ABSTRACT: The effect of respiration (aerobic cultivation in the presence of heme and vitamin K2) was compared with unsupplemented aerobic cultivation with Lactobacillus plantarum. Two-condition experiment, aerobic vs respiring cells. Biological replicates: 3 aerobic cultures, 3 respiring cultures, independently grown and harvested. One replicate per array. Respiring cultures are called reactor 1-3; Aerobic cultures are called reactor 4-6 In the subsequent analysis data from reactor 4 were not used. There was likely a mistake made during quenching. This was concluded as new labeling/hybridisation gave same (bad) results (128a); slide 128b was dye-swap.
Project description:The effect of nitrate reduction (anaerobic cultivation in the presence of heme, vitamin K2 and nitrate) was compared with anaerobic cultivation supplemented with citrate (Lactobacillus plantarum). The medium was chemically defined medium with mannitol as main carbon source Two-condition experiment, nitrate vs citrate reducing cells. Biological replicates: 4 nitrate reducing cultures, 4 citrate reducing cultures, independently grown and harvested. Two slides were used, each slide contained 8 Arrays. Citrate reducing cultures are called reactor 1-4, Nitrate reducing cultures are called reactor A-D
Project description:An aerobic Lactobacillus plantarum culture displayed growth stagnation during early growth. Transcriptome analysis revealed that regain of growth after stagnation correlated with activation of CO2-producing pathways suggesting that limiting CO2-concentration induced stagnation. Analogously providing increased CO2 gas partial pressure during aerobic fermentation prevented the temporal growth stagnation. Keywords: cell type comparison Two aerobic fermenters (biological replicates Land R) were sampled at two time points, before (1) and after (2) growth stagnation.
Project description:Lactobacillus plantarum WCFS1 was grown under anaerobic carbon-limited conditions in a chemostat with complete biomass retention (retentostat). In this cultivation system, the biomass concentration progressively increases while the dilution rate is kept constant, resulting in decreased specific susbtrate availibility, and hence, a progressive decrease in the specific growth rate. During the progressive transition from growth to virtually no growth, the global changes occurring at the level of metabolism and gene expression were studied using a genome-scale metabolic model and DNA microarrays. Four different time-points are compared, corresponding to 4 different specific growth rates, and hence, 4 different ratios of energy used for maintenance and growth. The samples taken at the start of retentostat cultivation serves as a a reference sample, to which the three other samples (taken after 3 days, 17 days, and 31 days under retentostat conditions) are compared. No biological replicates: all samples were taken from the same retentostat fermentation.
Project description:Lactobacillus reuteri is a heterofermentative lactic acid bacterium best known for its ability to co-ferment glucose and glycerol. Its genome sequence has recently been deduced enabling the implementation of genome-wide analysis. In this study we developed a dedicated cDNA microarray platform and a genome-scale metabolic network model of L. reuteri and use them to revisit the co-fermentation of glucose and glycerol. The model was used to simulate experimental conditions and to visualize and integrate experimental data in particular the global transcriptional response of L. reuteri to the presence of glycerol. We show how the presence of glycerol affects cell physiology and triggers specific regulatory mechanisms allowing simultaneously a better yield and more efficient biomass formation. Furthermore we were able to predict and demonstrate for this well-studied condition the involvement of previously unsuspected metabolic pathways for instance related to amino acids and vitamins. These could be used as leads in future studies aiming at the increased production of industrially relevant compounds such as vitamin B12 or 1 3- propanediol. Keywords: cell type comparison Dye swap
Project description:This SuperSeries is composed of the following subset Series: GSE11860: The impact of glycerol on the metabolism of Lactobacillus reuteri - Exploratory experiment GSE11861: The impact of glycerol on the metabolism of Lactobacillus reuteri - Main experiment Refer to individual Series
Project description:Lactobacillus reuteri has been shown to encode a vitamin B12 biosynthesis pathway that is phylogenetically related to the one present in some representatives of gamma-proteobacteria such as Salmonella and Yersinia. Here we present evidence supporting that the similarities between these otherwise unrelated organisms extend to their regulatory mechanisms. Keywords: cell type comparison Loop design
Project description:Recent functional genomics and genome-scale modeling approaches indicated that B12 production in Lactobacillus reuteri could be improved by medium optimization. Here we show that a series of systematic single amino acid omissions could significantly modulate the production of B12 from nearly undetectable levels (by isoleucine omission) to 20-fold higher than previously reported through omission of cysteine. We analyzed by cDNA microarray experiments the transcriptional response of L. reuteri to the medium lacking cysteine. These results supported the observed high B12 production and provided new avenues for future improvement of production of vitamin B12. Keywords: cell type comparison loop design
Project description:Medwakh smoking has radically expanded among the youth in the Middle East and around the world. The rising popularity of medwakh/dokha usage is linked to the onset of several chronic illnesses including cardiovascular diseases and cancers. The present study aims to elucidate changes in the salivary proteome of medwakh smokers and explore the resultant pathological alterations in comparison to non-smokers. Statistical measurements reveal significant alterations in the abundance of 74 protein profiles in medwakh smokers compared to non-smokers. Medwakh smoking affected proteins with roles in cell anchorage and adhesion (FERMT3, CAPZA2, ACTN1, TLN1), immune responses, and inflammation (CFI, PSME2, S100A12, CHI3L1, HRG, RNASE2, ORM2), oxidative and anti-oxidative stress responses (NCF4, ERP 29, AKRA1, NADPH, NCF1B) and various cell metabolic processes (G6PD, HEXB, HK3, EEF1A1, PYGL, UGP2, EEF1A1). In our investigation, several novel proteins such as CFI, RNASE2, ORM2, NQO2, SULT1A1, TSN, and UBA1 were also discovered. These proteins play key roles in the initiation of various pathologies and are unique in medwakh smokers. The high significant increase in the abundance of involucrin suggests an alarming squamous cell differentiation in medwakh smokers. In addition, various pathways related to mitochondrial damage, oxidative burst, cell adhesion, migration, differentiation, and proliferation were significantly altered in medwakh smokers. The knowledge gained would help to elucidate the adverse effects of medwakh smoking, especially among adolescents, raising awareness of plausible health hazards, thereby improving the quality of life.
Project description:Although genetically compact, HIV-1 commandeers vast arrays of cellular machinery that sustain and protect it during cycles of viral outgrowth. Transposon-mediated saturation linker scanning mutagenesis was used to isolate fully replication-competent viruses harboring a potent foreign epitope tag. Using these viral isolates, we performed differential isotopic labeling and affinity-capture mass spectrometric analyses on samples obtained from cultures of human lymphocytes to classify the vicinal interactomes of the viral Env and Vif proteins as they occur during natural infection. Importantly, interacting proteins were recovered without bias, regardless of their potential for positive, negative or neutral impact on viral replication. Specific host associations made with trimerized Env during its biosynthesis, at virological synapses, with innate immune effectors and with certain cellular signaling pathways (ex. Notch1) were identified. We also defined Vif associations with host proteins involved in the control of nuclear transcription and nucleoside biosynthesis as well as those that interact both stably and transiently with the cytoplasmic protein degradation apparatus. Our approach is broadly applicable to elucidating pathogen-host interactomes, providing high certainty identification of interactors by their direct access during cycling infection. Understanding the pathophysiological consequences of these associations is likely to provide strategic targets for antiviral intervention.