Filters








121 Hits in 6.3 sec

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

Caroline Colijn, Aaron Brandes, Jeremy Zucker, Desmond S. Lun, Brian Weiner, Maha R. Farhat, Tan-Yun Cheng, D. Branch Moody, Megan Murray, James E. Galagan, Jason A. Papin
<span title="2009-08-28">2009</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
In contrast to previous methods for metabolically interpreting gene expression data, E-Flux utilizes a model of the underlying metabolic network to directly predict changes in metabolic flux capacity.  ...  We tested our method using a model of mycolic acid biosynthesis as well as on a genome-scale model of M. tuberculosis metabolism.  ...  E-Flux, however, implicitly integrates across these different mechanisms by interpreting expression data through the lens of a metabolic network model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000489">doi:10.1371/journal.pcbi.1000489</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19714220">pmid:19714220</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2726785/">pmcid:PMC2726785</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nlrterreavhxvmxo5z4pdgcp34">fatcat:nlrterreavhxvmxo5z4pdgcp34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502154057/https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000489&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a3/66/a366a297665e3a068e4407927fd7fccd98544f6c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000489"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726785" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

Xin Fang, Anders Wallqvist, Jaques Reifman, Claus O. Wilke
<span title="2012-09-13">2012</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Given the microarray data for the alterations in gene expression, our model predicted reduced oxygen uptake, ATP production changes, and a global change from an oxidative to a reductive tricarboxylic acid  ...  The coupling of differential gene expression data with a metabolic network model allowed us to characterize the metabolic adaptations of M. tuberculosis H37Rv to hypoxia.  ...  We have developed a novel model to interpret M. tuberculosis H37Rv metabolic adjustment by combining gene transcription data with a genome-scale metabolic network model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002688">doi:10.1371/journal.pcbi.1002688</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23028286">pmid:23028286</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3441462/">pmcid:PMC3441462</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nyvfihr2vzfgfam5wkvoifj53i">fatcat:nyvfihr2vzfgfam5wkvoifj53i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015135833/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1002688&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f2/a8/f2a8902a6b5a5fd28062d3e3d249a012050171a1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1002688"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441462" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Systems-level modeling of mycobacterial metabolism for the identification of new (multi-)drug targets

Rienk A. Rienksma, Maria Suarez-Diez, Lucie Spina, Peter J. Schaap, Vitor A.P. Martins dos Santos
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b3ghs2okhzgt7jrif6kr2ovjne" style="color: black;">Seminars in Immunology</a> </i> &nbsp;
These limitations can be circumvented by combining expression data from in vivo samples with a validated CB model, creating an accurate description of pathogen metabolism in the host.  ...  Approximately one-fourth of the Mycobacterium tuberculosis (Mtb) genome contains genes that encode proteins directly involved in its metabolism.  ...  Acknowledgements We thank Anne Lemassu and Mamadou Daffé (Centre National de la Rescherche Scientifique) for their help on the dimycocerosate ester biosynthesis, mycolic acid biosynthesis and starch  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.smim.2014.09.013">doi:10.1016/j.smim.2014.09.013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25453232">pmid:25453232</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/opodniptb5abpdeb7d6ao4xwmm">fatcat:opodniptb5abpdeb7d6ao4xwmm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190216155942/https://core.ac.uk/download/pdf/82782249.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/01/66/0166710902093f04ea1ffc009ee3dc82d6d491bd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.smim.2014.09.013"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

System-level strategies for studying the metabolism of Mycobacterium tuberculosis

Dany J. V. Beste, Johnjoe McFadden
<span title="">2010</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zcnlz4nminfhjcp5esifetrr4u" style="color: black;">Molecular Biosystems</a> </i> &nbsp;
Despite decades of research many aspects of the biology of Mycobacterium tuberculosis remain unclear and this is reflected in the antiquated tools available to treat and prevent tuberculosis and consequently  ...  Important discoveries linking M. tuberculosis's metabolism and pathogenesis have renewed interest in this area of research.  ...  This 'E-flux' method applied to either the GSMN-TB or MAP correctly predicted that seven of the eight mycolic acid inhibitors tested in the experimental data negatively modulated mycolic acid metabolism  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c003757p">doi:10.1039/c003757p</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20938502">pmid:20938502</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3172586/">pmcid:PMC3172586</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bux5derombfihcejzzk67rb674">fatcat:bux5derombfihcejzzk67rb674</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190216042604/http://pdfs.semanticscholar.org/015f/1c6213cd83b4d9ad6337c2b0d0feb6223e9a.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/01/5f/015f1c6213cd83b4d9ad6337c2b0d0feb6223e9a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c003757p"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172586" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis

Christopher D. Garay, Jonathan M. Dreyfuss, James E. Galagan
<span title="2015-09-16">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
Mycobacterium tuberculosis (MTB) is the causal agent of the disease tuberculosis (TB). Metabolic  ...  This work was supported in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases National Institute of Health, Department of Health and Human Services, under  ...  Using E-Flux, we predicted the impact of drugs on MTB mycolic acid biosynthesis [46] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-015-0206-7">doi:10.1186/s12918-015-0206-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26377923">pmid:26377923</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4574064/">pmcid:PMC4574064</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ionkww5h4jfi7dy6djjccic55u">fatcat:ionkww5h4jfi7dy6djjccic55u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830052448/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/s12918-015-0206-7?site=http://bmcsystbiol.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/16/4f/164f55adccc28f56709b3121c9d8a6aa59901882.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-015-0206-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4574064" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Carbon flux rerouting during Mycobacterium tuberculosis growth arrest

Lanbo Shi, Charles D. Sohaskey, Carmen Pfeiffer, Pratik Datta, Michael Parks, Johnjoe McFadden, Robert J. North, Maria L. Gennaro
<span title="2010-10-06">2010</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/f55g362z2zdsnfvbumwdj3b53i" style="color: black;">Molecular Microbiology</a> </i> &nbsp;
A model describing carbon flux rerouting was formulated that (i) provides a coherent interpretation of the adaptation of M. tuberculosis metabolism to immunity-induced stress and (ii) identifies features  ...  Results of flux balance analysis using an in silico metabolic network were consistent with the transcript abundance data obtained in vivo.  ...  Acknowledgements We thank Ron LaCourse for mouse infections; Michelle Thissen for technical help with the enzyme assays; Gyanu Lamichhane, Lenny Mindich, Issar Smith and Xilin Zhao for critical reading  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-2958.2010.07399.x">doi:10.1111/j.1365-2958.2010.07399.x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21091505">pmid:21091505</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3072047/">pmcid:PMC3072047</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bgffk4r4wjaxvlhnjtjrvro4jy">fatcat:bgffk4r4wjaxvlhnjtjrvro4jy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150907204439/http://www.phri.org/news/Shi,MolMico10.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cb/58/cb58bdef46f8e73d3f33254dbd378fb95260a9e6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-2958.2010.07399.x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3072047" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

Dany JV Beste, Tracy Hooper, Graham Stewart, Bhushan Bonde, Claudio Avignone-Rossa, Michael E Bushell, Paul Wheeler, Steffen Klamt, Andrzej M Kierzek, Johnjoe McFadden
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Predictions of gene essentiality were also made by flux balance analysis simulation and were compared with global mutagenesis data for M. tuberculosis grown in vitro.  ...  The model provides a means to examine the metabolic flexibility of bacteria and predict the phenotype of mutants, and it highlights previously unexplored features of M. tuberculosis metabolism.  ...  GSMN) of Mycobacterium tuberculosis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2007-8-5-r89">doi:10.1186/gb-2007-8-5-r89</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17521419">pmid:17521419</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1929162/">pmcid:PMC1929162</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j4rzfr3dtbaftboxcbhbkzbnpu">fatcat:j4rzfr3dtbaftboxcbhbkzbnpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719140836/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2007-8-5-r89?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/cd/20/cd20a6a0e74eab8020a8276d480280e6b687b440.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2007-8-5-r89"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1929162" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions

Aarash Bordbar, Nathan E Lewis, Jan Schellenberger, Bernhard Ø Palsson, Neema Jamshidi
<span title="2010-10-19">2010</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oayrvwhnr5a2jm4pbva2dvz3ui" style="color: black;">Molecular Systems Biology</a> </i> &nbsp;
Metabolic coupling of Mycobacterium tuberculosis to its host is foundational to its pathogenesis.  ...  The model successfully predicted experimentally verified ATP and nitric oxide production rates in macrophages.  ...  Model predictions were improved for essential as well as non-essential genes when compared with experimental data. In total, the PM predicts 188 essential metabolic genes, while the HPM predicts 162.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/msb.2010.68">doi:10.1038/msb.2010.68</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20959820">pmid:20959820</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2990636/">pmcid:PMC2990636</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5ksm4nr6lvbiritqur4iyd5uvy">fatcat:5ksm4nr6lvbiritqur4iyd5uvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811134644/http://msb.embopress.org/content/msb/6/1/422.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dc/79/dc79b4462aa6a63e6cb64b09ff9a95b333838f6e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/msb.2010.68"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990636" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Flux through Trehalose Synthase Flows from Trehalose to the Alpha Anomer of Maltose in Mycobacteria

Farzana Miah, Hendrik Koliwer-Brandl, Martin Rejzek, Robert A. Field, Rainer Kalscheuer, Stephen Bornemann
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/v6fzdolajra2detrgb2pojrdpm" style="color: black;">Chemistry and Biology</a> </i> &nbsp;
Consistent with this direction of flux, trehalose levels in Mycobacterium tuberculosis decreased when TreS was overexpressed.  ...  Trehalose synthase (TreS) was thought to catalyze flux from maltose to trehalose, a precursor of essential trehalose mycolates in mycobacterial cell walls.  ...  This implies Mycobacterium smegmatis is not an appropriate model organism with respect to the metabolism of trehalose in Mycobacterium tuberculosis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.chembiol.2013.02.014">doi:10.1016/j.chembiol.2013.02.014</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23601637">pmid:23601637</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3918855/">pmcid:PMC3918855</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bulyyrwvrvgxvadbxrr5d3fjba">fatcat:bulyyrwvrvgxvadbxrr5d3fjba</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190412013257/https://core.ac.uk/download/pdf/82456824.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/90/bf/90bf7844445a6b1ecc28501ed4a88dc708d5a7f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.chembiol.2013.02.014"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3918855" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

Neema Jamshidi, Bernhard Ø Palsson
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
These models need to be able to assimilate data from large datasets and analyze them. Results: We completed a bottom up reconstruction of the metabolic network of Mycobacterium tuberculosis H37Rv.  ...  This functional in silico bacterium, iNJ661, contains 661 genes and 939 reactions and can produce many of the complex compounds characteristic to tuberculosis, such as mycolic acids and mycocerosates.  ...  Last year Raman et al [41] constructed and analyzed a model of the mycolic acid synthesis pathways and proposed additional targets in fatty acid metabolism.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-1-26">doi:10.1186/1752-0509-1-26</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17555602">pmid:17555602</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1925256/">pmcid:PMC1925256</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6bl4byhfijgwnfp2z3q3asm6ai">fatcat:6bl4byhfijgwnfp2z3q3asm6ai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428210638/https://escholarship.org/content/qt94s8m5r4/qt94s8m5r4.pdf?t=qaepeu" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-1-26"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1925256" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Flux balance analysis of biological systems: applications and challenges

K. Raman, N. Chandra
<span title="2009-03-15">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
In particular, constraint-based analyses of metabolic networks have gained considerable popularity for simulating cellular metabolism, of which flux balance analysis (FBA), is most widely used.  ...  matrix and a biologically relevant objective function to identify optimal reaction flux distributions.  ...  In a study of the mycolic acid pathway in Mycobacterium tuberculosis, we have evaluated two different objective functions describing the production of mycolic acids, illustrating how the biology is better  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbp011">doi:10.1093/bib/bbp011</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19287049">pmid:19287049</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/542cezsctjdmznnpwyfwpkdj3a">fatcat:542cezsctjdmznnpwyfwpkdj3a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308161612/http://pdfs.semanticscholar.org/eb2e/0b94172b26efdb2b2e3d1d0bdc0776136d5c.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/eb/2e/eb2e0b94172b26efdb2b2e3d1d0bdc0776136d5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbp011"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

GSMN-ML- a genome scale metabolic network reconstruction of the obligate human pathogen Mycobacterium leprae

Khushboo Borah, Jacque-Lucca Kearney, Ruma Banerjee, Pankaj Vats, Huihai Wu, Sonal Dahale, Sunitha Manjari Kasibhatla, Rajendra Joshi, Bhushan Bonde, Olabisi Ojo, Ramanuj Lahiri, Diana L. Williams (+2 others)
<span title="2020-07-06">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/23nqq3odsjhmbi5tqavvcn7cfm" style="color: black;">PLoS Neglected Tropical Diseases</a> </i> &nbsp;
The model was used to explore the growth and biomass production capabilities of the pathogen with a range of nutrient sources, such as amino acids, glucose, glycerol and metabolic intermediates.  ...  The GSMN-ML model is thereby a useful in silico tool that can be used to explore the metabolism of the leprosy bacillus, analyze functional genomic experimental data, generate predictions of nutrients  ...  M. tuberculosis GSMN-TB_2. Biomass production is shown for both the models on (A) various carbon substrates and (B) amino acids as carbon sources (C) various nitrogen sources.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pntd.0007871">doi:10.1371/journal.pntd.0007871</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32628669">pmid:32628669</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ctlzvzzoabezpoxpcdgp2vlq7y">fatcat:ctlzvzzoabezpoxpcdgp2vlq7y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200722043708/https://journals.plos.org/plosntds/article/file?id=10.1371%2Fjournal.pntd.0007871&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d3/8a/d38ae12d40fa1670a73ae95acc69f7d230c3a245.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pntd.0007871"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Systems approach to investigating host-pathogen interactions in infections with the biothreat agent Francisella. Constraints-based model of Francisella tularensis

Anu Raghunathan, Sookil Shin, Simon Daefler
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
Computational analysis with constraints derived from experimental data revealed a limited set of metabolic genes that are operational during infection.  ...  This systems biology approach demonstrated that changes in carbohydrate utilization and amino acid metabolism play a pivotal role in growth, acid resistance, and energy homeostasis during infection with  ...  Acknowledgements We thank Avellino Texiera for valuable suggestions on amino acid analysis using HPLC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-118">doi:10.1186/1752-0509-4-118</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20731870">pmid:20731870</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2933595/">pmcid:PMC2933595</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bmj4sv3at5fn3gyfsjg7rctaye">fatcat:bmj4sv3at5fn3gyfsjg7rctaye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830054310/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-4-118?site=http://bmcsystbiol.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3b/5b/3b5bdd3d680d91b4b585a22fd5f46e53ce50e101.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-118"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2933595" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Global Effects of Inactivation of the Pyruvate Kinase Gene in the Mycobacterium tuberculosis Complex

S. Chavadi, E. Wooff, N. G. Coldham, M. Sritharan, R. G. Hewinson, S. V. Gordon, P. R. Wheeler
<span title="2009-10-09">2009</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fu4cl5wxynclfn3telu2mfbrna" style="color: black;">Journal of Bacteriology</a> </i> &nbsp;
Overall, these data show that the loss of the pykA gene has powerful, global effects on proteins associated with central metabolism.  ...  To better understand the global effects of "natural" lesions in genes involved in the pyruvate metabolism in Mycobacterium bovis, null mutations were made in the Mycobacterium tuberculosis H37Rv ald and  ...  not interpret data on wall-bound mycolates or PDIMs when these constructs were used.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jb.00619-09">doi:10.1128/jb.00619-09</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19820096">pmid:19820096</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2786599/">pmcid:PMC2786599</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u3zqmrw7jfapjjcinqgiwxwo44">fatcat:u3zqmrw7jfapjjcinqgiwxwo44</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223155128/http://pdfs.semanticscholar.org/4779/96b6d5ec2b08acfbb1dea73b6cebc35c78c5.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/47/79/477996b6d5ec2b08acfbb1dea73b6cebc35c78c5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/jb.00619-09"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786599" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis

Xin Fang, Anders Wallqvist, Jaques Reifman
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
Moreover, we used the developed in vivo network to predict the effects of double-gene deletions on M. tuberculosis growth in the host environment, explore metabolic adaptations to life in an acidic environment  ...  During infection, Mycobacterium tuberculosis confronts a generally hostile and nutrient-poor in vivo host environment.  ...  Chenggang Yu for his providing comprehensive analysis on gene annotation of M. tuberculosis to obtain genes directly associated with metabolic processes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-160">doi:10.1186/1752-0509-4-160</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21092312">pmid:21092312</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3225870/">pmcid:PMC3225870</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fpivfqamafbuxjbq4swa2zbukq">fatcat:fpivfqamafbuxjbq4swa2zbukq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130409135811/http://bhsai.org/pubs/Fang_2010_Development_and_Analysis.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/63/db63b3a8a6b277d2aad6e6a7e81270e59bfb7890.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-160"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3225870" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 121 results