Biology subjects

Chaudhary, R.

Publications and source records attributed to Chaudhary, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Comparative Transcriptome Analysis Unveils Mechanisms of Salt Tolerance in Bluebunch Wheatgrass

Bluebunch wheatgrass (Pseudoroegneria spicata) exhibits substantial variation in its response to salt stress, making it a valuable model for studying salinity-tolerance mechanisms for use in crop improvement. In this study, we identified two P. spicata genotypes with contrasting responses to salt stress: the tolerant W6 56551, which maintained growth with green foliage under saline conditions, and the susceptible PI693916, which exhibited severe leaf chlorosis and stunted growth. To better understand the molecular basis of salt tolerance in blue-bunch wheatgrass, we conducted RNA-sequencing at 0, 1, and 4 days (D0, D1, and D4) after salt treatment at 160 mM level to examine changes in gene expression of salt-tolerant and salt-susceptible genotypes. Comparative analysis across time points identified 6,154 and 1,086 differentially expressed genes (DEGs) at D4 and D1 in PI693916, and 4,638 and 3,302 DEGs at D4 and D1 in W6 56551, respectively, relative to control (D0). Functional analysis of these DEGs showed that the salt-tolerant geno-type displayed an early and broad transcriptional reprogramming, including induction of photosynthesis, carbon metabolism, and flavonoid biosynthesis pathways, whereas the salt-susceptible genotype exhibited delayed and less coordinated responses, with enrichment of cyanoamino acid metabolism and repression of antioxidant-associated pathways. Notably, calcium signaling, ion transporter regulation, and osmolyte biosynthesis genes showed contrasting expression between genotypes, highlighting distinct strategies for ionic and osmotic homeostasis. Collectively, these results demonstrate that salt tolerance in P. spicata is associated with rapid metabolic adjustment, enhanced photosynthetic stability, and differential regulation of ion transport and osmoprotectant pathways.

genomics↗

bioRxiv2026

Soluble Urokinase Plasminogen Activator Receptor Primes Macrophages and Worsens Heart Failure with Preserved Ejection Fraction

BackgroundHeart failure with preserved ejection fraction (HFpEF) is a systemic inflammatory syndrome with few effective therapies. Soluble urokinase plasminogen activator receptor (suPAR), a circulating immune-derived glycoprotein, independently predicts adverse outcomes in HFpEF beyond natriuretic peptides, but whether it is a causal driver or a passive marker of inflammatory burden has remained unresolved. MethodsWe tested the hypothesis that elevated circulating suPAR is sufficient to amplify HFpEF by acting on the innate immune system. suPAR-transgenic (suPAR-Tg) and wild-type mice were subjected to a cardiometabolic two-hit model (high-fat diet plus L-NAME) for 15 weeks. Cardiac structure and diastolic function were assessed by serial echocardiography alongside blood pressure, glucose tolerance, and gravimetric endpoints, and left ventricular tissue was profiled by bulk RNA sequencing with in silico cellular deconvolution. Myeloid populations in the heart, spleen, and peripheral blood were quantified by spectral flow cytometry and corroborated by galectin-3 immunofluorescence, and the direct effect of suPAR on macrophages was tested by priming bone marrow-derived macrophages with recombinant suPAR before LPS and IFN-{gamma} stimulation. ResultsSustained suPAR elevation worsened the established HFpEF phenotype, producing greater diastolic dysfunction (higher E/e' and E/A ratios) and pulmonary congestion without altering blood pressure or ejection fraction, indicating a mechanism downstream of the canonical hemodynamic stimulus. Bulk RNA sequencing of left ventricular tissue revealed a coordinated transcriptional shift, with suppression of mitochondrial oxidative phosphorylation and amplification of innate and adaptive immune programs, including interleukin-1{beta} production, leukocyte chemotaxis, and antigen presentation. Spectral flow cytometry demonstrated stepwise expansion of CCR2 inflammatory monocytes and macrophages across cardiac, splenic, and peripheral compartments, corroborated in situ by increased galectin-3 macrophage density. In vitro, recombinant suPAR was not a stand-alone inflammatory ligand but instead primed bone marrow-derived macrophages to markedly amplify TNF-, IL-1{beta}, IL-6, and NLRP3 responses to LPS and IFN-{gamma}. ConclusionsTogether, these findings establish that elevated suPAR is sufficient to act as an upstream amplifier of HFpEF, identify the CCR2 inflammatory monocyte-macrophage axis as its proximate effector, and convert two decades of epidemiologic association into a mechanistically grounded, therapeutically tractable hypothesis with immediate relevance to clinical-stage anti-suPAR antibodies.

immunology↗

bioRxiv2026

Haplotype-resolved Genome Assemblies of Hybrid Wheatgrass and Bluebunch Wheatgrass Reveal the Stepwise Polyploid Origin and Biased Subgenome Dominance

Concerns over climate change have intensified the demand for stress resistant crops like hybrid wheatgrass (HWG; Elymus hoffmannii, StStStStHH), a perennial forage species known for its exceptional salt and drought tolerance. However, hexaploidy and high heterozygosity have complicated efforts to resolve its genomic structure and evolutionary history. Here, we present high-quality, haplotype-resolved, chromosome-level genome assemblies for HWG (CDC Saltking) and its putative progenitor, bluebunch wheatgrass (Pseudoroegneria spicata, StSt). By integrating PacBio HiFi and ultra-long Oxford Nanopore sequencing with Hi-C scaffolding, we assembled the 10.7 Gb HWG genome into 21 pseudochromosomes per haplotype. Our phylogenomic analysis redefines the origin of the H subgenome, positioning it as an intermediate between Old-World Hordeum marinum (sea barley) and Hordeum brevisubulatum. Notably, we identified significant chromosomal rearrangements, including a unique duplication on St chromosome 4. Transcriptome analysis across multiple tissues revealed a pronounced expression dominance of the H subgenome. This dominance was not associated with reduced LTR density, suggesting that selective pressures for rapid adaptation of the latest subgenome entrant may drive its dominance. Finally, using the f-branch statistic, population genomic analysis of 189 accessions representing eight Elymus and Pseudoroegneria species revealed extensive reticulate evolutionary relationships and identified P. spicata as a major, asymmetric genetic donor within the wheatgrass complex. These resources provide a foundational framework for future genomic research and genetic improvement in grasses and for the introgression of stress-tolerance traits into cereal crops such as wheat. Key MessagesO_LIDevelopment of world-first high-quality chromosomal-level haplotype-resolved genome assemblies of hexaploid HWG and diploid progenitor, Pseudoroegneria spicata, enabled the identification of the subgenome origins. C_LIO_LIThis study resolved the evolutionary placement of the St genome and clarified the history of polyploidization and hybridization in HWG. C_LIO_LIHomeolog expression bias in the H subgenome likely reflects selective pressure favoring greater gene retention and upregulation of functionally important genes, thereby enhancing hybrid fitness. C_LIO_LIPopulation structure analysis distinctly differentiates P. spicata, E. repens, E. hoffmannii from other European Pseudoroegneria species. C_LIO_LIThe findings reveal the complex patterns of interspecific gene flow and population dynamics within the Elymus and Pseudoroegneria species. C_LI

genomics↗

bioRxiv2026

High-quality genome assemblies of diploid Bromus species enhance understanding of genome complexity and uncover large DNA satellite structures.

Genus Bromus includes important cool-season forage grasses, but large genome sizes and complex ploidy hinder genomic studies. Here we carried out long read sequencing of two diploid genomes, Bromus riparius and Bromus squarrosus, generating highly contiguous assemblies with contig N50 values of 294.76 Mb and 98.78 Mb, respectively. These assemblies uncovered high-order centromeric repeats and two unique large sub-telomeric repeats on chromosome 5 and 7. Repeat expansion in Bromus appears relatively recent compared to speciation events ([~]9.75 million years ago); yet strong synteny persists across species. Transposable elements such as Angela, SIRE, Athila, CRM, and Retand were identified as major contributors to genome expansion in related Bromus species. Population structure analysis resolved six major subpopulations, with wild relatives exhibiting a higher genetic divergence than cultivated types. Hybrid bromegrass lines showed a higher proportion of genomic contribution from B. inermis than B. riparius. Together, these genomic resources provide a foundation for investigating traits of interest and advancing bromegrass breeding.

genomics↗

bioRxiv2025

Collagen remodeling promotes a GPCR-mediated mechanosensory immune checkpoint in ADGRG1+ CD8+ T cells and serves as a spatial biomarker of response to immunotherapy

Accessibility of immune cells to the tumor microenvironment (TME) in many solid tumors can be influenced by extracellular matrix (ECM) deposition, organization, and remodeling within tumor stroma. Specifically, lysyl hydroxylase-2 (LH2)-catalyzed lysine hydroxylation in type-I collagen telopeptides leads to formation of intermolecular collagen cross-links creating a stiffened and proteolytically resistant, stable ECM. Advanced head and neck squamous cell carcinomas (HNSCC) frequently exhibit desmoplasia with elevated LH2 expression, and Immune-checkpoint (ICI) therapy is effective in only <20% patients, suggesting that ECM remodeling mechanistically governs the composition and function of TME infiltrates. We show that elevated LH2 and collagen alignment promotes stromal accumulation of CD8 T-cells, and poor response to ICI in HPV-HNSCCs. Integration of clinical biopsies, transcriptomic datasets, and an immunocompetent syngeneic mouse model revealed that aligned collagen spatially restricts adhesion G protein-coupled receptor positive (ADGRG1) CD8 T-cells to activate a non-canonical GPCR-mediated mechanosensory program that drives dysfunction and exhaustion. Statement of significanceDesmoplasia is common in solid tumors, and immune checkpoint inhibitors benefit only some patients. Current biomarkers like PD-L1 and TMB have limited value. Our findings reveal a previously unrecognized collagen-ADGRG1 mechanosensory immune checkpoint, offering a clinically tractable, spatially resolved biomarker to better stratify patients for immunotherapy.

cancer biology↗

bioRxiv2025

Targeting Metabolic Dysfunction and Inflammation with Sotagliflozin Reverses Diastolic Dysfunction in Experimental HFpEF

BackgroundHeart failure with preserved ejection fraction (HFpEF) is increasingly prevalent and strongly associated with cardiometabolic comorbidities including obesity, hypertension, and metabolic dysfunction. While SGLT2 inhibitors have demonstrated clinical benefits in HFpEF, the mechanisms underlying dual SGLT1/2 inhibition remain incompletely understood. MethodsWe utilized a murine model of cardiometabolic HFpEF induced by high-fat diet combined with L-NAME administration. Following disease establishment, mice received sotagliflozin (30 mg/kg) or vehicle for 10 weeks. Comprehensive assessments included echocardiography, indirect calorimetry, cardiac metabolomics, bulk RNA sequencing with cell-type deconvolution, and high-dimensional immune profiling by flow cytometry and CyTOF. ResultsSotagliflozin significantly attenuated weight gain and improved glucose tolerance without normalizing blood pressure. Metabolic cage analyses revealed a sustained reduction in respiratory exchange ratio, indicating enhanced fatty acid oxidation, corroborated by elevated cardiac acylcarnitine intermediates including palmitoylcarnitine and dodecanoylcarnitine. Echocardiography demonstrated that sotagliflozin protected against diastolic dysfunction, normalizing isovolumic relaxation time and E/e ratio while reducing left ventricular mass and myocardial fibrosis. Transcriptomic profiling revealed upregulation of mitochondrial fatty acid {beta}-oxidation pathways and suppression of inflammatory signaling cascades including IL-1 processing and TLR pathways. Flow cytometric analysis demonstrated reduced cardiac infiltration of neutrophils, CCR2+ inflammatory monocytes/macrophages, and IL-1{beta}-expressing immune cells. Splenic immune cell expansion characteristic of systemic inflammation was similarly attenuated. ConclusionsDual SGLT1/2 inhibition with sotagliflozin exerts coordinated cardiometabolic benefits in experimental HFpEF through metabolic reprogramming toward enhanced lipid utilization and suppression of cardiac and systemic inflammation. These findings establish that sotagliflozin targets the intertwined metabolic-inflammatory axis central to HFpEF pathogenesis, providing mechanistic insight into the therapeutic efficacy of dual SGLT inhibition in cardiometabolic heart failure. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=96 SRC="FIGDIR/small/691021v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@146dfbforg.highwire.dtl.DTLVardef@ba784org.highwire.dtl.DTLVardef@122ecfcorg.highwire.dtl.DTLVardef@1f49a1a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2025

A novel role of circCPSF6 regulating antiviral innate immunity via miR-665 and PCBP2-IPS-1 axis

ObjectiveCircular RNAs are emerging as critical regulators of biological processes, yet their contribution to innate immune response during virus infection remains insufficiently defined. This study investigated the role of circCPSF6 in modulating host antiviral responses. MethodCircCPSF6 expression was validated in human and murine cells and tissue by RT-PCR and digital PCR. Its effect on virus replication was analysed by RT-PCR in human and murine primary cells and cytokine production at protein level was measured by ELISA. Luciferase assay, RNA immunoprecipitation, RNA pulldown assay, immunoblotting was performed to explore the circRNA-miRNA regulatory mechanism. CircCPSF6 interacting protein were identified by RNA pulldown followed by mass spectrometry and regulatory mechanism was analysed by immunoblotting and confocal microscopy. ResultCircCPSF6 identified as highly conserved circRNA, suppressed during virus infection, in vitro and in vivo. Functional analyses revealed antiviral role of circCPSF6. Mechanistically, circCPSF6 has dual cross-regulatory role by sequestering proviral miR-665 to relieve expression of key antiviral genes (MyD88, STAT2, IKK{varepsilon}) and interact with RNA binding protein PCBP2 to modulate IPS-1 degradation. ConclusionCircCPSF6 exert antiviral role and regulate host innate immune signaling by direct RNA-RNA and RNA-protein interaction, highlights circRNA mediated network as a potential therapeutic target in virus infection. HighlightsCircCPSF6 is evolutionarily conserved and suppressed during virus infection. CircCPSF6 act as antiviral factor by promoting inflammatory cytokine production. CircCPSF6 sponges proviral miR-665 and alleviate MyD88, STAT2, IKK{varepsilon} expression. CircCPSF6 bind to PCBP2, limit IPS-1 degradation and sustain antiviral signaling. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/686289v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@f59bedorg.highwire.dtl.DTLVardef@cff26eorg.highwire.dtl.DTLVardef@354ea5org.highwire.dtl.DTLVardef@1be4c63_HPS_FORMAT_FIGEXP M_FIG Mechanism of host innate immune regulation by circCPSF6 during virus infection. In cell cytoplasm circCPSF6 act as ceRNA for miR-665 and RNA binding protein PCBP2. Virus infection leads to reduced circCPSF6 and increased miR-665 expression, which inhibits expression of antiviral genes, MyD88, STAT2, IKK{varepsilon}. Additionally, reduced circCPSF6 leads to elevated free PCBP2 protein, hence, promote PCBP2 mediated IPS-1 degradation. Overall, these effects contribute to reduced innate immune response and increased viral replication. C_FIG

immunology↗

bioRxiv2025

Immunometabolic role of metabolic enzyme PANK4 in regulation of TLR7/9-mediated innate immunity

Innate immune responses are intimately linked to cellular metabolism, yet the molecular connections between metabolic reprogramming and antiviral defense remain incompletely defined. Here, we identify PANK4, an atypical member of pantothenate kinase family involved in coenzyme A (CoA) biosynthesis, as an unexpected regulator of RNA virus including influenza virus pathogenesis. Unlike other pantothenate kinases, PANK4 lacks canonical kinase activity but has been implicated in metabolic regulation. We show that influenza virus infection, in conjunction with pantothenic acid, induces PANK4 expression, which promotes viral replication by enhancing glucose uptake and glycolytic activity. Loss of PANK4 curtailed viral replication, reduced expression of glycolytic regulators, and heightened host antiviral defenses. Mechanistically, PANK4 interacts with UNC93B1 to suppress TLR7 and TLR9 mediated cytokine responses, thereby acting as a negative regulator of nucleic acid-sensing innate immune pathways in various cell-types. Furthermore, viral proteins NS1 and PB1 exploit PANK4 to amplify replication and immune evasion.

immunology↗

bioRxiv2025

A new subgenome of the Camelina genus reveals genome dominance is controlled by chromosomal proximity

Camelina sativa is an oilseed of the Brassicaceae, whose close relatives vary in ploidy number, providing a novel platform for studying plant genome evolution. The availability of diploid, tetraploid and hexaploid species of Camelina allow the evolutionary trajectory and fate of duplicated genes in the neopolyploid Camelina species to be elucidated. Here we report an improved assembly of the widely used C. sativa reference DH55 and three new genome assemblies of Camelina microcarpa; one tetraploid CN119243 (2n = 26), and two hexaploids with divergent chromosome numbers, Type 1 - CN119205 (2n=40) and Type 2 - CN120025 (2n=38). The tetraploid represents the first step in the evolutionary path to form C. sativa, while the hexaploids suggest three divergent lineages in the formation of higher ploidy Camelina species. The previously uncharacterized fourth subgenome found in C. microcarpa Type 2, although showing some homology to the C. sativa diploid progenitor genome, C. neglecta, showed numerous unique chromosomal rearrangements differentiating it from other subgenomes present in known Camelina species. Although this species was recently formed, the second subgenome showed gene expression dominance, which was in contrast to both 2n=40 Camelina species where the third subgenome was dominant. The expression dominance in Type 2 C. microcarpa contradicted the accepted two-step evolutionary process which led to the generation of related Brassicaceae species. However, the observed genome dominance in all Camelina species was negatively correlated with inter-subgenome chromatin interaction frequencies, suggesting that chromosome confirmation and proximity in the nucleus contributes to this mechanism of genome evolution. Despite the differences in genome structure, successful inter-specific hybridization provided evidence of chromosomal exchange between the divergent third sub-genomes of C. sativa and C. microcarpa Type 2, opening up a novel avenue to new diversity in the established oilseed. Key pointsO_LIAn improved genomic understanding of Camelina species and identification of distinct subgenome structures and relationships, which will facilitate strategies to increase the genetic diversity in C. sativa. C_LIO_LISubgenome evolution and subgenome dominance in polyploids is associated with chromosomal architecture and proximity in the nucleus. C_LIO_LIGenome assemblies representing all ploidy levels in the Camelina genus provide a unique and valuable platform for polyploid research. C_LI

genomics↗

bioRxiv2025

15-PGDH inhibition promotes hematopoietic recovery and enhances HSC function during aging

Hematopoietic aging is characterized by diminished stem cell regenerative capacity and an increased risk of hematologic dysfunction. We previously identified that the prostaglandin-degrading enzyme 15-hydroxyprostaglandin dehydrogenase (15-PGDH) regulates hematopoietic stem cell activity. Here, we expand on this work and demonstrate that in aged mice, (1) 15-PGDH expression and activity remain conserved in the bone marrow and spleen, suggesting it remains a viable therapeutic target in aging, (2) prolonged PGDH inhibition (PGDHi) significantly increases the frequency and number of phenotypic hematopoietic stem and progenitor cells across multiple compartments, with transcriptional changes indicative of enhanced function, (3) PGDHi-treated bone marrow enhances short-term hematopoietic recovery following transplantation, leading to improved peripheral blood output and accelerated multilineage reconstitution, and (4) PGDHi confers a competitive advantage in primary hematopoietic transplantation while mitigating age-associated myeloid bias in secondary transplants. Notably, these effects occur without perturbing steady-state blood production, suggesting that PGDHi enhances hematopoiesis under regenerative conditions while maintaining homeostasis. Our work identifies PGDHi as a translatable intervention to rejuvenate aged HSCs and mitigate hematopoietic decline. Significance StatementWe identify 15-hydroxyprostaglandin dehydrogenase inhibition (PGDHi) as a strategy to enhance hematopoietic stem cell function in aging. In aged mice, PGDHi expands stem and progenitor populations, accelerates hematopoietic recovery after transplantation, and reduces myeloid bias while maintaining steady-state blood production. These findings highlight a potential therapeutic approach to restore hematopoietic resilience and improve regenerative outcomes in aging. Graphical Abstract15-prostaglandin dehydrogenase inhibition ameliorates multiple facets of age-related hematopoietic decline. Schematic made using BioRender.com. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/648417v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1952ad9org.highwire.dtl.DTLVardef@30169aorg.highwire.dtl.DTLVardef@11bec0corg.highwire.dtl.DTLVardef@2617c8_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Genomic Analysis Reveals Genetic Diversity, Population Structure and Evolutionary Dynamics in Bluebunch wheatgrass (Pseudoroegneria species)

Bluebunch wheatgrass (BBWG: Pseudoroegneria species) is an outcrossing perennial grass of considerable ecological and agricultural importance due to its resilience in adverse environmental conditions. To gain a deeper understanding of the diversity, population structure, and genetic relationship within the Pseudoroegneria genus, we analyzed genomic variations of 145 genotypes representing seven species (P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata) from major global lineages, using genotyping-by-sequencing. Our results identify six distinct genetic clusters, with P. spicata (a North America species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutional history of Eurasian BBWG species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, which revealed potential gene flow events. Our findings suggest that the Eurasian BBWG species have undergone reticulate evolution, characterized by substantial gene flow.

genomics↗

bioRxiv2024

The global spectrum of tree crown architecture

Trees can differ enormously in their crown architectural traits, such as the scaling relationships that link their height and crown size to their stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of woody ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from >500,000 globally distributed trees, we explored how climate, disturbance, competition, functional traits, and evolutionary history constrain the height, crown size and shape of the worlds tree species. We found that variation in height scaling relationships was primarily controlled by water availability and light competition. Conversely, crown width was predominantly shaped by exposure to wind and fire, while also covarying with other functional traits related to mechanical stability and photosynthesis. Additionally, several plant lineages had crown architectures that defy their environments, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legumes in African savannas. Our study charts the global spectrum of tree crown architectural types. It provides a roadmap for integrating crown architecture with vegetation models and remote sensing observations, so that we may better understand the processes that shape the 3D structure of woody ecosystems.

ecology↗

bioRxiv2024

Comparative Analysis of Housing Temperature Impact on Heart Failure with Preserved Ejection Fraction in J vs N Strain C57BL/6 Mice

IntroductionHeart failure studies are conducted in preclinical animal models with different genotypic strains, 7-times higher metabolic rate, 5 to 6 times higher heart rate, and are housed in a cold-stressed environment of 23{degrees}C, unlike humans. These differences severely affect how animals respond to interventions, particularly those that lead to the development of metabolic syndrome, such as the two-hit model of diet-induced obesity (DIO) and N-nitro-L-arginine methyl ester (L-NAME) administration. A two-hit model of diet-induced obesity (DIO) and L-NAME administration has been proposed to induce heart failure with preserved ejection fraction (HFpEF) and mimic the hallmarks of metabolic syndrome and inflammation-induced heart failure in humans [1]. However, studies have reported conflicting results using this model. In this study, we examined the influence of mouse strain and environmental temperature on the development of metabolic syndrome and HFpEF using a two-hit model. MethodsEight-week-old, C57BL/6 mice (n=30) from the J and N strains were randomized to receive a high-fat diet (HFD) plus L-NAME versus a regular chow diet; and were randomized to be housed at a regular temperature of 23 {degrees}C versus a thermoneutral temperature of 30 {degrees}C. Glucose tolerance test (GTT, 2g/kg body weight), blood pressure via tail cuff, and echocardiography were conducted at baseline and, then at 5 and 15 weeks. Metabolic phenotyping was conducted at week 15 by using the Promethion Sable System. ResultsOur study revealed the significant effects of housing temperature and strain on the development of metabolic syndrome and HFpEF following the initiation of HFD +L-NAME over 5 and 15 weeks. At 5 weeks, both strains showed thermoneutral housing-induced attenuation of the effects of HFD + L-NAME on blood pressure and glucose tolerance, with the J strain exhibiting reduced diastolic dysfunction. By week 15, thermoneutral housing decreased energy expenditure (EE) and fat oxidation in both strains, while specifically reducing the respiratory exchange ratio (RER)_and glucose oxidation in J strain. Ejection fraction increased in both strains compared with the Chow group, except for J strain at 23 {degrees}C. Notably, physical activity levels remained constant across the groups, suggesting that the observed metabolic changes were not activity related. These findings highlight the complex physiological adaptations of these strains to different housing temperatures. ConclusionsThermoneutral housing conditions elicited strain-specific metabolic and cardiac effects in mice, with the J strain showing more pronounced responses. These findings highlight the critical influence of ambient temperature on experimental outcomes in rodent models, emphasizing the need to consider housing conditions when interpreting the results of metabolic and cardiovascular research.

immunology↗

bioRxiv2024

Harnessing genome prediction in Brassica napus through a nested association mapping population

Genome prediction (GP) significantly enhances genetic gain by improving selection efficiency and shortening crop breeding cycles. Using a nested association mapping (NAM) population a set of diverse scenarios were assessed to evaluate GP for vital agronomic traits in B. napus. GP accuracy was examined by employing different models, marker sets, population sizes, marker densities, and incorporating genome-wide association (GWAS) markers. Eight models, including linear and semi-parametric approaches, were tested. The choice of model minimally impacted GP accuracy across traits. Notably, two models, rrBLUP and RKHS, consistently yielded the highest prediction accuracies. Employing a training population of 1500 lines or more resulted in increased prediction accuracies. Inclusion of single nucleotide absence polymorphism (SNaP) markers significantly improved prediction accuracy, with gains of up to 15%. Utilizing the Brassica 60K Illumina SNP array, our study effectively revealed the genetic potential of the B. napus NAM panel. It provided estimates of genomic predictions for crucial agronomic traits through varied prediction scenarios, shedding light on achievable genetic gains. These insights, coupled with marker application, can advance the breeding cycle acceleration in B. napus. Core ideasO_LIGenome prediction (GP) enhances genetic gains by improving selection efficiency and shortening breeding cycles. C_LIO_LIFactors influencing GP accuracy include model choice, marker types, and population size. C_LIO_LIInclusion of SNaP markers and highly significant GWAS markers improves prediction accuracy, shedding light on achievable genetic gains. C_LI Plain SummaryGenome prediction (GP) is a powerful tool that helps us improve crops more efficiently. In this study, we assessed how well GP works for predicting important traits in Brassica napus plants. We tested different models and marker sets to see which ones were most accurate. We found that two models, rrBLUP and RKHS, were consistently the best. Also, including certain types of genetic markers, like SNaP markers and highly significant GWAS markers, improved the predictions. Overall, our study shows that GP can help us understand the genetic potential of B. napus plants and improve breeding strategies, which can be exploited to develop better varieties more quickly, which is good news for farmers and the food supply.

genomics↗

bioRxiv2024

Metabolic Adaptations in Adult Spiny Mouse (Acomys) Cardiomyocytes Facilitate Enhanced Cardiac Recovery Following Myocardial Infarction

The adult mammalian heart has limited regenerative capacity following injury, leading to progressive heart failure and mortality. Recent studies have identified the spiny mouse (Acomys) as a unique model for mammalian cardiac regeneration, exhibiting enhanced recovery after myocardial infarction compared to commonly used laboratory mouse strains. However, the cellular and molecular mechanisms underlying this regenerative response remain poorly understood. In this study, we performed a comprehensive characterization of the metabolic adaptations to ischemic injury in cardiomyocytes of Acomys in comparison to the non-regenerative Mus Musculus. To investigate the transcriptomic and metabolomic profiles of cardiomyocytes in response to myocardial infarction, we utilized single-nucleus RNA sequencing (snRNA-seq) in sham-operated animals and 1, 3, and 7 days post-myocardial infarction. Complementary targeted metabolomics, stable isotope-resolved metabolomics, and functional mitochondrial assays were performed on heart tissues from both species to validate the transcriptomic findings and elucidate the metabolic adaptations in cardiomyocytes following ischemic injury. Transcriptomic analysis revealed that Acomys cardiomyocytes upregulate genes associated with glycolysis, the pentose phosphate pathway, and glutathione metabolism while downregulating genes involved in oxidative phosphorylation following injury. These metabolic changes were linked to decreased production of reactive oxygen species and increased antioxidant capacity, evidenced by the upregulation of genes such as Prdx1, Sod1, Sod2, and G6pd. Our targeted metabolomic studies supported these findings, showing a shift from fatty acid oxidation to glycolysis and ancillary biosynthetic pathways in Acomys cardiomyocytes post-injury. Functional mitochondrial studies indicated a higher reliance on glycolysis in Acomys compared to Mus, underscoring the unique metabolic adaptations of Acomys cardiomyocytes. Stable isotope tracing experiments confirmed a shift in glucose utilization from oxidative phosphorylation in Acomys. In conclusion, our study identifies unique metabolic adaptations in Acomys cardiomyocytes that contribute to their enhanced regenerative capacity following myocardial infarction. These findings provide novel insights into the role of metabolism in regulating cardiomyocyte proliferation and cardiac repair in adult mammals. By targeting the specific metabolic pathways and regulators identified in Acomys, such as glycolytic enzymes and PCK2, we may be able to develop innovative therapies to promote cardiac regeneration in patients with ischemic heart disease. Our work highlights the importance of metabolic flexibility in determining cardiomyocyte regenerative responses and establishes Acomys as a valuable model for studying cardiac regeneration in adult mammals. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=119 SRC="FIGDIR/small/595229v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@dba53aorg.highwire.dtl.DTLVardef@3c8a74org.highwire.dtl.DTLVardef@a60251org.highwire.dtl.DTLVardef@e2142c_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

Overexpression of barley heat stress transcription factor HvHsfA6a provide thermotolerance by thermopriming

Adverse impacts of climate change, including high temperature on cereal crop production, have been evidenced globally. In plants, heat shock factors (HSFs) are crucial components of heat stress associated rescue mechanisms and are also required for normal biological processes. Here, we functionally characterized a highly heat stress responsive HvHSFA6a in barley by developing constitutively overexpressing transgenic lines. These transgenic lines showed heat tolerant phenotype via improved photosynthesis, antioxidants and upregulation of HSPs and metabolites involved in stress amelioration and keeping thermomemory as compared to wild type plants. Global transcriptomics and ChIP sequencing revealed that HvHSFA6a orchestrates the expression of several genes through direct binding with other HSFs containing consensus HSE in their promoter regions. A GC-MS based metabolomics analysis also revealed the alterations in key metabolic processes such as carbohydrate metabolism, citric acid cycle, amino acids and secondary metabolism. Higher accumulation of key metabolites such as sucrose, galactinol, shikimate and ascorbate has been observed under both control and heat stress in transgenic lines as compared to wild type plants. Taken together, the results suggest that overexpression of HvHsfA6a prime the plants for heat stress conditions by alteration in gene expression and metabolic status. HighlightPriming is a mechanism by which plants respond to various abiotic and biotic stresses. Through multi omics approach we found that barley HsfA6a provide thermotolernce in transgenic plants through priming effect on transcriptome and metabolome.

molecular biology↗

bioRxiv2023

TGF-β1 inhibits cholesterol metabolism in hepatocytes to facilitate cell death, EMT and signals for HSC activation.

Background and Aims: Transforming growth factor-{beta}1 (TGF-{beta}1) plays important roles in chronic liver diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD). MASLD involves various biological processes including dysfunctional cholesterol metabolism and contributes to progression to metabolic dysfunction-associated steatohepatitis (MASH) and hepatocellular carcinoma (HCC). However, the reciprocal regulation of TGF-{beta}1 signaling and cholesterol metabolism in MASLD is yet unknown. Methods: Changes in transcription of genes associated with cholesterol metabolism were assessed by RNA-Seq of murine hepatocyte cell line (AML12) and mouse primary hepatocytes (MPH) treated with TGF-{beta}1. Functional assays were performed on AML12 cells (untreated, TGF-{beta}1 treated, or subjected to cholesterol enrichment (CE) or depletion (CD)), and on mice injected with adeno-associated virus 8 (AAV8)-Control/TGF-{beta}1. Results: TGF-{beta}1 inhibited mRNA expression of several cholesterol metabolism regulatory genes, including rate-limiting enzymes of cholesterol biosynthesis in AML12 cells, MPHs, and AAV8-TGF-{beta}1-treated mice. Total cholesterol levels and lipid droplet accumulation in AML12 cells and liver tissue were also reduced upon TGF-{beta}1 treatment. Smad2/3 phosphorylation following 2 h TGF-{beta}1 treatment persisted after CE or CD and was mildly increased following CD, while TGF-{beta}1-mediated AKT phosphorylation (30 min) was inhibited by CE. Furthermore, CE protected AML12 cells from several effects mediated by 72 h incubation with TGF-{beta}1, including EMT, actin polymerization, and apoptosis. CD mimicked the outcome of long term TGF- {beta}1 administration, an effect that was blocked by an inhibitor of the type I TGF-{beta} receptor. Additionally, the supernatant of CE- or CD-treated AML12 cells inhibited or promoted, respectively, the activation of LX-2 hepatic stellate cells. Conclusions: TGF-{beta}1 inhibits cholesterol metabolism while cholesterol attenuates TGF-{beta}1 downstream effects in hepatocytes.

cell biology↗

bioRxiv2023

Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa

Vernalization requirement is an integral component of flowering in winter-type plants. The availability of winter ecotypes among Camelina species facilitated the mapping of QTL for vernalization requirement in C. sativa. An inter- and intraspecific crossing scheme between related Camelina species, where two different sources of the winter-type habit were used, resulted in the development of two segregating populations. Linkage maps generated with sequence-based markers identified three QTL associated with vernalization requirement in C. sativa; two from the inter-specific (chromosomes 13 and 20) and one from the intra-specific cross (chromosome 8). Notably, the three loci were mapped to different homologous regions of the hexaploid C. sativa genome. All three QTL were found in proximity to FLOWERING LOCUS C (FLC), variants of which have been reported to affect the vernalization requirement in plants. Temporal transcriptome analysis for winter-type Camelina alyssum demonstrated reduction in expression of FLC on chromosomes 13 and 20 during cold treatment, which would trigger flowering, since FLC would be expected to suppress floral initiation. FLC on chromosome 8 also showed reduced expression in the C. sativa ssp. pilosa winter parent upon cold treatment, but was expressed at very high levels across all time points in the spring-type C. sativa. The chromosome 8 copy carried a deletion in the spring-type line, which could impact its functionality. Contrary to previous reports, all three FLC loci can contribute to controlling the vernalization response in C. sativa and provide opportunities for manipulating this requirement in the crop. Significance StatementDeveloping winter C. sativa germplasm is an important breeding goal for this alternative oilseed, with application in the food, fuel and bioproduct industries. Studying the genetic architecture of the vernalization response has shown that contrary to previous reports all three FLC loci in Camelina species could be exploited to manipulate this important trait.

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