Drug repositioning for idiopathic epilepsy using gene expression signature data.

Epilepsy is one of the most common neurological disorders, affecting millions of patients with a substantial economic and human burden. About 30-40% of epileptic patients remain un-treated after the therapeutic option. Genetic or idiopathic epilepsy count about 40% of total epilepsy patients, showing a maximum percentage for drug-resistant epilepsy.

Unveiling the microbial diversity and functional dynamics of Shiv Kund, Sohna hot spring, India through a shotgun metagenomics approach.

In this research, we examined the microbial diversity in Sohna hot spring, Haryana, India using shotgun metagenome sequencing based on the Illumina Hiseq 4000 sequencing technology. The raw sequence data from metagenomic paired-end libraries were analysed for taxonomic classification, diversity, and functional annotation using MG-RAST online server. The results showed the presence of total of 57 phyla, 931 genera, and 2068 species, predominantly occupied by Moraxellaceae (Gammaproteobacteria).

The shape of chromatin: insights from computational recognition of geometric patterns in Hi-C data.

The three-dimensional organization of chromatin plays a crucial role in gene regulation and cellular processes like deoxyribonucleic acid (DNA) transcription, replication and repair. Hi-C and related techniques provide detailed views of spatial proximities within the nucleus. However, data analysis is challenging partially due to a lack of well-defined, underpinning mathematical frameworks.

Neutrophil extracellular trap formation and gene programs distinguish TST/IGRA sensitization outcomes among Mycobacterium tuberculosis exposed persons living with HIV.

Persons living with HIV (PLWH) have an increased risk for tuberculosis (TB). After prolonged and repeated exposure, some PLWH never develop TB and show no evidence of immune sensitization to Mycobacterium tuberculosis (Mtb) as defined by persistently negative tuberculin skin tests (TST) and interferon gamma release assays (IGRA). This group has been identified and defined as HIV+ persistently TB, tuberculin and IGRA negative (HITTIN).

A biallelic multiple nucleotide length polymorphism explains functional causality at 5p15.33 prostate cancer risk locus.

To date, single-nucleotide polymorphisms (SNPs) have been the most intensively investigated class of polymorphisms in genome wide associations studies (GWAS), however, other classes such as insertion-deletion or multiple nucleotide length polymorphism (MNLPs) may also confer disease risk. Multiple reports have shown that the 5p15.33 prostate cancer risk region is a particularly strong expression quantitative trait locus (eQTL) for Iroquois Homeobox 4 (IRX4) transcripts.

Accurate microRNA annotation of animal genomes using trained covariance models of curated microRNA complements in MirMachine.

The annotation of microRNAs depends on the availability of transcriptomics data and expert knowledge. This has led to a gap between the availability of novel genomes and high-quality microRNA complements. Using >16,000 microRNAs from the manually curated microRNA gene database MirGeneDB, we generated trained covariance models for all conserved microRNA families.

Structural and functional characterization of 6-phosphogluconate dehydrogenase in (3D7) and identification of its potent inhibitors.

The malarial parasite predominantly causes severe malaria and deaths worldwide. Moreover, resistance developed by to frontline drugs in recent years has markedly increased malaria-related deaths in South Asian Countries. Ribulose 5-phosphate and NADPH synthesized by Pentose Phosphate Pathway (PPP) act as a direct precursor for nucleotide synthesis and survival during oxidative challenges in the intra-erythrocytic growth phase .

Identification of CXCR4 inhibitors as a key therapeutic small molecule in renal fibrosis.

The final stage of almost all chronic kidney diseases is renal fibrosis. Simple wounds or persistent inflammation can cause tissue inflammation, which, in the case of the kidney, results in scarring. Vascular sclerosis, tubulointerstitial fibrosis and glomerular fibrosis are all types of kidney fibrosis.

Challenges of Diagnosing Mendelian Susceptibility to Mycobacterial Diseases in South Africa.

Inborn errors of immunity (IEI) are genetic disorders with extensive clinical presentations. They can range from increased susceptibility to infections to significant immune dysregulation that results in immune impairment. While IEI cases are individually rare, they collectively represent a significant burden of disease, especially in developing countries such as South Africa, where infectious diseases like tuberculosis (TB) are endemic.

Transcriptomic Maps of Colorectal Liver Metastasis: Machine Learning of Gene Activation Patterns and Epigenetic Trajectories in Support of Precision Medicine.

The molecular mechanisms of the liver metastasis of colorectal cancer (CRLM) remain poorly understood. Here, we applied machine learning and bioinformatics trajectory inference to analyze a gene expression dataset of CRLM. We studied the co-regulation patterns at the gene level, the potential paths of tumor development, their functional context, and their prognostic relevance.

Comprehensive interrogation of gene lists from genome-scale cancer screens with oncoEnrichR.

Genome-scale screening experiments in cancer produce long lists of candidate genes that require extensive interpretation for biological insight and prioritization for follow-up studies. Interrogation of gene lists frequently represents a significant and time-consuming undertaking, in which experimental biologists typically combine results from a variety of bioinformatics resources in an attempt to portray and understand cancer relevance. As a means to simplify and strengthen the support for this endeavor, we have developed oncoEnrichR, a flexible bioinformatics tool that allows cancer researchers to comprehensively interrogate a given gene list along multiple facets of cancer relevance.

HiBrowser: an interactive and dynamic browser for synchronous Hi-C data visualization.

With the development of chromosome conformation capture technology, the genome-wide investigation of higher-order chromatin structure by using high-throughput chromatin conformation capture (Hi-C) technology is emerging as an important component for understanding the mechanism of gene regulation. Considering genetic and epigenetic differences are typically used to explore the pathological reasons on the chromosome and gene level, visualizing multi-omics data and performing an intuitive analysis by using an interactive browser become a powerful and welcomed way. In this paper, we develop an effective sequence and chromatin interaction data display browser called HiBrowser for visualizing and analyzing Hi-C data and their associated genetic and epigenetic annotations.

Development of a versatile LCM-Seq method for spatial transcriptomics of fluorescently tagged cholinergic neuron populations.

Single-cell transcriptomics are powerful tools to define neuronal cell types based on co-expressed gene clusters. Limited RNA input in these technologies necessarily compromises transcriptome coverage and accuracy of differential expression analysis. We propose that bulk RNA-Seq of neuronal pools defined by spatial position offers an alternative strategy to overcome these technical limitations.

Genome sequence of an indole-3-acetic acid and siderophores producing SARCC-3054 with the potential as a microbial inoculant for enhanced crop production.

The genome of strain SARCC-3054 was sequenced after being confirmed as a potential plant growth-promoting rhizobacteria in both and assays. The 6.3 MB genome has a GC content of 60.

The Effect of Three Complexes of Iodine with Amino Acids on Gene Expression of Model Antibiotic Resistant Microorganisms ATCC BAA-196 and ATCC BAA-39.

Unlabelled: 1.

Background: Iodine is a broad-spectrum antimicrobial disinfectant for topical application. Recent studies have shown promising results on the applicability of an iodine-containing complex, FS-1, against antibiotic-resistant pathogens.

Annotated dataset for deep-learning-based bacterial colony detection.

Quantifying bacteria per unit mass or volume is a common task in various fields of microbiology (e.g., infectiology and food hygiene).

Polycomb proteins translate histone methylation to chromatin folding.

Epigenetic repression often involves covalent histone modifications. Yet, how the presence of a histone mark translates into changes in chromatin structure that ultimately benefits the repression is largely unclear. Polycomb group proteins comprise a family of evolutionarily conserved epigenetic repressors.

Immunologic and vascular biomarkers of mortality in critical COVID-19 in a South African cohort.

Introduction: Biomarkers predicting mortality among critical Coronavirus disease 2019 (COVID-19) patients provide insight into the underlying pathophysiology of fatal disease and assist with triaging of cases in overburdened settings. However, data describing these biomarkers in Sub-Saharan African populations are sparse.

Methods: We collected serum samples and corresponding clinical data from 87 patients with critical COVID-19 on day 1 of admission to the intensive care unit (ICU) of a tertiary hospital in Cape Town, South Africa, during the second wave of the COVID-19 pandemic.

Subunit composition of mitochondrial dehydrogenase complexes in diplonemid flagellates.

In eukaryotes, pyruvate, a key metabolite produced by glycolysis, is converted by a tripartite mitochondrial pyruvate dehydrogenase (PDH) complex to acetyl-coenzyme A, which is fed into the tricarboxylic acid cycle. Two additional enzyme complexes with analogous composition catalyze similar oxidative decarboxylation reactions albeit using different substrates, the branched-chain ketoacid dehydrogenase (BCKDH) complex and the 2-oxoglutarate dehydrogenase (OGDH) complex. Comparative transcriptome analyses of diplonemids, one of the most abundant and diverse groups of oceanic protists, indicate that the conventional E1, E2, and E3 subunits of the PDH complex are lacking.

Experimental Analysis of Passenger Comfort with Variable Preloaded Rear Springs on a Low-Cylinder Motorcycle.

The present study contains an experimental analysis of the vibratory response in a low-cylinder engine motorcycle at varying suspension preloads. Three different speed bumps of varying heights were used to subject the motorcycle to different vibrations. The analysis was carried out in three domains: time, frequency, and time-frequency.