Biology subjects

Goel, T.

Publications and source records attributed to Goel, T..

9 recordsLinked to original sources

bioRxiv2025

Drift, selection and convergence in the evolution of a nonribosomal peptide

Nonribosomal peptides play important roles in microbial ecology and medicine, for example as toxins and antibiotics such as penicillin1. Like ordinary proteins, nonribosomal peptides are subject to evolutionary change, which is driven by rampant recombinations of their synthetases2. This makes it difficult to study the evolutionary histories of nonribosomal peptides, because recombination is a serious challenge for phylogenetic inference3. Here we use recombination-aware phylogenetics and ancestral sequence reconstruction to retrace the evolution of GameXPeptides, nonribosomal peptides entomopathogenic bacteria use to kill their insect prey4. By untangling the complex histories of their synthetases, we discover dozens of new GameXPeptides and show striking patterns of structural convergence. In analogy to classic statistical test for natural selection acting on nucleotide mutations, we develop a similar test for whether selection acts to fix recombinations. We provide statistical and experimental evidence of both neutral genetic drift and natural selection in the diversification of GameXPeptides. GameXPeptides variants rapidly evolved highly insect specific toxicities, suggesting that their diversification may be driven by an evolutionary arms race. Our work suggests that small, fast evolving alteration to nonribosomal peptides can overcome host resistance on short timescales, with important implications for the evolution of resistance evading antibiotics.

evolutionary biology↗

bioRxiv2025

Prophage induction states drive structural and synergistic outcomes in marine bacterial biofilms

Microbes commonly live in biofilms, dense spatially structured assemblages where temperate phages can influence interactions amongst closely related strains. Yet, how these phage-host interactions impact biofilm architecture and ecological dynamics remains poorly understood, particularly in situations where antagonistic strains coexist in structured communities. In the marine Roseobacteraceae Sulfitobacter pontiacus, two genetically similar heteroimmune prophages, (termed A and D) establish lysogeny in their host. Depending on the host plasmid genotype, prophages are fixed in either high or low induction states, which consequently shape both biofilm structure and competitive outcomes. Using confocal scanning laser microscopy of fluorescently labeled lysogens, we investigated how prophage induction and phage genotype of phage-host coalitions influence monoculture and co-culture (competitive) S. pontiacus biofilms grown at a fluid-solid interface. Compared to their low induction counterparts, high-induction strains formed thicker and more voluminous monoculture biofilms, which primarily result from vertical protrusions arising from a basal monolayer. In co-culture experiments - mixing strains with reciprocal prophage genotypes that can mutually kill each other through phage-mediated allelopathy - we observed unexpected coexistence and synergistic biofilm enhancement rather than competitive exclusion. Reactive oxygen species (ROS) levels were significantly higher in co-cultures than monocultures and correlated with local cell density, suggesting that phage-mediated interactions generate hotspots of oxidative stress, which is expected to further promote prophage induction, creating a positive feedback loop that amplifies cell lysis and release of matrix components. These results suggest temperate phages can paradoxically stabilize and promote biofilm growth via mechanisms that combine antagonistic killing with cooperative matrix production, revealing how phage-mediated interactions can shape microbial community architecture in spatially structured environments. IMPORTANCEBacterial biofilms are ubiquitous in natural environments, yet understanding of how temperate bacteriophages shape biofilm development and microbial community dynamics remains limited. Here, we demonstrate that prophage induction state simultaneously drives antagonistic killing and cooperative biofilm enhancement in spatially structured microbial communities. Using Sulfitobacter pontiacus and its infecting temperate phages as a model system, we reveal that reciprocally antagonistic host-phage pairs, which can kill each other through phage-mediated allelopathy, form more robust biofilms when grown together rather than separately. These findings challenge traditional views of competition in dense microbial systems, highlighting the complex, multi-faceted roles that temperate phages play in microbial communities. Additionally, we propose that oxidative stress creates positive feedback loops that amplify prophage induction, promoting coexistence of host-phage pairs rather than driving competitive exclusion. These insights have broad implications for understanding microbial community assembly, maintenance of genetic diversity in biofilms, and evolutionary dynamics of host-phage interactions in structured environments.

microbiology↗

bioRxiv2025

Role of chrna5 in multi-substance preference and phenotypes comorbid with the development of substance dependence

Addiction to nicotine and alcohol continues to be a leading cause of death and loss of productivity as measured in disability-adjusted life years. Polymorphisms in the nicotinic acetylcholine receptor subunit 5 (CHRNA5) have been identified as risk factors associated with nicotine dependence in human genetic studies and rodent models. Whether the chrna5 function is independently relevant to phenotypes associated with disorders comorbid with substance use, and if genetic factors influence subsequent outcomes when exposure to psychoactive substances happens at an early age, are questions of interest. We generated a stable mutant line in zebrafish using the CRISPR-Cas9 technique. We found that the chrna5 mutant fish exhibit an increased acute preference to both nicotine and alcohol in the Self-Administration Zebrafish Assay (SAZA). When subjected to multi-day exposures to either, chrna5 mutants exhibited greater behavioural change, but reduced transcriptomic changes compared to WT siblings, suggesting an impaired homeostatic regulation following drug exposure. Further, chrna5 mutants exhibited drug-independent changes in appetite and circadian rhythms, suggesting a genetic predisposition to disorders often comorbid with substance dependence. We expect these results to give new insights into the operation of genes whose normal function modulates vulnerability to multi-substance use and comorbid disorders.

neuroscience↗

bioRxiv2024

You can do it! Using published undergraduate research on Hydra mouth opening to train undergraduates

Biophysical research is both exciting and challenging. It is exciting because physical approaches to biology can provide novel insights, and it is challenging because it requires knowledge and skills from multiple disciplines. We have developed an undergraduate biophysical laboratory module that is accessible to both biology and physics majors, teaches fundamental skills such as time-lapse microscopy, image analysis, programming, critical reading of scientific literature, and basics of scientific writing and peer-review. This module uses published research on the biomechanics of Hydra mouth opening as its framework because this work was co-first authored by an undergraduate student and featured in the public press, thus providing two anchors that make this research accessible and exciting to undergraduates. Students start with a critical reading and discussion of the publication. Then they execute some of the experiments and analysis from the paper, thereby learning fluorescence time-lapse microscopy and image analysis using ImageJ and/or MATLAB/Python, and compare their data to the literature. The module culminates in the students writing a short paper about their results following the Micropublication journal style, a blinded peer-review, and final paper submission. Here, we describe one possible implementation of this module with the necessary resources to reproduce it, and summarize student feedback from a pilot run. We also provide suggestions for more advanced exercises. Several students expressed that repeating a published study done by an undergraduate student inspired and motivated them, thus creating buy-in and assurance that they "can do it", which we expect to help with confidence and retention.

scientific communication and education↗

bioRxiv2024

Eco-evolutionary dynamics of temperate phages in periodic environments

Bacteriophage (viruses that exclusively infect bacteria) exhibit a continuum of infection mechanisms, including lysis and lysogeny in interactions with bacterial hosts. Recent work has demonstrated the near-term advantages of lysogeny over lysis in conditions of low host availability. Hence, temperate phage which can switch between lytic and lysogenic strategies -- both stochastically and responsively -- are hypothesized to have an evolutionary advantage in a broad range of conditions. To examine generalized drivers of viral strategies over the near- and long-term, we explore the eco-evolutionary dynamics of temperate viruses in periodic environments with varying levels of host availability and viral mortality. We use a nonlinear system of ordinary differential equation to simulate periodically-forced dynamics that separate a within-epoch phase and a between-epoch phase, in which a (potentially unequal) fraction of virus particles and lysogens survive. Using this ecological model and invasion analysis, we show and quantify how conflicts can arise between strategies in the near-term that may favor lysis and strategies in the long-term that may favor lysogeny. In doing so, we identify a wide range of conditions in which temperate strategies can outperform obligately lytic or lysogenic strategies. Finally, we demonstrate that temperate strategies can mitigate against the potential local extinction of viruses in stochastically fluctuating environments, providing further evidence of the eco-evolutionary benefits of being temperate.

ecology↗

bioRxiv2022

Inferring Spatially Resolved Transcriptomics Data from Whole Slide Images for the Assessment of Colorectal Tumor Metastasis: A Feasibility Study

Over 150,000 Americans are diagnosed with colorectal cancer (CRC) every year, and annually over 50,000 individuals will die from CRC, necessitating improvements in screening, prognostication, disease management, and therapeutic options. Tumor metastasis is the primary factor related to the risk of recurrence and mortality. Yet, screening for nodal and distant metastasis is costly, and invasive and incomplete resection may hamper adequate assessment. Signatures of the tumor-immune microenvironment (TIME) at the primary site can provide valuable insights into the aggressiveness of the tumor and the effectiveness of various treatment options. Spatially-resolved transcriptomics technologies offer an unprecedented characterization of TIME through high multiplexing, yet their scope is constrained by cost. Meanwhile, it has long been suspected that histological, cytological and macroarchitectural tissue characteristics correlate well with molecular information (e.g., gene expression). Thus, a method for predicting transcriptomics data through inference of RNA patterns from whole slide images (WSI) is a key step in studying metastasis at scale. In this work, we collected and preprocessed Visium spatial transcriptomics data (17,943 genes at up to 5,000 spots per patient sampled in a honeycomb pattern) from tissue across four stage-III matched colorectal cancer patients. We compare and prototype several convolutional, Transformer, and graph convolutional neural networks to predict spatial RNA patterns under the hypothesis that the transformer and graph-based approaches better capture relevant spatial tissue architecture. We further analyzed the models ability to recapitulate spatial autocorrelation statistics using SPARK and SpatialDE. Overall, results indicate that the transformer and graph-based approaches were unable to outperform the convolutional neural network architecture, though they exhibited optimal performance for relevant disease-associated genes. Initial findings suggest that different neural networks that operate on different scales are relevant for capturing distinct disease pathways (e.g., epithelial to mesenchymal transition). We add further evidence that deep learning models can accurately predict gene expression in whole slide images and comment on understudied factors which may increase its external applicability (e.g., tissue context). Our preliminary work will motivate further investigation of inference for molecular patterns from whole slide images as metastasis predictors and in other applications.

pathology↗

bioRxiv2021

Contingent-behavior assay shows zebrafish preference for alcohol is biphasic

Alcohol use disorders are complex, multifactorial phenomena with a large footprint within the global burden of diseases. Here, we report the development of an accessible, two-choice self-administration zebrafish assay (SAZA) to study the neurobiology of addiction. Using this assay, we first demonstrated that, while zebrafish avoid higher concentrations of alcohol, they are attracted to low concentrations. Pre-exposure to alcohol did not change this relative preference, but acute exposure to an alcohol deterrent approved for human use decreased alcohol self-administration. A pigment mutant used in whole-brain imaging studies displayed a similar relative alcohol preference profile, however, mutants in CCSER1, a gene associated with alcohol dependence in human genetic studies, showed a reversal in relative preference. The presence of a biphasic response (hormesis) in zebrafish validated a key aspect of vertebrate responses to alcohol. SAZA adds a new dimension for discovering novel alcohol deterrents, and studying the neurogenetics of addiction using the zebrafish.

neuroscience↗

bioRxiv2019

Linalool acts as a fast and reversible anesthetic in Hydra

The ability to make transgenic Hydra lines has opened the door for quantitative in vivo studies of Hydra regeneration and physiology. These studies commonly include excision, grafting and transplantation experiments along with high-resolution imaging of live animals, which can be challenging due to the animals response to touch and light stimuli. While various anesthetics have been used in Hydra studies over the years, they tend to be toxic over the course of a few hours or their long-term effects on animal health have not been studied. Here we show that the monoterpenoid linalool is a useful anesthetic for Hydra. Linalool is easy to use, non-toxic, fast acting, and reversible. It has no detectable long-term effects on cell viability or cell proliferation. We demonstrate that the same animal can be immobilized in linalool multiple times at intervals of several hours for repeated imaging over 2-3 days. This uniquely allows for in vivo imaging of dynamic processes such as head regeneration. We further directly compare linalool to currently used anesthetics and show its superior performance. Because linalool, which is frequently utilized in perfumes and cosmetic products, is also non-hazardous to humans, it will be a useful tool for Hydra research in both research and teaching contexts.

pharmacology and toxicology↗

bioRxiv2019

Mouth Function Determines The Shape Oscillation Pattern In Regenerating Hydra Tissue Spheres

Hydra is a small freshwater polyp capable of regeneration from small tissue pieces and from aggregates of cells. During regeneration, a hollow bilayered sphere is formed that undergoes osmotically driven shape oscillations of inflation and rupture. These oscillations are necessary for successful regeneration. Eventually, the oscillating sphere breaks rotational symmetry along the future head-foot axis of the animal. Notably, the shape oscillations show an abrupt shift from large amplitude, long period oscillations to small amplitude, short period oscillations. It has been widely accepted that this shift in oscillation pattern is linked to symmetry breaking and axis formation. However, recent work showed that regenerating tissue pieces inherit the parent animals body axis and thus are asymmetric from the beginning. Thus, there is no mechanistic explanation for the observed shift in oscillation pattern and no clear understanding of its significance for Hydra regeneration. Using in vivo manipulation and imaging, we quantified the shape oscillation dynamics and dissected the timing and triggers of the pattern shift. Our experiments demonstrate that the shift in the shape oscillation pattern in regenerating Hydra tissue pieces is caused by the formation of a functional mouth, thereby linking morphological readouts to physiologically relevant events during regeneration. This study shows the power of using modern experimental techniques to revisit old questions in pattern formation and development.

biophysics↗