Integrating biological pathways and genomic profiles with ChiBE 2

Cataloged from PDF version of article.Background: Dynamic visual exploration of detailed pathway information can help researchers digest and interpret complex mechanisms and genomic datasets. Results: ChiBE is a free, open-source software tool for visualizing, querying, and analyzing human biological pathways in BioPAX format. The recently released version 2 can search for neighborhoods, paths between molecules, and common regulators/targets of molecules, on large integrated cellular networks in the Pathway Commons database as well as in local BioPAX models. Resulting networks can be automatically laid out for visualization using a graphically rich, process-centric notation. Profiling data from the cBioPortal for Cancer Genomics and expression data from the Gene Expression Omnibus can be overlaid on these networks. Conclusions: ChiBE's new capabilities are organized around a genomics-oriented workflow and offer a unique comprehensive pathway analysis solution for genomics researchers

The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

<i>Trypanosoma brucei rhodesiense</i> transmitted by a single tsetse fly bite in vervet monkeys as a model of human African trypanosomiasis

Sleeping sickness is caused by a species of trypanosome blood parasite that is transmitted by tsetse flies. To understand better how infection with this parasite leads to disease, we provide here the most detailed description yet of the course of infection and disease onset in vervet monkeys. One infected tsetse fly was allowed to feed on each host individual, and in all cases infections were successful. The characteristics of infection and disease were similar in all hosts, but the rate of progression varied considerably. Parasites were first detected in the blood 4-10 days after infection, showing that migration of parasites from the site of fly bite was very rapid. Anaemia was a key feature of disease, with a reduction in the numbers and average size of red blood cells and associated decline in numbers of platelets and white blood cells. One to six weeks after infection, parasites were observed in the cerebrospinal fluid (CSF), indicating that they had moved from the blood into the brain; this was associated with a white cell infiltration. This study shows that fly-transmitted infection in vervets accurately mimics human disease and provides a robust model to understand better how sleeping sickness develops

Effect of environmental heat stress on Kıvırcık ram sperm parameters

ΔΕΝ ΔΙΑΤΙΘΕΤΑΙ ΠΕΡΙΛΗΨΗThe relationship between environmental conditions and reproduction has been in sight of research. Therefore, there has been a growing interest in effect of climate change, global warming and subsequently environmental heat stress on gametes in last decades. Thus, the present study was designed to investigate the effect of environmental heat stress on Kıvırcık ram sperm parameters. In this study, semen samples (n=72) were collected from six mature rams during a 12-month study period. The temperature and relative humidity of animal box were controlled daily. The mean monthly temperature humidity index (THI) values were calculated to determine heat stress and control periods. According to the mean monthly THI values, the 36 of 72 ejaculates, which were collected between May and October, were classified as heat stress period samples. The others (n=36), which were collected between November and April, were considered as control period samples. The heat stress period sperm samples had lower sperm concentration, motility, viability, membrane integrity and higher abnormal sperm rate compared to control period sperm samples (P&lt; 0.05). Semen volume, sperm DNA integrity and the ability of sperm to undergo acrosome reaction were detected similar between the heat stress and control periods. In conclusion, environmental heat stress was found deleterious for some sperm parameters in Kıvırcık rams.

The cBio cancer Genomics portal: An open platform for exploring multidimensional cancer genomics data

Cataloged from PDF version of article.The cBio Cancer Genomics Portal (http://cbioportal.org) is an open-access resource for interactive exploration of multidimensional cancer genomics data sets, currently providing access to data from more than 5,000 tumor samples from 20 cancer studies. The cBio Cancer Genomics Portal significantly lowers the barriers between complex genomic data and cancer researchers who want rapid, intuitive, and high-quality access to molecular profiles and clinical attributes from large-scale cancer genomics projects and empowers researchers to translate these rich data sets into biologic insights and clinical applications. © 2012 American Association for Cancer Research

Effect of seminal plasma on functional integrity of rabbit sperm membranes during storage at 4ºC or freezing

[EN] The effect of semen plasma removal either by simple centrifugation or by separation through a Percoll gradient on the integrity of plasma membranes of rabbit spermatozoa during storage at 4°C and freezing was evaluated in two successive experiments. A modifi ed hypo-osmotic swelling test procedure combined with supravital staining was employed to evaluate simultaneously membrane integrity of head and tail membranes of sperm cells. In the first experiment, the impact of semen plasma on membrane integrity of sperm cells was examined in Tris-citric acid-glucose extender at 4°C for 96 h. The percentage of sperm cells with disintegrated tail and head membranes increased in all groups in correlation with the length of storage. After storage for 96 h, removal of semen plasma, irrespective of the method of removal, resulted in signifi cant increase (P<0.01) in the percentage of sperm cells with disintegrated plasma membranes. The adverse effect of storage and removal of semen plasma was more prominent on the tail membranes, and especially during the fi rst 24 h of the storage period. In the second experiment, the impact of semen plasma on membrane integrity of sperm cells undergoing freezing was examined. A total of three groups were arranged as described in the fi rst experiment, and semen samples were frozen in straws using an extender including acetamide and methyl cellulose. Freezing of semen drastically reduced the percentage of sperm cells with intact plasma membranes in postthaw samples. However, removal of semen plasma, irrespective of the method of removal, did not affect the proportion of sperm cells with intact plasma membranes. In conclusion, the effect of semen plasma on plasma membranes varied signifi cantly relative to the preservation temperature of sperm cells. Although it exerted a protective infl uence during storage at 4°C, no protective impact was monitored during freezing.Aksoy, M.; Cankat Lehimcioglu, N.; Akman, O. (2010). Effect of seminal plasma on functional integrity of rabbit sperm membranes during storage at 4ºC or freezing. World Rabbit Science. 16(1). doi:10.4995/wrs.2008.64216

The Dispersal Ecology of Rhodesian Sleeping Sickness Following Its Introduction to a New Area

Tsetse-transmitted human and animal trypanosomiasis are constraints to both human and animal health in sub-Saharan Africa, and although these diseases have been known for over a century, there is little recent evidence demonstrating how the parasites circulate in natural hosts and ecosystems. The spread of Rhodesian sleeping sickness (caused by Trypanosoma brucei rhodesiense) within Uganda over the past 15 years has been linked to the movement of infected, untreated livestock (the predominant reservoir) from endemic areas. However, despite an understanding of the environmental dependencies of sleeping sickness, little research has focused on the environmental factors controlling transmission establishment or the spatially heterogeneous dispersal of disease following a new introduction. In the current study, an annually stratified case-control study of Rhodesian sleeping sickness cases from Serere District, Uganda was used to allow the temporal assessment of correlations between the spatial distribution of sleeping sickness and landscape factors. Significant relationships were detected between Rhodesian sleeping sickness and selected factors, including elevation and the proportion of land which was “seasonally flooding grassland” or “woodlands and dense savannah.” Temporal trends in these relationships were detected, illustrating the dispersal of Rhodesian sleeping sickness into more ‘suitable’ areas over time, with diminishing dependence on the point of introduction in concurrence with an increasing dependence on environmental and landscape factors. These results provide a novel insight into the ecology of Rhodesian sleeping sickness dispersal and may contribute towards the implementation of evidence-based control measures to prevent its further spread