Biology subjects

Singh, A.

Publications and source records attributed to Singh, A..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

High-Frequency Spinal Cord Stimulation Reorganizes Cortical Cross-Frequency Coupling in a Region- and Time-Dependent Manner

Pain management strategies have progressed beyond traditional pharmacologic and physical interventions, integrating advanced neuromodulation techniques such as deep brain stimulation, peripheral nerve stimulation, and high-frequency spinal cord stimulation (hSCS). Despite its clinical efficacy, the supraspinal mechanisms underlying hSCS remain poorly understood. Prior work in sheep demonstrated that hSCS modulates gamma ({gamma}) band (70-150 Hz) activity in the primary somatosensory and association cortices, implicating cortical involvement in pain modulation. Given, the interaction between low and high oscillations, we hypothesized that hSCS modulates {gamma} activity in a region- and time-dependent manner through specific coupling with theta ({square}) rhythms (4-8 Hz). Using 96-channel subdural electrocorticography (ECoG), we computed {square}-{gamma} phase-amplitude coupling (PAC) and the corresponding modulation index (MI) to quantify the effects of hSCS. While the preferred {square}phase of {gamma} activity remained consistent across conditions and regions, MI increased significantly post-stimulation--most prominently in the association cortex, where robust -{gamma} phase locking was observed. In contrast, the somatosensory cortex exhibited weaker and more variable locking. Temporally, both cortices demonstrated an early, rapid increase in MI post-hSCS, accompanied by a shift (association) and attenuation (somatosensory) of the secondary peak. These findings reveal distinct regional and temporal dynamics in PAC following hSCS and suggest complementary roles of somatosensory and association cortices in processing neuromodulatory input. hSCS appears to reorganize cortical cross-frequency interactions, supporting its role in reorganizing functional network dynamics relevant to sensory processing and the subjective pain experience.

neuroscience↗

bioRxiv2025

Monoallelic expression characterizes a distinct molecular and clinical group of breast tumors

In diploid cells, allelic imbalance occurs when gene alleles are expressed at different levels. To investigate the allelic imbalance landscape in tumor samples, we developed Interval-Based Allelic Imbalance Detection (IB-Aid), a quantitative framework that uses interval arithmetic to robustly distinguish monoallelic from biallelic gene expression by computing confidence intervals based on sequencing measurement uncertainty. We applied this approach to The Cancer Genome Atlas Breast Invasive Carcinoma tumor samples and through unsupervised gene enrichment analyses, identified a group of patients with a distinct monoallelic gene expression signature. Notably, these patients were enriched in Black/African American patients and had tumors which had not been previously classified into any established molecular subtype. Clinically, these tumors were associated with poor overall survival, with survival outcomes comparable to the aggressive basal subtype. These findings suggest a potential link between allelic imbalance and breast cancer development and point to genetic and epigenetic mechanisms that drive allelic imbalance as novel biomarkers for prognosis and design of targeted treatment strategies.

cancer biology↗

bioRxiv2025

Gut bacteria generate prodrugs in situ increasing systemic drug exposure

The human gut microbiome has been increasingly recognized as a metabolic compartment that influences health and therapeutic responses. While recent studies have cataloged diverse sets of drug biotransformation reactions as a result of microbial metabolism1-3, the pharmacological relevance of the resulting drug metabolites remains mostly uncharacterized. We investigated whether certain microbial drug metabolites can act as functional prodrugs. By systematically mining 871 putative drug metabolites produced by gut bacteria1, we identified microbial drug metabolites with key physicochemical properties of prodrugs. Using bacterial culturing, a genetic gain-of-function screen coupled to mass spectrometry and comparative genomics, we uncover that Bacteroidota bacteria encode conserved methyltransferases that can generate prodrugs through carboxyl methylation. As a case in point, we demonstrate that bezafibrate gets converted to a prodrug by a distinct bacterial enzyme, increasing epithelial drug permeability in vitro and systemic drug exposure in vivo in a gnotobiotic mouse model. Additionally, we tested 170 structurally and clinically diverse drugs, and demonstrate that microbial drug-prodrug conversion is a common result of gut bacterial drug biotransformation. Altogether, our findings suggest a novel mechanism of how the gut microbiota influences an individuals pharmacokinetics, and may generally cause interpersonal differences in microbiota-host metabolic interactions.

microbiology↗

bioRxiv2025

Abiotic Stress-Mediated Modulation of the tncRNome: Unraveling tRNA-Derived RNA Networks in Plant Adaptive Responses

Transfer RNA-derived non-coding RNAs (tncRNAs) are potential regulators of gene expression in plants, and its crucial to understand their diversity and functional roles in modulating plant stress responses. Here, we have investigated abiotic stress-responsive tncRNAs in two important crops, rice and chickpea, under drought and salt stress conditions. Small RNA sequencing revealed that 70.2% of tncRNAs in rice and 45% in chickpea were commonly expressed across multiple stress conditions. qRT-PCR validation showed that most tRF-5s were upregulated in both rice and chickpea under drought and salt stress. In rice, 3'tRHs were specifically induced by drought, whereas 5'tRHs responded predominantly to salt stress. In chickpea, tRF-3s were upregulated during drought but downregulated under salt stress. Furthermore, we confirmed the mRNA targets of these stress-associated tRNA fragments using RLM-RACE, thereby verifying the cleavage of specific target mRNAs in both species. Expression profiling of target genes revealed a negative association with their corresponding tRFs in both species. Subcellular localization demonstrated that OsGEM and OsPPR were primarily localized in the nucleus, while CaMIZ1 and CaSKP1 were detected at the plasma membrane. Overall, we identified abiotic stress-responsive tncRNAs from rice and chickpea that suggest their potential contribution to plant resilience under changing environmental conditions.

bioinformatics↗

bioRxiv2025

Domestication of the ancient grain Amaranthus cruentus L.

Grain amaranths are nutritious pseudocereals that have been domesticated in the Andes and North America mainly in Mexico. The repeated domestication of grain amaranths has recently been studied using genome-wide data. The results suggested independent processes of domestication from Amaranthus hybridus L. in different geographical regions. Although domestication process of the three grain amaranths has been partially elucidated, the detailed domestication centers remain unknown. Therefore, we study the geographic origin and center of domestication of A. cruentus within North America. We reveal a high genetic diversity and distinct history, using whole genome sequencing of 138 accessions belonging to A. cruentus and its closely related species (A. hypochondriacus L.) along with the wild relative A. hybridus mainly from South of Mexico and Guatemala. A. cruentus was most likely domesticated in central Mexico and then taken to Guatemala, where this species is most widely preferred and cultivated today. We identified three genomic groups of A. cruentus. Amaranthus cruentus group 1, representing the center of Mexico, A. cruentus group 2 mostly from Guatemala, and A. cruentus group 3 including individuals in Mexico, but distinct from group 1. Compared to A. hybridus, A. cruentus group 3 exhibited the lowest genetic differentiation and the highest genetic diversity among the A. cruentus groups. We find gene flow between A. cruentus group 1 and A. hybridus indicating the continuing interbreeding between wild and domesticated amaranth in its domestication center. Our results support the hypothesis of a Mexican origin of A. cruentus and a secondary center of domestication in Guatemala.

evolutionary biology↗

bioRxiv2025

Benchmarking cell-type deconvolution in cross-platform transcriptomic data

BackgroundTranscriptomic data from diverse measurement technologies are widely used to study tissue heterogeneity. Cell-type deconvolution, which resolves mixed transcriptomic signals into cellular components, is a key analytical approach. However, achieving accurate deconvolution across platforms remains challenging due to platform-specific experimental and technological biases. ResultsWe systematically benchmarked deconvolution performance using real-world cross-platform datasets and simulated data modeling distinct technological features. Our analyses provide practical guidelines for experimental design and promote more robust and comparable cross-platform transcriptomic analyses. ConclusionLog-normal regression methods such as SpatialDecon demonstrated the most reliable and consistent performance across both simulated and experimental settings, establishing a robust framework for accurate cross-platform transcriptomic deconvolution. Moreover, our results highlight potential caveats in deconvolution predictions arising from specific experimental conditions, providing guidance for more informed experimental design and interpretation Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=60 SRC="FIGDIR/small/690141v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@585cbdorg.highwire.dtl.DTLVardef@13088c7org.highwire.dtl.DTLVardef@163ea75org.highwire.dtl.DTLVardef@b5ccf7_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Stochastic Gene Expression under Sequestration: Noise Reduction and Emergent Distributions

Gene expression noise can be modulated by protein sequestration, a mechanism we investigate through a stochastic modeling framework. We examine how the distribution of free (non-sequestered) protein depends on sequestration cooperativity (monomers, dimers, multimers) and on the timescale separation between sequestration and protein turnover. For non-cooperative sequestration, faster kinetics drive the distribution from a high-noise to a lower-noise gamma form, while the right-tail remains governed by the high-noise limit -- revealing a non-commutativity between tail asymptotics and fast sequestration. For cooperative sequestration, the distribution departs from gamma, exhibiting left skewness or multi-modality. These results highlight how sequestration mechanisms shape protein variability in nontrivial ways.

systems biology↗

bioRxiv2025

Sexual dimorphism in zymosan-induced arthritis is linked with a higher IFN response in myeloid cell subsets that faithfully recapitulate RA synovial cell clusters

A key feature of rheumatoid arthritis (RA) is sexual dimorphism, with a higher incidence of RA in females. Myeloid cells are key drivers of the inflammatory effector phase of RA, but little is known about their contribution to a sexually dimorphic arthritis phenotype. We wished to utilize an arthritis model that recapitulates RA pathogenic myeloid cell subsets defined by single cell transcriptome analysis to investigate sex differences in human disease-relevant cell types and related molecular pathways. We developed a computational strategy that rigorously maps scRNAseq-defined mouse arthritis myeloid cells and clusters onto previously defined RA subsets. Synovial myeloid cells in the zymosan-induced arthritis (ZIA) model closely recapitulated four pathogenic RA myeloid cell subsets, strongly supporting the disease-relevance of the ZIA model. ZIA also effectively modeled myeloid cells in immune checkpoint inhibitor arthritis (ICI-A). These RA, ICI-A and ZIA myeloid cells express genes in TNF-NF-kB, PGE2, and IFN-STAT pathways. In ZIA, an induction phase dominated by cell clusters expressing NF-kB and PGE2 pathways transitioned to peak arthritis characterized by cell subsets co-expressing NF-kB and IFN pathways, as occurs in RA and various inflammatory diseases. Female mice exhibited increased arthritis linked with early induction of interferon-stimulated genes and increased expansion of IFN signature-expressing cell subsets. Our study identifies a computational strategy and animal model that enables investigation of recently described pathogenic myeloid cell subsets, and links increased arthritis in female mice with specific myeloid cell subsets that exhibit a stronger IFN response.

immunology↗

bioRxiv2025

Injury-induced tau pathology promotes aggressive behavior in Drosophila without neurodegeneration.

The microtubule-associated protein tau is implicated in neurodegenerative diseases, but its physiological roles remain poorly understood. Here, we find that pan-neuronal expression of human tau (HsTau) in Drosophila coupled with injury triggers hyper-aggression in male flies, which is absent in flies expressing non-phosphorylatable tau. These behavioral manifestations result from activation of dopaminergic circuits without neurodegeneration. Using in vitro reconstitution assays, we find that phosphorylated HsTau maintains microtubule binding but loses its ability to suppress catastrophes, thereby promoting microtubule dynamicity. In contrast, unphosphorylated HsTau and fly tau (DmTau) stabilize microtubules by reducing catastrophe frequency. Our findings challenge the canonical view of tau as a simple microtubule stabilizer and instead position it as a dynamic regulator of microtubule function and neuronal excitability. These results reveal how acute tau phosphorylation can alter neural circuit function and behavior prior to neurodegeneration, providing new insights into taus physiological and pathological roles.

neuroscience↗

bioRxiv2025

Spatiotemporal-multimodal integration reveals BCG-induced skin-blood crosstalk

Tuberculosis (TB) remains the leading cause of infectious death. The Bacille Calmette-Guerin (BCG) vaccine has been the only licensed vaccine available for TB prevention. Despite BCG being administered intradermally for over a century to >100 million individuals annually, the molecular events in the skin following BCG administration have not been investigated; as a result, measurable correlates of protection that could predict vaccine effectiveness already early after vaccination are lacking. Here we show that BCG immediately (within one day after vaccination) induces dynamic molecular waves that drive the acute human host response across space (layers of the skin and systemically in blood) and time (days). Integration of this data across space and time identified robust networks of interactive modules related to immune surveillance (e.g. Langerhans cells), cell trafficking (e.g. endothelial cells, ITGB5), and trained immunity (e.g. neutrophils, macrophages, {gamma}{delta}-T cell). Importantly, not only were we able to identify BCG-activated pathways associated with trained immunity such as mTOR signaling and glycolysis/gluconeogenesis, we were able to pinpoint the time-point and precise location (skin layer) of the initial activation of theses pathways. Combining tissue biopsies of human skin (spatial genomics) with liquid biopsies (cell-free blood plasma RNASeq) following BCG vaccination our data both confirmed known evidence (e.g. prominent {gamma}{delta}-T cell induction at the site of BCG administration; negative correlation of blood vs tissue myeloid-derived suppressor cells), but also generated promising new leads such as baseline levels of B cells, platelets and nuocytes in the skin prior to BCG administration predict eventual outcome, and that these predictive differences in baseline cellular composition can be captured non-invasively using high resolution images of the site of injection (dermatoscopy). Given this data represents the first holistic view of the acute molecular response to BCG in the skin in a human population at medium to high TB risk, we anticipate our findings of the immediate/early events following BCG vaccination, including non-invasive predictive assessment will support acceleration of vaccine development in the fight against TB.

systems biology↗

bioRxiv2025

FRG1 Regulates Nonsense-Mediated mRNA Decay by Modulating UPF1 Levels

FRG1 acts as a molecular double-edged sword: while its overexpression is linked to facioscapulohumeral muscular dystrophy (FSHD), its under expression activates tumorigenic signalling pathways--highlighting the importance of tightly regulated FRG1 levels. Although prior studies have hinted at FRG1s involvement in RNA biogenesis, its core molecular functions have remained largely elusive. Our previous work identified FRG1 as a transcriptional regulator of genes in the nonsense-mediated decay (NMD) pathway; however, the underlying mechanisms were not fully delineated. In this study, using a range of cellular models with altered FRG1 expression, we demonstrate that reduced FRG1 levels enhance NMD activity. We reveal that FRG1 is a structural component of both the spliceosome and the exon junction complex (EJC), and that it directly modulates NMD by interacting with UPF1--regulating its ubiquitination and degradation. Furthermore, we show that DUX4 inversely regulates the NMD machinery through FRG1, establishing a critical molecular axis. Despite its structural association with the EJC and spliceosome, the absence of FRG1 does not compromise the integrity of these complexes. Polysome profiling showed that FRG1 co-sediments with eIF4A3, a core EJC component, across translating ribosomal fractions. This interaction was further supported by proximity ligation assays confirming the close spatial proximity of FRG1 and eIF4A3. Importantly, we validated the impact of FRG1 perturbation on NMD efficiency and UPF1 levels in vivo using a transgenic FRG1 knockout zebrafish model. Together, these findings establish a direct, DUX4-independent role for FRG1 in regulating the NMD pathway and uncover a previously unrecognized function for FRG1 in post-transcriptional gene regulation. Our work provides mechanistic insight into FRG1s molecular roles and lays the groundwork for therapeutic strategies targeting diseases associated with its dysregulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/689056v2_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@1ef00e1org.highwire.dtl.DTLVardef@22cd63org.highwire.dtl.DTLVardef@da4080org.highwire.dtl.DTLVardef@c0d283_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

molecular biology↗

bioRxiv2025

Adipocyte IL-22RA1 signaling promotes structural and functional remodeling of white adipose tissue following acute intestinal damage.

Interleukin (IL)-22 has been shown to play an important role in intestinal host defense and ameliorating high-fat diet (HFD)-induced metabolic disorders primarily through signaling in intestinal epithelial cells. Adipocytes have emerged as key immune-metabolic regulators that influence intestinal inflammation in inflammatory bowel disease (IBD). However, the role of IL-22RA1 signaling in adipocytes has not been explored. In the present study, we examined the role of IL-22RA1 signaling in adipocytes in response to dextran sulfate sodium (DSS)-mediated gut inflammation. To do this, we subjected adipocyte specific Il22ra1 knockout mice (Il22ra1Adipo) to intestinal inflammation under normal chow and HFD conditions. Compared to littermate controls, Il22ra1Adipo mice displayed significant weight loss on day 9 of DSS treatment and showed altered expression of immune response- and lipid metabolism-related genes in white adipose tissue (WAT) under a normal chow diet. Notably, when mice were primed with HFD prior to DSS-induced intestinal injury, WAT from Il22ra1Adipo mice showed a significant reduction in Fabp4 expression and a marked increase in the proliferation marker Ki67. These findings indicate that loss of IL-22RA1 signaling in adipocytes disrupts adipocyte differentiation and lipid metabolism, leading to increased proliferation of preadipocytes or stromal cells without proper maturation. Importantly, this altered adipose tissue response occurred despite similar levels of colonic inflammation between knockout and control mice, suggesting a critical role for adipocyte IL-22RA1 signaling in maintaining metabolic and inflammatory homeostasis in WAT during combined metabolic and intestinal inflammatory stress.

pathology↗

bioRxiv2025

Antibiotic-resistance mutations in penicillin-binding protein 2 from the ceftriaxone-resistant Neisseria gonorrhoeae strain H041 strike a delicate balance between increasing resistance and maintaining transpeptidase activity

The mosaic penA allele (penA41) from H041, the most ceftriaxone-resistant Neisseria gonorrhoeae strain identified to date, encodes a variant of the essential Penicillin-Binding Protein 2 (PBP2) with 60 amino acid mutations compared to PBP2 from the antimicrobial-susceptible strain, FA19. Based on previous work from our lab and others, we identified a minimal set of 10 mutations that, when introduced into the {beta}-lactam antibiotic-susceptible penA allele from FA19 (penA19), confers two-thirds of the ceftriaxone and cefixime resistance compared to the penA41 allele. Three mutations (A311V, I312M, and V316P) are in the 2 helix of PBP2 containing the catalytic serine (Ser310), two (F504L and N512Y) are in the 3-4 loop that is important in binding and acylation, and one (G545S) interacts with conserved amino acids in the active site. The seventh mutation, T483S, confers substantial resistance to ceftriaxone within the minimal mutant set but requires the presence of three epistatic mutations located on the other side of the protein that do not alter resistance on their own yet are necessary to retain essential transpeptidase activity. These epistatic mutations change the backbone dihedral angles at position-447, which may increase flexibility of the enzyme and help restore essential transpeptidation. Our results highlight the complex balance necessary for evolving cephalosporin resistance while also retaining sufficient transpeptidase function in PBP2. Author SummaryIn this study, we set out to understand how Neisseria gonorrhoeae, the bacterium that causes gonorrhea, is able to resist the last remaining recommended antibiotic, ceftriaxone. Gonorrhea is a common sexually transmitted infection worldwide, and rising resistance threatens to make it untreatable. We focused on penicillin-binding protein 2 (PBP2), which is essential for the bacteriums survival and is the lethal target of ceftriaxone. By incorporating a subset of the 60 PBP2 mutations found in a highly resistant strain into PBP2 from an antibiotic-susceptible strain, we discovered that resistance evolved from a combination of mutations that work together to directly reduce the capacity of ceftriaxone to inactivate the protein and others that act as "supporting" mutations to keep the protein functional despite the presence of the resistance mutations. Our study highlights how N. gonorrhoeae successfully negotiates the delicate balance between resistance and function to escape the lethal action of antibiotics.

microbiology↗

bioRxiv2025

Differential Tissue Coupled Powering for Battery-Free Injectable Electroceuticals

Electroceutical implants that deliver targeted neural stimulation have shown therapeutic potential for a wide range of neurological and peripheral disorders, yet wirelessly powering ultra-miniaturized, fully injectable systems remains a critical challenge. Here we report a Thread-like Injectable Neural TechnologY (TINY), powered via a differential tissue-coupled powering (DTCP) scheme. DTCP employs mid-frequency differential potentials applied across external electrodes on a compact, wearable transmitter to deliver energy through tissue to an ultra-miniaturized, thread-like implant that integrates a custom ASIC and PEDOT-coated receiver and stimulation electrodes. Benchtop experiments in agar phantoms characterize the power-transfer efficiency (PTE) and reveal that PTE increases with implant length while maintaining strong tolerance to angular misalignment. In vivo tests in rat hindlimbs further demonstrate wireless activation of the sciatic nerve through tissue at centimeter-scale depths, confirming effective transcutaneous energy delivery for neurostimulation. A 20-day implantation study shows stable positioning of the device with minimal tissue response, indicating excellent chronic compatibility. These findings address long-standing challenges in wirelessly powering injectable electroceuticals and establish DTCP as a scalable and alignment-robust powering strategy for future minimally invasive neuromodulation therapies.

bioengineering↗

bioRxiv2025

Defining the Growth Stages of Mungbean (Vigna radiata L.) using the BBCH Scale

Mungbean (Vigna radiata L.) is a protein-rich food grain legume that fixes nitrogen and serves as a potential crop for the plant-based protein industry. It can fit in multiple cropping systems as a short-duration and low-water requirement crop. Phenological growth stages of mungbean are described here for the first time according to the BBCH (Biologische Bundesanstalt, Bundessortenamt, and Chemische Industrie) scale. We developed an extended BBCH chart with a two-digit scale to identify different phenological growth stages of mungbean. This study documented and illustrated the key growth stages of mungbean from germination to maturity, correlating them with the number of days after planting and accumulated growing degree days (GDD). It outlines the principal growth stages (PS) as follows: germination (PS-0), leaf development (PS-1), stem elongation (PS-3), flower bud development (PS-5), flowering (PS-6), fruit development (PS-7), ripening (PS-8), and senescence (PS-9). This chart can help track the key mungbean growth and developmental stages. Most importantly, this BBCH growth stages chart fills a gap in the literature by providing a practical tool for researchers and growers to standardize crop management practices, develop simulation models, and assess performance under various environmental conditions. The standardized scale enhances the precision of timing agricultural interventions, ultimately supporting improved mungbean production in the region.

plant biology↗

bioRxiv2025

Cryo-EM structures of Mycobacterium tuberculosis pyruvate carboxylase reveal allosteric activation and domain dynamics during catalysis

Pyruvate carboxylase (PC) is a biotin-dependent enzyme essential for anaplerotic flux into the tricarboxylic acid cycle and gluconeogenesis. Despite longstanding biochemical knowledge, the structural mechanisms governing its allosteric regulation and domain coordination remain poorly defined. Here, we present the cryo-EM structures of Mycobacterium tuberculosis PC (MtPC) captured in both apo and substrate-bound forms. In the absence of acetyl-CoA, MtPC forms a flexible and unstable tetramer that readily dissociates into subcomplexes. Upon binding of acetyl-CoA and the substrates, the enzyme transitions into a compact, ordered assembly, with acetyl-CoA acting as a molecular clamp that stabilizes inter-subunit interactions. Remarkably, we captured the mobile biotinylated domain simultaneously engaging each catalytic center within monomers, providing direct structural evidence for the two steps of the catalytic cycle. 3D variability analysis further revealed how this mobile domain translocates between the active sites during catalysis. Together, these findings demonstrate how acetyl-CoA stabilizes MtPC by reinforcing inter-subunit contacts and elucidate the conformational dynamics underlying domain coordination during catalysis. These findings provide new structural insights into the allosteric regulation of this essential metabolic enzyme.

biophysics↗

bioRxiv2025

AI-assisted Image-Based Phenotyping Reveals Genetic Architecture of Pod Traits in Mungbean (Vigna radiata L.)

Mungbean (Vigna radiata (L.) R. Wilczek) is a vital source of digestible proteins and is well-suited for the plant-based protein industry. In this study, we analyzed pod morphological traits in the Iowa Mungbean Diversity (IMD) panel with 372 genotypes (2022-23) with AI-assisted image phenotyping using 2,418 pod images. Pod morphological traits were extracted using deep learning image analysis, achieving excellent agreement with manual measurements (r>0.96 for pod length and seed per pod). Four complementary GWAS models identified 45 significant SNPs associated with pod curvature, length, width, and seed per pod traits. Notably, a significant SNP (5_35265704) on chromosome 1 was linked to pod dimensional traits, length, width, and curvature. A candidate gene, Vradi01g00001116, was located within the linkage disequilibrium (LD) region of this SNP, is part of the GH3 gene family, and has an Arabidopsis ortholog (AT4G27260) known for influencing organ elongation, pod, and seed development. Another SNP, 5_210437 on chromosome 2, has been found to be significantly associated with both pod length and seed per pod. A candidate gene, Vradi02g00003971, located in the LD region of this SNP, belongs to the potassium transporter family and shares homology with the HAK5 gene family (AT4G13420) in Arabidopsis, which influences pod and seed growth. Image-based measurements achieved genomic prediction accuracies ranging from 0.61 to 0.85 across various traits, exhibiting an improvement of 12-22% over manual methods. These results demonstrate the potential of AI-assisted phenomics integrated with genomic tools to accelerate selection for improved pod architecture in mungbean breeding programs across the Midwestern United States and globally.

genomics↗

bioRxiv2025

Programmable DNA-Silk fibroin hydrogel scaffold with temporal mechanical reinforcement for mesenchymal stem cells differentiation and accelerated wound healing in a full-thickness skin defect mice model

DNA-based hydrogels have attracted significant attention in biomedical applications due to their programmability, biocompatibility, and tunable functionalities. However, their clinical translation is hindered by high synthesis costs, limited mechanical strength, poor stability, and complex synthesis protocols. In this work, we present a novel DNA-silk fibroin hybrid hydrogel that overcomes these limitations by combining the unique biofunctionality of DNA with the superior mechanical and chemical properties of silk fibroin. Salmon-derived DNA, an abundant and low-cost source, was incorporated with silk fibroin to form hybrid networks via a simple, scalable process. Silk fibroin served as a robust scaffold, enhancing mechanical strength, controlling degradability, and improving structural stability, while the entangled DNA-silk network reduced rapid DNA degradation. The resulting hybrid hydrogel demonstrated temporal mechanical reinforcement and prolonged stability, with in vitro studies demonstrating that the developed hybrid hydrogel enhanced the chondrogenic and osteogenic differentiation of Infrapatellar Fat Pad Mesenchymal Stem Cells (IFP-MSCs). Additionally, hemostatic and in vivo studies demonstrated the potential of DNA-silk fibroin hydrogel as a promising biomaterial for rapid hemostasis and accelerated wound healing. Overall, the developed DNA-silk fibroin hybrid hydrogel offers strong potential for mesenchymal tissue engineering, hemostatic adjuvant and wound healing.

bioengineering↗