Methionine restriction slows down senescence in human diploid fibroblasts

Methionine restriction (MetR) extends lifespan in animal models including rodents. Using human diploid fibroblasts (HDF), we report here that MetR significantly extends their replicative lifespan, thereby postponing cellular senescence. MetR significantly decreased activity of mitochondrial complex IV and diminished the accumulation of reactive oxygen species. Lifespan extension was accompanied by a significant decrease in the levels of subunits of mitochondrial complex IV, but also complex I, which was due to a decreased translation rate of several mtDNA‐encoded subunits. Together, these findings indicate that MetR slows down aging in human cells by modulating mitochondrial protein synthesis and respiratory chain assembly.     

Evaluation of variant identification methods for whole genome sequencing data in dairy cattle

Background

Advances in human genomics have allowed unprecedented productivity in terms of algorithms, software, and literature available for translating raw next-generation sequence data into high-quality information. The challenges of variant identification in organisms with lower quality reference genomes are less well documented. We explored the consequences of commonly recommended preparatory steps and the effects of single and multi sample variant identification methods using four publicly available software applications (Platypus, HaplotypeCaller, Samtools and UnifiedGenotyper) on whole genome sequence data of 65 key ancestors of Swiss dairy cattle populations. Accuracy of calling next-generation sequence variants was assessed by comparison to the same loci from medium and high-density single nucleotide variant (SNV) arrays.

Results

The total number of SNVs identified varied by software and method, with single (multi) sample results ranging from 17.7 to 22.0 (16.9 to 22.0) million variants. Computing time varied considerably between software. Preparatory realignment of insertions and deletions and subsequent base quality score recalibration had only minor effects on the number and quality of SNVs identified by different software, but increased computing time considerably. Average concordance for single (multi) sample results with high-density chip data was 58.3% (87.0%) and average genotype concordance in correctly identified SNVs was 99.2% (99.2%) across software. The average quality of SNVs identified, measured as the ratio of transitions to transversions, was higher using single sample methods than multi sample methods. A consensus approach using results of different software generally provided the highest variant quality in terms of transition/transversion ratio.

Conclusions

Our findings serve as a reference for variant identification pipeline development in non-human organisms and help assess the implication of preparatory steps in next-generation sequencing pipelines for organisms with incomplete reference genomes (pipeline code is included). Benchmarking this information should prove particularly useful in processing next-generation sequencing data for use in genome-wide association studies and genomic selection.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-948) contains supplementary material, which is available to authorized users.     

Morphological variation of intervessel pit membranes and implications to xylem function in angiosperms

Pit membranes between xylem vessels have been suggested to have functional adaptive traits because of their influence on hydraulic resistance and vulnerability to embolism in plants. Observations of intervessel pit membranes in 26 hardwood species using electron microscopy showed significant variation in their structure, with a more than 25-fold difference in thickness (70-1892 nm) and observed maximum pore diameter (10-225 nm). In some SEM images, pit membrane porosity was affected by sample preparation, although pores were resolvable in intact pit membranes of many species. A significant relationship (r(2) = 0.7, P = 0.002) was found between pit membrane thickness and maximum pore diameter, indicating that the thinner membranes are usually more porous. In a subset of nine species, maximum pore diameter determined from SEM was correlated with pore diameter calculated from air-seeding thresholds (r(2) = 0.8, P < 0.001). Our data suggest that SEM images of intact pit membranes underestimate the porosity of pit membranes in situ. Pit membrane porosity based on SEM offers a relative estimate of air-seeding thresholds, but absolute pore diameters must be treated with caution. The implications of variation in pit membrane thickness and porosity to plant function are discussed.     

Hsp70 and cardiac surgery: molecular chaperone and inflammatory regulator with compartmentalized effects

Open heart surgery is a unique model to study the interplay between cellular injury, regulation of inflammatory responses and tissue repair. Stress-inducible heat shock protein 70-kDa (Hsp70) provides a molecular link between these events. In addition to molecular chaperoning, Hsp70 exerts modulatory effects on endothelial cells and leukocytes involved in inflammatory networks. Hsp70 residing in the intracellular compartment is part of an inhibitory feedback loop that acts on nuclear factor kappaB (NF-κB). In contrast, extracellular Hsp70 is recognized by multiple germline-encoded immune receptors, e.g., Toll-like receptor (TLR) 2, TLR4, LOX-1, CD91, CD94, CCR5 and CD40. Hsp70 is thereby able to enhance chemotaxis, phagocytosis and cytolytic activity of innate immune cells and stimulate antigen-specific responses. These apparent contradictory pro- and anti-inflammatory effects of endogenous Hsp70 in the context of cardiac surgery are still not fully understood. An all-embracing model of the compartmentalized effects of endogenous Hsp70 in the orchestration of inflammatory responses in cardiac surgery is proposed.     

Early Stages of Golgi Vesicle and Tubule Formation Require Diacylglycerol

We have investigated the role for diacylglycerol (DAG) in membrane bud formation in the Golgi apparatus. Addition of propranolol to specifically inhibit phosphatidate phosphohydrolase (PAP), an enzyme responsible for converting phosphatidic acid into DAG, effectively prevents formation of membrane buds. The effect of PAP inhibition on Golgi membranes is rapid and occurs within 3 min. Removal of the PAP inhibitor then results in a rapid burst of buds, vesicles, and tubules that peaks within 2 min. The inability to form buds in the presence of propranolol does not appear to be correlated with a loss of ARFGAP1 from Golgi membranes, as knockdown of ARFGAP1 by RNA interference has little or no effect on actual bud formation. Rather, knockdown of ARFGAP1 results in an increase in membrane buds and a decrease of vesicles and tubules suggesting it functions in the late stages of scission. How DAG promotes bud formation is discussed.     

R/qtl: high-throughput multiple QTL mapping

MOTIVATION: R/qtl is free and powerful software for mapping and exploring quantitative trait loci (QTL). R/qtl provides a fully comprehensive range of methods for a wide range of experimental cross types. We recently added multiple QTL mapping (MQM) to R/qtl. MQM adds higher statistical power to detect and disentangle the effects of multiple linked and unlinked QTL compared with many other methods. MQM for R/qtl adds many new features including improved handling of missing data, analysis of 10,000 s of molecular traits, permutation for determining significance thresholds for QTL and QTL hot spots, and visualizations for cis-trans and QTL interaction effects. MQM for R/qtl is the first free and open source implementation of MQM that is multi-platform, scalable and suitable for automated procedures and large genetical genomics datasets. AVAILABILITY: R/qtl is free and open source multi-platform software for the statistical language R, and is made available under the GPLv3 license. R/qtl can be installed from http://www.rqtl.org/. R/qtl queries should be directed at the mailing list, see http://www.rqtl.org/list/. CONTACT: kbroman@biostat.wisc.edu.