Biology subjects

Patel, R. R.

Publications and source records attributed to Patel, R. R..

7 recordsLinked to original sources

bioRxiv2026

A qPCR method facilitates study of absolute abundance, ecology, and inoculation fate of ciliate predators on the leaf surface

Predatory protists are important in shaping terrestrial microbial ecosystems, but their roles in the phyllosphere, or the communities on aerial plant surfaces, are poorly understood. Previous work found that the order Colpodida dominated heterotrophic protist communities in the phyllosphere. While most protists were sporadically present, a few Colpodida variants were prevalent and abundant, indicating that these variants may represent species adapted to the phyllosphere. To identify these organisms, we cultured colpodids from field-collected tomato leaves and performed phylogenetic analysis of the 18S rRNA gene. Five of nine independent isolates matched the most prevalent Colpodida variant previously identified as leaf-enriched through amplicon sequencing, and these isolates comprised a novel clade of Paracolpoda steinii. When compared to a maize root isolate of Colpoda inflata, an abundant rhizosphere ciliate, a P. steinii isolate was similar in size and growth yield on E. coli, but grew to higher yields and formed large cyst clusters when incubated with model phyllosphere bacteria prey Erwinia and Pseudomonas. We developed and validated quantitative PCR (qPCR) methods for detection and cell abundance estimation of the P. steinii phyllosphere clade, C. inflata, and the order Colpodida in environmental samples. In inoculated greenhouse plants, qPCR-estimated protist populations matched measured inoculum levels, and protist inoculum was still detectable after five days. In an uninoculated tomato field, P. steinii was detected on all plants, with greatest abundances observed in lower leaves and after a rain event. P. steinii comprised up to 18.7% of total leaf Colpodida populations, which were estimated at up to [~]1400 organisms per gram of fresh weight. The findings demonstrate that Colpodida communities are consistently present on tomato leaves, dynamically affected by the abiotic environment, and include significant populations of P. steinii. We propose that the P. steinii isolates and qPCR tools presented can be used as a model system to investigate colonization and distribution patterns, biotic interactions, genetic adaptations, and agricultural applications of leaf predation.

microbiology↗

bioRxiv2025

Social Exclusion Amplifies Behavioral Responses to Physical Pain via Insular Neuromodulation

The "Pain Overlap Theory" (1) proposes that the experience of social pain overlaps with and amplifies the experience of physical pain by sharing parts of the same underlying processing systems (2-6). In humans, the insular cortex has been implicated in this overlap of physical and social pain, but a mechanistic link has not been made (2,4,5,7-9). To determine whether social pain can subsequently impact responses to nociceptive stimuli via convergent electrical signals (spikes) or convergent chemical signals (neuromodulators), we designed a novel Social Exclusion paradigm termed the Fear of Missing Out (FOMO) Task which facilitates a mechanistic investigation in mice. We found that socially-excluded mice display more severe responses to physical pain, disrupted valence encoding, and impaired neural representations of nociceptive stimuli. We performed a systematic biosensor panel and found that endocannabinoid and oxytocin signaling in the insular cortex have opposing responses during trials where mice were attending or not attending to the Social Exclusion events respectively, demonstrating distinct neuromodulatory substrates that underpin different states of Social Exclusion. We also found that intra-insular blockade of oxytocin signaling increased the response to physical pain following Social Exclusion. Together these findings suggest Social Exclusion effectively alters physical pain perception using neuromodulatory signaling in the insular cortex.

neuroscience↗

bioRxiv2025

Rhizosphere-colonizing bacteria persist in the protist microbiome

Soils contain diverse predatory protists that affect the abundance and behavior of rhizosphere bacteria, including bacteria that may benefit plant health. Protists also harbor their own bacterial microbiomes, including transient and extracellular associates, but it is not known whether the protist microbiome affects the plant rhizosphere. To address this question, we profiled the bacterial microbiomes of eight evolutionarily diverse rhizosphere protist isolates after two years of continuous laboratory culture. We then compared the protist culture microbiomes to maize rhizosphere communities six weeks after protist inoculation. Introduction of protists enriched 13 protist-associated bacterial amplicon sequence variants (ASVs) in the rhizosphere, which comprised [~]10% of the rhizosphere bacterial community. Additional bacterial ASVs ranked highly in abundance in both rhizosphere and protist microbiomes; together, a median 47% of the protist microbiome was enriched or abundant in the rhizosphere. Inoculation with some of the protist cultures positively affected root biomass traits, but a protist mixture had no effect, indicating that the impact of protist holobionts on plant growth is context-dependent. Isolates of protist-associated bacteria had both positive and negative effects on protist growth in culture, suggesting that the bacteria use multiple strategies to survive in proximity to predators. This study demonstrates that even after prolonged laboratory culture, evolutionarily diverse rhizosphere protists host bacterial microbiomes dominated by plant-colonizing bacteria that impact the rhizosphere microbiome after inoculation. The findings suggest that protists may contribute to the rhizosphere as part of the soil microbial seedbank, and identify bacterial groups that may be important to the plant-protist interaction. ImportanceUnderstanding the impact of predatory protists on the plant microbiome will be essential to deploy protists in sustainable agriculture. This study shows that eight rhizosphere protist isolates hosted diverse and distinct bacterial communities, and that a large proportion of these bacteria could be found colonizing the maize root environment long after protists were introduced. This study demonstrates that maize rhizosphere bacteria can persist for years in the protist microbiome, indicating that extremely diverse eukaryotes could help select and maintain rhizosphere bacteria in the absence of the plant.

microbiology↗

bioRxiv2022

Amygdalostriatal transition zone neurons encode sustained valence to direct conditioned behaviors

To ensure survival, the brain must rapidly identify threats and maintain defensive behaviors for as long as danger is present. The amygdala has been studied as a key site for fear responses, but responses to threat cues in amygdala neurons are largely transient and shorter in duration than defensive responses observed. Here, we present the amygdalostriatal transition zone (ASt) as a missing piece of the circuits mediating fear responses. Using single-nucleus RNA sequencing (snRNA-seq), we demonstrate that the ASt is genetically distinct from adjacent striatal and amygdalar structures. In vivo electrophysiology and calcium imaging reveal that ASt neurons have robust, sustained responses to shock-predicting cues. Further, photostimulation of the ASt is sufficient to drive freezing and avoidance behaviors, and optogenetic inhibition experiments show that Drd2+ ASt neurons are necessary for cue-conditioned fear responses. Our findings establish the ASt as a previously unappreciated yet critical structure for encoding learned associations and directing defensive behaviors.

neuroscience↗

bioRxiv2021

Telomere-to-telomere genome assembly of Phaeodactylum tricornutum

Phaeodactylum tricornutum is a marine diatom with a growing genetic toolbox available and is being used in many synthetic biology applications. While most of the genome has been assembled, the currently available genome assembly is not a completed telomere-to-telomere assembly. Here, we used Oxford Nanopore long reads to build a telomere-to-telomere genome for Phaeodactylum tricornutum. We developed a graph-based approach to extract all unique telomeres, and used this information to manually correct assembly errors. In total, we found 25 nuclear chromosomes that comprise all previously assembled fragments, in addition to the chloroplast and mitochondrial genomes. We found that chromosome 19 has filtered long-read coverage and a quality estimate that suggests significantly less haplotype sequence variation than the other chromosomes. This work improves upon the previous genome assembly and provides new opportunities for genetic engineering of this species, including creating designer synthetic chromosomes.

genomics↗

bioRxiv2020

Alcohol dependence promotes systemic IFN-γ and IL-17 responses in mice

Alcohol use disorder (AUD) is a chronic relapsing disorder characterized by an impaired ability to stop or control alcohol use despite adverse social, occupational, or health consequences. AUD is associated with a variety of physiological changes and is a substantial risk factor for numerous diseases. We aimed to characterize systemic alterations in immune responses using a mouse model of chronic intermittent alcohol exposure to induce alcohol dependence. We exposed mice to chronic intermittent ethanol vapor for 4 weeks and used multiparametric flow cytometry to analyze the expression of cytokines IFN-{gamma}, IL-4, IL-10, IL-12 and IL-17 by different immune cells in the blood, spleen and liver of alcohol dependent and non-dependent control mice. We found increases in IFN-{gamma} and IL-17 expression in a cell type- and organ-specific manner. Often, B cells and neutrophils are primary contributors to increased IFN-{gamma} and IL-17 levels while other cell types play a secondary role. We conclude that chronic alcohol exposure promotes systemic pro-inflammatory IFN-{gamma} and IL-17 responses in mice. These responses are likely important in the development of alcohol-related diseases, but further characterization is necessary to understand the initiation and effects of systemic inflammatory responses to chronic alcohol exposure.

immunology↗

bioRxiv2020

Preferential Pharmacological Inhibition of Nav1.6, but not Nav1.1, Abolishes Epileptiform Activity Induced by 4-AP in Mouse Cortical Slices

Brain isoforms of voltage-gated sodium channels (VGSCs) have distinct cellular and subcellular expression patterns as well as functional roles that are critical for normal physiology as aberrations in their expression or activity lead to pathophysiological conditions. In this study, we asked how inhibition of select isoforms of VGSCs alters epileptiform activity to further parse out the roles of VGSCs in the brain. We first determined the relative selectivity of recently discovered small molecule, aryl sulfonamide, inhibitors (ICA-121431 and Compound 801) against Nav1.1, Nav1.2, and Nav1.6 activity using whole-cell patch clamp recordings obtained from HEK293 cells. To test the effects of these inhibitors on epileptiform activity, we obtained multielectrode array (MEA) recordings from mouse cortical slices in the presence of 4-aminopyridine (4-AP) to induce epileptiform activity. We found that the ICA-121431 and Compound 801 compounds are relatively selective for Nav1.1 and Nav1.6, respectively. From the MEA recordings, we found that inhibition of Nav1.6 and Nav1.2 with 500nM of the Compound 801 compound completely abolishes ictal local field potentials induced by 4-AP, whereas inhibition of Nav1.1 with 500nM of the ICA-121431 compound had minimal effect on epileptiform activity induced by 4-AP. Due to the prominent expression of Nav1.1 in inhibitory neurons, we asked whether inhibition of Nav1.1 alone alters activity. We found that, indeed, inhibition of Nav1.1 with the ICA-121431 compound increased basal activity in the absence of 4-AP. These findings expand our current understanding of the roles of VGSC isoforms in the brain and suggest that selective targeting of Nav1.6 may be a more efficacious treatment strategy for epileptic syndromes.

neuroscience↗