J. Lyu

Symmetry facilitated the evolution of specificity and high-order stoichiometry in vertebrate hemoglobin

This study investigates how vertebrate hemoglobin evolved from a homodimeric ancestor to a heterotetramer through simple genetic changes that exploited symmetry in its structure.

Using AlphaFold Multimer to discover interkingdom protein-protein interactions

The paper evaluates AlphaFold Multimer's ability to predict interkingdom protein-protein interactions through in-silico screening of pathogen-secreted immune hydrolase inhibitors.

Subtilase SBT5.2 inactivates flagellin immunogenicity in the plant apoplast

The paper shows that the subtilase SBT5.2 cleaves flagellin's flg22 epitope, inactivating its immunogenicity and controlling immune responses in plants.

Mechano-regulation of GLP-1 production by Piezo1 in intestinal L cells

This study shows that Piezo1 in intestinal L cells mechanically regulates GLP-1 production, affecting glucose tolerance and diabetes.

Structure-based discovery of positive allosteric modulators for the calcium sensing receptor

The paper uses structure-based virtual screening to identify novel CaSR PAMs with higher potency and reduced side effects compared to existing drugs.

AlphaFold2 structures template ligand discovery

This study evaluates AlphaFold2 models for ligand discovery, finding they perform similarly to experimental structures despite conformational differences, and identify potent agonists for the 5-HT2A receptor.

Covalent Targeting of Splicing in T Cells.

This study develops chemical probes to target splicing factors in T cells, showing state-dependent loss of ITK via SF3B1 and demonstrating covalent ligandability of splicing regulators.

Identification and Analysis of SARS-CoV-2 Mutation and Subtype using 2x tiled Primer Set with Oxford Nanopore Technologies Sequencing for Enhanced Variant Detection and Surveillance in Seoul, Korea

The paper uses long-read sequencing with a 2x tiled primer set to identify SARS-CoV-2 mutations and subtypes in Seoul, Korea, showing improved variant detection and genotype-patient characteristic correlation.

Linked regulation of genome integrity and senescence-associated inflammation by p53

This study identifies a mitochondria-regulated p53 circuit that links genomic instability and inflammation in senescent cells, showing p53 suppresses inflammation without affecting cell cycle arrest.

The proteome of agroinfiltrated Nicotiana benthamiana is shaped by extensive protein processing

The paper identifies extensive proteolytic processing of plant proteins in agroinfiltrated N. benthamiana using peptographs and mass spectrometry, revealing widespread proteoform modifications.

A peptide-centric local stability assay to unveil protein targets of diverse ligands

This paper introduces PELSA, a peptide-centric local stability assay that identifies ligand-binding regions across the proteome with high sensitivity and without ligand modification.

Mechanical force regulates ligand binding and function of PD-1

This study shows mechanical force is critical for PD-1 function, as soluble PD-L1 lacks the mechanical support needed to trigger PD-1 signaling.

Mechanotransduction governs CD40 function and underlies X-linked Hyper IgM syndrome

This study shows that CD40-CD40L interactions form catch bonds that enhance B cell signaling and antibody class-switch, and mutations in CD40L disrupt this mechanism, causing X-linked Hyper IgM syndrome.

Double and triple thermodynamic mutant cycles reveal the basis for specific MsbA-lipid interactions

The paper uses native mass spectrometry and mutant cycles to study the thermodynamics of MsbA-LPS interactions, revealing entropy-driven binding and conformational changes.

Zika virus infection induces IL-1β-mediated inflammatory responses by macrophages in the brain of an adult mouse model

This study investigates ZIKV-induced neuroinflammation in adult mice, finding that macrophage IL-1β expression and complement activation contribute to neuroinflammatory damage.

From whole genome to probiotic candidates: a study of potential Lactobacillus strain selection for vaginitis treatment

This study identifies two Lactobacillus strains with probiotic properties for vaginitis treatment using genomic analysis, in vitro tests, and in vivo experiments.

Tumor microenvironments impair T cell receptor affinity and function

This study shows that CD8+ T cells in the tumor microenvironment have reduced TCR-pMHC affinity and function, impairing their anti-tumor activity.

Structural basis for lipid and copper regulation of the ABC transporter MsbA

This study uses native mass spectrometry and structural analysis to show how copper and lipids regulate the ABC transporter MsbA, revealing a conserved KLA binding site that modulates ATPase activity.

Large library docking for novel SARS-CoV-2 main protease non-covalent and covalent inhibitors

The paper identifies novel non-covalent and covalent inhibitors of SARS-CoV-2 main protease through virtual docking and experimental validation.

Fertilizer reduction with bio-organic fertilizer to regulate the root soil microbial community structure to improve Baby Chinese cabbage yield

This study investigates how reducing chemical fertilizers and adding bio-organic fertilizer affects soil microbial communities and Baby Chinese cabbage yield in Gansu plateau, finding that T2 treatment yields the highest crop output.

An Acyclic Phosphonate Prodrug of HPMPC is Effective Against VZV in Skin Organ Culture and Mice

This study develops and evaluates USC-373, a phosphonate prodrug of HPMPC, showing efficacy against VZV in cell cultures and mouse models with improved potency and bioavailability.

SARS-CoV-2 Infection of Microglia Elicits Pro-inflammatory Activation and Apoptotic Cell Death

This paper shows SARS-CoV-2 directly infects human microglia, causing pro-inflammatory activation and apoptosis, which may contribute to neurological issues in COVID-19 patients.

Crystal structures of the σ2 receptor template large-library docking for selective chemotypes active in vivo

This study uses crystal structures of the σ2 receptor to dock and screen a large library, identifying new chemotypes with high affinity and selectivity for the receptor.

Phospholipidosis is a shared mechanism underlying the in vitro antiviral activity of many repurposed drugs against SARS-CoV-2

Newly identified proviruses in Thermotogota suggest that viruses are the vehicles on the highways of interphylum gene sharing.

The paper identifies 17 proviruses in Thermotogota, suggesting viruses mediate gene transfer between Firmicutes and Thermotogota.

An ABA Synthesis Enzyme Allele OsNCED2 Promotes the Aerobic Adaption in Upland Rice

This study identifies an OsNCED2 allele that enhances aerobic adaptation in upland rice by improving root development and drought tolerance through increased ABA synthesis.

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

This study investigates DNA methylation variation during maize domestication using WGS and WGBS, identifying DMRs linked to gene regulation and adaptation.