Recently Published Papers by Chs Staff/students in Researchgate-first

Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt. Olubisi Ashiru, Adriaan Willem Sturm and Prashini Moodley (co-authored) STRAINS OF MYCOBACTERIUM TUBERCULOSIS DIFFER IN AFFINITY FOR HUMAN OSTEOBLASTS AND ALVEOLAR CELLS IN VITRO ARTICLE in SPRINGERPLUS 5(163) · FEBRUARY 2016 with 6 READS DOI: 10.1186/s40064-016-1819-z Shrabanti Sarkar, Dlamini MG, Debapriya Bhattacharya Romona Govender (co-authored) MORE THAN SCALES AND TAPE MEASURES NEEDED TO ADDRESS OBESITY IN SOUTH AFRICA ARTICLE in OFFICIAL JOURNAL OF THE SOUTH AFRICAN ACADEMY OF FAMILY PRACTICE/PRIMARY CARE · FEBRUARY 2016 DOI: 10.1080/20786190.2016.1151643 R Ramlal ABSTRACT: Obesity is an emerging public health problem worldwide increasing from 857 million in 1980 to 2.1 billion by 2013. A study was done on a sample of 100 obese and overweight patients with a body mass index (BMI) above 25 kg/m2. The patients were asked to complete a questionnaire, which included socio-demographic data and perceptions regarding their weight.The patients were between the ages of 18 and 76 years old with 82% being female patients. The mean BMI for males was 41.7 kg/m2 (SD = 7.38112) and females 39.9 kg/m2 (SD = 7.90504). The results of this study confirm that 17% of overweight and obese patients saw themselves as having a normal weight and 97% felt that they were not unattractive. Of the sample, 96% affirmed that being obese was a health risk. The commonest reason cited for their obesity is by choice (70%).Although obese patients knew that obesity is a health risk, they have a positive image of obesity. The dramatic trend towards increasing obesity suggest that healthcare providers need to understand how people from different cultures view obesity. This will help them to promote key messages about the health risks associated with excess weight in a culturally sensitive way. Raziya Bobat (co-authored) LOW VITAMIN-D LEVELS COMBINED WITH PKP3-SIGIRR-TMEM16J HOST VARIANTS IS ASSOCIATED WITH TUBERCULOSIS AND DEATH IN HIV-INFECTED AND -EXPOSED INFANTS ARTICLE in PLOS ONE 11(2):E0148649 · FEBRUARY 2016 with 16 READS Impact Factor: 3.23 · DOI: 10.1371/journal.pone.0148649 ABSTRACT: Background: This study examined the associations of 25-hydroxyvitamin D and specific host genetic variants that affect vitamin D levels or its effects on immune function, with the risk of TB or mortality in children. Background: This study examined the associations of 25-hydroxyvitamin D and specific host genetic variants that affect vitamin D levels or its effects on immune function, with the risk of TB or mortality in children. Methods: A case-cohort sample of 466 South African infants enrolled in P1041 trial (NCT00080119) underwent 25-hydroxyvitamin D testing by chemiluminescent immunoassay. Single nucleotide polymorphisms (SNPs) that alter the effect of vitamin D [e.g. vitamin D receptor (VDR)], vitamin D levels [e.g. vitamin D binding protein (VDBP)], or toll like receptor (TLR) expression (SIGIRR including adjacent genes PKP3 and TMEM16J) were identified by realtime PCR. Outcomes were time to TB, and to the composite of TB or death by 192 weeks of follow-up. Effect modification between vitamin D status and SNPs for outcomes was assessed. Findings: Median age at 25-hydroxyvitamin D determination was 8 months; 11% were breastfed, 51% were HIV-infected and 26% had low 25-hydroxyvitamin D (<32ng/mL). By 192 weeks, 138 incident TB cases (43 definite/probable, and 95 possible) and 26 deaths occurred. Adjusting for HIV status and potential confounders, low 25-hydroxyvitamin D was associated with any TB (adjusted hazard ratio [aHR] 1.76, 95% CI 1.01-3.05; p = 0.046) and any TB or death (aHR 1.76, 95% CI 1.03-3.00; p = 0.038). Children with low 25-hydroxyvitamin D and TMEM 16J rs7111432-AA or PKP3 rs10902158-GG were at increased risk for probable/definite TB or death (aHR 8.12 and 4.83, p<0.05) and any TB or death (aHR 4.78 and 3.26, p<0.005) respectively; SNPs in VDBP, VDR, and vitamin D precursor or hydroxylation genes were not. There was significant interaction between low 25-hydroxyvitamin D and, TMEM 16J rs7111432-AA (p = 0.04) and PKP3 rs10902158-GG (p = 0.02) SNPs.