J. Johnson

Parallel phosphoproteomics and metabolomics map the global metabolic tyrosine phosphoproteome

The paper identifies and validates tyrosine phosphorylation sites on metabolic enzymes using parallel phosphoproteomics and metabolomics in MCF10A cells.

Characterization of West Nile virus Koutango lineage from Phlebotomine Sandflies in Kenya 2021

This study isolates and characterizes the West Nile virus Koutango lineage from phlebotomine sandflies in Kenya, revealing genetic variations and replication efficiency in mammalian and mosquito cells.

Resolved Genomes of Wastewater ESBL-Producing Escherichia coli and Metagenomic Analysis of Source Wastewater Samples

The paper analyzes ESBL-producing E. coli genomes and wastewater metagenomes to understand antibiotic resistance gene distribution and co-occurrence in Oregon wastewater systems.

The Chlamydia trachomatis Inc Tri1 interacts with TRAF7 to displace native TRAF7 interacting partners

This paper identifies the interaction between Chlamydia trachomatis effector Tri1 and host TRAF7, showing Tri1 displaces TRAF7's native binding partners to alter its signaling during infection.

High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune

This study examines phenotypic and genotypic variation in Schizophyllum commune strains, finding high diversity in mushroom development and lignocellulose degradation, with conserved genes for these traits across genomes.

Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease

This study tracks microbiome changes across four body sites in 86 participants over six years, revealing site-specific stability, individualized dynamics, and altered patterns in insulin-resistant individuals.

Multi-Channel smFRET study reveals a Compact conformation of EF-G on the Ribosome

This study uses multi-channel smFRET to show that EF-G adopts a compact conformation with specific mutations, impacting translocation and Poly(Phe) synthesis.

DAMM for the detection and tracking of multiple animals within complex social and environmental settings

The paper introduces DAMM, a pretrained object detector for localizing mice in complex environments, with robust performance in zero-shot and few-shot inference, and integrates it with SORT for tracking.

Differential early-life survival underlies the adaptive significance of temperature-dependent sex determination in a long-lived reptile

The study tests the survival-to-maturity hypothesis for temperature-dependent sex determination in alligators, finding male-promoting temperatures enhance hatchling survival regardless of sex.

Molecular pharmacology of selective NaV1.6 and dual NaV1.6 and NaV1.2 channel inhibitors that suppress excitatory neuronal activity ex vivo

This paper introduces selective NaV1.6 and dual NaV1.6/NaV1.2 inhibitors that suppress excitatory neuronal activity ex vivo, showing selectivity over NaV1.1 and efficacy in seizure models.

NaV1.6 inhibition drives the efficacy of voltage-gated sodium channel inhibitors to prevent electrically induced seizures in both wild type and Scn8aN1768D/+ gain-of-function mice

The paper shows that inhibiting NaV1.6 reduces seizures in both wild-type and Scn8aN1768D/+ mice, suggesting NaV1.6 is a key target for anti-seizure drugs.

A high-content screen reveals new regulators of nuclear membrane stability

This study identifies new regulators of nuclear membrane stability through a high-content siRNA screen and automated image analysis in cancer cells.

Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria at Amlakhadi canal

The study examines seasonal shifts in bacterial communities at Amlakhadi canal, showing a shift from Gammaproteobacteria to Betaproteobacteria in response to industrial pollution and seasonal changes.

Low Gut Microbial Diversity Augments Estrogen-driven Pulmonary Fibrosis in Female-Predominant Interstitial Lung Disease

The paper shows that low gut microbial diversity worsens estrogen-driven pulmonary fibrosis in female ILD by linking gut dysbiosis, estrogen, and inflammatory pathways.

Metaproteomic analysis of nasopharyngeal swab samples to identify microbial peptides and potential co-infection status in COVID-19 patients

This study uses metaproteomic analysis of nasopharyngeal swabs to identify microbial peptides and co-infections in COVID-19 patients, revealing potential pathogens and upregulated species in severe cases.

A monkeypox mRNA-lipid nanoparticle vaccine targeting virus binding, entry, and transmission drives protection against lethal orthopoxviral challenge

This paper develops an mRNA-lipid nanoparticle vaccine targeting four conserved MPXV surface proteins, showing superior protection against VACV compared to MVA.

JGI Plant Gene Atlas: An updateable transcriptome resource to improve structural annotations and functional gene descriptions across the plant kingdom

The paper introduces the JGI Plant Gene Atlas, a resource that improves gene function annotations by analyzing transcript abundance across 18 species and 604 tissues, identifying 64,620 genes with unknown functions.

The establishment of Populus x Laccaria bicolor ectomycorrhiza requires the inactivation of MYC2 coordinated defense response with a key role for root terpene synthases

This paper shows that MYC2.1 and MYC2.2 transcription factors in poplar repress defense genes, including terpene synthases, which are critical for Laccaria bicolor to establish ectomycorrhizal symbiosis.

A greenhouse-based high-throughput phenotyping platform for identification and genetic dissection of resistance to Aphanomyces root rot in field pea

This study develops a high-throughput phenotyping platform to assess Aphanomyces root rot resistance in field pea, identifies 260 SNPs associated with resistance, and discovers both known and novel genes involved in immunity.

Dysfunction of the Polycomb protein RYBP and of 5-methylcytosine oxidases leads to widespread CpG island hypermethylation and cell transformation

This study shows that dysfunction of RYBP and TET proteins causes CpG island hypermethylation and cell transformation in bronchial cells.

Dynamic Ins2 gene activity defines β-cell maturity states

This study shows that β-cell heterogeneity in insulin production is due to dynamic Ins2 gene activity states, with high activity linked to maturity and reduced viability.

Recapitulating Human Ovarian Aging Using Random Walks

This paper models human ovarian follicle activation using random walks to simulate ISR activity and recapitulates age-related follicle depletion patterns.

Temporal and spatial patterns of vertebrate extinctions during the Anthropocene

This study quantifies vertebrate extinctions since the 1400s, showing a rise in extinction rates linked to human population growth and industrialization.

A phospholipase assay screen identifies synergistic inhibitors of the P. aeruginosa toxin ExoU

This study identifies synergistic inhibitors of P. aeruginosa ExoU through a phospholipase assay screen, showing reduced cytotoxicity in vitro and in corneal assays.

MaxQuant and MSstats in Galaxy enable reproducible cloud-based analysis of quantitative proteomics experiments for everyone

The paper integrates MaxQuant and MSstats into Galaxy for reproducible cloud-based quantitative proteomics analysis, enabling accessible and transparent workflows for researchers.

Decoding the absolute stoichiometric composition and structural plasticity of α-carboxysomes

The paper uses mass spectrometry to determine the absolute stoichiometry of native and recombinant carboxysomes, revealing structural variability and assembly principles.

Proton export drives the Warburg Effect

This study shows that proton export drives the Warburg Effect by increasing intracellular alkalization, enhancing glycolytic flux, and promoting cancer aggressiveness.

NBI-921352, a First-in-Class, Na V 1.6 Selective, Sodium Channel Inhibitor That Prevents Seizures in Scn8a Gain-of- Function Mice, and Wild-Type Mice and Rats

This paper describes NBI-921352, a selective NaV1.6 inhibitor that prevents seizures in Scn8a gain-of-function mice and wild-type models, with better efficacy and tolerability than existing antiseizure drugs.

Mangrove forests mitigate coral bleaching under thermal stress from climate change

This study shows that coral reefs near mangroves are more resistant to bleaching under thermal stress than those without mangrove association.

SARS-COV-2 Recombinant Receptor-Binding-Domain (RBD) Induces Neutralising Antibodies Against Variant Strains of SARS-CoV-2 and SARS-CoV-1

This study shows that recombinant SARS-CoV-2 RBD induces neutralizing antibodies against variant strains and SARS-CoV-1, suggesting its potential as a vaccine candidate or booster.