Biology subjects

Kumar, R.

Publications and source records attributed to Kumar, R..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Functional Brain Mapping of Body Size Estimation Using a 3D Avatar

BackgroundBody size estimation--the ability to judge the size and shape of ones own body-- is a key perceptual component of body image. However, its neural basis, and the basis for inter-individual differences in accuracy, remain poorly understood, partly due to limitations in existing assessment tools. MethodsWe developed Somatomap 3D, an interactive fMRI-compatible task allowing participants to manipulate a rotatable 3D avatar by adjusting the size and shape of 26 individual body parts to match their perceived body. Twenty-eight healthy male and female adults completed the task during fMRI. Brain activity in a priori regions of interest from previous studies of body processing was modeled using a general linear model incorporating event-specific parameters and parametric modulators related to task performance. Inter-individual differences in body size estimation accuracy were calculated using multidimensional scaling of body part estimation errors, and scores were correlated with BOLD signal eigenvariates from regions of interest. ResultsTask engagement was associated with significant activation in hypothesized body-selective and multisensory regions, including bilateral extrastriate body area, right fusiform body area, right superior parietal lobule, and bilateral premotor cortex. Multidimensional scaling identified a primary subdimension reflecting distortions in body part girths, which was significantly associated with neural responses in the superior parietal lobule. No other brain regions showed significant associations with inter-individual differences in estimation accuracy. ConclusionsThese results suggest that body size estimation engages a distributed network of visual, motor, and parietal regions. Among these, only the superior parietal lobule showed a significant association with inter-individual variation in body size estimation accuracy for body part girths, supporting its role as a candidate neural substrate for altered body representation in psychiatric conditions such as eating disorders and body dysmorphic disorder.

neuroscience↗

bioRxiv2025

What's next for Indian Ornithology? 101 key research questions

India has a rich history of ornithology, and bird research in this field has expanded considerably in recent decades, spurred by a growing number of birdwatchers and ornithologists. Despite this progress, critical gaps remain. This paper highlights key areas where further research is needed and identifies pressing questions that will shape Indian ornithology in the coming years. Drawing from diverse inputs, we present a curated list of 101 research questions spanning across the various disciplines in ornithology - Natural History, Physiology and Disease Ecology, Behaviour, Population and Community Ecology, Habitat Ecology, Macroecology and Biogeography, Population Genetics and Evolution, Applied/Economic Ornithology and Conservation. The list was compiled through a multi-stage process, starting with a public open call for questions, followed by review and curation by a smaller panel of subject specialists. Each question was independently scored by a panel of experts based on three criteria: generality, novelty, and relevance. To account for variation in scoring styles, scores were normalised using Z-scores. The top 101 research questions were then selected based on these standardised scores. Each question is accompanied by an annotation that describes the significance of the question, and highlights opportunities to address it. While our list of research questions highlights significant research priorities, it is not intended to be exhaustive. Rather, it reflects the perspectives of those involved in its curation, who deemed these questions particularly relevant and impactful towards advancing Indian ornithology. We expect these questions to spark new project ideas among students, researchers, and citizen scientists, while guiding funders, managers, and policymakers toward priority research areas.

ecology↗

bioRxiv2025

Systematic discovery of bacterial symbionts in rumen ciliate protozoa

Microbial interactions are fundamental to global ecological and evolutionary processes, exemplified by endosymbiosis between prokaryotes and single-cell eukaryotes that gave rise to organelles. While such associations remain widespread and ecologically important, the diversity and evolutionary dynamics of intracellular symbioses in many microbial ecosystems remain poorly understood. Here, we uncover a hidden layer of microbial complexity in the rumen ecosystem by identifying multiple endosymbiotic associations between ciliate protozoa and bacteria. Using genome-resolved metagenomics on protozoa enriched rumen fractions, we reveal diverse bacterial genomes exhibiting hallmarks of an obligate intracellular lifestyle. These candidate symbionts span several bacterial phyla and include close relatives of known endosymbionts and parasites of protists as well as previously unclassified or presumed free-living bacterial lineages that likely represent overlooked symbiont specialists. Our findings therefore expand the known distribution of bacterial endosymbiosis, establish the rumen - a key site of global carbon and nitrogen cycling - as a promising model for symbiosis research, and demonstrate the power of our approach to uncover hidden symbiotic associations across complex microbial communities. Overall, our results highlight the ubiquity and evolutionary significance of intracellular symbiosis as a shaping force in microbial ecosystems.

microbiology↗

bioRxiv2025

Inhibiting ezrin triggers formin-mediated actin remodelling reducing cellular mechano-protection

Ezrin plays a crucial role in linking the cortical actin cytoskeleton to the plasma membrane in animal cells. Inactivated by small molecule ezrin inhibitors (EzrInh), ezrin is known to regulate cellular functions like adhesion and motility. However, whether ezrin plays any significant role in protecting cells against mechanical stresses is less explored. We use hypo-osmotic shock (HS) to challenge cells and study the mechano-protective role of ezrin. Inhibition of ezrin phosphorylation led to increased cell rupture rates on hypo-shock, with a greater impact at later time points ([~] 10 min). The time scales match with that of enhanced tension contrast at edges at the basal plane. We also observed a lowered relative retraction rate at protrusions created by hypo-shock and a less contractile mid-plane cortex - both indicate the role of a weakening of the cortex by EzrInh in compromising membrane integrity on hypo-shock. Concomitantly, EzrInh also increased stress fibres (SFs), traction forces and cell spreading clearly indicative of additional cellular pre-stress. Utilizing formin inhibitor (SMIFH2), we showed that formin-mediated actin polymerization was critical for the SF response to EzrInh while it also prevented the subsequent EzrInh-treatment from enhancing cell rupture rates. Together EzrInh reduced mechano-protection in cells by tilting of balance of actins organization from the cortex to SF enhancing formin-mediated SF assembly. HighlightsO_LIHypo-osmotically shocked CHO cells rupture more on ezrin inhibition C_LIO_LIEzrin inhibition weakens contractility of cortical actin but enhances stress fibre numbers at the base C_LIO_LIHypo-osmotic shock creates basal protrusions that are also retracted. C_LIO_LIRetractive potential in cells is weakened by ezrin inhibition C_LIO_LIFormin inhibitor prevents net increase in stress fibres by inhibition of ezrin C_LIO_LIOn pre-treatment with formin inhibitor, subsequent inhibition of ezrin doesnot render cells more vulnerable to hypo-osmotic shock C_LI

biophysics↗

bioRxiv2025

Hydrogen sulfide increases intracellular oxygen and regulates the HIF response

O2 sensing by hypoxia-inducible factor (HIF) is a principal mechanism by which aerobic organisms adjust cellular energy metabolism and adapt to O2 limitation. In this study, we show that H2S, a product of host and microbial metabolism, profoundly influences the threshold for HIF-dependent hypoxia-sensing by increasing intracellular O2. The dose-dependent destabilization of HIF by H2S is inversely correlated with sulfide quinone oxidoreductase, which oxidizes sulfide in the mitochondrion. Hypoxia sensors provide a quantitative estimate of the magnitude of H2S-induced perturbation. The O2 concentration in cells grown in a 2% O2 atmosphere is sensed as 5 or 15 % O2 in the presence of 25 or 100 ppm H2S, respectively. Sustained exposure to H2S elicits the hallmarks of hyperoxia-associated cytotoxicity, including loss of Fe-S proteins in cellular and murine models. H2S thus emerges as a powerful regulator of O2 sensing and signaling with possible implications for dysregulation in O2 toxicity diseases. Significance StatementThe mitochondrial electron transport chain (ETC) accounts for [~]90% of whole body O2 consumption. However, our understanding of how metabolites modify ETC flux and therefore, intracellular O2 availability, are poor. In this study, we demonstrate that hydrogen sulfide (H2S), which is produced by host and gut microbes alike, increases intracellular O2 by decreasing ETC flux, and destabilizes the principal hypoxia sensor, HIF-1. The upshift in intracellular O2 levels is quantitatively significant, such that 2% O2 is sensed as 5-15% O2 at varying H2S concentrations, with concomitant destabilization of Fe-S proteins, a signature of cellular hyperoxia. Our study identifies H2S as a HIF-1 regulator with important implications for the large class of mitochondrial diseases characterized by dysregulated O2 metabolism.

cell biology↗

bioRxiv2025

Integrated multi-omics analysis reveals divergent molecular responses in Palmer amaranth (Amaranthus palmeri) biotypes susceptible and resistant to glyphosate

Environmental stress triggers coordinated changes across genetic, transcriptomic, proteomic, and metabolomic levels in plants, yet the extent of synchronization across these omic layers remains underexplored. We captured transcriptomic, proteomic and metabolomic perturbation of glyphosate-resistant (GR) and glyphosate-susceptible (GS) Palmer amaranth (Amaranthus palmeri) biotypes 24 hours after herbicide treatment, quantifying 30,371 transcripts, 5,606 proteins, and 220 metabolites. Glyphosate perturbed threefold more transcripts and proteins in GS than in GR and caused the accumulation of shikimate intermediates in both biotypes. In GS, glyphosate severely disrupted primary metabolism, including photosynthesis and carbon fixation, leading to a collapse of energy production and impairment of phenylpropanoid and terpenoid biosynthesis, compromising defense and detoxification. In contrast, GR maintained cellular homeostasis, with minimal perturbation in carbon metabolism and upregulation of detoxifying pathways, indicating metabolic rerouting. Integrated multi-omics analysis captured stress responses hidden from single-omic analysis, including elevated glutathione metabolism, perturbation of the phenylpropanoid pathway and elevated raffinose family oligosaccharide metabolism in GR, and perturbation of taurine-hypotaurine metabolism in GS. Transcript and protein changes were broadly correlated, but GS exhibited signs of translational inhibition under glyphosate stress, indicating reduced protein synthesis. These findings reveal pervasive perturbation of glyphosate beyond the shikimate pathway within 24 hours after exposure, and underscore the importance of multi-omics integration to elucidate complex stress responses in plants.

plant biology↗

bioRxiv2025

Structural Validation of the Intermediate Leptomeningeal Layer in the Human Central Nervous System

Traditionally, the human central nervous system (CNS) is described as having three meningeal layers, from outer to inner: dura mater, arachnoid mater, and pia mater. The arachnoid and pia mater are called the leptomeninges, and the space between them is filled with cerebrospinal fluid (CSF). Using gross dissection, light microscopy, and ultrastructural analysis of fresh postmortem and cadaveric CNS specimens spanning fetal to adult ages (N=61), we demonstrate a fibrocellular intermediate leptomeningeal layer (ILL) from the cortex to the caudal end of the spinal cord. The ILL divides the subarachnoid space (SAS) into two distinct structural compartments, through which vessels and nerves pass. The ILL shows unique structural features, such as dips into the brains sulci and fissures, as a double-fold membrane that bears intra-layer trabeculae, carries vessels, and forms the perivascular sheath. Moreover, throughout the CNS, it appears to be a non-sieved barrier, characterized by the presence of tight and adherens junctions. ILL, predominantly in the spinal cord, contains macrophage-like cells, indicating its layer-specific immune properties. The ILL warrants recognition as a distinct human meningeal layer with potential barrier and immune functions. SignificanceO_ST_ABSAn Intermediate Leptomeningeal Layer encloses the Central Nervous System in HumansC_ST_ABSThe integrated analysis of our macroscopic, microscopic, and ultrastructural study provides robust support for an intermediate leptomeningeal layer (ILL) in the subarachnoid space (SAS) of the human central nervous system (CNS) along the entire neural axis. The ILL is a fibrocellular macroscopic structure, with restricted permeability, that divides the cerebrospinal fluid (CSF)-filled SAS into two distinct structural compartments. Uniquely, ILL revealed the presence of cells with macrophage-like properties, suggesting a possible role in immune surveillance. The ILL may redefine the established concept of protective coverings of CNS, CSF circulation dynamics, and the role of leptomeninges in health and disease, including drug delivery.

neuroscience↗

bioRxiv2025

A desert endophyte, Priestia megaterium SI1-IITJ, improves fluoride stress tolerance by reducing fluoride content of plant tissues and perturbing salt tolerance and defense genes of Arabidopsis thaliana

We isolated a fluoride (F-)-resistant bacterium, Priestia megaterium SI1-IITJ, from thse internal root tissues of several Thar Desert plants, Aerva javanica, Cyperus conglomeratus, Senna tora, and Tephrosia purpurea, tolerating up to 100 mM NaF. The root endophytic behavior of the isolate was confirmed by scanning electron microscopy. SI1-IITJ possesses plant growth-promoting properties, including auxin production (19.8 g mL-1), phosphate solubilization (index 3.64), ACC deaminase (0.54 mmol -ketobutyrate mL-1) and nitrate reductase (0.65 mol mL-1 nitrite) activities, revealed by biochemical tests and whole genome sequencing. SI1-IITJ extrudes F- from the cell, possibly through an F- efflux transporter, CrcB, identified in its genome. Significant growth improvements were observed in Arabidopsis thaliana under F- stress in hydroponics and soil culture upon coculture with SI1-IITJ, which improved the chlorophyll content by 1.6%, total nitrogen by 30.4%, and reduced reactive oxygen species by 48.9% and F- content by 63.9% in plant tissues. A differential gene expression analysis of A. thaliana by transcriptome sequencing indicated an unperturbed F- exporter, AtFEX1, but up-regulation of 55 genes regulating root meristem growth, cell wall modification, chlorophyll biosynthesis, Fe homeostasis, and high salt- and abiotic stress-responsive genes. On the other hand, 103 genes were down-regulated, suppressing systemic acquired resistance, plant defense, and H2O2 production. In conclusion, our results provide genomic insights into the mechanisms of F- toxicity alleviation and plant growth enhancement by a desert PGPR, highlighting Priestia megaterium SI1-IITJ as a potential biofertilizer for mitigating F- stress in plants.

plant biology↗

bioRxiv2025

Inflammasome activation differences underpin different Mycobacterium tuberculosis infection outcomes

The clinical outcome of Mycobacterium tuberculosis (Mtb) infection ranges from latent/non-progressive disease to active/progressive tuberculosis (TB), but the cellular events contributing to these variable outcomes remain unknown. Here, we report that progressive Mtb infection is associated with upregulation of guanylate-binding protein-1 (GBP1), hypoxia-inducible factor 1 (HIF-1) and elevated NLR family pyrin domain-containing (NLRP3) inflammasome activation pathways. Using rabbit lungs and in primary rabbit and human macrophages as well as human THP-1 cell line-derived macrophages for infection with laboratory (H37Rv) or clinical Mtb strains (HN878 or CDC1551) that differ in virulence, we show that NLRP3 inflammasome activation by HIF-1 and GBP1 leads to elevated mitochondrial stress, apoptosis and necrosis during progressive infection by HN878. These biological functions and pathways are dampened in rabbit lungs, primary rabbit and human macrophages during non-progressive infection by CDC1551. These findings are consistent with and confirmed by Mtb infection studies of macrophages knocked-down for HIF-1 or GBP1 expression. Our study indicates that differences in HIF-1- and GBP1-mediated NLRP3 inflammasome activation influence the outcome of Mtb infection to active or latent TB.

immunology↗

bioRxiv2025

Dietary glutamine supplementation alleviates age-related cardiac dysfunction by reducing elevated H3K27me3

BackgroundChanges to the epigenetic landscape play an important role in cardiovascular aging, where alterations in histone modifications influence gene expression by regulating DNA accessibility and chromatin structure. Our investigation into epigenetic changes during myocardial aging revealed that the repressive epigenetic mark H3K27me3 is significantly upregulated in aged mice and humans. This increase in H3K27me3 was shown to impair cardiomyocyte autophagy and drive metabolic reprogramming, key features of myocardial aging and causatively linked to dysfunction. Notably, by alleviating this repressive mark through a modified diet, we successfully mitigated the aged myocardial phenotype. MethodsHeart tissue from young and aged mice and humans was analyzed for H3K27me3 levels using immunoblotting and immunofluorescence staining. Genes regulated by H3K27me3 were identified through CUT&RUN-Seq and RNA-Seq, while metabolites were profiled using metabolomics. In neonatal rat ventricular myocytes (NRVMs), H3K27me3 levels were elevated by siRNA-mediated knockdown of UTX. Cellular metabolism was investigated using a Seahorse analyzer in cardiomyocytes with basal or elevated H3K27me3 levels. In further human studies, we assessed how circulating glutamine levels associate with the incidence of heart failure and the association of genetic variants within the SLC1A5 region with heart disease. In aged mice, H3K27me3 levels were reduced through a modified diet, and heart function was evaluated using echocardiography. Subsequently, hearts were processed for biochemical analysis, and autophagy was assessed using electron microscopy. ResultsH3K27me3 was significantly elevated in the aged mouse and human myocardium. This observed elevation in H3K27me3 was found to be attributed to impaired glutamine metabolism, resulting from reduced expression of the glutamine transporter SLC1A5 in the aged myocardium. Furthermore, elevation in H3K27me3 was found to contribute to impaired cardiomyocyte autophagy and metabolic dysfunction. In aged mice supplemented with a high glutamine diet this attenuated myocardial H3K27me3 and improved cardiac function. Furthermore, a high-glutamine diet reversed H3K27me3-mediated impairment in cardiac autophagy in aged mice. ConclusionsReduction in SLC1A5 during aging is likely to lead to increased myocardial H3K27me3 that results in impaired autophagy and metabolic reprogramming that contribute to the aged cardiac phenotype. Our findings also suggest glutamine may improve cardiac health in the aged population by lowering H3K27me3. Clinical PerspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIElevation in H3K27me3 during aging is likely to lead to impaired myocardial autophagy and metabolic reprogramming. C_LIO_LIReduction in SLC1A5 during aging in humans is likely to contribute to myocardial dysfunction C_LIO_LIDietary supplementation of glutamine improves cardiac function in aged mice. C_LI What are the clinical implications?O_LITargeting H3K27me3 in the aged population may to mitigate cardiovascular disease C_LIO_LIDietary glutamine supplementation offers a promising strategy to improve cardiac function during aging. C_LI

cell biology↗

bioRxiv2025

p53-induced RNA-binding protein ZMAT3 inhibits transcription of a hexokinase to suppress mitochondrial respiration

The tumor suppressor p53 is a transcription factor that controls the expression of hundreds of genes. Emerging evidence indicates that the p53-induced RNA-binding protein ZMAT3 acts as a key splicing regulator that contributes to p53-dependent tumor suppression in vitro and in vivo. However, the mechanism by which ZMAT3 functions within the p53 pathway remains largely unclear. Here, we discovered a function of ZMAT3 in inhibiting transcription of HKDC1, a hexokinase that regulates glucose metabolism and mitochondrial respiration. Quantitative proteomics revealed HKDC1 as the most significantly upregulated protein in ZMAT3-depleted colorectal cancer cells. ZMAT3 depletion resulted in increased mitochondrial respiration, which was rescued by simultaneous depletion of HKDC1, suggesting that HKDC1 is a critical downstream effector of ZMAT3. Unexpectedly, ZMAT3 did not bind to HKDC1 RNA or DNA; however, proteomic analysis of the ZMAT3 interactome identified its interaction with the oncogenic transcription factor JUN. ZMAT3 depletion enhanced JUN binding to the HKDC1 locus, leading to increased HKDC1 transcription that was rescued upon JUN depletion, suggesting that JUN activates HKDC1 transcription in ZMAT3-depleted cells. Collectively, these findings uncover a mechanism by which ZMAT3 regulates transcription through JUN and demonstrate that HKDC1 is a key component of the ZMAT3-regulated transcriptome in the context of mitochondrial respiration regulation.

cancer biology↗

bioRxiv2025

Acidification by nitrogen metabolism triggers extracellular biopolymer production in an oleaginous yeast

The oleaginous yeast Rhodotorula toruloides is a natural producer of lipids and carotenoids. However, its potential as a producer of extracellular biopolymers remains unexplored. Hence, we aimed to evaluate the R. toruloides CCT0783 for extracellular biopolymer production. We found that the carbon-to-nitrogen ratio influenced exopolysaccharide (EPS) production, reaching 5.84 {+/-} 0.45 g/L under glucose-rich conditions. We characterized the crude biopolymer using FTIR and GC-MS, identifying polysaccharide peaks, wherein EPS consisted of (%) glucose (88.83 {+/-} 4.87), galactose (5.50 {+/-} 1.50), mannose (4.80 {+/-} 1.57), and xylose and arabinose (0.87 {+/-} 0.04) monomers. The dried EPS also contained a fractional presence of protein (1.0%). Interestingly, inorganic, but not organic, nitrogen metabolism was associated with the acidification of the culture environment and simultaneous EPS production. A comparison between non-buffered and buffered media indicated that EPS was produced when the final pH was around or below 2, which was observed in the former but not in the latter. Finally, a comparative bioinformatics analysis allowed us to map a putative EPS biosynthesis and transport pathways, as well as regulators of intracellular pH maintenance. In conclusion, our study demonstrates R. toruloides potential as an extracellular microbial biopolymer producer, enabling its development as a cell factory. ImportanceMicrobial biopolymers are extensively investigated for their impact on the environment and health. However, developing a biotechnology process for producing such biopolymers remains challenging despite their potential for valuable applications. Considering this opportunity, we investigated the oleaginous yeast Rhodotorula toruloides as a producer of extracellular biopolymers. Our study describes the conditions of exopolysaccharide (EPS) biosynthesis in R. toruloides. This extracellular biopolymer could have a wide range of applications, from gelling agents in pharmaceuticals to emulsifiers in the food industry. Furthermore, our comparative bioinformatics analysis results could be useful for metabolic engineering and developing Rhodotorula cell factories.

microbiology↗

bioRxiv2025

Lamin A/C Deficiency Drives Genomic Instability and Poor Survival in Small-Cell Lung Cancer through Increased R-loop Accumulation

Lamin A/C (LMNA), a key component of the nuclear envelope, is essential for maintaining nuclear integrity and genome organization [1]. While LMNA dysregulation has been implicated in genomic instability across cancer and aging, the underlying mechanisms remain poorly understood [2]. Here, we investigate LMNAs role in small-cell lung cancer (SCLC), a highly aggressive malignancy characterized by extreme genomic instability [3, 4]. We demonstrate that LMNA depletion promotes R-loop accumulation, transcription-replication conflicts, replication stress, DNA breaks, and micronuclei formation. Mechanistically, LMNA loss disrupts nuclear pore complex distribution, reducing phenylalanine-glycine (FG)-nucleoporin incorporation and impairing RNA export efficiency. Furthermore, we show that LMNA expression is epigenetically repressed by EZH2 during SCLC differentiation from neuroendocrine (NE) to non-NE states. Clinically, low LMNA levels correlate with significantly worse survival in SCLC patients. These findings uncover a novel role for LMNA in safeguarding genome integrity and shaping tumor heterogeneity, with broad implications for cancer and aging. Significance StatementLamin A/C, a key structural component of the nuclear envelope, is frequently lost or mutated in cancer, laminopathies, and aging-related disorders. Lamin A/C loss is associated with genomic instability, but the underlying mechanisms remain incompletely understood. We demonstrate that LMNA loss drives genomic instability by promoting R-loop accumulation through disrupted nuclear pore dynamics and impaired RNA export. These findings reveal a previously unrecognized link between LMNA loss, nuclear envelope dysfunction, and genome instability. Targeting this pathway could help mitigate genomic instability in aging and laminopathies, while leveraging R-loop accumulation may enhance the efficacy of DNA-damaging therapies in cancer.

cancer biology↗

bioRxiv2025

Immunogenicity and Structural Features of a Stabilized Clade-C HIV-1 Env Derived from a Pediatric Elite-neutralizer

The envelope (Env) glycoprotein derived from circulating viruses in elite-neutralizers (who naturally develop broadly neutralizing antibodies (bNAbs)), serves as potential template for HIV-1 vaccine design. Herein, we report the structure and immunogenicity of soluble clade-C HIV-1 Env trimer (330) derived from a pediatric elite-neutralizer (AIIMS_330). Using SOSIP, NFL and ferritin-nanoparticle (NP) platforms, we engineered immunogens that preserved native-like Env conformation, exhibited high thermostability and nanomolar affinity for diverse bNAbs, with minimal reactivity to non-neutralizing antibodies. Cryo-EM structure solved at 5 [A] resolution of 330-SOSIP trimer-autologous bNAb 44m complex revealed interactions at GDIR motif, N332 supersite along with additional contacts at E293, K337, K446 and glycans N326, N442, N448, as compared to our previously reported BG505-44m structure. Rabbit immunizations with soluble and NP-displayed formats elicited autologous, and heterologous neutralization of tier-1 clade-C viruses. Herein we define a structurally resolved HIV-1 clade C Env that supports multivalent vaccine strategies and provides mechanistic insights toward rational HIV-1 immunogen design.

immunology↗

bioRxiv2025

Essential Role of Protein Kinase R in the Pathogenesis of Pulmonary Veno-occlusive Disease

Pulmonary veno-occlusive disease (PVOD) is a rare and severe subtype of pulmonary arterial hypertension, marked by progressive remodeling of small pulmonary arteries and veins with no therapies. Using a mitomycin C (MMC)-induced rat model, we previously demonstrated that protein kinase R (PKR)-mediated integrated stress response (ISR) drives endothelial dysfunction and vascular remodeling. To determine if PKR is the sole mediator of ISR and the pathogenesis, we treated control (Ctrl) and PKR knockout (KO) mice with the same dose of MMC. Consistent with rat data, Ctrl mice displayed ISR activation, vascular remodeling, and pulmonary hypertension after MMC treatment, while KO mice showed none of these phenotypes. Proteomic analysis revealed that MMC-mediated ISR activation attenuates protein synthesis in Ctrl but not in KO mice. These findings underscore the significance of PKR-dependent ISR activation and subsequent perturbation of proteostasis as central mechanisms driving PVOD pathogenesis and identifying PKR as a promising therapeutic target.

cell biology↗

bioRxiv2025

Loss-of-Function RUP-Variants Influence Ubiquitin-Proteasome System and Enhance Carotenoid and Folate Levels in Tomato

REPRESSOR OF UV-B PHOTOMORPHOGENESIS (RUP) negatively regulates UV- B signalling, yet its broader physiological roles in crop plants remain largely unexplored. We compared two tomato accessions bearing truncated RUP proteins--rup-1 and rup-2 (rup- variants)--with the cultivar Arka Vikas (AV), which harbours the native RUP protein. Seedlings of rup-variants exhibited enhanced tolerance to supplemental UV-B light. Red ripe (RR) fruits of rup-variants showed significantly elevated carotenoid and folate levels compared to AV. Introgression of rup-variants into AV confirmed that the increased carotenoid accumulation is genetically linked to RUP truncation. Metabolomic profiling of rup-variants revealed a substantial shift in primary metabolic homeostasis, particularly at the breaker stage, marked by a pronounced reduction in sugars and amino acids. Proteomic analyses of rup- variants across ripening stages identified that a significant proportion of differentially expressed proteins belonged to chaperones and ubiquitin-proteasome system (UPS). Upregulation of four key enzymes in the carotenoid biosynthesis pathway likely contributed to increased lycopene content in rup-variants. Elevated folate levels in rup-variants were associated with the upregulation of folate biosynthesis and C1 metabolism enzymes. Despite widespread metabolic reprogramming in rup-variants, hormonal regulatory pathways remained largely unaltered. Our results suggest that RUP modulates metabolic pathways during fruit ripening, and its loss triggers metabolic reprogramming associated with elevated folate/carotenoid levels.

plant biology↗

bioRxiv2025

Integrative Multi-omics and Supervised Learning Identifies an Epithelial Signature for Radiotherapy Response in Colorectal Cancer

Colorectal cancer (CRC) is the third most diagnosed cancer globally, accounting for 9.6% of all cancer cases, and the second leading cause of cancer deaths. Radiotherapy is a common treatment, but can demonstrate dangerous side effects and varying patient outcomes that reflects on CRC cancer heterogeneity at genetic, epigenetic, transcriptomics and proteomic levels. Identifying biomarkers capable of effectively predicting CRC patient responses to radiotherapy remains paramount, and an unmet need. We channeled both unsupervised and supervised approaches to assess radiotherapy response for 233 patients of the S:CORT Consortium. Splitting the cohort, we first integrated matched RNA, CNA, mutation, and methylation profiles of 117 patients using multi-omics factor analysis (MOFA). We identified a new radiotherapy signature of 101 biomarkers associated with patients who demonstrate a complete response to radiotherapy, and validated the signature using a random forest classifier on the internal validation dataset, and an independent testing cohort. Our signature effectively predicted treatment outcomes, achieving 89% accuracy with strong discriminatory performance (ROC_AUC = 0.85; PR_AUC = 0.71) to differentiate patients with complete response to radiotherapy compared to incomplete responders. Assessing human and murine scRNAseq datasets underscores that the signature is predominantly expressed in CRC epithelial cells, which underpin CRC heterogeneity and cellular diversity. Our identified signature enables pre-treatment identification of CRC patients that are unlikely to achieve a complete response to radiotherapy, thereby sparing these patients from unnecessary radiation exposure and off-target damage effects.

bioinformatics↗

bioRxiv2025

Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole-genome resequence and multi-environmental data

Breeding for stalk lodging resistance is of paramount importance to maintain and improve maize yield and quality and meet increasing food demand. The integration of environmental, phenotypic, and genotypic information offers the opportunity to develop genomic prediction strategies that can improve the genetic gain for complex traits such as stalk lodging. However, implementation of genomic predictions for stalk lodging resistance has been sparse primarily due to the lack of reliable and reproducible phenotyping strategies. In this study, we measured 10 traits related to stalk lodging resistance obtained from a novel phenotyping platform on approximately 31,000 individual stalks. These traits were combined with environmental information and whole-genome resequence data to investigate the predictive ability of different single and multi-environment genomic prediction models. In total, 555 maize inbred lines from the Wisconsin diversity panel were evaluated in four environments. The multi-environment models more than doubled the prediction accuracy compared to the single-environment model for most traits, particularly when predicting lines in a sparse testing design. Predictive correlations for stalk bending strength and stalk flexural stiffness, a non-destructive method for assessment of stalk lodging resistance, were moderately high and ranged between 0.32 to 0.89 and 0.26 to 0.88, respectively. In contrast, rind thickness was the most difficult trait to predict. Our results show that the use of multi-environmental data could improve genomic prediction accuracy for stalk lodging resistance and its intermediate phenotypes. This study will serve as a first step toward genetic improvement and the development of maize varieties resistant to stalk lodging. Core IdeasO_LIThe DARLING platform was successfully used to collect lodging resistance-related phenotypes C_LIO_LIProportion of variation explained by genotype by environment interaction was not negligible C_LIO_LIGenomic predictions for lodging resistance phenotypes ranged from moderate to high C_LIO_LIAccounting for genotype by environment interaction was found to be important for improved predictive performance C_LI Plain language summaryStalk lodging - when maize stalks break or fall over before harvest - can seriously reduce crop yields. Breeding maize that resists lodging is important to ensure reliable food production. We tested about 31,000 individual stalks for 10 traits related to lodging resistance using a new phenotyping system. These traits were combined with environmental information and whole-genome resequence data to investigate the predictive ability of single and multi-environment genomic prediction models. By analyzing 555 maize lines, we found that using data from multiple environments improved genomic prediction accuracy by more than twice as much as using data from a single environment. Traits such as bending strength and flexural stiffness were easier to predict, while rind thickness was more difficult. These results show that combining genetic, environmental, and phenotypic data can help breeders more accurately select maize plants with stronger stalks, leading to better, more resilient crops.

genetics↗