The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible. The uncharacterized complex Hdr/flox-1 (Dde_1207:13) is sometimes important alongside Rnf and may perform an electron bifurcation to generate more reduced ferredoxin from NADH to allow further ion pumping. Similarly, during the oxidation of malate or fumarate, the electron-bifurcating transhydrogenase NfnAB-2 (Dde_1250:1) is important and may generate reduced ferredoxin to allow additional ion pumping by Rnf. During formate oxidation, the periplasmic [NiFeSe] hydrogenase HysAB is required, which suggests that hydrogen forms in the periplasm, diffuses to the cytoplasm, and is used to reduce ferredoxin, thus providing a substrate for Rnf. During hydrogen utilization, the transmembrane electron transport complex Tmc is important and may move electrons from the periplasm into the cytoplasmic sulfite reduction pathway. Finally, mutants of many other putative electron carriers have no clear phenotype, which suggests that they are not important under our growth conditions, although we cannot rule out genetic redundancy

How is policy affecting classroom instruction?

Five-plus years into the experiment with new “college- and career-ready standards” (of which Common Core is the most notable and most controversial example), we know little about teachers’ implementation and the ways policy can support that implementation. This paper uses new state-representative teacher survey data to characterize the degree of standards implementation across three states—Kentucky, Ohio, and Texas. We also investigate teachers’ perceptions of the extent to which the policy environment supports them to implement the standards. We find a great deal of variation in perceptions of policy, with Ohio teachers perceiving policy to be less supportive than Kentucky or Texas teachers. Teachers in all states are mostly implementing the content in new standards, but they are also teaching a good deal of content they should not—content that has been deemphasized in their grade-level standards. Perceptions of policy do not explain much of the variation in instruction, contrary to our theory. If greater attention is not paid to supporting teachers to implement the standards and reduce coverage of deemphasized content, we worry the standards will not have much effect

Succenturiate Placental Lobe Abruption: a placental pathology complicating a dangerous delivery

The development of a placenta is a complex process that occurs without a clinically significant issue in most pregnancies. At times, however, the process develops in a way that isolates an island of placental tissue away from the main body, connected only by unprotected vasculature within the amniotic membranes. The vessels of this succenturiate lobe of the placenta are vulnerable both to compression or laceration, threatening the antepartum period with poor weight gain or the peripartum period with fetal distress, hemorrhage or retained products of conception. A majority of the time, this pathology is undiagnosed until recognized innocuously following delivery of the placenta. A placental abruption is a premature separation of the placenta from the uterus that can result in painful bleeding and fetal distress. This increased distress of mother or baby from continued blood loss usually necessitates delivery either vaginally, if stability is maintained, or by cesarean if it isn’t. The amount of distress correlates to where and how much of the placenta is affected. While succenturiate lobes of the placenta and placental abruptions are not routinely associated with each other, the abruption of only the succenturiate lobe of the placenta in this instance minimized the severity to the fetus, by allowing the main body of the placenta to remain intact. As the bleeding coagulated at the lobe, maternal well-being was maintained allowing enough time to complete a vaginal delivery

Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20.

UnlabelledThe genomes of sulfate-reducing bacteria remain poorly characterized, largely due to a paucity of experimental data and genetic tools. To meet this challenge, we generated an archived library of 15,477 mapped transposon insertion mutants in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. To demonstrate the utility of the individual mutants, we profiled gene expression in mutants of six regulatory genes and used these data, together with 1,313 high-confidence transcription start sites identified by tiling microarrays and transcriptome sequencing (5' RNA-Seq), to update the regulons of Fur and Rex and to confirm the predicted regulons of LysX, PhnF, PerR, and Dde_3000, a histidine kinase. In addition to enabling single mutant investigations, the D. alaskensis G20 transposon mutants also contain DNA bar codes, which enables the pooling and analysis of mutant fitness for thousands of strains simultaneously. Using two pools of mutants that represent insertions in 2,369 unique protein-coding genes, we demonstrate that the hypothetical gene Dde_3007 is required for methionine biosynthesis. Using comparative genomics, we propose that Dde_3007 performs a missing step in methionine biosynthesis by transferring a sulfur group to O-phosphohomoserine to form homocysteine. Additionally, we show that the entire choline utilization cluster is important for fitness in choline sulfate medium, which confirms that a functional microcompartment is required for choline oxidation. Finally, we demonstrate that Dde_3291, a MerR-like transcription factor, is a choline-dependent activator of the choline utilization cluster. Taken together, our data set and genetic resources provide a foundation for systems-level investigation of a poorly studied group of bacteria of environmental and industrial importance.ImportanceSulfate-reducing bacteria contribute to global nutrient cycles and are a nuisance for the petroleum industry. Despite their environmental and industrial significance, the genomes of sulfate-reducing bacteria remain poorly characterized. Here, we describe a genetic approach to fill gaps in our knowledge of sulfate-reducing bacteria. We generated a large collection of archived, transposon mutants in Desulfovibrio alaskensis G20 and used the phenotypes of these mutant strains to infer the function of genes involved in gene regulation, methionine biosynthesis, and choline utilization. Our findings and mutant resources will enable systematic investigations into gene function, energy generation, stress response, and metabolism for this important group of bacteria

Relationship between nitrate and nitrite stress responses of Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20

Many heavy metal-contaminated sites where nuclear weapons have been produced contain high concentrations of nitrate. Nitrate inhibits dissimilatory sulfate-reducing bacteria (SRB), bacteria known to precipitate heavy metals. An understanding of nitrate stress responses in SRB is necessary to predict responses in environmental settings. Desulfovibrio vulgaris Hildenborough and Desulfovibrio alaskensis G20, model SRB, offer the opportunity to identify the physiological and genetic changes that confer nitrate resistance. It is currently thought that nitrite production mediates nitrate inhibition of SRB (He et al., 2010). However, microarray studies have revealed few gene expression changes in common between nitrate- and nitrite-inhibited D. vulgaris cells (He et al., 2010). Since it has been shown that nitrite interacts with the dissimilatory sulfite reductase (Wolfe et al., 1994), it has been assumed that sulfite reduction is the sole target of nitrite inhibition (Haveman et al., 2004). Our results point to inhibition and resistance mechanisms for both nitrate and nitrite that are independent of sulfite reduction

Dissecting a complex chemical stress: chemogenomic profiling of plant hydrolysates.

The efficient production of biofuels from cellulosic feedstocks will require the efficient fermentation of the sugars in hydrolyzed plant material. Unfortunately, plant hydrolysates also contain many compounds that inhibit microbial growth and fermentation. We used DNA-barcoded mutant libraries to identify genes that are important for hydrolysate tolerance in both Zymomonas mobilis (44 genes) and Saccharomyces cerevisiae (99 genes). Overexpression of a Z. mobilis tolerance gene of unknown function (ZMO1875) improved its specific ethanol productivity 2.4-fold in the presence of miscanthus hydrolysate. However, a mixture of 37 hydrolysate-derived inhibitors was not sufficient to explain the fitness profile of plant hydrolysate. To deconstruct the fitness profile of hydrolysate, we profiled the 37 inhibitors against a library of Z. mobilis mutants and we modeled fitness in hydrolysate as a mixture of fitness in its components. By examining outliers in this model, we identified methylglyoxal as a previously unknown component of hydrolysate. Our work provides a general strategy to dissect how microbes respond to a complex chemical stress and should enable further engineering of hydrolysate tolerance

Electrocardiographic changes during haemodialysis and the potential impact on subcutaneous implantable cardioverter defibrillator eligibility

Acknowledgments The authors would like to acknowledge the kindness and support that they received from all of the patients and staff at the Chandler's Ford Dialysis Unit. Funding This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.Peer reviewedPublisher PD