G. Shi

Viral Syncytia Evolve to Resist Interferon

This study shows that SARS-CoV-2 syncytia reduce interferon and antibody effectiveness, explaining the evolution of fusogenic viral variants.

Unveiling unique microbial nitrogen cycling and novel nitrification drivers in coastal Antarctica

This study identifies unique microbial nitrogen cycling mechanisms in coastal Antarctica, highlighting the role of comammox Nitrospira in nitrification.

Use of Artificial Intelligence for Automated Detection and Surveillance of Red Imported Fire Ants Nests

This study develops an AI system using robotic dogs to detect red imported fire ant nests with 95% precision, improving surveillance and pesticide delivery in open fields.

Omicron Spike confers enhanced infectivity and interferon resistance to SARS-CoV-2 in human nasal tissue

This study shows Omicron SARS-CoV-2 has higher infectivity and interferon resistance in human nasal tissue compared to Delta, due to changes in Spike protein entry mechanisms.

A method for extracting effective interactions from Hi-C data with applications to interphase chromosomes and inverted nuclei

This paper introduces a method to extract effective interaction energies from Hi-C data to model chromosome organization, showing that heterochromatin attraction drives compartment formation in conventional and inverted nuclei.

Myofibrillar malformations that arise in mdx muscle fibers are driven by detyrosinated microtubules

This study identifies detyrosinated microtubules as a driver of myofibrillar malformations in dystrophic skeletal muscle fibers, linking increased deTyr-MT levels to structural impairments.

Structural basis for preservation of a subset of Topologically Associating Domains in Interphase Chromosomes upon cohesin depletion

The paper shows that some Topologically Associating Domains (TADs) persist without cohesin, supported by Hi-C data, polymer simulations, and 3D structural analysis in mouse and human cells.

Gaq-PKD/PKCμ regulates the IkB transcription to limit the NF-kB mediated inflammatory response essential for early pregnancy

This study shows that Gaq-PKD/PKCμ regulates IκB transcription to limit NF-κB-mediated inflammation, essential for successful early pregnancy.

Linear motif specificity in signaling through p38α and ERK2 mitogen-activated protein kinases

The paper identifies sequence motifs that determine docking site specificity for p38α and ERK2 MAPKs, revealing that p38 selectivity is driven by Lys residues and unique acidic residues in its docking groove.

Structural changes in chromosomes driven by multiple condensin motors during mitosis

The paper develops a computational framework to model loop extrusion by condensin I and II during mitosis, showing changes in loop size and structure across cell types.

Transcription-induced active forces suppress chromatin motion

The paper introduces a polymer model to explain how transcription-induced active forces suppress chromatin mobility during transcription.

A maximum-entropy model to predict 3D structural ensembles of chromatins from pairwise distances: Applications to Interphase Chromosomes and Structural Variants

This paper introduces a computational method to predict 3D chromatin structures from pairwise distances and applies it to analyze chromosome organization and structural variants.

Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors

The paper screens for MAPK docking motifs and interactors using a yeast-based genetic pipeline, identifying novel sequences and residues critical for binding to JNK1 and p38.

Evolution of Learning in Technology Adoption: The case of the U.S. Soybean Seed Industry.

The paper analyzes how learning evolution impacts technology adoption in U.S. soybean farming, showing reduced uncertainty over time and differing model fit across adoption stages.

Megakaryocyte derived immune-stimulating cells regulate host-defense immunity against bacterial pathogens

The paper identifies MK-derived immune-stimulating cells (MDICs) that enhance host defense against bacterial infections by interacting with myeloid cells and producing cytokines.

Modulating the selective utilization of carbon sources by engineering the 3rd and 4th helices of the DNA-binding domain of catabolite control protein A (CcpA) in Bacillus licheniformis

This study investigates how specific amino acids in the DNA-binding domain of CcpA affect carbon source utilization in Bacillus licheniformis through in vitro and in vivo experiments.

Rapalogs downmodulate intrinsic immunity and promote cell entry of SARS-CoV-2

This study shows rapalogs like rapamycin increase SARS-CoV-2 infection by reducing antiviral proteins through microautophagy, while ridaforolimus has less effect.

Chromatin dynamics controls epigenetic domain formation

The paper models chromatin dynamics to show how epigenetic domains form through nucleosome modification spreading and chromatin relaxation rates, with experimental validation in mouse embryonic stem cells.

Opposing activities of IFITM proteins in SARS-CoV-2 infection

This study identifies opposing roles of IFITM3 in restricting and enhancing SARS-CoV-2 infection through distinct mechanisms involving endosomal restriction and plasma membrane fusion.

Tubulin acetylation increases cytoskeletal stiffness to regulate mechanotransduction in striated muscle

The paper investigates how acetylated α-tubulin affects cytoskeletal stiffness and mechanotransduction in striated muscle by increasing its levels without changing detyrosinated α-tubulin.

Theory and Simulations of condensin mediated loop extrusion in DNA

The paper develops a theoretical model and simulations to explain condensin-mediated loop extrusion in DNA, showing how ATP binding induces conformational changes that drive loop formation.

From Hi-C Contact Map to Three-dimensional Organization of Interphase Human Chromosomes

This paper introduces HIPPS, a method to calculate 3D chromosome structures from Hi-C contact maps without assuming an energy function, showing conformational heterogeneity in human chromosomes.

Quantitative interactions drive Botrytis cinerea disease outcome across the plant kingdom

The paper investigates how Botrytis cinerea interacts with diverse plant hosts, finding that host species and pathogen strain differences are major sources of variation in disease outcomes.

Conformational Heterogeneity in Human Interphase Chromosome Organization Reconciles the FISH and Hi-C Paradox

The paper resolves the FISH-Hi-C paradox by showing that conformational heterogeneity in human interphase chromosomes explains discrepancies between Hi-C contact probabilities and FISH distances.

Endoplasmic reticulum associated degradation preserves hematopoietic stem cell quiescence and self-renewal by restricting mTOR activity

This study shows that ERAD preserves HSC quiescence and self-renewal by restricting mTOR activity, preventing HSC depletion and hyper-proliferation.

Changes in the Physicochemical Properties and Microbial Communities of Rhizospheric Soil after Cassava/Peanut Intercropping

This study examines how cassava/peanut intercropping affects rhizospheric soil physicochemical properties and microbial communities, finding improved nutrient content, pH, and microbial diversity.

Interphase Human Chromosome Exhibits Out of Equilibrium Glassy Dynamics

The paper models human interphase chromosomes as a self-avoiding polymer to study their glassy dynamics and shows agreement between simulations and experimental data.

Architecture of human interphase chromosome determines the spatiotemporal dynamics of chromatin loci

The paper uses a heteropolymer model with Hi-C data to study chromatin dynamics, finding that chromosome architecture determines spatiotemporal behavior and cell-to-cell variability.