Structure of an atypical periplasmic adaptor from a multidrug efflux pump of the spirochete Borrelia burgdorferi

Periplasmic adaptor proteins are essential components of bacterial tripartite multidrug efflux pumps. Here we report the 2.35 Å resolution crystal structure of the BesA adaptor from the spirochete Borrelia burgdorferi solved using selenomethionine derivatized protein. BesA shows the archetypal linear, flexible, multi-domain architecture evident among proteobacteria and retains the lipoyl, β-barrel and membrane-proximal domains that interact with the periplasmic domains of the inner membrane transporter. However, it lacks the α-hairpin domain shown to establish extensive coiled-coil interactions with the periplasmic entrance helices of the outer membrane-anchored TolC exit duct. This has implications for the modelling of assembled tripartite efflux pumps.     

Prevalence of BRCA1 Mutations in Familial and Sporadic Greek Ovarian Cancer Cases

Germline mutations in the BRCA1 and BRCA2 genes contribute to approximately 18% of hereditary ovarian cancers conferring an estimated lifetime risk from 15% to 50%. A variable incidence of mutations has been reported for these genes in ovarian cancer cases from different populations. In Greece, six mutations in BRCA1 account for 63% of all mutations detected in both BRCA1 and BRCA2 genes. This study aimed to determine the prevalence of BRCA1 mutations in a Greek cohort of 106 familial ovarian cancer patients that had strong family history or metachronous breast cancer and 592 sporadic ovarian cancer cases. All 698 patients were screened for the six recurrent Greek mutations (including founder mutations c.5266dupC, p.G1738R and the three large deletions of exon 20, exons 23–24 and exon 24). In familial cases, the BRCA1 gene was consequently screened for exons 5, 11, 12, 20, 21, 22, 23, 24. A deleterious BRCA1 mutation was found in 43/106 (40.6%) of familial cancer cases and in 27/592 (4.6%) of sporadic cases. The variant of unknown clinical significance p.V1833M was identified in 9/698 patients (1.3%). The majority of BRCA1 carriers (71.2%) presented a high-grade serous phenotype. Identifying a mutation in the BRCA1 gene among breast and/or ovarian cancer families is important, as it enables carriers to take preventive measures. All ovarian cancer patients with a serous phenotype should be considered for genetic testing. Further studies are warranted to determine the prevalence of mutations in the rest of the BRCA1 gene, in the BRCA2 gene, and other novel predisposing genes for breast and ovarian cancer.     

Using dynamic relative climate impact curves to quantify the climate impact of bioenergy production systems over time

The climate impact of bioenergy is commonly quantified in terms of CO₂ equivalents, using a fixed 100‐year global warming potential as an equivalency metric. This method has been criticized for the inability to appropriately address emissions timing and the focus on a single impact metric, which may lead to inaccurate or incomplete quantification of the climate impact of bioenergy production. In this study, we introduce Dynamic Relative Climate Impact (DRCI) curves, a novel approach to visualize and quantify the climate impact of bioenergy systems over time. The DRCI approach offers the flexibility to analyze system performance for different value judgments regarding the impact category (e.g., emissions, radiative forcing, and temperature change), equivalency metric, and analytical time horizon. The DRCI curves constructed for fourteen bioenergy systems illustrate how value judgments affect the merit order of bioenergy systems, because they alter the importance of one‐time (associated with land use change emissions) versus sustained (associated with carbon debt or foregone sequestration) emission fluxes and short‐ versus long‐lived climate forcers. Best practices for bioenergy production (irrespective of value judgments) include high feedstock yields, high conversion efficiencies, and the application of carbon capture and storage. Furthermore, this study provides examples of production contexts in which the risk of land use change emissions, carbon debt, or foregone sequestration can be mitigated. For example, the risk of indirect land use change emissions can be mitigated by accompanying bioenergy production with increasing agricultural yields. Moreover, production contexts in which the counterfactual scenario yields immediate or additional climate impacts can provide significant climate benefits. This paper is accompanied by an Excel‐based calculation tool to reproduce the calculation steps outlined in this paper and construct DRCI curves for bioenergy systems of choice.     

Salmonella SPI1 effector SipA persists after entry and cooperates with a SPI2 effector to regulate phagosome maturation and intracellular replication

Salmonellae employ two type III secretion systems (T3SSs), SPI1 and SPI2, to deliver virulence effectors into mammalian cells. SPI1 effectors, including actin-binding SipA, trigger initial bacterial uptake, whereas SPI2 effectors promote subsequent replication within customized Salmonella-containing vacuoles (SCVs). SCVs sequester actin filaments and subvert microtubule-dependent motors to migrate to the perinuclear region. We demonstrate that SipA delivery continues after Salmonella internalization, with dosage being restricted by host-mediated degradation. SipA is exposed on the cytoplasmic face of the SCV, from where it stimulates bacterial replication in both nonphagocytic cells and macrophages. Although SipA is sufficient to target and redistribute late endosomes, during infection it cooperates with the SPI2 effector SifA to modulate SCV morphology and ensure perinuclear positioning. Our findings define an unexpected additional function for SipA postentry and reveal precise intracellular communication between effectors deployed by distinct T3SSs underlying SCV biogenesis.     

A survey of the availability of primary bioinformatics web resources

The explosive growth of the bioinformatics field has led to a large amount of data and software applications publicly available as web resources. However, the lack of persistence of web references is a barrier to a comprehensive shared access. We conducted a study of the current availability and other features of primary bioinforo matics web resources （such as software tools and databases）. The majority （95%） of the examined bioinformatics web resources were found running on UNIX/Linux operating systems, and the most widely used web server was found to be Apache （or Apache-related products）. Of the overall 1,130 Uniform Resource Locators （URLs） examined, 91% were highly available （more than 90% of the time）, while only 4% showed low accessibility （less than 50% of the time） during the survey. Furthermore, the most common URL failure modes are presented and analyzed.     

Phosphate deposition during and after hypokinesia in phosphate supplemented and unsupplemented rats

The objective of this study was to show that prolonged restriction of motor activity (hypokinesia) could reduce phosphate (P) deposition and contribute to P loss with tissue P depletion. To this end, measurements were made of tissue P content, P absorption, plasma P levels, urinary and fecal P excretion of rats during and after hypokinesia (HK) and daily phosphate supplementation. Studies were conducted on male Wistar rats during a pre-hypokinetic period, a hypokinetic period and a post-hypokinetic period. All rats were equally divided into four groups: unsupplemented vivarium control rats (UVCR), unsupplemented hypokinetic rats (UHKR), supplemented vivarium control rats (SVCR) and supplemented hypokinetic rats (SHKR). Bone and muscle P content, plasma intact parathyroid hormone (iPTH) levels, P absorption, plasma P levels and urinary and fecal P excretion did not change in SVCR and UVCR compared with their pre-HK values. During HK, plasma P levels, urinary and fecal P excretion increased significantly (p<0.05) while muscle and bone P content, P absorption and plasma iPTH levels decreased significantly (p<0.05) in SHKR and UHKR compared with their pre-HK values and the values in their respective vivarium controls (SVCR and UVCR). During the initial 9-days of post-HK, plasma, urinary and fecal P levels decreased significantly (p<0.05), and plasma iPTH levels, muscle and bone P levels remained significantly (p<0.05) depressed in hypokinetic rats compared with their pre-HK values and the values in their respective vivarium control rats. By the 15th day, these values approached the control values. During HK and post-HK, changes in P absorption, plasma iPTH levels, and P levels in muscle, bone, plasma, urine and feces were significantly (p<0.05) greater in SHKR than in UHKR. Decreased tissue P content with increased P loss in animals receiving and not receiving P supplementation demonstrates decreased P deposition during HK. Higher P excretion with lower tissue content in SHKR and UHKR demonstrates that P deposition is decreased more with P supplementation than without. Because SHKR with a lower tissue P content showed higher P excretion than UHKR it was concluded that the risk of decreased P deposition with greater tissue P depletion is inversely related to P intake, that is, the higher the P intake the greater the risk for decreased P deposition and the greater tissue P depletion. It was shown that P (regardless of the intensity of its tissue depletion) is lost during HK unless factors contributing to the decreased P deposition are partially or totally reversed. It was concluded that dissociation between (decreased) tissue P content and (increased) P uptake indicates decreased P (absorption and) deposition as the main mechanisms of tissue P depletion during prolonged HK.     

Three's company: component structures bring a closer view of tripartite drug efflux pumps

Bacterial multidrug resistance is a serious clinical problem and is commonly conferred by tripartite efflux 'pumps' in the prokaryotic cell envelope. Crystal structures of the three components of a drug efflux pump have now been solved: the outer membrane TolC exit duct in the year 2000, the inner membrane AcrB antiporter in 2002 and the periplasmic adaptor MexA in 2004. These structures have enhanced our understanding of the principles underlying pump assembly and operation, and present pumps as new drug targets.     

Phosphorylation of the enteropathogenic E. coli receptor by the Src-family kinase c-Fyn triggers actin pedestal formation

Enteropathogenic Escherichia coli (EPEC) causes diarrhoeal disease worldwide. Pathogen adherence to host cells induces reorganization of the actin cytoskeleton into 'pedestal-like' pseudopods beneath the extracellular bacteria. This requires two bacterial virulence factors that mimic a ligand-receptor interaction. EPEC delivers its own receptor, the translocated intimin receptor (Tir), into the target cell plasma membrane, which is phosphorylated on interaction with the bacterial surface protein intimin. Tir phosphorylated on Tyr 474 (ref. 4) binds the cellular adaptor Nck, triggering actin polymerization. Nevertheless, despite its critical role, the mechanism of Tir Tyr 474 phosphorylation remains unknown. Here, by artificially uncoupling Tir delivery and activity, we show that Tir phosphorylation and Nck-dependent pedestal formation require the Src-family kinase (SFK) c-Fyn. SFK inhibitors prevent Tyr 474 phosphorylation, and cells lacking c-fyn are resistant to pedestal formation. c-Fyn exclusively phosphorylates clustered Tir in vitro, and kinase knockdown suppresses Tir phosphorylation and pedestal formation in cultured cells. These results identify the transient interaction with host c-Fyn as a pivotal link between bacterial Tir and the cellular Nck-WASP-Arp2/3 cascade, illuminating a tractable experimental system in which to dissect tyrosine kinase signalling.     

Behavioral and antioxidant activity of a tosylbenz[g]indolamine derivative. A proposed better profile for a potential antipsychotic agent

BACKGROUND: Tardive dyskinesia (TD) is a major limitation of older antipsychotics. Newer antipsychotics have various other side effects such as weight gain, hyperglycemia, etc. In a previous study we have shown that an indolamine molecule expresses a moderate binding affinity at the dopamine D2 and serotonin 5-HT1A receptors in in vitro competition binding assays. In the present work, we tested its p-toluenesulfonyl derivative (TPBIA) for behavioral effects in rats, related to interactions with central dopamine receptors and its antioxidant activity. METHODS: Adult male Fischer-344 rats grouped as: i) Untreated rats: TPBIA was administered i.p. in various doses ii) Apomorphine-treated rats: were treated with apomorphine (1 mg kg-1, i.p.) 10 min after the administration of TPBIA. Afterwards the rats were placed individually in the activity cage and their motor behaviour was recorded for the next 30 min The antioxidant potential of TPBIA was investigated in the model of in vitro non enzymatic lipid peroxidation. RESULTS: i) In non-pretreated rats, TPBIA reduces the activity by 39 and 82% respectively, ii) In apomorphine pretreated rats, TPBIA reverses the hyperactivity and stereotype behaviour induced by apomorphine. Also TPBIA completely inhibits the peroxidation of rat liver microsome preparations at concentrations of 0.5, 0.25 and 0.1 mM. CONCLUSION: TPBIA exerts dopamine antagonistic activity in the central nervous system. In addition, its antioxidant effect is a desirable property, since TD has been partially attributed, to oxidative stress. Further research is needed to test whether TPBIA may be used as an antipsychotic agent.     

Molecular mechanisms of type III hyperlipoproteinemia: The contribution of the carboxy-terminal domain of ApoE can account for the dyslipidemia that is associated with the E2/E2 phenotype

Apolipoprotein E2, which has an R158 for C substitution, has reduced affinity for the LDL receptor and is associated with type III hyperlipoproteinemia in humans. Consistent with these observations, we have found that following adenovirus-mediated gene transfer, full-length apoE2 aggravates the hypercholesterolemia and induces hypertriglyceridemia in E-deficient mice and induces combined hyperlipidemia in C57BL/6 mice. Unexpectedly, the truncated apoE2-202 form that has an R158 for C substitution when expressed at levels similar to those of the full-length apoE2 normalized the cholesterol levels of E-deficient mice without induction of hypertriglyceridemia. The apoE2 truncation increased the affinity of POPC-apoE particles for the LDL receptor, and the full-length apoE2 had a dominant effect in VLDL triglyceride secretion. Hyperlipidemia in normal C57BL/6 mice was prevented by coinfection with equal doses of each, the apoE2 and the apoE2-202-expressing adenoviruses, indicating that truncated apoE forms have a dominant effect in remnant clearance. Hypertriglyceridemia was completely corrected by coinfection of mice with an adenovirus-expressing wild-type lipoprotein lipase, whereas an inactive lipoprotein lipase had a smaller effect. The findings suggest that the apoE2-induced dyslipidemia is not merely the result of substitution of R158 for C but results from increased secretion of a triglyceride-enriched VLDL that cannot undergo lipolysis, inhibition of LpL activity, and impaired clearance of chylomicron remnants. Infection of E(-)(/)(-)xLDLr(-)(/)(-) double-deficient mice with apoE2-202 did not affect the plasma cholesterol levels, and also did not induce hypertriglyceridemia. In contrast, apoE2 exacerbated the hypercholesterolemia and induced hypertriglyceridemia, suggesting that the LDL receptor is the predominant receptor in remnant clearance.