 10">9 ?17</xref>
        ). It has been
proposed that a histone octamer-like substructure (formed by the
pairs TAF4-TAF12 and TAF6-TAF9) exists in TFIID, and such
a complex has been reconstituted in vitro with the yeast
proteins (
        <xref ref-type="bibr" rid="19 18">18, 19</xref>
        ). Moreover, immunolabeling experiments
coupled to EM studies as well as biochemical studies have
revealed that each histone-like pair in TFIID is present twice
in the complex, each pair being found in two different lobes
of TFIID (
        <xref ref-type="bibr" rid="21">20, 21</xref>
        ).
      </p>
      <p>
        Histone fold-containing TAFs (HFTs) are not sufficient to
form a stable subcomplex within TFIID, and the WD40
repeatcontaining TAF5 subunit appears important for integrating
HFTs into a single subcomplex (
        <xref ref-type="bibr" rid="22 23">22, 23</xref>
        ). In agreement, in yeast,
TAF5 and four HFTs (TAF6, TAF9, TAF10, and TAF12) are
shared between TFIID and the transcriptional co-activator
SAGA, suggesting that they form the structural core of these
complexes (
        <xref ref-type="bibr" rid="25">24, 25</xref>
        ). In metazoan SAGA, these HFTs are also
shared, with the exception of TAF5 and TAF6, which are
replaced by paralogues, namely TAF5L and TAF6L (
        <xref ref-type="bibr" rid="25">25</xref>
        ). In
addition, the other HFTs specific to TFIID are replaced in
SAGA by specific histone fold-containing subunits (Ada1, Spt3,
and Spt7L), suggesting a way to form two different multiprotein
transcriptional activators with the same structural core (
        <xref ref-type="bibr" rid="12 4">4, 12</xref>
        ).
      </p>
      <p>Although the histone fold motifs of the HFTs have drawn
most of the attention on these TAFs, those motifs have not kept
the high positive charge of the canonical histones, suggesting
that their primary role is not DNA binding but rather
dimerization, and possibly multimerization. In addition, the HFTs often
have additional regions whose role remains elusive. It is not
clear whether these additional regions, the histone fold motifs,
or both, are responsible for the assembly of higher order
structures within TFIID.</p>
      <p>
        TAF6 contains one of these additional regions. This region is
located at its C terminus and has been evolutionary conserved.
Surprisingly, despite this strong conservation, it has been
proposed that this region is not essential for TFIID assembly (
        <xref ref-type="bibr" rid="26">26</xref>
        ).
This result is, however, in contradiction with the fact that a
human TFIID complex incorporating the TAF6 isoform
TAF6 , which lacks the central part of its histone fold domain,
still retains all TAFs except TAF9 (
        <xref ref-type="bibr" rid="27">27</xref>
        ), suggesting that other
regions of TAF6 are required for integration of this TAF within
TFIID.
      </p>
    </sec>
    <sec id="2">
      <title>To address this issue, we have performed biochemical and</title>
      <p>structural studies on the conserved C-terminal region of TAF6.
This C-terminal region appears to be formed by two domains: a
small middle domain and a larger C-terminal domain. The
crystal structure of the larger C-terminal domain of TAF6 from
Antonospora locustae reveals that it is constituted of five HEAT
repeats, a motif generally involved in protein/protein
interactions. Surprisingly, mutations of conserved residues at the
surface of this C-terminal domain in full-length human TAF6
cause the weakening of the interactions between TAF6 and
TAF9. Moreover, introduction of these TAF6 mutants in the
context of a TAF5-TAF6-TAF9 complex appears to weaken
even further the TAF6-TAF9 complex, suggesting
conformational changes in the TAF6-TAF9 complex upon TAF5
binding. Expression of these mutants in HeLa cells shows that many
of them are less stable when compared with the wild type TAF6.
These results suggest that these mutants are poorly
incorporated within TFIID and submitted to degradation inside the
cell. Taken together, our results suggest that (i) formation of
histone fold-containing heterodimers within TFIID does not
simply rely on the histone fold motif of each partner and (ii)
TFIID assembly is an intricate process possibly requiring
conformational changes that may be important for TFIID function.</p>
      <sec id="2-1">
        <title>EXPERIMENTAL PROCEDURES</title>
        <sec id="2-1-1">
          <title>Cloning, Expression, and Purification?The various con</title>
          <p>
            structs used were amplified by standard PCR procedures and
inserted in the pnEA-tH (
            <xref ref-type="bibr" rid="28">28</xref>
            ) expression vector using NdeI and
BamHI restriction sites. Expression of all proteins was made
using Escherichia coli BL21(DE3) cells (Novagen) in 2 LB
medium for native proteins or using B834(DE3) cells (Novagen)
in M9 medium supplemented with selenomethionine (Sigma)
for selenomethionylated proteins. Cells were grown at 37 °C to
an absorbance of 0.3 at 600 nm, and the temperature was then
switched to 25 °C. Growth was then carried on until cells
reached an absorbance of 0.8 ?1.0 at 600 nm. Expression was
induced by adding a final concentration of 1 mM isopropyl-
D-thiogalactopyranoside (Euromedex), and cells were further
grown overnight at 25 °C. Cells were collected by low speed
centrifugation, resuspended in buffer A (10 mM Tris, pH 8.0;
400 mM NaCl), and lysed by sonication. The soluble fraction
recovered by high speed centrifugation was mixed with 1 ml of
Talon resin (Clontech). After a 1-h incubation, the supernatant
was removed, and the resin was washed extensively with buffer
A. The resin was then resuspended in 2 ml of buffer A, and
bovine thrombin (Sigma) was added overnight at 4 °C for
cleaving off the histidine tag. The supernatant was recovered and
applied onto a gel filtration column HiLoad 16/60 Superdex 75
(Amersham Biosciences) equilibrated with buffer A. The
purified proteins were concentrated on Microsep 10K Omega (Pall
Filtron) to a final concentration of around 5 mg/ml as assayed
with the Bio-Rad protein assay (Bio-Rad).
          </p>
          <p>Crystallization?The A. locustae TAF6C domain (residues
164 ?355) was crystallized by mixing 2 l of protein solution
with an equal volume of the reservoir solution containing 0.1 M
CHES (Sigma), pH 9.5, and 10% (w/v) PEG3350 (Fluka).
Crystals grew within a few days to reach an approximate size of
0.15 0.15 0.05 mm3. For data collection, crystals were
briefly transferred in a cryoprotectant solution of 0.1 M CHES,
pH 9.5, 10% (w/v) PEG3350, and 25% glycerol (Fluka) and
quickly frozen in liquid ethane.</p>
          <p>
            Data Collection and Structure Determination?Initial
inhouse data collection revealed that A. locustae TAF6C crystals
belong to space groups P21. To solve the phase problem,
crystals were grown with selenomethionylated protein. Due to the
relatively rapid decay of the crystals upon x-ray exposure at
synchrotron sources, only single wavelength anomalous
diffraction experiments could be performed on these crystals at
the selenium peak wavelength. Data collection on single native
and selenomethionylated crystals was carried out on beamline
ID14H4 at the European Synchrotron Radiation Facility. Data
at 1.9 Å resolution for native and 2.4 Å resolution for
selenomethionylated crystals were obtained (see Table 1). All data were
processed and scaled using HKL2000 (
            <xref ref-type="bibr" rid="29">29</xref>
            ). Location of
selenium atoms was done using Shake and Bake (
            <xref ref-type="bibr" rid="30">30</xref>
            ), their
positions were refined within the phasing program SHARP (
            <xref ref-type="bibr" rid="31">31</xref>
            ),
and the phases were further improved with the solvent
flattening program SOLOMON (
            <xref ref-type="bibr" rid="32">32</xref>
            ).
          </p>
          <p>
            Model Building and Refinement?Eight -helices could be
built in the initial single wavelength anomalous diffraction
experimental electron density map at 2.4 Å resolution.
Unfortunately, this information was not sufficient to improve the
quality of the map. We therefore used this initial model and the
native 1.9 Å resolution data for phase improvement within
ARP/wARP (
            <xref ref-type="bibr" rid="33">33</xref>
            ). The resulting map was of sufficient quality to
build the rest of the model. This model was further refined by
cycles of manual building within TURBO-FRODO and Coot
(
            <xref ref-type="bibr" rid="34">34</xref>
            ) and refinement with REFMAC (
            <xref ref-type="bibr" rid="35">35</xref>
            ) and BUSTER (
            <xref ref-type="bibr" rid="36">36</xref>
            ). The
structure shows good deviations from ideal geometry (see
Table 1), with no Ramachandran outliers.
          </p>
          <p>
            The TAF6C domains from A. locustae, yeast, and human
show almost identical values for pairwise identity (around 28%)
and similarity (around 47%). Based on these numbers, we could
confidently make models of yeast and human TAF6C domains
by using MODELLER (
            <xref ref-type="bibr" rid="37">37</xref>
            ). As expected, major differences were
located within the loop regions and in the last HEAT repeat,
which shows lower sequence similarity. We used this
information subsequently for the design of our mutants and chose
residues for mutations that were located in regions where the
confidence on model quality was high. The models are available
upon request.
          </p>
          <p>Purification of the Baculovirus-expressed Human
TAF6TAF9 and TAF5-TAF6-TAF9 Complexes?All hTAF6 mutants
were constructed using nested PCR protocols, and the cDNAs
were inserted in the pVL1392 vector to encode the full-length
human TAF6 with a FLAG tag at the N-terminal end of all the
mutant proteins. These vectors were used to produce
baculoviruses using standard procedures.</p>
          <p>
            Sf9 cells were simultaneously infected with the different
baculoviruses that express His-hTAF5, FLAG-hTAF6, or
FLAG-hTAF6 mutants, and hTAF9, respectively. All wild type
constructs used to generate the baculoviruses were described
previously (
            <xref ref-type="bibr" rid="38">38</xref>
            ).
          </p>
          <p>Cells were lysed 48 h after infection in a buffer containing
protease inhibitors, 400 mM KCl, 20 mM Tris-HCl (pH 7.9), 20%
glycerol, and 2 mM DTT by three cycles of freeze-thawing. Cells
were grown in a 75-cm2 Falcon flask, resuspended in 400 l of
buffer, lysed, and centrifuged, and the soluble proteins were
used for immunoprecipitation.</p>
          <p>Immunoprecipitation, Western Blot, and Coomassie Blue
Staining Analyses of TAF6-TAF9 and TAF5-TAF6-TAF9
Complexes?First, soluble Sf9 cell extracts were diluted to 100
mM KCl with immunoprecipitation buffer (25 mM Tris-Cl, pH
7.9, 10% (v/v) glycerol, 0.1% Nonidet P-40, 0.5 mM
dithiothreitol, 5 mM MgCl2). Next TAF6-containing complexes were
isolated by immunoprecipitation with a mouse monoclonal M2
antibody (ANTI-FLAG M2 affinity gel-purified
immunoglobulin beads, Sigma-Aldrich, product number A2220).
Immunoprecipitation was carried out by an overnight incubation of 250
l of diluted protein extract with 100 l of affinity-purified
ANTI-FLAG M2 antibody-coupled beads. Beads with M2
antibody-bound protein complexes were washed three times
with immunoprecipitation buffer containing 500 mM KCl
and twice with immunoprecipitation buffer containing 100
mM KCl. Immunoprecipitated proteins were eluted by an
excess (2 mg/ml) of the corresponding FLAG epitope
peptide and then boiled in sodium dodecyl sulfate (SDS) sample
buffer and separated by SDS-polyacrylamide gel
electrophoresis (PAGE).</p>
          <p>
            Proteins were either visualized by staining the gels with
Coomassie Blue or transferred to nitrocellulose membrane and
probed with the indicated primary antibodies.
Chemiluminescence detection was performed according to the
manufacturer?s instructions (Amersham Biosciences). The rabbit
polyclonal antibody (pAb 2282) raised against hTAF9 and the
monoclonal anti-hTAF6 (25TA 2G7) and anti-hTAF5 (1TA
1C2) antibodies were described previously (
            <xref ref-type="bibr" rid="39 23">23, 39</xref>
            ).
          </p>
          <p>In Vivo Expression in HeLa Cells?For cell transfection
assays, the wild type and mutant TAF6 proteins have been
cloned into the pCDNA3.1 vector using the NheI/NotI
restriction sites of this vector. The baculovirus vectors harboring
these different proteins have been used as templates for the
PCR reactions that were also used to FLAG tag the TAF6
proteins C-terminally. HeLa cells (5 106) were transfected in
90-mm dishes with 7 g of the different expression vectors by
using JetPEI (PolyPlus Transfection). Human HeLa cells were
lysed 48 h after transfection in 100 l of buffer/dish containing
protease inhibitors, 400 mM KCl, 20 mM Tris-HCl (pH 7.9), 20%
glycerol, and 2 mM DTT by three cycles of freeze-thawing.
Extracts were then centrifuged, and the soluble proteins were
used for immunoprecipitation (see above).</p>
        </sec>
      </sec>
      <sec id="2-2">
        <title>RESULTS</title>
        <p>
          Domain Organization of TAF6?The homology of the TAF6
histone fold with histone H4 has rapidly retained most of the
focus on this small N-terminal domain (
          <xref ref-type="bibr" rid="40 17 41">17, 18, 40 ? 42</xref>
          ).
However, the C-terminal region of TAF6 is also well conserved
throughout evolution, with the exception of its very C-terminus
(Fig. 1A). Specifically, the conserved C-terminal region of TAF6
is more than four times bigger than the histone fold motif and
starts immediately after the histone fold, suggesting that these
two regions may be functionally linked.
        </p>
        <p>
          To understand the functional role of the TAF6 C-terminal
region, we have started its biochemical and structural
characterization. The proteins from four organisms were used:
human, Saccharomyces cerevisiae (thereafter termed yeast),
and the two eukaryotic intracellular parasites Encephalitozoon
cuniculi and A. locustae. We use these two latter organisms as
model organisms for structural studies because their proteins
are generally shorter than their higher eukaryotic orthologues
but still retain the same domain organization (
          <xref ref-type="bibr" rid="46 43 45">43? 46</xref>
          ).
Specifically, the C-terminal region of the TAF6 proteins from these
two organisms ends exactly where the C-terminal conservation
of TAF6 finishes (Fig. 1A).
        </p>
        <p>Despite numerous trials, initial crystallization attempts of
the TAF6 conserved C-terminal region from the four
organisms studied were unsuccessful. Sequence analysis suggested
that this region can be divided into two domains. The first
domain (TAF6 middle domain; TAF6M) encompasses about 70
residues immediately after the histone fold motif. TAF6M is
separated from the second domain (TAF6 C-terminal
domain; TAF6C) by a poorly conserved stretch of 20 ?50
residues. The TAF6C domain forms the larger part of the
TAF6 conserved C-terminal region, spanning about 220
residues (Fig. 1, A and B).</p>
        <p>Secondary structure prediction suggests that both TAF6M
and TAF6C domains have different secondary structure
content. Specifically, predictions do not clearly indicate the kind of
secondary structure elements present in TAF6M, with
propensities for -helices, -strands, and coil being relatively equal
over the whole domain. In contrast, the TAF6C domain is
clearly predicted as purely -helical. We reasoned that the
putatively poorly folded TAF6M domain could have prevented
the crystallization of the full C-terminal region of TAF6. We
therefore expressed, purified, and submitted to crystallization
trials the TAF6C domains of the human, yeast, E. cuniculi, and
A. locustae TAF6 proteins.</p>
        <p>
          The Conserved TAF6C Domain Is Formed of Five HEAT
Repeats?Plate-shaped crystals were obtained with the
A. locustae construct. Despite their small thickness, some of the
crystals showed diffraction better than 2 Å resolution at
synchrotron sources, and a complete data set at 1.9 Å resolution
could be collected from a single crystal with good data
collection statistics (Table 1). Structure determination was carried
out by collecting single wavelength anomalous diffraction data
at 2.4 Å resolution on crystals grown with
selenomethioninesubstituted protein. After improvement of the initial single
wavelength anomalous diffraction map by solvent flattening, a
few helices could be located in the electron density but were not
sufficient for improving the quality of the map. Therefore, these
helices were positioned by rigid body in the 1.9 Å native map,
and the electron density was improved using ARP/wARP (
          <xref ref-type="bibr" rid="33">33</xref>
          ).
        </p>
        <p>The resulting map was of sufficient quality to build the rest
of the protein. The final model includes all but the last
C-terminal residue and 178 water molecules and has an R-factor
and an Rfree of 16.9 and 22.3%, respectively, with good
deviations from the ideal geometry (Table 1). Inspection of the
electron density also revealed the presence of two CHES
molecules at the interface of symmetry-related molecules,
explaining the absolute requirement for CHES in the
crystallization condition.</p>
        <p>Analysis of the final model revealed the presence of five
HEAT repeats tightly packed against each other, defining a
single structural domain (Fig. 2A). HEAT repeats are formed of a
single helical hairpin formed by two -helices ( A and B).</p>
        <p>
          HEAT repeats are known protein/protein interaction motifs
that are found repeated several times in many proteins (
          <xref ref-type="bibr" rid="47">47</xref>
          ).
        </p>
        <p>Specifically, when found in large numbers in proteins, these
repeats adopt a superhelix conformation. This is clearly not the
case in the TAF6C domain due to the small number of repeats,
which is not sufficient to adopt a helical conformation. In fact,
this domain resembles more a paving stone with six faces
(Fig. 2A).</p>
        <p>Because HEAT repeats are generally found repeated many
times in proteins harboring this kind of motif, the question
remains whether more repeats are present in TAF6. As already
mentioned, the TAF6M domain is not predicted to have a high
helical content and is separated from the TAF6C by a
nonconserved region of variable length, thus suggesting that it adopts a
different fold. Inspection of the conformation of the N-terminal
residues in our TAF6C structure confirms that their packing is
incompatible with the extension of the HEAT repeats at the N
terminus of TAF6C. Although it cannot be excluded that the
truncation of the protein leads to a different conformation of
these N-terminal residues, the poor helical propensity and the
poor conservation of the residues preceding the TAF6C
domain argue against an extension of the HEAT repeats at the
N terminus of the TAF6C.</p>
        <p>The A. locustae TAF6 protein terminates exactly with the
last HEAT repeat, which corresponds exactly to the position
where the conservation of the TAF6 finishes (Figs. 1 and 2A).</p>
        <p>Based on the A. locustae structure and our multiple sequence
alignment, we modeled the conserved yeast and human TAF6C
domains, which revealed that both proteins can adopt the same
fold without any steric clashes. Nonetheless, these latter two
proteins are longer than the A. locustae and E. cuniculi proteins
(about 50 and 250 additional residues for the yeast and human
TAF6, respectively). Secondary structure predictions suggest
the presence of helices in the remaining C-terminal region of
yeast and human TAF6, notably in the regions immediately
following the conserved TAF6C domain. Thus, it cannot be
excluded that the yeast and human TAF6 proteins encode a
small number of additional C-terminal HEAT repeats, but the
length of the TAF6 protein precludes that a large number of
these repeats are present in the TAF6 protein, as observed in
other proteins.</p>
        <p>Analysis of the electrostatic potential at the surface of the
TAF6C domain reveals a rather large positively charged patch
on one face of the TAF6C domain that could be indicative of a
specific electrostatic interaction surface (Fig. 2, B and C).
Interestingly, analysis of the electrostatic potential at the surface of
the modeled human and yeast TAF6C domains reveals that
only this positive patch is conserved between these three
domains (Fig. 3), suggesting that it is important for TFIID
assembly and/or function.</p>
        <p>The Conserved C-terminal Domain of Human TAF6 Is
Important for Interactions with TAF9 and TAF5?We next
sought to understand the role of the TAF6 HEAT repeats,
considering their strong evolutionary conservation. From (i) the
structure of the A. locustae TAF6C, (ii) the established models
of the yeast and human TAF6C, and (iii) the multiple sequence
alignment, we listed a certain number of exposed conserved or
semiconserved residues that could play a role by acting in
protein/protein interactions. Although many of these residues
were located in the vicinity of the positive electrostatic patch,
others were located on other faces of the TAF6C, suggesting
that the TAF6C could mediate multiple interactions.</p>
        <p>
          We decided to mutate these residues facewise (i.e. each
face of the TAF6C paving stone being mutated
independently from the others) in the human protein to investigate
the role of each face of the TAF6C domain. Due to the
presence of several conserved residues on all faces, multiple
residues were initially mutated together. Another mutant was lyzed by SDS-PAGE and Coomassie Blue staining. From this
made according to a known mutant from the literature (
          <xref ref-type="bibr" rid="48">48</xref>
          ). initial analysis, the exact amounts of sample to be loaded on an
Finally, two single mutants were made that involved half- SDS gel were estimated to keep the quantity of the different
buried and perfectly conserved residues. All mutants are TAF6 proteins constant. This second gel was then used for
listed in Table 2, and their locations are shown in Fig. 1B. To Western blotting TAF9 and, if necessary, TAF5, thus enabling
test the effect of these mutants, we used the TAF6-TAF9 quantification of the relative abundance of each subunit in the
complex, which is supposed to assemble through the histone complex.
fold motif of these two proteins, as well as the TAF5-TAF6- None of the mutants showed a complete loss of interaction
TAF9 complex, which appears to be sufficient to form the with TAF9 or TAF5-TAF9. Surprisingly, however, in the case of
three-lobed structure of TFIID and is important for human the TAF6-TAF9 complex, all mutants showed a weakening of
TFIID assembly (
          <xref ref-type="bibr" rid="22">22</xref>
          ). the interaction because lower amounts of TAF9 were
co-immu
        </p>
        <p>The human TAF6-TAF9 and TAF5-TAF6-TAF9 complexes, noprecipitated with the TAF6 mutants than with the wild type
containing either wild type or mutated TAF6, were reconsti- protein (Fig. 4, A and B). Specifically, the two mutants with
tuted by co-expressing all full-length proteins in insect cells single point mutations (mutants m7 and m8) showed the larger
using the baculovirus expression system. All TAF6 proteins decrease of interaction with TAF9. The residues mutated in
(wild type and mutated) contained a FLAG tag for affinity puri- these two mutants are highly conserved residues in TAF6C and,
fication. All the TAF6 mutants were expressed and soluble, contrary to most of the residues mutated in the other mutants,
showing that the mutations do not affect solubility of TAF6 these residues are half-buried within the domain. It might
(Fig. 4A). After affinity purification, the complexes were ana- therefore well be that these residues affect locally the structure
of the TAF6C and cause a stronger effect on the complex than
what would be expected by weakening direct interactions
between the two partners. Nonetheless, altogether these results
suggested that the TAF6C domain also participates in the
overall interaction between TAF6 and TAF9.</p>
        <p>We then analyzed the effect of the same mutants in the
context of the TAF5-TAF6-TAF9 complex. Once again, none of
the mutants caused a complete dissociation of the complex.</p>
        <p>However, all mutants were responsible for a weakening of the
interaction because lower amounts of both TAF5 and TAF9
were co-immunoprecipitated with TAF6 mutants when
compared with the wild type TAF6 (Fig. 4, C and D). Importantly,
some of the mutants appeared to have different effects when
introduced in the context of either the TAF6-TAF9 complex or
the TAF5-TAF6-TAF9 complex. Firstly, mutant m1, which
already reduced by more than 2-fold the quantity of TAF9
bound to TAF6 in the context of the dimeric complex,
appeared to have an even stronger effect on TAF9 binding in
the trimeric complex. Interestingly, this mutation had less
effect on TAF5 binding, suggesting that TAF5 interaction
FIGURE 3. Electrostatic potential at the surface of A. locustae, H. sapiens, with the TAF6-TAF9 complex may somehow weaken the
and S. cerevisiae TAF6C domains. The electrostatic potentials 7 and 7 interaction between these two HFTs, thus leading to a
stronkBT (kB, Boltzmann constant; T, temperature) are colored red and blue, respec- ger loss of TAF9 (Fig. 4).
tcirvyesltya.lTlohgerastprhuicctusrteruscutsuerde foanrdthethcealcmuoladteiolends asrteruthctousreeosfoAf. lHoc.usastpaieenTsAaFn6Cd In contrast, the effect of the mutants m7 and m8, which were
S. cerevisiae TAF6C domains built by homology using the A. locustae struc- the most deleterious for the TAF6-TAF9 complex, was much
ttautrieo.nTshoeftwA.oloocruiesntataetTioAnFs6sChodwispeldayceodrr einspFoign.d2tBo. tAheclueaprpceor nasnedrvloewdeproosriiteivne- milder for the ternary complex. As already mentioned, these
patch is observed in the three proteins in panel B. In contrast, the other side of two mutants could have destabilized, at least partially, the
the protein (panel A) does not seem to have conserved electrostatic features. structure of the TAF6C, and thus have an indirect effect on
Phenotype in Caenorhabditis elegans
Surface exposure
Conservation and surface exposure
Conservation and surface exposure
Conservation and surface exposure
Conservation
Conservation</p>
        <p>TAF9 binding. In the context of the ternary complex, binding of mutants m4, m5, and m6 are located on the surface of TAF6C
TAF5 to TAF6 could stabilize TAF6C and thus restore binding that has a strong positive charge.
of TAF9 to TAF6. In agreement, not only TAF9 binding, but Binding of Human TAF5 Modulates the Interaction between
also TAF5 binding to TAF6, was less affected. Human TAF6 and TAF9?The results obtained by these initial</p>
        <p>The remaining mutants (m2 to m6) affected more strongly mutational studies apparently imply an unexpected role of
TAF5 binding, with a loss of about 60% of the bound protein TAF6C in TAF9 binding, which appears further modulated by
(Fig. 4, C and D). Interestingly, these mutants can be split into TAF5 binding. Most of the mutants considered, however, were
two classes when considering their effect on TAF9 binding in composed of a large number of mutations, suggesting that these
the context of the TAF5-TAF6-TAF9 ternary complex. First, strong changes could have, in fact, an indirect effect on dimeric
mutants m2 and m3 showed similar amounts of TAF9 binding and trimeric complex formation (e.g. due to a large change of
as in the context of the dimeric complex. This suggests that the the overall electrostatic charge of TAF6). To address this issue,
effect of these mutants on TAF5 and TAF9 binding is not cou- we decided to create mutants with single point mutations that
pled, i.e. that the mutants affect nonoverlapping binding sur- should have less of an effect on the physicochemical properties
faces for TAF5 and TAF9. Contrasting with mutants m2 and of the TAF6 protein. The residues to be mutated were chosen
m3, mutants m4, m5, and m6 show a decrease of TAF9 binding within the initial m1 and m5 mutants that showed strong, albeit
when compared with their effect on the TAF6-TAF9 complex. different effects on TAF5 and TAF9 binding. The choice was
This effect appears, however, not as strong as for mutant m1 also made considering the position of the residues to be
but, once again, speaks in favor of a destabilization of the TAF6- mutated, looking for fully exposed residues, but also for
resiTAF9 complex upon binding of TAF5, suggesting structural dues that were not conserved between the TAF6 and TAF6L
rearrangements occurring during TFIID assembly. Of note, families. To increase the chances that these single mutations
would still show an effect on complex formation, we decided to
of the TAF6-TAF9 complex revealed that the mutations
introintroduce larger changes than only alanines, either with bulkier
side chains or, when applicable, residues observed in the human
TAF6L protein (mutants are shown in Table 3, and their
locations are shown in Fig. 1B).</p>
      </sec>
    </sec>
    <sec id="3">
      <title>In contrast to the results with the first set of mutants, analysis of the effect of these new single point mutants on the formation</title>
      <p>duced hardly have any influence (Fig. 5, A and B). Mutant m9
(R315A) appears the only exception, causing a decrease of
TAF9 binding, suggesting an important role for this residue in
the formation of the TAF6-TAF9 complex. In strong contrast,
introduction of these new single point mutants in the context of
the TAF5-TAF6-TAF9 complex shows drastic effects on
complex formation, affecting both TAF5 and TAF9 binding (Fig. 5,
C and D). These results reinforce the idea that TAF5 binding to
the TAF6-TAF9 complex causes destabilization of this latter
complex and also suggest that exposed TAF6L residues could
serve to discriminate between TAF5 and TAF5L in metazoans.</p>
      <sec id="3-1">
        <title>In Vivo Importance of the TAF6C Domain?We next investi</title>
        <p>gated whether the TAF6 mutants would incorporate in human
TFIID complex. For this purpose, vectors expressing
FLAGtagged human TAF6, either wild type or mutant forms, were
transfected in HeLa cells. 48 h after transfection, whole cell
extracts (WCEs) were prepared, and anti-FLAG purifications
were carried out to test how the exogenously expressed TAF6
proteins incorporate in TFIID complexes. Only mutant m1,
which harbored many mutations, was not considered for this
study.</p>
        <p>Surprisingly, when analyzing the overexpression levels of the
transfected FLAG-tagged mutants in WCEs in comparison
with endogenous TBP levels, we reproducibly observed lower
amounts of several mutants when compared with the
overexpressed wild type TAF6 (Fig. 6, A and B). This suggests that the
mutations might cause partial misincorporation of TAF6 in
endogenous TFIID and would thus lead to its partial
degradation.</p>
        <p>
          Nevertheless, we further analyzed some mutants by carrying
out FLAG purification to test their capability to incorporate in
endogenous TFIID complexes. Three mutants were chosen
according to their increasing stability in HeLa cells: m3, m6,
and m9. Analysis by Western blotting for the presence of other
TFIID subunits in these anti-FLAG immunoprecipitations did
not reveal a total loss or strong diminution of these subunits,
with a possible small effect on TAF5 for mutants m6 and m9
(Fig. 6C), suggesting that stabilization of the TAF6 mutants
occurs upon complex formation. Taken together, these
observations suggest that the observed diminution of the quantities
of each mutant is most likely due to the difficulties encountered
by the mutants to be incorporated into endogenous TFIID,
leading to their partial degradation, a phenomenon already
observed upon knockdown of different TFIID subunits in
Drosophila (
          <xref ref-type="bibr" rid="26">26</xref>
          ).
        </p>
        <p>Due to the complexity of TFIID assembly, it is difficult to
directly compare these in vivo results with the ones obtained on
the reconstitution of the TAF6-TAF9 and TAF5-TAF6-TAF9
subcomplexes by overexpression in insect cells. However, one
important aspect concerns the results obtained with TAF6
single point mutants. We showed that these mutants had little
effect on TAF6-TAF9 complex formation but, unexpectedly,
had strong effects on TAF5-TAF6-TAF9 complex formation
(Figs. 4 and 5). In the in vivo context, these mutants also appear
to show an effect, albeit less pronounced than the mutants with
several mutations. Thus, results obtained on the TAF6-TAF9
and TAF5-TAF6-TAF9 subcomplexes appear to be confirmed
in vivo (Fig. 6D).</p>
        <sec id="3-1-1">
          <title>DISCUSSION</title>
        </sec>
      </sec>
    </sec>
    <sec id="4">
      <title>Numerous biochemical and structural studies have shown</title>
      <p>
        that the histone fold motif plays a major role in TFIID and
SAGA assembly, enabling the formation of five distinct
histone-like pairs (
        <xref ref-type="bibr" rid="13 12 14 16 9">9, 11?17, 20</xref>
        ). Interestingly, almost all HFTs
harbor various additional regions that most likely convey
structural and/or functional roles. For instance, the
metazoan-specific TAF3 PHD domain and TAF4 homology domain
(TAFH) have been shown to recognize epigenetic marks and
activators (
        <xref ref-type="bibr" rid="50 49 7">6, 7, 49 ?51</xref>
        ). Other additional regions of HFTs
have been conserved throughout eukaryotic evolution and
are more likely to be involved in broader structural and
functional roles of TFIID. These roles, however, remain to be
determined.
      </p>
    </sec>
    <sec id="5">
      <title>We provide here results on the structure and the role of one</title>
      <p>
        of these conserved additional regions in the C-terminal region
of TAF6. This region, which immediately follows the histone
fold motif of TAF6, can be divided in two domains: a small
middle domain (TAF6M), which is separated from a larger
C-terminal domain (TAF6C) by a loop varying in sequence and
in length. The structure of the TAF6C domain from A. locustae
reveals that this domain is composed of five HEAT repeats that
appear conserved from yeast to human. HEAT repeats (and the
related ARM repeat) are known protein/protein interaction
motifs that are repeated many times in a wide variety of
proteins, forming superhelices that interact extensively with their
target proteins (
        <xref ref-type="bibr" rid="47">47</xref>
        ). These motifs are also used by other
transcriptional effectors to bind their targets, as shown recently for
the Iws1 and Mot1 proteins (
        <xref ref-type="bibr" rid="52 44">44, 52</xref>
        ).
      </p>
      <p>Importantly, our mutational analyses suggest that the
TAF6C domain modulates the TAF6/TAF9 interaction. This
modulation provides a more dynamic view of HFT assembly.</p>
      <p>
        Clearly, the TAF6C domain is not the driving force of the
interaction between TAF6 and TAF9. Indeed, the human TAF6
isoform is not able to interact with TAF9, although it still
harbors the TAF6C domain (
        <xref ref-type="bibr" rid="27">27</xref>
        ). In addition, our mutations are
only weakening the interaction between these two TAFs. The
molecular basis for this modulation is not clear. One possibility
could be that the TAF6C domain interacts directly with the
histone-like pair. Another possibility could be that TAF6C/
TAF6C interactions stabilize the TAF6-TAF9 complex. It
cannot be excluded that a combination of these two possibilities is
at work for modulating the TAF6/TAF9 interaction.
      </p>
      <p>
        Moreover, the addition of TAF5 to the TAF6-TAF9 complex
appears to enhance the modulator effect of TAF6C. Indeed,
single point mutants of TAF6C exert an effect on the formation
of the TAF6-TAF9 complex only when TAF5 is present. This
result highlights once again the importance of TAF5 for TFIID
assembly. Specifically, TAF5 is essential for the formation of a
larger TFIID subcomplex containing most HFTs and
contributes to the three-lobed architecture of TFIID (
        <xref ref-type="bibr" rid="22">22</xref>
        ). In addition,
TAF5 is the only non-HFT subunit of TFIID shared with yeast
SAGA. Interestingly, single point mutants, where residues of
human TAF6 (TFIID-specific) are changed into residues
present in human TAF6L (SAGA-specific), also show strong effects
upon TAF5 binding (mutants m10, m12, and m14).
Considering that in humans, TFIID-specific TAF5 is replaced by
SAGAspecific TAF5L, our results suggest that specific residues of
TAF5L most likely accommodate the changes observed
between TAF6 and TAF6L. Thus, human SAGA, in contrast to
yeast SAGA, seems to have evolved specific TAFs for dedicated
functions.
      </p>
      <p>
        Importantly, overexpression of the various mutants, but not
of wild type TAF6, in HeLa cells appears to affect TAF6
stability, suggesting that these mutants are poorly incorporated into
TFIID and partially degraded, as already observed upon
knockdown of specific TAFs in Drosophila (
        <xref ref-type="bibr" rid="26">26</xref>
        ). Interestingly, even
the single point mutants of TAF6 are affected, thus paralleling
and corroborating the results obtained with these mutants
upon reconstitution of the TAF5-TAF6-TAF9 complex.
      </p>
      <p>
        The experiments with the Drosophila melanogaster TAFs
also suggested that the TAF6 C-terminal region is not required
for TFIID assembly (
        <xref ref-type="bibr" rid="26">26</xref>
        ). In these experiments, the Drosophila
TAF6 was divided into an N-terminal part and a C-terminal
part. The N-terminal part, which was shown to be necessary for
TFIID assembly, is in fact composed of the histone fold motif,
the TAF6M domain, the following loop, and the first HEAT
repeat of the TAF6C domain. Therefore, it is difficult to
delineate a clear picture from these experiments. Notably, it remains
unclear which part of TAF6 is really required for TFIID
assembly. Specifically, our mutants located in the first HEAT repeat
(m1, m2, m14, and m15) show strong effects on the stability of
the TAF5-TAF6-TAF9 complex. Because the human TAF6
isoform is incorporated within TFIID, but not TAF9 (
        <xref ref-type="bibr" rid="27">27</xref>
        ), this
suggests in fact that the TAF6M domain and the first HEAT
repeat of the TAF6C domain are the most important regions of
TAF6 for its incorporation within TFIID. In agreement,
knockdown of Drosophila TAF9 does not lead to any degradation of
TAF6, whereas knockdown of TAF1, TAF2, TAF4, or TAF5
causes almost complete disappearance of Drosophila TAF6 in
WCEs (
        <xref ref-type="bibr" rid="26">26</xref>
        ).
      </p>
      <p>Although the remaining HEAT repeats of TAF6C appear,
from the Drosophila experiments, to be nonessential for TAF6
incorporation in TFIID, it cannot be excluded that these
repeats also participate, albeit less strongly, in this
incorporation. Our mutational data suggest such a role. On the other
hand, because HEAT repeats are protein/protein interaction
motifs, they may also be involved in other kinds of interactions.</p>
      <p>Specifically, these repeats could, in the context of the full
TFIID, interact with TFIID protein partners and/or DNA.</p>
      <p>Because the middle HEAT repeats of TAF6C define the surface
having a strongly conserved positive electrostatic charge, it is
likely that this surface is engaged in such interactions. Because
our mutational data suggest structural rearrangements
occurring at the TAF6/TAF9 interface upon TAF5 binding, it is
tempting to speculate that binding of other TAFs,
transcriptional effectors, and/or DNA to TAF6C might also trigger
conformational rearrangements (Fig. 6D).</p>
      <p>
        In agreement, it is interesting to note that binding of
TFIID to DNA upon recruitment by Rap1 and in the
presence of TFIIA induces conformational changes within TFIID
(
        <xref ref-type="bibr" rid="8">8</xref>
        ). Thus, conformational rearrangements between
subunits, as suggested by our data in the case of the formation of
the TAF5-TAF6-TAF9 subcomplex, could be essential. The
possibility to change from one conformation to another
upon recognition of a biological target could facilitate major
rearrangements and be of paramount importance for TFIID
and SAGA function.
      </p>
      <p>Acknowledgments?We thank members of the European Synchrotron
Radiation Facility-European Molecular Biology Laboratory
(ESRFEMBL) joint structural biology groups for the use of their beamline
facilities and for help during data collection.
Gene Regulation:
TFIID TAF6-TAF9 Complex Formation
Involves the HEAT Repeat-containing
C-terminal Domain of TAF6 and Is
Modulated by TAF5 Protein
 
Elisabeth Scheer, Frédéric Delbac, Laszlo
Tora, Dino Moras and Christophe Romier
J. Biol. Chem. 2012, 287:27580-27592.
doi: 10.1074/jbc.M112.379206 originally published online June 13, 2012
Access the most updated version of this article at doi: 10.1074/jbc.M112.379206
 
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d8f6415a393f50c1205f544a5f8f0d1e.pdf.

Cermine / Crossref / Grobid

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c3fce71cea0cf0daf58e9f916dabdb7c.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta />
    <article-meta>
      <abstract>
        <p>Your use of the JSTOR archive indicates your acceptance of the Terms &amp; Conditions of Use, available at http://www.jstor.org/page/ info/about/policies/terms.jsp JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact support@jstor.org.</p>
      </abstract>
      <volume>110</volume>
      <issue>9</issue>
      <fpage>844</fpage>
      <lpage>845</lpage>
      <pub-date>
        <year>2016</year>
      </pub-date>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>-</title>
      <p>Mathematical Association of America is collaborating with JSTOR to digitize, preserve and extend access to The American
Mathematical Monthly.
http://www.jstor.org</p>
      <p>This content downloaded from 129.199.129.11 on Fri, 15 Jan 2016 20:57:19 UTC</p>
      <p>All use subject to JSTOR Terms and Conditions
with 1 &lt; k &lt; n, let [n] denote {1, 2, ... , n}, andlet P be the discrete probabilityspace
consisting of the k-element subsets of [n], each equally likely. For S e P, let 7rs be
the permutationof [n] obtained by listing S in increasing orderfollowed by [n] - S in
increasing order. Let X (S) be the number of inversions in -rs (that is, the number of
instances of i, j E [n] such that j &lt; i and 7rs(j) &gt; Trs(i)). Prove that Var(X)/E(X)
does not depend on k.
11043. Proposed by Michael Golomb, Purdue University, WestLafayette, IN. Let f
and g be nonnegative real-valued L'1-functionson a finite interval I, and suppose that</p>
      <p>ff - g = 1.
(a) Show that for q E Z with q &gt; 2 there exists a subinterval J of I such that</p>
      <p>If</p>
      <p>=fga=
(b)* What happens if the restrictionto nonnegative functions is dropped?
11044. Proposed by Michel Bataille, Rouen, France. Let N be an odd integer greater
than 1. Let Ao = 1, and for k E N let</p>
      <p>Ak- reR -)</p>
      <p>H(r) i=1l1.2i
'
where R is the set of all k-tuples of nonnegative integers such that j= jr = k and
a (r) denotes y j= rj. For n E N, show that
1/q.</p>
      <p>kri
(1)n-1l(N
(--2n
-2kk--1 1 Ak= N2 (N
11045. Proposed by Manoj Prakash Singh, New Delhi, India. Prove that when n is a
sufficiently large positive integer there exists a finite set S of prime numbers such that
the sum of Ln/pJ over p E S is equal to n.
11046. Proposed by ChristophSoland, Neuchatel, Switzerland.Let ABC be a triangle,
let I be the incircle of ABC, and let r be the radius of I. Let K1, K2, and K3 be the
three circles outside I and tangent to I and to two of the three edges of ABC. Let ri
be the radius of Ki, for 1 &lt; i &lt; 3. Show that r = rYr2 + r2r3 + ,r3rI.</p>
    </sec>
    <sec id="2">
      <title>SOLUTIONS</title>
    </sec>
    <sec id="3">
      <title>Productsof Transpositions</title>
      <p>10913 [2001, 977]. Proposed by Donald E. Knuth,Stanford University,Stanford, CA.
Given a positive integer n, let akbe the transposition((k - 1) mod (n + 1), k mod (n +
1)), and let bkbe the transposition (k mod n, n). For example, for n = 3, we have
ao, al, a2, a3, a4, . . . = (3, 0), (0, 1), (1, 2), (2, 3), (3, 0), ....</p>
      <p>bo, bl, b2, b3, b4, . . . = (0, 3), (1, 3), (2, 3), (0, 3), (1, 3) ....</p>
      <p>Prove that aoal ... ak = bk... blbo for every k &gt; 0.
844</p>
      <p>@ THEMATHEMATICAALSSOCIATIONOFAMERICA [Monthly 110
Solution by Reiner Martin, New York,NY Let k = rn + s with 0 &lt; s &lt; n. Also, let
rt = (0, 1, .. . , s - 1, s, n), and let r = rt,_. We prove by induction on k that both
specified products equal rsTr, where k = rn + s with 0 &lt; s &lt; n. For bk... bIbo, the
induction step follows from bi ri-1 = ri for 0 &lt; i &lt; n.</p>
      <p>Next note that rai-r-j = ai+j for all positive integers i and j. With k = rn + s,
this yields
sTrak+l= = isar+k+1tr
= Tsar(n+l)+s+lTr
= tsas+lr.</p>
      <p>The last expression equals rs+Ir' if 0 &lt; s &lt; n - 1, while it equals rotr+l if s = n - 1.
Now aoal ... ak = t-r follows by induction on k, as desired.</p>
      <p>Also solved by G. Body (U. K.), D. Callan,R. Chapman(U. K.), B. Klimszova(CzechRepublic),P.Kordulova
(Czech Republic), J. H. Lindsey II, O. P. Lossers (Netherlands),J. Schlosberg (student),R. Stong, F. Szeged
(Hungary),L. Zhou, the GCHQ Problem Solving Group (U. K.), the National Security Agency Problems
Group,andthe proposer.</p>
      <p>A Sequenceof Integer Polynomials
10915 [2002, 77]. Proposed by C. P Rupert, Durham, NC. Given nonzero
polynomials p and q in Z[x] satisfying p2 + mq # 0 for 1 &lt; m &lt; 4, define polynomials t,
recursively by t,+2 = pt,+4 + qt, with initial conditions to = 0 and t1 = 1. With [
denoting the Mbbius function, prove for n &gt; 1 that the polynomial s E Q[x] defined
by s,(x) =</p>
      <p>tdg(n/d) actually belongs to Z[x].</p>
      <p>Solution byHRdlinchard Stong, Rice University, Houston, TX. Since s1(x) = tl = 1
Z[x], we assume n &gt; 1. The two roots of the characteristicpolynomial X2- p. - q
are ri = (p + p2 + 4q)/2 and r2 = (p - p2 +4q)/2. By assumption, p2 + 4q
0, and thus rl : r2. Solving the recurrencefor t, gives
n
rn - r2 r'n[(rl/r2)n - 1]
tn ri - r2 - - p24q</p>
      <p>For s, to be defined, we need tn, 0, which holds if r /r2 is not a root of unity.
Let f(X.) = + (p2/q + 2)X-+ 1. Note that rj/r2 is a zero of f, and that zeros of f
can only be-2roots of unity if (p2/q + 2) E {-2, -1, 0, 1, 2}. This is not the case, since
p 0 and p2 + mq A0 for I &lt; m &lt; 4.</p>
      <p>Now recall that Ed, n(n/d) = 0 for n &gt; 1. Also,qddn dlt(n/d) -=0(n), where 0
is Euler's totient function, and -dl xd - 1)g(n/d) =n- (x), where Oi is the nth
cyclotomic polynomial. Combining these facts shows that s, (x) = r20~) (r1/r2). Also,</p>
      <p>Sn(x) is a self-reciprocal polynomial in Z[x] of degree 0(n). Therefore, s,(x) is a
symmetric polynomial in rl and r2, and thus sn(x) e Z[r, + r2, rir2] = Z[p, -q] C
Z[x].</p>
      <p>Also solved by S. Amghibech (France),D. Callan, R. Chapman(U. K.), NSA ProblemsGroup,R. Richberg
(Germany),L. Zhou, and the proposer.</p>
      <p>Distancesto the Sides
10929 [2002, 298]. Proposed by Lajos Csete, Hungary. Let P be a point in the interior
of triangle ABC, and let rl, r2, r3 denote the distances from P to the sides of the
triangle with lengths a,, a2, a3, respectively. Let R be the circumradiusof ABC, and
let 0 &lt; a &lt; 1 be a real number.Let b = (2a)/(1 - a). Prove that</p>
      <p>+ b
rNao+vermab2e0rr0O3B]&lt;LEMA(N2RD(S)aSOL+UaTIONb)1-a</p>
      <p>PR
November 2003]</p>
      <p>PROBLEMSAND SOLUTIONS
845
845</p>
    </sec>
  </body>
  <back>
    <ref-list />
  </back>
</article>

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  <title line_height="10.8" font="Times-Bold">-)</title>
  <reference>Let be a2, a,, a3, lengths respectively. = - 1 be a real Let b
Prove number. that a). (2a)/(1 b ra r ra+ AND November b)1-a </reference>
  <reference>SOLUTION +a + (a 2003] &lt; PROBLEM(2R)S </reference>
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Exponential_Decay_Towards_Equilibrium_for_.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>Commun. Math. Phys.</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>Exponential Decay Towards Equilibrium for the Inhomogeneous Aizenman-Bak Model</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>J. A. Carrillo</string-name>
          <email>carrillo@mat.uab.es</email>
          <xref ref-type="aff" rid="2">2</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>L. Desvillettes</string-name>
          <xref ref-type="aff" rid="1">1</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>K. Fellner</string-name>
          <email>klemens.fellner@univie.ac.at</email>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <aff id="0">
          <label>0</label>
          <institution>Faculty of Mathematics, University of Vienna</institution>
          ,
          <addr-line>Nordbergstr. 15, 1090 Wien</addr-line>
          ,
          <country country="AT">Austria</country>
        </aff>
        <aff id="1">
          <label>1</label>
          <institution>CMLA, ENS Cachan, CNRS, PRES UniverSud</institution>
          ,
          <addr-line>61 Av. du Pdt. Wilson, 94235 Cachan Cedex</addr-line>
          ,
          <country country="FR">France</country>
        </aff>
        <aff id="2">
          <label>2</label>
          <institution>ICREA (Institucio? Catalana de Recerca i Estudis Avanc?ats) and Departament de Matema?tiques, Universitat Auto?noma de Barcelona</institution>
          ,
          <addr-line>E-08193 Bellaterra</addr-line>
          ,
          <country country="ES">Spain</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>The Aizenman-Bak model for reacting polymers is considered for spatially inhomogeneous situations in which they diffuse in space with a non-degenerate sizedependent coefficient. Both the break-up and the coalescence of polymers are taken into account with fragmentation and coagulation constant kernels. We demonstrate that the entropy-entropy dissipation method applies directly in this inhomogeneous setting giving not only the necessary basic a priori estimates to start the smoothness and size decay analysis in one dimension, but also the exponential convergence towards global equilibria for constant diffusion coefficient in any spatial dimension or for non-degenerate diffusion in dimension one. We finally conclude by showing that solutions in the one dimensional case are immediately smooth in time and space while in size distribution solutions are decaying faster than any polynomial. Up to our knowledge, this is the first result of explicit equilibration rates for spatially inhomogeneous coagulation-fragmentation models.</p>
      </abstract>
      <volume>451</volume>
      <issue>2008</issue>
      <fpage>433</fpage>
      <lpage>451</lpage>
      <pub-date>
        <year>2008</year>
      </pub-date>
      <history>
        <date date-type="accepted">
          <day>25</day>
          <month>7</month>
          <year>2007</year>
        </date>
        <date date-type="received">
          <day>18</day>
          <month>8</month>
          <year>2006</year>
        </date>
      </history>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>1. Introduction</title>
      <p>We analyze the spatial inhomogeneous version of a size-continuous model for reacting
polymers or clusters of aggregates:
?t f ? a(y)</p>
      <p>x f = Q( f, f ).</p>
      <p>Here, f = f (t , x , y) is the concentration of polymers/clusters with length/size y ? 0
at time t ? 0 and point x ? ? Rd , d ? 1. These polymers/clusters diffuse in the
environment . This set is assumed to be a smooth bounded domain with normalized
volume, i.e., | | = 1. In the one dimensional case, we will set = (0, 1). Equation
(1.1) is to be considered with homogeneous Neumann boundary condition
?x f (t , x , y) · ?(x ) = 0
on ?
(1.1)
with ? the outward unit normal to , so that there is no polymer flux through the physical
boundary. We assume the diffusion coefficient a(y) to be non-degenerate in the sense
that there exist a?, a? ? R+ such that</p>
      <p>0 &lt; a? ? a(y) ? a?.</p>
      <p>On the other hand, the reaction term Q( f, f ) of (1.1) models chemical
degradationbreak-up or fragmentation- and polymerization -coalescence or coagulation- of
polymers/clusters. More precisely, the full collision operator reads as</p>
      <p>Q( f, f ) = Qc( f, f ) + Qb( f, f ) = Q+( f, f ) ? Q?( f, f )</p>
      <p>= Qc+( f, f ) ? Qc?( f, f ) + Qb+( f, f ) ? Qb?( f, f )
with obvious definitions of the coagulation Qc( f, f ), fragmentation or break-up
Qb( f, f ), loss Q?( f, f ) and gain Q+( f, f ) operators which are determined from the
four basic terms in (1.4):
1. Coalescence of clusters of size y ? y and y ? y results in clusters of size y:
2. Polymerization of clusters of size y with other clusters of size y produces a loss in
its concentration:
3. Break-up of clusters of size y larger than y contributes to create clusters of size y:
(1.3)
(1.4)
(1.5)
(1.6)
(1.7)
(1.8)
0</p>
      <p>y
Qc+( f, f ) :=</p>
      <p>f (t, x , y ? y ) f (t, x , y ) d y .</p>
      <p>Qc?( f, f ) := 2 f (t, x , y)</p>
      <p>f (t, x , y ) d y .</p>
      <p>Qb+( f, f ) := 2
y
?</p>
      <p>f (t, x , y ) d y .</p>
      <p>Qb?( f, f ) := y f (t, x , y).</p>
      <p>0
?
0
?</p>
      <sec id="1-1">
        <title>4. Break-up of polymers of size y reduces its concentration:</title>
        <p>This kind of model finds its application not only in polymers and cluster aggregation
in aerosols [S16,S17,AB,Al,Dr] but also in cell physiology [PS], population dynamics
[Ok] and astrophysics [Sa]. Here, fragmentation and coagulation kernels are all set up to
constants as in the original Aizenman-Bak model [AB]. This will be of paramount
importance in the basic a-priori estimates. The conservation of the total number of monomers
at time t ? 0 quantified by</p>
        <p>N (t, x ) d x , where N (t, x ) :=
y f (t, x , y) d y
is the basic conservation law satisfied by Eq. (1.1) since the reaction term (1.4) satisfies
0
?</p>
        <p>y Q( f, f ) d y d x = 0,
and thus, assuming initially a positive total number of monomers, we formally conclude
y f (t, x , y) d y d x =</p>
        <p>N (t, x ) d x =</p>
        <p>N0(x ) d x := N? &gt; 0.</p>
        <p>(1.9)
Another macroscopic quantity of interest is the number density of polymers,
0
?
M (t, x ) :=
f (t, x , y) d y,
that together with the total number of monomers N (t, x ) satisfies the reaction-diffusion
system
(1.10)
(1.11)
(1.12)
(1.13)
(1.14)
(1.16)
(1.17)
(1.18)
?t N ?
?t M ?
x
x
?
?
0
0
ya(y) f (t, x , y) d y
a(y) f (t, x , y) d y
= 0,
= N ? M 2,
becoming a closed decoupled system in the constant diffusion case (a(y) := a):
with obvious notations.
for any smooth function ?, the function ? being the primitive of ? (?y ? = ?) such that
?(0) = 0.</p>
        <p>Let us consider the (free-energy) entropy functional associated to any positive density
f as
0
?
H ( f )(t, x ) =
( f ln f ? f ) d y,
and the relative entropy H ( f |g) = H ( f ) ? H (g) of two states f and g not necessarily
with the same L1y -norm. Then, the entropy formally dissipates as
d
dt</p>
        <p>H ( f ) d x = ?
a(y) |?x f |2 d y d x ?
f
? ?
f (y ) ? f (y) f (y ) (?(y) + ?(y ) ? ?(y )) d y d y
(1.15)
for any smooth function ?(y), where y = y + y and the dependence on (t, x ) of the
density function has been dropped for notational convenience. An alternative weak
formulation that can be useful in several arguments below is obtained integrating by parts
in the Qb+ part giving
&lt; Q( f, f ), ? &gt;= ? 2
f (y) f (y )?(y ) d y d y</p>
        <p>Global existence and uniqueness of classical solutions has been studied in [Am, AW]
for some particular cases, namely, for constant diffusion coefficient or dimension one
with additional restrictions for the coagulation and fragmentation kernel not including
the AB model. The initial boundary-value problem to (1.1)?(1.2) was then analyzed in
[LM02-1], for much more general coagulation and fragmentation kernels including the
AB model (1.5) ? (1.8), proving the global existence of weak solutions satisfying the
entropy dissipation inequality
0
t
H ( f (t )) d x +</p>
        <p>DH ( f (s)) ds ?</p>
        <p>H ( f0) d x
for all t ? 0.</p>
        <p>The equilibrium states for which the entropy dissipation vanishes are better
understood after applying a remarkable inequality proven in [AB, Props. 4.2 and 4.3]. A
modified version of this inequality (reviewed in Sect. 2) reads:
? ?
0
0
f
? f f
ln
f
f f
d y d y ? M H ( f | f?N ,N ) + 2(M ?
?N )2.</p>
        <p>(1.19)
Herein, f?N ,N denotes a distinguished, exponential-in-size distribution with the very
moments M = ?N and N :
y
f?N ,N (t , x , y) = e? ?N .</p>
        <p>These distributions f?N ,N appear as analogues to the so-called intermediate or local
equilibria in the study of inhomogeneous kinetic equation (e.g. [DV01, CCG, FNS, DV05,
FMS, NS]). Finally, the conservation of mass (1.9) identifies (at least formally) the global
equilibrium f? with constant moments M ?2 = N = N?:
y
f? = e? ?N? .</p>
        <p>The analogy to intermediate equilibria carries over to the following additivity of
relative entropies:</p>
        <p>H ( f | f?) = H ( f | f?N ,N ) + H ( f?N ,N | f?).</p>
        <p>It is worth pointing out that even if f?N ,N and f? do not have the same L 1y ?norm, its
global relative entropy
(1.20)
(1.21)
H ( f?N ,N | f?) d x = 2</p>
        <p>N d x ?
?</p>
        <p>N d x
? 0
is a nonnegative quantity, as easily checked via Jensens?s inequality. In [LM02-1], it is
proved that f? attracts all global weak solutions in L 1( × (0, ?)) of (1.1)-(1.2) but
no time decay rate is obtained. This result is the analogue to convergence results along
subsequences for the classical Boltzmann equation in [De].</p>
        <p>Other existence and uniqueness results for inhomogeneous
coagulation-fragmentation models were given in [CD] and the references therein. Finally, let us mention that
the conservation law (1.9) is known not to hold for certain coagulation-fragmentation
kernels, phenomena known as gelation [ELMP], and the convergence or not towards
typical self-similar profiles for the pure coagulation models is a related issue; we refer
to [Le,LM05,MP]. We refer finally to [LM02-1,LM03,LM04] for an extensive list of
related literature.</p>
        <p>Let us now discuss some works on the study of the long time asymptotics for
related models. Qualitative results concerning a discrete version of a
coagulation-fragmentation system, the Becker-Döring system, have been obtained in [CP,LW,LM02-2]
and the references therein. We emphasize that global explicit decay estimates towards
equilibrium were obtained for the Becker-Döring system without diffusion in [JN] by
entropy-entropy dissipation methods. Other techniques have recently been developed
for inhomogeneous kinetic equations. We refer to [MN] for a spectral approach and to
[V06] for a general description of the concept of hypocoercivity. Note that the presence
of diffusion instead of advection makes it possible in our present context, not to use the
concept of hypocoercivity.</p>
        <p>In this work we prove exponential decay towards equilibrium with explicit rates and
constants. Our key result, Lemma 2 in Sect. 2, establishes a functional inequality between
entropy and entropy dissipation provided lower and upper bounds on the moment M
and (1.3). We are able to apply this functional inequality to solutions of (1.1)-(1.2) in
the next two situations.</p>
        <p>In the special case of size-independent diffusion coefficients a(y) = a, we show, as
the first application of Lemma 2, the exponential decay towards equilibrium in all space
dimensions d ? 1 by exploiting the closed system (1.13)?(1.14) for N and M in Sect. 2.</p>
        <p>In the case of general diffusion coefficients a(y) satisfying (1.3) we prove in Sect. 3
a-priori estimates in the one-dimensional case d = 1, which entail an entropy-entropy
dissipation estimate with a constant sufficient to conclude exponential decay via a
suitable Gronwall argument (see Sect. 4). These two cases are summarized in the following
theorem:
Theorem 1. Let be a smooth bounded connected open set of Rd , d ? 1 and assume a
constant diffusion coefficient a(y) = a &gt; 0 or let be the interval (0, 1) and consider
a diffusion coefficient satisfying (1.3). Let us also assume that f0 = 0 is a nonnegative
initial datum such that (1 + y + ln f0) f0 ? L1((0, 1) × (0, ?)). In the case a(y) = a &gt; 0
assume further that initial moments M0(x ) and N0(x ) are L?( )-functions.</p>
        <p>Then, the global weak solutions f (t, x , y) of (1.1)?(1.2) decay exponentially to the
global equilibrium state (1.20) with explicitly computable constants C1, C2 and rate ?,
both in global relative entropy:
and in the L 1x,y sense:</p>
        <p>H ( f (t )| f?) d x ? C1</p>
        <p>H ( f0| f?) d x
f (t, ·, ·) ? f? L1x,y ? C2</p>
        <p>H ( f0| f?) d x
e?? t ,
e? ?2 t
(1.22)
(1.23)
for all t ? 0, where f? is defined by (1.20) and N? &gt; 0 is determined by the
conservation of mass (1.9).</p>
        <p>In the one dimensional case, it is further possible to interpolate the exponential
decay in a ?weak? norm like L1 with polynomially growing bounds in ?strong? norms
like (weighted) L1y (Hx1) in order to get an exponential decay in a ?medium? norm like
L1y (L ?x). Thus, the decay toward equilibrium can be extended to these stronger norms.</p>
      </sec>
      <sec id="1-2">
        <title>The following proposition is proved at the end of Sect. 4:</title>
        <p>Proposition 1. Under the assumptions of Theorem 1 for the case d = 1, for all t? &gt; 0
and q ? 0, there are explicitly computable constants C3, ? &gt; 0 such that whenever
t ? t?,
(1 + y)q f (t, ·, y) ? f?(y) L?x d y ? C3 e?? t .
(1.24)</p>
        <p>A bootstrap argument in the spirit of the proof of Proposition 1 allows to replace the
L ?x norm by any Sobolev norms in (1.24).</p>
        <p>g(y)g(y ) ln g(y + y ) d y d y ?
g(y) d y
g(y ) ln g(y ) d y
2. Entropy-Entropy Dissipation Estimate
Please note that in this section we will systematically use the shortcuts:
M =
f (x , y) d yd x ,</p>
        <p>N =
y f (x , y) d yd x .</p>
        <p>We start by reminding the reader of the following functional inequality:
Lemma 1 ([AB, Prop. 4.3]). Let g := g(y) be a function of L1+((0, ?)) with finite
entropy g ln g ? L1((0, ?)), then
? ?
0 0
? ?
0 0
while for the term
0
?
0
?
0
?
?</p>
        <p>.
f f
? ?
0
0
?
0
?
0
?
? f f ln f d y d y ,</p>
        <p>This inequality allows to show the dissipation inequality (1.19). Following the original
paper [AB] or the survey [LM04], one finds that
( f
? f f ) ln
d y d y
? M H ( f | f?N ,N ) + (M ?</p>
        <p>?N )2
g(y) d y</p>
        <p>(2.1)
+ M 2</p>
        <p>N N N
M 2 ln M 2 + 1 ? M 2
.</p>
        <p>(2.2)
In fact, after expanding the left-hand side of (2.2), one applies Lemma 1 to the term
one uses Jensen?s inequality for the convex function x ln x and further that
? ?
0
0
f f
f
f f
ln
f
f f</p>
        <p>d y d y
? ?
0
0</p>
        <p>f d y d y = N .</p>
        <p>Then, after directly calculating the remaining terms one obtains (2.2), as in [LM04], and
moreover the inequality (1.19) when applying the elementary inequality x ln(x )+1?x ?
(1 ? ?x )2 for x ? 0 to the last term on the right-hand side of (2.2).</p>
        <p>For the subsequent large-time analysis, we will rather study the relative entropy with
respect to the global equilibrium, which dissipates according to (1.18) and (1.19) as
d
dt</p>
        <p>We introduce a lemma enabling to estimate the entropy of f by means of its entropy
dissipation. This is a functional estimate, that is, the function f in this lemma does not
depend on t and has not necessarily something to do with the solution of our equation.
Lemma 2. Assume (1.3). Let f := f (x , y) ? 0 be a measurable function with moments
satisfying 0 &lt; M? ? M (x ) ? M L?x and 0 &lt; N? = N . Then, the following
entropy-entropy dissipation estimate holds:
with a constant C (M?, N?, a?, P( )) depending only on M?, N?, a? and the Poincaré
constant P( ).</p>
        <p>Proof. Step 1. We start with the right-hand side of (2.4) by using the additivity (1.21)
and calculating
and further, we obtain (2.6) by expanding ?N ? M 2L2 and Young?s inequality
x
?</p>
        <p>N ? M ? M + M 2L2 .</p>
        <p>x
M H ( f | f?N ,N ) d x + 2 M ?
?N 2L2
x
1 ?
2 N ? M 2L2x ?
Thus, we obtain (using 0 &lt; M? &lt; M )</p>
        <p>M ? M 2L2x ?
by the inequality (1.19)
f
? f f ln</p>
        <p>d y d y d x
f
f f
(2.4)
(2.5)
(2.6)
(2.7)
Step 3. Next, the variance of M , i.e. the last term on the right-hand side of (2.7) is
controlled by the first, ?Fisher?-type term of (2.3). Denoting with P( ) the constant of</p>
      </sec>
      <sec id="1-3">
        <title>Poincaré?s inequality, we estimate using Cauchy-Schwartz,</title>
        <p>0
provides a bound which does not seem sufficient to conclude as in Step 2.</p>
      </sec>
      <sec id="1-4">
        <title>Step 4. Finally, combining (2.7) and (2.8), we have</title>
        <p>Now, let us directly apply this entropy-entropy dissipation estimate to prove the
constant diffusion part of Theorem 1. In the constant diffusion case, the equations for the
first two moments M (t, x ) and N (t, x ) become the closed system (1.13)-(1.14). The
existence and uniqueness of global, classical solutions with global L? bounds from
below and above are standard thanks to the maximum principle applied to the equations
for N and further for M . We refer, for instance, to [Ro,Ki] for details, to conclude with:
Lemma 3. Let be a smooth bounded connected open set of Rd , d ? 1 and let us assume
that the initial data M0(x ) and N0(x ) = 0 are nonnegative L?( )-functions. Then,
there exist increasing functions t ? M?(t ), N?(t ) and decreasing functions t ? M ?(t ),
N ?(t ) such that the unique global bounded solutions of the system (1.13)-(1.14) satisfy
0 &lt; M?(t ) ? M (t, x ) ? M ?(t ) &lt; ?,
0 &lt; N?(t ) ? N (t, x ) ? N ?(t ) &lt; ?,
(2.9)
(2.10)
for all t &gt; 0.</p>
        <p>Proof of Theorem 1. Case a(y) = a constant, d ? 1. Let us fix t? &gt; 0. From
(2.9)(2.10), we have 0 &lt; M? ? M (t, x ) ? M? &lt; ? and 0 &lt; N? ? N (t, x ) ? N ? &lt; ?
for all t ? t?, and thus
for all t ? t? due to (2.4) with the constant C (M?, N?, a?, P( )) given in Lemma 2.</p>
      </sec>
      <sec id="1-5">
        <title>As a direct consequence, we get</title>
        <p>for all t ? t?. Gronwall?s lemma implies estimate (1.22).</p>
        <p>Next, convergence in L1 as stated in Theorem 1 follows from the functional inequality
of Csiszar-Kullback type [Cs,Ku]:
f (t, ·, ·) ? f? 2L1x,y ? 2</p>
        <p>M (t, x ) d x +</p>
        <p>N?</p>
        <p>H ( f (t )| f?) d x .</p>
        <p>(2.11)
The proof is standard, see [CCD] for related inequalities, and it is shown via a Taylor
expansion of the function ?( f ) = f ln( f ) ? f up to second order around f?. Indeed,
for a function ? (x , y) ? (inf{ f (x , y), f?(y)}, sup{ f (x , y), f?(y)}), we get
0
0
?
?
and the first term vanishes due to the conservation law (1.9). For the second term, we
apply Hölder?s inequality
f ? f? 2L1x,y ? ? L1x,y
( f ? f?)2 d y d x with ? L1x,y ?</p>
        <p>M d x +</p>
        <p>N .</p>
        <p>?
Noticing that t ? [0, t?] ? f (t, ·, ·) ? L 1x,y is bounded, we finally get (1.23), which
concludes the proof of Theorem 1.</p>
        <p>Remark 1. As a consequence of the previous result, we also showed that the unique
global bounded solutions of the system (1.13)-(1.14) satisfy M (t, x ) ? M? = ?N?
and N (t, x ) ? N? as t ? ? in L1( ) exponentially fast with explicit constants. In
fact, we first remark that H ( f | f?) = H ( f | f M,N ) + H ( f M,N | f?) with
E S :=</p>
        <p>H ( f M,N | f?)d x =</p>
        <p>N (? ln ? ? ? + 1)+</p>
        <p>N?</p>
        <p>N ?</p>
        <p>N?
?
2
d x ,
where ? = ?MN and
f M,N (t, x , y) =</p>
        <p>M 2
N</p>
        <p>e? MN y .</p>
        <p>M 2</p>
        <p>N
It is obvious that E S is nonnegative since the minimum of ? ln ? ? ? + 1 is zero, and it
can be written as</p>
        <p>H ( f M,N | f?) d x =</p>
        <p>M ln
? 2(M ?
?</p>
        <p>N ) + 2</p>
        <p>N? ?
?</p>
        <p>N
d x ,
by using the conservation of mass (1.9). Since H ( f | f M,N ) ? 0, then (1.22) implies
the exponential convergence to zero of E S by the above additivity property. Finally, a
simple Taylor expansion shows that, for all t ? t?,</p>
        <p>N (t ) ? M (t ) 2L2 +
x</p>
        <p>N (t ) ?</p>
        <p>N? 2L2x ? L</p>
        <p>H ( f M,N (t )| f?) d x ,
with</p>
        <p>L = max 1, ?</p>
        <p>M?</p>
        <p>N?
,
?</p>
        <p>N ? ,
that implies by trivial arguments the exponential convergence in L1( ) towards
equilibrium for M and N . In fact, the system (1.13)-(1.14) might have been studied by a
direct application of the techniques in [DF05,DF06].</p>
      </sec>
    </sec>
    <sec id="2">
      <title>3. A-priori Estimates</title>
      <p>In the sequel, we shall discuss the general diffusion coefficient, i.e., size dependent
verifying (1.3) but we restrict to the one dimensional case, d = 1 (we shall not recall this
fact in the various lemmas). We begin the proof of Theorem 1.</p>
      <p>Lemma 4. Assume that f0 = 0 is a non-negative initial datum such that (1 + y) f0 ?
L1((0, 1)×(0, ?)). Then, there exists M0? &gt; 0 such that solutions of (1.1)?(1.8) satisfy
f (t, x , y) d y d x ?</p>
      <p>M (t, x ) d x ? M0?.</p>
      <p>(3.1)
Proof. We estimate the L1( )-norm of M (t, x ) by integrating equality (1.14), obtaining
sup
t?0
d
dt
0
?
by Hölder?s inequality and the conservation of mass (1.9). Therefore, for all t ? 0,
M (t, x ) d x ? max
Lemma 5. Assuming that the nonnegative initial datum f0 = 0 satisfies (1 + y +
ln f0) f0 ? L1((0, 1) × (0, ?)). Then, the number density of polymers M ? L1 +
L?(0, ?; L?(0, 1)). More precisely, there exist m? &gt; 0 and an L1+(0, ?)-function
m1(t ) such that the solution of (1.1)?(1.8) satisfies
(3.2)
(3.3)
and as a consequence,
a.e. t ? 0.</p>
      <p>?</p>
      <p>sup f (t, x , y) d y ? m? + m1(t ),
0 0&lt;x&lt;1</p>
      <p>M (t, ·) L?x ? m? + m1(t )
Proof. In order to estimate the L ?x-norm of M (t, x ), we first use the entropy dissipation
(2.3) of H ( f | f?) to deduce that
2
0 0 0</p>
      <p>2
?x
f
d y d x dt ?
2 a?
2 a?
Now, we integrate
f (t, x , y) ?
f (t, x?, y) =</p>
      <p>f (t, ?, y) d?
x
?
x
2
?x
?
0
1
:= m1(t )
In particular, we have, due to (3.1) and (3.3), that
with respect to x? ? (0, 1) and estimate
sup
0&lt;x&lt;1
f (t, x , y) ?</p>
      <p>f (t, x?, y) d x?
0
1
Hence, after further integration with respect to y ? (0, ?), we apply Young?s and
Hölder?s inequalities to show
?</p>
      <p>sup f (t, x , y) d y ? 2
0 0&lt;x&lt;1
0 0
?x</p>
      <p>2
f (t, ?, y) d? d y + 2
?x
f (t, ?, y)</p>
      <p>d?.</p>
      <p>2
0 0
f (t, x?, y) d x? d y .
? m?</p>
      <sec id="2-1">
        <title>Finally,</title>
        <p>0
?
m1(t ) dt ? µ1 =</p>
        <p>H ( f0| f?) ,
2 a?</p>
        <p>m? = 2M0?.</p>
        <p>M (t, ·) L?x ?
?</p>
        <p>sup f (t, x , y) d y,
0 0&lt;x&lt;1
which completes the proof of Lemma 5.</p>
        <p>Note that the estimates (3.1) and (3.2) are somehow in duality, a fact that will become
essential below. We now prove a lemma showing that the total number of clusters
01 M (t, x ) d x is bounded below by a strictly positive constant:
Lemma 6. Assume that f0 = 0 is a nonnegative initial datum such that (1 + y + ln f0)
f0 ? L1((0, 1) × (0, ?)). Then, there exists a constant M0? &gt; 0 such that for all times
t ? 0, one has</p>
        <p>M (t, x ) d x ? M0?,
(3.4)
where f is a solution of (1.1)?(1.8).</p>
        <p>Proof. We recall that
d
dt 0</p>
        <p>1
so that
d
dt 0
1
0</p>
      </sec>
      <sec id="2-2">
        <title>Then,</title>
        <p>0
1
and, recalling µ1 ? 0+? m1(s) ds), we deduce
Distinguishing here between t &lt; 1 and t ? 1, for instance, we obtain
0
1
0
t
e?(t?s) m??µ1 ds
1 ? e?m? t
m?
0
1
0
1
which concludes the proof of Lemma 6.</p>
        <p>Next, we show the uniform control in time of all moments with respect to size y of
the solutions. Let us define the moment of order p &gt; 1 by</p>
        <p>M p( f )(t ) :=
1
0 0</p>
        <p>?y p f (t, x , y) d y d x
for all t ? 0.</p>
        <p>Lemma 7. We assume that f0 = 0 is a nonnegative initial datum such that (1 + y +
ln f0) f0 ? L1((0, 1) × (0, ?)). Then, the solution f of (1.1)?(1.8) has moments
M p( f )(t ) uniformly bounded in time t &gt; t? &gt; 0 and for any p &gt; 1, i.e., there exist
explicit constants M?p( f0, m?, m1, p) such that</p>
        <p>M p( f )(t ) ? M?p,
for a.e. t &gt; t? &gt; 0.</p>
        <p>(3.5)</p>
      </sec>
      <sec id="2-3">
        <title>Proof. We proceed in two steps:</title>
        <p>Step 1. We first assume that M p( f )(t?) &lt; ? for certain p &gt; 1 and t? &gt; 0. Using
the weak formulation (1.16), it is easy to check that
&lt; Q( f, f ), y p &gt;= ? 2
Taking into account Lemma 5 and (y + z) p ? C p (y p + z p), we deduce
&lt; Q( f, f ), y p &gt; ? 2(C p ? 1)
?y p f (y) d y [m? + m1(t )] ? pp ?+ 11 0?f (y) y p+1 d y
for all p &gt; 1. Integrating in space, we find that the evolution of the moment of order
p &gt; 1 is given by
d
dt
(3.6)
Trivial interpolation of the p + 1-order moment with the moment of order one implies
1
for a.e. t &gt; t?. According to Duhamel?s formula,</p>
        <p>M p( f )(t ) ? M p( f )(t?) exp 2(C p ? 1)
+ D
exp 2(C p ? 1)
m1(? ) d? ?
ds,</p>
        <p>(3.7)
s
t
t
t?
m1(s) ds ?
t ? t?</p>
        <p>2
t ? s
2
that
which shows that the moment M p( f )(t ) is bounded by a constant M?p for a.e. t &gt; t?
since m1(t ) ? L1((0, ?)) by Lemma 5.</p>
        <p>Moreover, it follows from (3.6) that the boundedness of M p(t?) immediately implies
for all T &gt; 0, and thus the finiteness of M p+1( f )(t ) for a.e. t &gt; t? and a simple induction
argument enables then to conclude the bounds on all higher moments.
Step 2. It remains to show that for given nontrivial initial data y f0 ? L 1x,y and for a p &gt; 1
and a time t? &gt; 0 we have that M p(t?) &lt; ?. We start with the following observation
[MW, Appendix A]: For a nonnegative integrable function g(y) = 0 on (0, ?), there
exists a concave function (y), depending on g, smoothly increasing from (0) &gt; 0
to (?) = ? such that</p>
        <p>M p+1( f )(t ) dt &lt; ?</p>
        <p>(y) g(y) d y &lt; ?.
t
t?</p>
        <p>T
t?
for 0 &lt; y &lt; y with C not depending on g. We refer to [MW, Appendix A] for all the
details of this ?by-now standard? construction.</p>
        <p>To show now that M p(t?) &lt; ? for a p &gt; 1 and a time t? &gt; 0, we take functions
(x , y) constructed for nontrivial y f0(x , y) ? L1y (0, ?) a.e. x ? (0, 1) and calculate
- similar to Step 1 - the moment</p>
        <p>M1, ( f )(t ) =</p>
        <p>y (x , y) f (x , y) d y d x .</p>
        <p>For the fragmentation part, we use (3.8) for 0 &lt; y &lt; y and estimate
y (y) Q f ( f ) = 2
y ( (y ) ?</p>
        <p>(y)) d y f (y)
1 ?
Moreover, the function
can be constructed to satisfy
(y) ?
(y ) ? C
for all ? &gt; 0 and a positive constant C?, where the (t, x )-dependence has been dropped
for notational convenience. Hence, by estimating the coagulation part similar to Step 1,
making use of the concavity of , we obtain that
d
dt</p>
        <p>M1, ( f )(t ) ? 3(m? + m1(t ))M1, ( f )(t ) ? C? M2??( f )(t ),
and boundedness of the moment M1, follows by interpolation as well as the finiteness
of M2??( f )(t?) analogously to Step 1.</p>
        <p>Next, we show that M and N are bounded below uniformly (with respect to t and x )
for all t ? t? &gt; 0.</p>
        <p>Proposition 2. Under the assumptions of Theorem 1, let t? &gt; 0 be given. Then, there
are strictly positive constants M? and N? such that for all t ? t? &gt; 0,
M (t, x ) ? M?
and</p>
        <p>N (t, x ) ? N?.</p>
      </sec>
      <sec id="2-4">
        <title>Proof. We write the equation satisfied by f in this way:</title>
        <p>where g1 is nonnegative. Then
?t f ? a(y) ?x x f = g1 ? y f ?</p>
        <p>M (t, ·) L?x f,
(?t + a(y) ?x x ) f et y+ 0t M(s,·) L?x ds
= g2,
where g2 is nonnegative.</p>
        <p>Now, we recall that the solution h := h(t, x ) of the heat equation</p>
        <p>?t h ? a ?x x h = G,
with homogeneous Neumann boundary condition on the interval (0, 1), where a &gt; 0 is
a constant and G := G(t, x) ? L1, is given by the formula</p>
        <p>1
h(t, x) = 2??
1
?1</p>
        <p>h?(0, z)
with h? and G? denoting the ?evenly mirrored around 0 in the x variable? functions h
and G.</p>
        <p>Therefore, for all t1, t ? 0, and x ? (0, 1), y ? R+,
f (t1 + t, x, y) e(t1+t) y+ 0t1+t M(s,·) L?x ds
so that when t ? [t?, 2t?] (and since |x ? z| &lt; 2):
and thus, for any A &gt; 0, we deduce
due to the conservation law (1.9) and</p>
        <p>N (t1 + t, x) ? C e?2t? A
Choosing now A, we get that N (t1 + t, x ) ? N? for some N? &gt; 0 which does not depend
on t1. Using Lemma 6,</p>
        <p>M (t1 + t, x ) ? C
1 ?
Once again choosing A, we get that M (t1 + t, x ) ? M?. Since M? does not depend on
t1, we get Proposition 2.
4. Proofs of Theorem 1 and Proposition 1 if
= (0, 1).</p>
        <p>With Proposition 2 and Lemma 5 providing the moment bounds required by the
entropyentropy dissipation Lemma 2 in the one dimensional case = (0, 1), we turn now to
the
Proof of Theorem 1. Case</p>
        <p>= (0, 1). According to Lemma 2,
H ( f | f?) d x ? ?D( f ) ? ?</p>
        <p>Knowing that m1(t ) ? Lt1 with 0? m1(t ) dt ? µ1, we consider the sets A := {s &gt; 0 :
m1(s) ? 1} and Bt := {s ? [0, t ] : m1(s) &lt; 1}. We readily find that
m1(t ) dt ? µ1
and
|Bt | = t ?</p>
        <p>ds ? t ? µ1.</p>
        <p>A?[0,t]
0
1
d
dt 0</p>
        <p>1
| A| =</p>
        <p>A</p>
        <p>ds ?</p>
      </sec>
      <sec id="2-5">
        <title>Moreover,</title>
        <p>t
t?
M L?x
ds ?</p>
        <p>Bt
?</p>
        <p>C C</p>
        <p>M L?x ds ? ? (1 + m?) (t ? µ1),
finishing the proof of (1.22). The proof of the L1-decay estimate (1.23) follows the same
arguments as in the case of constant diffusion done in Sect. 2 using Csiszar-Kullback
type inequalities.</p>
        <p>Finally, we show Proposition 1. Let us denote by CT any constant of the form C (t ) (1+
T )s , where s ? R and C (t ) is bounded on any interval [t?, +?) with t? &gt; 0.
0 0 0 0</p>
        <p>According to the properties of the heat kernel (cf. [DF06] for example), we know that
for any ? &gt; 0 and t? &gt; 0,
f (·, ·, y) L3??([t?,T ]× ) ? CT
f (0, ·, y) L1 + Q+( f, f )(·, ·, y) L1([0,T ]× ) .</p>
        <p>x
Then, for all r ? [2, 3[,
0
?
0
?
(1 + y)q</p>
        <p>Q+( f, f )(·, ·, y) Lr/2([t?,T ]× ) d y</p>
        <p>(1 + y)q f (·, ·, y) L3??([t?,T ]× ) d y ? CT .
Proof of Proposition 1. We observe using the bounds (3.5) and (3.1) that for all q ? 0,
? (1 + y)q+1
?
+</p>
        <p>0
? CT +
0
?</p>
        <p>q + 1
(1 + y)q
?</p>
        <p>?
0
0
0
?
0
?
0
?
0
?
f (·, ·, y) Lr ([t?,T ]× ) d y</p>
        <p>f (·, ·, y ) f (·, ·, y ? y ) d y Lr/2([t?,T ]× ) d y
(1 + y + z)q f (·, ·, y) f (·, ·, z) Lr/2([t?,T ]× ) d yd z
? CT + 2q?1
(1 + y)q f (·, ·, y) Lr ([t?,T ]× )d y
2
? CT .</p>
        <p>Using again the properties of the heat kernel (still described in [DF06]), we see that for
any s ? [1, ?) and t? &gt; 0,
The above argument can now be used with r = 4 and shows that</p>
        <p>(1 + y)q f (·, ·, y) Ls ([t?,T ]× )d y ? CT .
(1 + y)q</p>
        <p>Q+( f, f )(·, ·, y) L2([t?,T ]× ) d y ? CT .</p>
        <p>As a consequence, the standard energy estimate on the heat kernel implies that</p>
        <p>(1 + y)q f (T , ·, y) Hx1 d y ? CT .
Then, using a Gagliardo-Niremberg type interpolation and Theorem 1, we obtain
?
0
?</p>
        <p>0
×
?
×
?
0
0
?
(1 + y)q f (T , ·, y) ? f?(y) L?x d y
(1 + y)q f (T , ·, y) ? f?(y) 3H/x14
which concludes the proof of Proposition 1.</p>
        <p>Acknowledgements. JAC acknowledges the support from DGI-MEC (Spain) project MTM2005-08024. KF
is partially supported by the WWTF (Vienna) project ?How do cells move?? and the Wittgenstein Award 2000
of Peter A. Markowich. JAC and KF appreciate the kind hospitality of the ENS de Cachan. The authors want
to express their gratitude to the reviewer who helped us to improve this work.
[AB]</p>
        <p>Aizenman, M., Bak, T.: Convergence to equilibrium in a system of reacting polymers. Commun.
Math. Phys. 65, 203?230 (1979)
Aldous, D.J.: Deterministic and stochastic models for coalescence (aggregation, coagulation):
a review of the mean-field theory for probabilists. Bernoulli 5, 3?48 (1999)
Amann, H.: Coagulation-fragmentation processes. Arch. Rat. Mech. Anal. 151, 339?366 (2000)
Amann, H., Walker, C.: Local and global strong solutions to continuous
coagulationfragmentation equations with diffusion. J. Differ. Eqs. 218, 159?186 (2005)
Cáceres, M.J., Carrillo, J.A., Dolbeault, J.: Nonlinear stability in lp for solutions of the
vlasovpoisson system for charged particles. SIAM J. Math. Anal. 34, 478?494 (2002)
Cáceres, M.J., Carrillo, J.A., Goudon, T.: Equilibration rate for the linear inhomogeneous
relaxation-time boltzmann equation for charged particles. Comm. Partial Differ. Eqs. 28,
969?989 (2003)
Chae, D., Dubovskii, P.: Existence and uniqueness for spatially inhomogeneous
coagulationcondensation equation with unbounded kernels. J. Integ. Eqs. Appl. 9, 219?236 (1997)
Csiszár, I.: Information-type measures of difference of probability distributions and indirect
observations. Studia Sci. Math. Hungar 2, 299?318 (1967)
Collet, J.F., Poupaud, F.: Asymptotic behaviour of solutions to the diffusive
fragmentationcoagulation system. Phys. D 114, 123?146 (1998)
Desvillettes, L.: Convergence to equilibrium in large time for boltzmann and b.g.k.
equations. Arch. Rat. Mech. Anal. 110, 73?91 (1990)
Desvillettes, L., Fellner, K.: Exponential decay toward equilibrium via entropy methods for
reaction-diffusion equations. J. Math. Anal. Appl. 319, 157?176 (2006)
Desvillettes, L., Fellner, K.: Entropy methods for Reaction-Diffusion Equations: Degenerate
Diffusion and Slowly Growing A-priori bounds. To appear in Rev. Matem. Iber.</p>
        <p>Desvillettes, L., Villani, C.: On the trend to global equilibrium in spatially inhomogeneous
entropy-dissipating systems: the linear fokker-planck equation. Comm. Pure Appl. Math. 54,
1?42 (2001)
Desvillettes, L., Villani, C.: On the trend to global equilibrium for spatially inhomogeneous
kinetic systems: the boltzmann equation. Invent. Math. 159, 245?316 (2005)
Drake, R.L.: ?A general mathematical survey of the coagulation equation?. Topics in Current
Aerosol Research (part 2), International Reviews in Aerosol Physics and Chemistry, Oxford:
Pergamon Press, 1972, pp. 203?376
[Ku]
[LM02-2]
[LM03]
[LM04]
[LM05]
[LW]
[Le]
[MP]
[MW]
[MN]
[NS]
[Ok]
[PS]
[Ro]
[Sa]
[S16]
[S17]
[V06]
Communicated by A. Kupiainen</p>
      </sec>
    </sec>
  </body>
  <back>
    <ref-list />
  </back>
</article>

<?xml version="1.0"?>
<pdf>
  <title line_height="18.47" font="MTSYN">:=</title>
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system of reacting polymers. Commun. Math. Phys. 65, 203-230
(1979)</reference>
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coalescence (aggregation, coagulation): a review of the mean-efild theory
for probabilists. Bernoulli 5, 3-48 (1999)</reference>
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Rat. Mech. Anal. 151, 339-366 (2000)</reference>
  <reference>[CCD]</reference>
  <reference>[CCG]</reference>
  <reference>[CD]</reference>
  <reference>[Cs]</reference>
  <reference>[CP]</reference>
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Dolbeault, J.: Nonlinear stability in lp for solutions of the vlasov-
poisson system for charged particles. SIAM J. Math. Anal. 34, 478-494
(2002) Cc&#xE1;eres, M.J., Carrillo, J.A., Goudon, T.: Equilibration rate
for the linear inhomogeneous relaxation-time boltzmann equation for charged
particles. Comm. Partial Differ. Eqs. 28, 969-989 (2003) Chae, D.,
Dubovskii, P.: Existence and uniqueness for spatially inhomogeneous
coagulation- condensation equation with unbounded kernels. J. Integ. Eqs.
Appl. 9, 219-236 (1997) Csiszr&#xE1;, I.: Information-type measures of
difference of probability distributions and indirect observations. Studia
Sci. Math. Hungar 2, 299-318 (1967) Collet, J.F., Poupaud, F.: Asymptotic
behaviour of solutions to the diffusive fragmentation- coagulation system.
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110, 73-91 (1990) Desvillettes, L., Fellner, K.: Exponential decay toward
equilibrium via entropy methods for reaction-diffusion equations. J. Math.
Anal. Appl. 319, 157-176 (2006) Desvillettes, L., Fellner, K.: Entropy
methods for Reaction-Diffusion Equations: Degenerate Diffusion and Slowly
Growing A-priori bounds. To appear in Rev. Matem. Iber. Desvillettes, L.,
Villani, C.: On the trend to global equilibrium in spatially inhomogeneous
entropy-dissipating systems: the linear fokker-planck equation. Comm. Pure
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Incorporation_of_magnesium_in_mesostructur.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>Phys. Chem. Chem. Phys.</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>Incorporation of magnesium in mesostructured and mesoporous aluminophosphates¤</article-title>
      </title-group>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Yaroslav Z. Khimyak</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jacek Klinowski</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <aff id="0">
          <label>0</label>
          <institution>Department of Chemistry, University of Cambridge</institution>
          ,
          <addr-line>L ensÐeld Road, Cambridge, UK CB2 1EW . E-mail : jk18=cam.ac.uk</addr-line>
        </aff>
      </contrib-group>
      <abstract>
        <p>Mesostructured and mesoporous MgAPOs and MgAPSOs were synthesised using cationic templating in the presence of various relative amounts of Mg2` and the silica source. The products were characterised by X-ray di†raction, 27Al, 31P and 29Si solid-state NMR, thermal and elemental analyses and nitrogen adsorption. Magnesium is incorporated into the structure substituting for either the Al3` units or the surfactant cations, with a consequent decrease of mesoscopic ordering. Incorporation of large amounts of magnesium in either mesostructured AlPO or SAPO gives products with signiÐcantly larger pore diameters than those of MgAPO and MgAPSO with lower Mg content, or AlPO or SAPO made using the same P O : Al O ratio. Introduction of Si into the framework leads to an increased degree of condensatio2n of the inorganic 5 2 3 framework, and improves the thermal stability of the products. ¤ Electronic Supplementary Information available. See http : // www.rsc.org/suppdata/cp/b0/b010029n</p>
      </abstract>
      <volume>3</volume>
      <fpage>1544</fpage>
      <lpage>1551</lpage>
      <pub-date>
        <year>2001</year>
      </pub-date>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>Introduction</title>
      <p>The considerable Ñexibility of the aluminophosphate
framework makes it possible to incorporate heteroatoms with
similar size and coordination in microporous AlPO structures.
Such a modiÐcation often leads to the generation of sites with
either acidic or redox properties, which is of considerable
interest for the design of new catalysts.1 Generally, three main
mechanisms for the incorporation of heteroatoms can be
envisaged : impregnation, ion exchange and isomorphous
substitution.1 In the latter method, a compound containing the
heteroatom is added directly to the synthesis mixture.
Although isomorphous substitution is regarded as a complex
phenomenon, heteroatoms such as Be, B, Mg, Si, Ti, V, Cr,
Mn, Fe, Co, Zn, Zr, Ge, Ga have been reported to replace
Al3` and/or P5` in the structure of microporous AlPO.2
However, detailed information on the heteroatom location is
difficult to obtain, since in most of cases their concentration in
the structure is very low.</p>
      <p>The degree of the incorporation of the heteroatoms in the
structure of microporous crystalline AlPO -n molecular sieves
4
depends on the particular structure. However, recent work
suggests that there is no upper limit to the amount of the
heteroatom being incorporated.2 Moreover, microporous
phosphates containing no aluminium, such as cobalt3h5 and
zinc6,7 phosphates, have also been synthesized.</p>
      <p>Incorporation of magnesium into the microporous AlPO
has been achieved for di†erent structures.8h11 Substitution of
divalent Mg2` for Al3` gives molecular sieves in which the
generated negative charge can be balanced by protons, to
form BrÔnsted acid sites.12 In most cases the 31P MAS NMR
conÐrms substitution of aluminium by magnesium, as
resonances attributable to the P(OAl)4~n(OMg)n structural units
are observed.11,13h15 In addition, several unique structures
have been reported only as MgAPOs. These include
largepore DAF-1,16 and organically templated STA-117 and
STA2.18 Syntheses of organically templated magnesium
phosphates such as UiO-16 with a layered structure19 and
open-framework UiO-20 with the DFT topology20 have also
been reported.</p>
      <p>Following previous studies on the synthesis and structure of
mesostructured and mesoporous AlPO,21h24 we describe the
synthesis and characterisation of Mg-modiÐed mesostructured
and mesoporous AlPOs and SAPOs. In the presence of
tetraalkylammonium hydroxides, the supramolecular assembly in
the AlPOÈC TMACl system gives mesocomposites with
dif16
ferent structures and properties. XRD allowed us to identify
three hexagonal (Hex-1, Hex-2, Hex-3) and three mesolamellar
(L1, L2 and L3) products synthesized under di†erent
conditions.21h23 The inorganic component of mesostructured
AlPOs varies in the degree of condensation, the P : Al ratio
and the population ratio of 6- and 4-coordinate Al. The
C TMA` cations are the only organic species in the
produ1c6ts. The di†erences in the mesocomposites are also reÑected
in the speciÐc organisation of the surfactant arrays. Thus, at
ambient temperatures, Hex-1, Hex-2 and L2 show
predominant gauche disordered conformation of the aliphatic chains,
while in L1 and L3 they are in the all-trans conformation.24</p>
      <p>
        Incorporation of magnesium into Hex-1 and Hex-2 AlPO
and SAPO is of interest because these mesocomposites are
thermally stable and upon calcination at 500 ¡C give solids
with a tubular pore system. Hexagonal AlPOs can be
obtained at ambient temperature from synthesis mixtures with
similar compositions. For the mixtures with the same P/Al
ratio, water and surfactant content, Hex-1 is obtained at pH
7.20È7.40, while Hex-2 precipitates at higher pH 7.60È7.80.
The inorganic component of Hex-1 consists of alternating
octahedral Al and tetrahedral P units. Even though some
Al(
        <xref ref-type="bibr" rid="4">4</xref>
        ) units are present, the low-Ðeld 31P chemical shifts
suggest the absence of extended regions of alternating
phosphate and aluminate tetrahedra. The surfactant head groups
at the inorganic/organic interface form electrostatic bonds
with the phosphate tetrahedra, which are probably connected
to two Al(H O) (OP) or Al(H O) (OP) units. Further from
the interface2, th3e num3 ber of w2ater4 mol2ecules in the
coordination sphere of Al(
        <xref ref-type="bibr" rid="6">6</xref>
        ) decreases. As a result, the inorganic
network consists of O2P(OAl(H2O)nO5~n)3 (n \ 2, 3) units.
Al(
        <xref ref-type="bibr" rid="4">4</xref>
        ) tetrahedra are accommodated in the bulk of the
inorganic component, leading to a small contribution of the units
.
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      </p>
      <p>
        OÈP(OAlO3)k(OAl(H O)nO )
P atoms are connecte2d to b5o~tnh3~k (n \ 2, 3 ; k \ 1, 2), where
Al(
        <xref ref-type="bibr" rid="4">4</xref>
        ) and Al(
        <xref ref-type="bibr" rid="6">6</xref>
        ). We note that
the inorganic component in Hex-n AlPOs is amorphous. The
di†erences between Hex-1 and Hex-2 AlPOs are related to the
increased number of H O molecules in the coordination
sphere of Al(
        <xref ref-type="bibr" rid="6">6</xref>
        ) units, as r2eÑected in the downÐeld shift of the
Al(
        <xref ref-type="bibr" rid="6">6</xref>
        ) peak in the 27Al NMR spectra. At the same time, the
proportion of the sites where the phosphate tetrahedra are
connected to only two or one Al atoms increases.
      </p>
      <p>Incorporation of di†erent heteroatoms has been achieved
for mesoporous silicate molecular sieves.25,26 However, only a
few studies on the synthesis and characterisation of
heteroatom-substituted mesoporous AlPO have been
published.27,28 The structure and properties of SAPOs
obtained by di†erent research groups appear to vary
substantially despite quite similar synthesis routes. Kevan and
coworkers obtained and characterised mesoporous AlPO
containing manganese and vanadium.27,29 However, no
systematic study has been performed on the mechanism of the
incorporation of di†erent heteroatoms in the structure, and
the comparison between heteroatom-substituted microporous
and mesoporous aluminophosphates. We will show that
incorporation of the heteroatoms in mesoporous and
mesostructured AlPO can improve their thermal stability, and that
incorporation of magnesium into AlPO and SAPO inÑuences
the pore diameter of the products.</p>
    </sec>
    <sec id="2">
      <title>Experimental</title>
      <sec id="2-1">
        <title>Synthesis</title>
        <p>Syntheses of hexagonal MgAPO and MgAPSO were carried
out at ambient conditions. In the Ðrst step, Al(OC Hiso) was
dispersed in water and stirred for 30 min. Th3e r7eq3uired
amount of H PO was then added (P O : Al O \ 2.0) and
the mixture 3was 4stirred for 60 min.2 A5 mag2nes3ium source
(Mg(OCOCH ) É 4H O, Aldrich) was added to the synthesis
mixture. A s3o2lution2 of cetyltrimethylammonium chloride
(CTAC) (Aldrich) was then added. After stirring for 1 h, a 25%
aqueous solution of tetramethylammonium hydroxide
(TMAOH) (Lancaster) was added dropwise. Magnetic stirring
of the mixtures was used during the whole course of the
synthesis. After 48È96 h the products were Ðltered and dried at
50 ¡C overnight. During the synthesis of SAPO the Si source
(TEOS, Aldrich) was added to the synthesis mixture after the
addition of the surfactant and before the addition of
TMAOH. The products were calcined at 500 ¡C in air for 12
h. The composition of the starting mixtures used for the
synthesis of hexagonal MgAPO and MgAPSO is given in Table
1. MgAPOs and MgAPSOs are referred to as MgAPO[Mg-n]
and MgAPSO[Si-m ; Mg-n] where n is the Al : Mg ratio and
m is the Al : Si ratio in the synthesis mixture.</p>
      </sec>
      <sec id="2-2">
        <title>Powder X-ray di†raction</title>
        <p>XRD patterns were recorded using a Philips 1710 powder
diffractometer with Cu-Ka radiation (40 kV, 40 mA), 0.020¡ step
size and 0.5È2.0 s counting time per step.</p>
      </sec>
      <sec id="2-3">
        <title>Solid-state NMR</title>
        <p>NMR spectra were recorded at 9.4 T using a Chemagnetics
CMX-400 spectrometer with zirconia rotors 4 mm in diameter
spun in dry nitrogen at 8 kHz. 27Al magic-angle-spinning
(MAS) NMR spectra were acquired at 104.20 MHz with
pulses shorter than p/10 (0.3 ls pulse length). 1000 scans were
acquired with a recycle time of 0.5 s. The position of 27Al
resonances is quoted in ppm from external Al(H O) 3`. 31P
MAS NMR spectra were measured at 161.89 MHz 6with
zir2
conia rotors 7.5 mm in diameter spun in nitrogen at 5.5 kHz,
p/2 (6.5 ls) pulses, 8 scans and 120 s recycle delays. 31P
chemical shifts are quoted with respect to external 85% H PO .
Solid-state 29Si MAS NMR spectra were recorded at3 79.444
MHz using zirconia rotors 7.5 mm in diameter spun in
nitrogen at 4.0 kHz. p/3 pulses of 4.0 ls duration were used with a
recycle delay of 300 s. 29Si chemical shifts are quoted in ppm
from external TMS. 1HÈ29Si cross-polarized (CP)/MAS NMR
experiments were performed using 1H p/2 pulse of 6.5 ls
length and 10 s repetition time with the contact time t in the
1.0È25.0 ms range. The HartmannÈHahn condition wams
established using kaolinite.</p>
      </sec>
      <sec id="2-4">
        <title>Thermogravimetry</title>
        <p>Thermogravimetric analysis was carried out using a Polymer
Laboratories TGA 1500 instrument under a Ñow of nitrogen,
and with a heating rate of 10 ¡C min~1 in the 20È800 ¡C
temperature range.</p>
      </sec>
      <sec id="2-5">
        <title>Elemental analysis</title>
        <p>Samples were analysed for carbon, hydrogen and nitrogen
using a Carlo Erba elemental analyser. Phosphorous was
determined colorimetrically. JEOL 5800 and JEOL 2101
scanning electron microscopes with energy-dispersive X-ray (EDS)
attachments, operating at 15 and 200 kV respectively, were
used to determine the Al : P : Mg ratio.</p>
        <p>N2 adsorption–desorption
Nitrogen adsorptionÈdesorption measurements were carried
out using the volumetric method with a Coulter SA3100
sorptometer at [196 ¡C. Before analysis, calcined samples were
dried at 120 ¡C and evacuated for 8 h at 200 ¡C under vacuum.
The surface area was calculated using the BET method on the
basis of the adsorption branch in the 0.05È0.20 partial
pressure (p/p ) range. The pore volume was determined from the
amount o0f N adsorbed at p/p \ 0.99. The pore size was
calculated using2the HorvathÈKawazoe method.30</p>
        <p>0</p>
      </sec>
    </sec>
    <sec id="3">
      <title>Results and discussion</title>
      <sec id="3-1">
        <title>Synthesis and X-ray di†raction</title>
        <p>Mesostructured MgAPOs were synthesised using starting
mixtures with di†erent contents of magnesium. An increased
amount of Mg2` reduces the pH in comparison to the
heteroatom-free synthesis. For Hex-1 MgAPO, the pH
decreases from 7.35 for Hex-1 AlPO to 7.20 for
MgAPO[MgTCaTbAleC 1: AlC2Oom3 \pos0i.t7io1)n of the starting mixtures used for the synthesis of mesostructured MgAPO and MgAPSO (P2O5 : Al2O3 \ 2.0,
5.0]. During the synthesis of the mesostructured MgAPSOs
the pH decreases signiÐcantly with the increase of the content
of both Mg2` and TEOS.</p>
        <p>XRD patterns of hexagonal MgAPOs are similar to those
of Hex-1 and Hex-2 AlPO. Hex-1 MgAPOs show a relatively
narrow (100) di†raction peak with d \ 37.4È38.7 AŽ (Fig.
1(a)), while Hex-2 MgAPOs give 10b0roader peaks with
d \ 39.1È40.7 AŽ (Fig. 1(b)). The general appearance of the
100
XRD patterns does not change substantially until the Al : Mg
ratio falls below 5.0. A further rise in the Mg2` content
reduces the intensity of the (100) and (110) peaks, indicating a
decline in the mesoscopic ordering. The solids obtained at pH
7.1È7.2 with Al : Mg \ 2.5 show a single, poorly resolved
diffraction peak at 45.2 AŽ . An increase of the TMAOH content
to a level required for the synthesis of Hex-2 produces
mesocomposites with slightly lower d \ 41.7 AŽ. The XRD
patterns of such solids contain no (110100) peak, which indicates a
much lower degree of mesoscopic organisation compared to
MgAPO with a lower Mg2` content.</p>
        <p>Hex-1 MgAPSO[Si-5.0, 2.0 ; Mg P 5.0] have d \ 37.5 AŽ .</p>
        <p>As for Hex-1 MgAPOs, an increase of Mg-conten1t00in the
synthesis mixtures to Al : Mg \ 2.5 shifts the single di†raction
peak to a larger d-spacing (d \ 45.0 AŽ ). A similar e†ect is
observed for Hex-2 MgAPS O10s0. Solids obtained at low and
medium Mg2` contents display broader di†raction peaks
with slightly higher d-spacing (d \ 40.0 AŽ), which also
increases (to 43.0 AŽ) after the increa10se0 of the Mg2` content to
Al : Mg \ 2.5.</p>
        <p>The e†ect of the reduction of the mesoscopic ordering with
the increased content of the heteroatom has been reported
during the synthesis of modiÐed silica-based mesoporous
molecular sieves31 and mesoporous AlPO modiÐed with
silicon or manganese.29 Note that for MgAPO and MgAPSO
an increased Mg content leads to a signiÐcant increase of the
d spacing, even though mesoscopic ordering is decreased.</p>
        <p>T1h0i0s e†ect is most distinct for the syntheses with the highest
content of magnesium.</p>
      </sec>
      <sec id="3-2">
        <title>Composition and thermogravimetric analysis</title>
        <p>As in hexagonal AlPOs, the C H N(CH ) ` cations are the
only organic species in the 1s6tru3c3ture o3f 3Mg2`-containing
mesocomposites. The increased Mg2` content reduces the
amount of the incorporated template. Thus, for Hex-2
MgAPO a rise of the Mg2` content from Al : Mg \ 50.0 to
3.3 is accompanied by a decrease of the surfactant content
from 53.0 to 36.0 wt.%. The decreasing amount of
C H N(CH ) ` cations in the structure with the increased
he1t6ero3a3tom c3on3tent indicates the changes in the organic/
inorganic interface in the mesocomposites.</p>
        <p>The Al : P : Mg ratio shows an increased relative content of
magnesium incorporated in the Hex-1 and Hex-2 MgAPOs
with the increase of Mg content in the syntheses mixtures
(Table 2). Hex-2 incorporate a larger amount of Mg2` than
Hex-1 MgAPOs obtained at the same Al : Mg starting ratio.
It is clear that substitution of aluminium by Mg2` takes
place, as the increased Mg content in the products is
accompanied by a reduced Al content. We also note that the
(Al ] Mg)/P ratio increases with the increased Mg content.
Mesocomposites obtained at Al : Mg \ 2.5 have a much
lower Al : P ratio than those synthesised at lower Mg
contents. The latter could in part contribute to the substantial
di†erences of the mesocomposites with the highest content of
Mg from other hexagonal MgAPOs.</p>
        <p>EDS analysis of hexagonal MgAPSOs shows that the
amounts of the heteroatoms incorporated in the
aluminophosphate framework follow their relative contents in the
synthesis mixtures (Table 3). Incorporation of magnesium a†ects
the amount of Si in the structure, which decreases with the
increased amount of Mg2`.</p>
        <p>
          We note that composition of the mesostructured AlPO
expressed in terms of the Al : P ratio is not constant and,
unlike microporous AlPO, the Al : P D 1 and varies over a
broad interval.23,32 It seems that during the synthesis some of
the Mg2` can replace the surfactant cations and have a
charge-balancing role leading to the formation of MgÈOÈP
bonds at the inorganic/organic interface. This can explain the
increase of the (Al ] Mg)/P ratio with the increased Mg
content. Incorporation of heteroatoms changes the
contributions of di†erent steps in the TG curves.¤ Three main thermal
events are observed during the calcination of mesostructured
MgAPO and MgAPSO. The Ðrst, at 90È110 ¡C, is related to
the loss of water (physisorbed water at 80È90 ¡C and
chemisorbed water at 100È110 ¡C). The second and third steps, at
250È270 and 330È370 ¡C, respectively, can be attributed to the
decomposition of the template. Generally, Hex-2 MgAPO
have a larger contribution of step II in the TG curves than
Hex-1 (Fig. 2). Incorporation of Mg2` and/or of Si increases
the relative contribution of step III. We assume that steps II
and III represent the template species with di†erent strengths
of bonding to the inorganic network. Step II is attributable to
the decomposition of the occluded template species, while step
III represents processes involving template electrostatically
bound to the MgAPO network in the form of either parent
surfactant cations or protonated amine species, formed as a
result of their decomposition at lower temperatures.33 In this
case, the substitution of Al3` by Mg2` or P5` by Si4` in the
network leads to the formation of additional negatively
charged sites in the structure, the latter being reÑected in the
increase of the relative contribution of step III.
.
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27Al MAS NMR spectra of mesostructured MgAPOs are
analogous to those reported for Hex-1 and Hex-2 AlPOs.
Aluminium is predominantly in an octahedral coordination (Fig.
3). Al(
          <xref ref-type="bibr" rid="4">4</xref>
          ) sites are found at ca. 43.0 ppm, while the Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) peak is
between [5.3 and [5.8 ppm for Hex-1 MeAPOs and
between [2.5 and [4.1 ppm for Hex-2 MgAPOs. The Al(
          <xref ref-type="bibr" rid="4">4</xref>
          )/
Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) ratio is virtually independent of the Mg2` content,
except for the solids synthesised with the highest content of
magnesium. Hex-1 MgAPOs have a higher relative content of
Al(
          <xref ref-type="bibr" rid="4">4</xref>
          ) sites than Hex-2 MgAPOs. For Hex-1 MgAPO obtained
from the synthesis mixtures with Al : Mg [ 2.5 the ratio of the
occupancies Al(
          <xref ref-type="bibr" rid="4">4</xref>
          )/Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) \ 0.24È0.28. Hex-2 MgAPO obtained
at the same Mg contents show Al(
          <xref ref-type="bibr" rid="4">4</xref>
          )/Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) \ 0.15È0.19.
MgAPO[Mg-2.5] has a higher proportion of tetrahedral sites :
Al(
          <xref ref-type="bibr" rid="4">4</xref>
          )/Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) \ 0.32 for Hex-1 and 0.29 for Hex-2.
        </p>
        <p>
          27Al MAS NMR of hexagonal MgAPSO and SAPO34
shows that it is the incorporation of Si into the
aluminophosphate framework which a†ects the Al(
          <xref ref-type="bibr" rid="4">4</xref>
          )/Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) ratio. The
position of the Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) peak in the Hex-2 MgAPSOs is shifted
downÐeld to between [3.1 and [4.0 ppm for Al : Si \ 5.0,
and to between [4.7 and [5.3 ppm for Al : Si \ 2.0 (Fig. 4).
Solids synthesised at higher Si contents in the starting
mixtures have a much higher Al(
          <xref ref-type="bibr" rid="4">4</xref>
          )/Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) ratio. We note that an
increase of the Mg content in the synthesis mixture reduces
the contribution of Al(
          <xref ref-type="bibr" rid="4">4</xref>
          ) sites both for Hex-1 and Hex-2
MgAPSO. This is more marked for solids obtained at higher
Si contents which hence give more intense Al(
          <xref ref-type="bibr" rid="4">4</xref>
          ) peaks. We
believe this e†ect to result from the decreased Si content upon
the increased Mg content in the products.
31P MAS NMR
The 31P MAS NMR spectra show signiÐcant di†erences
between Hex-1 and Hex-2 MgAPOs. In contrast to 27Al
NMR, 31P MAS NMR spectra reÑect substantial structural
changes upon the incorporation of Mg2` cations. Those are
reÑected in the gradual increase of the contribution of the
resonances at between [7 and [10 ppm both for Hex-1 (Fig.
5) and Hex-2 (Fig. 6) at the expense of the sites at lower or
higher Ðelds. As for mesostructured AlPO, Hex-2 MgAPOs
have a less condensed inorganic framework than Hex-1
MgAPOs, as the contribution of the sites at low Ðeld (above
[4.0 ppm) is much higher.
        </p>
        <p>31P MAS NMR spectra of Hex-1 MgAPSO[Si-5.0]
obtained at various Mg contents are shown in Fig. 7. An
increased Si content shifts the main broad resonance upÐeld
and decreases the contribution of the lines at lower Ðeld. An
increase in Mg2` content increases the contribution of the
peaks in the range from [8.0 to [13.0 ppm. A similar trend
is observed for Hex-2 MgAPSOs with a less condensed
inorganic component. The spectrum of Hex-2 MgAPSO[Si-5.0 ;
Mg-20.0] is dominated by the peaks above [4.0 ppm, while
the main resonance in the spectrum of Hex-2
MgAPSO[Si5.0 ; Mg-2.5] is found at [7.1 ppm. Incorporation of Mg into
MgAPSO[Si-2.0] shifts the main peak from [15.1 ppm for
MgAPSO[Si-2.0 ; Mg-20.0] to [7.7 ppm for
MgAPSO[Si2.0 ; Mg-2.5].</p>
        <p>The 31P and 27Al MAS NMR spectra of the calcined
MgAPOs are identical to those of calcined AlPO. The 27Al
MAS NMR spectra show a predominantly tetrahedral
coordination of Al atoms, while the 31P MAS NMR spectra show a
single broad resonance centred at ca. [23.0 ppm, indicating a
signiÐcant decrease of the mesoscopic ordering upon
calcination.</p>
        <p>SigniÐcant di†erences in the 31P MAS NMR spectra of
hexagonal MgAPO, synthesised at di†erent magnesium contents
and practically no di†erence in the 27Al MAS NMR spectra,
conÐrm substitution of Al3` by Mg2`. The peaks in the
middle range of 31P chemical shifts (between [7.0 and [10.0
ppm) can be attributed to the P sites where some of the Al
decreased contribution of the pe4a~kxa(Ot[M1e).0 ppm suggests that
atoms are substituted by P(OAl) x metal cations. The
.
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        <p>Mg2` cations also play a charge balancing role substituting
the C H N(CH ) ` cations at the organic/inorganic
interface. T1h6is is in agr3e3ement with the results of thermal and
ele33
mental analyses. For MgAPSO the appearance of the 31P
MAS NMR spectra depends on the contents of both
magnesium and silicon. Introduction of the Si sites leads to the
signiÐcant increase of the degree of the condensation of the
inorganic network reÑected in the increased population of
tetrahedral Al and an upÐeld shift of the main lines in the 31P
MAS NMR spectra. By analogy to the earlier reports on the
mechanisms of isomorphous substitution by Si in the
microporous AlPO,10,11 we assume that P5` atoms are replaced by
the silicate tetrahedra.</p>
        <p>31P MAS NMR was used to estimate the Mg content in the
framework of crystalline microporous MgAPO molecular
sieves, as the lines corresponding to P atoms coordinated to
di†erent numbers of the Mg atoms are easily
distinguishable.11,13,15 For mesoporous and mesostructured MgAPO
and MgAPSO, accurate quantitative analysis cannot be
carried out because of the substantial overlapping and large
widths of peaks corresponding to di†erent structural units.
29Si MAS NMR
The 29Si MAS NMR spectra of mesostructured MgAPSO
obtained at di†erent contents of Si show broad resonances
with the maxima at between [94.1 and [98.1 ppm. The
maxima in the spectra are observed at between [93.5 and
[96.5 ppm for MgAPSO[Si-5.0], and between [96.5 and
[98.1 ppm for MgAPSO[Si-2.0] with a higher Si content.
Comparison of the spectra with those reported for the
microporous SAPO and mesoporous silicates suggests that the
shouldered peak at d [ [92.0 ppm can be ascribed to the
silicon atoms coordinated to four aluminium atoms
(Si(OAl) ).10,11 The peak at ca. [95.0 ppm probably
represents t4he units in which one of the Al atoms is substituted
by a silicon atom (Si(OAl) (OSi)). The assignment of the peak
at ca. [102.0 ppm is more3difficult. This peak might represent
a site with a larger content of Si atoms in the Ðrst
coordination sphere or with some of the Al or Si atoms substituted
by OH groups. It is clear that the 29Si resonance in
mesostructured SAPO is shifted to a lower Ðeld compared to the
peaks for mesostructured silicates with a much higher
contribution of the peaks from Si(OSi) units. The very low intensity
of the peaks at ca. [112.0 ppm 4corresponding to such sites in
mesostructured SAPO indicates the absence of extended
regions of silica in the structure.</p>
        <p>
          1HÈ29Si CP/MAS NMR spectra of mesostructured
MgAPSO with di†erent contents of Si and Mg measured with
relatively short contact times (t \ 4.0 ms) show maxima
m
shifted by ca. 2 ppm downÐeld compared to the Bloch decay
spectra. The most efficient CP is observed at t B 4.0 ms.
m
Longer contact times lead to an overall lower intensity of the
spectra and increased contribution of the resonance at higher
Ðeld, indicating larger distances between silicon and protons
for these sites. At the same time the relative intensity of the
shouldered peak at ca. [83 ppm attributed to Si(OAl) units
4
decreases with the increased contact time suggesting that
cross-polarization for these sites proceeds mainly from the
protons from water molecules coordinated to Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) sites. As
for 29Si MAS NMR spectra, solids with higher content of Si
show increased contribution of the sites at higher Ðeld.
        </p>
      </sec>
      <sec id="3-3">
        <title>Characterisation of calcined MgAPO and MgAPSO</title>
        <p>XRD patterns of calcined MgAPOs and MgAPSO are typical
of solids with a disordered tubular pore system27,35,36 as a
single broad di†raction peak is observed. For calcined Hex-1
MgAPO the di†raction peak is narrower and the d spacing
100
is smaller than for calcined Hex-2 MgAPO synthesised with
the same Mg content (Fig. 8). For Hex-1 MgAPO[Mg-2.5]
d \ 39.1 AŽ , while for Hex-2 MgAPO[Mg-2.5] d \ 36.5
AŽ100(XRD patterns are given as Electronic Supp1le0m0entary
Imformation¤). Both values are much larger than for the
products with a lower Mg content. For both MgAPO and
MgAPSO the increase in the heteroatom content reduces the
quality of the tubular pore system, indicated by the reduced
intensity of the di†raction peak.</p>
        <p>
          The dependence of the thermal stability of Mg2`-modiÐed
AlPOs on the amount of Mg2` in the structure and type of
the mesophase is illustrated by the N adsorptionÈdesorption
isotherms (Fig. 9), which identify 2calcined MgAPOs and
MgAPSOs as mesoporous solids.37 A substantial lowering of
the mesoscopic ordering upon increase in the Mg content is
indicated by the decrease in S and V (Table 4). For Hex-1
and Hex-2 this occurs at AlB:EMTg \ 10.0 and Al : Mg \ 5.0,
ads
respectively. Calcined Hex-1 MgAPOs give a hysteresis loop
at p/p [ 0.5 attributable to the textural mesoporosity.36
Generally,0 Hex-1 MgAPOs show a much larger textural
mesoporosity than Hex-2 MgAPOs. The relative contribution of
the textural mesopores increases with the increased Mg
content. The tubular pore systems of mesoporous MgAPSO
correspond to medium values of S and adsorbed volume
(Table 4). Apart from Hex-1 MgABPETSO[Si-2.0] with a
relatively small surface area and pore volume, other MgAPSOs
obtained at di†erent pH and Si and Mg contents show
S [ 600 m2 g~1 and the framework-conÐned adsorbed
voBEluTme V [ 0.30 ml g~1.
We also note that the decrease in the pore diameter upon
calcination of mesostructured MgAPO and MgAPSO
synthesised at Al : Mg \ 2.5 is substantially smaller than for solids
with a lower Mg content. The decreased pore diameter and
decreased degree of ordering upon calcination of
mesostructured AlPO can be explained by the dehydration of the
Al(
          <xref ref-type="bibr" rid="6">6</xref>
          ) units, which are responsible for most of the aluminium in
the structure, into Al(
          <xref ref-type="bibr" rid="4">4</xref>
          ) units. For MgAPO and MgAPSO one
can assume that Mg is in the octahedral coordination.
Although lower coordination states of Mg have been
reported,20 it is unlikely that calcination would change the
coordination of the Mg sites in the structure. For products with high
Mg contents this would contribute to a much smaller
reduction of pore diameter upon calcination than for
mesostructured AlPO, where the increase in the pore diameter is
observed with increased Al : P ratio.23,32 One should also
mention other methods of regulating the pore diameters in
AlPO systems based on the organic component. These involve
increasing the length of the aliphatic chains in the surfactant
or introduction of auxiliary organic molecules, such as
triisopropylbenzene, in the synthesis mixtures.38
        </p>
      </sec>
    </sec>
    <sec id="4">
      <title>Conclusions</title>
      <p>
        Direct synthesis of mesostructured AlPO and SAPO in the
presence of magnesium cations results in the incorporation of
the heteroatom into the inorganic framework. Incorporation
of relatively small amounts of the Mg leads to a slight decline
of the mesoscopic ordering for both Hex-1 and Hex-2
MgAPO and MgAPSO. Syntheses carried out using a high
content of Mg give solids with signiÐcantly larger pore
dimensions. 27Al and 31P MAS NMR, elemental and
thermogravimetric analyses show that Mg2` cations can, on the one hand,
replace the surfactant cations, reducing the amount of the
organic template incorporated and, on the other hand,
substitute Al3` units in the inorganic framework. The latter is
shown by the 31P MAS NMR spectra, with the increased
conwith increased Mg content. The 4p~rexs(OenMceg)oxf (xsi\lico1n,2)inuntihtes
tribution of peaks from the P(OAl)
structure leads to the increased degree of condensation of the
inorganic framework, shown by the increased population of
the Al(
        <xref ref-type="bibr" rid="4">4</xref>
        ) units and shift of the 31P NMR peaks upÐeld.
Substitution of P5` units by Si4` units is very likely to occur.
Nitrogen adsorptionÈdesorption isotherms show that the
pore diameter of the mesoporous MgAPO and MgAPSO can
be regulated by changing the Al : Mg ratio. For Hex-1
MgAPO, the D (HK) increases from 17.1 AŽ for
MgAPO[Mg20.0] to 23.8 AŽaMvgAPO[Mg-2.5]. A similar e†ect is observed
for Hex-2 MgAPO. As for Hex-1 and Hex-2 MgAPO, the
pore diameters of calcined MgAPSO increase with the
amount of incorporated magnesium.
      </p>
      <p>Comparison of the pore volumes and surface areas of
MgAPO and MgAPSO shows that the introduction of Si into
the structure improves the quality of the pore system, which is
particularly noticeable for the products containing a relatively
high amount of magnesium. This can be attributed to the
increased degree of condensation of the MgAPSO in
comparison with MgAPO, as conÐrmed by 27Al and 31P MAS NMR.</p>
      <p>The e†ect of an increased pore diameter with the increased
Mg content can be explained by the fact that the MgÈO bond
(1.93 AŽ ) is signiÐcantly longer than the AlÈO bond (1.70 AŽ ).</p>
      <p>N adsorption parameters of mesoporous MgAPO and MgAPSOa
2
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      <p>However, one cannot rule out the possibility of the two Si
atoms substituting for the Al3`ÈP5` pair. In this case some
silica-rich domains might be present in the structure.
However, 29Si MAS NMR shows that even if these are
present, their content is quite low compared to other
Si(OÈAl)4vx(OÈSi)x (x \ 0, 1, 2) sites.</p>
      <p>Calcination of the mesostructured MgAPO and MgAPSO
gives solids with tubular pore systems. Increased amount of
incorporated Mg leads to the increased pore diameter in the
products, especially for solids made at Al : Mg \ 2.5. This
may be due to the larger radius of the Mg2` cations in
comparison with the substituted Al3` units. For both MgAPO
and MgAPSO the content of Mg2` can be used to obtain the
products with the desired pore diameters. Introduction of Si
into the structure improves its thermal stability. As a result,
MgAPSOs with high Mg content have larger surface areas
and pore volumes compared to the corresponding MgAPO.</p>
    </sec>
    <sec id="5">
      <title>Acknowledgements</title>
      <p>We are grateful to the Cambridge Oppenheimer Fund for the
Research Fellowship for YK.</p>
    </sec>
  </body>
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Tick-Borne_Rickettsioses,_Neglected_Emergi.pdf.

Cermine / Crossref / Grobid

<?xml version="1.0" encoding="UTF-8"?>
<article>
  <front>
    <journal-meta>
      <journal-title-group>
        <journal-title>Neglected Emerging Diseases in Rural Senegal. PLoS Negl
Trop Dis 4(9): e821. doi:10.1371/journal.pntd.0000821</journal-title>
      </journal-title-group>
    </journal-meta>
    <article-meta>
      <title-group>
        <article-title>Tick-Borne Rickettsioses, Neglected Emerging Diseases in Rural Senegal</article-title>
      </title-group>
      <article-id pub-id-type="doi">10.1371/journal.pntd.0000821</article-id>
      <contrib-group>
        <contrib contrib-type="author">
          <string-name>Oleg Mediannikov</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Georges Diatta</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Florence Fenollar</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Cheikh Sokhna</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Jean-Franc¸ ois Trape</string-name>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="author">
          <string-name>Didier</string-name>
          <email>didier.raoult@gmail.com</email>
          <xref ref-type="aff" rid="0">0</xref>
        </contrib>
        <contrib contrib-type="editor">
          <string-name>Pamela L. C. Small, University of Tennessee, United States of America</string-name>
        </contrib>
        <aff id="0">
          <label>0</label>
          <institution>URMITE, UMR IRD 198/CNRS 6236, Medical Faculty, Mediterranean University</institution>
          ,
          <addr-line>Marseille, France and Dakar</addr-line>
          ,
          <country country="SN">Senegal</country>
        </aff>
      </contrib-group>
      <abstract>
        <p>Background: Rickettsioses are one of the most important causes of systemic febrile illness among travelers from developed countries, but little is known about their incidence in indigenous populations, especially in West Africa. Methodology/Principal Findings: Overall seroprevalence evaluated by immunofluorescence using six rickettsial antigens (spotted fever and typhus group) in rural populations of two villages of the Sine-Saloum region of Senegal was found to be 21.4% and 51% for spotted fever group rickettsiae for Dielmo and Ndiop villages, respectively. We investigated the role of tick-borne rickettsiae as the cause of acute non-malarial febrile diseases in the same villages. The incidence of rickettsial DNA in 204 blood samples from 134 (62M and 72F) febrile patients negative for malaria was studied. DNA extracted from whole blood was tested by two qPCR systems. Rickettsial DNA was found in nine patients, eight with Rickettsia felis (separately reported). For the first time in West Africa, Rickettsia conorii was diagnosed in one patient. We also tested 2,767 Ixodid ticks collected in two regions of Senegal (Niakhar and Sine-Saloum) from domestic animals (cows, sheep, goats, donkeys and horses) by qPCR and identified five different pathogenic rickettsiae. We found the following: Rickettsia aeschlimannii in Hyalomma marginatum rufipes (51.3% and 44.8% in Niakhar and Sine-Saloum region, respectively), in Hyalomma truncatum (6% and 6.8%) and in Rhipicephalus evertsi evertsi (0.5%, only in Niakhar); R. c. conorii in Rh. e. evertsi (0.4%, only in Sine-Saloum); Rickettsia massiliae in Rhipicephalus guilhoni (22.4%, only in Niakhar); Rickettsia sibirica mongolitimonae in Hyalomma truncatum (13.5%, only in Sine-Saloum); and Rickettsia africae in Rhipicephalus evertsi evertsi (0.7% and 0.4% in Niakhar and Sine-Saloum region, respectively) as well as in Rhipicephalus annulatus (20%, only in SineSaloum). We isolated two rickettsial strains from H. truncatum: R. s. mongolitimonae and R. aeschlimannii. Conclusions/Significance: We believe that together with our previous data on the high prevalence of R. africae in Amblyomma ticks and R. felis infection in patients, the presented results on the distribution of pathogenic rickettsiae in ticks and the first R. conorii case in West Africa show that the rural population of Senegal is at risk for other tick-borne rickettsioses, which are significant causes of febrile disease in this area.</p>
      </abstract>
      <volume>4</volume>
      <issue>9</issue>
      <pub-date>
        <day>14</day>
        <month>9</month>
        <year>2010</year>
      </pub-date>
      <history>
        <date date-type="accepted">
          <day>12</day>
          <month>8</month>
          <year>2010</year>
        </date>
        <date date-type="received">
          <day>14</day>
          <month>4</month>
          <year>2010</year>
        </date>
      </history>
    </article-meta>
  </front>
  <body>
    <sec id="1">
      <title>-</title>
      <p>Funding: The authors have no support or funding to report.</p>
      <p>Competing Interests: The authors have declared that no competing interests exist.</p>
    </sec>
    <sec id="2">
      <title>Introduction</title>
      <p>
        Cases of tick-borne rickettsiosis have been regularly reported in
North [
        <xref ref-type="bibr" rid="1">1</xref>
        ] and South Africa [
        <xref ref-type="bibr" rid="3 2">2,3</xref>
        ] since 1910. Despite Pijper?s
suggestions [4], all cases of spotted fevers in sub-Saharan Africa
were considered to be Mediterranean spotted fever (MSF) with
Rickettsia conorii as an agent [
        <xref ref-type="bibr" rid="5">5</xref>
        ]. Rickettsia conorii was isolated in
Tunisia in 1932 [
        <xref ref-type="bibr" rid="6">6</xref>
        ]. Since that time, multiple cases of the disease
and isolations of the agent have been reported, mostly in countries
in the Mediterranean region. R. conorii conorii has also been
detected in ticks in Kenya, Somalia, South Africa, and Chad [
        <xref ref-type="bibr" rid="7">7</xref>
        ].
In 1992, however, a case of another spotted fever group (SFG)
rickettsiosis in a 36-year-old woman presenting with tick bite fever
at a hospital in Zimbabwe was described [
        <xref ref-type="bibr" rid="8">8</xref>
        ]. Authors succeeded in
isolating the etiological agent. By PCR and restriction fragment
length polymorphism they proved that the obtained strain differed
from all other SFG rickettsiae, including Rickettsia conorii. The new
strain was not, however, absolutely unique. It was
indistinguishable from the strains isolated earlier from the Ixodid tick,
Amblyomma variegatum, collected in Ethiopia [
        <xref ref-type="bibr" rid="9">9</xref>
        ] and from isolates
recovered from another tick of the same genus, Amblyomma
hebraeum, collected in Zimbabwe in the 1980s [
        <xref ref-type="bibr" rid="10">10</xref>
        ]. Rickettsia africae,
a SFG rickettsia that causes African tick-bite fever (ATBF)
officially received its name in 1996 [
        <xref ref-type="bibr" rid="11">11</xref>
        ]. R. africae seems to be
very widely distributed in the continent. It has been either isolated
or found by PCR in a number of African countries, including
Niger, Mali, Burundi, Sudan [
        <xref ref-type="bibr" rid="12">12</xref>
        ], Chad, Ethiopia [
        <xref ref-type="bibr" rid="13">13</xref>
        ], and in
most countries of equatorial and Southern Africa [
        <xref ref-type="bibr" rid="14">14</xref>
        ]. The
majority of strains and cases are reported in South Africa [
        <xref ref-type="bibr" rid="15 11">11,15</xref>
        ].
Recently, we have reported the high prevalence of R. africae in A.
variegatum in Senegal [16].
      </p>
      <p>
        Moreover, many proven and potential rickettsial pathogens
were discovered in Africa [
        <xref ref-type="bibr" rid="14">14</xref>
        ], mostly in ticks. Rickettsia sibirica
mongolitimonae, the agent of lymphangitis-associated rickettsiosis
Spotted fever rickettsioses are endemic diseases known
since the beginning of the 21st century. They may be
severe, like Rocky Mountain Spotted fever in the Americas,
and are always transmitted by the tick bite. In Africa, little
is known about the prevalence of these diseases; most
available data is from the travelers who felt ill after coming
back to Europe and USA. We have studied the distribution
of bacteria causing different spotted fevers (rickettsiae) in
rural Senegal, as well as the role of these bacteria in human
pathology among indigenous population. We have found
that up to half of tested villagers have serological evidence
of contact with rickettsiae and in some cases these
bacteria may be found in the blood of feverish patients.
      </p>
      <sec id="2-1">
        <title>From the other side, almost all species of ticks that may be</title>
        <p>collected in the villages on domestic animals also harbor
the pathogenic bacteria. In total, six different species of
rickettsiae were identified in ticks. We believe that our data
cast light on the problem of unexplained fevers in West</p>
      </sec>
      <sec id="2-2">
        <title>Africa.</title>
        <p>
          (LAR) was identified in ticks in Niger 10 years after its first
isolation in China in 1991 [
          <xref ref-type="bibr" rid="12">12</xref>
          ]. Rickettsia slovaca, which causes
tickborne lymphadenopathy (TIBOLA) in Europe, was found in
Dermacentor marginatus ticks in Morocco by PCR [
          <xref ref-type="bibr" rid="17">17</xref>
          ]. Two
Ixodesassociated rickettsiae, Rickettsia helvetica and Rickettsia monacensis,
were also detected in ticks in North Africa [
          <xref ref-type="bibr" rid="17 18">17,18</xref>
          ]. Both were
reported several times as probable human pathogens, although
more information is required regarding their pathogenicity [14].
Beginning in 1994, another SFG rickettsia, Rickettsia massiliae, was
repeatedly detected in Rhipicephalus spp. ticks in Central African
Republic, Mali, Algeria and Morocco [
          <xref ref-type="bibr" rid="12 17 20">12,17,19,20</xref>
          ]. The first
human case of spotted fever caused by this rickettsia was identified
in 2005 [21]. Rickettsia aeschlimannii was first isolated in Morocco in
1992 from the Hyalomma marginatum marginatum tick [
          <xref ref-type="bibr" rid="22">22</xref>
          ].
Genotypically similar or identical strains were reported in many
regions, including Kazakhstan, Southern Europe, Zimbabwe,
Mali, Niger, and Algeria [
          <xref ref-type="bibr" rid="14 19">14,19</xref>
          ]. These strains are almost always
associated with almost always associated with Hyalomma ticks.
Several human cases have been reported in Africa, including the
sub-Saharan regions [14]. Many other SFG rickettsiae not
previously associated with human diseases have been reported in
Ixodid ticks in Africa. Some of them are genetically described and
registered under Candidatus status [
          <xref ref-type="bibr" rid="23">23</xref>
          ].
        </p>
        <p>
          Tick-borne rickettsioses play a very important role in public
health. A recent worldwide report demonstrated a 5.6% incidence
of rickettsial infection in a group of travelers who developed acute
febrile infections after returning from sub-Saharan Africa. It is one
of the most frequently identified etiology for systemic febrile illness
among travelers, following malaria [
          <xref ref-type="bibr" rid="25 24">24,25</xref>
          ].
        </p>
        <p>
          The precise serological identification of the etiological agent of
spotted fever in humans may be difficult because of the strong
cross-reactivity in serological studies [
          <xref ref-type="bibr" rid="26">26</xref>
          ]. In some cases,
crossabsorption studies and western blots may help [
          <xref ref-type="bibr" rid="27">27</xref>
          ], but these
techniques may only work in cases in which the suspected agent is
known and isolated. In all cases of new and emerging rickettsioses,
the serological study may indicate only the group etiology (SFG).
One of the first studies performed with R. conorii antigen showed
the strikingly high incidence of rickettsial antibodies is human sera
from many African countries, including Angola, Burkina Faso,
Central African Republic, Mali, Cote d?Ivoire [
          <xref ref-type="bibr" rid="28">28</xref>
          ], Zambia [
          <xref ref-type="bibr" rid="29">29</xref>
          ],
and other countries [
          <xref ref-type="bibr" rid="33 32 34 40 37 39">30?40</xref>
          ]. The percentage of seroprevalence
found in different studies is shown in Figure 1.
        </p>
        <p>
          The growing number of newly discovered rickettsial species
outlines the indispensable role of molecular methods in
microbiology. However, the studies are still in early stages because the
distribution of many agents of rickettsioses is incompletely described.
West Africa, including Senegal, remains incompletely studied in
terms of tick-borne rickettsioses. Despite recent reports of high rates
of infection of A. variegatum ticks in Senegal [
          <xref ref-type="bibr" rid="16">16</xref>
          ], other tick species
were never studied for the presence of rickettsial agents. Thirty-three
species of Ixodid ticks are known in Senegal [
          <xref ref-type="bibr" rid="41">41</xref>
          ]; many of them are
associated with domestic animals and readily bite humans.
        </p>
        <p>The present work was performed in order to enlarge the scant
knowledge about tick-borne rickettsioses in Senegal.</p>
      </sec>
    </sec>
    <sec id="3">
      <title>Materials and Methods</title>
      <sec id="3-1">
        <title>Human sample collection and treatment</title>
        <p>
          The study was performed in two Senegalese villages, Dielmo
(13u439N;16u249W) and Ndiop (13u419N;16u229W), situated in the
Sine-Saloum region. Since 1990, a longitudinal study of malaria
and tick-borne relapsing fever has been ongoing in these villages
[
          <xref ref-type="bibr" rid="43 42">42,43</xref>
          ]. The project consists of long-term investigations of
hostparasite relationships in the entire village population, which was
enrolled in a longitudinal prospective study. The project was
approved by the National Ethics Committee of Senegal [42] and
the Local Ethics Committee (Marseille, France). Written
individual informed consent was obtained from each participant,
including the parents or legal guardians of all children, at the
beginning of the current study. Dielmo and Ndiop villagers are
settled agricultural workers. Millet and peanut crops are cultivated
during the rainy season, and market gardening is the main
agricultural activity during the dry season.
        </p>
        <p>Here we used the serological techniques to detect immune
response to different rickettsial species. We tested the samples from
the serological bank created for the above-mentioned longitudinal
study and collected in 2008. In total, 238 serum samples collected
in Dielmo in 2008 (mean age 26618, range from 3 to 78, 117 men
and 121 women) and 241 samples from Ndiop (mean age 25617,
range from 5 to 82, 112 men and 129 women) were tested.</p>
        <p>Another part of the study was to investigate the role of
tickborne rickettsiae as the causes of acute non-malarial febrile disease
in rural populations of the same villages. Interviews and sampling
were conducted in the same two villages from December 2008
through June 2009. During the period between November 2008
and July 2009, a total of 204 samples from 134 patients (62M and
72F) were included in this study. In this study, we included patients
who came into the dispensary with a recent fever and had negative
test results for malaria; 103 (77%) were from Dielmo (468
inhabitants) and 31 (23%) from Ndiop (628 inhabitants); 90
(67.2%) were younger than 10 years, including 64 (47.8%) under
five years. No one died during the study.</p>
        <p>Medical examinations were performed by a medical attendant
for each individual with fever (defined by an axillary temperature
.37.5uC). A questionnaire was completed for each individual.
Whole blood was collected from the fingertip by lancet stick and
then applied to glass microscope slides. Thick and thin blood
smears were stained with Giemsa and analyzed by microscopy for
the trophozoites and gametocytes of malaria. If the malaria test
was negative, 200 ml of whole blood (3?4 drops) were collected for
DNA extraction. The first stages of DNA extraction (digesting,
binding and washing) was performed directly in the village
dispensary using the QIAamp kit (QIAGEN, Hilden, Germany).
The columns with the bound and dry DNA inside were then
stored at 4uC before transportation and final elution, which was
performed in URMITE, Marseilles, France.</p>
      </sec>
      <sec id="3-2">
        <title>Ticks</title>
        <p>
          In November-December 2008, ticks were collected from
domestic animals (cows, goats, sheep, horses, donkeys) in two
regions of Senegal: Sine-Saloum and Niakhar (Table 1, Figure 2).
A total of 406 ticks were collected from four villages in the
SineSaloum region and 2361 ticks from the Niakhar region. They were
stored in 70% ethanol. Twenty adult Hyalomma truncatum ticks were
preserved alive in a flask at 90?95% of relative humidity. The
species and sex were identified according to standard taxonomic
keys for adult ticks [
          <xref ref-type="bibr" rid="45 44">44,45</xref>
          ].
        </p>
      </sec>
      <sec id="3-3">
        <title>Culture</title>
        <p>
          Live H. truncatum ticks were used for bacterial culture and were
not included in the overall statistics. Each was washed in a 10%
water solution of a commercial disinfectant-detergent
(Amphomousse, Hydenet S.A., Sainghin-en-Melantois, France), then
rinsed in sterile water and placed in a 1% solution of sodium
hypochlorite for 10 min. After rinsing with distilled water, they
were incubated in 70% ethanol for 15 min. A final rinse in sterile
phosphate buffer saline preceded inoculation. Ticks were placed in
a sterile 1.5 ml plastic tube, where they were triturated with a
sterile micropestle in 300 ml of Minimum Essential Medium
(MEM) supplied with 4% of fetal bovine serum (FBS). Isolation
was done according to the well-known shell-vial technique with
modifications [
          <xref ref-type="bibr" rid="46">46</xref>
          ]. We used 300 ml of whole tick suspension for
inoculation of a vial with a monolayer of L929 cells. After
centrifugation, the supernatant was removed and conserved. The
cells were covered with culture media (MEM, 4% FBS).
Antibiotics were not used during the cultivation.
        </p>
      </sec>
      <sec id="3-4">
        <title>Molecular biology</title>
        <p>
          DNA from homogenized ticks that were conserved in ethanol,
supernatants collected after shell-vial inoculation, as well as
supernatants of cell culture were extracted using the BioRobot
MDx Workstation (Qiagen, Courtaboeuf, France) with a
customized extraction protocol following the manufacturer?s instructions.
DNA was stored at 4uC until use in PCR amplifications. Rickettsial
DNA was initially detected by Rickettsia genus-specific quantitative
PCR (qPCR) reactions that were performed using LightCycler 2.0
equipment and software (Roche Diagnostics GmbH, Mannheim,
Germany). Master mixtures were prepared by following the
instructions of the manufacturer with primers RKND03F and
RKND03R and a probe, whose sequences are specific for the
sequence of the rickettsial citrate synthase gene. PCR cycling and
melting curve conditions have been described previously [
          <xref ref-type="bibr" rid="47">47</xref>
          ]. A
new qPCR system based on rickettsial sca1 gene and specific for R.
aeschlimannii was designed and tested for specificity and sensitivity.
The sequences of the primers and probe are as follows: forward
primer R_aesSca1_F
39-AAGCGGCACTTTAGGTAAAGAAA59, reverse primer R_aesSca1_R
39-CATGCTCTGCAAATGAACCA-59, probe
6-FAMH-TGGGGAAATATGCCGTATACGCAAGC-TAMRAH. Specificity was tested with 26 species and
strains of different rickettsiae and sensitivity was compared with
RKND03 by serial dilutions [
          <xref ref-type="bibr" rid="47">47</xref>
          ].
        </p>
        <p>
          Chosen positive samples were subjected to simple PCR using
primers manufactured by Eurogentec, Seraing, Belgium. They
amplified almost the complete genetic sequence of rickettsial
citrate synthase (gltA), as previously described [
          <xref ref-type="bibr" rid="49 48">48,49</xref>
          ].
Additionally, a 632 bp fragment of the ompA gene was amplified using Rr.
190.70 and Rr. 190.701 primers [50].
        </p>
        <p>
          The screening of DNA from human samples for SFG rickettsiae
was also performed with the Rickettsia genus-specific RKND03
qPCR system. The positive results were then confirmed by the
??1029 system?? based on the RC0338 gene (referenced by R. conorii
genome AE006914) coding for hypothetical protein and present in
all rickettsiae of spotted fever group [
          <xref ref-type="bibr" rid="51">51</xref>
          ]. A nested PCR was later
used to obtain the larger portion of the rickettsial gltA gene for the
subsequent sequencing of the amplicons derived from positive
samples. For the nested PCR, CS2d and CSendR primers were
used to amplify most of the full-length gltA gene, and the primers
RpCS409p and RpCS877p were subsequently used as described
above.
        </p>
        <p>
          We used the amplification of the beta actin gene by specific
qPCR [
          <xref ref-type="bibr" rid="51">51</xref>
          ] as the control for appropriate handling and extraction
of DNA from human samples.
        </p>
        <p>
          DNA extracted from uninfected ticks from colonies at the Unite´
des Rickettsies, Marseille, France and sterile cardiac valve biopsies
were used as negative controls, and DNA extracted from the cell
culture supernatant of Rickettsia bellii served as a positive control.
Polymerase chain reactions were performed in automated DNA
thermal cyclers (GeneAmp 2400 and 9700; Applied Biosystems,
Foster City, CA, USA). PCR products were visualized by
electrophoresis on a 1.5% agarose gel, stained with ethidium
bromide, and examined using an ultraviolet transilluminator. The
PCR products were purified using a QIAquick Spin PCR
Purification Kit (Qiagen) according to the manufacturer?s
instructions. Sequencing of amplicons was performed using the
BigDye Terminator Cycle Sequencing Kit (Perkin Elmer Applied
Biosystems) with an ABI automated sequencer (Applied
Biosystems). Obtained sequences were assembled (ChromasPro 1.49
beta, Technelysium Pty Ltd, Tewantin, Australia), edited by
BioEdit Sequence alignment editor v. 7.0.9.0 [
          <xref ref-type="bibr" rid="52">52</xref>
          ], and compared
with those available in GenBank by NCBI BLAST (http://blast.
ncbi.nlm.nih.gov/Blast.cgi). Sequences of gltA genes from
Rickettsiae species chosen in GenBank for comparison were concatenated
and aligned with the ClustalW program, and a neighbor-joining
phylogenetic tree was constructed with Geneious 4.7.6 software
(Biomatters Ltd, Australia).
        </p>
      </sec>
      <sec id="3-5">
        <title>Serological studies</title>
        <p>Titers of IgG and IgM antibodies in serum samples obtained
from each person were determined using an indirect
immunofluorescence assay with antigens generated in-house. We tested sera
with the following antigens: R. conorii conorii strain Malish (ATCC
VR-613), R. africae strain ESF-5, R. aeschlimanni strain MC16,
Rickettsia sibirica mongolitimonae strain HA-91 (ATCC VR-1526),
Rickettsia felis strain Marseille (ATCC VR-1525), and R. typhi strain
Wilmington. All serum samples were diluted at ratios of 1:25, 1:50,
and 1:100 and were screened for total immunoglobulin. If the
serological screening with any rickettsial antigen was positive, final
titers for IgG and IgM were determined for all anti-rickettsial
antibodies.</p>
      </sec>
      <sec id="3-6">
        <title>Statistical analysis</title>
        <p>Data were analyzed using Epi Info software, version 3.4.1
(Centers for Disease Control and Prevention, Atlanta, GA, USA).
Non-parametric values were compared using a x2 test. Statistical
significance was defined as p,0.05.</p>
      </sec>
    </sec>
    <sec id="4">
      <title>Results</title>
      <sec id="4-1">
        <title>Human samples</title>
        <p>We have found that that 51/238 (21.4%) and 123/241 (51%) of
randomly screened healthy population of the Dielmo and Ndiop
villages of Sine-Saloum region of Senegal, respectively, had
serological evidence of contact with rickettsiae (Table 2). We have
noted that the prevalence of anti-rickettsial antibodies in sera was
higher in young villagers, with the positive ratio declining with age.
This tendency was always true for Ndiop; however, in Dielmo only
inhabitants older than 40 showed a higher seroprevalence
compared with the younger population (Table 2). In most cases,
sera reacted with several rickettsial antigens, and the titers of total
Ig were low and did not exceed 1/100 (94.1% of positive results in
Dielmo and 88% in Ndiop). We found IgM in 2 out of 3 sera with
high antibody levels from Dielmo and in 13 of 15 from Ndiop,
indicating recent infection. The highest titers for IgG and IgM
were 1/256, and both sera were from Ndiop. We identified the
antibodies against R. typhi in 6 cases (2.4%) from Dielmo and in 7
cases (2.9%) from Ndiop, but in all cases sera also reacted with
rickettsiae of SFG with at least the same titers. Only one patient
from Dielmo had low titer (1/50) antibodies against R. felis. His
serum also reacted with R. typhi and all SFG rickettsiae. We noted
that among all antigens tested, R. africae reacted most often with
the tested sera; 49 of 51 (96%) and 110 of 123 (89%) reacted with
its antigen in Dielmo and Ndiop respectively; it constitutes 20.6%
and 45.6% of tested villagers, respectively. The second most
commonly reactive rickettsia was R. sibirica mongolitimonae with 35
sera of 51 (68.6% and 14.7% of tested villagers) positive sera from
Dielmo and 93 sera of 123 (75.6% and 35.6% of tested villagers)
positive sera from Ndiop.</p>
        <p>
          As for rickettsial DNA, nine patients who presented in the
dispensary with acute fever of non-malarial origin were positive.
We considered patients positive only in samples in which the
qPCRs for both rickettsial genes were positive and the subsequent
standard PCR/sequencing produced the rickettsial gltA gene. Data
for eight of the patients positive for the DNA of R. felis were
already reported [
          <xref ref-type="bibr" rid="51">51</xref>
          ]. In one patient, we have successfully
amplified the DNA of Rickettsia conorii conorii. The patient was a
4-year-old girl with tachycardia and a fever that appeared on the
same day (27 March 2009). No rash or eschar was noticed during
her examination. Paracetamol was prescribed and the girl was sent
home. The fever resolved within several days without antibiotics.
        </p>
      </sec>
      <sec id="4-2">
        <title>Ticks</title>
        <p>
          We have collected ticks of seven different species on domestic
animals (Table 3), 491 ticks from four villages in the Sine-Saloum
region and 2494 ticks from 16 villages of the Niakhar region. The
results of studies of Amblyomma variegatum ticks have already been
reported (74/85 (87.1%) and 101/133 (79.7%) positive for R.
africae, respectively, for both regions) [
          <xref ref-type="bibr" rid="16">16</xref>
          ]. The majority of ticks in
both regions (268 of 406 (66%) and 2090 of 2361 (88.5%)) were
represented by Rhipicephalus evertsi evertsi (Figure 3). In our study,
Rhipicephalus guilhoni was the predominantly collected species in the
Niakhar region (49 of 50 ticks collected). Most of the ticks (85.7%)
were collected from donkeys. We have collected only five
Rhipicephalus (Boophilus) annulatus ticks and these ticks were all
collected in the Sine-Saloum region. Another species, Rhipicephalus
(B.) decoloratus, was only collected in the Niakhar region. Two
species of the Hyalomma genus were collected in both regions.
Hyalomma marginatum rufipes was less common than Hyalomma
truncatum in Sine-Saloum (58 ticks collected versus 74) when
compared with Niakhar (115 versus 67).
        </p>
      </sec>
      <sec id="4-3">
        <title>Molecular identification of rickettsiae in ticks</title>
        <p>
          We found three different rickettsial species in Rh. e. evertsi, with a
low rate of infection from 0.4 to 0.7% (Table 3). In the
SineSaloum region, one tick collected from the horse was infected with
R. conorii conorii, the agent of MSF. One tick from Sine-Saloum and
14/2090 (0.7%) total were infected with R. africae, the agent of
African tick-bite fever. This finding represents the first time that it
was found in Rh. e. evertsi. In the Niakhar region, 10 (0.5%) ticks
were infected by R. aeschlimannii. In both regions we were able to
amplify and sequence almost complete gltA gene (all samples
positive by qPCR were subjected to standard PCR and
sequencing). The gltA sequence was not absolutely identical to
P value
the R. africae reference strain (ESF-5), the clonality of which was
previously based on analysis of strains isolated from patients and A.
variegatum ticks [
          <xref ref-type="bibr" rid="53">53</xref>
          ]. Moreover, the sequence of the gltA gene of R.
aeschlimannii found in Rh. e. evertsi differed slightly from all GenBank
records. The phylogenetic positions of these rickettsiae are shown
in Figure 4.
        </p>
        <p>We have identified only one rickettsia in Rh. guilhoni and
only in the Niakhar region. All samples positive by qPCR were
subjected to a standard PCR (ompA and gltA genes) and
amplicons were sequenced. Both genes showed 100% identity
with R. massiliae strain Bar29 isolated from Rh. sanguineus
from Spain. The rate of infection in the Niakhar region is
22.4%; in Sine-Saloum the only collected tick was negative by
PCR.</p>
        <p>We have also tested two species of Rhipicephalus (Boophilus)
ticks; R. africae was also detected in one Rh. (B.) annulatus tick
from Sine-Saloum. The gltA and ompA sequences were identical
to the reference strain, ESF-5. All of our Rhipicephalus (B.)
decoloratus ticks were negative when tested by rickettsial
genusspecific qPCR. We found that 44.8% and 51.3% of H.
marginatum rufipes ticks in the Sine-Saloum and Niakhar regions,
respectively, are infected with R. aeschlimannii. In our study, it
was the only species of rickettsiae identified in this species of
tick. All ticks positive by genus-specific qPCR were subjected to
a R. aeschlimannii-specific qPCR and all were found to be
positive. In 6.8% and 4.6% of H. truncatum ticks from the
SineSaloum and Niakhar regions, respectively, we found a variant of
R. aeschlimannii that insignificantly differed from the one found in
Rh. e. evertsi and H. m. rufipes (Figure 4). We also identified R. s.
mongolitimonae in 13.5% of ticks, but only in the Sine-Saloum
region. All ticks positive by genus-specific qPCR were tested for
R. aeschlimannii-specific qPCR. Positive ticks were considered to
harbor R. aeschlimannii and all negative ticks were subjected to a
standard PCR with sequencing. The gltA gene of R. s.
mongolitimonae was identified in all positive ticks.</p>
      </sec>
      <sec id="4-4">
        <title>Rickettsial strains</title>
        <p>
          We have also succeeded in isolating two strains of rickettsiae from
Hyalomma truncatum collected in Dielmo village, in the region of
Sine-Saloum. Both strains were deposited in official collection of
Unite´ des Rickettsies, Medical Faculty, Marseilles, France (http://
ifr48.timone.univ-mrs.fr/portail2/index.php?option = com_content&amp;
task = view&amp;id = 96) under the following references: CSUR R175 for
R. s. mongolitimonae strain RH05 and CSUR R176 for R. aeschlimannii
strain RH15. Sequences of the rrs, gltA, ompA, ompB, and sca4 genes of
R. sibirica mongolitimonae, strain RH05, were deposited in GenBank
under the accession numbers HM050271, HM050296, HM050272,
HM050273, and HM050295, respectively. Sequences of the rrs, gltA,
ompA, ompB, and sca4 genes of R. aeschlimannii, strain RH15, were
deposited in GenBank under the accession numbers HM050274,
HM050276, HM050277, HM050278, and HM050275, respectively.
According to the proposed criteria for species definition in
rickettsiology [
          <xref ref-type="bibr" rid="54">54</xref>
          ], the isolated bacteria do not belong to a new
species. Strain RH05 was close but not identical to R. s. mongolitimonae.
Strain RH15 was also close but not identical to R. aeschlimannii. The
degree of divergence of the five above-mentioned genes from the
closest relative (R. s. mongolitimonae for RH05 and R. aeschlimannii for
RH15) was less than that required for the definition of a new species.
Genes of both strains were almost completely identical with sequenced
amplicons from H. truncatum ticks.
        </p>
        <p>Sequenced amplicons from the ticks were registered in GenBank
under the following accession numbers: gltA and ompA genes of R. s.
mongolitimonae from H. truncatum voucher #90105 (HM050279 and
HM050280); gltA and ompA genes of R. aeschlimannii from H. truncatum
voucher #90361 (HM050282 and HM050281); gltA and ompA genes
of R. aeschlimannii from H. m. rufipes voucher #83512 (HM050283 and
HM050284); voucher #83467 (HM050285 and HM050286); gltA and
ompA genes of R. africae from Rh. e. evertsi voucher #83298 (HM050288
and HM050287); gltA and ompA genes of R. aeschlimannii from Rh. e.
evertsi voucher #92200 (HM050289 and HM050290); gltA and ompA
genes of R. massiliae from Rh. guilhoni voucher #93995 (HM050293 and
HM050294); and gltA and ompA genes of R conorii from Rh. e.
evertsi.voucher#90310 (HM050292 and HM050291).</p>
      </sec>
    </sec>
    <sec id="5">
      <title>Discussion</title>
      <p>
        Entomological studies performed in two regions of Senegal
confirmed that Ixodid ticks, the potential vectors of spotted fevers
in Senegal, are highly prevalent in domestic animals and that the
close contact of humans with ticks is continual and permanent.
Seven different tick species of 33 known in Senegal were collected
in the studied regions. The most abundant species, Rhipicephalus
evertsi evertsi, is one of the most common ticks that feed not only on
domestic animals, but also many species of wild animals in Africa
[
        <xref ref-type="bibr" rid="55 41">41,55</xref>
        ]. The species is confined to the Afrotropical
zoogeographical region in sub-Saharan Africa [44]. This species, although very
common and prevalent, has not been frequently studied as the
vector of agents of humans and animal diseases. To date, it has
been known to transmit the protozoa Babesia bigemina [
        <xref ref-type="bibr" rid="56">56</xref>
        ],
Crimean-Congo hemorrhagic fever virus (CCHFV) [
        <xref ref-type="bibr" rid="57">57</xref>
        ], and
Ehrlichia ruminantium [
        <xref ref-type="bibr" rid="58">58</xref>
        ]. Rickettsial agents have not been
previously reported in these ticks, although tick hemolymph tests
showed the presence of rickettsial-like organisms [
        <xref ref-type="bibr" rid="10">10</xref>
        ]. Here, we
report the first identification of R. conorii in Senegal and in this tick.
This report also provides the first evidence of the role of this tick
species in the epidemiology of MSF. Despite its very low infection
rate (that is, in fact, always very low for all vectors of MSF [
        <xref ref-type="bibr" rid="7">7</xref>
        ]), the
abundance of this tick and its close contact with humans who take
care of and often live close to animals increases the probability of
infection. Two other rickettsial species, R. africae and R.
aeschlimannii, were not previously reported in Rh. e. evertsi.
      </p>
      <p>
        Rh. guilhoni is a member of the Rhipicephalus sanguineus group. It
can be a common tick in the drier areas in a horizontal band south
of the Sahara. Cattle, sheep, horses, and dogs, as well as wild
carnivores and birds are the preferred hosts of adult Rh. guilhoni
[
        <xref ref-type="bibr" rid="44">44</xref>
        ]. The only previously known pathogenic agent associated with
this species is CCHFV [
        <xref ref-type="bibr" rid="57">57</xref>
        ], although the disease itself has never
been reported to result from a bite by this tick. R. massiliae, a
recently emerged pathogen [
        <xref ref-type="bibr" rid="21">21</xref>
        ], was found in our study of this
tick. Interestingly, this rarely studied species was collected from
donkeys and ruminants and not from dogs, which are the usual
hosts for ticks of the R. sanguineus group.
      </p>
      <p>
        Ticks of the Boophilus sub-genus of Rhipicephalus are one-host
ticks with a monotropic type of behavior. Rhipicephalus (Boophilus)
annulatus transmits the protozoans Babesia bigemina and Babesia bovis
to cattle, both of which cause bovine babesiosis. It also transmits
Anaplasma marginale and Eh. ruminantium to cattle [
        <xref ref-type="bibr" rid="44">44</xref>
        ]. R. africae has
also been found in the closely related species, Rhipicephalus (B.)
microplus [
        <xref ref-type="bibr" rid="59">59</xref>
        ]. Rhipicephalus (B.) decoloratus was already shown to
harbor R. africae in Botswana [
        <xref ref-type="bibr" rid="60">60</xref>
        ]. Our finding of typical R. africae
in Rh. (B.) annulatus is not surprising. The low percentage of
infection compared with A. variegatum collected in the same region
from the same animals may be explained by lower genus/species
susceptibility to R. africae.
      </p>
      <p>
        H. marginatum rufipes is the most widespread Hyalomma in Africa
and is notorious as a vector of the CCHF virus [
        <xref ref-type="bibr" rid="61">61</xref>
        ]. The feeding
of adults on cattle often causes large lesions at the attachment sites,
leading to the formation of severe abscesses. It has also been
identified as a host of R. aeschlimannii [
        <xref ref-type="bibr" rid="22">22</xref>
        ], which our data
supported. H. truncatum is found predominantly in sub-Saharan
Africa where it may be the most common Hyalomma. This species
of tick is notorious for causing many types of direct damage to its
hosts. Certain strains of H. truncatum have a toxin in their saliva
that causes the skin disease known as sweating sickness in cattle
[
        <xref ref-type="bibr" rid="62">62</xref>
        ], particularly calves. H. truncatum also transmits the protozoan
Babesia caballi to horses [
        <xref ref-type="bibr" rid="44">44</xref>
        ]. Rickettsia-like organisms have been
previously observed microscopically in this species [
        <xref ref-type="bibr" rid="10">10</xref>
        ]. We found
R. s. mongolitimonae, which causes lymphangitis-associated
rickettsiosis, in this aggressive tick that readily bites humans.
Interestingly, the reported clinical picture of the illness caused by this
rickettsia strikingly resembles the description of the disease of
??young shepherds?? mentioned by the village chiefs. The theory
that rickettsiae are responsible for this disease is also supported by
the highest seroprevalence in the younger members of the village
population.
      </p>
      <p>
        Finally, we have identified five different pathogenic rickettsial
species in tick vectors with an incidence up to 51.3% (R.
aeschlimannii in H. marginatum rufipes). R. africae is a pathogen
known to be responsible for African tick-bite fever. The high
incidence (87.1%) of this rickettsia in A. variegatum ticks was
previously reported. We have found that, although to a lesser
degree, two other species of ticks, Rh. e. evertsi and Boophilus
(Rhipicephalus) annulatus, may harbor this pathogen. R. aeschlimannii
is a recently recognized pathogen [
        <xref ref-type="bibr" rid="63">63</xref>
        ]. The properties of
aggressivity, abundance, and the high rate of infection of vectors
that are characteristic of ticks of the Hyalomma genus may enhance
the probability of this infection.
      </p>
      <p>
        We suppose that ticks in Senegal may play an important role in
the transmission of vector-borne diseases, primarily because of the
elevated probability of contact with humans and because of high
levels of rickettsial infection in ticks. Indirect evidence of the role of
Ixodid ticks in vector-borne diseases may be obtained from local
populations. The village chiefs of Dielmo and Ndiop told us, for
instance, that the beginning of the field activities of children
coincides with the appearance of multiple eschar-like lesions on
the child?s ankles that is often associated with a fever. This
description perfectly corresponds with many rickettsial diseases,
including African tick-bite fever (Table 4). Several publications
from other regions confirm that Ixodid ticks, and especially tick
larvae, may be a serious pest, causing ??skin disease?? [
        <xref ref-type="bibr" rid="64 65">64,65</xref>
        ]. Here
and in previous works [16], we have shown that A. variegatum, H.
marginatum rufipes, H. truncatum, and Rh. evertsi evertsi are among the
most important species that may have a contact with humans.
      </p>
      <p>
        The results of the serological screening confirmed our
assumption. They showed a very high prevalence (21.4% and
51% in Dielmo and Ndiop, respectively) of sera that react with
rickettsial antigens (spotted fever group) in a generally healthy
population of rural Senegal. Generally, our results correspond with
the previous data from Burkina Faso, Central African Republic,
Mali, Cote d?Ivoire, and Guinea-Bissau where an incidence of
rickettsial antibodies in human sera of up to 36% was shown [
        <xref ref-type="bibr" rid="28">28</xref>
        ].
Preliminary results show that two rickettsial species, R. africae and
R. sibirica mongolitimonae, which show a greater affinity with human
sera may play a more important role in human pathology in the
studied regions. R. aeschlimannii, which is most prevalent in ticks, is
not as pathogenic as two above-mentioned rickettsiae, however,
because of cross-reactivity among rickettsiae of spotted-fever group
and R. felis, based on performed serological studies we may not say
exactly which species of rickettsia play the most important role in
elevated seroprevalence in West Africa.
      </p>
      <p>
        We have also studied the role of rickettsial infections as possible
causes of acute fevers in the indigenous population of rural
Senegal. It was found that rickettsioses may be responsible for up
to 6.7% of cases of recent acute non-malarial fever in the rural
dispensary. Although most of the cases were found to be caused by
flea-borne rickettsiosis caused by R. felis [
        <xref ref-type="bibr" rid="51">51</xref>
        ], in 0.7% the origin of
the fever was tick-borne rickettsia. The identified case was from
Dielmo village, and the tick positive for R. conorii (Rh. e. evertsi) was
collected in Medina, a small village not far from Ndiop. Despite
the very low percentage of infected ticks, we succeeded in the
identification of this rickettsia in the blood of a febrile girl that was
evidently ill with Mediterranean spotted fever.
      </p>
      <p>
        The prevalence of five tick-borne and one flea-borne rickettsiae in
the same region poses a question about cross-protection. To the best
of our knowledge, no other region in the world has yet been found to
present such a variety of pathogenic rickettsiae. The model studies
that have been performed in animals since the beginning of 20th
century often showed opposite results (Table 5), even when the same
animals and rickettsiae were tested, for instance R. conorii and R.
africae on guinea pigs [
        <xref ref-type="bibr" rid="67 66">66,67</xref>
        ]. Usually, broader cross-protection was
seen when sublethal doses of live rickettsiae were used for
immunization [
        <xref ref-type="bibr" rid="69">68,69</xref>
        ] when compared with inactivated bacteria.
No studies in humans have been performed. In Senegal, the natural
condition favors simultaneous contact of the rural population with
different rickettsiae, so further studies on the dynamics of antibody
levels over several years and their protective significance should be
performed. Moreover, the prevalence Q fever in humans and its
causative agent, C. burnetii, in ticks in the same regions [
        <xref ref-type="bibr" rid="70">70</xref>
        ] shows
that these regions of rural Senegal present a natural reservoir of at
least several emerging zoonoses.
      </p>
      <p>In conclusion, we have to emphasize that the pathogenic
spotted fever rickettsiae are very common in rural Senegal. Both
occasional travelers and local villagers have a very high probability
of being infected. Unfortunately, the modern reader is familiar</p>
      <p>H.truncatum, H. asiaticum, H.truncatum
H. anatolicum excavatum,
Rh. pusillus
H. m. marginatum, H. m. H.truncatum,H.
rufipes, H. aegyptium, m. rufipes, Rh.</p>
      <p>Haemaphysalis inermis e. evertsi
Unnamed (one
case)</p>
      <p>Rh. sanguineus, Rh.
turanicus, Rh. muhsamae,
Rh. lunulatus, Rh. sulcatus</p>
      <p>Rh. guilhoni
Rh. e. evertsi
Rh. e. evertsi,
Rh. (B.) annulatus
Tick species
associated Fever, Diffuse Eschar,
(present study) % rash, % %
Reported
mortality</p>
      <p>Lymphadenopathy Lymphangitis rates,%
100
92
100
Yes
Yes
97
43
78
Yes
Yes
72
98%,
often
multiple
89%
Yes
Yes</p>
      <p>Rare
Yes
55%
?
?</p>
      <p>
        No
No
?
?
Yes, up
to 44%
1?5
Very low
0
0
0
Animal model
Guinea pigs
Guinea pigs
Guinea pigs
Guinea pigs
Guinea pigs
Guinea pigs
Guinea pigs
almost exclusively with rickettsioses as the cause of returning
travelers? fever [
        <xref ref-type="bibr" rid="25">25</xref>
        ]. The fevers in returning travelers are easy to
identify, because these people are usually intently observed after
returning. In contrast, little is known about rickettsioses in the local
indigenous African population. The only known report is from
Cameroon [
        <xref ref-type="bibr" rid="71">71</xref>
        ], where seven cases were described based on the
molecular identification of R. africae in the blood of febrile patients.
The integral approach applied in our work (studies of vectors,
seroprevalence, and causes of acute fevers) allowed us to reveal the
important role of rickettsial diseases in public health in Western
Africa.
      </p>
      <p>Our results are compatible with previously reported data, and the
very high prevalence of spotted fevers may be explained by the
surprising number of pathogenic rickettsiae identified in the studied
region (R. conorii conorii, R. africae, R. sibirica mongolitimonae, R.
aeschlimannii, and R. massiliae). We have summarized the clinical and
epidemiological data concerning spotted fevers caused by all five
tick-borne rickettsiae (Table 4). In addition, our study contributes to
the discovery of the origin of unexplained fevers in Africa. We
showed that up to 6.7% (9 of 134) of acute non-malarial fevers in
rural Africa may have rickettsial (R. felis and R. conorii) origin.</p>
      <p>
        Based on these data, we concluded that tick-borne rickettsioses
together with Q fever [
        <xref ref-type="bibr" rid="70">70</xref>
        ], flea-borne rickettsiosis caused by R. felis
[
        <xref ref-type="bibr" rid="51">51</xref>
        ], Tropheryma whipplei infection [
        <xref ref-type="bibr" rid="72">72</xref>
        ], and tick-borne relapsing
fever [
        <xref ref-type="bibr" rid="43">43</xref>
        ] are major public health problems in West Africa.
Taking into consideration that the role of tick-borne fevers in West
Africa was previously underestimated, it is very important to
perform long-term surveys on the distribution of vector ticks and
rickettsiae, as well as screening targeted groups, both tourists and
the indigenous population. We suggest implementing diagnostic
      </p>
      <p>Antigen
Sublethal doses alive
rickettsiae
Sublethal doses alive
rickettsiae
Sublethal doses alive
rickettsiae
Sublethal doses alive
rickettsiae
Sublethal doses alive
rickettsiae
Sublethal doses alive
rickettsiae
Sublethal doses alive
rickettsiae</p>
      <p>
        Results of the study
Absence of cross-immunity
Reciprocal cross-protection
Absence of cross-immunity
Reciprocal cross-protection
Absence of cross-immunity
Reciprocal cross-protection
Reciprocal cross-protection
[
        <xref ref-type="bibr" rid="73 69">69,73</xref>
        ]
Reference
[66]
[
        <xref ref-type="bibr" rid="67">67</xref>
        ]
[
        <xref ref-type="bibr" rid="74">74</xref>
        ]
[
        <xref ref-type="bibr" rid="75">75</xref>
        ]
[
        <xref ref-type="bibr" rid="76">76</xref>
        ]
[
        <xref ref-type="bibr" rid="77">77</xref>
        ]
procedures and adapted treatments in the field to enhance the
health of the people living in rural sub-Saharan Africa.
      </p>
    </sec>
    <sec id="6">
      <title>Supporting Information</title>
      <p>Alternative Language Abstract S1 Translation of the abstract
of the article Tick-borne rickettsioses, neglected emerging diseases
in rural Senegal into Russian language by author O. Mediannikov
Found at: doi:10.1371/journal.pntd.0000821.s001 (0.00 MB
DOC)
Alternative Language Abstract S2 Translation of the abstract
of the article Tick-borne rickettsioses, neglected emerging diseases
in rural Senegal into French language by author O. Mediannikov
Found at: doi:10.1371/journal.pntd.0000821.s002 (0.02 MB
DOC)
Checklist S1 STROBE checklist
Found at: doi:10.1371/journal.pntd.0000821.s003 (0.10
DOC)
MB</p>
    </sec>
    <sec id="7">
      <title>Acknowledgments</title>
      <p>We thank Denis Pyak and Geetha Subramanian for the technical
assistance.</p>
    </sec>
    <sec id="8">
      <title>Author Contributions</title>
      <p>Conceived and designed the experiments: OM GD FF J-FT DR.
Performed the experiments: OM GD. Analyzed the data: OM GD FF
CS J-FT. Contributed reagents/materials/analysis tools: CS J-FT DR.
Wrote the paper: OM DR.
www.plosntds.org</p>
    </sec>
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  <title line_height="18.29" font="BENKKD+AdvP40319B">Tick-Borne
Rickettsioses, Neglected Emerging Diseases in Rural Senegal</title>
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language by author O. Mediannikov Found at:
doi:10.1371/journal.pntd.0000821.s002 (0.02 MB DOC) Checklist S1 STROBE
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