Led by Dapeng Xiong, Yunguang Qiu, Junfei Zhao, Yadi Zhou, and Dongjin Lee, the Yu lab and collaborators have published an article in Nature Biotechnology that presents an ensemble deep learning framework, termed PIONEER (Protein–protein InteractiOn iNtErfacE pRediction), that predicts protein-binding partner-specific interfaces for all known protein interactions in humans, and seven other common model organisms to generate comprehensive structurally informed protein...

Bill Loftus, our Director of Operations, has been awarded a President’s Award for Employee Excellence, Thoughtful Leader Award. Read more about the President’s Awards...

Inle Bush (undergraduate student in the Han Lab) has been awarded a CAS Undergraduate Research Program grant, supporting the project: “Identification of Golgi Outpost Formation and Maturation Pathways in Drosophila melanogaster Neurons.” Congrats,...

Xander Lacrampe, a BCMB Graduate student in the Hu lab, has been awarded a Graduate School Dean’s Scholars Provost Diversity Fellowship. Congrats, Xander! Click here for more information about this...

A publication by Rebecca Z. Zawistowski (graduate student in the Crane Lab) in The Journal of Molecular Biology discusses how high pressure affects the structure of a protein called cytochrome c peroxidase (CcP). It shows that while the outer parts of the protein shrink and shift slightly under pressure, the core remains stable, protecting its key functions from...

TAR DNA-binding protein 43 (TDP-43) is a DNA/RNA binding protein predominantly localized in the nucleus under physiological conditions. TDP-43 proteinopathy, characterized by cytoplasmic aggregation and nuclear loss, is associated with many neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Thus it is crucial to understand the molecular mechanism regulating TDP-43 homeostasis. Here, we show that the uptake of oligodeoxynucleotides (ODNs) from the extracellular space induces reversible TDP-43 cytoplasmic puncta formation in both neurons and glia. ODNs facilitate the liquid-liquid phase separation of TDP-43 in vitro. Importantly, persistent accumulation of DNA in the cytoplasm leads to nuclear depletion of TDP-43 and...

Lilijana Oliver is a doctoral student in plant biology from Rush, New York. She earned her B.S. at Yale University and now studies polyploidy in plant development under the guidance of Adrienne Roeder at Cornell. What is your area of research and why is it important? My research focuses on the role of polyploidy in plant development using the model organism Arabidopsis thaliana. Polyploidy occurs when a whole genome duplication event results in more than two copies of a genome per somatic cell. This may occur across every cell of an entire organism or only in specific cells. Polyploidy is widespread amongst plants, and has been linked to everything from their evolution, to stress response, to cell and organ size, and more. I aim to understand the mechanisms by which polyploidy alters...

Bella and Adrienne discuss their investigation into robustness in the developing Arabidopsis...

Led by graduate student Xinchen Chen, members of the Han Lab (in collaboration with researchers at the USC) have published an article in PLOS Genetics about a new CRISPR toolkit to knock out specific genes in different types of cells in fruit fly tissues, particularly focusing on the neuromuscular junction (NMJ). Using this method, researchers from the Han lab identified important genes that help maintain the NMJ structure and regulate communication between nerve and muscle...

Organ development is a robust process, resulting in a reproducible organ size and shape across organisms. Altering the rates of cell division has been shown to not affect this robustness, as cells can compensate by changing their size and shape. However, the mechanisms that control this remain unclear. Here, Isabella Burda, Adrienne Roeder and colleagues investigate this robustness in the developing Arabidopsis thaliana sepal, the leaf-like organ that encloses the flower bud, by looking at a combination of mutants that affect cell division and cell growth rate heterogeneity. Using live imaging and cell growth tracking, the authors find that, in wild-type plants and plants with an increased or decreased number of cell divisions, the organ-scale growth pattern remains unaltered....

Dr. Adrienne Roeder was featured in the latest episode of InSDB’s “Behind The Bench” interview series, where she discusses her research into the intersection of patterning and morphogenesis in Arabidopsis development, and the value of bridging the gaps between science disciplines to foster collaborative interdisciplinary...

Dr. Megan Keller, graduate of the Doerr Lab, was awarded the CHIMID Fellowship, which offers postdoctoral scholars financial and professional development support to study host-microbe interactions. The Cornell Institute of Host-Microbe Interactions and Disease (CIHMID) is composed of researchers representing multiple departments and colleges at Cornell University, united in the common pursuit of understanding host-microbe biology. This fellowship, which is supported by a National Institutes of Health training grant, encourages collaborations across multiple Cornell labs and fosters intellectual independence in research that spans various disciplines. Dr. Keller’s research will focus on repurposing antibiotics into new combinational therapy for treating clinical infections. By...

The 2024 Louisa Gross Horwitz Prize will be awarded to Scott Emr and Wesley Sundquist for discovering the ESCRT pathway and revealing how it works. Defects in ESCRT function can lead to uncontrolled cell growth and tumor formation, contributing to cancer, neurodegeneration, and Parkinson’s disease. In addition, many viruses, including HIV, hijack ESCRT machinery to exit an infected host...

In a recent paper from the Roeder lab published in Developmental Cell, Shuyao Kong and Mingyuan Zhu investigate how a mutation in the protein coding gene DRMY1 in Arabidopsis plants affects the consistent formation of sepals, which protect the flower bud. The mutation reduces protein production, leading to a disruption in signals that normally control sepal development, causing variability in their number and...

During animal development, the spatiotemporal properties of molecular events largely determine the biological outcomes. Conventional gene analysis methods lack the spatiotemporal resolution for precise dissection of developmental mechanisms. Although optogenetic tools exist for manipulating designer proteins in cultured cells, few have been successfully applied to endogenous proteins in live animals. Here, we report OptoTrap, a light-inducible clustering system for manipulating endogenous proteins of diverse sizes, subcellular locations, and functions in Drosophila. This system turns on fast, is reversible in minutes or hours, and contains variants optimized for neurons and epithelial cells. By using OptoTrap to disrupt microtubules and inhibit kinesin-1 in neurons, we show that...

Ubiquitination is a posttranslational modification in eukaryotes that plays a significant role in the infection of intracellular microbial pathogens, such as Legionella pneumophila. While the Legionella-containing vacuole (LCV) is coated with ubiquitin (Ub), it avoids recognition by autophagy adaptors. Here, we report that the Sdc and Sde families of effectors work together to build ubiquitinated species around the LCV. The Sdc effectors catalyze canonical polyubiquitination directly on host targets or on phosphoribosyl-Ub conjugated to host targets by Sde. Remarkably, Ub moieties within poly-Ub chains are either modified with a phosphoribosyl group by PDE domain-containing effectors or covalently attached to other host substrates via Sde-mediated phosphoribosyl-ubiquitination....

A new paper from the Baskin lab (in collaboration with Smolka Lab and scientists at Weill Cornell Medicine) in Nature Cell Biology reports a system for mitosis-specific protein recruitment to the plasma membrane. The work was led by graduate student Xiaofu...

Lamins are intermediate filament proteins that contribute to numerous cellular functions, including nuclear morphology and mechanical stability. The N-terminal head domain of lamin is crucial for higher order filament assembly and function, yet the effects of commonly used N-terminal tags on lamin function remain largely unexplored. Here, we systematically studied the effect of two differently sized tags on lamin A (LaA) function in a mammalian cell model engineered to allow for precise control of expression of tagged lamin proteins. Untagged, FLAG-tagged and GFP-tagged LaA completely rescued nuclear shape defects when expressed at similar levels in lamin A/C-deficient (Lmna–/–) MEFs, and all LaA constructs prevented increased nuclear envelope ruptures in these cells. N-terminal tags,...

Antimicrobial peptides (AMPs) are a promising tool with which to fight rising antibiotic resistance. However, pathogenic bacteria are equipped with several AMP defense mechanisms, whose contributions to AMP resistance are often poorly defined. Here, we evaluate the genetic determinants of resistance to an insect AMP, cecropin B, in the opportunistic pathogen Enterobacter cloacae. Single-cell analysis of E. cloacae’s response to cecropin revealed marked heterogeneity in cell survival, phenotypically reminiscent of heteroresistance (the ability of a subpopulation to grow in the presence of supra-MIC concentration of antimicrobial). The magnitude of this response was highly dependent on initial E. cloacae inoculum. We identified 3 genetic factors which collectively contribute...

This recent article from the Baskin Lab introduces a method for direct visualization of phospholipid transport mechanisms within the cell, specifically between the plasma membrane and the endoplasmic reticulum. Special fluorescent markers allowed them to study the roles of lipid transfer proteins in the interorganelle distribution of...