B. Ma

Deep learning of protein energy landscape and conformational dynamics from experimental structures in PDB

This study develops DeepConformer, a diffusion model that learns protein conformational dynamics and energy landscapes from PDB structures and coevolution data, reproducing MD simulation results without using MD data.

Ultra-sensitivity metaproteomics redefines the gut dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal inflammatory diseases.

The paper introduces uMetaP, an ultra-sensitive metaproteomic method that enhances detection of the gut dark metaproteome and identifies drug targets in intestinal inflammatory diseases.

Discovery and Synthesis of GS-7682, a Novel Prodrug of a 4'-CN-4-Aza-7,9-Dideazaadenosine C-Nucleoside with Broad-Spectrum Potency Against Pneumo- and Picornaviruses and Efficacy in RSV-Infected African Green Monkeys.

This paper describes the discovery and synthesis of GS-7682, a prodrug with broad antiviral activity against RSV and other viruses, showing efficacy in RSV-infected monkeys.

de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination

This paper presents a method to sequence polyclonal IgG antibodies from human plasma post-SARS-CoV-2 vaccination, generating recombinant antibodies with neutralizing capabilities.

Chitinase 3-like-1 (CHI3L1) Inhibits Innate Anti-Tumor and Tissue Remodeling ImmuneResponses by Regulating CD47-SIRPα and CD24-Siglec10-Mediated Phagocytosis

This study shows CHI3L1 inhibits macrophage phagocytosis by modulating CD47-SIRPα and CD24-Siglec10 pathways, contributing to immune evasion in cancer and COPD.

The receptor VLDLR binds East Equine Encephalitis virus through multiple distinct modes

This study identifies VLDLR as an EEEV receptor and characterizes its binding modes through cryo-EM and biochemical analyses, revealing mutations that enhance viral attachment.

Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function

This paper introduces FISH-scRACS-Seq, a method to identify and sequence single cells with specific metabolic functions, revealing a new cyclohexane-degrading enzyme system in marine bacteria.

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects

The paper presents a new microbial reference set with paired isolates from China, showing probiotic and cardiometabolic effects on hosts.

Chitinase 3-like-1 (CHI3L1) in the Pathogenesis of Epidermal Growth Factor Receptor Mutant Non-Small Cell Lung Cancer

This study shows CHI3L1 is induced by EGFR activation in NSCLC and promotes EGFR signaling, with anti-CHI3L1 antibodies reversing TKI resistance and inhibiting metastasis.

Targeted Protein O-GlcNAcylation Using Bifunctional Small Molecules

This paper develops OGTACs, bifunctional small molecules that enable protein-specific O-GlcNAcylation in cells, with applications for studying and targeting this modification in disease.

Lepidoptera proboscis pollens are mainly derived from nectar

The study shows that pollens on the proboscis of Lepidoptera are mainly from nectar, supporting their role in pollination and pollen germination on stigmas.

Premature Aging and Reduced Cancer Incidence Associated with Near-Complete Body-Wide Myc Inactivation

This study investigates the effects of near-complete Myc inactivation in mice, finding premature aging features but reduced cancer incidence and linking Myc dysregulation to aging and cancer.

Early immunomodulatory program triggered by pro-tolerogenic Bifidobacterium pseudolongum drives cardiac transplant outcomes

This study identifies Bifidobacterium pseudolongum as inducing an early anti-inflammatory response that influences cardiac transplant outcomes.

CHI3L1 Enhances Melanoma Lung Metastasis via Regulation of T cell Co-stimulators and CTLA-4/B7 Axis

This study shows CHI3L1 promotes melanoma lung metastasis by inhibiting T cell co-stimulators and stimulating CTLA-4/B7 axis, with combined anti-CHI3L1 and anti-CTLA-4 antibodies showing synergistic antitumor effects.

Generation and Functional Characterization of PLAP CAR-T Cells against Cervical Cancer Cells

This study generates and evaluates PLAP CAR-T cells for cervical cancer, showing their ability to kill tumor cells and secrete anti-tumor molecules.

Highly specialized carbohydrate metabolism capability in Bifidobacterium strain associated with intestinal barrier maturation in early preterm infants

Persistence and in vivo evolution of vaginal bacterial strains over a multi-year time period

This study identifies persistent bacterial strains in the vaginal microbiota over one year, showing their ability to evolve and co-exist in communities.

Conformational Flexibility in Neutralization of SARS-CoV-2 by Naturally Elicited Anti-SARS-CoV-2 Antibodies

This study evaluates the neutralizing activity of nine anti-SARS-CoV-2 monoclonal antibodies against variants of concern and reveals their structural mechanisms of action.

Structural visualization of the tubulin folding pathway directed by eukaryotic chaperonin TRiC

The paper visualizes the tubulin folding pathway mediated by TRiC using cryoEM, showing how TRiC's structure guides the folding of β-tubulin through specific interactions.

Strain-specific alterations in gut microbiome and host immune responses elicited by Bifidobacterium pseudolongum

This study compares two Bifidobacterium pseudolongum strains to determine strain-specific effects on gut microbiota and host immune responses.

Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule

This paper uses a computational method to simulate the binding mechanism of bosentan to hETB, identifying key steps like fly-casting and ligand-sliding.

Host Chitinase 3-like-1 is a Universal Therapeutic Target for SARS-CoV-2 Viral Variants in COVID 19

This study shows that targeting CHI3L1 inhibits SARS-CoV-2 variants' infection of epithelial cells, suggesting it as a universal therapeutic target.

Hypoxia Dynamically Regulates DBC1 Ubiquitination and Stability by SIAH2 and OTUD5 in Breast Cancer Progression

This study identifies hypoxia-regulated ubiquitination of DBC1 by SIAH2 and OTUD5 as a mechanism driving breast cancer progression.

Genetic Encoding of A Nonhydrolyzable Phosphotyrosine Analog in Mammalian Cells

This paper introduces a method to genetically incorporate a nonhydrolyzable phosphotyrosine analog into mammalian proteins to study tyrosine phosphorylation without dynamic interconversion complications.

Structural Basis of Substrate Recognition by the Mitochondrial ADP/ATP Transporter

The paper identifies a new substrate recognition site in the mitochondrial ADP/ATP transporter AAC, revealing its role in ADP selectivity and transport mechanism.

Quantitative Profiling of Adaptation to Cyclin E Overproduction

This study examines how mammalian cells adapt to chronic cyclin E overproduction, revealing that adaptation involves downregulation of G1-regulated genes and partial resistance to replication stress.

Insight into the ecology of vaginal bacteria through integrative analyses of metagenomic and metatranscriptomic data

The paper analyzes metagenomic and metatranscriptomic data to understand factors driving vaginal microbiota composition and function, finding that transcriptional activity varies with community context.

Simeprevir suppresses SARS-CoV-2 replication and synergizes with remdesivir

The paper identifies simeprevir as a potent inhibitor of SARS-CoV-2 replication that synergizes with remdesivir in vitro.

Young and Undamaged rMSA Improves the Longevity of Mice

This study shows that young and undamaged recombinant mouse serum albumin (rMSA) extends the lifespan and healthspan of C57BL/6N mice by 17.6% and 20.3% respectively.

Chitinase 3-like-1 Stimulates PD-L1 and Other Immune Checkpoint Inhibitors

This study shows Chi3l1 promotes PD-L1 and other immune checkpoint inhibitors in melanoma, suggesting combined targeting of Chi3l1 and PD-1-PD-L1 as a therapeutic strategy for pulmonary metastasis.