Identification of tag single-nucleotide polymorphisms in regions with varying linkage disequilibrium

We compared seven different tagging single-nucleotide polymorphism (SNP) programs in 10 regions with varied amounts of linkage disequilibrium (LD) and physical distance. We used the Collaborative Studies on the Genetics of Alcoholism dataset, part of the Genetic Analysis Workshop 14. We show that in regions with moderate to strong LD these programs are relatively consistent, despite different parameters and methods. In addition, we compared the selected SNPs in a multipoint linkage analysis for one region with strong LD. As the number of selected SNPs increased, the LOD score, mean information content, and type I error also increased.     

Protein arginine methylation of non-histone proteins and its role in diseases

Protein arginine methyltransferases (PRMTs) are a family of enzymes that can methylate arginine residues on histones and other proteins. PRMTs play a crucial role in influencing various cellular functions, including cellular development and tumorigenesis. Arginine methylation by PRMTs is found on both nuclear and cytoplasmic proteins. Recently, there is increasing evidence regarding post-translational modifications of non-histone proteins by PRMTs, illustrating the previously unknown importance of PRMTs in the regulation of various cellular functions by post-translational modifications. In this review, we present the recent developments in the regulation of non-histone proteins by PRMTs.     

Collective motion of surfactant-producing bacteria imparts superdiffusivity to their upper surface

Swarming bacteria move on agar surfaces in groups, using flagella as motive organelles. Motility depends critically on surface wetness, which is enabled by osmotic agents and surfactants secreted by the bacteria. In a recent study, the upper surface of an Escherichia coli swarm was found to be stationary, as determined from the motion of MgO particles deposited on the swarm. This led to the remarkable conclusion that the bacteria move between two stationary surfaces—the agar gel below and the liquid/air interface above. That study suggested that secreted surfactants may contribute to immobilizing the upper surface of a swarm. Here, we test this proposition using two robust surfactant-producing bacteria. We find antithetically that the upper surfaces of both these swarms are mobile, showing a superdiffusive behavior in swarms with stronger surfactant activity. Superdiffusive behavior was not observed on the surface of a drop of bacterial culture, on bacteria-free culture supernatant, or on nonswarming surfactant-producer colonies, which suggests that superdiffusion is an emergent property resulting from the interaction of the collective motion of the bacteria within the swarm with the surfactant layer above. Swarming not only allows bacteria to forage for food, but also confers protective advantages against antimicrobial agents. Our results are therefore relevant to superdiffusive strategies in biological foraging and survival.     

Evaluation of dairy cattle manure as a supplement to improve net energy gain in fermentative hydrogen production from sucrose

This study evaluated fermentative biohydrogen production from sucrose supplemented with dairy cattle manure at different sucrose:manure ratios. Hydrogen yields found in this study (2.9-5.3 M hydrogen/M sucrose) at ambient temperature are higher than literature results obtained at mesophilic temperatures. This study demonstrated that dairy cattle manure could serve as a buffering agent to maintain recommended pH levels; as a nutrient source to provide the required nutrients for hydrogen production; as a seed to produce hydrogen from sucrose; and as a co-substrate to improve the hydrogen yield. Based on an analysis of the net energy gain, it is concluded that positive net energy gains can be realized with non-thermal pretreatment and/or by combining dark fermentation with anaerobic digestion or microbial fuel cells to extract additional energy from the aqueous products of dark fermentation.     

The RcsCDB signaling system and swarming motility in Salmonella enterica serovar typhimurium: dual regulation of flagellar and SPI-2 virulence genes

The Rcs phosphorelay is a multicomponent signaling system that positively regulates colanic acid synthesis and negatively regulates motility and virulence. We have exploited a spontaneously isolated mutant, IgaA(T191P), that is nearly maximally activated for the Rcs system to identify a vast set of genes that respond to the stimulation, and we report new regulatory properties of this signaling system in Salmonella enterica serovar Typhimurium. Microarray data show that the Rcs system normally functions as a positive regulator of SPI-2 and other genes important for the growth of Salmonella in macrophages, although when highly activated the system completely represses the SPI-1/SPI-2 virulence, flagellar, and fimbrial biogenesis pathways. The auxiliary protein RcsA, which works with RcsB to positively regulate colanic acid and other target genes, not only stimulates but also antagonizes the positive regulation of many genes in the igaA mutant. We show that RcsB represses motility through the RcsB box in the promoter region of the master operon flhDC and that RcsA is not required for this regulation. Curiously, RcsB selectively stimulates expression of the flagellar type 3 secretion genes fliPQR; an RcsAB box located downstream of fliR influences this regulation. We show that excess colanic acid impairs swimming and inhibits swarming motility, consistent with the inverse regulation of the two pathways by the Rcs system.     

Respiratory supercomplexes: structure,function and assembly

The mitochondrial respiratory chain consists of 5 enzyme complexes that are responsible for ATP generation. The paradigm of the electron transport chain as discrete enzymes diffused in the inner mitochondrial membrane has been replaced by the solid state supercomplex model wherein the respiratory complexes associate with each other to form supramolecular complexes. Defects in these supercomplexes, which have been shown to be functionally active and required for forming stable respiratory complexes, have been associated with many genetic and neurodegenerative disorders demonstrating their biomedical significance. In this review, we will summarize the functional and structural significance of supercomplexes and provide a comprehensive review of their assembly and the assembly factors currently known to play a role in this process.     

An update on complex I assembly: the assembly of players

Defects in Complex I assembly is one of the emerging underlying causes of severe mitochondrial disorders. The assembly of Complex I has been difficult to understand due to its large size, dual genetic control and the number of proteins involved. Mutations in Complex I subunits as well as assembly factors have been reported to hinder its assembly and give rise to a range of mitochondria disorders. In this review, we summarize the recent progress made in understanding the Complex I assembly pathway. In particularly, we focus on the known as well as novel assembly factors and their role in assembly of Complex I and human disease.     

DNA sequence organization in Phycomyces blakesleeanus

Reassociation analysis shows that the genome of the Zygomycete Phycomyces blakesleeanus consists of repetitive and single copy sequences arranged in a long period interspersion pattern. The average lengths of the interspersed repetitive (16 kb) and single copy (25 kb) sequences appear to be very large. The sequence organization resembles that reported for the Oomycete Achlya (Hudspeth et al., 1977).     

On the Analysis of Genome-Wide Association Studies in Family-Based Designs: A Universal,Robust Analysis Approach and an Application to Four Genome-Wide Association Studies

For genome-wide association studies in family-based designs, we propose a new, universally applicable approach. The new test statistic exploits all available information about the association, while, by virtue of its design, it maintains the same robustness against population admixture as traditional family-based approaches that are based exclusively on the within-family information. The approach is suitable for the analysis of almost any trait type, e.g. binary, continuous, time-to-onset, multivariate, etc., and combinations of those. We use simulation studies to verify all theoretically derived properties of the approach, estimate its power, and compare it with other standard approaches. We illustrate the practical implications of the new analysis method by an application to a lung-function phenotype, forced expiratory volume in one second (FEV1) in 4 genome-wide association studies.