Molecular characterization and phylogenetic analysis of babA gene of Helicobacter pylori isolated from Indian patients with gastrointestinal diseases.

Introduction: Outer membrane protein (OMP) of Helicobacter pylori (H. pylori) i.e.

Primary antibiotic resistance of Helicobacter pylori in India over the past two decades: A systematic review.

Background: Helicobacter pylori antibiotic resistance has undergone vast changes in the last two decades. No systematic review has been done on the prevalence of antibiotic resistant H. pylori in India in the last two decades.

Network analysis of transcriptomic data uncovers molecular signatures and the interplay of mRNAs, lncRNAs, and miRNAs in human embryonic stem cells.

Growing evidence has shown that besides the protein coding genes, the non-coding elements of the genome are indispensable for maintaining the property of self-renewal in human embryonic stem cells and in cell fate determination. However, the regulatory mechanisms and the landscape of interactions between the coding and non-coding elements is poorly understood. In this work, we used weighted gene co-expression network analysis (WGCNA) on transcriptomic data retrieved from RNA-seq and small RNA-seq experiments and reconstructed the core human pluripotency network (called PluriMLMiNet) consisting of 375 mRNA, 57 lncRNA and 207 miRNAs.

Assigning new supergroups V and W to the diversity.

are endosymbiotic and alphaproteobacteria that belong to the order Rickettsiales. They are known to infect half of the insect population and cause host manipulation, and have been categorized into 19 monophyletic lineages called supergroups. Recently, two strains, wCfeJ and wCfeT were isolated from cat fleas (Ctenocephalides felis), but their supergroup relationships were not assigned.

Inference of Dynamic Growth Regulatory Network in Cancer Using High-Throughput Transcriptomic Data.

Growth is regulated by gene expression variation at different developmental stages of biological processes such as cell differentiation, disease progression, or drug response. In cancer, a stage-specific regulatory model constructed to infer the dynamic expression changes in genes contributing to tissue growth or proliferation is referred as a dynamic growth regulatory network (dGRN). Over the past decade, gene expression data has been widely used for reconstructing dGRN by computing correlations between the differentially expressed genes (DEGs).

Recombination in sarbecovirus lineage and mutations/insertions in spike protein are linked to the emergence and adaptation of SARS-CoV-2.

The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Wuhan city, China in December 2019 and thereafter its spillover across the world has created a global pandemic and public health crisis. Right after, there has been intense interest in understanding how the SARS-CoV-2 originated and evolved. This paper also aims to shed light on the origin and evolution of SARS-CoV- 2.

Design, synthesis and antimicrobial activity of novel quinoline derivatives: an and study.

A series of new quinoline derivatives has been designed, synthesized and evaluated as antibacterial and antifungal agents functioning as peptide deformylase enzyme (PDF) inhibitors and fungal cell wall disruptors on the basis of computational and experimental methods. The molecular docking and ADMET assessment aided in the synthesis of quinoline derivatives starting from 6-amino-4-methyl-1-quinoline-2-one substituted with different types of sulfonyl/benzoyl/propargyl moieties. These newly synthesized compounds were evaluated for their antibacterial and antifungal activity.

(2-Cyclohexyl-1-methylpropyl) cyclohexane isolated from garlic extract exhibits antidepressant-like activity: extraction, docking, drug-like properties, molecular dynamics simulations and MM/GBSA studies.

Depressive disorders are among most common psychiatric diseases and second most common form of psychiatric illness globally. Commonly available chemical drugs used for treatment of nervous system disorders exert undesirable effects. Therefore, there is a growing need towards exploring novel antidepressants of herbal origin.

Analysis of Functional Status of Genetically Diverse OipA Gene in Indian Patients with Distinct Gastrointestinal Disease.

Helicobacter pylori (H. pylori,) a genetically diversified bacteria which colonizes human gastric epithelium, is now established causative agent for gastric cancer worldwide. Outer membrane protein (OMP)-coding genes of H.

The LCNetWork: An electronic representation of the mRNA-lncRNA-miRNA regulatory network underlying mechanisms of non-small cell lung cancer in humans, and its explorative analysis.

Advancement in genomics technologies have made it possible to identify the genes and their interaction/regulation involved in NSCLC, but the interaction information are scattered over the literature. Thus, there is a need of assembling all the available interaction/regulation information in a single platform which will provide a complete view of NSCLC mechanisms. Further, analysis of the mechanisms underlying NSCLC in humans would benefit substantially from easy access to an electronic network.

Comparative molecular dynamics simulation analysis of G20 and C92 mutations in c-di-GMP I riboswitch and the wild type with docked c-di-GMP ligand.

Riboswitch, a bacterial regulatory RNA consists of an aptamer (specific ligand binding unit) and an expression platform (gene expression modulation unit), which act as a potential drug target as it regulates critical genes. Therefore, it is of interest to glean information on the binding of c-di-GMP ligand to mutated conserved G20 and C92 residues of cyclic diguanosine monophosphate I (c-di-GMP I) riboswitch using molecular dynamics simulation. The result shows that the binding energy of wild/native type riboswitch-ligand complex (3IRW) is lower than the mutant complexes suggesting that the binding affinity for c-di-GMP ligand decreases in case of mutant riboswitches.

Common miRNAs, candidate genes and their interaction network across four subtypes of epithelial ovarian cancer.

Epithelial ovarian cancer (EOC) is categorized into four major histological subtypes such as clear cell carcinoma (CCC), endometrioid carcinoma (EC), mucinous carcinoma (MC), and serous carcinoma (SC). Heterogeneity of the EOC leads to different clinical outcomes of the disease, although all the subtypes are originated from the same layer of tissue. Therefore, it is of interest to identify the common candidate genes, miRNA and their interaction network in four the subtypes of EOC.

In silico design, synthesis and anti-HIV activity of quinoline derivatives as non-nucleoside reverse transcriptase inhibitors (NNRTIs).

A series of quinoline derivatives has been designed, synthesized and screened for their anti-HIV properties. The drug-like properties of compounds were evaluated first and then molecular docking using DS v20.1.

Transcriptomic Analysis of Human Naïve and Primed Pluripotent Stem Cells.

Over the last decade, RNA-Sequencing (RNA-Seq) has revolutionized the field of transcriptomics due to its sheer advantage over previous technologies for studying gene expression. Even the domain of stem cell bioinformatics has benefited from these advancements. It has helped look deeper into how the process of pluripotency is maintained by stem cells and how it may be exploited for application in regenerative medicine.

The Synergistic Role of Tip α, Nucleolin and Ras in Helicobacter pylori Infection Regulates the Cell Fate Towards Inflammation or Apoptosis.

Infection with Helicobacter pylori (H. pylori) leads to a fork in the road situation where it is critical and complex to judge the fate of the cell. We propose for the first time an in silico representation of a protein level network model that can unfold the mystery behind the cell fate decision between inflammation or cell proliferation or cell death.

Design, synthesis, and molecular dynamics simulation studies of quinoline derivatives as protease inhibitors against SARS-CoV-2.

A new series of quinoline derivatives has been designed and synthesized as probable protease inhibitors (PIs) against severe acute respiratory syndrome coronavirus 2. studies using DS v20.1.

Decoding molecular markers and transcriptional circuitry of naive and primed states of human pluripotency.

Pluripotent stem cells (PSCs) have been observed to occur in two distinct states - naive and primed. Both naive and primed state PSCs can give rise to tissues of all the three germ layers in vitro but differ in their potential to generate germline chimera in vivo. Understanding the molecular mechanisms that govern these two states of pluripotency in human can open a plethora of opportunities for studying early embryonic development and in biomedical applications.

RNA-Seq analysis reveals pluripotency-associated genes and their interaction networks in human embryonic stem cells.

Insight into the key genes of pluripotency in human and their interrelationships is necessary for understanding the underlying mechanism of pluripotency and hence their successful application in regenerative medicine. The recent advances in transcriptomics technologies have created new opportunities to decipher the genes involved in pluripotency, genetic network that governs the unique properties of embryonic stem cells and lineage differentiation mechanisms in a deeper scale. There are a large number of experimental studies on human embryonic stem cells (hESCs) being routinely conducted for unfolding the underlying biology of embryogenesis and their clinical prospects.

Geographically distinct North-East Indian strains are highly sensitive to clarithromycin but are levofloxacin resistant.

Purpose: Helicobacter pylori causes various gastro-intestinal diseases. Antibiotic resistance to commonly used antibiotics for the treatment of H. pylori infection is the major cause for treatment failure.

Causes, consequences and solutions of phylogenetic incongruence.

Phylogenetic analysis is used to recover the evolutionary history of species, genes or proteins. Understanding phylogenetic relationships between organisms is a prerequisite of almost any evolutionary study, as contemporary species all share a common history through their ancestry. Moreover, it is important because of its wide applications that include understanding genome organization, epidemiological investigations, predicting protein functions, and deciding the genes to be analyzed in comparative studies.

Derivation of an interaction/regulation network describing pluripotency in human.

Identification of the key genes/proteins of pluripotency and their interrelationships is an important step in understanding the induction and maintenance of pluripotency. Experimental approaches have accumulated large amounts of interaction/regulation data in mouse. We investigate how far such information can be transferred to human, the species of maximum interest, for which experimental data are much more limited.

The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications.

Background: Analysis of the mechanisms underlying pluripotency and reprogramming would benefit substantially from easy access to an electronic network of genes, proteins and mechanisms. Moreover, interpreting gene expression data needs to move beyond just the identification of the up-/downregulation of key genes and of overrepresented processes and pathways, towards clarifying the essential effects of the experiment in molecular terms.

Methodology/principal Findings: We have assembled a network of 574 molecular interactions, stimulations and inhibitions, based on a collection of research data from 177 publications until June 2010, involving 274 mouse genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its plugins.

ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work.

Background: Experimentalists are overwhelmed by high-throughput data and there is an urgent need to condense information into simple hypotheses. For example, large amounts of microarray and deep sequencing data are becoming available, describing a variety of experimental conditions such as gene knockout and knockdown, the effect of interventions, and the differences between tissues and cell lines.

Results: To address this challenge, we developed a method, implemented as a Cytoscape plugin called ExprEssence.

ML or NJ-MCL? A comparison between two robust phylogenetic methods.

Large-scale gene sequencing gives an opportunity to reconstruct the tree of life and histories of multigene species phylogenies from very large datasets. A primary need for reconstructing large-scale phylogenies is a computationally efficient and accurate method. Current efforts to achieve such a goal include NJ-MCL2 described by Tamura et al.

The effect of heterotachy in multigene analysis using the neighbor joining method.

Sequence alignments of multiple genes are routinely used to infer phylogenetic relationships among species. The analysis of their concatenation is more likely to give correct results under an assumption of homotachy (i.e.