Himanshu Mishra’s Post

Quorum sensing is a communication system that enables bacteria to detect and respond to the density of their population. Through this process, bacteria release signaling molecules called autoinducers. When the concentration of these molecules reaches a threshold due to increased bacterial population, it triggers coordinated changes in gene expression across the bacterial community. This can lead to behaviors like biofilm formation, virulence factor production, and bioluminescence. One of the most fascinating aspects of quorum sensing is its role in bacterial pathogenicity. For example, the notorious Pseudomonas aeruginosa, an opportunistic pathogen, uses quorum sensing to regulate genes responsible for virulence and antibiotic resistance, making infections particularly difficult to treat. Understanding quorum sensing can provide new avenues for disrupting bacterial communication and developing novel antimicrobial strategies. Image credit - https://lnkd.in/eHuDgSMu #microbiology #medicalmicrobiology #health #funfacts #beatricesargin #quorumsensing

The authors have created the workflow ARGprofiler to process large amounts of raw sequencing reads for studying the composition, distribution, and function of antibiotic resistance gene (ARGs). ARGprofiler tackles the challenge of deciding which reference database to use by providing the PanRes database of 14 078 unique ARGs that combines several existing collections into one. Our pipeline is designed to not only produce abundance tables of genes and microbes but also to reconstruct the flanking regions of ARGs with ARGextender. https://lnkd.in/evsTd-DH

Decreased calcium permeability caused by biallelic TRPV5 mutation leads to autosomal recessive renal calcium-wasting hypercalciuria. #RareDisease #Genetics In this study, they explored the genetic cause of hypercalciuria driven by renal Ca2+ wasting in a family of consanguineous parents and three affected individuals. Whole-exome sequencing of the proband revealed a homozygous ultra-rare variant in TRPV5(NM_019841.7:c.1792G>A; p.(Val598Met)), which encodes for a renal Ca2+-selective ion channel. The variant segregates with the three individuals with hypercalciuria. Biochemical and functional analyses on the mutated TRPV5 channel demonstrated failure to increase plasma membrane Ca2+ permeability in HEK293 cells and increased proteasomal degradation. https://lnkd.in/dWmspEHS

'-- Next, a comparison of gene expression patterns between CR responding and non-responding strains revealed unique sets of genes and pathways and regulators of CR response. We found that responding wild strains uniquely adapted to increase mitochondrial translation coupled with oxidative phosphorylation and ATP biosynthesis under high glucose conditions. -- This data suggests that under high glucose conditions (2%), negatively responding strains might have decreased mitochondrial capacity for energy derivation by oxidative phosphorylation ... ...' Excellent - combine with ... ... https://lnkd.in/eberRK4V Excellent - combine with - '3-Hydroxybutyric acid exists in all living species, ranging from bacteria through yeast into humans' https://lnkd.in/eberRK4V

🧬 New insights into the VILLIN (VLN) gene family in cotton! Akash Deep and Dhananjay K. Pandey explore how VLN genes are involved in stress responses in Gossypium spp. in their genome-wide analysis. 🔊 This study reveals that VLN genes are crucial for regulating the actin cytoskeleton, contributing to plant responses to environmental stresses and development. 🗝 Key findings include the identification of 14 GhVLNs in Gossypium hirsutum and their significant role in stress, hormone, and light-response mechanisms. Read more here: https://lnkd.in/exQa8CRg #PlantBiology #CottonResearch #Genomics #StressResponse #MolecularBiology #AgriculturalResearch

Download our new app note! See how duet evoC allows for cfDNA fragment size profiles, copy number variation information, differentially methylated regions, variant-associated methylation, and achieves superior genetic and epigenetic accuracy throughout. Learn more: https://lnkd.in/g6NgFWKa #genetics #epigenetics #evoC

【Expression Pattern, Interaction Network, and Functional Analysis of the Arabidopsis Botrytis Susceptible1 Interactor】 Full article: https://lnkd.in/g_N6_T5w (Authored by Jianzhong Huang, et al., from Fuzhou Medical University, China.) #E3_ubiquitin_ligases play an important role in the ubiquitin-proteasome pathway, which is among the most important protein degradation pathway in eukaryotic organisms. Arabidopsis RING E3 ubiquitin ligase (referred to as RING E3 protein) has been reported to be involved in various processes, including the responses to biotic and abiotic stresses. Botrytis susceptible1 interactor (BOI) is an RING type E3 ligase, and mediates the ubiquitination of BOS1 (Botrytis susceptible1), a transcription factor participated in stress and pathogen responses. This study utilizes diversified methods to comprehensively analyze the #expression_pattern, #interaction_network and function of BOI gene. #Arabidopsis

Map of the genetic determinants of #heterogeneity in #Type2Diabetes, and their relation to #cardiometabolic traits. Contributions from Steno Diabetes Center Copenhagen and Novo Nordisk Foundation Center for Basic Metabolic Research and others to this collaborative #Nature study. https://lnkd.in/dZqYxiP9 #Omics #PrecisionMedicine #Genetics #DIabetes

Excited to share a recent paper I co-authored with Lilan Hoang and Mountasser Abdelkhalki, under the supervision of Professor Josemari Elizari. Our project focuses on the critical role of single nucleotide polymorphisms (SNPs) in understanding the genetic basis of human diseases. Tools like PolyPhen-2 and SIFT predict the effect of such mutations on protein function, helping interpret genetic mutation data in patients. However, their accuracy needs validation against a benchmark dataset, such as ClinVar, which classifies SNPs as benign or pathogenic. We compared these predictions to ClinVar, assessed the tools' performance and visualized it using ROC (Receiver Operating Characteristic) plots. Additionally, to conduct the biological analysis of SNP impact prediction, we first obtained results for two specific SNPs within the BRCA1 gene using the Variant Effect Predictor (VEP) tool. Following this, we evaluated the sequence conservation and structural implications of these variants through PolyPhen-2, providing a comprehensive assessment of their potential pathogenicity. #bioinformatics #biomedical #uva #vu #SNPs #machine_learning #genomics #polyphen #polyphen_2 #SIFT #VEP #systemsbiology

Transposable elements are DNA segments capable of moving between different locations1. They are widespread across all domains of life and have significantly affected genome diversity and evolution. Transposable elements can modulate gene expression, disseminate virulence and antibiotic resistance cassettes and are associated with numerous diseases. Several transposases rely on transposon-encoded regulators, including molecular matchmakers such as those found in Tn7, bacteriophage Mu and CRISPR RNA-guided elements, which belong to the ATPases associated with various cellular activities (AAA+) family of ATPases. The smallest and most abundant type of DNA transposons only contains proteins implicated in the transposition reaction. In bacteria, these are termed insertion sequences (ISs). The IS21 family is particularly widespread, has been found in clinically important multidrug-resistant strains and has shaped the evolution of human pathogens. Here you can see a cryoEM structure of the IstA-IstB strand transfer complex from Geobacillus stearothermophilus (PDB code: 8Q4D) Rendering by Francisco J. Enguita (@paco.enguita) made with #ProteinImager https://lnkd.in/d_Y7-67D #molecularart #transposon #transposase #complex #dna #mobile #cryoem