Biology subjects

Sharma, V.

Publications and source records attributed to Sharma, V..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

Immunopeptidomics reveals peptide antigens preferentially presented in psoriasis lesional skin of HLA-C*06:02 carriers

BackgroundHuman leukocyte antigen (HLA)-C*06:02 is a major genetic risk factor for psoriasis and understanding the HLA-C*06:02-presented peptide antigen repertoire (immunopeptidome) in the skin of patients is crucial for identifying autoantigens. Yet, no skin immunopeptidome data from patients stratified by their HLA-C*06:02 status exists. ObjectiveWe analysed biopsies from lesional and non-lesional skin of patients with psoriasis vulgaris (n=12), guttate psoriasis (n=8), or from skin of healthy controls (n=16). MethodsHLA class I and class II peptide complexes were isolated by serial immunoprecipitation and HLA-bound peptides identified by liquid chromatography-tandem mass spectrometry. HLA-C*06:02 genotyping was performed by polymerase chain reaction. ResultsOver 99,000 non-redundant peptide ligands were identified across all samples. Substantially more HLA class I and class II peptides were detected in lesional psoriatic skin compared to matched non-lesional and healthy skin. Three peptides predicted to bind HLA-C*06:02, including MRASSFLIV from the known psoriasis marker peptidase inhibitor 3 (PI3), were identified in all lesions of HLA-C*06:02-positive patients but were rarely detected or absent in HLA-C*06:02-negative patient lesional skin and not detected at all in unaffected skin. Keratinocyte differentiation-associated protein (KRTDAP) was a notable source of lesion-specific HLA class II ligands contributing three out of six peptides detected in more than half of the lesional samples. ConclusionActive psoriatic lesions display an altered and expanded immunopeptidome compared to unaffected skin. We have identified numerous unreported, lesion-specific HLA-bound peptides and their source proteins. These findings offer insights into the pathobiology of psoriasis and provide a resource for future functional studies. CAPSULE SUMMARYA selection of immunopeptides is presented exclusively in lesional skin of HLA-C*06:02+ patients with psoriasis that may represent antigenic drivers of disease.

immunology↗

bioRxiv2026

Molecular and Energetic Basis of Histidine Switch Dynamics in Respiratory Complex I

The respiratory complex I in mitochondria and bacteria drives the two-electron reduction of quinone to pump protons across the membrane. The molecular basis of this catalytic reaction remains enigmatic despite significant progress in structural characterization of the complex. A highly conserved histidine residue in the distal antiporter-like subunit of its membrane domain has been shown to undergo conformational changes in molecular simulations and cryo-EM structures. However, the function of histidine switch dynamics, and energetics of its conformational transitions remain unclear. Here, by applying enhanced sampling simulations, we evaluate the energetics of the histidine switch dynamics and demonstrate that it is coupled to the charge state of lysine residues ca. 10 [A] apart, which cause hydrogen bond restructuring and stabilize histidine in specific conformations. Hybrid QM/MM metadynamics simulations show that the histidine participates in gated proton transfer and may function as a proton confurcation device in complex I and related proteins. Importance of workProton pumping by the mitochondrial respiratory chain enzymes needs to be highly directional so that the ATP production occurs as efficiently as possible during high energy demands. With the protons being hard to detect by most methods of structural biology, computer simulation approaches as applied in this work offer critical information on how molecular gates within respiratory complexes can function and help elucidate the challenging questions in the field of mitochondrial bioenergetics.

biophysics↗

bioRxiv2026

A continuous viral vaccine biomanufacturing platform utilizing multiple bioreactor configurations

Scalable, continuous biomanufacturing processes have grown in importance to meet demand for smaller bioreactor sizes, lowered production costs, and improved quality attributes. The Sf9/recombinant baculovirus (rBV) expression system demonstrates promise for virus-like particle (VLP) vaccine and gene therapy production. Here, we present a continuous rBV platform integrating an infection plug flow reactor (PFR) between stirred tank growth (gCSTR) and production (pCSTR) bioreactors. Cell expansion in the gCSTR included a ramp-up stage followed by continuous growth, reaching a steady state of 5x106 cells/mL and >90% viability. Peclet number-fit tracer studies confirmed near-ideal plug flow in the PFR, yielding a 10 h residence time and progressive infection as measured by gp64 signaling. Finally, a pCSTR with a residence time of 48 h exhibited sustained recombinant protein production. An integrated pilot cascade incorporating all reactors ran continuously for 5 days, maintaining stable CSTR cell densities and a measurable increase in infected cell diameter from 14.5 m to 16.1 m. Western blotting and EM of [~]100 nm VLPs in pCSTR effluent demonstrated platform success. Digital twin mechanistic models across four distinct stages of bioreactor operation and Hill-type relationships for rBV infection kinetics predicted cell growth and death for a 7-day run, demonstrating promise for designing continuous systems in silico and building a quantitative framework for scale-up and optimization. Our multi-stage reactor configuration represents a cell host- and product-agnostic production scheme, particularly for processes prone to product heterogeneity, and paves the way towards a true end-to-end continuous platform for myriad modalities in the future.

bioengineering↗

bioRxiv2025

Fitness at the Expanding Front: An Exploration-Exploitation Trade-off in Phenotypic Switching

Phenotypic switching is a key bet-hedging strategy for navigating the exploration-exploitation trade-off in fluctuating environments, yet its interplay with spatial population dynamics during range expansions remains poorly understood. We use an individual-based spatial simulation to investigate how switching strategies shape fitness (expansion speed) in heterogeneous landscapes. Maximizing expansion speed requires balancing exploration and exploitation, leading to an optimal intermediate switching rate in these spatial settings. Critically, we incorporate a phenotypic switching lag, representing the biophysical cost of adaptation. We demonstrate this lag imposes a hard fitness constraint, forcing the optimal strategy toward slower switching rates as lag duration increases and reducing maximum expansion speed. Contrasting with models focusing on irreversible mutations, we show reversible switching enhances resilience by allowing recovery from maladaptation, influencing specialist persistence boundaries. Spatial structure also generates emergent phenomena: we find clustering provides collective protection, enhancing the survival of disadvantaged phenotypes. Additionally, our simulations show that conditioning on lineage survival alone is sufficient to generate the apparent stagnancy of deleterious sectors reported experimentally, revealing this observational bias as a crucial factor when characterizing selection effects at expanding fronts. This work integrates bethedging theory with adaptation costs and spatial dynamics, offering a quantitative framework for fitness at expanding fronts.

evolutionary biology↗

bioRxiv2025

Sensitivity to ATR-CHK1 pathway inhibition in AML/MDS is enhanced by SRSF2 mutations and reduced by RUNX1 loss

SRSF2 mutations occur in up to 25% of acute myeloid leukemia (AML) and 17% of myelodysplastic syndrome (MDS) cases and are associated with poor prognosis, yet no mutation-directed therapy exists. Here, we aimed to identify therapeutically targetable vulnerabilities in MDS/AML with SRSF2 mutations. Ex vivo drug-sensitivity testing of bone marrow cells from AML patients and healthy donors showed that SRSF2-mutant cells are sensitive to inhibitors of CHK1, and WEE1 DNA damage response (DDR) kinases. To test causality, we engineered isogenic K562 cell line clones expressing SRSF2P95H/L/R mutations. RNA sequencing confirmed splicing aberrations characteristic of MDS/AML in these clones. We found that SRSF2P95H/L/R sensitize leukemia cells to ATR-CHK1-WEE1 inhibition. Bone marrow progenitors from Srsf2P95H and U2AF1S34F knock-in mice showed heightened sensitivity to CHK1 inhibition, corroborating the human data. In contrast, RUNX1 mutations were linked to resistance against CHK1 and WEE1 inhibition in SRSF2-mutant AML samples. Runx1 loss also caused resistance to CHK1 inhibitors in knock-in mouse progenitors harboring Srsf2P95H or U2AF1S34F, indicating that RUNX1 loss is a mechanism of resistance. In conclusion, SRSF2 and U2AF1 mutations are biomarkers of sensitivity to ATR-CHK1 pathway inhibitors, while RUNX1 mutations cause resistance. These biomarkers can support patient stratification in MDS/AML.

cancer biology↗

bioRxiv2025

Molecular attributes of intrinsically disordered regions in secretomes influence fungal pathogenesis

Secretory proteins are crucial for establishing fungal infection through biomolecular interactions with the host. Accumulating evidence suggest that intrinsically disordered regions (IDRs) in proteins facilitate molecular interactions. How do IDRs of secretory proteins influence fungal pathogenesis? By analyzing 195,359 secretory proteins of 73 fungal species, we find that IDRs in plant pathogen extracellular non-effectors are enriched for weak polyampholytes and polyelectrolytes. These could adopt beads-on-string conformation effectively promoting assembly of diverse enzymes aiding swift degradation of host cell wall. Both animal pathogen secretory proteins and intracellular plant pathogen effectors show enrichment for strong polyampholytes, potentially aiding phase-separation and organizing intracellular biological matter to hijack or suppress host machinery. Importantly, IDRs of plant pathogen effectors which mimic host IDRs could have emerged through convergent evolution, while those of non-effectors might have evolved de novo. Thus, specific molecular attributes of fungal secretome IDRs can influence initiation, establishment and long-term persistence of infection.

systems biology↗

bioRxiv2025

Dynamical models reveal distance to criticality in ageing brain dynamics.

Understanding how the brain changes with age remains a central question in neuroscience. Here, we combine magnetoencephalography (MEG) recordings from young and older adults with a whole-brain dynamical model to explore how brain dynamics evolve across the lifespan. Using a network of coupled Stuart-Landau oscillators constrained by empirical structural connectivity, we systematically vary three model parameters to identify the settings that best reproduce alpha-band features observed in MEG data. Our findings reveal age-related shifts in these model parameters: older individuals exhibit stronger global coupling and more positive values of the bifurcation parameter, consistent with a transition to a supercritical regime. These results align with prior work suggesting altered excitation-inhibition balance in ageing and indicate a systematic reconfiguration of whole-brain dynamics. By situating empirical observations within a dynamical systems framework, this study provides a principled approach for quantifying the brains distance to criticality and lays the groundwork for future clinical applications. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/678711v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@248e37org.highwire.dtl.DTLVardef@1f4bf00org.highwire.dtl.DTLVardef@127d894org.highwire.dtl.DTLVardef@fbdd23_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

A Protein Antibiotic Inhibits the BAM Complex to Kill Without Cell Entry

Many antibiotics are ineffective against Gram-negative pathogens such as Pseudomonas aeruginosa because they cannot penetrate the bacterial outer membrane. Here, we show that protein antibiotics called L-type pyocins kill P. aeruginosa by inhibiting the {beta}-barrel assembly machinery (BAM) complex at the cell surface, halting outer-membrane protein assembly. Using single-particle cryo-electron microscopy, we show that L-type pyocins bind a surface-exposed region of BamA and deploy a C-terminal peptide that competitively inhibits the BAM complex, demonstrating that cell entry is not required for antibiotic activity. We combine genetics, multi-omics and cryo-electron tomography to show that BAM complex inhibition by L-type pyocins or the peptide antibiotic darobactin triggers a multifaceted transcriptomic, proteomic and morphological response. Despite this, BAM inhibition ultimately leads to a catastrophic loss of membrane integrity and cell death. These results validate BAM as a target for antibiotics that do not enter the cell and define an engineerable system for their development.

microbiology↗

bioRxiv2025

Whole genome sequencing-based multi-locus association mapping for kernel iron, zinc and protein content in groundnut

Malnutrition is a major global challenge, especially in the developing regions, where improving the nutritional content of staple crops is a significant step towards alleviating hidden hunger. Groundnut, a nutrient rich legume contains several mineral nutrients, high protein, essential amino-acids and vitamins that are required for human health. In this study, multi-season phenotyping data for kernel iron (Fe), zinc (Zn) content and protein content (PC) and whole genome re-sequencing (WGRS) data on mini-core collection, were used to perform genome-wide association study (GWAS) analysis. Phenotypic variability analysis revealed a large variation in the Fe (7.6 - 42.8 ppm), Zn (10.9 - 62.4 ppm) and PC (12.7 - 33.6%). GWAS analysis identified a total of 15 marker-trait associations (MTAs) and 28 candidate genes for pooled season data, as well as 44 MTAs and 62 candidate genes for individual seasons. Key candidate genes like MYB transcription factor (Arahy.QI0PHV, Arahy.1I6ZSS), Zn finger MYM type protein, RING finger MYM type protein (Arahy.7P97F6, Arahy.9R964H, Arahy.I3B88T) and NAC domain protein (Arahy.LV3APC), associated with the Fe and Zn homeostasis pathway, genes related to protein homeostasis, such as protein kinase family protein (Arahy.4D7KBI), and E3 ubiquitin-protein ligase (Arahy.PE3CF6), were also identified within significant MTA regions. These findings provide basis for the detection and characterization of the possible candidate genes related to the nutritional quality traits. Single nucleotide polymorphism (SNP)-based KASP (Kompetitive Allele Specific Polymerase Chain Reaction) markers for 9 SNPs were designed and validated. Of these, three markers (snpAH00636, snpAH00641 and snpAH00644) showed polymorphism which could be deployed in the genomics-assisted breeding for the development of nutrient-rich groundnut varieties.

plant biology↗

bioRxiv2025

Dissecting genomic regions and candidate genes for pod borer resistance and component traits in pigeonpea minicore collection

BackgroundPigeonpea is an important leguminous food crop primarily grown in tropical and subtropical regions of the world and is a rich source of high-quality protein. The biotic (weed, disease, and insect-pests) and abiotic stresses have significantly reduced the production and productivity of pigeonpea. Helicoverpa armigera, also known as pod borer, is a major pest in pigeonpea. A substantial investigations needed for comprehending the genetic and genomic underpinnings of resistance to H. armigera. Genetic improvement by genomics-assisted breeding (GAB) is an effective approach for developing high yielding H. armigera resistance cultivars. Still yet, no genetic markers and genes linked to this key trait have been detected in pigeonpea. In this context, a set of 146 pigeonpea minicore accessions were evaluated for four H. armigera resistance component traits namely pod borer resistance (PBR), days to 50% flowering (DF), days to maturity (DM), and grain yield (GY) for three consecutive seasons under field conditions. ResultsPhenotypic data of pod borer resistance and component traits, along with the whole-genome resequencing (WGRS) data for 4,99,980 SNPs, were utilized to perform multi-locus genome-wide association study (GWAS) analysis. Two models (SUPER, and FarmCPU) detected 14 significant marker-trait associations (MTAs) for PBR and three component traits. The MTAs with significant effect were mainly identified on chromosomes CcLG02, CcLG04, CcLG05, CcLG07 and CcLG11. These MTAs subsequently delineated with key candidate genes associated with pod borer resistance (Probable carboxylesterase 15, microtubule-associated protein 5, FAR1-RELATED SEQUENCE, and Omega-hydroxypalmitate O-feruloyl transferase 4), days to maturity (RING-H2 finger protein ATL7 and Leucine-rich repeat receptor-like protein kinase), and grain yield (Secretory carrier-associated membrane protein, and Glutaredoxin-C5 chloroplastic). ConclusionThese research findings reported significant MTAs and candidate genes associated with pod borer resistance and component traits. Further lab-based pod bioassay screening identified four minicore accessions, namely ICP 10503, ICP 655, ICP 9691 and ICP 9655 (moderately resistance genotypes), showing least damage rating and larval weight gain %, compared to the susceptible checks. After validating the significant MTAs, the associated SNP markers can be effectively utilised in indirect selection, which offers potential gains for such quantitative traits with low heritability and can improve insect management more sustainably. The significant MTAs, candidate genes and resistant accessions, reported in this study may be utilized for the development of pod borer-resistant pigeonpea varieties.

plant biology↗

bioRxiv2025

Microbial Scl1 Activates TGFBR1 receptor kinase signalling to Drive Fibrosis-Inflammation Axis in Alcohol-Associated Liver Disease

Background and AimsAlcohol consumption alters gut microbiota, which can affect metabolism, immune regulation, and signalling pathways and lead to alcohol-associated liver disease (ALD). We investigated how alcohol-associated gut microbiota (AGMs) modulate liver kinome signalling to drive inflammation and fibrosis in ALD. MethodLiver kinome and metaproteome changes were studied in rats (n=6/group) colonized with stool of severe alcohol-related hepatitis (SAH) patients (SAH[->]healthy-rats) or healthy human donors (HD[->]ALD-rats). AGM-associated liver kinome changes were cross-correlated with bacterial genera. A bacterial protein; Streptococcal collagen-like protein 1 (Scl1) was identified with affinity for TGF{beta}R1. This was validated by molecular docking and immunoprecipitation-LCMS assay. Expression of Streptococcus pneumonia and pyogenes was done in stool of SAH patients (n=10). Also, Scl1 was quantified in patient stool (n=24) and liver tissue (n=19) samples. Validation was performed by assessing Scl1 level in plasma and Streptococcus level in stool samples before and after fecal microbiota transplantation (FMT) in SAH patients. ResultsStool metaproteomics showed significant increase in 10 bacterial genera (Streptococcus, Staphylococcus, and Clostridium) in SAH[->]Healthy-rats, mirroring changes seen in ALD-rats (FC>1.5, p<0.05). Clusters of Orthologous Groups analysis indicated increased post-translational modifications (PTMs) and decreased lipid metabolism in ALD-rats and SAH[->]Healthy-rats. Liver kinome profiling showed 85 upregulated kinases in SAH[->]Healthy-rats, with 34 overlapping with ALD-rats, associated with inflammation (Mapk14, Map3k10 and others), fibrosis (Tgfbr1, Igf1r, and others), lipid metabolism (Cdk14, Cdk18) and regeneration (Met, Bmpr1a and others). FMT from healthy human-donors to ALD-rats reversed the expression of Streptococcus (10-fold), Staphylococcus (3-fold), and Clostridium (5-fold), along with 18 kinases associated with inflammation (Btk, Camk4, Nuak1) and fibrosis (Tgfbr1, Col4a1, Fgfr2 and others). Strong association (r{superscript 2}>0.9, p<0.05) was seen between Streptococcus abundance and fibrosis and inflammation-related kinases. Level of Scl1 was significantly high in SAH and ALD-rat stool samples (FC>2, p<0.05). It showed strong affinity for TGF{beta}R1, as validated by molecular docking (>86%confidence) and immunoprecipitation assays (>100FC,p<0.05), indicating it as a potential ligand for TGF{beta}R1. Concordantly, expression of Scl1 was highest amongst all the known ligands for TGF{beta}R1 (p<0.05) suggesting Scl1 is a major contributor for TGF{beta}R1 activation and its downstream signalling in these patients. Following fecal microbiota transplantation, expression of Scl1 in plasma and Streptococcus levels in stool were significantly reduced by 2.1-folds and 1.9 folds respectively in SAH patients. Further, Scl1 levels SAH plasma is capable of predicting poor therapeutic response and 30-day mortality with high accuracy (AUC=0.92, cutoff >70 normalized abundance). ConclusionAlcohol induced gut dysbiosis alters the liver kinome, promoting inflammation, fibrosis, and lipid dysregulation. Streptococcal Scl1 is identified as a bacterial protein mimicking human collagen and capable of activating fibrotic signalling pathway through TGF{beta}R1in liver and is capable of predicting poor response in SAH. FMT from healthy donor restores microbial imbalance and harmful microbial-host interactions.

microbiology↗

bioRxiv2025

In situ Structure of the Human Gap Junction

Gap junction plaques (GJPs) enable direct intercellular communication and consist of connexin channels arranged into two-dimensional lattices. While structures of purified connexin channels have informed models of gating, they omit key intracellular regions and lack native context. Here, we use cryogenic electron tomography and focused ion beam milling to determine the in situ structure of human connexin-43 (Cx43) GJPs in HEK293 cells at 14 [A] resolution. We discover a previously unresolved structural role for the large C-terminal domain in mediating lateral channel-channel interactions critical for plaque assembly. Coarse-grained molecular dynamics simulations reveal how lipids and cholesterol occupy the space between adjacent connexins. These findings resolve a decades-old question regarding gap junction organization and highlight a mechanistic function for the C-terminal domain, likely regulated by phosphorylation. Our study provides a structural blueprint for understanding how connexin diversity and regulation shape tissue-level communication in health and disease.

cell biology↗

bioRxiv2025

Liver Kinome Profiling Identifies PS1145 as a Potential Therapeutic molecule for amelioration of Systemic Inflammation in Alcohol-related Liver Disease

Background and aimsAlcohol-related liver disease (ALD) has high mortality due to systemic inflammation. We analysed liver and monocyte kinome profiles in a chronic ethanol-fed pre-clinical rat model to identify therapeutic targets that could mitigate inflammation in ALD. MethodKinome profile was performed in liver and circulating monocytes at baseline, and after 8,12,16,20 and 24-weeks of 40% ethanol administration. Pathway-specific inhibitors, including PS1145 (IKK-phosphorylation inhibitor), PH-797804 (MAPK14 inhibitor), resveratrol and prednisolone were tested for their anti-inflammatory effects in ALD-rats, PBMC from patients and NIAAA mouse model. ResultsKinome profiling identified 497 liver and 345 monocyte kinases in ALD rats (FDR<0.01). A time-dependent increase in MAPK14-associated kinases was observed in both tissues (FC>1.5, p<0.05). By 24 weeks, 172 liver and 48 monocyte kinases were significantly upregulated, particularly those linked to MyD88-TLR4, PI3K-Akt, TNF, TGF{beta}, and cellular senescence pathways. Key contributors included TGF{beta}R1, ROS-generating kinases, and IL-1-driven MAPK14 and IKK phosphorylation. Targeting this axis, PS1145 (an IKK inhibitor) suppressed NF{kappa}B activation and inflammation in THP1 and HepG2 cells, as well as PBMCs from healthy and SAH patients, outperforming PH797804, resveratrol, and prednisolone (p<0.05, FC>1.5). PS1145 significantly reduced IL-6, TNF, and NF{kappa}B, while increasing IL-10. In vivo, PS1145 treatment in the NIAAA mouse model markedly reduced hepatic steatosis, cellular stress and inflammatory pathways (cytokine signalling, IL-36 signalling and others) more effectively than standard therapies, Notably, it also downregulated IL36R, impairing TLR receptor dimerization, suggesting a dual mechanism of action (p<0.05) highlighting its therapeutic potential in ameliorating systemic inflammation in ALD. ConclusionOur study highlights the key role of MAPK14 and MYD88-TLR4 pathway kinases in driving systemic inflammation in SAH. The IKK inhibitor PS1145, by blocking both IKK phosphorylation and TLR dimerization, effectively suppresses inflammatory signalling and improves liver pathology, positioning it as a promising targeted therapy for ALD.

pharmacology and toxicology↗

bioRxiv2025

Mapping Fusarium Wilt and Sterility Mosaic Disease Resistance-Associated Genomic Regions and Haplotype Variants in Pigeonpea

The occurrence of fusarium wilt and sterility mosaic disease in genial conditions causes significant yield losses in pigeonpea. The present genome-wide association study (GWAS) was employed on 176-genotype panel to identify candidate genomic regions associated with FW and SMD resistance in pigeonpea. A total of 869,447 filtered SNP markers were used for GWAS analysis. GWAS analysis identified significant genomic regions for FW on chromosomes 05, 10, and 11 and for SMD on chromosome 09. Four resistant sources, namely, ICP20096, ICP20097, ICPL87119 and ICP13304 were identified as a resistance source for both FW and SMD. Total 12 markers from chromosome 11 for FW and 4 markers from chromosome 09 for SMD were validated using the KASP genotyping approach. We have identified resistant haplotypes for FW on chromosome 10 and 11 and for SMD on chromosome 09. Moreover, we have identified four InDels for FW on chromosome 5 in Two component response regulator gene (Cc_11098) and four InDels for SMD on chromosome 9 in genes, namely, LRR and NB-ARC domain disease resistance protein (Cc_21069), Flavonoid 3, 5-hydroxylase (Cc_21070) respectively. For FW, Cc_10507586 region from chromosome 5 is identified in ICPL87119 and ICPL20096 donors. A region Cc_21637656 from chromosome 11 is identified in the ICPL87119 but not in the ICPL20096. Similarly, a region Cc_4438493 from chromosome 10 is identified in the ICPL20096 but not in the ICPL87119. For SMD, Cc_24131177 region is identified in both the SMD resistance donors (ICPL20096 and ICPL87119). Ccsmd04 region from chromosome 4 has been identified in ICPL87119 but not in the ICPL20096. These genomic regions can be brought together into single elite genetic background with the help of the markers identified in this study. The validated markers and donor lines in this study offer valuable tools and resources for the genetic improvement of pigeonpea cultivars with enhanced FW and SMD resistance.

genomics↗

bioRxiv2025

InDels in an intronic region of gene Ccsmd04 coding for dormancy/auxin-associated protein controls sterility mosaic disease resistance in pigeonpea

Sterility mosaic disease presents a significant challenge to pigeonpea cultivation in the Indian subcontinent, potentially leading to total crop failure. The development of diagnostic molecular markers for SMD resistance can aid in improving SMD-resistant varieties. In this context, a QTL-seq approach identified genomic regions associated with SMD resistance using a recombinant inbred line generated from ICP8863 x ICPL87119. In total, 6,105 high-confidence variants were identified in the genomic region, namely, smdCc04 based on the delta SNP index. A genomic region smdCc04 on chromosome Cc04 spans 3.2 Mb (9.3 - 12.5 Mb) comprised of 6 missense variants and eight indels. A total of 211 candidate genes were identified from this region. 1 bp insertion, 21 bp insertion, 9 bp deletion, and 3 bp insertion at different intronic positions in 22 susceptible line leads to downregulation of Dormancy/auxin associated protein (Ccsmd04) resulting in loss of signaling in disease resistance pathways. The identified sites recognize four important disease and plant growth related transcription factors. A total of 4 Indels and 8 SNPs were validated from smdCc04 genomic regions using whole genome re-sequencing data and KASP genotyping on resistant and susceptible pigeonpea lines respectively. These markers will be used in pigeonpea breeding programs.

genomics↗

bioRxiv2025

Genomic analysis reveals the interplay between ABA-GA in determining dormancy duration in groundnut

Groundnut is an important leguminous crop however; its productivity and seed quality are frequently reduced due to lack of fresh seed dormancy (FSD). To address this challenge, a mini-core collection of 184 accessions was phenotyped to identify donors in each agronomic type, in addition to analysing data on whole genome re-sequencing and multi-season phenotypic evaluations to identify stable marker-trait associations (MTAs) associated with FSD. Phenotypic analysis revealed substantial variability in dormancy durations, with days to 50% germination (DFG) ranging from 1 to 30 days. Multi-locus genome-wide association studies (ML-GWAS) identified 27 MTAs in individual seasons and 12 MTAs in pooled seasons data, respectively. Key candidate genes identified included Cytochrome P450 superfamily proteins, protein kinase superfamily proteins, and MYB transcription factors involved in the Abscisic acid (ABA) pathway, as well as F-box interaction domain proteins, ATP-binding ABC transporters, associated with the Gibberellic acid (GA) pathway. SNP-based KASP (Kompetitive Allele-Specific Polymerase chain reaction) markers for 12 SNPs were developed and validated, of these 6 markers (snpAH00577, snpAH00580, snpAH00582, snpAH00585, snpAH00586 and snpAH00588) showed polymorphism between dormant and non-dormant lines. Incorporating favourable dormant alleles into breeding strategies could enable the development of high-yielding cultivars with a dormancy period of 2-3 weeks.

genomics↗

bioRxiv2025

Metabolomic Profiling of Ashwagandha (Withania somnifera): Linking Bioactive Compounds to Functional Therapeutic Roles

IntroductionWithania somnifera (Ashwagandha) is a widely used medicinal plant with established roles in traditional systems of medicine. Known for diverse pharmacological effects, including neuroprotection, hepatoprotection, enhancement of male fertility, and anti-inflammatory activity. Despite its longstanding use, a deeper understanding of its phytochemical composition and bioactive mechanisms is required to bridge traditional knowledge with modern therapeutic applications. MethodsA comprehensive metabolomics profiling of Withania somnifera was performed to identify and quantify its bioactive secondary metabolites. Focus was placed on major classes such as alkaloids, phenolic compounds, and terpenoids. Known compounds were annotated and categorized based on their abundance, chemical class, and reported biological functions. Particular attention was given to compounds implicated in neuroprotection, liver health, reproductive support, and inflammation-modulation. ResultsThe analysis revealed a rich but low-abundance of known metabolites. Alkaloids such as Gentianaine (8.44%) and Sauroxine (2.94%), and phenolics like Mulberrofuran A (14.58%) and Sulphuretin (9.61%), were among the most prominent. These compounds are associated with antioxidative, anti-inflammatory, and neuroregenerative activities. Terpenoids including Pinocarvone and Ergosterol contributed to hepatoprotective and anti-inflammatory properties. Compounds such as Gomphrenin-I, Sitosterol, Pfaffic acid, beta-Carotene and others (>3%) supported spermatogenesis, while Embelin and Kievitone enhanced oxidative stress response. Although most identified compounds were individually present in low percentages (<0.30%), their collective activity suggests synergistic effects. ConclusionMetabolomic analysis of Withania somnifera confirms high abundance of bioactive secondary metabolites that have hepatoprotective, neuroprotective, anti-oxidant and spermatogenesis-enhancing effects. These findings justify protective and beneficial effect of Withania in promoting stress relief, energy, and overall wellness. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/659832v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1ae8e5forg.highwire.dtl.DTLVardef@105300corg.highwire.dtl.DTLVardef@1958320org.highwire.dtl.DTLVardef@d3ba13_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

Proton transfer through a charged conduit in respiratory complex I - long range effects and conformational gating

Energy coupling processes in respiratory complex I - a large redox-driven proton pump in the inner mitochondrial membrane - remains one of the most enigmatic problems in modern bioenergetics. Recent high-resolution cryo EM structures of complex I revealed extensive hydration in the interior of the protein, including the buried E channel, which is an acidic charged conduit that bridges the quinone binding cavity with the extended membrane domain of the enzyme. Despite the general agreement that E channel participates in proton transfer, absence of proton density in the cryo-EM maps pose a significant challenge to develop viable models of proton pumping. By adhering to the hypothesis that E channel catalyzes transfer of proton(s) from the quinone binding cavity to the membrane-bound proton pumping site(s), we performed hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations using the ~2.4 A cryo-EM structure of mitochondrial complex I from Mus musculus. By combining classical atomistic MD simulations with the hybrid QM/MM free energy calculations, we identify several energetically favorable Grotthuss-competent proton transfer paths in the E channel region. As part of the long-range coupling in complex I, our calculations show that protonation of a single acidic amino acid residue in the distal MM surroundings can alter the dynamics of proton transfer in the E channel region. Additionally, we pinpoint the gating function of a highly conserved tyrosine residue in the E channel, which undergoes conformational flipping to establish an energetically favorable proton transfer path. In the context of the redox-coupled proton pumping mechanism of complex I, we propose a stepping-stone model of proton transfer through the E channel.

biochemistry↗