Predictive models for anti-tubercular molecules using machine learning on high-throughput biological screening datasets

<p>Abstract</p> <p>Background</p> <p>Tuberculosis is a contagious disease caused by <it>Mycobacterium tuberculosis </it>(Mtb), affecting more than two billion people around the globe and is one of the major causes of morbidity and mortality in the developing world. Recent reports suggest that Mtb has been developing resistance to the widely used anti-tubercular drugs resulting in the emergence and spread of multi drug-resistant (MDR) and extensively drug-resistant (XDR) strains throughout the world. In view of this global epidemic, there is an urgent need to facilitate fast and efficient lead identification methodologies. Target based screening of large compound libraries has been widely used as a fast and efficient approach for lead identification, but is restricted by the knowledge about the target structure. Whole organism screens on the other hand are target-agnostic and have been now widely employed as an alternative for lead identification but they are limited by the time and cost involved in running the screens for large compound libraries. This could be possibly be circumvented by using computational approaches to prioritize molecules for screening programmes.</p> <p>Results</p> <p>We utilized physicochemical properties of compounds to train four supervised classifiers (Naïve Bayes, Random Forest, J48 and SMO) on three publicly available bioassay screens of Mtb inhibitors and validated the robustness of the predictive models using various statistical measures.</p> <p>Conclusions</p> <p>This study is a comprehensive analysis of high-throughput bioassay data for anti-tubercular activity and the application of machine learning approaches to create target-agnostic predictive models for anti-tubercular agents.</p

Combinations of Plant Water-Stress and Neonicotinoids Can Lead to Secondary Outbreaks of Banks Grass Mite (Oligonychus Pratensis Banks)

Spider mites, a cosmopolitan pest of agricultural and landscape plants, thrive under hot and dry conditions, which could become more frequent and extreme due to climate change. Recent work has shown that neonicotinoids, a widely used class of systemic insecticides that have come under scrutiny for non-target effects, can elevate spider mite populations. Both water-stress and neonicotinoids independently alter plant resistance against herbivores. Yet, the interaction between these two factors on spider mites is unclear, particularly for Banks grass mite (Oligonychus pratensis; BGM). We conducted a field study to examine the effects of water-stress (optimal irrigation = 100% estimated evapotranspiration (ET) replacement, water stress = 25% of the water provided to optimally irrigated plants) and neonicotinoid seed treatments (control, clothianidin, thiamethoxam) on resident mite populations in corn (Zea mays, hybrid KSC7112). Our field study was followed by a manipulative field cage study and a parallel greenhouse study, where we tested the effects of water-stress and neonicotinoids on BGM and plant responses. We found that water-stress and clothianidin consistently increased BGM densities, while thiamethoxam-treated plants only had this effect when plants were mature. Water-stress and BGM herbivory had a greater effect on plant defenses than neonicotinoids alone, and the combination of BGM herbivory with the two abiotic factors increased the concentration of total soluble proteins. These results suggest that spider mite outbreaks by combinations of changes in plant defenses and protein concentration are triggered by water-stress and neonicotinoids, but the severity of the infestations varies depending on the insecticide active ingredient

Mitochondrial function as a determinant of life span

Average human life expectancy has progressively increased over many decades largely due to improvements in nutrition, vaccination, antimicrobial agents, and effective treatment/prevention of cardiovascular disease, cancer, etc. Maximal life span, in contrast, has changed very little. Caloric restriction (CR) increases maximal life span in many species, in concert with improvements in mitochondrial function. These effects have yet to be demonstrated in humans, and the duration and level of CR required to extend life span in animals is not realistic in humans. Physical activity (voluntary exercise) continues to hold much promise for increasing healthy life expectancy in humans, but remains to show any impact to increase maximal life span. However, longevity in Caenorhabditis elegans is related to activity levels, possibly through maintenance of mitochondrial function throughout the life span. In humans, we reported a progressive decline in muscle mitochondrial DNA abundance and protein synthesis with age. Other investigators also noted age-related declines in muscle mitochondrial function, which are related to peak oxygen uptake. Long-term aerobic exercise largely prevented age-related declines in mitochondrial DNA abundance and function in humans and may increase spontaneous activity levels in mice. Notwithstanding, the impact of aerobic exercise and activity levels on maximal life span is uncertain. It is proposed that age-related declines in mitochondrial content and function not only affect physical function, but also play a major role in regulation of life span. Regular aerobic exercise and prevention of adiposity by healthy diet may increase healthy life expectancy and prolong life span through beneficial effects at the level of the mitochondrion

LKB1 is an essential regulator of spermatozoa release during spermiation in the mammalian testis

LKB1 acts as a master upstream protein kinase regulating a number of kinases involved in diverse cellular functions. Recent studies have suggested a role for LKB1 in male fertility. Male mice with reduced total LKB1 expression, including the complete absence of the major splice variant in testis (LKB1(S)), are completely infertile. We sought to further characterise these mice and determine the mechanism underlying this infertility. This involved expression studies of LKB1 in developing germ cells, morphological analysis of mature spermatozoa and histological studies of both the testis and epididymis using light microscopy and transmission electron microscopy. We conclude that a defect in the release of mature spermatids from the seminiferous epithelium (spermiation) during spermatozoan development is a major cause of the infertility phenotype. We also present evidence that this is due, at least in part, to defects in the breakdown of the junctions, known as ectoplasmic specialisations, between the sertoli cells of the testis epithelium and the heads of the maturing spermatids. Overall this study uncovers a critical role for LKB1 in spermiation, a highly regulated, but poorly understood process vital for male fertility

Prevalence and sociodemographic determinants of tobacco use among adults in Pakistan: findings of a nationwide survey conducted in 2012.

BACKGROUND: Smoking is one of the leading causes of preventable mortality. The World Health Organization recommends that countries should monitor tobacco use regularly. In Pakistan, the last national study on smoking in the general population was conducted in 2002 to 2003. METHODS: We conducted a cross-sectional survey of a nationally representative sample of men and women living in rural and urban areas of four main provinces of Pakistan from March through April 2012. Face-to-face in-house interviews were undertaken using a pre-tested structured questionnaire that asked about smoking and other forms of tobacco use. Multistage stratified random area probability sampling was used. To determine the national prevalence of tobacco use, the sample was weighted to correspond to rural-urban population proportions in each of the four provinces as in the 1998 census conducted by Pakistan's Population Census Organization. Associations between sociodemographic variables and tobacco use were investigated using multivariable robust regression. RESULTS: Out of 2,644 respondents (1,354 men and 1,290 women), 354 men and 4 women reported being current cigarette smokers. The weighted prevalence of current cigarette smoking was 15.2% (95% confidence interval [CI]; 11.2, 19.3) overall, 26.6% (95% CI: 19.1, 34.1) among males, and 0.4% (95% CI: -0.2, 1.0) among females. Among females, 1.8% (95% CI: 0.4, 3.1) used any smoked tobacco and 4.6% (95% CI: 1.8, 7.4) used any smokeless tobacco daily or on some days of the week. Among males, odds of current cigarette smoking decreased with increasing level of education (OR = 0.75; 95% CI: 0.68, 0.84) and increased with having a father who used tobacco (OR = 2.11; 95% CI: 1.39, 3.22) after adjusting for other sociodemographic characteristics. Lower household income was associated with current cigarette smoking among rural males only (odds ratio [OR] = 0.67; 95% CI: 0.48, 0.92 per category increase in monthly household income). CONCLUSION: A large proportion of males smoked cigarettes. Cigarette use was negligible among females, but they used other forms of tobacco. Low education was a determinant of cigarette smoking among males irrespective of socioeconomic status and area of residence. Tobacco control campaigns should target uneducated and rural poor men and monitor all forms of tobacco used by the population