In silico drug design of potential novel anti malarial agents

This thesis project incorporates the principles of rational and computer aided drug design in the quest for an improved anti-malarial agent. The target, a pathway for isoprenoid biosynthesis (the deoxy-D-xylulose-5-phosphate (DOXP) pathway) occurs in the parasite plastid – the apicoplast, and among the factors that make it an excellent target for an anti-malarial agent is its uniqueness from the pathway in the host, thus accounting for its specificity and low toxicity. A library of 18 potential anti malarial analogues/ ligands were designed and tested in silico against the receptor using molecular docking. The analogue L ο (omicron) - {3-[acetyl(hydroxy)amino]-1-hydroxypropyl} phosphonic acid was found to be the most promising anti malarial analogue and it may be worthwhile to subject the molecule to further analysis and comprehensive evaluation

Modelling Energy Consumption based on Resource Utilization

Power management is an expensive and important issue for large computational infrastructures such as datacenters, large clusters, and computational grids. However, measuring energy consumption of scalable systems may be impractical due to both cost and complexity for deploying power metering devices on a large number of machines. In this paper, we propose the use of information about resource utilization (e.g. processor, memory, disk operations, and network traffic) as proxies for estimating power consumption. We employ machine learning techniques to estimate power consumption using such information which are provided by common operating systems. Experiments with linear regression, regression tree, and multilayer perceptron on data from different hardware resulted into a model with 99.94\% of accuracy and 6.32 watts of error in the best case.Comment: Submitted to Journal of Supercomputing on 14th June, 201

Correlation between Disease Severity and the Intestinal Microbiome in Mycobacterium tuberculosis-Infected Rhesus Macaques

Why some but not all individuals infected with Mycobacterium tuberculosis develop disease is poorly understood. Previous studies have revealed an important influence of the microbiota on host resistance to infection with a number of different disease agents. Here, we investigated the possible role of the individual’s microbiome in impacting the outcome of M. tuberculosis infection in rhesus monkeys experimentally exposed to this important human pathogen. Although M. tuberculosis infection itself caused only minor alterations in the composition of the gut microbiota in these animals, we observed a significant correlation between an individual monkey’s microbiome and the severity of pulmonary disease. More importantly, this correlation between microbiota structure and disease outcome was evident even prior to infection. Taken together, our findings suggest that the composition of the microbiome may be a useful predictor of tuberculosis progression in infected individuals either directly because of the microbiome’s direct influence on host resistance or indirectly because of its association with other host factors that have this influence. This calls for exploration of the potential of the microbiota composition as a predictive biomarker through carefully designed prospective studies.The factors that determine host susceptibility to tuberculosis (TB) are poorly defined. The microbiota has been identified as a key influence on the nutritional, metabolic, and immunological status of the host, although its role in the pathogenesis of TB is currently unclear. Here, we investigated the influence of Mycobacterium tuberculosis exposure on the microbiome and conversely the impact of the intestinal microbiome on the outcome of M. tuberculosis exposure in a rhesus macaque model of tuberculosis. Animals were infected with different strains and doses of M. tuberculosis in three independent experiments, resulting in a range of disease severities. The compositions of the microbiotas were then assessed using a combination of 16S rRNA and metagenomic sequencing in fecal samples collected pre- and postinfection. Clustering analyses of the microbiota compositions revealed that alterations in the microbiome after M. tuberculosis infection were of much lower magnitude than the variability seen between individual monkeys. However, the microbiomes of macaques that developed severe disease were noticeably distinct from those of the animals with less severe disease as well as from each other. In particular, the bacterial families Lachnospiraceae and Clostridiaceae were enriched in monkeys that were more susceptible to infection, while numbers of Streptococcaceae were decreased. These findings in infected nonhuman primates reveal that certain baseline microbiome communities may strongly associate with the development of severe tuberculosis following infection and can be more important disease correlates than alterations to the microbiota following M. tuberculosis infection itself

Multi-omics: Differential expression of IFN-γ results in distinctive mechanistic features linking chronic inflammation, gut dysbiosis, and autoimmune diseases

Low grade, chronic inflammation is a critical risk factor for immunologic dysfunction including autoimmune diseases. However, the multiplicity of complex mechanisms and lack of relevant murine models limit our understanding of the precise role of chronic inflammation. To address these hurdles, we took advantage of multi-omics data and a unique murine model with a low but chronic expression of IFN-γ, generated by replacement of the AU-rich element (ARE) in the 3’ UTR region of IFN-γ mRNA with random nucleotides. Herein, we demonstrate that low but differential expression of IFN-γ in mice by homozygous or heterozygous ARE replacement triggers distinctive gut microbial alterations, of which alteration is female-biased with autoimmune-associated microbiota. Metabolomics data indicates that gut microbiota-dependent metabolites have more robust sex-differences than microbiome profiling, particularly those involved in fatty acid oxidation and nuclear receptor signaling. More importantly, homozygous ARE-Del mice have dramatic changes in tryptophan metabolism, bile acid and long-chain lipid metabolism, which interact with gut microbiota and nuclear receptor signaling similarly with sex-dependent metabolites. Consistent with these findings, nuclear receptor signaling, encompassing molecules such as PPARs, FXR, and LXRs, was detectable as a top canonical pathway in comparison of blood and tissue-specific gene expression between female homozygous vs heterozygous ARE-Del mice. Further analysis implies that dysregulated autophagy in macrophages is critical for breaking self-tolerance and gut homeostasis, while pathways interact with nuclear receptor signaling to regulate inflammatory responses. Overall, pathway-based integration of multi-omics data provides systemic and cellular insights about how chronic inflammation driven by IFN-γ results in the development of autoimmune diseases with specific etiopathological features

Defective IgA response to atypical intestinal commensals in IL-21 receptor deficiency reshapes immune cell homeostasis and mucosal immunity

Despite studies indicating the effects of IL-21 signaling in intestinal inflammation, its roles in intestinal homeostasis and infection are not yet clear. Here, we report potent effects of commensal microbiota on the phenotypic manifestations of IL-21 receptor deficiency. IL-21 is produced highly in the small intestine and appears to be critical for mounting an IgA response against atypical commensals such as segmented filamentous bacteria and Helicobacter, but not to the majority of commensals. In the presence of these atypical commensals, IL-21R-deficient mice exhibit reduced numbers of germinal center and IgA⁺ B cells and expression of activation-induced cytidine deaminase in Peyer’s patches as well as a significant decrease in small intestine IgA⁺ plasmablasts and plasma cells, leading to higher bacterial burdens and subsequent expansion of Th17 and Treg cells. These microbiota-mediated secondary changes in turn enhance T cell responses to an oral antigen and strikingly dampen Citrobacter rodentium-induced immunopathology, demonstrating a complex interplay between IL-21-mediated mucosal immunity, microbiota, and pathogens

Conventional Co-Housing Modulates Murine Gut Microbiota and Hematopoietic Gene Expression

Specific-pathogen-free (SPF) mice have improved hematopoietic characteristics relative to germ-free mice, however, it is not clear whether improvements in hematopoietic traits will continue when the level of microorganism exposure is further increased. We co-housed SPF C57BL/6 mice in a conventional facility (CVT) and found a significant increase in gut microbiota diversity along with increased levels of myeloid cells and T cells, especially effector memory T cells. Through single cell RNA sequencing of sorted KL (c-Kit+Lin−) cells, we imputed a decline in long-term hematopoietic stem cells and an increase in granulocyte-monocyte progenitors in CVT mice with up-regulation of genes associated with cell survival. Bone marrow transplantation through competitive repopulation revealed a significant increase in KSL (c-Kit+Sca-1+Lin−) cell reconstitution in recipients of CVT donor cells which occurred when donors were co-housed for both one and twelve months. However, there was minimal to no gain in mature blood cell engraftment in recipients of CVT donor cells relative to those receiving SPF donor cells. We conclude that co-housing SPF mice with mice born in a conventional facility increased gut microbiota diversity, augmented myeloid cell production and T cell activation, stimulated KSL cell reconstitution, and altered hematopoietic gene expression

Additional file 7: Figure S7. of Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy

Repeat experiment demonstrating reproducibility of key findings observed during treatment. See Additional file 6: Figure S6 for description with the following exceptions: C57BL/6J female mice were used and treatment was terminated at month 7 of Mtb infection, and mice were not monitored post cessation of therapy. n = 3–5. (PDF 657 kb

Additional file 13: Figure S13. of Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy

Unweighted and weighted UniFrac analysis of the sequences from the four groups described in Additional file 1: Figure S1. Each sphere represents a single animal and all animals from all time points were included in this analysis including the samples excluded in Figs. 1b, 2b, and 5b. The size of the sphere increases with respect to time. n = 4–5 for each time point except W20 time point of TB group where n = 3. (PDF 1103 kb

Additional file 6: Figure S6. of Longitudinal profiling reveals a persistent intestinal dysbiosis triggered by conventional anti-tuberculosis therapy

Repeat experiment demonstrating reproducibility of major differences observed during as well as post treatment. a Outline of experimental plan for longitudinal analysis of alterations in the microbiota induced by ATT in Mtb-infected C57BL/6J-CD45a(Ly5a) female mice. Two groups of mice (TB and TB + HRZ) were employed with each group consisting of four animals. Stool sample collection time points are indicated as colored circles (TB, red; TB + HRZ, orange). For the purpose of consistency, the time points shown refer to the month (M) of stool sample collection relative to the date of infection rather than treatment. In the case of the TB + HRZ group, treatment was ceased at M5 and post HRZ samples (yellow circles) were collected at M8. H, Isoniazid; R, Rifampin; Z, Pyrazinamide. b Community diversity in the TB and TB + HRZ animal groups for every stool sample collected was calculated from 16S sequences using Chao1 (left) and Shannon (right) indices. Error bars indicate maximum and minimum values. Significance tests were performed between the corresponding time points in the two groups. *p < 0.05, Wilcoxon-rank sum test. c Principal coordinate (PC) analysis of unweighted (left) and weighted (right) UniFrac distances of the sequences from the animal groups. Each sphere represents a single animal with the size of the sphere referring to the sample collection time point (early to late time points indicated as a gradient in the size of the spheres from small to large). d LEfSe analysis was performed to identify genera that are differentially abundant between the TB and TB + HRZ groups. Taxa significantly enriched in the TB or TB + HRZ groups depicted with red or orange bars, respectively. Data are filtered for p < 0.01 and LDA score >2. n = 4. (PDF 719 kb