P. Kumar

SIC50: Determination of IC50 by an optimized Sobel operator and a vision transformer

SIC50 uses a vision transformer and Sobel operator to determine IC50 from phase-contrast images, validated with four drugs and 1536-well plates.

Molecular basis for antiviral activity of pediatric neutralizing antibodies targeting SARS-CoV-2 Spike receptor binding domain

This study identifies two potent neutralizing antibodies, EH3 and EH8, from a pediatric patient that cross-neutralize SARS-CoV-2 variants and provide in vivo protection against the Delta VOC.

Melanoma cells appropriate pericyte:endothelial cell crosstalk during perivascular invasion in the brain

This study identifies how melanoma cells use pericyte:endothelial cell signaling during brain invasion, showing that Sox9hi mesenchymal cells use Snail1-dependent mechanisms while Sox10hi cells form clusters.

A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome

The paper updates the M. tuberculosis H37Rv reference genome using Bact-Builder, revealing 6.4 kb of new sequence and ten new regions in widely used strains.

Development of amidase-dependent pyrazinoic acid prodrugs with activity against pyrazinamide resistant Mycobacterium tuberculosis

This paper develops amidase-dependent pyrazinoic acid prodrugs that bypass PncA activation, showing efficacy against PZA-resistant Mtb.

Optimizing multifunctional fluorescent ligands for intracellular labeling

The paper designs cell-permeable multifunctional ligands for HaloTag fusions that enable protein labeling and translocation, using Si-rhodamines with low KL-Z and high logD7.4 values.

Losartan controls immune checkpoint blocker-induced edema and improves survival in glioblastoma

Losartan prevents ICB-induced cerebral edema and improves survival in glioblastoma mice, with a predictive immune signature identified.

Simultaneous Multisheet Multichannel Imaging Cytometry (SMMIC) System Powered by Adaptive Vertically-Aligned Multi-Sheet Array (VAMSA) PSF

The paper introduces a high-throughput imaging cytometry system (SMMIC) that enables volumetric interrogation of live specimens with high resolution and flow rate.

Epistasis between promoter activity and coding mutations shapes gene evolvability

The paper shows that expression level masks the effects of coding mutations, demonstrating that expression level dictates their fitness impact.

SAM-dependent viral MTase inhibitors: herbacetin and caffeic acid phenethyl ester, structural insights into dengue MTase

The paper identifies herbacetin and caffeic acid phenethyl ester as inhibitors of dengue and chikungunya virus MTases, revealing their mechanism of action and antiviral efficacy.

LKB1 is the gatekeeper of carotid body chemo-sensing and the hypoxic ventilatory response

This study identifies LKB1 as essential for carotid body chemosensing and the hypoxic ventilatory response, showing divergence in LKB1 and AMPK dependency between the carotid body and the HVR.

Mindin differentially regulates fibroblast subpopulations via distinct members of the Src family kinases during fibrogenesis.

This study shows Mindin regulates distinct fibroblast subpopulations through different Src family kinases during fibrosis and cancer.

Structural dynamics of Zika Virus NS1 via a reductionist approach reveal the disordered nature of its beta roll domain in isolation

This study uses molecular dynamics simulations and experimental validation to show that the ZIKV NS1 beta-roll domain is intrinsically disordered and the beta-ladder domain is highly flexible.

Architecture of the chikungunya virus replication organelle

This study uses cryo-electron tomography to reveal the architecture of CHIKV spherules and presents a mathematical model explaining their membrane remodeling.

Bidirectional regulation between AP-1 and SUMO genes modulates inflammatory signaling during Salmonella Typhimurium infection

This study shows that Salmonella Typhimurium modulates SUMOylation by regulating AP-1 transcription factors, affecting inflammatory responses and infection outcomes.

A Single Multipurpose FSH-Blocking Therapeutic for Osteoporosis and Obesity

This paper develops and tests a first-in-class FSH-blocking antibody, MS-Hu6, showing efficacy in preventing obesity and osteoporosis in mice and safety in monkeys.

Stable nebulization and muco-trapping properties of Regdanvimab/IN-006 support its development as a potent, dose-saving inhaled therapy for COVID-19

This paper demonstrates that IN-006, a reformulated Regdanvimab, effectively traps SARS-CoV-2 virus-like particles in human airway mucus and achieves higher lung concentrations in rats when nebulized compared to intravenous delivery.

HIV-1 Vpu restricts Fc-mediated effector functions in vivo

This study shows that HIV-1 Vpu reduces nnAb recognition and ADCC resistance, with nnAb Fc-effector functions dependent on Env's open conformation.

Dual Inhibition of Cathepsin L and 3CL-Pro by GC-376 Constrains SARS Cov2 Infection Including Omicron Variant

This study shows that dual inhibition of cathepsin-L and 3CL-Pro by GC-376 effectively inhibits SARS-CoV-2 infection, including the Omicron variant, in highly susceptible cell lines.

Mindin is essential for cutaneous fibrogenesis in a new mouse model of systemic sclerosis

This study identifies Mindin as a key driver of fibrosis in a new mouse model of systemic sclerosis, showing its role in inducing inflammation and collagen production in fibroblasts.

Mitoxantrone dihydrochloride, an FDA approved drug, binds with SARS-CoV-2 NSP1 C-terminal

The paper investigates the binding of the FDA-approved drug Mitoxantrone dihydrochloride to the C-terminal region of SARS-CoV-2 NSP1 and suggests potential therapeutic implications.

Structure, dynamics, and inhibition of Staphylococcus aureus m1A22-tRNA methyltransferase

This study characterizes the structure, dynamics, and inhibition of Staphylococcus aureus TrmK, identifying a cryptic binding pocket for drug discovery.

Investigating the conformational dynamics of Zika virus NS4B protein

This study investigates the conformational dynamics of Zika virus NS4B protein using molecular dynamics simulations and experiments, identifying the cytosolic region as intrinsically disordered and showing its dynamic behavior under different conditions.

Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities

The paper develops ACE2-Fc molecules that neutralize SARS-CoV-2 and show Fc-effector activity, effectively treating lethal infection in mice.

Clinically observed deletions in SARS-CoV-2 Nsp1 affect protein stability and its ability to inhibit translation

The paper investigates how deletions in SARS-CoV-2 Nsp1 affect protein stability and translation inhibition, finding that certain deletions reduce translation inhibition while others impact interferon response.

Engineered neuron-targeting, placental mesenchymal stromal cell-derived extracellular vesicles for in utero treatment of myelomeningocele

This paper engineers neuron-targeting extracellular vesicles for in utero treatment of myelomeningocele, showing improved neuroprotection and reduced apoptosis in a rodent model.

An anti-SARS-CoV-2 non-neutralizing antibody with Fc-effector function defines a new NTD epitope and delays neuroinvasion and death in K18-hACE2 mice

Allosteric cooperation in β-lactam binding to a non-classical transpeptidase

The paper identifies an allosteric site in a L,D-transpeptidase that binds the sugar moiety of PG substrates and a second β-lactam molecule, revealing cooperative binding with the catalytic site.

Acropetal and basipetal cardenolide transport in Erysimum cheiranthoides (wormseed wallflower)

This study investigates cardenolide transport patterns in Erysimum cheiranthoides, finding maternal control of seed cardenolides and root cardenolide profiles determined by aboveground genotype.

Cryo-ET of a human GBP coatomer governing cell-autonomous innate immunity to infection

The paper solves the native structure of a human GBP coatomer that coats cytosolic bacteria and functions as an antimicrobial signaling platform.