Characterization of Adherent Bacteroidales from Intestinal Biopsies of Children and Young Adults with Inflammatory Bowel Disease

There is extensive evidence implicating the intestinal microbiota in inflammatory bowel disease [IBD], but no microbial agent has been identified as a sole causative agent. Bacteroidales are numerically dominant intestinal organisms that associate with the mucosal surface and have properties that both positively and negatively affect the host. To determine precise numbers and species of Bacteroidales adherent to the mucosal surface in IBD patients, we performed a comprehensive culture based analysis of intestinal biopsies from pediatric Crohn's disease [CD], ulcerative colitis [UC], and control subjects. We obtained biopsies from 94 patients and used multiplex PCR or 16S rDNA sequencing of Bacteroidales isolates for species identification. Eighteen different Bacteroidales species were identified in the study group, with up to ten different species per biopsy, a number higher than demonstrated using 16S rRNA gene sequencing methods. Species diversity was decreased in IBD compared to controls and with increasingly inflamed tissue. There were significant differences in predominant Bacteroidales species between biopsies from the three groups and from inflamed and uninflamed sites. Parabacteroides distasonis significantly decreased in inflamed tissue. All 373 Bacteroidales isolates collected in this study grew with mucin as the only utilizable carbon source suggesting this is a non-pathogenic feature of this bacterial order. Bacteroides fragilis isolates with the enterotoxin gene [bft], previously associated with flares of colitis, were not found more often at inflamed colonic sites or within IBD subjects. B. fragilis isolates with the ability to synthesize the immunomodulatory polysaccharide A [PSA], previously shown to be protective in murine models of colitis, were not detected more often from healthy versus inflamed tissue

Genome-Wide RNA Sequencing of Human Trabecular Meshwork Cells Treated with TGF-β1: Relevance to Pseudoexfoliation Glaucoma

Pseudoexfoliation glaucoma (XFG) is an aggressive form of secondary open angle glaucoma, characterised by the production of exfoliation material and is estimated to affect 30 million people worldwide. Activation of the TGF-β pathway by TGF-β1 has been implicated in the pathogenesis of pseudoexfoliation glaucoma. To further investigate the role of TGF-β1 in glaucomatous changes in the trabecular meshwork (TM), we used RNA-Seq to determine TGF-β1 induced changes in the transcriptome of normal human trabecular meshwork (HTM) cells. The main purpose of this study was to perform a hypothesis-independent RNA sequencing analysis to investigate genome-wide alterations in the transcriptome of normal HTMs stimulated with TGF-β1 and investigate possible pathophysiological mechanisms driving XFG. Our results identified multiple differentially expressed genes including several genes known to be present in exfoliation material. Significantly altered pathways, biological processes and molecular functions included extracellular matrix remodelling, Hippo and Wnt pathways, the unfolded protein response, oxidative stress, and the antioxidant system. This cellular model of pseudoexfoliation glaucoma can provide insight into disease pathogenesis and support the development of novel therapeutic interventions

Size matters: the value of small populations for wintering waterbirds

Protecting systematically selected areas of land is a major step towards biodiversity conservation worldwide. Indeed, the identification and designation of protected areas more often than not forms a core component of both national and international conservation policies. In this paper we provide an overview of those Special Protection Areas and Ramsar Sites that have been classified in Great Britain as of 1998/99 for a selection of wintering waterbird species, using bird count data from the Wetland Bird Survey. The performance of this network of sites is remarkable, particularly in comparison with published analyses of networks elsewhere in the world. Nevertheless, the current site-based approach, whilst having the great benefit of simplicity, is deliberately biased towards aggregating species at the expense of the more dispersed distribution species. To ensure that the network continues successfully to protect nationally and internationally important waterbird populations, efforts now need to concentrate on the derivation of species-specific representation targets and, in particular, the ways in which these can be incorporated into the site selection process. Although these analyses concern the performance of protected areas for waterbirds in Great Britain, the results have wide-ranging importance for conservation planning in general and the design of protected area networks

Extensive Aerosol Optical Properties and Aerosol Mass Related Measurements During TRAMP/TexAQS 2006 – Implications for PM Compliance and Planning

Extensive aerosol optical properties, particle size distributions, and Aerodyne quadrupole aerosol mass spectrometer measurements collected during TRAMP/TexAQS 2006 were examined in light of collocated meteorological and chemical measurements. Much of the evident variability in the observed aerosol-related air quality is due to changing synoptic meteorological situations that direct emissions from various sources to the TRAMP site near the center of the Houston-Galveston-Brazoria (HGB) metropolitan area. In this study, five distinct long-term periods have been identified. During each of these periods, observed aerosol properties have implications that are of interest to environmental quality management agencies. During three of the periods, long range transport (LRT), both intra-continental and intercontinental, appears to have played an important role in producing the observed aerosol. During late August 2006, southerly winds brought super-micron Saharan dust and sea salt to the HGB area, adding mass to fine particulate matter (PM2.5) measurements, but apparently not affecting secondary particle growth or gas-phase air pollution. A second type of LRT was associated with northerly winds in early September 2006 and with increased ozone and sub-micron particulate matter in the HGB area. Later in the study, LRT of emissions from wildfires appeared to increase the abundance of absorbing aerosols (and carbon monoxide and other chemical tracers) in the HGB area. However, the greatest impacts on Houston PM2.5air quality are caused by periods with low-wind-speed sea breeze circulation or winds that directly transport pollutants from major industrial areas, i.e., the Houston Ship Channel, into the city center

The structure of tris(chloromethyl)amine in the gas phase using quantum chemical calculations and gas electron diffraction and as a solid and melt using Raman spectroscopy

The equilibrium structure of tris(chloromethyl)amine, N(CH2Cl)3, has been determined in the gas phase using electron diffraction. Single-step distance corrections (representing the differences between the interatomic distances from the equilibrium structure and those from the vibrationally averaged structure) and amplitudes of vibration have been computed using semi-empirical molecular dynamics (SE-MD) simulations in order to treat accurately the description of the low-frequency, large-amplitude vibrational modes associated particularly with one CH2Cl group. A series of complementary theoretical calculations using the SOGGA11-X DFT functional with correlation-consistent basis sets of double-, triple-, and quadruple-ζ quality is also presented. The agreement between the experimental and theoretical equilibrium structural parameters attests to the accuracy of the applied theoretical calculations and of our gas-phase structural solution. Raman spectra have been recorded over a range of temperatures, allowing the solid and the melt to be studied, and the Raman-active intramolecular modes to be identified. Free from the influence of intermolecular interaction, the structure of tris(chloromethyl)amine in the gas phase is markedly different to that reported in the literature for the single crystal. This is discussed, and evidence for the anomeric effect in tris(chloromethyl)amine is evaluated

The structural basis of rubisco phase separation in the pyrenoid

Approximately one-third of global CO2 fixation occurs in a phase-separated algal organelle called the pyrenoid. The existing data suggest that the pyrenoid forms by the phase separation of the CO2-fixing enzyme Rubisco with a linker protein; however, the molecular interactions underlying this phase separation remain unknown. Here we present the structural basis of the interactions between Rubisco and its intrinsically disordered linker protein Essential Pyrenoid Component 1 (EPYC1) in the model alga Chlamydomonas reinhardtii. We find that EPYC1 consists of five evenly spaced Rubisco-binding regions that share sequence similarity. Single-particle cryo-electron microscopy of these regions in complex with Rubisco indicates that each Rubisco holoenzyme has eight binding sites for EPYC1, one on each Rubisco small subunit. Interface mutations disrupt binding, phase separation and pyrenoid formation. Cryo-electron tomography supports a model in which EPYC1 and Rubisco form a codependent multivalent network of specific low-affinity bonds, giving the matrix liquid-like properties. Our results advance the structural and functional understanding of the phase separation underlying the pyrenoid, an organelle that plays a fundamental role in the global carbon cycle

Design of a Potent, Selective, and Brain-Penetrant Inhibitor of Wnt-Deactivating Enzyme Notum by Optimization of a Crystallographic Fragment Hit

Notum is a carboxylesterase that suppresses Wnt signaling through deacylation of an essential palmitoleate group on Wnt proteins. There is a growing understanding of the role Notum plays in human diseases such as colorectal cancer and Alzheimer's disease, supporting the need to discover improved inhibitors, especially for use in models of neurodegeneration. Here, we have described the discovery and profile of 8l (ARUK3001185) as a potent, selective, and brain-penetrant inhibitor of Notum activity suitable for oral dosing in rodent models of disease. Crystallographic fragment screening of the Diamond-SGC Poised Library for binding to Notum, supported by a biochemical enzyme assay to rank inhibition activity, identified 6a and 6b as a pair of outstanding hits. Fragment development of 6 delivered 8l that restored Wnt signaling in the presence of Notum in a cell-based reporter assay. Assessment in pharmacology screens showed 8l to be selective against serine hydrolases, kinases, and drug targets

International meta-analysis of PTSD genome-wide association studies identifies sex- and ancestry-specific genetic risk loci.

The risk of posttraumatic stress disorder (PTSD) following trauma is heritable, but robust common variants have yet to be identified. In a multi-ethnic cohort including over 30,000 PTSD cases and 170,000 controls we conduct a genome-wide association study of PTSD. We demonstrate SNP-based heritability estimates of 5-20%, varying by sex. Three genome-wide significant loci are identified, 2 in European and 1 in African-ancestry analyses. Analyses stratified by sex implicate 3 additional loci in men. Along with other novel genes and non-coding RNAs, a Parkinson's disease gene involved in dopamine regulation, PARK2, is associated with PTSD. Finally, we demonstrate that polygenic risk for PTSD is significantly predictive of re-experiencing symptoms in the Million Veteran Program dataset, although specific loci did not replicate. These results demonstrate the role of genetic variation in the biology of risk for PTSD and highlight the necessity of conducting sex-stratified analyses and expanding GWAS beyond European ancestry populations