Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility.

Cytoplasmic incompatibility is a selfish reproductive manipulation induced by the endosymbiont Wolbachia in arthropods. In males Wolbachia modifies sperm, leading to embryonic mortality in crosses with Wolbachia-free females. In females, Wolbachia rescues the cross and allows development to proceed normally. This provides a reproductive advantage to infected females, allowing the maternally transmitted symbiont to spread rapidly through host populations. We identified homologs of the genes underlying this phenotype, cifA and cifB, in 52 of 71 new and published Wolbachia genome sequences. They are strongly associated with cytoplasmic incompatibility. There are up to seven copies of the genes in each genome, and phylogenetic analysis shows that Wolbachia frequently acquires new copies due to pervasive horizontal transfer between strains. In many cases, the genes have subsequently acquired loss-of-function mutations to become pseudogenes. As predicted by theory, this tends to occur first in cifB, whose sole function is to modify sperm, and then in cifA, which is required to rescue the cross in females. Although cif genes recombine, recombination is largely restricted to closely related homologs. This is predicted under a model of coevolution between sperm modification and embryonic rescue, where recombination between distantly related pairs of genes would create a self-incompatible strain. Together, these patterns of gene gain, loss, and recombination support evolutionary models of cytoplasmic incompatibility.Wellcome Trust grant number WT094664MA - Wellcome Trust grant number WT202888/Z/16/Z - ERC grant 28166

Computer Model for Prediction of PCB Dechlorination and Biodegradation Endpoints,”

Mathematical modeling of polychlorinated biphenyl (PCB) transformation served as a means of predicting possible endpoints of bioremediation, thus allowing evaluation of several of the most common transformation patterns. Correlation between laboratory-observed and predicted endpoint data was, in some cases, as good as 0.98 (perfect correlation = 1.0)

Investigation of 91 proteins implicated in neurobiological processes identifies multiple candidate plasma biomarkers of stroke outcome

The inter-individual variation in stroke outcomes is large and protein studies could point to potential underlying biological mechanisms. We measured plasma levels of 91 neurobiological proteins in 209 cases included in the Sahlgrenska Academy Study on Ischemic Stroke using a Proximity Extension Assay, and blood was sampled in the acute phase and at 3-month and 7-year follow-ups. Levels were also determined once in 209 controls. Acute stroke severity and neurological outcome were evaluated by the National Institutes of Health Stroke Scale. In linear regression models corrected for age, sex, and sampling day, acute phase levels of 37 proteins were associated with acute stroke severity, and 47 with 3-month and/or 7-year outcome at false discovery rate < 0.05. Three-month levels of 8 proteins were associated with 7-year outcome, of which the associations for BCAN and Nr-CAM were independent also of acute stroke severity. Most proteins followed a trajectory with lower levels in the acute phase compared to the 3-month follow-up and the control sampling point. Conclusively, we identified multiple candidate plasma biomarkers of stroke severity and neurological outcome meriting further investigation. This study adds novel information, as most of the reported proteins have not been previously investigated in a stroke cohort

A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver

Characterizing the relationship between genetic, epigenetic (e.g., deoxyribonucleic acid [DNA] methylation), and transcript variation could provide insights into mechanisms regulating hemostasis and potentially identify new drug targets. Several hemostatic factors are synthesized in the liver, yet high-resolution DNA methylation data from human liver tissue is currently lacking for these genes. Single-nucleotide polymorphisms (SNPs) can influence DNA methylation in cis which can affect gene expression. This can be analyzed through allele-specific methylation (ASM) experiments. We performed targeted genomic DNA- and bisulfite-sequencing of 35 hemostatic genes in human liver samples for SNP and DNA methylation analysis, respectively, and integrated the data for ASM determination. ASM-associated SNPs (ASM-SNPs) were tested for association to gene expression in liver using in-house generated ribonucleic acid-sequencing data. We then assessed whether ASM-SNPs associated with gene expression, plasma proteins, or other traits relevant for hemostasis using publicly available data. We identified 112 candidate ASM-SNPs. Of these, 68% were associated with expression of their respective genes in human liver or in other human tissues and 54% were associated with the respective plasma protein levels, activity, or other relevant hemostatic genome-wide association study traits such as venous thromboembolism, coronary artery disease, stroke, and warfarin dose maintenance. Our study provides the first detailed map of the DNA methylation landscape and ASM analysis of hemostatic genes in human liver tissue, and suggests that methylation regulated by genetic variants in cis may provide a mechanistic link between noncoding SNPs and variation observed in circulating hemostatic proteins, prothrombotic diseases, and drug response

Bio-Energy Production from Anaerobic Digestion of Animal and Farm Wastes

Track II: Transportation and BiofuelsIncludes audio file (20 min.)US produces annually huge amount of animal and farm wastes (e.g. only cow manure in amount of about 1.8 billion tons). These wastes can be valuable source of renewable energy besides overcoming the environmental problems caused by them such as greenhouse gas effect of methane emission of 22 times worse than carbon dioxide, surface and ground water contamination, odor, dust, ammonia leaching, etc. In this project we systematically studied the process, kinetics, microorganisms interaction and population, and the effects of design and operating parameters on reactor design and scale up of cow manure digestion for bioenergy production and for wastes treatment by developing and implementing advanced imaging, visualization and computational techniques such as computational fluid dynamics (CFD), novel multiple radioactive particles tracking technique (MRPT), novel dual source computed tomography (DSCT), and microbiology imaging techniques. New design and conditions of anaerobic digesters that can reduce significantly the inactive volume and improve the digesters performance have been identified and recommended. In addition, for the first time, the energy produced has been related to the energy introduced in order to maximize the energy output while minimizing the energy input through the mixing power consumed. It is hoped that the findings will be applied in the field to promote bioenergy production and eliminate major environmental pollution problems

Associations of sedentary behaviour, physical activity, blood pressure and anthropometric measures with cardiorespiratory fitness in children with cerebral palsy

Background - Children with cerebral palsy (CP) have poor cardiorespiratory fitness in comparison to their peers with typical development, which may be due to low levels of physical activity. Poor cardiorespiratory fitness may contribute to increased cardiometabolic risk. Purpose - The aim of this study was to determine the association between sedentary behaviour, physical activity and cardiorespiratory fitness in children with CP. An objective was to determine the association between cardiorespiratory fitness, anthropometric measures and blood pressure in children with CP. Methods- This study included 55 ambulatory children with CP [mean (SD) age 11.3 (0.2) yr, range 6-17 yr; Gross Motor Function Classification System (GMFCS) levels I and II]. Anthropometric measures (BMI, waist circumference and waist-height ratio) and blood pressure were taken. Cardiorespiratory fitness was measured using a 10 m shuttle run test. Children were classified as low, middle and high fitness according to level achieved on the test using reference curves. Physical activity was measured by accelerometry over 7 days. In addition to total activity, time in sedentary behaviour and light, moderate, vigorous, and sustained moderate-to-vigorous activity (≥10 min bouts) were calculated. Results - Multiple regression analyses revealed that vigorous activity (β = 0.339, p<0.01), sustained moderate-to-vigorous activity (β = 0.250, p<0.05) and total activity (β = 0.238, p<0.05) were associated with level achieved on the shuttle run test after adjustment for age, sex and GMFCS level. Children with high fitness spent more time in vigorous activity than children with middle fitness (p<0.05). Shuttle run test level was negatively associated with BMI (r2 = -0.451, p<0.01), waist circumference (r2 = -0.560, p<0.001), waist-height ratio (r2 = -0.560, p<0.001) and systolic blood pressure (r2 = -0.306, p<0.05) after adjustment for age, sex and GMFCS level. Conclusions - Participation in physical activity, particularly at a vigorous intensity, is associated with high cardiorespiratory fitness in children with CP. Low cardiorespiratory fitness is associated with increased cardiometabolic risk

Insertion Sequence Inversions Mediated by Ectopic Recombination between Terminal Inverted Repeats

Transposable elements are widely distributed and diverse in both eukaryotes and prokaryotes, as exemplified by DNA transposons. As a result, they represent a considerable source of genomic variation, for example through ectopic (i.e. non-allelic homologous) recombination events between transposable element copies, resulting in genomic rearrangements. Ectopic recombination may also take place between homologous sequences located within transposable element sequences. DNA transposons are typically bounded by terminal inverted repeats (TIRs). Ectopic recombination between TIRs is expected to result in DNA transposon inversions. However, such inversions have barely been documented. In this study, we report natural inversions of the most common prokaryotic DNA transposons: insertion sequences (IS). We identified natural TIR-TIR recombination-mediated inversions in 9% of IS insertion loci investigated in Wolbachia bacteria, which suggests that recombination between IS TIRs may be a quite common, albeit largely overlooked, source of genomic diversity in bacteria. We suggest that inversions may impede IS survival and proliferation in the host genome by altering transpositional activity. They may also alter genomic instability by modulating the outcome of ectopic recombination events between IS copies in various orientations. This study represents the first report of TIR-TIR recombination within bacterial IS elements and it thereby uncovers a novel mechanism of structural variation for this class of prokaryotic transposable elements

Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant?

The expansion of genome sequencing projects has produced accumulating evidence for lateral transfer of genes between prokaryotic and eukaryotic genomes. However, it remains controversial whether these genes are of functional importance in their recipient host. Nikoh and Nakabachi, in a recent paper in BMC Biology, take a first step and show that two genes of bacterial origin are highly expressed in the pea aphid Acyrthosiphon pisum. Active gene expression of transferred genes is supported by three other recent studies. Future studies should reveal whether functional proteins are produced and whether and how these are targeted to the appropriate compartment. We argue that the transfer of genes between host and symbiont may occasionally be of great evolutionary importance, particularly in the evolution of the symbiotic interaction itself

Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group

The obligate intracellular bacterium Wolbachia pipientis strain wPip induces cytoplasmic incompatibility (CI), patterns of crossing sterility, in the Culex pipiens group of mosquitoes. The complete sequence is presented of the 1.48-Mbp genome of wPip which encodes 1386 coding sequences (CDSs), representing the first genome sequence of a B-supergroup Wolbachia. Comparisons were made with the smaller genomes of Wolbachia strains wMel of Drosophila melanogaster, an A-supergroup Wolbachia that is also a CI inducer, and wBm, a mutualist of Brugia malayi nematodes that belongs to the D-supergroup of Wolbachia. Despite extensive gene order rearrangement, a core set of Wolbachia genes shared between the 3 genomes can be identified and contrasts with a flexible gene pool where rapid evolution has taken place. There are much more extensive prophage and ankyrin repeat encoding (ANK) gene components of the wPip genome compared with wMel and wBm, and both are likely to be of considerable importance in wPip biology. Five WO-B–like prophage regions are present and contain some genes that are identical or highly similar in multiple prophage copies, whereas other genes are unique, and it is likely that extensive recombination, duplication, and insertion have occurred between copies. A much larger number of genes encode ankyrin repeat (ANK) proteins in wPip, with 60 present compared with 23 in wMel, many of which are within or close to the prophage regions. It is likely that this pattern is partly a result of expansions in the wPip lineage, due for example to gene duplication, but their presence is in some cases more ancient. The wPip genome underlines the considerable evolutionary flexibility of Wolbachia, providing clear evidence for the rapid evolution of ANK-encoding genes and of prophage regions. This host–Wolbachia system, with its complex patterns of sterility induced between populations, now provides an excellent model for unraveling the molecular systems underlying host reproductive manipulation

CO2 dissolution and design aspects of a multiorifice oscillatory baffled column

Dissolution of CO2 in water was studied for a batch vertical multiorifice baffled column (MOBC) with varying orifice diameters (d0) of 6.4-30 mm and baffle open area (α) of 15-42%. Bubble size distributions (BSDs) and the overall volumetric CO2 mass transfer coefficient (KLa) were experimentally evaluated for very low superficial gas velocities, UG of 0.12-0.81 mm s-1, using 5% v/v CO2 in the inlet gas stream at a range of fluid oscillations (f = 0-10 Hz and x0 = 0-10 mm). Remarkably, baffles presenting large do = 30 mm and α = 36%, therefore in the range typically found for single-orifice oscillatory baffled columns, were outperformed with respect to BSD control and CO2 dissolution by the other baffle designs or the same aerated column operating without baffles or fluid oscillations. Flow visualization and bubble tracking experiments also presented in this study established that a small do of 10.5 mm combined with a small value of α = 15% generates sufficient, strong eddy mixing capable of generating and trapping an extremely large fraction of microbubbles in the MOBC. This resulted in increased interfacial area yielding KLa values up to 65 ± 12 h-1 in the range of the UG tested, representing up to 3-fold increase in the rate of CO2 dissolution when compared to the unbaffled, steady column. In addition, a modi fied oscillatory Reynolds number, Re′o and Strouhal number, St' were presented to assist on the design and scale-up of gas-liquid systems based on multiorifice oscillatory ba ffled columns. This work is relevant to gas-liquid or multiphase chemical and biological systems relying on efficient dissolution of gaseous compounds into a liquid medium.BBSRC -European Commissio