R. Das

Phage genome architecture and GC content: Structural genes and where to find them

The paper analyzes 45 phage genomes to show a relationship between structural genes, GC content, and genome size, suggesting environmental adaptation influences phage evolution.

Exploring Probiotic Potential: A Comparative Genomics and In Silico Assessment of Genes within the Genus Geobacillus

This study assesses the probiotic potential of Geobacillus by analyzing its genomic features, revealing safety traits and absence of virulence factors.

Novel 4,400-year-old ancestral component in a tribe speaking a Dravidian language

This study identifies a fourth ancestral component in Dravidian-speaking tribes, suggesting a Proto-Dravidian ancestry originating around 4,400 years ago, distinct from other known sources.

Structural analysis of genetic variants of the human tumor suppressor Palb2 coiled-coil domain

The paper determines the structure of the human Palb2 coiled-coil domain and shows how mutations affect its function in homologous recombination.

Ribonanza: deep learning of RNA structure through dual crowdsourcing

The paper introduces RibonanzaNet, a deep learning model trained on crowdsourced RNA chemical mapping data to predict RNA structure and related properties.

E41K Mutation Activates Brutons Tyrosine Kinase by Stabilizing an Inositol Hexakisphosphate Dependent Invisible Dimer

The paper investigates the E41K mutation in BTK, showing it stabilizes an IP6-dependent PH-TH dimer, activating BTK independently of PIP3 binding.

Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses

This paper determines the 3D structures of SL5 RNA domains from six coronaviruses, revealing conserved tertiary features with implications for protein-binding and antiviral targets.

Fusobacterium nucleatum present in the saliva of oral cancer subjects can activate niche defense of oral squamous cell carcinoma

The paper investigates how Fusobacterium nucleatum in saliva activates a tumor stemness defense phenotype in oral cancer stem cells, contributing to cancer progression and relapse.

Metallo-protease Peptidase M84 from Bacillus altitudinis induces ROS dependent apoptosis in ovarian cancer cells by targeting PAR-1

This paper identifies Peptidase M84 from Bacillus altitudinis as an apoptosis inducer in ovarian cancer cells via PAR-1 mediated oxidative stress, showing anti-tumor effects in vitro and in vivo.

Evaluation of morpho-physiological and yield-associated traits of rice (Oryza sativa L.) landraces combined with marker-assisted selection under high temperature stress and elevated atmospheric CO2 levels

This study evaluates NEI rice landraces under high temperature and elevated CO2 stress, identifying two landraces with better performance and genetic variation for breeding stress-tolerant rice.

Enhancing gene transfer to renal tubules and podocytes by context-dependent selection of AAV capsids

This study identifies AAV capsids that enhance gene delivery to renal tubules and podocytes, showing context-dependent effectiveness based on delivery route and disease state.

Molecular basis of VEGFR1 autoinhibition at the plasma membrane

This study identifies a mechanism by which VEGFR1 remains constitutively inactive through juxtamembrane inhibition and phosphatase activity, explaining its differential regulation compared to VEGFR2.

Insights into the genomic features, lifestyle and therapeutic potential of B1 sub-cluster mycobacteriophages

This study functionally annotates and experimentally characterizes B1 sub-cluster mycobacteriophages, revealing their genomic features, lifestyle, and therapeutic potential against drug-resistant M. smegmatis.

Bacterial deamidases modulate ubiquitin structure and dynamics to dysregulate ubiquitin signaling

This study shows that deamidation of ubiquitin by bacterial enzymes creates salt bridges that disrupt its structure and dynamics, impairing ubiquitin signaling.

Assessment of three-dimensional RNA structure prediction in CASP15

This paper evaluates RNA 3D structure prediction methods in CASP15, finding that non-deep learning groups outperformed deep learning models, with challenges in fine details and model ranking.

Whole Body PBPK Model of Nasal Naloxone Administration to Measure Repeat Dosing Requirements During Fentanyl Overdose

The paper develops a whole-body PBPK model to determine repeat naloxone dosing requirements during fentanyl overdose based on opiate amount and respiratory response.

Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis

The paper uses simulations to show that cell size polydispersity and deformability explain the viscosity plateau in non-confluent zebrafish tissue beyond a critical packing fraction.

RNA structure landscape of S. cerevisiae introns

The paper characterizes RNA structures in S. cerevisiae introns using DMS probing and identifies new structural elements that influence intron retention.

Plasticity of the proteasome-targeting signal Fat10 enhances substrate degradation

This study shows that the structural plasticity of the Fat10 proteasome-targeting tag enhances substrate degradation by creating partially unstructured regions and reducing resistance to mechanical unfolding.

Further antibody escape by Omicron BA.4 and BA.5 from vaccine and BA.1 serum

This study shows that BA.4 and BA.5 variants are more resistant to neutralization by vaccine and BA.1 immune sera compared to BA.1 and BA.2.

RNase H1 exists as phase-separated assemblies in association with elongating RNA Polymerase II during transcription

The paper shows RNase H1 forms phase-separated assemblies with RNA Polymerase II during transcription, regulating R-loop levels through liquid-liquid phase separation.

The Biomechanics of the Locust Ovipositor Valves: a Unique Digging Apparatus

This paper studies the biomechanics of locust ovipositor valves, showing that mature females have stiffer valves that resist mechanical failure and are anisotropic in stiffness.

Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers

The paper investigates how mechanical feedback in growing tissue monolayers leads to dynamical memory effects through cell division and intercellular interactions.

An evolutionary divergent thermodynamic brake in ZAP-70 finetunes the kinetic proofreading in T cell

This study identifies a thermodynamic brake in ZAP-70 that regulates T cell signaling kinetics and ligand selectivity, with evolutionary implications for immune system divergence.

Cyclic constrained immunoreactive peptides from crucial P. falciparum proteins: potential implications in malaria diagnostics

The paper identifies three cyclic constrained peptides from P. falciparum proteins that show immunoreactivity and diagnostic potential in field-collected samples.

Identification and targeting of a pan-genotypic influenza A virus RNA structure that mediates packaging and disease.

This paper identifies a conserved RNA structure in influenza A virus that mediates packaging and disease, showing that targeting it inhibits virus production and reduces disease severity.

Microbial byproducts determine reproductive fitness of free-living and parasitic nematodes

The paper identifies microbial byproducts that influence reproductive fitness in both free-living and parasitic nematodes using C. elegans and Trichuris muris.

A Combined Spectroscopic and Molecular Modeling Study on Structure-Function-Dynamics under Chemical Modification: Alpha-Chymotrypsin with Formalin Preservative

This study examines how formalin modifies alpha-chymotrypsin's structure and function, showing reduced catalytic activity and altered substrate binding due to cross-linking.

Comparative in vitro antioxidant and antibacterial activities of leaf extract fractions of Crimson bottlebrush, Callistemon citrinus (Curtis.) Skeels

This study compares the antioxidant and antibacterial activities of different extract fractions from Callistemon citrinus leaves, finding the aqueous fraction has highest antioxidant activity while petroleum ether has highest antibacterial activity.

Functional characterization of a DNA-dependent AAA ATPase in SimranZ1, a F cluster mycobacteriophage

This study functionally characterizes Gp65, a DNA-dependent AAA ATPase from mycobacteriophage SimranZ1, showing its role in DNA repair/maintenance mechanisms.