Tissue resolved, gene structure refined equine transcriptome.

BackgroundTranscriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.ResultsThis equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.ConclusionsWe have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome

An alternative approach to using LiDAR remote sensing data to predict stem diameter distributions across a temperate forest landscape

© 2017 by the authors. We apply a spatially-implicit, allometry-based modelling approach to predict stem diameter distributions (SDDs) from low density airborne LiDAR data in a heterogeneous, temperate forest in Ontario, Canada. Using a recently published algorithm that relates the density, size, and species of individual trees to the height distribution of first returns, we estimated parameters that succinctly describe SDDs that are most consistent with each 0.25-ha LiDAR tile across a 30,000 ha forest landscape. Tests with independent validation plots showed that the diameter distribution of stems was predicted with reasonable accuracy in most cases (half of validation plots had R2 ≥ 0.75, and another 23% had 0.5 ≤ R2 < 0.75). The predicted frequency of larger stems was much better than that of small stems (8 ≤ x < 11 cm diameter), particularly small conifers. We used the predicted SDDs to calculate aboveground carbon density (ACD; RMSE = 21.4 Mg C/ha), quadratic mean diameter (RMSE = 3.64 cm), basal area (RMSE = 6.99 m2/ha) and stem number (RMSE = 272 stems/ha). The accuracy of our predictions compared favorably with previous studies that have generally been undertaken in simpler conifer-dominated forest types. We demonstrate the utility of our results to spatial forest management planning by mapping SDDs, the proportion of broadleaves, and ACD at a 0.25 ha resolution

Disclosing 3' UTR cis-elements and putative partners involved in gene expression regulation in Leishmania spp.

To identify putative cis-elements involved in gene expression regulation in Leishmania, we previously conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L. major, L. infantum, and L. braziliensis. Here, the CICS databank was explored to search for sequences that were present in the untranslated regions (UTRs) of groups of genes showing similar expression profiles during in vitro differentiation. Using a selectable marker as a reporter gene, flanked by either an intact 3' UTR or a UTR lacking the conserved element, the regulatory role of a CICS was confirmed. We observed that the pattern of modulation of the mRNA levels was altered in the absence of the CICS. We also identified putative CICS RNA-binding proteins. This study suggests that the publicly available CICS database is a useful tool for identifying regulatory cis-elements for Leishmania genes and suggests the existence of post-transcriptional regulons in Leishmania

Evaluation of the use of Pycnoporus sanguineus fungus for phenolics and genotoxicity decay of a pharmaceutical effluent treatment

If not properly and efficiently treated, wastes produced by the chemical industry can contaminate the environment. Using fungi able to degrade organic compounds (e.g. phenol) seems to be a prominent method to treat pharmaceutical wastewaters, in particular, the white-rot fungus. The aim of this work was to treat pharmaceutical effluent by the Pycnoporus sanguineus fungus. Three effluent samples were collected in a pharmaceutical industry. The production of enzymes such as laccase and manganese peroxidase was determined. Their production increased throughout the treatment with the P. sanguineus fungus, reaching maximum concentration of 4.48 U.mL-1 (Effluent 1), 8.16 U.mL-1 (Effluent 2), 2.8 U.mL-1 (Effluent 3) and 0.03 Abs.min-1 (Effluent 2), respectively, during 96 hours of biological treatment. Genotoxic effects of the raw and treated effluents were also investigated using the in vivo mouse bone marrow micronucleus (MN) assay. Results showed the biological treatment reduced the frequency of MN, in a dose-dependent manner, when compared to untreated sample. The decreasing of around 20% and 45% of phenolics concentration was observed throughout the treatment, confirming that laccase production can be related to the degradation of toxic compounds present in the effluent. Therefore, the biodegradation by the P. sanguineus fungus seems a promising method for the mineralization of recalcitrant compounds present in pharmaceutical effluent

Gastro-protective effect of Crossopteryx febrifuga in Wistar rats

Preparations of Crossopteryx febrifuga (Afzel.) Benth. (Rubiaceae) are  widely used in Northern Nigeria in the therapeutic management of trypanosomiasis, malaria and painful inflammatory disorders. Previous studies have shown that the methanolic stem bark extract of Crossopteryx febrifuga possesses significant analgesic and anti-inflammatory properties possibly mediated via Non-selective inhibition of cyclo-oxygenase pathways. In the present study, the methanolic stem bark extract of Crossopteryx febrifuga was evaluated against ethanol- and piroxicam-induced ulceration in rats. Histopathological studies of the rat stomach tissues were also carried out in order to determine its safety profile on the gastrointestinal tract (git). The extract (25, 50 and100 mg extract/kg body weight) significantly (

A cross-sectional study of physical activity and sedentary behaviours in a Caribbean population: combining objective and questionnaire data to guide future interventions

Abstract Background Current understanding of population physical activity (PA) levels and sedentary behaviour in developing countries is limited, and based primarily on self-report. We described PA levels using objective and self-report methods in a developing country population. Methods PA was assessed in a cross-sectional, representative sample of the population of Barbados (25–54 years), using a validated questionnaire (RPAQ) and individually calibrated combined heart rate and movement sensing monitors. The RPAQ collects information on recalled activity in 4 domains: home, work, transport, and leisure. Physical inactivity was defined according to World Health Organization (WHO) guidelines; sedentary lifestyle was defined as being sedentary for 8 h or more daily; PA overestimation was defined as perceiving activity to be sufficient, when classified as ‘inactive’ by objective measurement. Results According to objective estimates, 90.5 % (95 % CI: 83.3,94.7) of women and 58.9 % (48.4,68.7) of men did not accumulate sufficient activity to meet WHO minimum recommendations. Overall, 50.7 % (43.3,58.1) of the population was sedentary for 8 h or more each day, and 60.1 % (52.8,66.9) overestimated their activity levels. The prevalence of inactivity was underestimated by self-report in both genders by 28 percentage points (95 % CI: 18,38), but the accuracy of reporting differed by age group, education level, occupational grade, and overweight/obesity status. Low PA was greater in more socially privileged groups: higher educational level and higher occupational grade were both associated with less objectively measured PA and more sedentary time. Variation in domain-specific self-reported physical activity energy expenditure (PAEE) by educational attainment was observed: higher education level was associated with more leisure activity and less occupational activity. Occupational PA was the main driver of PAEE for women and men according to self-report, contributing 57 % (95 % CI: 52,61). The most popular leisure activities for both genders were walking and gardening. Conclusions The use of both objective and self-report methods to assess PA and sedentary behaviour provides important complementary information to guide public health programmes. Our results emphasize the urgent need to increase PA and reduce sedentary time in this developing country population. Women and those with higher social economic position are particularly at risk from low levels of physical activity

Acquired trichostasis in postoperative site: a case report

This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

Cluster J Mycobacteriophages: Intron Splicing in Capsid and Tail Genes

Bacteriophages isolated on Mycobacterium smegmatis mc2155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu gene not previously identified as a mycobacterial attB site for phage integration. The Cluster J genomes provide two examples of intron splicing within the virion structural genes, one in a major capsid subunit gene, and one in a tail gene. These genomes also contain numerous free-standing HNH homing endonuclease, and comparative analysis reveals how these could contribute to genome mosaicism. The unusual Cluster J genomes provide new insights into phage genome architecture, gene function, capsid structure, gene mobility, intron splicing, and evolution. © 2013 Pope et al

Topoisomer Differentiation of Molecular Knots by FTICR MS: Lessons from Class II Lasso Peptides

Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminalmacrolactamring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collisioninduced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECDspectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c\bullet/z from c/z\bullet) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions {\eth}b0In{\TH}. We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z\bullet and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture