J. R. Yates

Diverse competitor B cell responses to a germline-targeting priming immunogen in human Ig loci transgenic mice

The paper analyzes B cell responses to a germline-targeting immunogen in human Ig loci transgenic mice, finding diverse non-VRC01-class B cells and competitor B cells recognizing epitopes near the VRC01 epitope.

Wiskott-Aldrich Syndrome Protein Regulates Nucleolar Organization and Function in Innate Immune Response

This study shows that WASP regulates nucleolar structure and function, affecting rRNA transcription and inflammatory cytokine response in macrophages.

Evolving spike-protein N-glycosylation in SARS-CoV-2 variants

This study compares N-glycan processing in SARS-CoV-2 spike-proteins across variants to understand immune evasion mechanisms.

Comparative membrane proteomics reveals diverse cell regulators concentrated at the nuclear envelope

The paper identifies novel transmembrane proteins enriched at the nuclear envelope using proteomics and validates their localization and function.

Shared and distinctive neighborhoods of emerin and LBR revealed by proximity labeling and quantitative proteomics

The paper uses proximity labeling and proteomics to identify proteins interacting with emerin and LBR at the inner nuclear membrane, revealing shared and distinct partners.

Targeted protein S-nitrosylation of ACE2 as potential treatment to prevent spread of SARS-CoV-2 infection

This paper develops aminoadamantane nitrate compounds that inhibit SARS-CoV-2 infection by S-nitrosylating ACE2 and blocking viral entry, showing efficacy in vitro and in a Syrian hamster model.

Heat shock chaperone HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition

This study shows HSPB1 regulates cytoplasmic TDP-43 phase separation and liquid-to-gel transition, with implications for neurodegenerative diseases like ALS.

Unconventional tonicity-regulated nuclear trafficking of NFAT5 mediated by KPNB1, XPOT and RUVBL2

This study identifies KPNB1 and RUVBL2 as key regulators of NFAT5's unconventional tonicity-dependent nuclear trafficking.

DeGlyPHER: an ultrasensitive method for analysis of viral spike N-glycoforms

DeGlyPHER is an ultrasensitive method to analyze viral spike N-glycoforms, assessing glycan occupancy and processing from high-mannose to complex forms at each N-glycosylation site.

Mitotic R-loops direct Aurora b kinase to maintain centromeric cohesion

This study identifies mitotic R-loops as regulators of centromeric cohesion through their interaction with Aurora B kinase and the Chromosome Passenger Complex.

Aurora Kinase A proximity interactome reveals centriolar satellites as regulators of its function during primary cilium biogenesis

This study identifies AURKA's proximity interactome, revealing centriolar satellites as regulators of AURKA function during primary cilium biogenesis.

Visualization of the HIV-1 Env Glycan Shield Across Scales

This study uses cryo-EM, computational modeling, and mass-spectrometry to analyze the HIV-1 Env glycan shield's structure and dynamics, revealing how heterogeneity and interactions affect epitope accessibility and trimer stability.

Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate

The paper uses cryo-EM and glycan analysis to study the structure of a full-length SARS-CoV-2 spike protein in a vaccine candidate, revealing its stable prefusion conformation and novel trimer interactions.

TDP-43 and HSP70 phase separate into anisotropic, intranuclear liquid spherical annuli

The paper shows acetylation of TDP-43 drives its phase separation into intranuclear spherical annuli with liquid properties, regulated by HSP70 chaperone activity and proteasome function.

The versatility of Ascorbate Peroxidase-aided mapping uncovers insights of thenuclear lamina interactions and function

This paper introduces an APEX2-based method to map proteins, RNA, and DNA associated with the nuclear lamina, revealing new insights into its regulatory roles and dynamic interactions.

Covalent Protein Painting Reveals Structural Changes in the Proteome in Alzheimer Disease

The paper introduces CPP, a method to quantify lysine accessibility in proteins, and finds altered lysine accessibility in Alzheimer's disease patients.

HIV-1 Envelope and MPER antibody structures in lipid assemblies

This study presents methods to incorporate full-length HIV-1 Env into lipid assemblies for structural analysis, revealing the quaternary epitope of an MPER antibody and Env tilting during neutralization.

Amyloidogenic Proteins Drive Hepatic Proteostasis Remodeling in an Induced Pluripotent Stem Cell Model of Systemic Amyloid Disease

This study uses iPSC-derived hepatic cells to show that liver proteostasis factors and UPR signaling correlate with TTR amyloid production and can reduce amyloid secretion through ER stress-independent activation.

A non-acidic method using hydroxyapatite and phosphohistidine monoclonal antibodies allows enrichment of phosphopeptides containing non-conventional phosphorylations for mass spectrometry analysis.

This paper introduces a non-acidic method using hydroxyapatite and phosphohistidine antibodies to enrich non-conventional phosphopeptides for mass spectrometry analysis, detecting 425 unique phosphorylation sites.

RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia

This study shows RNA nucleates phase separation of glycolysis enzymes into G bodies in yeast under hypoxia, revealing their biophysical properties and structural integrity.

Quantitative Analysis of Global Protein Stability Rates in Tissues

This paper introduces QUAD, a method to quantify global protein stability in tissues, revealing tissue-specific stability patterns and age-related changes in brain protein stability.

Identification of new transmembrane proteins concentrated at the nuclear envelope using organellar proteomics of mesenchymal cells

The paper identifies five new transmembrane proteins enriched at the nuclear envelope in mesenchymal cells using proteomics and immunofluorescence validation.

The Heterotaxy Gene, CCDC11, is Essential for Cytokinesis and Cell-Cell Adhesion Via RhoA Regulation

This study shows CCDC11 is essential for cytokinesis and cell-cell adhesion via RhoA regulation, linking it to heterotaxy disease pathogenesis.

Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic β-cell function

This study uses in vivo proteomics and nutrient tracing to show age-related metabolic changes in pancreatic β-cells improve glucose-stimulated insulin secretion.

DNA replication-mediated error correction of ectopic CENP-A deposition maintains centromere identity

The paper shows DNA replication removes CENP-A from chromosome arms, preserving centromere identity by maintaining CENP-A at centromeres.

Quantitative Temporal Analysis of Protein Dynamics in Maladaptive Cardiac Remodeling

The paper uses proteomic analysis to study protein dynamics in mouse cardiac remodeling, identifying adaptive and maladaptive changes and their underlying mechanisms.

Defective RNA Polymerase III is negatively regulated by the SUMO-Ubiquitin-Cdc48 Pathway

The paper identifies the SUMO-Ubiquitin-Cdc48 pathway as a negative regulator of RNA polymerase III in budding yeast, leading to proteasomal degradation of Pol III subunits and repression of transcription.

HILAQ: A Novel Strategy for Newly Synthesized Protein Quantification

HILAQ quantifies newly synthesized proteins with higher sensitivity than QuaNCAT in HEK293T cells.