Classification of T cell movement tracks allows for prediction of cell function.
Identifieur interne : 003984 ( PubMed/Corpus ); précédent : 003983; suivant : 003985Classification of T cell movement tracks allows for prediction of cell function.
Auteurs : Reka K. Kelemen ; Gengen F. He ; Hannah L. Woo ; Thomas Lane ; Caroline Rempe ; Jun Wang ; Ian A. Cockburn ; Rogerio Amino ; Vitaly V. Ganusov ; Michael W. BerrySource :
- International journal of computational biology and drug design [ 1756-0756 ] ; 2014.
English descriptors
- KwdEn :
- MESH :
- immunology : Malaria.
- physiology : T-Lymphocytes.
- Animals, Cell Movement, Mice.
Abstract
Using a unique combination of visual, statistical, and data mining methods, we tested the hypothesis that an immune cell's movement pattern can convey key information about the cell's function, antigen specificity, and environment. We applied clustering, statistical tests, and a support vector machine (SVM) to assess our ability to classify different datasets of imaged flouresently labelled T cells in mouse liver. We additionally saw clusters of different movement patterns of T cells of identical antigenic specificity. We found that the movement patterns of T cells specific and non-specific for malaria parasites are differentiable with 72% accuracy, and that specific cells have a higher tendency to move towards the parasite than non-specific cells. Movements of antigen-specific T cells in uninfected mice vs. infected mice were differentiable with 69.8% accuracy. We additionally saw clusters of different movement patterns of T cells of identical antigenic specificity. We concluded that our combination of methods has the potential to advance the understanding of cell movements in vivo.
DOI: 10.1504/IJCBDD.2014.061655
PubMed: 24878724
Links to Exploration step
pubmed:24878724Le document en format XML
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He</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Woo, Hannah L" sort="Woo, Hannah L" uniqKey="Woo H" first="Hannah L" last="Woo">Hannah L. Woo</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lane, Thomas" sort="Lane, Thomas" uniqKey="Lane T" first="Thomas" last="Lane">Thomas Lane</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Rempe, Caroline" sort="Rempe, Caroline" uniqKey="Rempe C" first="Caroline" last="Rempe">Caroline Rempe</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Cockburn, Ian A" sort="Cockburn, Ian A" uniqKey="Cockburn I" first="Ian A" last="Cockburn">Ian A. Cockburn</name><affiliation><nlm:affiliation>Department of Pathogens and Immunity, John Curtin School of Medical Research, Australian National University, GPO Box 334, Canberra City ACT 2600, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Amino, Rogerio" sort="Amino, Rogerio" uniqKey="Amino R" first="Rogerio" last="Amino">Rogerio Amino</name><affiliation><nlm:affiliation>Unité de Biologie et Génétique du Paludisme, Institut Pasteur, 75724, Paris Cedex 15, France.</nlm:affiliation></affiliation></author><author><name sortKey="Ganusov, Vitaly V" sort="Ganusov, Vitaly V" uniqKey="Ganusov V" first="Vitaly V" last="Ganusov">Vitaly V. Ganusov</name><affiliation><nlm:affiliation>Department of Microbiology, University of Tennessee, M409 Walters Life Science Building, 1414 West Cumberland Avenue, Knoxville, TN 37996-0845, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Berry, Michael W" sort="Berry, Michael W" uniqKey="Berry M" first="Michael W" last="Berry">Michael W. Berry</name><affiliation><nlm:affiliation>EECS Department, University of Tennessee, 401 Min H. Kao Building, Knoxville, TN 37996, USA.</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24878724</idno><idno type="pmid">24878724</idno><idno type="doi">10.1504/IJCBDD.2014.061655</idno><idno type="wicri:Area/PubMed/Corpus">003984</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">003984</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Classification of T cell movement tracks allows for prediction of cell function.</title><author><name sortKey="Kelemen, Reka K" sort="Kelemen, Reka K" uniqKey="Kelemen R" first="Reka K" last="Kelemen">Reka K. Kelemen</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="He, Gengen F" sort="He, Gengen F" uniqKey="He G" first="Gengen F" last="He">Gengen F. He</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Woo, Hannah L" sort="Woo, Hannah L" uniqKey="Woo H" first="Hannah L" last="Woo">Hannah L. Woo</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Lane, Thomas" sort="Lane, Thomas" uniqKey="Lane T" first="Thomas" last="Lane">Thomas Lane</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Rempe, Caroline" sort="Rempe, Caroline" uniqKey="Rempe C" first="Caroline" last="Rempe">Caroline Rempe</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation><nlm:affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Cockburn, Ian A" sort="Cockburn, Ian A" uniqKey="Cockburn I" first="Ian A" last="Cockburn">Ian A. Cockburn</name><affiliation><nlm:affiliation>Department of Pathogens and Immunity, John Curtin School of Medical Research, Australian National University, GPO Box 334, Canberra City ACT 2600, Australia.</nlm:affiliation></affiliation></author><author><name sortKey="Amino, Rogerio" sort="Amino, Rogerio" uniqKey="Amino R" first="Rogerio" last="Amino">Rogerio Amino</name><affiliation><nlm:affiliation>Unité de Biologie et Génétique du Paludisme, Institut Pasteur, 75724, Paris Cedex 15, France.</nlm:affiliation></affiliation></author><author><name sortKey="Ganusov, Vitaly V" sort="Ganusov, Vitaly V" uniqKey="Ganusov V" first="Vitaly V" last="Ganusov">Vitaly V. Ganusov</name><affiliation><nlm:affiliation>Department of Microbiology, University of Tennessee, M409 Walters Life Science Building, 1414 West Cumberland Avenue, Knoxville, TN 37996-0845, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Berry, Michael W" sort="Berry, Michael W" uniqKey="Berry M" first="Michael W" last="Berry">Michael W. Berry</name><affiliation><nlm:affiliation>EECS Department, University of Tennessee, 401 Min H. Kao Building, Knoxville, TN 37996, USA.</nlm:affiliation></affiliation></author></analytic><series><title level="j">International journal of computational biology and drug design</title><idno type="ISSN">1756-0756</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Cell Movement</term><term>Malaria (immunology)</term><term>Mice</term><term>T-Lymphocytes (physiology)</term></keywords><keywords scheme="MESH" qualifier="immunology" xml:lang="en"><term>Malaria</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>T-Lymphocytes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Cell Movement</term><term>Mice</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Using a unique combination of visual, statistical, and data mining methods, we tested the hypothesis that an immune cell's movement pattern can convey key information about the cell's function, antigen specificity, and environment. We applied clustering, statistical tests, and a support vector machine (SVM) to assess our ability to classify different datasets of imaged flouresently labelled T cells in mouse liver. We additionally saw clusters of different movement patterns of T cells of identical antigenic specificity. We found that the movement patterns of T cells specific and non-specific for malaria parasites are differentiable with 72% accuracy, and that specific cells have a higher tendency to move towards the parasite than non-specific cells. Movements of antigen-specific T cells in uninfected mice vs. infected mice were differentiable with 69.8% accuracy. We additionally saw clusters of different movement patterns of T cells of identical antigenic specificity. We concluded that our combination of methods has the potential to advance the understanding of cell movements in vivo.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24878724</PMID><DateCreated><Year>2014</Year><Month>06</Month><Day>02</Day></DateCreated><DateCompleted><Year>2014</Year><Month>09</Month><Day>25</Day></DateCompleted><DateRevised><Year>2014</Year><Month>06</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1756-0756</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><Issue>2-3</Issue><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>International journal of computational biology and drug design</Title><ISOAbbreviation>Int J Comput Biol Drug Des</ISOAbbreviation></Journal><ArticleTitle>Classification of T cell movement tracks allows for prediction of cell function.</ArticleTitle><Pagination><MedlinePgn>113-29</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1504/IJCBDD.2014.061655</ELocationID><ELocationID EIdType="pii" ValidYN="Y">IJCBDD.2014.061655</ELocationID><Abstract><AbstractText>Using a unique combination of visual, statistical, and data mining methods, we tested the hypothesis that an immune cell's movement pattern can convey key information about the cell's function, antigen specificity, and environment. We applied clustering, statistical tests, and a support vector machine (SVM) to assess our ability to classify different datasets of imaged flouresently labelled T cells in mouse liver. We additionally saw clusters of different movement patterns of T cells of identical antigenic specificity. We found that the movement patterns of T cells specific and non-specific for malaria parasites are differentiable with 72% accuracy, and that specific cells have a higher tendency to move towards the parasite than non-specific cells. Movements of antigen-specific T cells in uninfected mice vs. infected mice were differentiable with 69.8% accuracy. We additionally saw clusters of different movement patterns of T cells of identical antigenic specificity. We concluded that our combination of methods has the potential to advance the understanding of cell movements in vivo.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kelemen</LastName><ForeName>Reka K</ForeName><Initials>RK</Initials><AffiliationInfo><Affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>He</LastName><ForeName>Gengen F</ForeName><Initials>GF</Initials><AffiliationInfo><Affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Woo</LastName><ForeName>Hannah L</ForeName><Initials>HL</Initials><AffiliationInfo><Affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lane</LastName><ForeName>Thomas</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rempe</LastName><ForeName>Caroline</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jun</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>UT-ORNL Graduate School of Genome Science and Technology, Center for Environmental Biotechnology, and Departments of Civil and Environmental Engineering, Geography, and Microbiology, University of Tennessee, F337 Walters Life Science, Knoxville, TN 37996-0840, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cockburn</LastName><ForeName>Ian A</ForeName><Initials>IA</Initials><AffiliationInfo><Affiliation>Department of Pathogens and Immunity, John Curtin School of Medical Research, Australian National University, GPO Box 334, Canberra City ACT 2600, Australia.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Amino</LastName><ForeName>Rogerio</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Unité de Biologie et Génétique du Paludisme, Institut Pasteur, 75724, Paris Cedex 15, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ganusov</LastName><ForeName>Vitaly V</ForeName><Initials>VV</Initials><AffiliationInfo><Affiliation>Department of Microbiology, University of Tennessee, M409 Walters Life Science Building, 1414 West Cumberland Avenue, Knoxville, TN 37996-0845, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berry</LastName><ForeName>Michael W</ForeName><Initials>MW</Initials><AffiliationInfo><Affiliation>EECS Department, University of Tennessee, 401 Min H. Kao Building, Knoxville, TN 37996, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>05</Month><Day>28</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Int J Comput Biol Drug Des</MedlineTA><NlmUniqueID>101479540</NlmUniqueID><ISSNLinking>1756-0756</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002465" MajorTopicYN="N">Cell Movement</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008288" MajorTopicYN="N">Malaria</DescriptorName><QualifierName UI="Q000276" MajorTopicYN="N">immunology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013601" MajorTopicYN="N">T-Lymphocytes</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="Y">physiology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>6</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>6</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>9</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24878724</ArticleId><ArticleId IdType="pii">IJCBDD.2014.061655</ArticleId><ArticleId IdType="doi">10.1504/IJCBDD.2014.061655</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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