med2ris failure
Bruce Hayward <[email protected]> Mon, 15 Oct 2007 10:56:47 +0100
| Newsgroups | gmane.text.refdb.general |
|---|---|
| Message-ID | <[email protected]> |
Recently I've been getting lots of failures when I try to convert a Pubmed xml file to ris format. I've attached a couple of offending files. Failure 1: med2ris pubmed_031007.xml > pubmed_031007.ris junk after document element at line 216, column 4, byte 11204 at /usr/local/lib/perl5/site_perl/5.8.8/mach/XML/Parser.pm line 187 In this case the ris file contains only the first reference Failure 2: med2ris pubmed_081007.xml > pubmed_081007.ris not well-formed (invalid token) at line 3, column 27, byte 44 at /usr/local/lib/perl5/site_perl/5.8.8/mach/XML/Parser.pm line 187 In this case the ris file is empty. ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Refdb-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/refdb-users
pubmed_031007.xml
(text/xml, 35.6 KB)
<PubmedArticle>
<MedlineCitation Owner="NLM" Status="MEDLINE">
<PMID>16764814</PMID>
<DateCreated>
<Year>2006</Year>
<Month>07</Month>
<Day>31</Day>
</DateCreated>
<DateCompleted>
<Year>2006</Year>
<Month>10</Month>
<Day>27</Day>
</DateCompleted>
<DateRevised>
<Year>2006</Year>
<Month>11</Month>
<Day>15</Day>
</DateRevised>
<Article PubModel="Print-Electronic">
<Journal>
<ISSN IssnType="Print">0003-2697</ISSN>
<JournalIssue CitedMedium="Print">
<Volume>355</Volume>
<Issue>2</Issue>
<PubDate>
<Year>2006</Year>
<Month>Aug</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
<Title>Analytical biochemistry</Title>
<ISOAbbreviation>Anal. Biochem.</ISOAbbreviation>
</Journal>
<ArticleTitle>Magnetic bead-based solid phase for selective extraction of genomic DNA.</ArticleTitle>
<Pagination>
<MedlinePgn>285-97</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>Magnetic bead-based solid phases are widely used for the separation of nucleic acids from complex mixtures. The challenge to selectively separate specific DNA molecules (via complementary hybridization) in a single step is the selection of a linker between the capture probe and the solid support that can be exposed to high temperatures in the presence of a high salt media. This article presents a general platform for the fabrication of a magnetic bead-based selective solid phase that can be used for subtractive hybridization or sequence capture applications. Phosphorus dendrimers are used for the first time as linkers in a magnetic bead-based selective solid phase for capture of genomic DNA. Aside from providing a high loading capacity, they render a stable bond between the capture probe and the surface under the high temperature and salt conditions required for denaturation and capture to proceed in a single step. The thermal stability of the solid phase under these conditions is first demonstrated by hybridizing a Cy3-labeled target. The selective capture of DNA targets in a single step is then demonstrated by subtractive hybridization of fragmented human genomic DNA. The specificity and selectivity of the solid phase are demonstrated by the recovery of adenovirus serotype 4 DNA spiked into the human DNA target. The effect of steric and electrostatic constraints was also investigated by using dendrimers of different generations that vary in their size and the number of branches. The results demonstrate that this platform can be used for single-step subtractive hybridization applications with better performance over the conventional two-step method using streptavidin-coated magnetic beads.</AbstractText>
</Abstract>
<Affiliation>Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC 20375, USA.</Affiliation>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Archer</LastName>
<ForeName>Marie J</ForeName>
<Initials>MJ</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Lin</LastName>
<ForeName>Baochuan</ForeName>
<Initials>B</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Wang</LastName>
<ForeName>Zheng</ForeName>
<Initials>Z</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Stenger</LastName>
<ForeName>David A</ForeName>
<Initials>DA</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType>Journal Article</PublicationType>
<PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
<PublicationType>Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2006</Year>
<Month>05</Month>
<Day>24</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>United States</Country>
<MedlineTA>Anal Biochem</MedlineTA>
<NlmUniqueID>0370535</NlmUniqueID>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Carbocyanines</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Fluorescent Dyes</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Salts</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>cyanine dye 3</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>9007-49-2</RegistryNumber>
<NameOfSubstance>DNA</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>9013-20-1</RegistryNumber>
<NameOfSubstance>Streptavidin</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Adenoviridae</DescriptorName>
<QualifierName MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Carbocyanines</DescriptorName>
<QualifierName MajorTopicYN="N">chemistry</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">DNA</DescriptorName>
<QualifierName MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Electrophoresis, Polyacrylamide Gel</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Fluorescent Dyes</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Genetic Techniques</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Genome</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Magnetics</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Nucleic Acid Denaturation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Nucleic Acid Hybridization</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Polymerase Chain Reaction</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Salts</DescriptorName>
<QualifierName MajorTopicYN="N">pharmacology</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Serotyping</DescriptorName>
<QualifierName MajorTopicYN="N">methods</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Streptavidin</DescriptorName>
<QualifierName MajorTopicYN="N">chemistry</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Temperature</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="received">
<Year>2006</Year>
<Month>3</Month>
<Day>8</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised">
<Year>2006</Year>
<Month>5</Month>
<Day>1</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="accepted">
<Year>2006</Year>
<Month>5</Month>
<Day>4</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="aheadofprint">
<Year>2006</Year>
<Month>5</Month>
<Day>24</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2006</Year>
<Month>6</Month>
<Day>13</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2006</Year>
<Month>10</Month>
<Day>28</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pii">S0003-2697(06)00336-8</ArticleId>
<ArticleId IdType="doi">10.1016/j.ab.2006.05.005</ArticleId>
<ArticleId IdType="pubmed">16764814</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>
<PubmedArticle>
<MedlineCitation Owner="NLM" Status="MEDLINE">
<PMID>10603244</PMID>
<DateCreated>
<Year>2001</Year>
<Month>03</Month>
<Day>08</Day>
</DateCreated>
<DateCompleted>
<Year>2001</Year>
<Month>05</Month>
<Day>31</Day>
</DateCompleted>
<DateRevised>
<Year>2006</Year>
<Month>11</Month>
<Day>15</Day>
</DateRevised>
<Article PubModel="Print">
<Journal>
<ISSN IssnType="Print">0003-2697</ISSN>
<JournalIssue CitedMedium="Print">
<Volume>276</Volume>
<Issue>2</Issue>
<PubDate>
<Year>1999</Year>
<Month>Dec</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
<Title>Analytical biochemistry</Title>
<ISOAbbreviation>Anal. Biochem.</ISOAbbreviation>
</Journal>
<ArticleTitle>Real-time measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer.</ArticleTitle>
<Pagination>
<MedlinePgn>204-14</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>When capture oligonucleotides are tethered on planar surfaces, mass transport limitations influence the kinetics of solid-phase nucleic acid hybridizations. By diffusion theory, however, hybridization of oligonucleotides on microparticles should be reaction-rate limited. In an initial effort to understand the kinetics of microparticle hybridization reactions, we developed a fluorescence resonance energy transfer method for monitoring oligonucleotide hybridization on microparticles. Microparticles were coated with a fluoresceinated oligomer at surface densities of 20, 40, and 80% saturation, hybridized to a complementary oligonucleotide labeled with tetramethylrhodamine, and monitored over time for quenching of the fluorescein signal as hybridization occurred on the particle surface. Association rate constants were compared for microparticle-based hybridization and solution-phase hybridization. Rate constants for hybridizations on the particle surface were about an order of magnitude less than those for hybridization in solution, but decreasing the surface density of the capture oligonucleotide to 20% saturation improved particle hybridization rates. Although a bimolecular reaction model adequately described solution-phase hybridization kinetics, oligonucleotide hybridization on microparticles did not fit this model but exhibited biphasic reaction kinetics. Based on two different lines of reasoning, we argue that microparticle-based oligonucleotide hybridization was indeed reaction-rate limited in our system and not diffusion-rate limited.</AbstractText>
<CopyrightInformation>Copyright 1999 Academic Press.</CopyrightInformation>
</Abstract>
<Affiliation>Department of Biomedical Engineering, Robert R. McCormick School of Engineering and Applied Science, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA. [email protected]</Affiliation>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Henry</LastName>
<ForeName>M R</ForeName>
<Initials>MR</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Wilkins Stevens</LastName>
<ForeName>P</ForeName>
<Initials>P</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Sun</LastName>
<ForeName>J</ForeName>
<Initials>J</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Kelso</LastName>
<ForeName>D M</ForeName>
<Initials>DM</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType>Journal Article</PublicationType>
<PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo>
<Country>UNITED STATES</Country>
<MedlineTA>Anal Biochem</MedlineTA>
<NlmUniqueID>0370535</NlmUniqueID>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Oligonucleotide Probes</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>9007-49-2</RegistryNumber>
<NameOfSubstance>DNA</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">DNA</DescriptorName>
<QualifierName MajorTopicYN="Y">genetics</QualifierName>
<QualifierName MajorTopicYN="Y">isolation & purification</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Fluorometry</DescriptorName>
<QualifierName MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Kinetics</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Microspheres</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Models, Chemical</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Nucleic Acid Hybridization</DescriptorName>
<QualifierName MajorTopicYN="Y">methods</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Oligonucleotide Probes</DescriptorName>
<QualifierName MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Spectrometry, Fluorescence</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="pubmed">
<Year>1999</Year>
<Month>12</Month>
<Day>22</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2001</Year>
<Month>6</Month>
<Day>2</Day>
<Hour>10</Hour>
<Minute>1</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">10603244</ArticleId>
<ArticleId IdType="medline">20072531</ArticleId>
<ArticleId IdType="doi">10.1006/abio.1999.4344</ArticleId>
<ArticleId IdType="pii">S0003-2697(99)94344-0</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>
<PubmedArticle>
<MedlineCitation Owner="NLM" Status="MEDLINE">
<PMID>8599632</PMID>
<DateCreated>
<Year>1996</Year>
<Month>04</Month>
<Day>29</Day>
</DateCreated>
<DateCompleted>
<Year>1996</Year>
<Month>04</Month>
<Day>29</Day>
</DateCompleted>
<DateRevised>
<Year>2006</Year>
<Month>11</Month>
<Day>15</Day>
</DateRevised>
<Article PubModel="Print">
<Journal>
<ISSN IssnType="Print">0006-3495</ISSN>
<JournalIssue CitedMedium="Print">
<Volume>69</Volume>
<Issue>6</Issue>
<PubDate>
<Year>1995</Year>
<Month>Dec</Month>
</PubDate>
</JournalIssue>
<Title>Biophysical journal</Title>
<ISOAbbreviation>Biophys. J.</ISOAbbreviation>
</Journal>
<ArticleTitle>The biophysics of DNA hybridization with immobilized oligonucleotide probes.</ArticleTitle>
<Pagination>
<MedlinePgn>2243-55</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>A mathematical model based on receptor-ligand interactions at a cell surface has been modified and further developed to represent heterogeneous DNA-DNA hybridization on a solid surface. The immobilized DNA molecules with known sequences are called probes, and the DNA molecules in solution with unknown sequences are called targets in this model. Capture of the perfectly complementary target is modeled as a combined reaction-diffusion limited irreversible reaction. In the model, there are two different mechanisms by which targets can hybridize with the complementary probes: direct hybridization from the solution and hybridization by molecules that adsorb nonspecifically and then surface diffuse to the probe. The results indicate that nonspecific adsorption of single-stranded DNA on the surface and subsequent two-dimensional diffusion can significantly enhance the overall reaction rate. Heterogeneous hybridization depends strongly on the rate constants for DNA adsorption/desorption in the non-probe-covered regions of the surface, the two-dimensional (2D) diffusion coefficient, and the size of probes and targets. The model shows that the overall kinetics of DNA hybridization to DNA on a solid support may be an extremely efficient process for physically realistic 2D diffusion coefficients, target concentrations, and surface probe densities. The implication for design and operation of a DNA hybridization surface is that there is an optimal surface probe density when 2D diffusion occurs; values above that optimum do not increase the capture rate. Our model predicts capture rates in agreement with those from recent experimental literature. The results of our analysis predict that several things can be done to improve heterogeneous hybridization: 1) the solution phase target molecules should be about 100 bases or less in size to speed solution-phase and surface diffusion; 2) conditions should be created such that reversible adsorption and two-dimensional diffusion occur in the surface regions between DNA probe molecules; 3) provided that 2) is satisfied, one can achieve results with a sparse probe coverage that are equal to or better than those obtained with a surface totally covered with DNA probes.</AbstractText>
</Abstract>
<Affiliation>Department of Chemical Engineering, University of Pennsylvania, Philadelphia, USA.</Affiliation>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Chan</LastName>
<ForeName>V</ForeName>
<Initials>V</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Graves</LastName>
<ForeName>D J</ForeName>
<Initials>DJ</Initials>
</Author>
<Author ValidYN="Y">
<LastName>McKenzie</LastName>
<ForeName>S E</ForeName>
<Initials>SE</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType>Comparative Study</PublicationType>
<PublicationType>Journal Article</PublicationType>
</PublicationTypeList>
</Article>
<MedlineJournalInfo>
<Country>UNITED STATES</Country>
<MedlineTA>Biophys J</MedlineTA>
<NlmUniqueID>0370626</NlmUniqueID>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>DNA Probes</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Ligands</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Receptors, Cell Surface</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>9007-49-2</RegistryNumber>
<NameOfSubstance>DNA</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Base Composition</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">DNA</DescriptorName>
<QualifierName MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">DNA Probes</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Ligands</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Mathematics</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Models, Theoretical</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Nucleic Acid Conformation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Nucleic Acid Hybridization</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Receptors, Cell Surface</DescriptorName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="pubmed">
<Year>1995</Year>
<Month>12</Month>
<Day>1</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>1995</Year>
<Month>12</Month>
<Day>1</Day>
<Hour>0</Hour>
<Minute>1</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">8599632</ArticleId>
<ArticleId IdType="medline">96167203</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>
<PubmedArticle>
<MedlineCitation Owner="NLM" Status="MEDLINE">
<PMID>15653637</PMID>
<DateCreated>
<Year>2005</Year>
<Month>01</Month>
<Day>17</Day>
</DateCreated>
<DateCompleted>
<Year>2005</Year>
<Month>02</Month>
<Day>10</Day>
</DateCompleted>
<DateRevised>
<Year>2006</Year>
<Month>11</Month>
<Day>15</Day>
</DateRevised>
<Article PubModel="Electronic-Print">
<Journal>
<ISSN IssnType="Electronic">1362-4962</ISSN>
<JournalIssue CitedMedium="Internet">
<Volume>33</Volume>
<Issue>1</Issue>
<PubDate>
<Year>2005</Year>
</PubDate>
</JournalIssue>
<Title>Nucleic acids research</Title>
<ISOAbbreviation>Nucleic Acids Res.</ISOAbbreviation>
</Journal>
<ArticleTitle>Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres.</ArticleTitle>
<Pagination>
<MedlinePgn>366-75</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>Hybridization kinetics of DNA sequences with known secondary structures and random sequences designed with similar melting temperatures were studied in solution and when one strand was bound to 5 mum silica microspheres. The rates of hybridization followed second-order kinetics and were measured spectrophotometrically in solution and fluorometrically in the solid phase. In solution, the rate constants for the model sequences varied by almost two orders of magnitude, with a decrease in the rate constant with increasing amounts of secondary structure in the target sequence. The random sequences also showed over an order of magnitude difference in the rate constant. In contrast, the hybridization experiments in the solid phase with the same model sequences showed almost no change in the rate constant. Solid phase rate constants were approximately three orders of magnitude lower compared with the solution phase constants for sequences with little or no single-stranded structure. Sequences with a known secondary structure yielded solution phase rate constants as low as 3 x 10(3) M(-1) s(-1) with solid phase rate constants for the same sequences measured at 2.5 x 10(2) M(-1) s(-1). The results from these experiments indicate that (i) solid phase hybridization occurs three orders of magnitude slower than solution phase, (ii) trends observed in structure-dependent kinetics of solution phase hybridization may not be applicable to solid phase hybridization and (iii) model probes with known secondary structure decrease reaction rates; however, even random sequences with no known internal single-stranded structure can yield a broad range of reaction rates.</AbstractText>
</Abstract>
<Affiliation>Department of Chemistry, State University of New York at New Paltz 75 S. Manheim Blvd, New Paltz, NY 12561, USA.</Affiliation>
<AuthorList CompleteYN="Y">
<Author ValidYN="Y">
<LastName>Sekar</LastName>
<ForeName>Michael M A</ForeName>
<Initials>MM</Initials>
</Author>
<Author ValidYN="Y">
<LastName>Bloch</LastName>
<ForeName>Will</ForeName>
<Initials>W</Initials>
</Author>
<Author ValidYN="Y">
<LastName>St John</LastName>
<ForeName>Pamela M</ForeName>
<Initials>PM</Initials>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList>
<PublicationType>Comparative Study</PublicationType>
<PublicationType>Journal Article</PublicationType>
<PublicationType>Research Support, Non-U.S. Gov't</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2005</Year>
<Month>01</Month>
<Day>14</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<Country>England</Country>
<MedlineTA>Nucleic Acids Res</MedlineTA>
<NlmUniqueID>0411011</NlmUniqueID>
</MedlineJournalInfo>
<ChemicalList>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Oligonucleotide Probes</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance>Solutions</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>7631-86-9</RegistryNumber>
<NameOfSubstance>Silicon Dioxide</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>9007-49-2</RegistryNumber>
<NameOfSubstance>DNA</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">DNA</DescriptorName>
<QualifierName MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Kinetics</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Microspheres</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="Y">Nucleic Acid Hybridization</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Oligonucleotide Probes</DescriptorName>
<QualifierName MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName MajorTopicYN="N">Silicon Dioxide</DescriptorName>
<QualifierName MajorTopicYN="Y">chemistry</QualifierName>
</MeshHeading>
<MeshHeading>
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pubmed_081007.xml
(text/xml, 11.6 KB)
<PubmedArticle>
<MedlineCitation Owner Status>
<PMID>17909015</PMID>
<DateCreated>
<Year>2007</Year>
<Month>10</Month>
<Day>02</Day>
</DateCreated>
<Article PubModel>
<Journal>
<ISSN IssnType>0008-5472</ISSN>
<JournalIssue CitedMedium>
<Volume>67</Volume>
<Issue>19</Issue>
<PubDate>
<Year>2007</Year>
<Month>Oct</Month>
<Day>1</Day>
</PubDate>
</JournalIssue>
<Title>Cancer research</Title>
<ISOAbbreviation>Cancer Res.</ISOAbbreviation>
</Journal>
<ArticleTitle>Epigenetic Inactivation of a Cluster of Genes Flanking MLH1 in Microsatellite-Unstable Colorectal Cancer.</ArticleTitle>
<Pagination>
<MedlinePgn>9107-16</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>Biallelic promoter methylation and transcriptional silencing of the MLH1 gene occurs in the majority of sporadic colorectal cancers exhibiting microsatellite instability due to defective DNA mismatch repair. Long-range epigenetic silencing of contiguous genes has been found on chromosome 2q14 in colorectal cancer. We hypothesized that epigenetic silencing of MLH1 could occur on a regional scale affecting additional genes within 3p22, rather than as a focal event. We studied the levels of CpG island methylation and expression of multiple contiguous genes across a 4 Mb segment of 3p22 including MLH1 in microsatellite-unstable and -stable cancers, and their paired normal colonic mucosa. We found concordant CpG island hypermethylation, H3-K9 dimethylation and transcriptional silencing of MLH1 and multiple flanking genes spanning up to 2.4 Mb in microsatellite-unstable colorectal cancers. This region was interspersed with unmethylated genes, which were also transcriptionally repressed. Expression of both methylated and unmethylated genes was reactivated by methyltransferase and histone deacetylase inhibitors in a microsatellite-unstable colorectal carcinoma cell line. Two genes at the telomeric end of the region were also hypermethylated in microsatellite-stable cancers, adenomas, and at low levels in normal colonic mucosa from older individuals. Thus, the cluster of genes flanking MLH1 that was specifically methylated in the microsatellite-unstable group of cancers extended across 1.1 Mb. Our results show that coordinate epigenetic silencing extends across a large chromosomal region encompassing MLH1 in microsatellite-unstable colorectal cancers. Simultaneous epigenetic silencing of this cluster of 3p22 genes may contribute to the development or progression of this type of cancer. [Cancer Res 2007;67(19):9107-16].</AbstractText>
</Abstract>
<Affiliation>Departments of Medical Oncology and Colorectal Surgery, St. Vincent's Hospital.</Affiliation>
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<Author ValidYN>
<LastName>Hitchins</LastName>
<ForeName>Megan P</ForeName>
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<Author ValidYN>
<LastName>Lin</LastName>
<ForeName>Vita Ap</ForeName>
<Initials>VA</Initials>
</Author>
<Author ValidYN>
<LastName>Buckle</LastName>
<ForeName>Andrew</ForeName>
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<LastName>Cheong</LastName>
<ForeName>Kayfong</ForeName>
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<LastName>Halani</LastName>
<ForeName>Nimita</ForeName>
<Initials>N</Initials>
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<Author ValidYN>
<LastName>Ku</LastName>
<ForeName>Su</ForeName>
<Initials>S</Initials>
</Author>
<Author ValidYN>
<LastName>Kwok</LastName>
<ForeName>Chau-To</ForeName>
<Initials>CT</Initials>
</Author>
<Author ValidYN>
<LastName>Packham</LastName>
<ForeName>Deborah</ForeName>
<Initials>D</Initials>
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<LastName>Suter</LastName>
<ForeName>Catherine M</ForeName>
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<LastName>Meagher</LastName>
<ForeName>Alan</ForeName>
<Initials>A</Initials>
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<LastName>Stirzaker</LastName>
<ForeName>Clare</ForeName>
<Initials>C</Initials>
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<LastName>Clark</LastName>
<ForeName>Susan</ForeName>
<Initials>S</Initials>
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<Author ValidYN>
<LastName>Hawkins</LastName>
<ForeName>Nicholas J</ForeName>
<Initials>NJ</Initials>
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<Author ValidYN>
<LastName>Ward</LastName>
<ForeName>Robyn L</ForeName>
<Initials>RL</Initials>
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<Language>eng</Language>
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<PublicationType>Journal Article</PublicationType>
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<Country>United States</Country>
<MedlineTA>Cancer Res</MedlineTA>
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<Month>10</Month>
<Day>3</Day>
<Hour>9</Hour>
<Minute>0</Minute>
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<Year>2007</Year>
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<PMID>17911167</PMID>
<DateCreated>
<Year>2007</Year>
<Month>10</Month>
<Day>03</Day>
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<Journal>
<ISSN IssnType>0964-6906</ISSN>
<JournalIssue CitedMedium>
<Volume>16 Spec No 2</Volume>
<PubDate>
<Year>2007</Year>
<Month>Oct</Month>
<Day>15</Day>
</PubDate>
</JournalIssue>
<Title>Human molecular genetics</Title>
<ISOAbbreviation>Hum. Mol. Genet.</ISOAbbreviation>
</Journal>
<ArticleTitle>Status of genomic imprinting in human embryonic stem cells as revealed by a large cohort of independently derived and maintained lines.</ArticleTitle>
<Pagination>
<MedlinePgn>R243-51</MedlinePgn>
</Pagination>
<Abstract>
<AbstractText>Investigation of the epigenetic stability of human embryonic stem cells (hESCs) is a crucial step for their use in cell-replacement therapies, as well as for assessing whether hESCs model epigenetic regulation in human pre-implantation cell types. To address these issues, we have examined the expression of imprinted genes in a previous study and more recently in 46 individual hESC lines as part of the International Stem Cell Initiative. Our results show that nearly all hESC lines examined possessed a substantial degree of epigenetic stability, despite differences in genetic background and in their derivation and initial propagation conditions. However, some hESCs did show loss of allele-specific expression, which could have implications for hESC differentiation and epigenetic stability (both in vitro and after clinical transplantation). A benefit of our and other recent studies of genomic imprinting in hESCs was the identification of imprinted genes that provide a useful indication of epigenetic stability. SNRPN, IPW and KCNQ1OT1 were highly stable and thus appeared insensitive to perturbation; in contrast, H19, IGF2 and MEG3 were more variable and thus could potentially provide a sensitive indication of epigenetic status. In this review, we examine the differences between imprinted genes in their susceptibility to perturbation and discuss the potential molecular basis for these differences. This examination provides insight into the regulation of genomic imprinting in hESCs and the corresponding peri-implantation stages of human development.</AbstractText>
</Abstract>
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<LastName>Rugg-Gunn</LastName>
<ForeName>Peter J</ForeName>
<Initials>PJ</Initials>
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<LastName>Ferguson-Smith</LastName>
<ForeName>Anne C</ForeName>
<Initials>AC</Initials>
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<LastName>Pedersen</LastName>
<ForeName>Roger A</ForeName>
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