Biology subjects

Patel, M. K.

Publications and source records attributed to Patel, M. K..

12 recordsLinked to original sources

bioRxiv2026

Generative Deep Learning and Molecular Dynamics Reveal Design Principles for Amyloid-Like Antimicrobial Peptides

Antimicrobial peptides (AMPs) are emerging as promising alternatives to conventional antibiotics, and growing evidence indicates a fundamental link between antimicrobial activity and amyloid-like self-assembly. Many AMPs are known to form amyloid-like fibrils, while several amyloidogenic peptides exhibit intrinsic antimicrobial properties, suggesting shared underlying physicochemical determinants such as amphipathicity, {beta}-sheet propensity, and charge distribution. However, the rational design of peptides that simultaneously encode these dual functionalities remains a significant challenge. Here, we present amyAMP, a generative deep-learning framework based on a Wasserstein generative adversarial network with gradient penalty (WGAN-GP), designed to learn and generate peptides with integrated antimicrobial and amyloidogenic properties. Trained on curated datasets of antimicrobial and amyloid-forming peptides, amyAMP captures the latent sequence-property relationships governing dual functionality. Statistical and latent-space analyses demonstrate that the generated peptides closely overlap with biologically relevant peptide space while remaining distinct from random sequences, indicating successful learning of key biochemical features. To validate functional behavior, we performed extensive coarse-grained molecular dynamics simulations to probe membrane interaction, peptide self-assembly, and membrane disruption. The simulations reveal rapid membrane adsorption, stable amphipathic insertion, and strong peptide-peptide aggregation. Notably, cooperative clustering of peptides on membrane surfaces induces membrane thinning and curvature perturbations, highlighting a mechanistic coupling between aggregation and antimicrobial activity. Collectively, these results establish that amyAMP effectively captures the shared physicochemical principles underlying antimicrobial action and amyloid-like self-assembly. This work provides a generalizable framework for the AI-guided design of multifunctional peptides to advance the development of next-generation therapeutics targeting antimicrobial resistance.

biophysics↗

bioRxiv2025

Base Editing Rescue of Seizures and SUDEP in SCN8A Developmental Epileptic Encephalopathy

SCN8A encodes the voltage-gated sodium channel Nav1.6 which plays a key role in facilitating neuronal excitability. Mutations in SCN8A, particularly gain-of-function missense variants, are associated with SCN8A developmental and epileptic encephalopathy (DEE), a severe epilepsy syndrome characterized by spontaneous seizures, movement disorders, cognitive dysfunction, and sudden unexpected death in epilepsy (SUDEP). The recurrent SCN8A variant R1872W destabilizes inactivation of the sodium channel, resulting in neuronal hyperexcitability and onset of seizures. Current treatments, including anti-seizure medications (ASMs) that broadly target sodium channels, are often ineffective in SCN8A DEE patients and are associated with significant side effects, highlighting the need for targeted therapies. In this study, we utilized base editing as a therapeutic strategy to correct the patient derived R1872W SCN8A variant. Using two engineered mammalian cell line screens, we identified several targeting constructs that successfully reverted the R1872W variant to the reference allele. Our most effective construct, a modified adenine base editor, along with a paired successful guide RNA, was selected and packaged within a dual PhP.eB-adeno-associated virus (AAV) delivery system. This dual AAV therapy, referred to as SCN8A-ABE, was administered to mice expressing the R1872W variant at P2. Treatment with SCN8A-ABE significantly increased survival of mice expressing R1872W and either significantly reduced or completely inhibited seizure occurrence. Assessment of editing efficiencies revealed approximately 30% conversion of the mutant tryptophan to wildtype arginine observable in RNA transcripts from hippocampal and cortex tissue. Electrophysiological recordings revealed a rescue of seizure-associated neuronal hyperexcitability and a suppression of the pathogenic sodium channel behavior in treated mice. Associated comorbidities, including movement disorders and anxiety-like behaviors, were also improved in treated mice. These findings demonstrate the profound potential of base editing as a targeted and effective therapeutic approach for SCN8A DEE, addressing the underlying genetic mutation driving the disease.

bioengineering↗

bioRxiv2025

FG-Nup Sequence Length Polydispersity Enhances Selectivity of NPC Translocation

The central channel of the nuclear pore complex (NPC) exhibits polydispersity in FG-nucleoporin (FG-Nup) sequence length, with longer FG-Nups on the periphery and shorter FG-Nups in the interior of the pore. The functional role of FG-Nup polydispersity in NPC transport was investigated using a minimal, coarse-grained model and Langevin dynamics simulations. The NPC was modelled as a cylindrical pore lined with a random copolymer brush composed of hydrophobic and hydrophilic segments, mimicking FG-Nups. The total number of hydrophobic segments corresponded to the fraction of FG-repeats, f, in the FG-Nups. The translocation of karyopherin-bound spherical cargo (12 nm spherical tracers) was simulated through two model NPCs; a homogeneous NPC (h-NPC) with uniform FG-Nup lengths and an inhomogeneous NPC (ih-NPC) featuring shorter FG-Nups in the middle and longer FG-Nups at the periphery. The ih-NPC demonstrated enhanced selectivity and significantly higher passage probabilities for karyopherin-bound tracers, with an increase of up to 90% compared to h-NPC. Analysis of binding contacts between tracers and FG-Nup hydrophobic segments revealed that tracer translocation was facilitated by a handover process between successive FG-Nups along the NPC length. The enhanced selectivity of the ih-NPC was attributed to an increase in binding contacts of the tracer with the shorter FG-Nups in its middle region. These findings provide a biophysical basis for the evolutionary significance of FG-Nup polydispersity in selective NPC transport.

biophysics↗

bioRxiv2024

A Brain Reward Circuit Inhibited By Next-Generation Weight Loss Drugs

Glucagon-like peptide-1 receptor agonists (GLP1RAs) effectively reduce body weight and improve metabolic outcomes, yet established peptide-based therapies require injections and complex manufacturing. Small-molecule GLP1RAs promise oral bioavailability and scalable manufacturing, but their selective binding to human versus rodent receptors has limited mechanistic studies. Here, we developed humanized GLP1R mouse models to investigate how small-molecule GLP1RAs influence feeding behavior. This approach revealed that these compounds regulate both homeostatic and hedonic feeding through parallel neural circuits. Beyond engaging canonical hypothalamic and hindbrain networks that control metabolic homeostasis, GLP1RAs recruit a discrete population of Glp1r-expressing neurons in the central amygdala, which selectively suppress the consumption of palatable foods by reducing dopamine release in the nucleus accumbens. Stimulating these central amygdalar neurons curtail hedonic feeding, whereas targeted deletion of the receptor in this cell population specifically diminishes the anorectic efficacy of GLP1RAs for reward-driven intake. These findings reveal a dedicated neural circuit through which small molecule GLP1RAs modulate reward processing, suggesting broad therapeutic potential in conditions of dysregulated dopamine signaling including substance use disorder and binge eating.

neuroscience↗

bioRxiv2024

Microenvironment T-Type calcium channels regulate neuronal and glial processes to promote glioblastoma growth

BackgroundGlioblastoma (GBM) is the most common primary malignant brain tumor. The aim of this study was to elucidate the role of microenvironment and intrinsic T-type calcium channels (Cav3) in regulating tumor growth and progression. MethodsWe grafted syngeneic GBM cells into Cav3.2 knockout mice to assess the role of microenvironment T-Type calcium channels on GBM tumor growth. We performed single-cell RNA-seq (scRNA-seq) of tumors from WT and Cav3.2 KO mice to elucidate the regulation of tumors by the microenvironment. We used neurons from WT and Cav3.2 KO mice in co-culture with GBM stem cells (GSC) to assess the effects of Cav3.2 on neuron/GSC synaptic connections and tumor cell growth. ResultsCav3.2 KO in the microenvironment led to significant reduction of GBM growth and prolongation of animal survival. scRNA-seq showed that microenvironment Cav3.2 regulates neuronal and glial biological processes. Microenvironment Cav3.2 downregulated numerous genes associated with regulating the OPC cell state in GBM tumors such as SOX10 and Olig2. Neuronal Cav3.2 promoted neuron/GSC synaptic connections and GSC growth. Treatment of GSCs with the Cav3 blocker mibefradil downregulated genes associated with neuronal processes. The Cav3 blocker drug mibefradil synergized with temozolomide (TMZ) and radiation to reduce in vivo tumor growth and prolong animal survival. ConclusionsTogether these data reveal a role for microenvironment Cav3 in promoting GBM tumor progression through regulating neuronal and glial processes particularly associated with the OPC-cell state. Targeting both intrinsic and microenvironment Cav3 with the inhibitor mibefradil significantly enhanced the anti-GBM effects of TMZ and radiation. Key PointsO_LIMicroenvironment Cav3.2 promotes GBM progression C_LIO_LIMicroenvironment Cav3.2 promotes neuronal and glial processes C_LIO_LIPharmacological targeting of intrinsic and microenvironment Cav3 synergizes with TMZ/radiation C_LI Importance of the StudyIn this study, we demonstrate for the first time that microenvironment Cav3.2 contributes to GBM progression and growth by regulating neuronal and glial processes. Our findings highlight the importance of T-type calcium channels in the microenvironment as well as the tumor and provides preclinically relevant data for the use of mibefradil to inhibit GBM growth in combination with standard of care therapies.

cancer biology↗

bioRxiv2024

Cdhr1a and pcdh15b link photoreceptor outer segments with inner segment calyceal processes revealing a potential mechanism for cone-rod dystrophy.

Cone rod dystrophy (CRD) is a macular degeneration disorder characterized by initial cone cell photoreceptor degeneration and subsequently of rod photoreceptors. Mutations in CDHR1, a photoreceptor specific cadherin have been found to be associated with the incidence of cone-rod dystrophy and recapitulated in mouse CDHR1 knockouts. However, the molecular function of CDHR1 remains unknown. CDHR1 has been shown to localize at the leading edge of murine rod nascent outer segment (OS) making junctions to an unknown partner in the inner segment. Using Structured Illumination Microscopy (SIM), we observed that the localization of zebrafish cdhr1a extends from basal nascent OS discs above the periciliary ridge of the inner segment to a considerable length along the OS, akin to calyceal process (CPs). When labeling the CPs using pcdh15b, a CP specific cadherin, we observed that cdhr1a at the leading edge of OS juxtaposes with pcdh15b in the CP. Similar localization patterns were detected in human, macaque, xenopus, ducks, and various rodent PRCs indicating conservation. Importantly, using immunoprecipitation and K652 cell aggregation assays we demonstrate that pcdh15b and cdhr1a can interact and potentially link the OS and CP. To analyze the consequences of OS-CP interactions in CRD, we established a zebrafish cdhr1a mutant line (cdhr1afs*146) and analyzed CRD progression at high temporal resolution. Homozygous cdhr1afs*146 mutants begin to exhibit minor cone OS morphology defects starting at 15 dpf (days post fertilization) and severe OS disruption and cell loss by 3 months. Rod OS defects were delayed until 3-6 months. Furthermore, we show that loss of cdhr1a function leads to disorganization and shortening of CPs coinciding with cone outer OS defects which is significantly exacerbated when combined with the loss of pcdh15b. In conclusion, we propose that cdhr1a and pcdh15b function to link cone OSs with CPs to maintain proper OS homeostasis thus revealing a potential novel mechanism for CRD.

developmental biology↗

bioRxiv2024

Parvalbumin Interneuron Impairment Leads to Synaptic Transmission Deficits and Seizures in SCN8A Epileptic Encephalopathy

SCN8A epileptic encephalopathy (EE) is a severe epilepsy syndrome resulting from de novo mutations in the voltage-gated sodium channel Nav1.6, encoded by the gene SCN8A. Nav1.6 is expressed in both excitatory and inhibitory neurons, yet previous studies have primarily focused on the impact SCN8A mutations have on excitatory neuron function, with limited studies on the importance of inhibitory interneurons to seizure onset and progression. Inhibitory interneurons are critical in balancing network excitability and are known to contribute to the pathophysiology of other epilepsies. Parvalbumin (PV) interneurons are the most prominent inhibitory neuron subtype in the brain, making up about 40% of inhibitory interneurons. Notably, PV interneurons express high levels of Nav1.6. To assess the role of PV interneurons within SCN8A EE, we used two mouse models harboring patient-derived SCN8A gain-of-function mutations, Scn8aD/+, where the SCN8A mutation N1768D is expressed globally, and Scn8aW/+-PV, where the SCN8A mutation R1872W is selectively expressed in PV interneurons. Expression of the R1872W SCN8A mutation selectively in PV interneurons led to the development of spontaneous seizures in Scn8aW/+-PV mice and seizure-induced death, decreasing survival compared to wild-type. Electrophysiology studies showed that PV interneurons in Scn8aD/+ and Scn8aW/+-PV mice were susceptible to depolarization block, a state of action potential failure. Scn8aD/+ and Scn8aW/+-PV interneurons also exhibited increased persistent sodium current, a hallmark of SCN8A gain-of-function mutations that contributes to depolarization block. Evaluation of synaptic connections between PV interneurons and pyramidal cells showed an increase in synaptic transmission failure at high frequencies (80-120Hz) as well as an increase in synaptic latency in Scn8aD/+ and Scn8aW/+-PV interneurons. These data indicate a distinct impairment of synaptic transmission in SCN8A EE, potentially decreasing overall cortical network inhibition. Together, our novel findings indicate that failure of PV interneuron spiking via depolarization block along with frequency-dependent inhibitory synaptic impairment likely elicits an overall reduction in the inhibitory drive in SCN8A EE, leading to unchecked excitation and ultimately resulting in seizures and seizure-induced death.

neuroscience↗

bioRxiv2024

The endophytic fungus Serendipita indica alters auxin distribution in Arabidopsis thaliana roots through alteration of auxin transport and conjugation to promote plant growth

Plants share their habitats with a multitude of different microbes. This close vicinity promoted the evolution of inter-organismic interactions between plants and many different microorganisms that provide mutual growth benefits both to the plant and the microbial partner. The symbiosis of Arabidopsis thaliana with the beneficial root colonizing endophyte Serendipita indica represents a well-studied system. Co-colonization of Arabidopsis roots with S. indica significantly promotes plant growth. Due to the notable phenotypic alterations of fungus-infected root systems, the involvement of a reprogramming of plant hormone levels, especially that of indole-3-acetic acid, has been suggested earlier. However, until now, the molecular mechanism by which S. indica promotes plant growth remains largely unknown. This study used comprehensive transcriptomics, metabolomics, reverse genetics, and life cell imaging to reveal the intricacies of auxin-related processes that affect root growth in the symbiosis between A. thaliana and S. indica. Our experiments revealed the essential role of tightly controlled auxin conjugation in the plant-fungus interaction. It particularly highlighted the importance of two GRETCHEN HAGEN 3 (GH3) genes, GH3.5 and GH3.17, for the fungus infection-triggered stimulation of biomass production, thus broadening our knowledge about the function of GH3s in plants. Furthermore, we provide evidence for the transcriptional alteration of the PIN2 auxin transporter gene in roots of Arabidopsis seedlings infected with S. indica and demonstrate that this transcriptional adjustment affects auxin signaling in roots, which results in increased plant growth.

plant biology↗

bioRxiv2023

Emergence of selectivity and specificity in a coarse-grained model of the nuclear pore complex with sequence-agnostic FG-Nups

The role of hydrophobicity of phenylalanine-glycine nucleoporins (FG-Nups) in determining transport of receptor-bound cargo across the nuclear pore complex (NPC) is investigated using Langevin dynamics simulations. A coarse-grained, minimal model of the NPC, comprising a cylindrical pore and hydrophobic-hydrophilic random copolymers for FG-Nups was employed. Karyopherin-bound receptor-cargo complexes (Kaps) were modeled as rigid, coarse-grained spheres without (inert) and with (patchy) FG-binding hydrophobic domains. With a sequence-agnostic description of FG-Nups and the absence of any anisotropies associated with either NPC or cargo, the model described tracer transport only as a function of FG-Nup hydrophobicity, f. The simulations showed the emergence of two important features of cargo transport, namely, NPC selectivity and specificity. NPC selectivity to patchy tracers emerged due to hydrophobic Kap-FG interactions and despite the sequence-agnostic description of FG-Nups. Further, NPC selectivity was observed only in a specific range of FG-hydrophobic fraction, 0.05 [≤] f [≤] 0.20, resulting in specificity of NPC transport with respect to f. Significantly, this range corresponded to the number fraction of FG-repeats observed in both S. cerevisiae and H. sapiens NPCs. This established the centrality of FG-hydrophobic fraction in determining NPC transport, and provided a biophysical basis for conservation of FG-Nup hydrophobic fraction across evolutionarily distant NPCs. Specificity in NPC transport emerged from the formation of a hydrogel-like network inside the pore with a characteristic mesh size dependent on f. This network rejected cargo for f > 0.2 based on size exclusion which resulted in an enhanced translocation probability for 0.05 [≤] f [≤] 0.20. Thus, the NPC model provides a template for designing synthetic, biomimetic nanopores for macromolecular separations with high degrees of selectivity and specificity.

biophysics↗

bioRxiv2021

DNA Methyltransferase 1 and 3a Expression in the Frontal Cortex Regulates Palatable Food Consumption

DNA methylation is an important regulatory mechanism in the control of neuronal function. Both during development and following exposure to salient stimuli, plasticity in the methylation of cytosine residues leads to a change in neuron excitability that subsequently sculpts animal behavior. However, although the response of DNA methyltransferase enzymes in adult neurons to stimuli such as drugs of abuse have been described, less is known about how these enzymes regulate methylation at specific loci to change the drive to ingest natural rewards. Specifically, we do not understand how changes in methylation within important brain areas known to regulate palatable food intake can affect ingestion, while a detailed investigation of the neurophysiological and genomic effects of perturbing methyltransferase function has not been pursued. By deleting DNA methyltransferase 1 and 3a in the mouse prefrontal cortex, we observed the requirement for these enzymes in the regulation of nutrient rich food consumption in the absence of any effect on the intake of low fat and low sugar chow. We also determined that the deletion profoundly affected neuron excitability within pyramidal cells resident in superficial layers II/III of the cortex but had little effect in deep layer V neurons. Finally, reduced representation bisulfite sequencing revealed both hypo and hypermethylation in response to methyltransferase deletion, an effect that was observed in binding sites for retinoic acid receptor beta (RAR{beta}) located within regulatory regions of genes known to affect neuronal function. Together, our data suggest that alterations in the actions of RAR{beta} could shift neuronal activity to reduce palatable food intake.

neuroscience↗

bioRxiv2021

Somatostatin-positive Interneurons Contribute to Seizures in SCN8A Epileptic Encephalopathy

SCN8A epileptic encephalopathy is a devastating epilepsy syndrome caused by mutant SCN8A which encodes the voltage-gated sodium channel NaV1.6. To date, it is unclear if and how inhibitory interneurons, which express NaV1.6, influence disease pathology. We found that selective expression of the R1872W mutation in somatostatin (SST) interneurons was sufficient to convey susceptibility to audiogenic seizures. SST interneurons from mutant mice were hyperexcitable but hypersensitive to action potential failure via depolarization block under normal and seizure-like conditions. Remarkably, GqDREADD-mediated activation of wild-type SST interneurons resulted in prolonged electrographic seizures and was accompanied by SST hyperexcitability and depolarization block. Aberrantly large persistent sodium currents, a hallmark of SCN8A mutations, were observed and were found to contribute directly to aberrant SST physiology in computational and pharmacological experiments. These novel findings demonstrate a critical and previously unidentified contribution of SST interneurons to seizure generation not only in SCN8A encephalopathy, but epilepsy in general.

neuroscience↗

bioRxiv2021

Coordinated overexpression of OsSUT1, OsSWEET11 and OsSWEET14 in rice impairs carbohydrate metabolism that has implications in plant growth, yield and susceptibility to Xanthomonas oryzae pv oryzae (Xoo)

Enhancing carbohydrate export to sink tissues is considered as a feasible approach for improving photosynthetic efficiency and crop yield. In Oryza sativa Sucrose Transporter OsSUT1 located in companion cells and Sugars Will Eventually be Exported Transporters (SWEETs); OsSWEET11 and OsSWEET14 present in phloem parenchyma mesophyll cell plasma membranes are involved in long distance sucrose transport. OsSWEET11 and OsSWEET14 also play important role in host-pathogen interaction of rice plants and Xanthomonas oryzae pv oryzae (Xoo) that causes bacterial leaf blight. Three genes, OsSUT1, OsSWEET11, and OsSWEET14 were overexpressed under the control of their native promoters in rice to modulate long distance sugar transport and disease resistance. The transgenics displayed several phenotypic aberrations such as reduced plant height and seed weight due to altered sucrose transport and metabolism. Lower sucrose transport rate in transgenics than the WT resulted in reduced sucrose, fructose and glucose and increased starch accumulation in their leaves at the end of dark period. Transcriptional analysis revealed a reduction in the expression of genes involved in sucrose synthesis pathway in transgenics. Normal growth and development of transgenic seedlings were restored in growth media supplemented with 3% sucrose demonstrating in planta sucrose limitation. Remarkably, transgenic lines had diminished susceptibility to Xoo than the WTs due to low sugar content in the leaves demonstrating that rice plants maintain an optimum level of SWEETs for proper plant growth and development, and upregulation of these SWEETs in rice mimicks Xoo attack impelling plants to reduce sugar content in the apoplasm to inhibit pathogen growth.

plant biology↗