Biology subjects

Rout, S.

Publications and source records attributed to Rout, S..

6 recordsLinked to original sources

bioRxiv2026

Divergent Behavioral and Circuit-Level Adaptations to Acute and Chronic Gastric Electrical Stimulation

Anxiety disorders are highly prevalent and often refractory to existing treatments, motivating the development of alternative neuromodulatory strategies. Peripheral bioelectronic approaches targeting the gut-brain axis such as vagus nerve stimulation (VNS) demonstrate that modulation of visceral afferent pathways can influence central emotional circuits. Gastric electrical stimulation (GES) is a clinically established therapy for gastrointestinal motility disorders. While the stomach is densely innervated by vagal afferents, the effect of GES on anxiety-related behavior has not been systematically examined. We sought to identify neural pathways engaged by GES and effects of continuous chronic GES on behavior. To do this, we developed a gastric stimulation platform for rodents, a fully implantable, untethered system enabling chronic neuromodulation in freely moving rats. We combined this with cross-species whole-brain activity mapping in mice to interrogate circuit-level mechanisms. Using open field and elevated plus mazes, together with machine-learning-based behavioral tracking and multivariate modeling, we show that acute GES induces a robust, context-dependent anxiogenic phenotype characterized by reduced exploration and increased freezing, particularly in novel open-field environments. In contrast, chronic GES produces a divergent post-stimulation behavioral profile marked by enhanced exploratory behavior relative to acutely stimulated animals, indicating temporally dynamic reorganization of anxiety-related behavior. Principal component analysis and hierarchical clustering further revealed that stimulation reshapes the multivariate structure of behavioral features rather than shifting animals along a single anxiety continuum. Whole-brain c-Fos mapping revealed anatomically distributed modulation of limbic-cortical networks following gastric stimulation, including suppression of ventral medial entorhinal cortex, excitation of nucleus tractus solitarii and heterogeneous recruitment of amygdalar and hippocampal subregions. These circuit-level patterns align with the behavioral dissociation between contextual exploration and explicit threat avoidance, providing convergent cross-species evidence that gastric stimulation engages distributed anxiety-related networks. Together, these findings establish the first freely moving behavioral model of chronic gastric neuromodulation, demonstrate temporally dynamic and context-sensitive effects on anxiety-like behavior, and provide systems-level validation that the stomach can serve as a viable peripheral access point for modulating central emotional circuits.

bioengineering↗

bioRxiv2026

Genetic code expansion enables programmable covalent protein design

Covalent chemistry has transformed small-molecule drug discovery, yet analogous strategies for proteins remain largely inaccessible because covalent warheads cannot be readily integrated into biologics. Conventional genetic code expansion requires engineering a dedicated aminoacyl-tRNA synthetase for each new amino acid, rendering broad warhead screening impractical. Here we introduce AminoX, a platform that bypasses this limitation through direct tRNA acylation, enabling site-specific incorporation of chemically diverse non-standard amino acids (nsAAs), including covalent warhead nsAAs compatible with scalable biologic manufacturing and multifunctional nsAAs. Using a pooled mRNA display workflow, we screened more than 2,000 warhead-position combinations in machine learning-designed de novo miniproteins targeting CTLA-4, enabling parallel interrogation of covalent chemistry, linker geometry, and incorporation site. We confirmed covalent engagement on cells together with enhanced functional blockade. Finally, we demonstrate multifunctional nsAAs that combine covalent warheads with fluorogenic reporters for real-time detection of target engagement, as well as dual nsAA incorporation for macrocyclization and fluorescent imaging of covalent binding on cell surfaces. By uniting synthetic biology, chemical biology, generative protein design, and high-throughput functional selection, AminoX compresses covalent protein engineering timelines by orders of magnitude, accelerating the development of next-generation therapeutics, biosensors, and chemical probes.

synthetic biology↗

bioRxiv2026

Females are protected from semaglutide-induced muscle loss in ob/ob mice

Obesity is a major contributor to cardiometabolic disease, and pharmacological therapies such as semaglutide are increasingly used to induce weight loss. However, the commonly used diet-induced obesity model in C57BL/6J mice is limited by relative resistance to weight gain in females, complicating the study of sex-specific effects. Here, we used leptin-deficient ob/ob mice, which develop severe early-onset obesity in both sexes, to investigate sex-specific responses to semaglutide on skeletal muscle mass, function, and mitochondrial metabolism. The ob/ob mice were treated daily with semaglutide or vehicle for three weeks, followed by assessments of body composition, muscle and organ mass, muscle contractile function, and mitochondrial efficiency. Semaglutide induced comparable reductions in body weight and food intake in both sexes but elicited distinct sex-specific changes in body composition. Male mice exhibited losses in both skeletal muscle and organ mass, whereas female mice preferentially lost fat and organ mass while preserving skeletal muscle. Despite these divergent structural adaptations, muscle force generation remained intact in both sexes. Collectively, these findings reveal pronounced sexual dimorphism in skeletal muscle and metabolic remodeling during pharmacologically induced weight loss, highlighting the importance of considering biological sex when evaluating the metabolic and therapeutic effects of anti-obesity interventions. Article HighlightO_LIC57BL/6J mice are limited by relative resistance to weight gain in females, complicating the study of sex-specific effects. So, we wanted to determine the sex-specific effect of semaglutide on skeletal muscle function, and mitochondrial metabolism in ob/ob mice. C_LIO_LIWe assessed body composition and ex-vivo muscle force following the treatment and found that the female ob/ob mice are protected from semaglutide-induced skeletal muscle mass loss. C_LIO_LIThese findings demonstrate sex-specific effects of semaglutide, highlighting the need to consider biological sex in GLP-1RA-based therapies. C_LI

physiology↗

bioRxiv2026

Mitochondrial Bioenergetic Uncoupling and Strain-Dependent Adaptations in a High-Fat, High-Salt Model of Metabolic Dysfunction-Associated Kidney Disease

Metabolic dysfunction-associated kidney disease (MDAKD) is closely linked to dietary excess, but models that capture early kidney injury without obesity are limited. We fed male C57BL/6J (6J) and C57BL/6N (6N) mice a high-fat, high-sodium (HF/HNa) or control diet for 16 weeks. HF/HNa feeding did not alter body weight, adiposity, or total food intake; however, it increased dietary energy and sodium exposure, kidney mass, water intake, and urine volume. GFR declined modestly in 6J mice, whereas 6N mice maintained or slightly increased GFR. Both substrains showed increased urinary albumin, creatinine, KIM-1, and NGAL, while cystatin C rose predominantly in 6N mice, indicating strain-dependent tubular injury. Whole-kidney trichrome staining revealed increased fibrotic area with HF/HNa, particularly in 6N mice, without significant changes in glomerular morphology. In isolated renal mitochondria, oxygen consumption was preserved, but ATP production and ATP:O ratios were reduced, with unchanged citrate synthase activity and OXPHOS protein abundance, consistent with early mitochondrial bioenergetic uncoupling. Exploratory urinary proteomics in 6J mice identified HF/HNa-associated changes in proteins linked to tubular stress and extracellular matrix remodeling. These findings define an early MDAKD-like renal phenotype with strain-specific functional responses, tubular injury, fibrosis, and impaired mitochondrial ATP efficiency. Translational StatementMetabolic Dysfunction-Associated Kidney Disease (MDAKD) is a leading driver of chronic kidney disease (CKD) in the world. In addition to obesity and related comorbidities, renal mitochondrial dysfunction is thought to be a key contributor to the development of CKD in patients with MDAKD; however, few models recapitulate the progression of MDAKD. We couple well-established mouse models of obesity, namely the C57Bl/6J and C57Bl/6N mouse lines, with a high-fat, high-salt diet to induce renal mitochondrial dysfunction, leading to early stages of MDAKD as indicated by widespread fibrosis and mild reduction in glomerular filtration rate, though these effects were strain-dependent. We identify diet-induced mitochondrial dysfunction as a common feature in both mouse strains, suggesting impairments in mitochondrial respiration and oxidative ATP production are indeed a contributing factor to the development of MDAKD. This study highlights the role of energetic impairments in the pathogenesis of MDAKD and may guide future therapies for CKD.

physiology↗

bioRxiv2024

Muscle-specific Keap1 deletion enhances force production but does not prevent inactivity-induced muscle atrophy in mice

Immobilization-associated muscle atrophy and weakness appear to be driven in part by oxidative stress. Nuclear Factor Erythroid 2-Related Factor 2 (NRF2) is a critical redox rheostat that regulates oxidative stress responses, and its deletion is known to accelerate muscle atrophy and weakness during aging (sarcopenia) or denervation. Conversely, pharmacologic activation of NRF2 extends mouse lifespan and attenuates sarcopenia. Similarly, deletion of Kelch-like ECH-associated Protein 1 (Keap1), negative regulator of NRF2, enhances exercise capacity. The purpose of this study was to determine whether muscle-specific Keap1 deletion is sufficient to prevent muscle atrophy and weakness in mice following 7-days of hindlimb unloading (HU). To test this hypothesis, control (Ctrl) and tamoxifen inducible, muscle-specific Keap1 knockout (mKO) mice were subjected to either normal housing (Sham) or HU for 7 days. Activation of NRF2 in muscle was confirmed by increased mRNA of NRF2 targets thioredoxin 1 (Txn1) and NAD(P)H quinone dehydrogenase 1 (NQO1) in mKO mice. Keap1 deletion had an effect to increase force-generating capacity at baseline. However, muscle masses, cross sectional area, and ex vivo force were not different between mKO and Ctrl HU mice. In addition, muscle 4-hydroxynonenal-modified proteins and protein carbonyls were unaffected by Keap1 deletion. These data suggest NRF2 activation improves muscle force production during ambulatory conditions but is not sufficient prevent muscle atrophy or weakness following 7-days of HU. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=95 SRC="FIGDIR/small/616570v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@433d1eorg.highwire.dtl.DTLVardef@61996dorg.highwire.dtl.DTLVardef@19fe734org.highwire.dtl.DTLVardef@104205f_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Unravelling ATP processing by the AAA+ protein p97 at the atomic level

The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of homeostasis and impactful pharmacological target. The hexameric complex undergoes substantial conformational changes in the course of its catalytic cycle. Here, we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and MD simulations. p97 populates a metastable reaction intermediate, the ADP.Pi state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.

biophysics↗