S. Shi

Emergence of Functional Heart-Brain Circuits in a Vertebrate

This study tracks the development of heart-brain circuits in larval zebrafish, revealing three stages of functional maturation involving vagal motor, sympathetic, and sensory pathways.

Selected humanization of yeast U1 snRNP leads to global suppression of pre-mRNA splicing and mitochondrial dysfunction in the budding yeast

The paper humanizes yeast U1 snRNP components to study 5 ss recognition, finding that U1C ZnF substitution causes splicing defects and mitochondrial dysfunction.

Biochemical, biophysical, and structural investigations of two mutants (C154Y and R312H) of the human Kir2.1 channel involved in the Andersen-Tawil syndrome.

This study investigates two Kir2.1 mutants linked to Andersen-Tawil syndrome, showing they impair channel function through distinct mechanisms, with C154Y causing dominant-negative effects.

Defining the SPCA2C interactome identifies unique links to store-operated calcium entry

This study identifies novel SPCA2C interactors involved in calcium signaling and vesicular transport using BioID and validates key interactions with STIM1, ESYT1, and CCDC47.

Seasonal Variation in Bacterial Community Structures of Mangrove Sediments

This study examines seasonal variations in mangrove sediment bacterial communities and identifies factors influencing their assembly mechanisms.

Computational insights into the conformational transition of STING: mechanistic, energetic considerations, and the influence of crucial mutations

This study investigates the conformational transition of STING upon cGAMP binding, identifying mutations that affect the energetic landscape and suggesting V147L may not be a gain-of-function mutation.

Semiconductor augumented valuable chemical photosynthesis from Rhodospirillum rubrum and mechanism study

This paper constructs a Rhodospirillum rubrum-CdS biohybrid system and investigates its enhanced photosynthetic activity and electron transfer mechanisms.

Targeting the Immune-Fibrosis Axis in Myocardial Infarction and Heart Failure

The paper identifies a fibroblast trajectory associated with cardiac fibrosis and shows that macrophage-fibroblast crosstalk via IL-1β signaling drives fibrosis.

A Vaccinia-based system for directed evolution of GPCRs in mammalian cells

This paper develops a Vaccinia-based system to evolve GPCRs in mammalian cells, improving stability and expression, and demonstrating functional receptor properties.

DNA transposons of maT family in the Cnidaria

The paper analyzes the distribution and evolution of maT/DD37D and mosquito/DD37E transposons in cnidarians, revealing their unique evolutionary patterns and species-specific dynamics.

Illumination of a progressive allosteric mechanism mediating the glycine receptor activation

The paper uses fluorescence and simulations to reveal a progressive conformational change in the glycine receptor that precedes channel activation.

Trophoblast and blood vessel organoid cultures recapitulate the role of WNT2B in promoting intravillous vascularization in human intrauterine and ectopic pregnancy

The paper uses organoid models to show that WNT2B promotes vascularization in pregnancies, linking trophoblast function to vascular development in both intrauterine and ectopic pregnancies.

Prediction and validation of host cleavage targets of SARS-CoV-2 3C like protease

This study predicts and validates host cleavage targets of SARS-CoV-2 3CL protease using bioinformatics and experimental methods, identifying new targets like Obscurin and linking them to cardiac dysfunction in COVID-19.

Nucleocapsid 203 mutations enhance SARS-CoV-2 immune evasion

This study shows that the nucleocapsid 203 mutation, combined with spike L452R, enhances SARS-CoV-2 immune evasion and fitness, contributing to the dominance of variants like Delta and Omicron.

Two decades of suspect evidence for adaptive molecular evolution - Negative selection confounding positive selection signals

This paper investigates the concordance between two methods for detecting positive selection and finds that they often disagree, suggesting negative selection variation may mislead positive selection inferences.

Mutation N501Y in RBD of Spike Protein Strengthens the Interaction between COVID-19 and its Receptor ACE2

This study investigates how the N501Y mutation in the SARS-CoV-2 spike protein's RBD enhances its binding to ACE2, contributing to increased transmissibility of variants.

Crosstalk between myosin II and formin functions in the regulation of force generation and actomyosin dynamics in stress fibers

The paper measures traction forces and actomyosin dynamics in stress fibers, revealing that actin turnover and traction forces depend on both myosin II and formin activities.

Rapid and Visible RPA-Cas12a fluorescence Assay for Accurate Detection of Zoonotic Dermatophytes

This paper develops a RPA-Cas12a fluorescence assay for rapid, accurate detection of zoonotic dermatophytes with high sensitivity and specificity.

MLC Seq: De novo sequencing of full-length tRNA isoforms by mass ladder complementation

This paper introduces MLC-Seq, a method to sequence full-length tRNA isoforms and quantify RNA modifications, demonstrating its application on yeast and mouse tRNAs.

Actin polymerization and crosslinking drive left-right asymmetry in single cell and cell collectives

The paper identifies actin polymerization regulators that drive chiral actin swirling and left-right asymmetry in single cells and cell collectives.

In the absence of reproductive isolation - Extensive gene flow after speciation

The paper sequenced two mangrove species to show extensive gene flow after speciation, with many small introgression blocks and genomic islets contributing to speciation.

The intestinal microbiota-driven dopamine level influences social interaction and innate color preference in zebrafish larvae

This study shows that gut microbiota influence dopamine levels, which in turn affect social interaction and color preference in zebrafish larvae.

Apoptotic Extracellular Vesicles (ApoEVs) Safeguard Liver Homeostasis and Regeneration via Assembling an ApoEV-Golgi Organelle

This study shows that apoptotic extracellular vesicles (apoEVs) protect liver homeostasis and regeneration by forming a chimeric organelle with the Golgi apparatus and restoring hepatic ploidy.

ILRUN downregulates ACE2 expression and blocks infection of human cells by SARS-CoV-2

This study shows that ILRUN inhibits SARS-CoV-2 replication by downregulating ACE2 expression and blocking viral entry into human cells.

Germline Selection by Meiosis Defends the Transmission of defective Mitochondria with mtDNA variants

The paper investigates mtDNA variants in human polar bodies and mouse oocytes, showing meiotic selection removes defective mitochondria.

The Formin Inhibitor, SMIFH2, Inhibits Members of the Myosin Superfamily

The paper shows SMIFH2 inhibits myosin ATPase activity and actin filament translocation, affecting myosin 2A, myosin 10, and other non-muscle myosins, suggesting caution in using SMIFH2 to infer formin function.

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

This study uses stable isotope-informed genome-resolved metagenomics to trace carbon flow in rhizosphere soil and identify microbial interactions with plants and phages.

PIWIL1 Promotes Gastric Cancer via a piRNA-Independent Mechanism

This paper shows PIWIL1 promotes gastric cancer independently of piRNA by interacting with the NMD pathway.

Two decades of suspect evidence for adaptive DNA-sequence evolution - Failure in consistent detection of positive selection

The paper re-examines evidence for adaptive DNA sequence evolution using MK and PAML tests on Drosophila and Arabidopsis data, finding little overlap and suggesting unreliable results.

Two decades of suspect evidence for adaptive DNA-sequence evolution - Less negative selection misconstrued as positive selection

The paper investigates whether apparent signals of positive selection in DNA sequences are actually due to relaxed negative selection, finding strong fluctuations in negative selection strength across species.