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The purpose of this study was to evaluate the safety and efficacy of buprenorphine compared with placebo in prolonging the duration of analgesia in single-injection peripheral nerve block. The systematic review and meta-analysis were conducted following the PRISMA statement and Review Manager was used for meta-analysis. Outcomes were calculated using the mean difference (MD) with 95% confidence interval (CI) for continuous data. For dichotomous outcomes, effect sizes were estimated by calculating pooled risk ratio (RR) with 95% CI. Statistical heterogeneity was estimated by the I2 statistic. Compared with placebo, buprenorphine prolonged the duration of analgesia by an average of 8 hours (MD, 8.01; 95% CI, 6.79 to 9.24; P < .00001). The cumulative pain scores within 24 hours (MD, -0.8; 95% CI, -1.21 to -0.40; P < .0001) and the 24-hour opioid consumption (MD, -5.56; 95% CI, -10.60 to -0.52; P = .03) after surgery was lower with buprenorphine group. Conversely, buprenorphine increased the incidence of postoperative nausea and vomiting (PONV) (RR, 1.67; 95% CI, 1.16 to 2.39; P = .006). Buprenorphine is effective in prolonging analgesia, decreasing pain scores and opioid consumption, however, it increases the risk of PONV. [ABSTRACT FROM AUTHOR]

The trophic ecology of eight circumglobal meso- and bathypelagic fishes (Anoplogaster cornuta, Chauliodus sloani, Coccorella atlantica, Gigantura chuni, G. indica, Omosudis lowii, Photostomias guernei, and Stomias affinis) with contrasting vertical migration habits (vertical migrators vs. non-migrators) were examined using stable isotope analysis (SIA). Mean δ13C values of these predators were similar among species, ranging from –18.17 to –18.99 ‰, suggesting that all species are supported by a similar carbon source. This finding was supported by mixing-model analysis; all of these deep-living predators received the majority (>73%) of their carbon from epipelagic food resources. Mean δ15N values of the predators ranged from 9.18 to 11.13 ‰, resulting in trophic position estimates between the third and fourth trophic level, although significant shifts in δ15N with increasing body size suggest that some of these species undergo ontogenetic shifts in trophic position. Bayesian standard ellipses, used to estimate isotopic niche areas, differed in size among species, with those occupying the highest relative trophic positions possessing the largest isotopic niches. These results, which provide the first trophic descriptions using dietary tracers for several of these species, offer insight into the trophic structure of deep-sea ecosystems and will help inform the construction of ecosystem-based models. [ABSTRACT FROM AUTHOR]

Relationships between abundance of post-larval and juvenile carangid (jacks) fishes and physical oceanographic conditions were examined in the northern Gulf of Mexico (GoM) in 2011 with high freshwater input from the Mississippi River. Generalized additive models ( GAMs) were used to explore complex relationships between carangid abundance and physical oceanographic data of sea surface temperature ( SST), sea surface height anomaly ( SSHA) and salinity. The five most abundant carangid species collected were: Selene setapinnis (34%); Caranx crysos (30%); Caranx hippos (10%); Chloroscombrus chrysurus (9%) and Trachurus lathami (8%). Post-larval carangids (median standard length [ SL] = 10 mm) were less abundant during the spring and early summer, but more abundant during the late summer and fall, suggesting summer to fall spawning for most species. Juvenile carangid (median SL = 23 mm) abundance also increased between the mid-summer and early fall. Most species showed increased abundance at lower salinities and higher temperatures, suggesting entrainment of post-larval fishes or feeding aggregations of juveniles at frontal convergence zones between the expansive river plume and dynamic mesoscale eddy water masses. However, responses were species- and life-stage specific, which may indicate fine-scale habitat partitioning between species. Ordination methods also revealed higher carangid abundances at lower salinities for both post-larval and juvenile life stages, with species- and life-stage specific responses to SST and SSHA, further suggesting habitat separation between species. Results indicate strong links between physical oceanographic features and carangid distributions in the dynamic northern GoM. [ABSTRACT FROM AUTHOR]

Presented here is the first description of the geographic and depth distributions of pelagic decapod shrimps in the area located around the Deepwater Horizon oil spill, based on the National Oceanic and Atmospheric Administration (NOAA) National Resource Damage Assessment (NRDA) samples collected from April to June 2011. This information is important in ecosystem models investigating trophic effects of the spill because pelagic decapod shrimps are consumed by organisms occupying higher trophic levels. One of the most abundant and diverse groups is the family Oplophoridae; however, past research on their distribution and reproductive biology has been limited. In the northeastern Gulf of Mexico (GOM), all previous studies have been conducted at Standard Station (27°N, 86°W). The present study: (1) provides data from a larger area of the northeastern GOM, where oplophorids have never been studied; (2) allows for comparisons of distributions and abundances of oplophorid species in both the mesopelagic and bathypelagic zones by using a continuous data set; and (3) compares assemblages from two distinct bathymetric environments, slope (200- to 1000-m bottom depth) and offshore (>1000 m). Our post-spill data set can be compared with data obtained during future Deep Pelagic Nekton Dynamics (DEEPEND Consortium of the GOM) cruises to monitor changes, or lack thereof, in the assemblage afterexposure to Deepwater Horizon oil and dispersants in the water column. [ABSTRACT FROM AUTHOR]

The domestic dog, Canis familiaris, is a well-established model system for mapping trait and disease loci. While the original draft sequence was of good quality, gaps were abundant particularly in promoter regions of the genome, negatively impacting the annotation and study of candidate genes. Here, we present an improved genome build, canFam3.1, which includes 85 MB of novel sequence and now covers 99.8% of the euchromatic portion of the genome. We also present multiple RNA-Sequencing data sets from 10 different canine tissues to catalog ∼175,000 expressed loci. While about 90% of the coding genes previously annotated by EnsEMBL have measurable expression in at least one sample, the number of transcript isoforms detected by our data expands the EnsEMBL annotations by a factor of four. Syntenic comparison with the human genome revealed an additional ∼3,000 loci that are characterized as protein coding in human and were also expressed in the dog, suggesting that those were previously not annotated in the EnsEMBL canine gene set. In addition to ∼20,700 high-confidence protein coding loci, we found ∼4,600 antisense transcripts overlapping exons of protein coding genes, ∼7,200 intergenic multi-exon transcripts without coding potential, likely candidates for long intergenic non-coding RNAs (lincRNAs) and ∼11,000 transcripts were reported by two different library construction methods but did not fit any of the above categories. Of the lincRNAs, about 6,000 have no annotated orthologs in human or mouse. Functional analysis of two novel transcripts with shRNA in a mouse kidney cell line altered cell morphology and motility. All in all, we provide a much-improved annotation of the canine genome and suggest regulatory functions for several of the novel non-coding transcripts. [ABSTRACT FROM AUTHOR]

A comprehensive gene-based map of a genome is a powerful tool for genetic studies and is especially useful for the positional cloning and positional candidate approaches. The availability of gene maps for multiple organisms provides the foundation for detailed conserved-orthology maps showing the correspondence between conserved genomic segments. These maps make it possible to use cross-species information in gene hunts and shed light on the evolutionary forces that shape the genome. Here we report a radiation hybrid map of mouse genes, a combined project of the Whitehead Institute/Massachusetts Institute of Technology Center for Genome Research, the Medical Research Council UK Mouse Genome Centre, and the National Center for Biotechnology Information. The map contains 11,109 genes, screened against the T31 RH panel and positioned relative to a reference map containing 2,280 mouse genetic markers. It includes 3,658 genes homologous to the human genome sequence and provides a framework for overlaying the human genome sequence to the mouse and for sequencing the mouse genome. [ABSTRACT FROM AUTHOR]

Chromatin accessibility plays a fundamental role in gene regulation. Nucleosome placement, usually measured by quantifying protection of DNA from enzymatic digestion, can regulate accessibility. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC (MNase accessibility), quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both nucleosome location and accessibility in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares histone and non-histone protection. We find that changes in accessibility at enhancers, promoters and other regulatory regions do not correlate with changes in nucleosome occupancy. Moreover, high nucleosome occupancy does not necessarily preclude high accessibility, which reveals novel principles of chromatin regulation.

Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs), and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach to identify regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. Surprisingly, most chromatin remains unchanged; a majority of rearrangements appear to affect a single nucleosome. RoDs are enriched at genes and regulatory elements, including enhancers associated with pluripotency and differentiation. RoDs co-localize with binding sites of key developmental regulators, including the reprogramming factors Klf4, Oct4/Sox2, and c-Myc. Nucleosomal landscapes in ESC enhancers are extensively altered, exhibiting lower nucleosome occupancy in pluripotent cells than in somatic cells. Most changes are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of cell differentiation and reprogramming and likely identify regulatory regions essential for these processes.

ATRX alterations occur at high frequency in neuroblastoma of adolescents and young adults. Particularly intriguing are the large N-terminal deletions of ATRX (Alpha Thalassemia/Mental Retardation, X-linked) that generate in-frame fusion (IFF) proteins devoid of key chromatin interaction domains, while retaining the SWI/SNF-like helicase region. We demonstrate that ATRX IFF proteins are redistributed from H3K9me3-enriched chromatin to promoters of active genes and identify REST as an ATRX IFF target whose activation promotes silencing of neuronal differentiation genes. We further show that ATRX IFF cells display sensitivity to EZH2 inhibitors, due to derepression of neurogenesis genes, including a subset of REST targets. Taken together, we demonstrate that ATRX structural alterations are not loss-of-function and put forward EZH2 inhibitors as a potential therapy for ATRX IFF neuroblastoma. • ATRX IFFs are redistributed genome wide and are enriched at active promoters • The neuronal silencing transcription factor REST is an ATRX IFF target gene • REST and EZH2 silence neuronal gene programs in ATRX IFF NB • REST loss or EZH2 inhibition induces neuronal gene expression programs and NB cell death Qadeer et al. show that ATRX in-frame fusions (IFF), found in a subset of neuroblastomas, are redistributed from wild-type ATRX-binding sites to other genomic regions, including the REST promoter. REST expression silences neuronal differentiation genes, which can be derepressed with EZH2 inhibitors to suppress ATRX IFF cell growth. [ABSTRACT FROM AUTHOR]