Evaluative Profiling of Arsenic Sensing and Regulatory Systems in the Human Microbiome Project Genomes

The influence of environmental chemicals including arsenic, a type 1 carcinogen, on the composition and function of the human-associated microbiota is of significance in human health and disease. We have developed a suite of bioinformatics and visual analytics methods to evaluate the availability (presence or absence) and abundance of functional annotations in a microbial genome for seven Pfam protein families: As(III)-responsive transcriptional repressor (ArsR), anion-transporting ATPase (ArsA), arsenical pump membrane protein (ArsB), arsenate reductase (ArsC), arsenical resistance operon transacting repressor (ArsD), water/glycerol transport protein (aquaporins), and universal stress protein (USP). These genes encode function for sensing and/or regulating arsenic content in the bacterial cell. The evaluative profiling strategy was applied to 3,274 genomes from which 62 genomes from 18 genera were identified to contain genes for the seven protein families. Our list included 12 genomes in the Human Microbiome Project (HMP) from the following genera: Citrobacter, Escherichia, Lactobacillus, Providencia, Rhodococcus , and Staphylococcus. Gene neighborhood analysis of the arsenic resistance operon in the genome of Bacteroides thetaiotaomicron VPI-5482, a human gut symbiont, revealed the adjacent arrangement of genes for arsenite binding/transfer (ArsD) and cytochrome c biosynthesis (DsbD_2). Visual analytics facilitated evaluation of protein annotations in 367 genomes in the phylum Bacteroidetes identified multiple genomes in which genes for ArsD and DsbD_2 were adjacently arranged. Cytochrome c , produced by a posttranslational process, consists of heme-containing proteins important for cellular energy production and signaling. Further research is desired to elucidate arsenic resistance and arsenic-mediated cellular energy production in the Bacteroidetes

Public knowledge and beliefs about depression among urban and rural Malays in Malaysia

BACKGROUND: This study examined knowledge and beliefs about depression among Malaysian Malays varying in socioeconomic status. METHODS: A total of 153 urban and 189 rural participants completed a questionnaire in which they had to identify two cases of depression and rate a series of items about the causes and best treatments for depression. RESULTS: Results showed that urban participants were more likely to use psychiatric labels ('depression') for the two vignettes, whereas rural participants tended to use more generic terms ('emotional stress'). CONCLUSION: Principal components analysis (PCA) showed that beliefs about the causes of depression factored into five components, of which stressful life events was most strongly endorsed by both groups. PCA of treatment items revealed four stable components, of which religious factors were most strongly endorsed. There were also a number of significant between-group differences in the endorsement of these factors (eta(p) (2) = .03-.11), with rural participants generally rating supernatural and religious factors more strongly than urban Malays. These results are discussed in relation to mental health literacy programmes in Malaysia

First Nigerian Bioinformatics Conference (FNBC): Towards a dynamic bioinformatics community

The human genome project, which was completed in 2003, ushered in a new era of scientific applications in medicine and bioscience, and also enhanced the generation of high-throughput data which required laboratory and computational analytical approaches in fields known as genomics and bioinformatics respectively. Internationally, specific advances have been achieved which involved the formation and emergence of strong scientific communities to sustain these technological advancements. On the African continent and regionally, the Human Hereditary and Health in Africa (H3Africa), Biosciences eastern and central Africa - International Livestock Research Institute (BecA - ILRI) Hub, and the Alliance for Accelerated Crop Improvements in Africa (ACACIA), are helping to push some of these advances in human health, biosciences, and agriculture respectively. In Nigeria, we believe that significant advances have also been made by various groups since the human genome project was completed. However, a scientific gathering platform to sustainably enable scientists discuss and update these progresses remained elusive. In this article, we report the First Nigerian Bioinformatics Conference (FNBC) hosted by the Nigerian Bioinformatics and Genomics Network (NBGN) in collaboration with the Nigerian Institute of Medical Research (NIMR). The conference was held from 24th - 26th June, 2019, with the theme: “Bioinformatics in the era of genomics in Africa”. Quantitatively, the conference recorded 195 online registered participants, and up to 186 actual participants; comprising of 8 keynote speakers, 6 invited speakers, 25 oral presenters, 83 poster presenters, and up to 73 non-presenting participants. Attendees with national (up to 179) and international (up to 16) affiliations also participated at the conference. Qualitatively, broad scope of bioinformatics, genomics and molecular biology presentations in biomedicine, health, and biosciences were featured at the conference. We discuss the conference structure and activities, lessons learned, and way forward for future bioinformatics conferences in Nigeria. We further discuss the relevance of the conference which presents an increased visibility for the Nigerian bioinformatics community, positions Nigeria as a dynamic community player within the African bioinformatics space, and provides a platform for national impact through the application and implementation of the benefits of bioinformatics