Biology subjects

Rao, R. P.

Publications and source records attributed to Rao, R. P..

6 recordsLinked to original sources

bioRxiv2026

Enteroscape: An agent-based model for simulating microbial dynamics and host responses in the gut ecosystem

Understanding microbial interactions within the gut microbiome is challenging due to the sheer number of microorganisms present. Each additional microbe introduces new layers of complexity, especially when studying the conditions and dynamics of infectious progression. To address this challenge, we have developed Enteroscape: an in silico agent-based model, grounded in previous research, laboratory experiments, and in vivo assays. Enteroscape enables simulation of diverse microbial interactions within a nematode host environment. In this study, we used Enteroscape to model the progression of pathogenic yeast infection and evaluate the effects of probiotic yeast treatment in the Caenorhabditis elegans intestine. Drawing upon empirical and literature-based behavioral rules for individual microbes, Enteroscape simulations produced emergent behaviors of the microbial population that mirror experimentally observed infection dynamics, including visual patterns of infectious progression, as well as the effect of probiotic treatment on the host lifespan. Enteroscape demonstrates how computational models can generate testable predictions that deepen our insight into microbial community interactions and their impact on host biology. Author SummaryThe human microbiome is a complicated ecosystem, consisting of trillions of microbes of hundreds of different species that live in the human intestine. Understanding how different species interact to maintain a healthy balanced microbiological ecosystem that keeps pathogenic microbes at bay is critically important to human health. We have developed a simple experimental system that allows us to examine the interactions of just a few thousand microbes at a time in a living host, the microscopic nematode worm, C. elegans. In prior laboratory work, we have demonstrated how ingestion by the worm of the human pathogenic microbe C. albicans shortens the worms lifespan, while co-ingestion of various probiotic microbial species restores a longer lifespan. In this paper, we report the creation of a computational model of this system, which we named Enteroscape. We show that Enteroscape mimics the results of the experimental system, including the visual progression of infection by a pathogenic species, the effects on worm lifespan, and the amelioration of the pathogens effects by a probiotic species. Enteroscape will allow us to develop and test hypotheses about the mechanisms underlying remediation by probiotic microbes, with potential applications to better probiotic treatment of human infections.

microbiology↗

bioRxiv2023

A correlative study of the genomic underpinning of virulence traits and drug tolerance of Candida auris

Candida auris is an opportunistic fungal pathogen with high mortality rates that presents a clear and present threat to public health. The risk of C. auris infection is high because it can colonize the body, resist antifungal treatment, and evade the immune system. The genetic mechanisms for these traits are not well-known. Identifying them could lead to new targets for new treatments. To this end, we present an analysis of the genetics and gene expression patterns of C. auris carbon metabolism, drug resistance, and macrophage interaction. We chose to study two C. auris isolates simultaneously, one drug sensitive (B11220 from Clade II) and one drug resistant (B11221 from Clade III). Comparing the genomes, we found that B11220 was missing a 12.8 kb gene cluster encoding proteins related to alternative sugar utilization, possibly L-rhamnose. We show that B11221, which has the cluster, more readily assimilates and utilizes D-galactose and L-rhamnose. B11221 also exhibits increased adherence and drug resistance compared to B11220 when grown in these sugars. Transcriptomic analysis of both strains grown on glucose or galactose showed that genes associated with translation were upregulated in B11221, and the putative L-rhamnose gene cluster was upregulated when grown on D-galactose. These findings reinforce the growing evidence of a link between metabolism and tolerance. Since immune system evasion depends heavily on the cell surface, we characterized cell wall composition and macrophage evasion for the two strains. We found that B11221 has far less {beta}-1,3-glucan exposure, a key determinant of immune system evasion, and resists phagocytosis by macrophages compared to B11220. In a transcriptomic analysis of both strains co-cultured with macrophages we found that B11221 upregulates genes associated with early stages of growth and transcription factors that regulate transport. These key differences in growth and membrane composition could explain the resistance to phagocytosis and increased stress tolerance in general of B11221, and indicates another connection between metabolism and immune system evasion. Taken together, these data show that membrane composition, metabolism, and transport all correlate with colonization, drug resistance, and immune system evasion in C. auris.

microbiology↗

bioRxiv2021

mDrop-seq: Massively parallel single-cell RNA-seq of Saccharomyces cerevisiae and Candida albicans

Advances in high-throughput single-cell mRNA sequencing (scRNA-seq) have been limited till date by technical challenges like tough cell walls and low RNA quantity that prevented transcriptomic profiling of microbial species at throughput. We present microbial Drop-seq or mDrop-seq, a high-throughput scRNA-seq technique that is used on two yeast species, Saccharomyces cerevisiae, a popular model organism and Candida albicans, a common opportunistic pathogen. We benchmarked mDrop-seq for sensitivity and specificity and used it to profile 35,109 S. cerevisiae cells to detect variation in mRNA levels between them. As a proof of concept, we quantified expression differences in heat-shocked S. cerevisiae using mDrop-seq. We detected differential activation of stress response genes within a seemingly homogenous population of S. cerevisiae under heat-shock. We also applied mDrop-seq to C. albicans cells, a polymorphic and clinically relevant yeast species with thicker cell wall compared to S. cerevisiae. Single cell transcriptomes in 39,705 C. albicans cells was characterized using mDrop-seq under different conditions, including exposure to fluconazole, a common anti-fungal drug. We noted differential regulation in stress response and drug target pathways between C. albicans cells, changes in cell cycle patterns and marked increases in histone activity. These experiments are among the first high throughput single cell RNA-seq on different yeast species and demonstrate mDrop-seq as an affordable, easily implementable, and scalable technique that can quantify the variability in gene expression in different yeast species. We hope that mDrop-seq will lead to better understanding of genetic variation in yeasts in response to stimuli and find immediate applications in investigating drug resistance and infection outcome.

genomics↗

bioRxiv2020

Secondary metabolites from food-derived yeasts inhibit virulence of Candida albicans

Beneficial microbes in the intestine are thought to control pathogen overgrowth by competing for limited nutrients. Our findings modify this prevailing paradigm of a passive, microbial antagonistic mode of action to an active, directed mechanism mediated by specific secondary metabolites. We describe two food-derived yeasts, Saccharomyces cerevisiae and Issatchenkia occidentalis, that inhibit virulence traits of Candida albicans, including hyphal morphogenesis, biofilms formation and adhesion to intestinal epithelial cells. These yeasts also protect the model host Caenorhabditis elegans from C. albicans infection. We demonstrate that the protective activity is primarily retained in the secretome of the beneficial yeasts and the protection they provide as a physical barrier is minimal. Mutant analysis demonstrates that phenylethanol and tryptophol are necessary for protection and experiments with commercially procured compounds indicates that they are sufficient to inhibit C. albicans virulence. We propose food-derived yeasts as an alternative or combination therapy to conventional antifungal therapy for C. albicans infection.

microbiology↗

bioRxiv2019

Subject sex and partner sex modulate social touch responses across multiple cortical areas

Touch is a fundamental aspect of mammalian social, parental and sexual behavior. Human affective touch is critical for healthy child development and shows great promise as a novel therapeutic strategy for mental disorders characterized by social dysfunction, such as anxiety, depression and autism spectrum disorder. However, despite our detailed knowledge about cortical processing of non-social touch, we still know very little about how social touch modulates cortical circuits. We investigated the activity patterns of single neurons (N = 1156) across five sensory and frontal cortical areas in both male and female rats (N = 28) engaging in naturalistic social facial touch with male and female conspecifics. We found that information about social touch is widely available across cortex. Besides touch, the sex of the interaction partner (a biologically significant feature) is a major determinant of single neuron activity, and across cortex we observed 25.7% touch and 11.9% sex-touch responses. Although all areas investigated had access to social touch and partner sex information, social touch modulated different cortical areas in different ways. Finally, we found that network activity patterns during social touch depend on both subject sex and partner sex. Interestingly, these sex-differences in network activity patterns were differences in response magnitude and would not be evident without single cell resolution. Our observations suggest that socio-sexual characteristics of touch (subject and partner sex) widely modulate cortical activity and need to be investigated with cellular resolution.

neuroscience↗

bioRxiv2018

Coordinated host-pathogen transcriptional dynamics revealed using sorted subpopulations and single, Candida albicans infected macrophages

The outcome of fungal infections depends on interactions with innate immune cells. Within a population of macrophages encountering C. albicans, there are distinct host-pathogen trajectories; however, little is known about the molecular heterogeneity that governs these fates. We developed an experimental system to separate interaction stages and single macrophage cells infected with C. albicans from uninfected cells and assessed transcriptional variability in the host and fungus. Macrophages displayed an initial up-regulation of pathways involved in phagocytosis and proinflammatory response after C. albicans exposure that declined during later time points. Phagocytosed C. albicans shifted expression programs to survive the nutrient poor phagosome and remodeled the cell wall. The transcriptomes of single infected macrophages and phagocytosed C. albicans revealed a tightly coordinated shift in gene expression co-stages and revealed expression bimodality and differential splicing that may drive infection outcome. This work establishes an approach for studying host-pathogen trajectories to resolve heterogeneity in dynamic populations.

genomics↗