Collybistin and gephyrin are novel components of the eukaryotic translation initiation factor 3 complex

<p>Abstract</p> <p>Background</p> <p>Collybistin (CB), a neuron-specific guanine nucleotide exchange factor, has been implicated in targeting gephyrin-GABA_Areceptors clusters to inhibitory postsynaptic sites. However, little is known about additional CB partners and functions.</p> <p>Findings</p> <p>Here, we identified the p40 subunit of the eukaryotic translation initiation factor 3 (eIF3H) as a novel binding partner of CB, documenting the interaction in yeast, non-neuronal cell lines, and the brain. In addition, we demonstrated that gephyrin also interacts with eIF3H in non-neuronal cells and forms a complex with eIF3 in the brain.</p> <p>Conclusions</p> <p>Together, our results suggest, for the first time, that CB and gephyrin associate with the translation initiation machinery, and lend further support to the previous evidence that gephyrin may act as a regulator of synaptic protein synthesis.</p

A call for transparent reporting to optimize the predictive value of preclinical research

The US National Institute of Neurological Disorders and Stroke convened major stakeholders in June 2012 to discuss how to improve the methodological reporting of animal studies in grant applications and publications. The main workshop recommendation is that at a minimum studies should report on sample-size estimation, whether and how animals were randomized, whether investigators were blind to the treatment, and the handling of data. We recognize that achieving a meaningful improvement in the quality of reporting will require a concerted effort by investigators, reviewers, funding agencies and journal editors. Requiring better reporting of animal studies will raise awareness of the importance of rigorous study design to accelerate scientific progress

Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines

An increasing number of cis-regulatory RNA elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems. Effective computational tools for large-scale identification of novel regulatory RNAs are strongly desired to facilitate our exploration of gene regulation mechanisms and regulatory networks. We present a new computational program named RSSVM (RNA Sampler+Support Vector Machine), which employs Support Vector Machines (SVMs) for efficient identification of functional RNA motifs from random RNA secondary structures. RSSVM uses a set of distinctive features to represent the common RNA secondary structure and structural alignment predicted by RNA Sampler, a tool for accurate common RNA secondary structure prediction, and is trained with functional RNAs from a variety of bacterial RNA motif/gene families covering a wide range of sequence identities. When tested on a large number of known and random RNA motifs, RSSVM shows a significantly higher sensitivity than other leading RNA identification programs while maintaining the same false positive rate. RSSVM performs particularly well on sets with low sequence identities. The combination of RNA Sampler and RSSVM provides a new, fast, and efficient pipeline for large-scale discovery of regulatory RNA motifs. We applied RSSVM to multiple Shewanella genomes and identified putative regulatory RNA motifs in the 5′ untranslated regions (UTRs) in S. oneidensis, an important bacterial organism with extraordinary respiratory and metal reducing abilities and great potential for bioremediation and alternative energy generation. From 1002 sets of 5′-UTRs of orthologous operons, we identified 166 putative regulatory RNA motifs, including 17 of the 19 known RNA motifs from Rfam, an additional 21 RNA motifs that are supported by literature evidence, 72 RNA motifs overlapping predicted transcription terminators or attenuators, and other candidate regulatory RNA motifs. Our study provides a list of promising novel regulatory RNA motifs potentially involved in post-transcriptional gene regulation. Combined with the previous cis-regulatory DNA motif study in S. oneidensis, this genome-wide discovery of cis-regulatory RNA motifs may offer more comprehensive views of gene regulation at a different level in this organism. The RSSVM software, predictions, and analysis results on Shewanella genomes are available at http://ural.wustl.edu/resources.html#RSSVM

Symptoms of common mental disorder and cognitive associations with seropositivity among a cohort of people coming for testing for HIV/AIDS in Goa, India: a cross-sectional survey.

BACKGROUND: The majority of research on HIV/AIDS and mental health has been carried out among clinical populations: the time of onset of comorbid depression and the mechanisms for this are therefore unclear. Although there is evidence to suggest that asymptomatic people living with HIV/AIDS exhibit some cognitive deficits, the prevalence of poor cognitive functioning among people in low income settings at an early, pre-clinical stage has not yet been investigated. METHODS: We used a cross-sectional survey design to test the hypotheses that symptoms of Common Mental Disorder (CMD) and low scores on cognitive tests would be associated with seropositivity among participants coming for testing for HIV/AIDS. Participants were recruited at the time of coming for testing for HIV/AIDS; voluntary informed consent was sought for participation in research interviews and data linkage with HIV test results. Baseline questionnaires including sociodemographic variables and measures of mental health (PHQ-9, GAD-7, panic disorder questions, AUDIT and delayed word list learning and recall and animal naming test of verbal fluency) were administered by trained interviews. HIV status data was extracted from clinical records. RESULTS: CMD and scoring below the educational norm on the test of verbal fluency were associated with testing positive for HIV/AIDS in bivariate analysis (OR = 2.26, 1.31-3.93; OR = 1.77, 1.26-2.48, respectively). After controlling for the effects of confounders, the association between CMD and seropositivity was no longer statistically significant (AOR = 1.56, 0.86-2.85). After adjusting for the effects of confounders, the association between low scores on the test of verbal fluency and seropositivity was retained (AOR = 1.77, 1.27-2.48). CONCLUSIONS: Our findings provide tentative evidence to suggest that low cognitive test scores (and possibly depressive symptoms) may be associated with HIV status among people who have yet to receive their HIV test results. Impaired cognitive functioning and depression-like symptoms may be the result of the same underlying neurological damage. CMD and cognitive impairment may overlap to a greater extent than previously assumed. If replicated, this may have implications for the way in which we measure and treat CMD and cognitive functioning among people living with HIV/AIDS