RNA-seq of Mycobacterium tuberculosis H37rv in response with 5 different drugs
Ontology highlight
ABSTRACT:
INSTRUMENT(S): NextSeq 500
ORGANISM(S): Mycobacterium tuberculosis H37Rv
SUBMITTER: Etienne Kornobis
PROVIDER: E-MTAB-12306 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:L. plantarum is known to possess an L-lactate inducible lactate racemase activity (Goffin et al. 2005. J. Bacteriol. 187:6750). In the present study, microarrays were used in order to identify all genes that are up-regulated by L-lactate, but not by a racemic mixture of D- and L-lactate. A mutant of L. plantarum NCIMB8826 deficient for NAD-dependent L-lactate activity (TF101; Ferain et al. 1994. 176:596), and thus producing no L-lactate, was grown in MRS medium at 28°C until mid-exponential phase (OD600nm 0.75). The culture was then divided into 3 sub-cultures. Optically pure sodium L-lactate (200 mM) was added to the first sub-culture (TF101 + L-lac 200 mM). An equimolar mixture of sodium D- and L-lactate (100 mM each) was added to the second sub-culture (TF101 + L/D-lac 200 mM). The third sub-culture was not treated (TF101; reference sample). The three sub-cultures were further incubated at 28°C for 1h30 (a time known to be sufficient for induction of lactate racemase activity by L-lactate). Cells were harvested by centrifugation. Microarray data were used ot identify genes that are specifically induced by L-lactate (comparison of TF101 with TF101 + L-lac 200 mM), but not by DL-lactate (comparison of TF101 with T101 + L/D-lac 200 mM). There are no biological replicates.
2013-07-01 | E-GEOD-43518 | biostudies-arrayexpress
Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 30 °C in chemostats, as previously described (for more information see Esteve-Núñez, A., M. M. Rothermich, M. Sharma, and D. R. Lovley. 2004. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol.:in press.), with acetate (5 mM) as the electron donor and fumarate (27.5 mM) as the electron acceptor. For growth in the absence of fixed nitrogen, the ammonium chloride (4.7 mM) was omitted from the medium and fumarate served as the electron acceptor. Therefore, cultures with ammonium chloride were limited by acetate while cultures without ammonium chloride were limited by nitrogen. Cultures were maintained at a dilution rate of 0.05 h-1 for 5 culture vessel volumes to ensure that cells were at steady-state prior to harvesting. Cells were harvested by centrifugation at 4 °C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 °C prior to RNA extraction. Cells grown in the absence of ammonium had acetylene reduction rates of 0.012 nmol/hr compared to 0.003 nmol/hr in ammonium-grown cells, providing evidence that these cells were fixing nitrogen.. The steady-state concentration of cells in the nitrogen-fixing chemostats (0.178 mg/mL + 0.011; mean + standard deviation, n=3) was significantly lower than chemostats provided with ammonium (0.45 mg/mL + 0.007). Three cultures of acetate limited growth with fumarate as the electron acceptor and three cultures of nitrogen limited growth with fumarate as the electron acceptor were grown. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment.
2005-01-01 | E-TIGR-82 | biostudies-arrayexpress
Project description:Burkholderia cenocepacia J2315 was repeatedly and intermittently exposed to tobramycin, ciprofloxacin or meropenem. Bacteria were grown on cryobeads submerged in liquid BHI medium. After 24 hours, the beads were washed and fresh medium with of without antibiotics added. After another 24 hours of incubation, the beads were washed, the bacteria removed from the beads, and used for inoculation of fresh beads. This was repeated to a total of up to ten cycles. Evolved lineages were then DNA-sequenced to screen for genome changes.
2022-08-18 | E-MTAB-12092 | biostudies-arrayexpress
Project description:Pseudomonas aeruginosa AA2 was repeatedly and intermittently exposed to tobramycin, ciprofloxacin or meropenem. Bacteria were grown on cryobeads submerged in liquid BHI medium. After 24 hours, the beads were washed and fresh medium with of without antibiotics added. After another 24 hours of incubation, the beads were washed, the bacteria removed from the beads, and used for inoculation of fresh beads. This was repeated to a total of up to ten cycles. Evolved lineages were then DNA-sequenced to screen for genome changes.
2022-08-18 | E-MTAB-12091 | biostudies-arrayexpress
Project description:Pseudomonas aeruginosa was repeatedly and intermittently exposed to tobramycin. Bacteria were grown in synthetic cystic fibrosis medium in wells of a 96-well microtiter plate. After 24 hours, more medium with or without tobramycin was added. After another 24 hours of incubation, a subsample of the well content was used to inoculate fresh synthetic cystic fibrosis medium in a 96-well microtiter plate. This was repeated for a total of 15 cycles. Evolved lineages were then DNA-sequenced to screen for genome changes.
2022-08-18 | E-MTAB-11894 | biostudies-arrayexpress
Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 23 °C in batch culture. Both control and experimental populations were grown with 10mM acetate as the electron donor while Fe(III) as 55 mM ferric citrate served as the electron acceptor for the control populations and graphite anodes as the electron acceptor for the experimental populations. Controls populations were harvested at a concentration of 30 mM Fe(II). Fuel cell power output was monitored by measuring the voltage across a known resistance in the fuel cell and experimental populations were harvested when current production reached a steady state of 0.6 milliamperes. Cells were harvested at log phase by centrifugation at 4 °C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 °C prior to RNA extraction. Three cultures of control and experimental populations were collected. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment. Additional information regarding the fuel cell experimental set up and culture conditions for this experiment can be found in both the current reference and the following reference: Bond DR and Lovley DR. Electricity production by Geobacter sulfurreducens attached to electrodes. 2003. Applied and Environmental Microbiology 69: 1548-1555.
2007-07-02 | E-TIGR-5001 | biostudies-arrayexpress
Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 23 �Â�°C in batch culture. Both control and experimental populations were grown with 10mM acetate as the electron donor while Fe(III) as 55 mM ferric citrate served as the electron acceptor for the control populations and graphite anodes as the electron acceptor for the experimental populations. Controls populations were harvested at a concentration of 30 mM Fe(II). Fuel cell power output was monitored by measuring the voltage across a known resistance in the fuel cell and experimental populations were harvested when current production reached a steady state of 0.6 milliamperes. Cells were harvested at log phase by centrifugation at 4 �Â�°C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 �Â�°C prior to RNA extraction. Three cultures of control and experimental populations were collected. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment. Additional information regarding the fuel cell experimental set up and culture conditions for this experiment can be found in both the current reference and the following reference: Bond DR and Lovley DR. Electricity production by Geobacter sulfurreducens attached to electrodes. 2003. Applied and Environmental Microbiology 69: 1548-1555.
2006-01-26 | E-TIGR-83 | biostudies-arrayexpress
Project description:A mutant of L. plantarumWCFS1 (deletion of lp_2991) was compared with the wildtype grown in standard MRS broth. Cells were sampled at OD1 for mRNA extraction. Knockout vs wildtype. Technical replicates (same mRNA isolation) used for a dye swap.
2010-04-01 | E-GEOD-20515 | biostudies-arrayexpress
Project description:Several strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of specific cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in probiotic-host interactions remains obscure. Through genome mining and mutagenesis we constructed derivatives of L. plantarum WCFS1 that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. Transcriptome analysis revealed the genetic determinants involved in backbone switching. Human dendritic cells secreted drastically decreased levels of pro-inflammatory cytokines after stimulation with the WTA mutants, and indicated LTA contributes to TLR-2/6 signalling, whereas WTA attenuates TLR-2 and TLR-1/2 signalling in a backbone-alditol dependent manner. Overall, the engineering of WTA and its consequences for immune system interaction advances our molecular understanding of host-microbe communication, and underpins the strain-specificity of probiotics. All samples were hybridized twice (each dye once) in a triangular design, hybridizing all samples
2011-05-01 | E-GEOD-27683 | biostudies-arrayexpress
Project description:Specific Lactobacillus strains are marketed as probiotics i.e. health promoting organisms. As previously shown in vivo, L. plantarum WCFS1 modulates immune responses via nuclear factor (NF)kB in a growth phase dependent manner, likely caused by changed microbial cell surface characteristics. Here, we identified the differential cell-surface proteome composition of L. plantarum WCFS1 cells derived from the mid-logarithmic and late stationary growth phase by surface trypsination of intact bacterial cells, followed by a combined 1D- and 2D-LC-MS shotgun proteomics strategy, and growth phase dependent transcriptome analysis. Overall, these analyses led to the identification of 31 surface proteins differentially present in the logarithmic and stationary phase, whereas additional 17 and 33 proteins appeared solely present in stationary and logarithmic phase of growth, respectively. From 75% of predicted surface related genes displaying relatively high expression levels, the corresponding proteins were detected, demonstrating a high correlation between transcriptome and proteome profiles. The impact of cell-surface peptide fractions on cellular host responses was evaluated using NFkB promoter activation assays in intestinal epithelial cells, revealing that only late stationary phase derived peptides are capable of attenuating flagellin and cell envelope induced NFkB activation. Overall our data mechanistically expand earlier observations that revealed growth-phase dependent immunomodulation by L. plantarum WCFS1, leading to a typical adjuvant- or tolerance-like response after exposure to stationary phase harvested bacterial cells. Sub-fractionation of the late stationary phase peptide fraction revealed a sub-set of strong attenuator peptides able to manipulate NFkB related pathways to hereby attenuate pro-inflammatory signaling. Samples were hybridizedin a loop design linking each timepoint to the next as well as the previous timepoint. Additional hybridizations were introduced linking each sample three timepoints forward and three timepoints back. All samples were hybridized unsing at least each of the two dyes once.
2012-01-01 | E-GEOD-31000 | biostudies-arrayexpress