The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Excess intra-abdominal adipose tissue accumulation, often termed visceral obesity, is part of a phenotype including dysfunctional subcutaneous adipose tissue expansion and ectopic triglyceride storage closely related to clustering cardiometabolic risk factors. Hypertriglyceridemia; increased free fatty acid availability; adipose tissue release of proinflammatory cytokines; liver insulin resistance and inflammation; increased liver VLDL synthesis and secretion; reduced clearance of triglyceride-rich lipoproteins; presence of small, dense LDL particles; and reduced HDL cholesterol levels are among the many metabolic alterations closely related to this condition. Age, gender, genetics, and ethnicity are broad etiological factors contributing to variation in visceral adipose tissue accumulation. Specific mechanisms responsible for proportionally increased visceral fat storage when facing positive energy balance and weight gain may involve sex hormones, local cortisol production in abdominal adipose tissues, endocannabinoids, growth hormone, and dietary fructose. Physiological characteristics of abdominal adipose tissues such as adipocyte size and number, lipolytic responsiveness, lipid storage capacity, and inflammatory cytokine production are significant correlates and even possible determinants of the increased cardiometabolic risk associated with visceral obesity. Thiazolidinediones, estrogen replacement in postmenopausal women, and testosterone replacement in androgen-deficient men have been shown to favorably modulate body fat distribution and cardiometabolic risk to various degrees. However, some of these therapies must now be considered in the context of their serious side effects. Lifestyle interventions leading to weight loss generally induce preferential mobilization of visceral fat. In clinical practice, measuring waist circumference in addition to the body mass index could be helpful for the identification and management of a subgroup of overweight or obese patients at high cardiometabolic risk.

Pathophysiology of Human Visceral Obesity: An Update

Autism spectrum disorders (ASDs) represent a formidable challenge for psychiatry and neuroscience because of their high prevalence, lifelong nature, complexity and substantial heterogeneity. Facing these obstacles requires large-scale multidisciplinary efforts. Although the field of genetics has pioneered data sharing for these reasons, neuroimaging had not kept pace. In response, we introduce the Autism Brain Imaging Data Exchange (ABIDE)-a grassroots consortium aggregating and openly sharing 1112 existing resting-state functional magnetic resonance imaging (R-fMRI) data sets with corresponding structural MRI and phenotypic information from 539 individuals with ASDs and 573 age-matched typical controls (TCs; 7-64 years) (http://fcon_1000.projects.nitrc.org/indi/abide/). Here, we present this resource and demonstrate its suitability for advancing knowledge of ASD neurobiology based on analyses of 360 male subjects with ASDs and 403 male age-matched TCs. We focused on whole-brain intrinsic functional connectivity and also survey a range of voxel-wise measures of intrinsic functional brain architecture. Whole-brain analyses reconciled seemingly disparate themes of both hypo- and hyperconnectivity in the ASD literature; both were detected, although hypoconnectivity dominated, particularly for corticocortical and interhemispheric functional connectivity. Exploratory analyses using an array of regional metrics of intrinsic brain function converged on common loci of dysfunction in ASDs (mid- and posterior insula and posterior cingulate cortex), and highlighted less commonly explored regions such as the thalamus. The survey of the ABIDE R-fMRI data sets provides unprecedented demonstrations of both replication and novel discovery. By pooling multiple international data sets, ABIDE is expected to accelerate the pace of discovery setting the stage for the next generation of ASD studies.

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The autism brain imaging data exchange: towards a large-scale evaluation of the intrinsic brain architecture in autism

Elements Of X Ray Diffraction

Medicinal plants of India with anti-diabetic potential.

Comparative toxicity evaluation of cyanobacterial cyclic peptide toxin microcystin variants (LR, RR, YR) in mice.

How instructive cues present on the cell surface have their precise effects on the actin cytoskeleton is poorly understood. Semaphorins are one of the largest families of these instructive cues and are widely studied for their effects on cell movement, navigation, angiogenesis, immunology and cancer. Semaphorins/collapsins were characterized in part on the basis of their ability to drastically alter actin cytoskeletal dynamics in neuronal processes, but despite considerable progress in the identification of semaphorin receptors and their signalling pathways, the molecules linking them to the precise control of cytoskeletal elements remain unknown. Recently, highly unusual proteins of the Mical family of enzymes have been found to associate with the cytoplasmic portion of plexins, which are large cell-surface semaphorin receptors, and to mediate axon guidance, synaptogenesis, dendritic pruning and other cell morphological changes. Mical enzymes perform reduction-oxidation (redox) enzymatic reactions and also contain domains found in proteins that regulate cell morphology. However, nothing is known of the role of Mical or its redox activity in mediating morphological changes. Here we report that Mical directly links semaphorins and their plexin receptors to the precise control of actin filament (F-actin) dynamics. We found that Mical is both necessary and sufficient for semaphorin-plexin-mediated F-actin reorganization in vivo. Likewise, we purified Mical protein and found that it directly binds F-actin and disassembles both individual and bundled actin filaments. We also found that Mical utilizes its redox activity to alter F-actin dynamics in vivo and in vitro, indicating a previously unknown role for specific redox signalling events in actin cytoskeletal regulation. Mical therefore is a novel F-actin-disassembly factor that provides a molecular conduit through which actin reorganization-a hallmark of cell morphological changes including axon navigation-can be precisely achieved spatiotemporally in response to semaphorins.

/pdf/mical-links-semaphorins-to-f-actin-disassembly-46c0wcniof.pdf

Mical links semaphorins to F-actin disassembly

Considerable evidence exists for the place of mind body medicine in the treatment of anxiety disorders. Excessive anxiety is maladaptive. It is often considered to be the major component of unhealthy lifestyle that contributes significantly to the pathogenesis of not only psychiatric but also many other systemic disorders. Among the approaches to reduce the level of anxiety has been the search for healthy lifestyles. The aim of the study was to study the short-term impact of a comprehensive but brief lifestyle intervention, based on yoga, on anxiety levels in normal and diseased subjects. The study was the result of operational research carried out in the Integral Health Clinic (IHC) at the Department of Physiology of All India Institute of Medical Sciences. The subjects had history of hypertension, coronary artery disease, diabetes mellitus, obesity, psychiatric disorders (depression, anxiety, 'stress'), gastrointestinal problems (non ulcer dyspepsia, duodenal ulcers, irritable bowel disease, Crohn's disease, chronic constipation) and thyroid disorders (hyperthyroidism and hypothyroidism). The intervention consisted of asanas, pranayama, relaxation techniques, group support, individualized advice, and lectures and films on philosophy of yoga, the place of yoga in daily life, meditation, stress management, nutrition, and knowledge about the illness. The outcome measures were anxiety scores, taken on the first and last day of the course. Anxiety scores, both state and trait anxiety were significantly reduced. Among the diseased subjects significant improvement was seen in the anxiety levels of patients of hypertension, coronary artery disease, obesity, cervical spondylitis and those with psychiatric disorders. The observations suggest that a short educational programme for lifestyle modification and stress management leads to remarkable reduction in the anxiety scores within a period of 10 days.

/pdf/effect-of-yoga-based-lifestyle-intervention-on-state-and-40zxq0nqkd.pdf

Effect of yoga based lifestyle intervention on state and trait anxiety.

Historically, many technologies have been associated with societal controversies, leading to public rejection of their use. It is therefore important to understand the psychological determinants of societal acceptance of emerging technologies. Socio-psychological determinants of public acceptance of 10 (controversial) technologies are reviewed. The results indicate that there has been an increased interest in and focus on public acceptance of technologies in academia. Risk, trust, perceived benefit, knowledge, individual differences and attitude were found to have been a focus of research in 60% of articles. The results of correspondence analysis suggest that some determinants have been used more extensively in association with some technologies compared to others. As the published research has predominantly been conducted in North America and Europe, research across different cultural contexts internationally is required if globally relevant conclusions are to be reached. Implications for future research are discussed.

/pdf/socio-psychological-determinants-of-public-acceptance-of-2l4l432rq6.pdf

Socio-psychological determinants of public acceptance of technologies: A review

To meet stringent emission standards stipulated by regulatory agencies, the oil industry is required to make a huge investment to bring down the sulfur content in diesel to the desired level, using conventional hydrodesulfurization (HDS) technology, by which sulfur is catalytically converted to hydrogen sulfide in the presence of hydrogen. These reactions proceed rapidly only at high temperature and pressure and therefore the capital cost as well as the operating cost associated with HDS very high. Biological desulfurization has the potential of being developed as a viable technology downstream of classical HDS. Various attempts have been made to develop biotechnological processes based on microbiological desulfurization employing aerobic and anaerobic bacteria. However, there are several bottlenecks limiting commercialization of the process. This review discusses various aspects of microbial desulfurization and the progress made towards its commercialization.

Nidhi Gupta

Papers

Comparative toxicity evaluation of cyanobacterial cyclic peptide toxin microcystin variants (LR, RR, YR) in mice.

Mical links semaphorins to F-actin disassembly

Effect of yoga based lifestyle intervention on state and trait anxiety.

Socio-psychological determinants of public acceptance of technologies: A review

Biotechnology of desulfurization of diesel: prospects and challenges.