Compounds that select against the tetracycline-resistance efflux pump

This is the author accepted manuscript. The final version is available from Nature Research via the DOI in this recordAccession codes. The sequences reported in this article have been deposited in the National Center for Biotechnology Information Sequence Read Archive database (accession number SRP073071).We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline.National Institute of Allergy and Infectious DiseasesUS National Institutes of HealthEuropean Union FP7National Science Foundatio

Withholding or withdrawing invasive interventions may not accelerate time to death among dying ICU patients

We considered observational data available from the MIMIC-III open-access ICU database and collected within a study period between year 2002 up to 2011. If a patient had multiple admissions to the ICU during the 30 days before death, only the first stay was analyzed, leading to a final set of 6,436 unique ICU admissions during the study period. We tested two hypotheses: (i) administration of invasive intervention during the ICU stay immediately preceding end-of-life would decrease over the study time period and (ii) time-to-death from ICU admission would also decrease, due to the decrease in invasive intervention administration. To investigate the latter hypothesis, we performed a subgroups analysis by considering patients with lowest and highest severity. To do so, we stratified the patients based on their SAPS I scores, and we considered patients within the first and the third tertiles of the score. We then assessed differences in trends within these groups between years 2002-05 vs. 2008-11. Comparing the period 2002-2005 vs. 2008-2011, we found a reduction in endotracheal ventilation among patients who died within 30 days of ICU admission (120.8 vs. 68.5 hours for the lowest severity patients, p<0.001; 47.7 vs. 46.0 hours for the highest severity patients, p=0.004). This is explained in part by an increase in the use of non-invasive ventilation. Comparing the period 2002-2005 vs. 2008-2011, we found a reduction in the use of vasopressors and inotropes among patients with the lowest severity who died within 30 days of ICU admission (41.8 vs. 36.2 hours, p<0.001) but not among those with the highest severity. Despite a reduction in the use of invasive interventions, we did not find a reduction in the time to death between 2002-2005 vs. 2008-2011 (7.8 days vs. 8.2 days for the lowest severity patients, p=0.32; 2.1 days vs. 2.0 days for the highest severity patients, p=0.74)

Upper Limits for the Visible Counterpart of the Hulse-Taylor Binary Pulsar

The time-averaged intensity of visible pulses from PSR 1913+16 is fainter than V = 23 mag. The absence of visible objects at the pulsar position on the Sky Survey implies a rough limit of M > 3 for the absolute magnitude of the pulsar's binary companion

Proteomic analysis of the cerebrospinal fluid of patients with restless legs syndrome/Willis-Ekbom disease

BACKGROUND: Restless Legs Syndrome/Willis-Ekbom Disease (RLS/WED) is a sensorimotor disorder that causes patients to experience overwhelming and distressing sensations in the legs compelling the patient to move their legs to provide relief. The purpose of this study was to determine if biomarkers in the cerebrospinal fluid can distinguish RLS/WED patients from neurological controls. METHODS: We obtained CSF samples by lumbar puncture from 5 early-onset RLS/WED patients and 5 controls. We performed 2-dimensional difference in-gel electrophoresis (2D-DIGE). Proteins that were significantly altered were identified by Student’s t-test. Protein spots that were differentially expressed (p ≤ 0.05, Av. Ratio ≥ 2.0) between RLS/WED and control CSF samples were identified using MALDI-TOF-MS. Statistical analyses of the validation immunoblot assays were performed using Student’s t-test. RESULTS: In this discovery study we identified 6 candidate CSF protein markers for early-onset RLS/WED. Four proteins (Cystatin C, Lipocalin-type Prostaglandin D2 Synthase, Vitamin D binding Protein, and β-Hemoglobin) were increased and 2 proteins (Apolipoprotein A1 and α-1-acid Glycoprotein) were decreased in RLS/WED patients. CONCLUSIONS: Our results reveal a protein profile in the RLS/WED CSF that is consistent with clinical findings of disruptive sleep, cardiovascular dysfunction and painful symptoms. Moreover, protein profiles are consistent with neuropathological findings of activation of hypoxia inducible factor (HIF) pathways and alterations in dopaminergic systems. These data indicate the CSF of RLS/WED patients may provide information relevant to biological basis for RLS/WED, treatment strategies and potential new treatment targets

Sporulenes, Heptaprenyl Metabolites from Bacillus subtilis Spores

Sporulene, a C35-terpenoid hydrocarbon with an unusual pentacyclic structure, is produced by Bacillus subtilis during sporulation.Earth and Planetary SciencesMolecular and Cellular Biolog

GABA-modulating bacteria of the human gut microbiota.

The gut microbiota affects many important host functions, including the immune response and the nervous system1. However, while substantial progress has been made in growing diverse microorganisms of the microbiota2, 23-65% of species residing in the human gut remain uncultured3,4, which is an obstacle for understanding their biological roles. A likely reason for this unculturability is the absence in artificial media of key growth factors that are provided by neighbouring bacteria in situ5,6. In the present study, we used co-culture to isolate KLE1738, which required the presence of Bacteroides fragilis to grow. Bioassay-driven purification of B. fragilis supernatant led to the isolation of the growth factor, which, surprisingly, is the major inhibitory neurotransmitter GABA (γ-aminobutyric acid). GABA was the only tested nutrient that supported the growth of KLE1738, and a genome analysis supported a GABA-dependent metabolism mechanism. Using growth of KLE1738 as an indicator, we isolated a variety of GABA-producing bacteria, and found that Bacteroides ssp. produced large quantities of GABA. Genome-based metabolic modelling of the human gut microbiota revealed multiple genera with the predicted capability to produce or consume GABA. A transcriptome analysis of human stool samples from healthy individuals showed that GABA-producing pathways are actively expressed by Bacteroides, Parabacteroides and Escherichia species. By coupling 16S ribosmal RNA sequencing with functional magentic resonance imaging in patients with major depressive disorder, a disease associated with an altered GABA-mediated response, we found that the relative abundance levels of faecal Bacteroides are negatively correlated with brain signatures associated with depression

Composition and temporal patterns of larval fish communities in Chesapeake and Delaware Bays, USA

Comparing larval fish assemblages in different estuaries provides insights about the coastal distribution of larval populations, larval transport, and adult spawning locations. We simultaneously compared the larval fish assemblages entering 2 Middle Atlantic Bight (MAB) estuaries(Delaware Bay and Chesapeake Bay, USA) through weekly sampling from 2007 to 2009. In total,43 taxa (32 families) and 36 taxa (24 families) were collected in Delaware and Chesapeake Bays,respectively. Mean taxonomic diversity, mean richness, and evenness were generally lower in Delaware Bay. Communities of both bays were dominated by Anchoaspp., Gobiosomaspp.,Micropogonias undulatus, and Brevoortia tyrannus; Paralichthys spp. was more abundant in Delaware Bay and Microgobius thalassinus was more abundant in Chesapeake Bay. Inter-annual variation in the larval fish communities was low at both sites, with a relatively consistent composition across years, but strong seasonal (intra-annual) variation in species composition occurred in both bays. Two groups were identified in Chesapeake Bay: a ‘winter’ group dominated by shelf-spawned species and a ‘summer’ group comprising obligate estuarine species and coastal species.In Delaware Bay, 4 groups were identified: a ‘summer’ group of mainly obligate estuarine fishes being replaced by a ‘fall’ group; ‘winter’ and ‘spring’ groups were dominated by shelf-spawned and obligate estuarine species, respectively. This study demonstrates that inexpensive and simultaneous sampling in different estuaries provides important insights into the variability in community structure of fish assemblages at large spatial scales

Dimensions of biodiversity in Chesapeake Bay demersal fishes: patterns and drivers through space and time

Biodiversity has typically been described in terms of species richness and composition, but theory and growing empirical evidence indicate that the diversity of functional traits, the breadth of evolutionary relationships, and the equitability with which individuals or biomass are distributed among species better characterize patterns and processes within ecosystems. Yet, the advantages of including such data come at the expense of measuring traits, sequencing genes, and counting or weighing individuals, and it remains unclear whether this greater resolution yields substantial benefits in describing diversity. We summarized a decade of high-resolution trawl data from a bimonthly trawl survey to investigate spatial and seasonal patterns of demersal fish diversity in the Chesapeake Bay, USA, with the goal of identifying areas and times of mismatch between different dimensions of diversity, and their response to environmental forcing. We found moderate to strong positive relationships among all metrics of diversity, and that functional and phylogenetic differences were well-reflected in an index derived from taxonomic (Linnaean) hierarchy. Compared with species richness and species diversity, functional, phylogenetic, and taxonomic indices peaked later in the year, which was a consequence of the distribution of biomass among functionally and evolutionarily divergent species. Generalized additive models revealed that spatial, temporal, and environmental variables explained roughly similar proportions of deviance across all aspects of diversity, suggesting that these three factors do not differentially affect the functional and phylogenetic aspects of community structure. We conclude that an index of diversity derived from taxonomic hierarchy served well as a practical surrogate for functional and phylogenetic diversity of the demersal fish community in this system. We also emphasize the importance of evenness in understanding diversity patterns, especially since most ecological communities in nature are dominated by one or few species

Selection for High Oridonin Yield in the Chinese Medicinal Plant Isodon (Lamiaceae) Using a Combined Phylogenetics and Population Genetics Approach

Oridonin is a diterpenoid with anti-cancer activity that occurs in the Chinese medicinal plant Isodon rubescens and some related species. While the bioactivity of oridonin has been well studied, the extent of natural variation in the production of this compound is poorly known. This study characterizes natural variation in oridonin production in order to guide selection of populations of Isodon with highest oridonin yield. Different populations of I. rubescens and related species were collected in China, and their offspring were grown in a greenhouse. Samples were examined for oridonin content, genotyped using 11 microsatellites, and representatives were sequenced for three phylogenetic markers (ITS, rps16, trnL-trnF). Oridonin production was mapped on a molecular phylogeny of the genus Isodon using samples from each population as well as previously published Genbank sequences. Oridonin has been reported in 12 out of 74 species of Isodon examined for diterpenoids, and the phylogeny indicates that oridonin production has arisen at least three times in the genus. Oridonin production was surprisingly consistent between wild-collected parents and greenhouse-grown offspring, despite evidence of gene flow between oridonin-producing and non-producing populations of Isodon. Additionally, microsatellite genetic distance between individuals was significantly correlated with chemical distance in both parents and offspring. Neither heritability nor correlation with genetic distance were significant when the comparison was restricted to only populations of I. rubescens, but this result should be corroborated using additional samples. Based on these results, future screening of Isodon populations for oridonin yield should initially prioritize a broad survey of all species known to produce oridonin, rather than focusing on multiple populations of one species, such as I. rubescens. Of the samples examined here, I. rubescens or I. japonicus from Henan province would provide the best source of oridonin