A. Gupta

VISUALIZING GAUSSIAN-CHAIN LIKE STRUCTURAL MODELS OF HUMAN alpha-SYNUCLEIN IN MONOMERIC PRE-FIBRILLAR STATE: SOLUTION SAXS DATA AND MODELING ANALYSIS

The paper uses SAXS data and modeling to analyze the conformational ensemble of monomeric pre-fibrillar human alpha-synuclein, concluding a shifting equilibrium of curved models with low alpha-helical content.

E. coli cells advance into phase-separated (biofilm-simulating) extracellular polymeric substance containing DNA, HU, and lipopolysaccharide

The paper shows E. coli cells enter phase-separated extracellular polymeric substances containing HU, DNA, and LPS, with LPS modulating liquidity and structural integrity of biofilms.

Molecular patterns and mechanisms of tumorigenesis in HPV-associated and HPV-independent sinonasal squamous cell carcinoma

This study identifies molecular differences between HPV-associated and HPV-independent SNSCC, showing HPV drives tumorigenesis and suggesting YAP/TAZ and PI3K inhibition as therapeutic targets.

Hepatic lipopolysaccharide binding protein partially uncouples inflammation from fibrosis in MAFLD

This study shows that reducing hepatic LBP in mice limits inflammation but not fibrosis in MAFLD, suggesting inflammation may not be a primary driver of fibrosis.

Cancer Cachexia in STK11/LKB1-mutated NSCLC is Dependent on Tumor-secreted GDF15

This study shows that tumor-secreted GDF15 drives cachexia in STK11/LKB1-mutated NSCLC, and blocking GDF15 reduces cachexia symptoms in mice.

Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling

This study uses Visium HD spatial transcriptomics to map immune cell populations in colorectal cancer tumor microenvironments, identifying spatially distinct macrophage and T cell subpopulations.

Causal discovery in biodiversity-mediated social-ecological systems

This study develops a framework to discover causal links in social-ecological systems using literature and data, finding consistent negative links between global change and biodiversity-ecosystem function.

GSK-3alpha-BNIP3 axis promotes mitophagy in human cardiomyocytes under hypoxia

This study identifies a novel mechanism by which GSK-3 promotes mitophagy in human cardiomyocytes under hypoxia through BNIP3 upregulation and interaction.

Exploiting gene expression profiles of circulating extracellular vesicles for breast cancer detection

This study identifies five circulating extracellular vesicle RNAs that can diagnose breast cancer independently of subtypes and detect metastatic states.

Mixed evidence for species diversity affecting ecological forecasts in constant versus declining light

This study investigates how species diversity affects ecological forecasts under constant and declining light conditions, finding mixed evidence of an interactive effect on forecast accuracy.

APOBEC3 mutagenesis drives therapy resistance in breast cancer

This study identifies APOBEC3 mutagenesis as a common driver of therapy resistance in breast cancer, associated with poorer clinical outcomes.

Unveiling inverted D genes and D-D fusions in human antibody repertoires unlocks novel antibody diversity

The paper identifies inverted D genes and D-D fusions in human antibody repertoires, revealing new diversity and functionality through a comprehensive analysis of NGS data.

Natural compound screening predicts novel GSK-3 isoform-specific inhibitors

This study identifies two natural compounds, Psoralidin and Rosmarinic acid, as GSK-3 isoform-specific inhibitors with differential potency against GSK-3 and GSK-3β.

Evaluation of the gene fusion landscape in early onset sporadic rectal cancer reveals association with chromatin architecture and genome stability

The paper evaluates gene fusions in early-onset sporadic rectal cancer, linking them to chromatin architecture and genome stability.

A Deep Learning-Driven Sampling Technique to Explore the Phase Space of an RNA Stem-Loop

This paper adapts a deep learning-driven sampling technique for RNA stem-loop folding, showing it can efficiently explore phase space with lower computational cost than traditional methods.

TOTEM: A web TOol for Tissue-EnrichMent analysis on gene lists

TOTEM calculates tissue-specific gene enrichment from user gene lists using single-cell expression atlases, enabling analysis of gene function in specific tissues.

A random mutagenesis screen enriched for missense mutations in bacterial effector proteins.

The paper presents a yeast-based method to identify informative missense mutations in bacterial effector proteins and validates it using three effectors from Legionella pneumophila.

Pf bacteriophages hinder sputum antibiotic diffusion via electrostatic binding

This study shows Pf phages and sputum polymers reduce antibiotic diffusion through electrostatic binding and liquid crystal formation in chronic Pseudomonas aeruginosa infections.

Testing a Method for Quantifying Microplastic Content in Mytilus californianus

The paper tests a method to isolate and quantify microplastics in Mytilus californianus using digestion, sonication, and fluorescent microscopy.

Multimodal intrinsic activation of GPCRs in ultrastable plasma membrane nanodomains

This paper quantifies GPCR intrinsic activation at the plasma membrane, revealing spatial multimodality with most receptors showing negligible spontaneous activation.

Expression of Plasmodium Major Facilitator Superfamily Protein in Transporters-Delta Candida Identifies a Drug Transporter

The paper assesses the functional relevance of a Plasmodium MFS protein as a drug transporter using Candida glabrata, showing antifungal resistance and antimalarial properties.

Phylochemical mapping of natural products onto the plant tree of life using text mining and large language models.

This paper maps natural products onto the plant tree of life using text mining and large language models, revealing lineage-specific distributions and demonstrating automation potential.

Integrative analysis of nanopore direct RNA sequencing data reveals a role of PUS7-dependent pseudouridylation in regulation of m6A and m5C modifications

The paper introduces NanoPsiPy, a pipeline for detecting pseudouridylation sites using nanopore sequencing, and shows PUS7-dependent pseudouridylation affects m6A and m5C levels.

Serotonin Promotes Vesicular Association and Fusion by Modifying Lipid Bilayers

This study shows serotonin enhances vesicle association and fusion with lipid bilayers by altering their mechanical properties through water content changes.

Ser/Thr Phosphorylation of Mycobacterium tuberculosis Type II Rel TA module by Protein Kinase K interferes with toxin neutralization: A novel mode of TA regulation.

This study identifies Ser/Thr phosphorylation by PknK as a novel regulatory mechanism for Type II TA modules in M. tuberculosis, disrupting toxin-antitoxin interactions.

A Novel AI-Designed Antimicrobial Peptide Synergistically Potentiates Aminoglycosides against Colistin- and Carbapenem-Resistant Acinetobacter baumannii

This study designs AI-generated antimicrobial peptides that synergize with aminoglycosides to combat colistin- and carbapenem-resistant Acinetobacter baumannii, showing potent antibacterial activity and biofilm eradication.

Progression of herpesvirus infection remodels mitochondrial organization and metabolism

This study shows how herpesvirus infection alters mitochondrial structure and metabolism during infection progression.

The Role of Electron Spin, Chirality, and Charge Dynamics in Promoting thePersistence of Nascent Nucleic Acid-Peptide Complexes

This study shows how chirality and spin enhance protein-DNA complex stability through the chiral-induced spin selectivity effect.

Disrupted Cholesterol Biosynthesis and Hair Follicle Stem Cell Impairment in the Onset of Alopecia

This study investigates how disrupted cholesterol biosynthesis affects hair follicle stem cell function and hair follicle cycling in alopecia, finding that cholesterol inhibition leads to stem cell impairment and apoptosis.

The nutrient sensor CRTC & Sarcalumenin / Thinman represent a new pathway in cardiac hypertrophy

This study identifies CRTC and Sarcalumenin/TMN as a novel conserved pathway involved in cardiac hypertrophy through genetic and functional analyses in Drosophila and zebrafish.