MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/m_dormancy_lipidome_metabolite_profiling_mass_spectrometry_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/s_Dormancy Lipidome.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/a_dormancy_lipidome_metabolite_profiling_mass_spectrometry.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R48_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R48_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R24_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R24_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R48_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R48_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R24_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_01_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_02_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R144_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_03_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R144_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R72_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_03_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_02_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_01_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_01_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_02_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_01_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_03_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_02_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R72_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R72_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_03_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R72_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R72_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R144_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R72_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R72_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R144_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R72_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R144_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R144_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R144_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R72_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R48_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_03_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R24_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R48_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R48_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R24_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R144_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_01_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_01_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R48_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R24_03.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_02_Dormant.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_03_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_R48_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R24_01.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150919_BR2_R24_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R144_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150921_BR3_02_Control.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/20150918_BR1_R24_02.rawftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304ftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/metexplore_mapping.jsonftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/auditftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS304/__MACOSXprimaryOK2000000Sajith RaghunandananMetaboLightsPublicSYNAPT G2 HDMS (Waters)The SYNAPT® G2 High Definition MS™ System mass spectrometer was operated in positive resolution mode with electrospray ionization (ES+) source over a mass range of 50 to 1500 Da. Each spectrum was acquired for 0.25 s with an interscan delay of 0.024 s. Ion source and desolvation gas (nitrogen) temperatures were kept at 130 °C and 450 °C, respectively. The cone and desolvation gas flow rates were 80 l/h and 600 l/h, respectively. Capillary voltage was set at 3.0 kV. Sampling cone voltage was set at 30 kV. The lock mass acquisition was performed every 30 s by leucine-enkephalin (556.2771 [M + H] +) for accurate on-line mass calibration.Analysis of lipids was performed using a Waters ACQUITY UPLC system (Waters, Milford, MA, USA) coupled to a Quadrupole-Time of Flight (Q- TOF) mass spectrometer (SYNAPT-G2, Waters). Both the systems were operated and controlled by MassLynx4.1 SCN781 software (Waters Corp, Milford, MA). The lipidomic separation was achieved using reverse-phase liquid chromatographic technique employing a C18 (high-strength silica 2.1 x 100 mm, 1.8 µm; Waters) column.</br>Briefly, a 7.5 µl aliquot of each sample was injected into the column with the column temperature maintained at 40 °C. For each sample, the run time was 20 min with a flow rate of 400 µl/min. The mobile phase consisted of aqueous (A) and organic (B) solvent components, where A was 0.1% formic acid in ultrapure water, and B was 0.1% formic acid in acetonitrile. The gradient was 0 min, 1% B; 2 min, 10% B; 6 min, 30% B; 8 min, 50% B; 12 min, 75% B; 15 min, 99% B and 20 min, 1% B. Each sample was injected thrice with blank injections between each sample.Comparative label-free lipidomic analysis of Mycobacterium tuberculosis during dormancy and reactivation. 10.1038/s41598-019-40051-5. PMID:30842473Rajiv Gandhi Centre For BiotechnologyMycobacterium tuberculosismass spectrometrySamples were centrifuged for 10 min x 4,000 rpm at 27 °C. Cell pellets were washed twice in 10 ml sterile water at room temperature and centrifuged for 10 min x 4,000 rpm at 25 °C. Cell pellets (400 mg) from each condition were resuspended in 1 ml of CH3OH, transferred to a 50 ml centrifuge tube with 25 ml of CHCl3/CH3OH (2:1, /v) and incubated overnight. CHCl3/CH3OH suspensions were shaken on an Orbitron rotator for at least 1 hr after overnight incubation. After centrifugation (4,000 rpm x 10 min), supernatants were transferred to new tubes, and the pellets were subjected to two additional extractions using CHCl3:CH3OH at 1:1 (v/v) and 1:2 (v/v) ratios. Prior to extraction, the samples were spiked with internal standards phenylalanine (1 µg/ml in water), reserpine (1 µg/ml in methanol) and sulfadimethoxine (1 µg/ml in methanol). All extracts were pooled together and dried under nitrogen gas. One milligram of dried lipids was weighed from all samples and resuspended in 1 ml CH3OH, vortexed and used for further analysis.https://www.ebi.ac.uk/metabolights/MTBLS304Vipin Gopinath.Sajith Raghunandanan.Kumar Ajay. Scientist E-II. Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram.. rakumar@rgcb.res.in. 9447800305.Leny Jose.Ramakrishnan Ajay Kumar.R Sajith. PhD Student. Mycobacterium Research Group, Rajiv Gandhi Centre for Biotechnology, Thycaud P.O., Thiruvananthapuram.. sajithr@rgcb.res.in. 9544057605.The data were acquired in centroid mode and processed using MassLynx software. MassLynx4.1 SCN781 (Waters) was used for data acquisition and collection. Markerlynx XS software (Waters) was employed for peak/feature picking and raw data de-convolution. Markerlynx performs noise filtering, peak detection, isotope peak removal, alignment of retention time and mass, as well as optional peak/feature normalization. Method parameters for Markerlynx processing were as follows: peak width at 5% height - 1 s; marker intensity threshold - 10 counts; mass window - 0.05 Da and retention time window - 0.2 min.GroupVirulent M. tuberculosis strain H37Rv (collected from Tuberculosis Research Centre Chennai, India) at different time points of dormancy and reactivation (R24, R48, R72, and R144).Metabolomicsultra-performance liquid chromatography-mass spectrometryTuberculosisHypoxiauntargeted metabolitesdormancy processultra-performance liquid chromatography-mass spectrometryTuberculosisdormancy processHypoxiauntargeted metaboliteswhole organismRaw data were processed by XCMS for noise filtering, peak picking, and de-convolution to resolve co-eluting ions and peak alignment across replicates so that features with equivalent AMRT values are aligned across biological conditions and their intensities reported in a final data matrix. MassLynx4.1 SCN781 (Waters) was used for data acquisition and collection. Markerlynx XS software (Waters) was employed for peak/feature picking and raw data de-convolution, noise filtering, peak detection, isotope peak removal, alignment of retention time and mass, as well as optional peak/feature normalization. Method parameters for Markerlynx processing were as follows: peak width at 5% height - 1 S; marker intensity threshold - 10 counts; mass window - 0.05 Da and retention time window - 0.2 min. Automatic naming of compound was performed whose m/z matched within 5 ppm range and further validated by comparing the m/z with MycoMass and MTB Lipid DB databases.lyso phosphatidic acidsmenaquinonesdiacylglycerolsphosphatidylglycerolsphosphatidic acidslysophosphatidylethanolaminesphosphatidylinositolscarboxymycobactinsglycopeptidolipids IIa/IVunknownlysophosphatidylglycerolsmycocerosic acidsmycolipodienic acidmycolactonestriacyltrehalosesmycobactinsphosphatidylethanolamineslysophosphatidylinositolscardiolipindimycocerosatesmannosylphosphomycoketidesdiacyltrehalosesglycopeptidolipids ItriacylglycerolsphophomycoketidesmonoacylglycerolsMycobacterium tuberculosis employs several strategies to combat and adapt to adverse conditions encountered inside the host. The non-replicative dormant state of the bacterium is linked to drug resistance and slower response to anti-tubercular therapy. It is known that alterations in lipid content allow dormant bacteria to acclimatize to cellular stress. Employing comparative lipidomic analysis we profiled the changes in lipid metabolism in M. tuberculosis using a modified Wayne's model of hypoxia-induced dormancy. Further we subjected the dormant bacteria to resuscitation, and analyzed their lipidomes until the lipid profile was similar to that of normoxially grown bacteria. An enhanced degradation of cell wall-associated and cytoplasmic lipids during dormancy, and their gradual restoration during reactivation, were clearly evident. This study throws light on distinct lipid metabolic patterns that M. tuberculosis undergoes to maintain its cellular energetics during dormancy and reactivation.Comparative label-free lipidomic analysis of Mycobacterium tuberculosis during dormancy and reactivation.Raghunandanan Sajith S, Jose Leny L, Gopinath Vipin V, Kumar Ramakrishnan Ajay RAmulticellular organismal catabolic process, single-organism catabolic process, lipids, host organism, Mycobacterium tuberculosis variant tuberculosis, determination, drug susceptibility/resistance, Deficiencies, dormancy, Visible Light, eubacteria, composed of, Ly113, Oxygen Deficiency, Oxygen Deficiencies, Metabolism, Mycobacterium tuberculosis var. hominis, responsivity, hnu, Kochs disease, Tuberculosis, light, drug resistance, foton, Walls, Koch's Disease, Cell Walls, Bacillus tuberculosis, treatment, reactivity, Resuscitations, study, Bacterium tuberculosis, Koch Disease, Eubacteria, lipid metabolism, Infections, catabolism, Lichtquant, composition, Visible, Mycobacterium tuberculosis Infections, Monera, Oxygen, Bacteria <bacteria>, Prokaryotae, TB, disease management, photon, Mycobacterium tuberculosis, fungi, Procaryotae, TR2, associated, gamma, bacteria, Radiation, Kochs Disease, degradation, Drug resistance, Light, compositionality, CD258, Cell, tuberculosis disease, Anoxia, LIGHT, Lipid, chemical analysis, lethargus., Resistance, Infection, prokaryotes, Tuberculoses, diapause, Visible Radiations, Radiations, Wall, Visible Radiation, breakdown, HVEML, distinct, HVEM-L, Mycobacterium tuberculosis H37Rv, content, response to drug, Photoradiation, Hypoxemia, LTg, Drug, Deficiency, light quantum, Photoradiations, prokaryote, lethargus, structure, assay, response, Mycobacterium tuberculosis Infection, Anoxemia, active tuberculosis, Prokaryota, Mycobacterium tuberculosis typus humanusBacillus tuberculosis, Bacterium tuberculosis, Mycobacterium tuberculosis variant tuberculosis, determination, Mycobacterium tuberculosis var. hominis, chemical analysis, Mycobacterium tuberculosis H37Rv, lethargus., assay, dormancy, diapause, free, Mycobacterium tuberculosis typus humanusmulticellular organismal catabolic process, single-organism catabolic process, lipids, host organism, Mycobacterium tuberculosis variant tuberculosis, determination, drug susceptibility/resistance, Deficiencies, dormancy, Visible Light, eubacteria, composed of, Ly113, Oxygen Deficiency, Oxygen Deficiencies, Metabolism, Mycobacterium tuberculosis var. hominis, responsivity, hnu, Kochs disease, Tuberculosis, light, drug resistance, foton, Walls, Koch's Disease, Cell Walls, Bacillus tuberculosis, treatment, reactivity, Resuscitations, study, Bacterium tuberculosis, Koch Disease, Eubacteria, lipid metabolism, Infections, catabolism, Lichtquant, composition, Visible, Mycobacterium tuberculosis Infections, Monera, Oxygen, Bacteria <bacteria>, Prokaryotae, TB, disease management, photon, Mycobacterium tuberculosis, fungi, Procaryotae, TR2, associated, gamma, bacteria, Radiation, Kochs Disease, degradation, Drug resistance, Light, compositionality, CD258, Cell, tuberculosis disease, Anoxia, LIGHT, Lipid, chemical analysis, lethargus., Resistance, Infection, prokaryotes, Tuberculoses, diapause, Visible Radiations, Radiations, Wall, Visible Radiation, breakdown, HVEML, distinct, HVEM-L, Mycobacterium tuberculosis H37Rv, content, response to drug, Photoradiation, Hypoxemia, LTg, Drug, Deficiency, light quantum, Photoradiations, prokaryote, lethargus, structure, assay, response, Mycobacterium tuberculosis Infection, Anoxemia, active tuberculosis, Prokaryota, Mycobacterium tuberculosis typus humanusBacillus tuberculosis, Bacterium tuberculosis, Mycobacterium tuberculosis variant tuberculosis, determination, Mycobacterium tuberculosis var. hominis, chemical analysis, Mycobacterium tuberculosis H37Rv, lethargus., assay, dormancy, diapause, free, Mycobacterium tuberculosis typus humanus0.00.00.00.00.00trueComparative label-free lipidomic analysis of Mycobacterium tuberculosis during dormancy and reactivationMycobacterium tuberculosis employs several strategies to combat and adapt to adverse conditions encountered inside the host. The non-replicative dormant state of the bacterium is linked to drug resistance and slower response to anti-tubercular therapy. It is known that alterations in lipid content allow dormant bacteria to acclimatize to cellular stress. Employing comparative lipidomic analysis we profiled the changes in lipid metabolism in M. tuberculosis using a modified Wayne's model of hypoxia-induced dormancy. Further we subjected the dormant bacteria to resuscitation, and analyzed their lipidomes until the lipid profile was similar to that of normoxially grown bacteria. An enhanced degradation of cell wall-associated and cytoplasmic lipids during dormancy, and their gradual restoration during reactivation, were clearly evident. This study throws light on distinct lipid metabolic patterns that M. tuberculosis undergoes to maintain its cellular energetics during dormancy and reactivation.2018-10-222016-01-20MTBLS304MTBLC32957MTBLC18035MTBLC90454MTBLC31870MTBLC16038MTBLC17517MTBLC16337MTBLC17855MTBLC28494MTBLC17408MTBLC25185MTBLC64574MTBLC62579MTBLC2887430842473CHEBI:28874CHEBI:32957CHEBI:25185CHEBI:31870CHEBI:28494CHEBI:17517CHEBI:17408CHEBI:16038CHEBI:17855CHEBI:64574CHEBI:90454CHEBI:16337CHEBI:18035CHEBI:62579