Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media and then pelleted and transferred to another media when they reached stationary phase. The Choline mutant was transferred to lacte/sulfate minimal media and choline/sulfate minimal media. The LysX mutant was transferred to minimal media with lysine and rich media. G20 was transferred to minimal media, choline/sulfate minimal media, lactate/choline/sulfate minimal media, minimal media with lysine, and rich media. We aimed to confirm or expand the regulons of each of the transposon interupted regulator mutants and compare gene expression responses of the regulators in different growth conditions. 10 samples were collected: 2 regulator mutants (2 conditions each), Desulfovibrio alaskensis G20 (5 conditions), 2 replicates for G20 minimal media condition. Control sample -G20 rich media.
Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase. We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants. 12 samples were collected: 10 regulator mutants, 1 mutant in a secretory protein and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.
Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media. Pellets collected at mid-log growth phase. We aimed to confirm or expand the predicted regulons of each of the transposon interrupted regulator mutants. 8 samples were collected: 7 regulator mutants and 1 control sample Desulfovibrio alaskensis G20. 1 replicate for each condition.
Project description:Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis or Methanospirillum hungatei in chemostats at a low growth rate of 0.027h-1. 7 samples of Desulfovibrio alaskensis strain G20 grown in syntrophic coculture on lactate with either Methanococcus maripaludis (4 replicates) or Methanospirillum hungatei (3 replicates), and 5 samples of sulfate-limited monoculture growth of strain G20 on lactate.
Project description:Expression data for Desulfovibrio alaskensis strain G20 grown on lactate in sulfate-limited monoculture and syntrophic coculture with Methanococcus maripaludis in chemostats at a high growth rate of 0.047h-1 5 replicates of coculture and 3 replicates of sulfate-limited monoculture
Project description:Pyruvate fermentation pathway and energetics of Desulfovibrio alaskensis strain G20 under syntrophic coculture and fermentative monoculture conditions Expression data for Desulfovibrio alaskensis strain G20 grown in chemostats on pyruvate under respiratory conditions (sulfate-limited and pyruvate-limited monoculture, dilution rate 0.047 and 0.027 h-1), fermentative conditions (monoculture, dilution rate 0.036 h-1), and syntrophic conditions (coculture with Methanococcus maripaludis or Methanospirillum hungatei, dilution rate of 0.047 and 0.027 h-1) 2 replicates each for syntrophic coculture (M. maripaludis or M. hungatei pairing) and respiratory (sulfate- or pyruvate-limited) monoculture for both growth rates (0.027 and 0.047 h-1), and 4 replicates fermentative monoculture (gas flow rate through head space of bioreactor 10 ml/min (chemostats C91 and C93) or 1 ml/min (chemostats C92 and C94)
Project description:Platinum and palladium are highly sought-after noble metals that due to their low abundance have high value and because of their stability and their roles in catalytic processes are very desirable for industrial purposes. Bacteria are able to produce nanoparticles of platinum and palladium at low temperatures and from low concentration feedstocks contrary to chemical methods and so pose a potentially untapped ‘green’ resource for nanoparticle synthesis. We have used the bacterium Desulfovibrio alaskensis G20 to reduce Pt and Pd ions to zero-valent nanoparticle forms and used differential shotgun proteomics to identify proteins responsible for this reduction . There was found to be a core set of 13 proteins common to both datasets as well as 7 proteins specific to Pt and Pd individually. Over expression of one of Pt-specific genes; the NiFe hydrogenase small subunit, resulted in the formation of larger nanoparticles. For the first time the proteins involved in the metal reduction pathway have been pinpointed and it is our hope that these target genes can then be used for nanoparticle production to tailor specific properties for industrial purposes at the genetic level rather than post-production.
Project description:Gene expression was compared from adult C. elegans after RNAi Triplicate control RNAi (Empty vector), control RNAi, choline treated, sams-1(RNAi) and sams-1(RNAi) choline treated animals were grown to young adulthood and RNA was extracted
Project description:The experiment aimed to find how Campylobacter responds to oxidative stress using hydrogen peroxide. This was done by using previously made TraDIS libraries (https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02835-8) and putting them under oxidative stress. The strains used were C. jejuni 11168, C. coli 15-537360 and C. coli CCN182.
Project description:Managing tradeoffs through gene regulation is believed to maintain resilience of a microbial community in a fluctuating resource environment. To investigate this hypothesis we imposed a fluctuating environment that required the sulfate-reducing generalist Desulfovibrio vulgaris to manage tradeoffs associated with repeated ecologically-relevant shifts between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with the hydrogen consuming Methanococcus maripaludis. Strikingly, the microbial community became progressively less proficient at restoring the environmentally-relevant physiological state after each perturbation. Most cultures collapsed within 3-7 shifts with only a few collapsing later. We demonstrate that the collapse was caused by conditional gene regulation, which drove precipitous decline in intracellular abundance of essential transcripts and proteins, imposing greater energetic burden of regulation to restore function in a fluctuating environment. The microbial community collapse was rescued by a single regulatory mutation that could then potentially serve as a stepping stone for further adaptive evolution in a variable resource environment. Co-culture strains of M. maripaludis wild type and either wild type or DVU0744::Tn5 mutant of D. vulgaris strains were grown anaerobically in replicates. Samples were transitioned between syntrophic and sulfate respiratory growth conditions at early log phases.