Biology subjects

Kumar, A.

Publications and source records attributed to Kumar, A..

At least 217 records · Page 12Linked to original sources

bioRxiv2025

Essential role of hsa-miR-203a-3p in type I Interferons immune homeostasis during Influenza and NDV infection

MicroRNAs (miRNAs) are small, non-coding molecules that act as essential post-transcriptional regulators in various biological processes. Many studies suggest that miRNAs may modulate the hosts immune response during virus infections. We analyzed publicly available transcriptomics data involving infection with different RNA viruses and identified the most prominent candidate, miR-203a-3p. This miRNA is upregulated during H7N9, HCV, and DENV2 infections. Interestingly, pathway analysis of microRNA-targeted genes shows that miR-203a-3p targets multiple genes of the type-I interferon and JAK-STAT pathway. In this study, we reported the novel role of miR-203a-3p as it is elevated in response to polyinosinic-polycytidylic acid [poly(I:C)] transfection and infection with various RNA viruses such as Newcastle Disease Virus (NDV) and A/PR8/H1N1 influenza virus. We found that miR-203a-3p promotes the A/PR8/H1N1 virus replication by suppressing the hosts type-I interferons and interferon-stimulated genes. We demonstrated that the miR-203a-3p overexpression reduced the expression of ISGs and is attributed to the direct binding of miR-203a-3p to 3 UTRs of Janus-activated kinase 1 (JAK1), STAT1, SOCS3, and multiple IFNA transcripts. Altogether, these findings strongly suggest that miR-203a-3p plays a pivotal role in immune homeostasis by regulation of type I IFN and supports A/PR8/H1N1 and NDV infection by targeting multiple genes of the hosts type I IFNs and JAK-STAT signaling pathways.

immunology↗

bioRxiv2025

Temporal and Spatial Scales of Resting-state Human Cortical Activity Throughout Lifespan

Sensorimotor and cognitive abilities undergo substantial changes throughout the human lifespan, but the corresponding changes in the functional properties of cortical networks remain poorly understood. This can be studied using temporal and spatial scales of functional magnetic resonance imaging (fMRI) signals, which provide a robust description of the topological structure and temporal dynamics of neural activity. For example, timescales of resting-state fMRI signals parsimoniously predict a significant amount of the individual variability in functional connectivity networks identified in adult human brains. In the present study, we quantified and compared temporal and spatial scales in resting-state fMRI data collected from 2,352 subjects between the ages of 5 and 100 in Developmental, Young Adult, and Aging datasets from the Human Connectome Project. For most cortical regions, we found that both temporal and spatial scales decreased with age throughout the lifespan, with the visual cortex and the limbic network consistently showing the largest and smallest scales, respectively. For some prefrontal regions, however, these two scales displayed non-monotonic trajectories and peaked around the same time during adolescence and decreased throughout the rest of the lifespan. We also found that cortical myelination increased monotonically throughout the lifespan, and its rate of change was significantly correlated with the changes in both temporal and spatial scales across different cortical regions in adulthood. These findings suggest that temporal and spatial scales in fMRI signals, as well as cortical myelination, are closely coordinated during both development and aging. Significance StatementTemporal and spatial scales of resting-state cortical activity in humans measured by fMRI largely decreased throughout the lifespan, except that for some regions in the prefrontal cortex they peaked similarly during adolescence. In addition, whereas cortical myelination consistently increased throughout the lifespan, its variation across different cortical networks and the rate of age-related changes were correlated with the dynamics of temporal and spatial scales of rs-fMRI activity, suggesting that the spatio-temporal scales of cortical activity and cortical myelination might be co-regulated during development and aging.

neuroscience↗

bioRxiv2025

Heterogeneity across mammalian- and avian-origin A(H1N1) influenza viruses influences viral infectivity following incubation with host bacteria from the human respiratory tract

Influenza A viruses (IAV) are primarily transmitted between mammals by the respiratory route, and encounter bacteria in the respiratory tract before infecting susceptible epithelial cells. Previous studies have shown that mammalian-origin IAV can bind to the surface of different bacterial species and purified bacterial lipopolysaccharides (LPS), but despite the broad host range of IAV, few studies have included avian-origin IAV in these assessments. Since IAV that circulate in humans and birds are well-adapted to replication in the human respiratory and avian gastrointestinal tracts, respectively, we investigated the ability of multiple human and avian A(H1N1) IAV to associate with bacteria and their surface components isolated from both host niches. Binding interactions were assessed with microbial glycan microarrays, revealing that seasonal and avian IAV strains exhibited binding diversity to multiple bacterial glycans at the level of the virus and the bacterium, independent of sialic acid binding preference of the virus. Co-incubation of diverse IAV with LPS derived from Pseudomonas aeruginosa (P. aeruginosa), a respiratory tract bacterium, led to reduced retention of viral infectivity in a temperature dependent manner which was not observed when co-incubated with LPS from Escherichia coli, a gut bacterial isolate. Reduction of viral infectivity was supported by disruption of IAV virions following incubation with P. aeruginosa LPS using electron microscopy. Our findings highlight that both human and avian IAV can bind to bacterial surface components from different host sites resulting in differential functional interactions early after binding, suggesting the need to study IAV-bacteria interactions at the host range interface.

microbiology↗

bioRxiv2025

Hyperactivation of TAK1 causes skeletal muscle pathology reminiscent of inflammatory myopathies

Loss of skeletal muscle mass and strength is a debilitating consequence of various chronic diseases, inflammatory myopathies, and neuromuscular disorders. Inflammation plays a major role in the perpetuation of myopathy in degenerative muscle diseases. TAK1 is a major signaling protein that mediates the activation of multiple signaling pathways in response to inflammatory cytokines and microbial products. Recent studies have demonstrated that TAK1 is essential for the growth and maintenance of skeletal muscle mass in adult mice. However, the effects of overstimulation of TAK1 activity in the regulation of skeletal muscle mass remain unknown. In the present study, using AAV vectors, we investigated the effect of varying levels of TAK1 activation on skeletal muscle in adult mice. Our results demonstrate that while low levels of TAK1 activation improve skeletal muscle mass, sustained hyperactivation of TAK1 causes myopathy in adult mice. Excessive stimulation of TAK1 manifests pathological features, such as myofiber degeneration and regeneration, cellular infiltration, increased expression of proinflammatory molecules, and interstitial fibrosis. Hyperactivation of TAK1 also upregulates proteolytic systems and various catabolic signaling pathways in skeletal muscle of adult mice. Altogether, our study demonstrates that physiological levels of activation of TAK1 lead to myofiber hypertrophy, whereas its hyperactivation results in myofiber damage and other pathological features resembling inflammatory myopathies.

cell biology↗

bioRxiv2025

Studies on Gene Enhancer with KSHV mini-chromatin

Kaposis sarcoma-associated herpesvirus (KSHV) genome contains a terminal repeats (TR) sequence. Previous studies demonstrated that KSHV TR functions as a gene enhancer for inducible lytic gene promoters. Gene enhancers anchor bromodomain-containing protein 4 (BRD4) at specific genomic region, where BRD4 interacts flexibly with transcription-related proteins through its intrinsically disordered domain and exerts transcription regulatory function. Here, we generated recombinant KSHV with reduced TR copy numbers and studied BRD4 recruitment and its contributions to the inducible promoter activation. Reducing the TR copy numbers from 21 (TR21) to 5 (TR5) strongly attenuated viral gene expression during de novo infection and impaired reactivation. The EF1 promoter encoded in the KSHV BAC backbone also showed reduced promoter activity, suggesting a global attenuation of transcription activity within TR5 latent episomes. Isolation of reactivating cells confirmed that the reduced inducible gene transcription from TR-shortened DNA template and is mediated by decreased efficacies of BRD4 recruitment to viral gene promoters. Separating the reactivating iSLK cell population from non-responders showed that reactivatable iSLK cells harbored larger LANA nuclear bodies (NBs) compared to non-responders. The cells with larger LANA NBs, either due to prior transcription activation or TR copy number, supported KSHV reactivation more efficiently than those with smaller LANA NBs. With auxin-inducible LANA degradation, we confirmed that LANA is responsible for BRD4 occupancies on latent chromatin. Finally, with purified fluorescence-tagged proteins, we demonstrated that BRD4 is required for LANA to form liquid-liquid phase-separated dots. The inclusion of TR DNA fragments further facilitated the formation of larger BRD4-containing LLPS in the presence of LANA, similar to the "cellular enhancer dot" formed by transcription factor-DNA bindings. These results suggest that LANA binding to TR establishes an enhancer domain for infected KSHV episomes. The strength of this enhancer, regulated by TR length or transcription memory, determines the outcome of KSHV replication. ImportanceGene enhancers are genomic domains that regulate frequency and duration of transcription burst at gene promoters, with BRD4 playing a critical role in their enhancer functions. KSHV latent mini-chromosome also contains an enhancer domain made with multiple copies of 801 bp identical repeat DNA fragments, terminal repeats. Here, we utilized manipulable mini-scale chromatins with convenient inducible KSHV reactivation to systematically examine the association between enhancer strength and the outcome of inducible promoter activation. This study illustrated the amount of BRD4 recruitment at the enhancer associated with frequencies of BRD4 distribution to the inducible promoters during KSHV reactivation and, therefore, KSHV lytic replication. Recruitment of BRD4 to the TR is specifically regulated by KSHV latent protein, LANA. KSHV evolves clever enhancer elements designed to be regulated by the KSHV own latent protein, LANA.

microbiology↗

bioRxiv2025

Artesunate Alleviate Kidney Fibrosis by Restoring Klotho Protein and Suppressing Wnt/β-Catenin Signalling Pathway

Chronic kidney disease (CKD) is a global health concern that often progresses to renal failure and premature death. Regardless of etiology of CKD, kidney fibrosis is the main determinant of progressive CKD. Renal fibrosis is characterized by excessive collagen and extracellular-matrix (ECM) deposition, which impairs renal function with an irreversible loss of nephrons. Currently, there are no effective antifibrotic therapies to halt the progression of CKD to the end-stage kidney failure (ESKF). Artesunate has recently shown antifibrotic effects in various animal models, but its efficacy in renal fibrosis remains unexplored. In this study, the efficacy of artesunate was evaluated in a unilateral ureteral obstruction (UUO) mouse model and in primary human kidney fibroblasts (HKF). Mechanistic investigation including immunoblot analysis, immunohistochemistry, gene expression assay, enzyme-linked immunosorbent assay (ELISA) and other tools were used to study the underlying molecular mechanisms of antifibrotic effects of artesunate. Results of this study showed that artesunate ameliorated multiple profibrotic pathways including transforming growth factor-beta (TGF-{beta}) expression in UUO model and reduced profibrotic markers including alpha-smooth muscle actin (-SMA), fibronectin, collagen I, and vimentin in both in-vivo and in-vitro models. Mechanistic studies indicated that artesunate treatment abrogated the TGF-{beta}/SMAD pathway, restored klotho-protein expression and attenuated both PI3K/Akt and Wnt/{beta}-catenin pathways. Additionally, artesunate inhibited cell proliferation in UUO and induced ferroptosis in HKF cell culture. In conclusions our study demonstrates that artesunate treatment abrogated fibroblast activation, attenuated canonical and non-canonical TGF-{beta} pathways, inhibited cell proliferation in UUO and selectively induced ferroptosis in HKF cell culture, which may offer a potential treatment to attenuate kidney fibrosis and progressive CKD. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=121 SRC="FIGDIR/small/644310v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1d70fe3org.highwire.dtl.DTLVardef@5423e7org.highwire.dtl.DTLVardef@12866org.highwire.dtl.DTLVardef@37f1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

KCa3.1 Contributes to Neuroinflammation and Nigral Dopaminergic Neurodegeneration in Experimental models of Parkinson's Disease

Chronic neuroinflammation and misfolded -synuclein (Syn) have been identified as key pathological correlates driving Parkinsons disease (PD) pathogenesis; however, the contribution of ion channels to microglia activation in the context of -synucleinopathy remains elusive. Herein, we show that KCa3.1, a calcium-activated potassium channel, is robustly upregulated within microglia in multiple preclinical models of PD and, most importantly, in human PD and dementia with Lewy bodies (DLB) brains. Pharmacological inhibition of KCa3.1 via senicapoc or TRAM-34 inhibits KCa3.1 channel activity and the associated reactive microglial phenotype in response to aggregated Syn, as well as ameliorates of PD like pathology in diverse PD mouse models. Additionally, proteomic and transcriptomic profiling of microglia revealed that senicapoc ameliorates aggregated Syn-induced, inflammation-associated pathways and dysregulated metabolism in primary microglial cells. Mechanistically, FYN kinase in a STAT1 dependent manner regulates KCa3.1 mediated the microglial reactive activation phenotype after -synucleinopathy. Moreover, reduced neuroinflammation and subsequent PD-like neuropathology were observed in SYN AAV inoculated KCa3.1 knockout mice. Together, these findings suggest that KCa3.1 inhibition represents a novel therapeutic strategy for treating patients with PD and related -synucleinopathies.

neuroscience↗

bioRxiv2025

Electrochemical Paper Fluidic Device for Extended Real-time Cocaine Monitoring in Simulated Sweat

Cocaine and other illicit substances are known to excrete from the body into sweat, making sweat an advantageous matrix for non-invasive detection and monitoring of substance use and abuse. However, existing detection of illicit substances in sweat remain single-use technologies that arent suitable for real-time, continuous monitoring over the course of an entire day. Long-term, continuous detection is hampered by large, bulky instrumentation, limited sensor stability for multi-hour measurements, and fluidic systems not optimized for minute and variable sweat flow rates. We demonstrate the continuous detection of 0.5 mM cocaine in simulated sweat via a paper fluidic device over the course of 17 hours. Our sensing system uses a biosensor functionalized with a cocaine-binding aptamer and a miniaturized electrochemical potentiostat. Our fluidics are driven by evaporation flow at physiological sweat rates (0.3-0.5 {micro}L/min/cm2). Our development lays critical groundwork towards wearable, continuous detection of illicit substances in sweat.

biochemistry↗

bioRxiv2025

Schwann cells modified to secrete MANF is a potential cellular therapy for peripheral nerve regeneration

Despite several decades of research, an effective therapy for peripheral nerve regeneration is still lacking. The lack of knowledge of molecular candidates that equally promote axon regeneration and glial cell dynamics essential for regeneration poses challenges in developing effective therapies. Improper optimization of potential therapies leading to failures in ensuring their local availability in nerves also poses additional challenges. Here, we showed that the neurotrophic factor, the mesencephalic astrocyte-derived neurotrophic factor (MANF), equally promotes axon regeneration and glial cell dynamics favorable for nerve regeneration. We showed that while endogenous expression of MANF is primarily restricted to non-peptidergic sensory neurons in adult rats, exogenous MANF promotes the growth of all subtypes of adult rat sensory neurons. We also demonstrated that exogenous MANF promotes the proliferation and migration of adult rat primary Schwann Cells (SCs). Further, we found that local and repeated administration of exogenous MANF to injured mouse nerve promote axon regeneration. Finally, we devised a therapeutic approach by programming nerve resident SCs to locally and continuously deliver MANF to injured rat nerves and showed that this approach improved nerve regeneration indices. Overall, this work developed a therapeutic approach by harnessing the power of SCs as a local delivery system of MANF for improving nerve regeneration.

neuroscience↗

bioRxiv2025

Decoding stress specific transcriptional regulation by causality aware Graph-Transformer deep learning

Cells respond to environmental stimuli through transcriptional reprogramming orchestrated by transcription factors (TFs), which interpret cis-regulatory DNA sequences to determine the timing and location of gene expression. The diversification of TFs and their interactions with cis-regulatory elements (CREs) underpins plant adaptation to stress through the formation of gene regulatory networks (GRNs). However, deciphering condition-specific GRNs and identifying transcription factor binding motifs (TFBMs) for spatio-temporal gene expression remain major challenges in plant biology. To decipher the conditional networks governing TF-Target gene interactions, we developed CTF-BIND, a novel computational framework designed to reason about the spatio-temporal dynamics of TF activity. Leveraging over [~]23TB of multi-omics data (ChIP-seq, RNA-seq, and protein-protein interaction data), we constructed Bayesian causal networks capable of explaining TF activity across diverse conditions. These networks, validated against extensive experimental data, were then integrated into a Graph Transformer deep learning system. This system uses expression information of network components to quantitatively determine TF activity levels. Models were developed for 110 abiotic stress-related TFs, enabling accurate condition-specific detection of TF binding directly from RNA-seq data, eliminating the need for separate ChIP-seq experiments. CTF-BIND achieved a high average accuracy of [~]93% when tested against experimentally established data from various conditions. It is implemented as an interactive, open-access web server, it not only provides TF binding profiles but also facilitates downstream functional analysis. Furthermore, we developed CTF-BIND-DB, (https://hichicob.ihbt.res.in/ctfbind/) a database capturing dynamic shifts in regulatory pathways, providing information on TGs, network ontology, and binding motifs. CTF-BIND and CTF-BIND-DB represent a transformative approach for understanding and determining TF activity in plant stress responses, offering a powerful tool for crop improvement and bypassing the limitations of traditional methods and extensive experimental validation.

bioinformatics↗

bioRxiv2025

Gluconeogenesis plays a critical role in mycobacterial biofilm formation

Gluconeogenesis is an important pathway for bacteria and humans as it maintains the glucose levels in the system. These glucose molecules can be utilized as substrates for several cellular functions. Gluconeogenesis genes are important for the intracellular survival and pathogenicity of Mycobacterium tuberculosis (Mtb). A few reports have shown the role of gluconeogenesis in biofilm formation in other bacteria. Similarly, we utilized gluconeogenesis genes and explored their role in biofilm formation in Mtb. For this study, we have taken the pyruvate carboxylase (pca) gene, which catalyzes the conversion of pyruvate into oxaloacetate and diverts the carbon flux into the gluconeogenesis pathway. We observed that the transposon mutant of pca was deficient in pellicle and submerged biofilm formation and was defective in colony morphology. This phenomenon was recovered upon either gene complementation or external addition of glucose into the medium. In addition to glucose, we also observed the regaining of biofilm phenomenon in the case of pyruvate supplementation. These observations led us to hypothesize that the glucose molecules generated from the gluconeogenesis pathway can be utilized to generate carbohydrates or polysaccharides, such as cellulose, which can be integrated into the extracellular polymeric substances of the biofilm matrix. Cellulose, whose primary subunit is glucose, can be synthesized from these generated glucose molecules, thereby integrating into the biofilm matrix of mycobacteria. This study provides a novel mechanism of cellulose production through a non-canonical pathway in Mtb, which is important in the biofilm formation of this pathogenic bacterium.

microbiology↗

bioRxiv2025

Effect of perchlorate on biocementation capable bacteria and Martian bricks

With the recent discovery of perchlorate (0.5-1%) in Martian regolith, more experiments related to the impact of perchlorate on microbial life are crucial to understanding the possibility of earth life forms that could sustain on the Martian terrain. While we are familiar with the idea of bioconsolidated Martian bricks made via Microbially Induced Calcite Precipitation (MICP), studies on the effect of perchlorate on Martian bricks & biocementation capable microbes have been obscure. In this work, we investigated the effect of perchlorate (MgClO4- salt) on a lab-isolated biocementation capable bacteria & Martian bricks bioconsolidated by the same, with 1% perchlorate in Mars Global Simulant-1 (MGS-1). The screening of biocementation-capable bacteria involved phenol red assay for urease activity followed by Scanning Electron Microscopy (SEM) and X-ray diffraction (XRD) study of the precipitate formed through MICP via ureolytic pathway. The biocementation capable bacterium SI_IISc_isolate was found phylogenetically closest to Sporosarcina pasteurii strain S2135, its draft genome being approximately 3.69 Mb. To understand the effect of perchlorate on SI_IISc_isolate, we majorly relied on Gram-staining & SEM. The negative effect of perchlorate stress on the isolate was evident by its decreased growth in the presence of varying concentrations of perchlorate through plate assays, growth curve studies in broth & live-dead staining. Gram-staining study and SEM both revealed that perchlorate induces the release of extracellular matrix (ECM) and promotes clustering of cells by the bacteria, which we termed as multicellularity-like behavior. Further, we constructed Martian bricks with Martian Global Simulant (MGS-1) along with 1% perchlorate, utilizing the microbially induced calcite precipitation ability of the Sporosarcina sp. strain SI_IISc_isolate via ureolysis, following an established protocol at our lab. The bioconsolidation experiments showed that in the presence of a natural adhesive - guar gum, perchlorate tends to significantly improve the compressive strength of Martian bricks. However, the end result eventually relies on the overall effect of various additives in the regolith.

bioengineering↗

bioRxiv2025

Resistance to Radiation Enhances Metastasis by Altering RNA Metabolism

The cellular programs that mediate therapy resistance are often important drivers of metastasis, a phenomenon that needs to be understood better to improve screening and treatment options for cancer patients. Although this issue has been studied extensively for chemotherapy, less is known about a causal link between resistance to radiation therapy and metastasis. We investigated this problem in triple-negative breast cancer (TNBC) and established that radiation resistant tumor cells have enhanced metastatic capacity, especially to bone. Resistance to radiation increases the expression of integrin {beta}3 (ITG{beta}3), which promotes enhanced migration and invasion. Bioinformatic analysis and subsequent experimentation revealed an enrichment of RNA metabolism pathways that stabilize ITG{beta}3 transcripts. Specifically, the RNA binding protein heterogenous nuclear ribonucleoprotein L (HNRNPL), whose expression is regulated by Nrf2, mediates the formation of circular RNAs (circRNAs) that function as competing endogenous RNAs (ceRNAs) for the family of let-7 microRNAs that target ITG{beta}3. Collectively, our findings identify a novel mechanism of radiation-induced metastasis that is driven by alterations in RNA metabolism.

cancer biology↗

bioRxiv2025

Insights into the structure and modulation of human TWIK-2

The Tandem of pore domain in a Weak Inward Rectifying K+ channel 2 (TWIK-2; KCNK6) is a member of the Two-Pore Domain K+ (K2P) channel family, which is associated with pulmonary hypertension, lung injury, and inflammation. The structure and regulatory mechanisms of TWIK-2 remain largely unknown. Here, we present the cryo-electron microscopy (cryo-EM) structure of human TWIK-2 at [~]3.7 [A] and highlight its conserved and unique features. Using automated whole-cell patch clamp recordings, we demonstrate that gating in TWIK-2 is voltage-dependent and insensitive to changes in the extracellular pH. We identify key residues that influence TWIK-2 activity by employing structure and sequence-guided site-directed mutagenesis and provide insights into the possible mechanism of TWIK-2 regulation. Additionally, we demonstrate the application of high-throughput automated whole-cell patch clamp platforms to screen small molecule modulators of TWIK-2. Our work serves as a foundation for designing high-throughput small molecule screening campaigns to identify specific high-affinity TWIK-2 modulators, including promising new anti-inflammatory therapeutics.

biophysics↗

bioRxiv2025

Melatonin-mediated methylglyoxal homeostasis and regulation of autophagy during seed germination under PEG-induced drought stress in upland cotton

Methylglyoxal (MGO), toxic byproduct of glycolysis, acts as a signaling molecule at low levels, but its over-accumulation during drought stress disrupts redox balance and accelerates cell death. Contrarily, melatonin maintains redox balance, particularly during stress. The redox status and MGO level might differ in drought-sensitive and drought-tolerant varieties, so shall the melatonins effect. The study evaluated the effect of melatonin-priming on MGO detoxification and autophagy during polyethylene glycol (PEG)-induced drought stress during seed germination in drought-sensitive (L-799) and drought-tolerant (Suraj) varieties of upland cotton. Melatonin-priming increased endogenous melatonin content, reduced MGO accumulation and advanced glycation end-products (AGEs), and downregulated the expression of MGO biosynthesis genes in L-799 under stress. The expression and activities of glyoxalases and non-glyoxalases were upregulated, showing melatonins effectiveness in MGO detoxification. Additionally, priming upregulated the expression of TPI1, PGK5, and PK1 and downregulated HK3 expression, allowing better conversion of glucose to pyruvate, leading to reduced MGO in L-799. The downregulation of necrosis-related genes with reduced cell death in L-799 shows the potential of priming in maintaining cell viability under stress. Furthermore, upregulated expression of SnRK1.1, SnRK2.6 genes and KIN10 protein levels, with enhanced autophagy markers (ATGs, MDC-stained bodies, lipidated-ATG8), confirmed improved autophagy in melatonin-primed L-799 under stress. Despite lowered ABA, melatonin-mediated MGO homeostasis likely activated MAPK6, inducing autophagy independent of ABA in stressed plants. Conversely, Suraj, with higher endogenous melatonin and inherent stress tolerance, showed limited response to priming. Thus, the study illustrates melatonins role in regulating MGO homeostasis and autophagy under drought stress in cotton.

plant biology↗

bioRxiv2025

Design, development, and evaluation of gene therapeutics specific to KSHV-associated diseases

Kaposis sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposis sarcoma (KS) and two human lymphoproliferative diseases: primary effusion lymphoma and AIDS-related multicentric Castlemans disease. KSHV-encoded latency-associated nuclear antigen (LANA) is expressed in KSHV-infected cancer cells and is responsible for maintaining viral genomes in infected cells. Thus, LANA is an attractive target for therapeutic intervention for KSHV-associated diseases. Here, we devised a cancer gene therapy vector using the adeno-associated virus (AAV), which capitalizes the LANAs function to maintain terminal repeat (TR) containing circular genome in latently infected cells and the TRs enhancer function for KSHV inducible gene promoters. By including two TR copies with a lytic inducible gene promoter (TR2-OriP), we prepared an AAV vector, which expresses an engineered thymidine kinase (TK) selectively in KSHV-infected cells. Ganciclovir (GCV), an anti-herpesvirus drug, effectively eradicated multiple KSHV-infected cells that include iPSC-derived epithelial colony-forming cells, but not non-KSHV-infected counterparts in the presence of AAV8-TR2-OriP-TK. In addition, AAV8-TR2-OriP-TK prevents KSHV virion production from reactivated cells, spreading KSHV infections from reactivated cells. Anti-cancer drugs, known to reactivate KSHV, stimulated TK expression from the vector and, therefore, synergized with AAV8 TR2-OriP-TK to induce KSHV-infected cancer cell death. Finally, the AAV8-TR2-OriP-TK with GCV completely diminished KSHV-infected cancer cells in the xenograft tumor model. The new cancer gene therapeutics should augment the current clinical protocol for KS.

microbiology↗

bioRxiv2025

DMRU: Generative Deep-Learning to unravel condition specific cytosine methylation in plants

Methylation at cytosines in plants influence spatio-temporal gene expression by regulating chromatin structure and accessibility. Some algorithms have been developed to identify DNA methylation but none of them are capable to tell the condition specific DNA methylation, making them hardly of any use. Here, we report a first of its kind an explainable Deep Encoders-Decoders generative system, DMRU, which learns the relationship between transcritpome status and DNA methylation states at any given time. It was also found that GC similarity is more relevant to the specificity of DNA methylation patterns than homology, concurring with reports of direct involvement of GC content in providing regulatory switches for DNA accessibility. Leveraging on which DMRU could perform with same level of accuracy in cross-species universal manner. In a comprehensive testing and benchmarking study across a huge volume of experimental data covering 85 different conditions, and multiple plant species, it has consistently achieved >90% accuracy. With this all, DMRU brings a completely new chapter in methylated cytosine discovery, giving a strong alternative to costly bisulfite sequencing experiments. DMRU may prove critical turning point in plant regulatory research and its acceleration.

bioinformatics↗

bioRxiv2025

Exploration of the Anticancer Activity of Selaginella bryopteris-derived Silver Nanoparticles

AbstractOvarian cancer is characterized by chronic hormonal imbalances and associated symptoms like irregular menstruation, fertility problems and abdominal discomfort. Poly ADP-ribose polymerases (PARPs) are proteins that play a crucial role in DNA repair pathways like base excision repair (BER). PARP family proteins exhibit catalytic activities which facilitate the transport of ADP-ribose to targeted proteins. Inhibition of PARP proteins in cancer cells with BRAC1/2 gene mutations impairs the process of Single Strand Break (SSBs) repairs followed by Double Strand Breaks (DSBs), stalling replication, leading to apoptosis. PARP1 protein inhibition is an innovative therapeutic approach in cancer treatment. Commercially available drugs like Olaparib and Rucaparib are used as PARP1 inhibitors to treat ovarian cancer, however the development of effective new therapeutic drugs is urgently needed to overcome drug toxicity and resistance. In this study, we synthesized silver nanoparticles (AgNPs) from the leaf extract of Selaginella bryopteris demonstrating their cytotoxic nature against the ovarian cancer SKOV-3 cell line, with an IC50 value of 7.81{micro}g/ml. We also observed cell death in cancer cells with an ROS upsurge induced by S. bryopteris AgNPs. Our findings also elaborate on the role of Rhamnetin, a S. bryopteris phytochemical that exhibits active site targeting of PARP-1 residues.

biochemistry↗