Biology subjects

Patel, S. R.

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

6 recordsLinked to original sources

bioRxiv2025

Amenability to Engineering of the Homologation Enzyme, HphA, through Homologous-Based Site-Directed Mutagenesis

Homologation of amino acids, the addition or deletion of a methylene group onto their side chains, has the potential to increase the biostability and bioavailability of peptide natural products. The first enzyme in the homologation pathway, HphA, has been previously characterized and is substrate selective. Bioinformatics studies were used to identify amino acids in the active site of HphA, which may play a role in substrate selection, by comparison to homologous enzymes, homocitrate synthase (HCS) and 2-isopropylmalate synthase (IPMS). Single point mutants to five amino acid residues in the HphAs active site were created to mimic those of HCS and IPMS. Their activities were measured via time-course assays with the natural substrates for HCS and IPMS. Residue A73 was identified as important in the substrate specificity of HphA; therefore, six different additional mutations were generated and tested with nine substrates with various side chains. The HphA A73L mutant exhibited the highest activity compared to the other mutants, showing activity with counterparts of L-Tyr (HphA natural substrate), L-Val (IPMS natural substrate), L-Leu, L-Ser, L-Trp, and L-Asp. Kinetic assays were taken with HphA A73L with the active substrates and compared with kinetic data from HphA WT, HCS, and IPMS. These results demonstrated that the A73L mutation significantly relaxed the substrate specificity of HphA, indicating its amenability to engineering. This research will serve as the foundation for future metabolic engineering studies on the enzymatic homologation pathway of amino acids.

bioengineering↗

bioRxiv2023

Pax Protein Depletion in Proximal Tubules Triggers Conserved Mechanisms of Resistance to Acute Ischemic Kidney Injury and Prevents Transition to Chronic Kidney Disease

Acute kidney injury (AKI) is a common condition that lacks effective treatments. In part this shortcoming is due to an incomplete understanding of the genetic mechanisms that control pathogenesis and recovery. Pax2 and Pax8 are homologous transcription factors with overlapping functions that are critical for kidney development and are re-activated in AKI. In this report, we examined the role of Pax2 and Pax8 in recovery from ischemic AKI. We found that Pax2 and Pax8 are upregulated after severe AKI and correlate with chronic injury. Surprisingly, we then discovered that proximal-tubule-selective deletion of Pax2 and Pax8 resulted in a less severe chronic injury phenotype. This effect was mediated by protection against the acute insult, similar to preconditioning. Prior to injury, Pax2 and Pax8 mutant mice develop a unique subpopulation of S3 proximal tubule cells that display features usually seen only in acute or chronic injury. The expression signature of these cells was strongly enriched with genes associated with other mechanisms of protection against ischemic AKI including caloric restriction, hypoxic preconditioning, and female sex. Taken together, our results identify a novel role for Pax2 and Pax8 in mature proximal tubules that regulates critical genes and pathways involved in both injury response and protection from ischemic AKI. TRANSLATIONAL STATEMENTIdentifying the molecular and genetic regulators unique to the nephron that dictate vulnerability to injury and regenerative potential could lead to new therapeutic targets to treat ischemic kidney injury. Pax2 and Pax8 are two homologous nephron-specific transcription factors that are critical for kidney development and physiology. Here we report that proximal-tubule-selective depletion of Pax2 and Pax8 protects against both acute and chronic injury and induces an expression profile in the S3 proximal tubule with common features shared among diverse conditions that protect against ischemia. These findings highlight a new role for Pax proteins as potential therapeutic targets to treat AKI.

pathology↗

bioRxiv2022

Notch-1 mediates epithelial-mucosal healing during murine colitis recovery phase

Inflammatory bowel disease (IBD) is marked by inflammation mediated epithelial-mucosal damage. The intestinal epithelial forms a tight barrier displaying two contrasting functions: restricting the entry of potentially harmful substances while, on the other hand allowing the selective passage of nutrients. The damaged epithelial-mucosal barrier causes the exposure of mucosa layers to luminal inflammatory contents. This eventually leads to the leaky epithelium, exposing the immune cells, release of various cytokines, and results in loss of epithelial homeostasis. Therefore, maintenance of healthy epithelial-mucosal lining is critical during IBD recovery. Notch signaling is an evolutionarily conserved molecular pathway crucial for the development and homeostasis of most tissues. Notably, the deregulation of Notch signaling is involved in IBD (Ulcerative colitis and Crohns disease). Notch signaling also plays a vital role in wound healing and tissue repair. Here, we investigated the role of Notch-1 signaling in wound healing and regeneration of colonic epithelium during colitis recovery phase by using conditional deletion of Notch-1 in colonic epithelium of mice. We used colonic carcinoma cell line HCT116 transiently transfected with Notch1 intracellular domain (NICD) to support in vivo data. We observed that deletion of Notch1 among mice was associated with compromised healing after colitis. Therefore, targeting the Notch-1 pathway might provide a novel therapeutic strategy for the patients recovering from colitis.

immunology↗

bioRxiv2020

The neural computations for stimulus presence and modal identity diverge along a shared circuit

The brain is comprised of neural circuits that are able to flexibly represent the complexity of the external world. In accomplishing this feat, one of the first attributes the brain must code for is whether a stimulus is present and subsequently what sensory information that stimulus contains. One of the core characteristics of that information is which sensory modality(ies) are being represented. How information regarding both the presence and modal identity of a given stimulus is represented and transformed within the brain remains poorly understood. In this study, we investigated how the brain represents the presence and modal identity of a given stimulus while tactile, audio, and audio-tactile stimuli were passively presented to non-human primates. We recorded spiking activity from primary somatosensory (S1) and ventral pre-motor (PMv) cortices, two areas known to be instrumental in transforming sensory information into motor commands for action. Using multivariate analyses to decode stimulus presence and identity, we found that information regarding stimulus presence and modal identity were found in both S1 and PMv and extended beyond the duration of significant evoked spiking activity, and that this information followed different time-courses in these two areas. Further, we combined time-generalization decoding with cross-area decoding to demonstrate that while signaling the presence of a stimulus involves a feedforward-feedback coupling between S1-PMv, the processing of modal identity is largely restricted to S1. Together, these results highlight the differing spatiotemporal dynamics of information flow regarding stimulus presence and modal identity in two nodes of an important cortical sensorimotor circuit. Significance StatementIt is unclear how the structure and function of the brain support differing sensory functions, such as detecting the presence of a stimulus in the environment vs. identifying it. Here, we used multivariate decoding methods on monkey neuronal data to track how information regarding stimulus presence and modal identity flow within a sensorimotor circuit. Results demonstrate that while neural patterns in both primary somatosensory (S1) and ventral pre-motor (PMv) cortices can be used to detect and discriminate between stimuli, they follow different time-courses. Importantly, findings suggest that while information regarding the presence of a stimulus flows reciprocally between S1 and PMv, information regarding stimulus identity is largely contained in S1.

neuroscience↗

bioRxiv2019

Whole-Genome Association Analyses of Sleep-disordered Breathing Phenotypes in the NHLBI TOPMed Program

Sleep-disordered breathing (SDB) is a common disorder associated with significant morbidity. Through the NHLBI Trans-Omics for Precision Medicine (TOPMed) program we report the first whole-genome sequence analysis of SDB. We identified 4 rare gene-based associations with SDB traits in 7,988 individuals of diverse ancestry and 4 replicated common variant associations with inclusion of additional samples (n=13,257). We identified a multi-ethnic set-based rare-variant association (p = 3.48 x 10-8) on chromosome X with ARMCX3. Transcription factor binding site enrichment identified associations with genes implicated with respiratory and craniofacial traits. Results highlighted associations in genes that modulate lung development, inflammation, respiratory rhythmogenesis and HIF1A-mediated hypoxic response.

genetics↗

bioRxiv2018

Epigenome-wide association analysis of daytime sleepiness in the Multi-Ethnic Study of Atherosclerosis reveals African-American specific associations

Study ObjectivesExcessive daytime sleepiness (EDS) is a consequence of inadequate sleep, or of a primary disorder of sleep-wake control. Population variability in prevalence of EDS and susceptibility to EDS are likely due to genetic and biological factors as well as social and environmental influences. Epigenetic modifications (such as DNA methylation-DNAm) are potential influences on a range of health outcomes. Here, we explored the association between DNAm and daytime sleepiness quantified by the Epworth Sleepiness Scale (ESS).\n\nMethodsWe performed multi-ethnic and ethnic-specific epigenome-wide association studies for DNAm and ESS in 619 individuals from the Multi-Ethnic Study of Atherosclerosis. Replication was assessed in the Cardiovascular Health Study (CHS). Genetic variants in genes proximal to ESS-associated DNAm were analyzed to identify methylation quantitative trait loci and followed with replication of genotype-sleepiness associations in the UK Biobank.\n\nResults61 methylation sites were associated with ESS (FDR [≤] 0.1) in African Americans only, including an association in KCTD5, a gene strongly implicated in sleep. One association (cg26130090) replicated in CHS African Americans (p-value 0.0004). We identified a sleepiness-associated methylation site in the gene RAI1, a gene associated with sleep and circadian phenotypes. In a follow-up analysis, a genetic variant within RAI1 associated with both DNAm and sleepiness score. The variants association with sleepiness was replicated in the UK Biobank.\n\nConclusionsOur analysis identified methylation sites in multiple genes that may be implicated in EDS. These sleepiness-methylation associations were specific to African Americans. Future work is needed to identify mechanisms driving ancestry-specific methylation effects.\n\nStatement of SignificanceExcessive daytime sleepiness is associated with negative health outcomes such as reduction in quality of life, increased workplace accidents, and cardiovascular mortality. There are race/ethnic disparities in excessive daytime sleepiness, however, the environmental and biological mechanisms for these differences are not yet understood. We performed an association analysis of DNA methylation, measured in monocytes, and daytime sleepiness within a racially diverse study population. We detected numerous DNA methylation markers associated with daytime sleepiness in African Americans, but not in European and Hispanic Americans. Future work is required to elucidate the pathways between DNA methylation, sleepiness, and related behavioral/environmental exposures.

genomics↗