Biology subjects

Kalia, R.

Publications and source records attributed to Kalia, R..

7 recordsLinked to original sources

bioRxiv2026

Sex-specific roles for yawning in the Emperor cichlid Boulengerochromis microlepis

Yawning is a poorly understood, yet spontaneous and ubiquitous behaviour. Three main hypotheses explain the function of yawns, most notably stimulating arousal. Yawns can also play a role in social cohesion through their "contagious" nature, eliciting an unconscious yawn in an observer. Yawn contagion has been observed in mammals and birds, and has been suggested in fish. Yawning also contributes to sexual dimorphisms, whereby males and females display differences in yawn frequency or function. Here, we examine these hypotheses in juveniles of the African cichlid, Boulengerochromis microlepis. By re-analyzing hundreds of hours of video recordings and nearly 3000 observed yawns we find support for all three yawn hypotheses in fish and two temporally and sexually distinct effects for yawns. First, our results suggest yawns at night and dawn induce arousal by delaying transitions into sleep. In contrast, daytime yawns induced rapid yawn contagion in neighbouring fish. Our analyses also demonstrate clear differences between sexes, with increased yawning in males at night and dawn associated with less sleep, whereas females displayed more robust social yawning. Together, our results expand the evolutionary context for yawning, and raise further questions about its functions in sleep and social cohesion across animals, and across sexes.

animal behavior and cognition↗

bioRxiv2026

Integrating Diffusion and Liquid AI Models for Predicting Peptide Affinity from mRNA Display Selections

In vitro selection and directed evolution technologies such as mRNA display, explore large libraries ([≥]1014 variants) and generate thousands to millions of functional polypeptide ligands to a variety of targets. Denoising diffusion implicit machine learning models (DDIMs) trained using display-derived deep sequencing data can greatly expand these functional sequences beyond what is accessible experimentally. However, methods are needed to predict peptide properties such as binding free energies ({Delta}G{degrees}). Here, we applied machine learning methods to predict binding free energies of both experimental and DDIM-generated peptide ligands against a target of interest, the oncogenic protein Bcl-xL. To do this, we trained a Closed-form Continuous (CfC) neural network using a dataset of 15,700 peptide ligands where pairs of sequences and their corresponding binding free energies ({Delta}G{degrees}) were used as inputs. This type of model was chosen due to its ability to represent irregular series. The resulting CfC model accurately predicts the rank order, within error, and binding free energies ({Delta}G{degrees}) for both experimental and DDIM-generated peptides, identifying five DDIM-generated peptides with single-digit picomolar affinities. Combining trained DDIM and CfC models offers a unified route to expand the scope of experimental ligand discovery, predict the molecular properties of both experimental and generated ligands, and highlights the utility of large quantitative datasets for making accurate in silico predictions of high-affinity peptide candidates. StatementHigh-throughput sequencing analysis of mRNA display libraries enables generating novel peptide ligands and expands the scope of functional sequences beyond what is accessible experimentally. Closed-form Continuous neural networks trained using sequences and their corresponding free energies accurately predict the binding free energies of both experimental and machine learning-generated peptides, enabling a route to quantitatively predict peptide properties using directed evolution data.

bioengineering↗

bioRxiv2021

Design and immunogenicity of a Pan-SARS-CoV-2 synthetic DNA vaccine

Here we have employed SynCon(R) design technology to construct a DNA vaccine expressing a pan-Spike immunogen (INO-4802) to induce broad immunity across SARS-CoV-2 variants of concern (VOC). Compared to WT and VOC-matched vaccines which showed reduced cross-neutralizing activity, INO-4802 induced potent neutralizing antibodies and T cell responses against WT as well as B.1.1.7, P.1, and B.1.351 VOCs in a murine model. In addition, a hamster challenge model demonstrated that INO-4802 conferred superior protection following intranasal B.1.351 challenge. Protection against weight loss associated with WT, B.1.1.7, P.1 and B.1.617.2 challenge was also demonstrated. Vaccinated hamsters showed enhanced humoral responses against VOC in a heterologous WT vaccine prime and INO-4802 boost setting. These results demonstrate the potential of the pan-SARS-CoV-2 vaccine, INO-4802 to induce cross-reactive immune responses against emerging VOC as either a standalone vaccine, or as a potential boost for individuals previously immunized with WT-matched vaccines.

immunology↗

bioRxiv2021

INO-4800 DNA Vaccine Induces Neutralizing Antibodies and T cell Activity Against Global SARS-CoV-2 Variants

Global surveillance has identified emerging SARS-CoV-2 variants of concern (VOC) associated with broadened host specificity, pathogenicity, and immune evasion to vaccine induced immunity. Here we compared humoral and cellular responses against SARS-CoV-2 VOC in subjects immunized with the DNA vaccine, INO-4800. INO-4800 vaccination induced neutralizing antibodies against all variants tested, with reduced levels detected against B.1.351. IFN{gamma} T cell responses were fully maintained against all variants tested.

immunology↗

bioRxiv2019

The mechanisms of dynamin-actin interaction

Cell-cell fusion is an indispensable process in the conception, development and physiology of multicellular organisms. Here we demonstrate a direct and noncanonical role for dynamin, best known as a fission GTPase in endocytosis, in cell-cell fusion. Our genetic and cell biological analyses show that dynamin colocalizes within the F-actin-enriched podosome-like structures at the fusogenic synapse, which is required for generating invasive membrane protrusions and myoblast fusion in vivo, in an endocytosis-independent manner. Biochemical, negative stain EM and cryo-electron tomography (cryo-ET) analyses revealed that dynamin forms helices that directly bundles actin filaments by capturing multiple actin filaments at their outer rim via interactions with dynamins proline-rich domain. GTP hydrolysis by dynamin triggers disassembly of the dynamin helix, exposes the sides of the actin filaments, promotes dynamic Arp2/3-mediated branched actin polymerization, and generates a mechanically stiff actin network. Thus, dynamin functions as a unique actin-bundling protein that enhances mechanical force generation by the F-actin network in a GTPase-dependent manner. Our findings have universal implications for understanding dynamin-actin interactions in various cellular processes beyond cell-cell fusion.

cell biology↗

bioRxiv2018

Vms1p is a release factor for the Ribosome-associated Quality control Complex

Eukaryotic cells employ the Ribosome-associated Quality control Complex (RQC) to maintain homeostasis despite defects that cause ribosomes to stall. The RQC comprises the E3 ubiquitin ligase Ltn1p, the ATPase Cdc48p, and the novel proteins Rqc1p and Rqc2p1-3. Following recognition and subunit splitting of stalled ribosomes, the RQC detects and assembles on 60S subunits that hold incomplete polypeptides linked to a tRNA (60S:peptidyl-tRNA)4-8. Ltn1p cooperates with Rqc1p to facilitate ubiquitination of the incomplete nascent chain, marking it for degradation7,9,10. Rqc2p stabilizes Ltn1p on the 60S3-5,8 and recruits charged tRNAs to the 60S to catalyze elongation of the nascent protein with Carboxy-terminal Alanine and Threonine extensions, or CAT tails, via a mechanism that is distinct from canonical translation4,10. CAT-tailing mobilizes and exposes lysine residues in the nascent chain, especially those stalled within the exit tunnel, thereby supporting efficient ubiquitination10,11. If the ubiquitin-proteasome system is overwhelmed or unavailable, CAT-tailed nascent chains aggregate in the cytosol or within organelles like the mitochondria12-14. Here we identify Vms1p as the tRNA hydrolase that releases nascent polypeptides for extraction and degradation in the RQC pathway.

biochemistry↗

bioRxiv2017

Structural Basis of Mitochondrial Receptor Binding and GTP Driven Conformational Constriction by Dynamin-Related Protein 1

Mitochondrial inheritance, genome maintenance, and metabolic adaptation all depend on organelle fission by Dynamin-Related Protein 1 (DRP1) and its mitochondrial receptors. DRP1 receptors include the paralogs Mitochondrial Dynamics 49 and 51 (MID49/MID51) and Mitochondrial Fission Factor (MFF), but the mechanisms by which these proteins recruit DRP1 and regulate its activities are unknown. Here we present a cryoEM structure of human, full-length DRP1 bound to MID49 and an analysis of structure- and disease-based mutations. We report that GTP binding allosterically induces a remarkable elongation and rotation of the G-domain, Bundle-Signaling Element (BSE) and connecting hinge loops of DRP1. In this nucleotide-bound conformation, a distributed network of multivalent interactions promotes DRP1 copolymerization into a linear filament with MID49, MID51 or both. Subsequent GTP hydrolysis and exchange within the filament leads to receptor dissociation, shortening through disassembly, and concomitant curling of DRP1 oligomers into closed rings. The dimensions of the closed DRP1 rings are consistent with DRP1-constricted mitochondrial tubules observed in human cells. These structures are the first views of full-length, receptor- and nucleotide-bound dynamin-family GTPases and--in comparison with nucleotide-free crystal structures--teach us how these molecular machines perform mechanical work through nucleotide-driven allostery.

biophysics↗