Validated In Silico Model for Biofilm Formation in .

Using as the representative biofilm former, we report here the development of an in silico model built by simulating events that transform a free-living bacterial entity into self-encased multicellular biofilms. Published literature on ∼300 genes associated with pathways involved in biofilm formation was curated, static maps were created, and suitably interconnected with their respective metabolites using ordinary differential equations. Precise interplay of genetic networks that regulate the transitory switching of bacterial growth pattern in response to environmental changes and the resultant multicomponent synthesis of the extracellular matrix were appropriately represented.

Blood progenitor redox homeostasis through olfaction-derived systemic GABA in hematopoietic growth control in Drosophila.

The role of reactive oxygen species (ROS) in myeloid development is well established. However, its aberrant generation alters hematopoiesis. Thus, a comprehensive understanding of events controlling ROS homeostasis forms the central focus of this study.

Medicalisation and Ayurveda: the need for pluralism and balance in global health systems.

The current global economic and biomedical perspectives contribute content, strategy, and values to global health systems, like objectification and competition, which encourage the medicalisation of the system. Medicalisation overlooks our interdependence with other beings, the environment and biosphere. In contrast, ancient health traditions like Ayurveda, derived from Asian cultures, provide knowledge of the human being's composition of five basic states of nature that need to remain in constant equilibrium to ensure health (Svasthya).

Role of Cel5H protein surface amino acids in binding with clay minerals and measurements of its forces.

Our previous study on the binding activity between Cel5H and clay minerals showed highest binding efficiency among other cellulase enzymes cloned. Here, based on previous studies, we hypothesized that the positive amino acids on the surface of Cel5H protein may play an important role in binding to clay surfaces. To examine this, protein sequences of Bacillus licheniformis Cel5H (BlCel5H) and Paenibacillus polymyxa Cel5A (PpCel5A) were analyzed and then selected amino acids were mutated.

Neuronal and cardiac toxicity of pharmacological compounds identified through transcriptomic analysis of human pluripotent stem cell-derived embryoid bodies.

Concurrent with the '3R' principle, the embryonic stem cell test (EST) using mouse embryonic stem cells, developed in 2000, remains the solely accepted in vitro method for embryotoxicity testing. However, the scope and implementation of EST for embryotoxicity screening, compliant with regulatory requirements, are limited. This is due to its technical complexity, long testing period, labor-intensive methodology, and limited endpoint data, leading to misclassification of embryotoxic potential.

Azaindole Based Potentiator of Antibiotics against Gram-Negative Bacteria.

We discovered azaindole-based compounds with weak innate activity that exhibit substantial potentiation of antibacterial activities of different antibiotics, viz., rifampicin, erythromycin, solithromycin, and novobiocin in Gram-negative bacteria. In the presence of the azaindole derivatives, these antibiotics exhibited submicromolar minimum inhibitory concentrations (MICs) against , , , and .

Cargo-specific recruitment in clathrin- and dynamin-independent endocytosis.

Spatially controlled, cargo-specific endocytosis is essential for development, tissue homeostasis and cancer invasion. Unlike cargo-specific clathrin-mediated endocytosis, the clathrin- and dynamin-independent endocytic pathway (CLIC-GEEC, CG pathway) is considered a bulk internalization route for the fluid phase, glycosylated membrane proteins and lipids. While the core molecular players of CG-endocytosis have been recently defined, evidence of cargo-specific adaptors or selective uptake of proteins for the pathway are lacking.

Structure and function relationship of OqxB efflux pump from Klebsiella pneumoniae.

OqxB is an RND (Resistance-Nodulation-Division) efflux pump that has emerged as a factor contributing to the antibiotic resistance in Klebsiella pneumoniae. OqxB underwent horizontal gene transfer and is now seen in other Gram-negative bacterial pathogens including Escherichia coli, Enterobacter cloacae and Salmonella spp., further disseminating multi-drug resistance.

APOE4 Affects Basal and NMDAR-Mediated Protein Synthesis in Neurons by Perturbing Calcium Homeostasis.

Apolipoprotein E (APOE), one of the primary lipoproteins in the brain has three isoforms in humans, APOE2, APOE3, and APOE4. APOE4 is the most well-established risk factor increasing the predisposition for Alzheimer's disease (AD). The presence of the APOE4 allele alone is shown to cause synaptic defects in neurons and recent studies have identified multiple pathways directly influenced by APOE4.

DEELIG: A Deep Learning Approach to Predict Protein-Ligand Binding Affinity.

Protein-ligand binding prediction has extensive biological significance. Binding affinity helps in understanding the degree of protein-ligand interactions and is a useful measure in drug design. Protein-ligand docking using virtual screening and molecular dynamic simulations are required to predict the binding affinity of a ligand to its cognate receptor.

Mass Spectrometric Analysis of Cyclotides from Clitoria ternatea: Xxx-Pro Bond Fragmentation as Convenient Diagnostic of Pro Residue Positioning.

Cyclotides, a class of macrocyclic plant peptides, characterized by a cyclic backbone and three inter-locking disulfide bonds, may be divided into two major structural subfamilies, Möbius and Bracelet, based on the presence or absence of a specific proline residue. The present study describes the suite of cyclotides obtained from Clitoria ternatea, characterized by LC-MS and MS/MS techniques. Notable variations in product ion distributions were observed in cyclotides belonging to different structural subfamilies based on the number and positions of proline residues.

Disulfide-Rich Cyclic Peptides from Protect against β-Amyloid Toxicity and Oxidative Stress in Transgenic .

Neurotoxic aggregation of β-amyloid (Aβ) peptides is a hallmark of Alzheimer's disease and increased reactive oxygen species (ROS) is an associated process. In the present study, we report the neuroprotective effects of disulfide-rich, circular peptides from () (butterfly pea) on Aβ-induced toxicity in transgenic . Cyclotides (∼30 amino acids long) are a special class of cyclic cysteine knot peptides.

Total polyphenols and antihyperglycemic activity of aqueous fruits extract of Abelmoschus esculentus: Modeling and optimization of extraction conditions.

Aqueous fruits extract of Abelmoschus esculentus (L.) Moench (Malvaceae) has been used traditionally in several communities to alleviate elevated blood glucose levels. However, optimized extraction conditions have not been reported.

Photo-mediated optimized synthesis of silver nanoparticles using the extracts of outer shell fibre of L. fruit and detection of its antioxidant, cytotoxicity and antibacterial potential.

Presently, photo-mediated optimized synthesis of SNPs (CS-AgNPs) was carried out with the help of aqueous extracts of coconut () outer shell fibre. Green synthesis of CS-AgNPs was undertaken under laboratory light conditions and characterized by several standard techniques such as UV-visible spectrophotometer (UV-Vis), X-ray diffraction pattern (XRD), Fourier transform infrared (FT-IR), and scanning electron microscopy (SEM) images and energy dispersive spectroscopy (EDX). UV-Vis spectra displayed a surface plasmon resonance peak at 468 nm equivalent to CS-AgNPs, and the FT-IR spectra confirmed the association of biological molecules from the extract in the synthesis process.

Molecular and functional characterization of buffalo nasal epithelial odorant binding proteins and their structural insights by and biochemical approaches.

The olfactory system is capable of detecting and distinguishing thousands of environmental odorants that play a key role in reproduction, social behaviours including pheromones influenced classical events. Membrane secretary odorant binding proteins (OBPs) are soluble lipocalins, localized in the nasal membrane of mammals. They bind and carry odorants within the nasal epithelium to putative olfactory transmembrane receptors (ORs).

Asymmetric chromosome segregation and cell division in DNA damage-induced bacterial filaments.

Faithful propagation of life requires coordination of DNA replication and segregation with cell growth and division. In bacteria, this results in cell size homeostasis and periodicity in replication and division. The situation is perturbed under stress such as DNA damage, which induces filamentation as cell cycle progression is blocked to allow for repair.

A knowledge-driven protocol for prediction of proteins of interest with an emphasis on biosynthetic pathways.

This protocol describes a stepwise process to identify proteins of interest from a query proteome derived from NGS data. We implemented this protocol on transcriptome to identify proteins involved in secondary metabolite and vitamin biosynthesis and ion transport. This knowledge-driven protocol identifies proteins using an integrated approach involving sensitive sequence search and evolutionary relationships.

'Population self-reliance in health' and COVID-19: The need for a 4th tier in the health system.

The COVID-19 pandemic is straining health systems globally. The current international biomedical focus for disease control and policies fails to include the resource of a population's capacity to be self-reliant in its health care practices. The ancient wisdom of Ayurveda ('the knowledge of life') and Local Health Traditions (LHTs) in India understand that health is about , 'being rooted within'; a concept that includes the relationship and balance between the individual, their families, communities and the environment in creating and maintaining their own health.

Differential effect of Ayurvedic nootropics on C. elegans models of Parkinson's disease.

Background: Globally, there is increased incidence of Parkinson's Disease (PD), which is the second most common age-related neurodegenerative disease. The currently available PD-therapeutics provide only symptomatic relief. Thus, there is an urgent need to devise an effective and safe treatment strategy for PD.

Transcriptomic profiling of the medicinal plant Clitoria ternatea: identification of potential genes in cyclotide biosynthesis.

Clitoria ternatea a perennial climber of the Fabaceae family, is well known for its agricultural and medical applications. It is also currently the only known member of the Fabaceae family that produces abundant amounts of the ultra-stable macrocyclic peptides, cyclotides, across all tissues. Cyclotides are a class of gene-encoded, disulphide-rich, macrocyclic peptides (26-37 residues) acting as defensive metabolites in several plant species.

Controversial identities of medicinal plants in classical literature of Ayurveda.

India's medical heritage across its two streams of experiential knowledge viz. the classical (codified) and folk (oral) reveals an incredible range and depth of knowledge of medicinal plants. In the classical stream of Ayurveda, across the period from 1500 BCE to 1900 CE, there is information of more than 12,000 distinct Sanskrit plant names with overlaps across texts.

Star anise (Illicium verum): Chemical compounds, antiviral properties, and clinical relevance.

Medicinal herbs are one of the imperative sources of drugs all over the world. Star anise (Illicium verum), an evergreen, medium-sized tree with star-shaped fruit, is an important herb with wide distribution throughout southwestern parts of the Asian continent. Besides its use as spice in culinary, star anise is one of the vital ingredients of the Chinese medicinal herbs and is widely known for its antiviral effects.

Early fate of exogenous promoters in E. coli.

Gene gain by horizontal gene transfer is a major pathway of genome innovation in bacteria. The current view posits that acquired genes initially need to be silenced and that a bacterial chromatin protein, H-NS, plays a role in this silencing. However, we lack direct observation of the early fate of a horizontally transferred gene to prove this theory.

The basis for non-canonical ROK family function in the -acetylmannosamine kinase from the pathogen .

In environments where glucose is limited, some pathogenic bacteria metabolize host-derived sialic acid as a nutrient source. -Acetylmannosamine kinase (NanK) is the second enzyme of the bacterial sialic acid import and degradation pathway and adds phosphate to -acetylmannosamine using ATP to prime the molecule for future pathway reactions. Sequence alignments reveal that Gram-positive NanK enzymes belong to the Repressor, ORF, Kinase (ROK) family, but many lack the canonical Zn-binding motif expected for this function, and the sugar-binding EGH motif is altered to EGY.