An Extended Nomenclature for Mammalian V-ATPase Subunit Genes and Splice Variants

The vacuolar-type H+-ATPase (V-ATPase) is a multisubunit proton pump that is involved in both intra- and extracellular acidification processes throughout the body. Multiple homologs and splice variants of V-ATPase subunits are thought to explain its varied spatial and temporal expression pattern in different cell types. Recently subunit nomenclature was standardized with a total of 22 subunit variants identified. However this standardization did not accommodate the existence of splice variants and is therefore incomplete. Thus, we propose here an extension of subunit nomenclature along with a literature and sequence database scan for additional V-ATPase subunits. An additional 17 variants were pulled from a literature search while 4 uncharacterized potential subunit variants were found in sequence databases. These findings have been integrated with the current V-ATPase knowledge base to create a new V-ATPase subunit catalogue. It is envisioned this catalogue will form a new platform on which future studies into tissue- and organelle-specific V-ATPase expression, localization and function can be based

Finding Rare AGN: X-ray Number Counts of Chandra Sources in Stripe 82

We present the first results of a wide area X-ray survey within the Sloan Digital Sky Survey (SDSS) Stripe 82, a 300 deg$^2$ region of the sky with a substantial investment in multi-wavelength coverage. We analyzed archival {\it Chandra} observations that cover 7.5 deg$^2$ within Stripe 82 ("Stripe 82 ACX"), reaching 4.5$\sigma$ flux limits of 7.9$\times10^{-16}$, 3.4$\times10^{-15}$ and 1.8$\times10^{-15}$ erg s$^{-1}$ cm$^{-2}$ in the soft (0.5-2 keV), hard (2-7 keV) and full (0.5-7 keV) bands, to find 774, 239 and 1118 X-ray sources, respectively. Three hundred twenty-one sources are detected only in the full band and 9 sources are detected solely in the soft band. Utilizing data products from the {\it Chandra} Source Catalog, we construct independent Log$N$-Log$S$ relationships, detailing the number density of X-ray sources as a function of flux, which show general agreement with previous {\it Chandra} surveys. We compare the luminosity distribution of Stripe 82 ACX with the smaller, deeper CDF-S + E-CDFS surveys and with {\it Chandra}-COSMOS, illustrating the benefit of wide-area surveys in locating high luminosity AGN. We also investigate the differences and similarities of X-ray and optical selection to uncover obscured AGN in the local Universe. Finally, we estimate the population of AGN we expect to find with increased coverage of 100 deg$^2$ or 300 deg$^2$, which will provide unprecedented insight into the high redshift, high luminosity regime of black hole growth currently under-represented in X-ray surveys.Comment: Accepted for publication in MNRAS, 15 pages, 6 Figures, 2 Table

Soil management and engineering for blue-green infrastructure

As urban areas continue to expand, the value of urban blue-green infrastructure (BGI) for increasing the social, environmental and economic sustainability of cities is increasingly recognised. However, there remains an inherent lack of knowledge and awareness around the fundamental contribution that soils make to the functioning of ecosystems within urban BGI. Urban landscapes are a nexus of environmental, engineered and socio-economic factors, which combine to create multifunctional spaces for people to live and work, all underpinned by the soil beneath us. In this chapter, we first outline the characteristics of urban soils and their importance for providing a range of beneficial ecosystem services, such as food production, flood mitigation, carbon storage and opportunities for recreation. We then highlight the key challenges and opportunities around the management and creation of soils within urban BGI. We conclude by emphasising the urgent need for better recognition of urban soils within planning policy and setting out a series of land-use specific management recommendations that will better enable urban soils to support the delivery of ecosystem services and, ultimately, enhance human health and wellbeing

Determining a minimum detection threshold in terminal restriction fragment length polymorphism analysis

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a common technique used to characterize soil microbial diversity. The fidelity of this technique in accurately reporting diversity has not been thoroughly evaluated. Here we determine if rare fungal species can be reliably detected by T-RFLP analysis. Spores from three arbuscular mycorrhizal fungal species were each mixed at a range of concentrations (1%, 10%, 50%, and 100%) with Glomus irregulare to establish a minimum detection threshold. T-RFLP analysis was capable of detecting diagnostic peaks of rare taxa at concentrations as low as 1%. The relative proportion of the target taxa in the sample and DNA concentration influenced peak detection reliability. However, low concentrations produced small, inconsistent electropherogram peaks contributing to difficulty in differentiating true peaks from signal noise. The results of this experiment suggest T-RFLP is a reproducible and high fidelity procedure, which requires careful data interpretation in order to accurately characterize sample diversity

Massively Parallel Sequencing of Human Urinary Exosome/Microvesicle RNA Reveals a Predominance of Non-Coding RNA

Intact RNA from exosomes/microvesicles (collectively referred to as microvesicles) has sparked much interest as potential biomarkers for the non-invasive analysis of disease. Here we use the Illumina Genome Analyzer to determine the comprehensive array of nucleic acid reads present in urinary microvesicles. Extraneous nucleic acids were digested using RNase and DNase treatment and the microvesicle inner nucleic acid cargo was analyzed with and without DNase digestion to examine both DNA and RNA sequences contained in microvesicles. Results revealed that a substantial proportion (∼87%) of reads aligned to ribosomal RNA. Of the non-ribosomal RNA sequences, ∼60% aligned to non-coding RNA and repeat sequences including LINE, SINE, satellite repeats, and RNA repeats (tRNA, snRNA, scRNA and srpRNA). The remaining ∼40% of non-ribosomal RNA reads aligned to protein coding genes and splice sites encompassing approximately 13,500 of the known 21,892 protein coding genes of the human genome. Analysis of protein coding genes specific to the renal and genitourinary tract revealed that complete segments of the renal nephron and collecting duct as well as genes indicative of the bladder and prostate could be identified. This study reveals that the entire genitourinary system may be mapped using microvesicle transcript analysis and that the majority of non-ribosomal RNA sequences contained in microvesicles is potentially functional non-coding RNA, which play an emerging role in cell regulation

Long-term personalized low FODMAP diet improves symptoms and maintains luminal Bifidobacteria abundance in irritable bowel syndrome

Acknowledgements The authors thank the patients who agreed to participate in this long-term follow up study. We are grateful to Monash University, Melbourne, Australia, for access to their FODMAP food composition database for analysis of FODMAP intake. The initial study was funded by the National Institute for Health Research and the long term follow-up was funded by King’s College London, neither of whom played a role in the study design, data collection, data analysis, data interpretation or writing of the manuscript.Peer reviewedPostprin

Forum: Critical Decision Dates for Drought Management in Centraland Northern Great Plains Rangeland

Ranchers and other land managers of central and northern Great Plains rangelands face recurrent droughts that negatively influence economic returns and environmental resources for ranching enterprises. Accurately estimating annual forage production and initiating drought decision-making actions proactively early in the growing season are both critical to minimize financial losses and degradation to rangeland soil and plant resources. Long-term forage production data sets from Alberta, Kansas, Montana, Nebraska, North Dakota, South Dakota, and Wyoming demonstrated that precipitation in April, May, and June (or some combination of these months) robustly predict annual forage production. Growth curves from clipping experiments and ecological site descriptions (ESDs) indicate that maximum monthly forage growth rates occur 1 mo after the best spring month (April to June) precipitation prediction variable. Key for rangeland managers is that the probability of receiving sufficient precipitation after 1 July to compensate for earlier spring precipitation deficits is extremely low. The complexity of human dimensions of drought decision-making necessitates that forage prediction tools account for uncertainty in matching animal demand to forage availability, and that continued advancements in remote sensing applications address both spatial and temporal relationships in forage production to inform critical decision dates for drought management in these rangeland ecosystems

Volatile Organic Compounds in Feces Associate With Response to Dietary Intervention in Patients With Irritable Bowel Syndrome

Background & Aims Dietary interventions are effective in management of patients with irritable bowel syndrome (IBS), although responses vary. We investigated whether fecal levels of volatile organic compounds (VOCs) associate with response to dietary interventions in patients with IBS. Methods Adults who fulfilled the Rome III criteria for IBS were recruited to a 2x2 factorial randomized controlled trial. Patients were randomly assigned to a group counselled to follow a diet low in fructans, galacto-oligosaccharides, lactose, fructose, and polyols (low-FODMAP diet, n = 46) or a group that received placebo dietary advice (sham diet, n = 47) for 4 weeks. Patients from each group were also given either a multi-strain probiotic or placebo supplement. Response was defined as a reduction of 50 points or more on the validated IBS symptom scoring system. Fecal samples were collected from participants at baseline and end of the 4-week study period; VOCs were analyzed by a gas-chromatography sensor device. VOC profiles were determined using a pipeline involving wavelet transformation followed by feature selection based on random forest. A partial least squares classifier was constructed to classify VOC profiles by response and accuracies were determined using 10-fold cross-validation. Results Data from 93 patients who completed the study (63 female) were used in the final analysis. More patients responded to the low-FODMAP diet (37/46, 80%) than the sham diet (21/47, 45%) (P < .001), but there was no difference in response between patients given the probiotic (31/49, 63%) vs the placebo (27/44, 61%) (P = .850), with no interaction between the diet and supplement interventions. At baseline, VOC profiles contained 15 features that classified response to the low-FODMAP diet with a mean accuracy of 97% (95% CI, 96%–99%) and 10 features that classified response to probiotic with a mean accuracy of 89% (95% CI, 86%–92%). End of treatment models achieved similar predictive powers and accuracies. Conclusion Fecal VOC profiling is a low cost, non-invasive tool that might be used to predict responses of patients with IBS to low-FODMAP diet and probiotics and identify their mechanisms of action. ISRCTN registry no: 02275221

Clinical impairment in premanifest and early Huntington's disease is associated with regionally specific atrophy.

TRACK-HD is a multicentre longitudinal observational study investigating the use of clinical assessments and 3-Tesla magnetic resonance imaging as potential biomarkers for future therapeutic trials in Huntington's disease (HD). The cross-sectional data from this large well-characterized dataset provide the opportunity to improve our knowledge of how the underlying neuropathology of HD may contribute to the clinical manifestations of the disease across the spectrum of premanifest (PreHD) and early HD. Two hundred and thirty nine gene-positive subjects (120 PreHD and 119 early HD) from the TRACK-HD study were included. Using voxel-based morphometry (VBM), grey and white matter volumes were correlated with performance in four domains: quantitative motor (tongue force, metronome tapping, and gait); oculomotor [anti-saccade error rate (ASE)]; cognition (negative emotion recognition, spot the change and the University of Pennsylvania smell identification test) and neuropsychiatric measures (apathy, affect and irritability). After adjusting for estimated disease severity, regionally specific associations between structural loss and task performance were found (familywise error corrected, P < 0.05); impairment in tongue force, metronome tapping and ASE were all associated with striatal loss. Additionally, tongue force deficits and ASE were associated with volume reduction in the occipital lobe. Impaired recognition of negative emotions was associated with volumetric reductions in the precuneus and cuneus. Our study reveals specific associations between atrophy and decline in a range of clinical modalities, demonstrating the utility of VBM correlation analysis for investigating these relationships in HD