WormBase 2016: expanding to enable helminth genomic research

WormBase (www.wormbase.org) is a central repository for research data on the biology, genetics and genomics of Caenorhabditis elegans and other nematodes. The project has evolved from its original remit to collect and integrate all data for a single species, and now extends to numerous nematodes, ranging from evolutionary comparators of C. elegans to parasitic species that threaten plant, animal and human health. Research activity using C. elegans as a model system is as vibrant as ever, and we have created new tools for community curation in response to the ever-increasing volume and complexity of data. To better allow users to navigate their way through these data, we have made a number of improvements to our main website, including new tools for browsing genomic features and ontology annotations. Finally, we have developed a new portal for parasitic worm genomes. WormBase ParaSite (parasite.wormbase.org) contains all publicly available nematode and platyhelminth annotated genome sequences, and is designed specifically to support helminth genomic research

Safety of the Malaria Vaccine Candidate, RTS,S/AS01E in 5 to 17 Month Old Kenyan and Tanzanian Children

The malaria vaccine candidate, RTS,S/AS01E, showed promising protective efficacy in a trial of Kenyan and Tanzanian children aged 5 to 17 months. Here we report on the vaccine's safety and tolerability. The experimental design was a Phase 2b, two-centre, double-blind (observer- and participant-blind), randomised (1∶1 ratio) controlled trial. Three doses of study or control (rabies) vaccines were administered intramuscularly at 1 month intervals. Solicited adverse events (AEs) were collected for 7 days after each vaccination. There was surveillance and reporting for unsolicited adverse events for 30 days after each vaccination. Serious adverse events (SAEs) were recorded throughout the study period which lasted for 14 months after dose 1 in Korogwe, Tanzania and an average of 18 months post-dose 1 in Kilifi, Kenya. Blood samples for safety monitoring of haematological, renal and hepatic functions were taken at baseline, 3, 10 and 14 months after dose 1. A total of 894 children received RTS,S/AS01E or rabies vaccine between March and August 2007. Overall, children vaccinated with RTS,S/AS01E had fewer SAEs (51/447) than children in the control group (88/447). One SAE episode in a RTS,S/AS01E recipient and nine episodes among eight rabies vaccine recipients met the criteria for severe malaria. Unsolicited AEs were reported in 78% of subjects in the RTS,S/AS01E group and 74% of subjects in the rabies vaccine group. In both vaccine groups, gastroenteritis and pneumonia were the most frequently reported unsolicited AE. Fever was the most frequently observed solicited AE and was recorded after 11% of RTS,S/AS01E doses compared to 31% of doses of rabies vaccine. The candidate vaccine RTS,S/AS01E showed an acceptable safety profile in children living in a malaria-endemic area in East Africa. More data on the safety of RTS,S/AS01E will become available from the Phase 3 programme

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

OBJECTIVE: Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired β-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology. RESEARCH DESIGN AND METHODS: We have conducted a meta-analysis of genome-wide association tests of ∼2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates. RESULTS: Nine SNPs at eight loci were associated with proinsulin levels (P < 5 × 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 × 10(-4)), improved β-cell function (P = 1.1 × 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 × 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets. CONCLUSIONS: We have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis

A genome-wide association search for type 2 diabetes genes in African Americans.

African Americans are disproportionately affected by type 2 diabetes (T2DM) yet few studies have examined T2DM using genome-wide association approaches in this ethnicity. The aim of this study was to identify genes associated with T2DM in the African American population. We performed a Genome Wide Association Study (GWAS) using the Affymetrix 6.0 array in 965 African-American cases with T2DM and end-stage renal disease (T2DM-ESRD) and 1029 population-based controls. The most significant SNPs (n = 550 independent loci) were genotyped in a replication cohort and 122 SNPs (n = 98 independent loci) were further tested through genotyping three additional validation cohorts followed by meta-analysis in all five cohorts totaling 3,132 cases and 3,317 controls. Twelve SNPs had evidence of association in the GWAS (P<0.0071), were directionally consistent in the Replication cohort and were associated with T2DM in subjects without nephropathy (P<0.05). Meta-analysis in all cases and controls revealed a single SNP reaching genome-wide significance (P<2.5×10(-8)). SNP rs7560163 (P = 7.0×10(-9), OR (95% CI) = 0.75 (0.67-0.84)) is located intergenically between RND3 and RBM43. Four additional loci (rs7542900, rs4659485, rs2722769 and rs7107217) were associated with T2DM (P<0.05) and reached more nominal levels of significance (P<2.5×10(-5)) in the overall analysis and may represent novel loci that contribute to T2DM. We have identified novel T2DM-susceptibility variants in the African-American population. Notably, T2DM risk was associated with the major allele and implies an interesting genetic architecture in this population. These results suggest that multiple loci underlie T2DM susceptibility in the African-American population and that these loci are distinct from those identified in other ethnic populations

An Unexpected Forest

https://works.swarthmore.edu/alum-books/4839/thumbnail.jp

White Dog Fell From The Sky

https://works.swarthmore.edu/alum-books/2352/thumbnail.jp

Elevated representational similarity of voluntary action and inhibition in Tourette syndrome

Many people with Tourette syndrome (TS) are able to volitionally suppress tics, under certain circumstances. To better understand the neural mechanisms that underlie this ability, we used functional magnetic resonance neuroimaging (fMRI) to track regional brain activity during performance of an intentional inhibition task. On some trials, TS and comparison (non-TS) participants chose to make or withhold a motor action (a button press), while on other trials, they followed ‘Go’ and ‘NoGo’ instructions to make or withhold the same button press action. Using representational similarity analysis, an fMRI multivariate pattern analysis technique, we assessed how TS and comparison participants differed in neural activity when internally choosing to make or to withhold an action, relative to externally-cued responses on Go and NoGo trials. Analyses were pre-registered, and the data and code are publicly available. We considered similarity of action representations within regions implicated as critical to motor action release or inhibition, and to symptom expression in TS, namely the pre-supplementary motor area (preSMA), inferior frontal gyrus (IFG), insula, caudate nucleus, and primary motor cortex (M1). Strikingly, in the TS compared to comparison group, neural activity within preSMA displayed greater representational similarity across all action types. There was lower response-specific differentiation within preSMA of action and inhibition plans, and of internally chosen and externally-cued actions, implicating the region as a functional nexus in the symptomatology of TS. Correspondingly, patients with TS may experience volitional tic suppression as an effortful and tiring process because, at the top of the putative motor decision hierarchy, activity within the population of neurons facilitating action is overly similar to activity within the population of neurons promoting inhibition. Group differences in representational similarity were also present in M1. Here, representations of internally-chosen and externally-cued inhibition were more differentiated in the TS group than in the comparison group, potentially a consequence of a weaker voluntary capacity earlier in the motor hierarchy to proactively suppress action. Tic severity and premonitory sensations correlated with M1 and caudate nucleus representational similarity, but these effects did not survive correction for multiple comparisons. In summary, more rigid preSMA neural coding across action categories may constitute a central feature of TS, which can account for patients’ experience of ‘unvoluntary’ tics, and effortful tic suppression

Development and pilot testing of the “focus on the person” form: Supporting care transitions for people with dementia

When people with dementia are hospitalised, their capacity to communicate with the staff may be limited, compounding risks of distress and other adverse outcomes. Opportunities for carers to share relevant information to inform appropriate person-centred care are also limited. This four-phase mixed methods study aimed to develop an evidence-based family carer–staff communication form, the Focus on the Person form, to address this concern. In Phase I, a literature review plus consultation with clinicians and carers informed form development. In Phase II, the professionally formatted form was piloted by 31 family carers, who were then interviewed about their experiences. These data, combined with data from 30 hospital staff members who participated in Phase III focus groups, led to final, Phase IV, refinements of the form. The form now provides an opportunity for families to inform the person-centred care of people with dementia in hospital, potentially improving outcomes for this vulnerable group