rTANDEM, an R/Bioconductor package for MS/MS protein identification.

SUMMARY: rTANDEM is an R/Bioconductor package that interfaces the X!Tandem protein identification algorithm. The package can run the multi-threaded algorithm on proteomic data files directly from R. It also provides functions to convert search parameters and results to/from R as well as functions to manipulate parameters and automate searches. An associated R package, shinyTANDEM, provides a web-based graphical interface to visualize and interpret the results. Together, those two packages form an entry point for a general MS/MS-based proteomic pipeline in R/Bioconductor. AVAILABILITY AND IMPLEMENTATION: rTANDEM and shinyTANDEM are distributed in R/Bioconductor, http://bioconductor.org/packages/release/bioc/. The packages are under open licenses (GPL-3 and Artistice-1.0). CONTACT: frederic.fournier@crchuq.ulaval.ca or arnaud.droit@crchuq.ulaval.ca SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Regulation of skeletal muscle transcriptome in elderly men after 6 weeks of endurance training at lactate threshold intensity.

A compromised muscle function due to aging, sarcopenia and reduced level of physical activity can lead to metabolic complications and chronic diseases. Endurance exercise counters these diseases by inducing beneficial adaptations whose molecular mechanisms remain unclear. We have investigated the transcriptomic changes following mild-intensity endurance training in skeletal muscle of elderly men. Seven healthy subjects followed an exercise program of cycle ergometer training at lactate threshold (LT) level for 60 min/day, five times/week during six weeks. Physiological and transcriptomic changes were analyzed before and after training. LT training decreased percentage body fat and fasting levels of plasma glucose, while increasing high-density lipoprotein cholesterol and lecithin-cholesterol acyltransferase levels. Transcriptomic analysis revealed fast-to-slow fiber type transition, increased amount of mtDNA encoded transcripts and modulation of 12 transcripts notably related to extracellular matrix (ECM), oxidative phosphorylation (OXPHOS), as well as partially characterized and novel transcripts. The training simultaneously induced the expression of genes related to slow fiber type transition, OXPHOS and ECM, which might contribute to the improvement of glucose and lipid metabolisms and whole body aerobic capacity.

An environmentally relevant organochlorine mixture impairs sperm function and embryo development in the porcine model.

We evaluated the effects of an environmentally relevant mixture of more than 15 organochlorines on the development of pig oocytes and sperm during in vitro fertilization (IVF). Oocytes were cocultured with sperm in IVF medium containing increasing concentrations of an organochlorine mixture, similar to that found in women of highly exposed populations. Exposure to the organochlorine mixture diminished oocyte penetration rates and polyspermy in a linear manner. The mixture did not affect rates of cleavage nor development to multicell embryos. However, rates of development to the blastocyst stage were lower at the highest concentration at which oocyte penetration was observed. The same experiment was performed using oocytes that were preexposed during in vitro maturation. This greater exposure to the mixture also reduced penetration in a dose-response manner and affected polyspermy. Frozen-thawed pig sperm were also cultured in IVF medium containing the same organochlorine concentrations. Sperm motility parameters were immediately reduced in a dose-dependent manner by the organochlorines, followed by diminished viability 2 h later. From these results, it appears that reduced sperm quality would account for decreases in fertilization, polyspermy, and blastocyst formation. These results suggest that exposing porcine oocytes and sperm to an environmentally pertinent organochlorine mixture in vitro disrupts the oocyte block to polyspermy, sperm fertility, and further embryonic development, and supports recent concerns that such pollutants harm reproductive health in humans and other species.