Physiological Genomics

IntroductionObesity is a major health issue associated with metabolic and psychological comorbidities, as well as an increased prevalence of disorders of gut-brain interaction (DGBI). Obesity and DGBI share common mechanisms such as inflammation, gut barrier dysfunction, and alterations of gut microbiota, which are all known to be regulated by stress. Glutamine (Gln), which is essential to maintain intestinal integrity and immune response, may counteract these alterations. This study aimed to evaluate the effects of oral Gln supplementation on stress-induced response in obese mice. MethodsSeven-week-old male leptin-deficient ob/ob mice were assigned to four groups: control, chronic restraint stress (CRS), Gln-supplemented, or both CRS and Gln-supplemented. Gln was administered in drinking water for two weeks, and CRS was performed during the final 4 days. Metabolic parameters, intestinal permeability, inflammatory markers, gene and protein expression, and gut microbiota composition were assessed. ResultsStress increased plasma corticosterone levels but had a limited effect on metabolic parameters. In obese mice without stress, Gln supplementation reduced body weight gain, improved body composition and reduced inflammation in the visceral adipose tissue. These effects were lost under stress conditions, with an increase in fasting glycaemia. Stress reduced occludin protein levels, while Gln exerted context-dependent effects, decreasing gene expression of Tjp3, Cldn15 and Ccl2 in unstressed mice but increasing gene expression of multiple tight junction (Tjp2, Tjp3, Cldn12, Cgn, F11r, Marveld2) and inflammatory markers (Tlr2, Myd88, Irf3) under stress. Interestingly, in unstressed obese mice, Gln altered the composition of the gut microbiota, with changes in key bacterial taxa (Thermodesulfobacteriota and Clostridiaceae). This was associated with decreased levels of cecal short-chain fatty acids and increased levels of branched-chain fatty acids. ConclusionIn conclusion, Gln improves metabolic and adipose inflammatory parameters in genetically obese mice. However, these benefits are no longer observed when mice are under stress conditions. Since, Gln has been found to increase fasting glycaemia and colonic inflammation, in association with alterations of gut microbiota.

Angiotensinogen (AGT) deletion in hepatocytes reduces Western diet-induced adiposity and hepatic steatosis in mice maintained under conventional room-temperature (RT) housing. Given the high metabolic activity of mice, this temperature imposes adaptive metabolic responses in this species. Whether this metabolic protection persists independent of increased thermogenic demand remains unclear. In this study, we first determined whether thermoneutral housing (TN, 30 {degrees}C) alters Western diet-induced metabolic phenotypes compared with RT housing (20 {degrees}C) in wild-type mice. Although body weight did not differ significantly between housing conditions, Western diet-fed mice housed at TN exhibited brown adipose tissue whitening and more pronounced hepatic steatosis than mice housed at RT, confirming that thermoneutrality exacerbated diet-induced metabolic dysfunction. We then housed hepatocyte Agt deficient (hepAGT-/-) mice and wild-type (hepAGT+/+) littermates at TN and fed them Western diet for 12 weeks. Despite enhanced metabolic dysfunction under TN, hepatocyte AGT deletion resulted in reductions in diet-induced body weight gain, fat mass, liver weight, and hepatic triglyceride accumulation. Bulk RNA sequencing of liver revealed hepatocyte AGT deficiency-dependent alterations in lipid-metabolic pathways. Cross-temperature analysis of RT and TN housing identified 35 shared differentially expressed genes, including 27 concordantly downregulated genes enriched in lipid metabolism and transport. Extended Western diet feeding for 24 weeks confirmed sustained reductions in body weight gain, liver weight, and hepatic lipid accumulation in hepAGT-/- mice. These findings demonstrate that hepatocyte AGT deletion provides sustained protection against Western diet-induced metabolic dysfunction under thermoneutral housing, a condition that more closely recapitulates human basal metabolism. NEW & NOTEWORTHYThis study investigated hepatocyte angiotensinogen (AGT) biology during Western diet feeding in mice under thermoneutral housing, a condition relevant to human metabolism. By minimizing adaptive thermogenesis induced by standard room temperature housing, thermoneutrality more closely recapitulates human basal metabolic conditions. Under this condition, hepatocyte AGT deletion remains protective against adipo and hepatic lipid accumulation, despite exacerbated Western diet-induced metabolic dysfunction in wild-type mice, demonstrating that this protection persists in a human-relevant thermal environment. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/742617v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1ac7094org.highwire.dtl.DTLVardef@131cfforg.highwire.dtl.DTLVardef@d4dba6org.highwire.dtl.DTLVardef@a09acc_HPS_FORMAT_FIGEXP M_FIG C_FIG

BackgroundsEarly-life environmental insults cause persistent neurodevelopmental abnormalities accompanied by transcriptional and epigenetic dysregulation despite removal of the original insult or postnatal intervention. However, transcriptomic and epigenomic responses to developmental insults and subsequent treatment during active neurodevelopment remain insufficiently characterized. Developmental iron deficiency (ID) provides a unique model for investigating this question because iron is an essential cofactor for TET DNA dioxygenases and developmental ID causes persistent behavioral and molecular alterations despite iron repletion. ResultsWe integrated the hippocampal transcriptome, DNA methylome (5mC), and hydroxymethylome (5hmC) in male rats at postnatal day 15 following developmental ID and postnatal iron treatment, using Oxford Nanopore sequencing for native DNA modification profiling. Developmental ID induced substantial transcriptional and epigenetic alterations associated with synaptic function, neurodevelopment, and neuroinflammation. Postnatal iron treatment induced a hierarchical response across molecular layers: while transcriptomic alterations largely normalized, 5mC showed only partial recovery, and 5hmC showed extensive de novo modifications. Recovered, persistent, and newly emerged epigenetic marks were associated with increasingly specialized biological functions, from broad neurodevelopmental processes to specific pathways. Furthermore, while 5mC enrichment was associated with transcriptionally suppressed pathways, 5hmC enrichment showed weaker coupling with concurrent transcriptomic activity, suggesting epigenetic poising rather than immediate transcriptional output. MergeOmics integration identified key driver genes showing post-treatment epigenetic regulation despite transcriptional recovery. ConclusionsMolecular recovery following developmental ID extends beyond transcriptomic normalization, involving persistent and extensive epigenetic remodeling. This study provides a framework for understanding molecular responses following early-life environmental insults and highlights the importance of delineating persistent regulatory reprogramming.

The liver of laying hens plays a central role in metabolism and reproduction, supporting the synthesis of egg yolk precursors under strong hormonal regulation. Despite its physiological importance, a high-resolution cellular reference of the adult chicken liver is still lacking. Here, we generated a single-nucleus RNA sequencing atlas of the adult laying hen liver from eight individuals, providing a comprehensive view of its cellular composition and transcriptional landscape. Using this framework, we identified major hepatic cell populations, including hepatocytes, endothelial cells, cholangiocytes, hepatic stellate cells, and diverse immune cell types, revealing a broadly conserved vertebrate liver architecture. However, hepatocyte zonation, a key feature of mammalian liver organization, was not observed, consistent with the absence of hepatocyte zonation reported in birds. Importantly, we demonstrate that the use of an enriched genome annotation, incorporating additional protein-coding and long non-coding RNA models, substantially improves transcript detection and enhances cell-type resolution in single-nucleus datasets. This improved resolution allows more accurate marker-based assignment of hepatocyte subpopulations and refines the interpretation of hepatic cellular heterogeneity. Within hepatocytes, we uncovered transcriptionally distinct subpopulations associated with lipid metabolism and reproductive function, including estrogen-responsive programs involving cytochrome P450 genes such as CYP2C23A and CYP2C23B. In parallel, we characterized a complex immune compartment composed of resident macrophages and adaptive immune cells, highlighting the dual metabolic and immunological roles of the avian liver. Overall, this atlas provides a high-resolution reference for avian liver biology and demonstrates that improved genome annotation enhances the resolution and interpretation of cellular heterogeneity in single-cell transcriptomic studies.

Objective: Circadian rhythms are frequently disrupted in patients in the intensive care unit (ICU), potentially worsening clinical outcomes. Continuous enteral nutrition throughout the day and night is common in the ICU, but eliminates feeding-fasting cycles that serve as important timing cues for the circadian system. The objective of this study was to determine the effect of providing enteral nutrition in a cyclic daytime pattern, compared with continuous administration, on circadian rhythmicity in critically ill patients in the ICU. Design: Single-center randomized controlled trial Setting: Mixed medical-surgical tertiary intensive care unit in the Netherlands Patients: Adult ICU patients ([≥]18 yr) receiving enteral nutrition. Intervention: Patients were randomized to receive either continuous, or cyclic daytime enteral feeding (08:00-20:00), initiated from the start of nutritional support. Measurements and Main Results: Sixty-two ICU patients were enrolled, of whom 51 were included in the per-protocol analysis. While the amplitude of the 24-hour rhythm in core body temperature did not differ significantly between the cyclic daytime and continuous feeding groups (0.17 [interquartile range: 0.09-0.24] vs. 0.20 [0.13-0.30], p=0.182), the 24-hour rhythm in heart rate was enhanced in patients receiving cyclic daytime feeding, as reflected by significantly higher amplitudes and more synchronized peak times. No significant differences in 24-hour rhythmicity were observed between groups for the other vital signs or melatonin. Conclusions: Our findings suggest that cyclic daytime feeding may strengthen circadian rhythms in critically ill patients. Further studies are warranted to evaluate its impact on clinical outcomes.

Background Sepsis is the primary driver of mortality in intensive care. Personalized medicine requires an accurate understanding of the syndrome, and plasma proteomics is increasingly used to characterize its molecular alterations. Comorbidities, demographics and postoperative sterile inflammation complicate this task, and proteins associated with them may be mistaken as sepsis-specific. Methods We compared 343 sepsis patients with two independent perioperative control cohorts (n = 73 and n = 75) sampled before and after surgery. Plasma was analyzed by mass spectrometry, and analyzed using linear models adjusted for age, sex and cohort-specific comorbidities. Propensity score matching was used to characterize renal comorbidities and Elastic Net classifiers were trained per cohort and time point. Results We show that renal comorbidities had the strongest impact on the plasma proteome and affected sepsis-associated proteins including Cystatin-C and Beta-2-microglobulin. Eleven proteins were robustly associated with sepsis, among them established acute phase proteins and the less well characterized Beta-1,4-galactosyltransferase 1. Feature importance analysis confirmed this core set and identified further proteins that contributed in a cohort- and time point-specific manner. Classifiers performed very well except against control patients at day 3 after surgery, when sterile inflammation peaked. Conclusions Sepsis, comorbidities and sterile inflammation may alter the same acute phase and renal proteins, differing in magnitude rather than in the type of response. We disentangled these influences and report a robust set of sepsis-associated proteins together with confounder-associated proteins, providing a basis for future studies and the development of diagnostic and therapeutic strategies.

Maternal hyperglycemia can affect offspring development and metabolism, but how its effects on skeletal muscle change during postnatal life remains unclear. We investigated skeletal muscle phenotypes in male offspring of streptozotocin-induced hyperglycemic mice at 4 and 8 weeks of age, representing early post-weaning and later postnatal stages, respectively. Maternal hyperglycemia resulted in lower offspring body and skeletal muscle weights at both time points. Myofiber cross-sectional area was reduced without a reduction in total myofiber number, indicating impaired myofiber growth rather than myofiber loss. At 4 weeks, skeletal muscle showed type I/IIA hybrid myofibers and increased expression of fetal, myogenic, and proliferation-associated genes. This immature profile was not maintained at 8 weeks; instead, the transcriptional profile shifted toward reduced mitochondrial and oxidative metabolism. DNA methylation changes at 4 weeks showed limited correspondence with transcriptional alterations. Taken together, maternal hyperglycemia impaired postnatal myofiber growth at both time points, with distinct molecular profiles at 4 and 8 weeks.

Preeclampsia (PE) is a hypertensive pregnancy-specific disorder and a leading cause of maternal and fetal mortality. A common feature of PE placentas and maternal plasma is dyslipidemia, or abnormal lipid levels, which can increase oxidative stress and endothelial dysfunction. However, the precise transcriptional, post-transcriptional, and epigenetic mechanisms underlying these abnormalities remain poorly characterized. Identifying such changes may clarify disease mechanisms and identify lipid-related PE biomarkers. We conducted a large-scale meta-analysis integrating public placental datasets from NCBI GEO, comprising four DNA methylation (DNAm) datasets (n = 172), three RNA-sequencing datasets (n = 92), and an independent RNA microarray validation cohort (n =146). We evaluated differential DNAm (limma), gene expression (DESeq2), transcript-level shifts (Swish), and alternative splicing (rMATS) in PE versus control placentas, with all analyses stratified by fetal sex via an interaction term model. We also performed placental cell-type deconvolution to quantify PE-associated cell-type proportion changes. Our results demonstrated that lipid-related regulation changes in PE placentas occur primarily at the gene and transcript level, with DNAm showing no changes. We also identified significant isoform switching in PE that were undetected by differential gene expression analysis, and primarily driven by alternative transcription initiation and termination sites rather than alternative splicing. A subset of these isoform switches mapped to pathways dysregulated in PE and were predicted to cause functional protein changes. An interaction term model identified several sex-specific differentially expressed genes (DEGs) in PE, including a subset of male-specific downregulated genes involved in oxidative metabolism. However, many of the remaining sex-specific DEGs across both sexes were previously uncharacterized in the literature. These findings suggest that transcriptional and isoform-level regulation play a role in PE-associated dyslipidemia, with certain regulatory pathways displaying fetal sex-specific patterns. Highlights- Preeclampsia-associated dyslipidemia manifests at the gene and transcript level - Reciprocal isoform switches were missed by standard gene-level analyses - Alternative transcript initiation and termination drove isoform switching - Sex-interaction modeling identified sex-specific transcriptional shifts in PE

ABSTRACT Objective: Skeletal muscle growth rate differs substantially among diverse pig breeds. In the present study, RNA-seq was performed to identify differentially expressed genes (DEGs) across pig breeds with distinct growth rates. CCND2 showed obvious differential expression among pig breeds. Although CCND2 is essential for cell cycle control, its biological function in skeletal muscle differentiation has rarely been reported. This work aims to identify DEGs in pig breeds with different growth rates and explore CCND2 role in porcine skeletal muscle development. Methods: RNA-seq was performed to identify differentially expressed genes (DEGs) across pig breeds with distinct growth rates. Weighted gene co-expression network analysis (WGCNA) was used to identify gene modules potentially associated with skeletal muscle growth and development. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis was performed to validate the role of CCND2 in skeletal muscle differentiation. Results We identified 5,416, 4,846, and 2,777 DEGs in the Duroc pig (DU) vs. Jiangquan black pig (JQ), DU vs. Laiwu pigs (LW), and JQ vs. LW comparison groups, respectively. WGCNA identified two gene modules (lightgreen and darkmagenta) potentially associated with skeletal muscle growth and development. CCND2 exhibited differential expression in comparisons between DU vs JQ and DU vs LW, with higher expression observed in Duroc pigs. qRT-PCR analysis revealed that overexpression of CCND2 at day 6 (D6) of cell differentiation significantly increased the expression levels of CCND2 gene and markers of myogenic differentiation (p < 0.05). Conversely, knockdown of CCND2 significantly decreased the expression levels of CCND2 gene and myogenic differentiation markers (p < 0.05). Conclusions This study identified breed-specific DEGs and key gene modules in porcine skeletal muscle and verified that CCND2 promotes myogenic differentiation. These findings provide a genetic theoretical basis for further investigations into skeletal muscle growth and development. Keywords pig, skeletal muscle, transcriptome, WGCNA, CCND2

Introduction: Adipose tissue fibrosis has been associated with metabolic dysfunction-associated steatotic liver disease (MASLD) and suboptimal weight loss after bariatric surgery. The objective was to characterize changes in adipose tissue fibrosis and extracellular matrix (ECM) components in adipose tissues from two abdominal fat compartments, subcutaneous and omental, in response to bariatric surgery; and determine the effect of weight loss on the association between adipose tissue fibrosis and MASLD feature changes with weight loss. Methods: Liver and adipose tissue biopsy samples were obtained before and after weight loss from patients who underwent two-stage bariatric surgery. Adipose tissue pericellular fibrosis was evaluated histologically with picrosirius red staining for collagen quantification and normalized to adipocyte count per microscope field. Transcript levels of ECM remodeling and inflammatory genes were measured by RNA sequencing in subcutaneous adipose tissue pre- and post-surgery. Results: At baseline, adipose tissue pericellular fibrosis did not associate with MASLD features, metabolic dysfunction-associated steatohepatitis or hepatic fibrosis in patients with severe obesity. Changes in liver histology after surgery were unrelated to changes in adipose tissue fibrosis. Transcripts for most genes involved in ECM remodeling and inflammation were downregulated in subcutaneous fat one year after bariatric surgery. Omental, but not subcutaneous, adipose tissue fibrosis decreased after surgery when adjusted for cell number (mean {+/-} SD: 0.41 {+/-} 0.12 vs 0.32 {+/-} 0.08 {micro}m2/cell, p<0.005). Higher subcutaneous adipose tissue fibrosis correlated with reduced weight loss (estimate {+/-} SE: -2.04 {+/-} 0.99, p<0.05) and BMI loss (-0.73 {+/-} 0.35, p<0.05), while increased omental adipose tissue fibrosis after weight loss was associated with worsening hepatic fibrosis (0.31 {+/-} 0.14, p<0.05). Conclusion: In individuals with severe obesity undergoing bariatric surgery, adipose tissue fibrosis is poorly correlated with MASLD features. Notably, pericellular fibrosis in subcutaneous abdominal, but not omental, adipose tissue was associated with a reduced weight-loss response to surgery.

Ketogenic (keto) diets have gained popularity due to their potential benefits on weight loss and metabolic conditions. However, the consequences of consuming a keto diet before, during, and after pregnancy on maternal and offspring health remain incompletely understood. To investigate this, female Swiss Webster mice were randomly assigned to either a keto or control diet. After 6 weeks on diet, females were mated and maintained on their respective diets throughout pregnancy and lactation. In experiment 1, glucose tolerance tests (GTT) were performed on pregnant dams at gestational day (GD) 16.5. At GD 17.5, dams were euthanized, urine was collected for ketone analysis, and fetal and placental weights were recorded. In experiment 2, dams delivered naturally and one male and one female offspring per dam were retained and weighed weekly. At 12 weeks of age, offspring underwent GTT, followed by euthanasia and serum collection for insulin and leptin analysis. Compared with controls, keto dams exhibited increased body weight, impaired glucose tolerance, elevated urinary ketones, and reduced circulating insulin during late gestation (p<0.05). Fetuses from keto dams were significantly smaller (p<0.05), whereas placental weight and placental efficiency were unchanged. Offspring from keto dams weighed less than controls during early postnatal development but demonstrated catch-up growth by 12 weeks of age. At 12 weeks, keto offspring exhibited a modest but statistically significant improvement in glucose tolerance compared to control offspring (p<0.05). Male keto offspring had significantly decreased serum insulin (p<0.05) compared to male control offspring, while no differences were observed in females. Serum leptin levels did not differ between diet groups, although sex differences present in control offspring were not observed in keto offspring. Together, these findings suggest that maternal ketogenic diet consumption is associated with altered maternal glucose homeostasis during pregnancy and reduced fetal growth in this mouse model. Although offspring exhibited only modest metabolic alterations during early adulthood, the observed changes in growth trajectory and sex-specific metabolic profiles support further investigation into the long-term consequences of maternal ketogenic diet exposure during pregnancy.

Nitrogenous waste excretion is essential for all developmental stages of fish. Embryonic fish excrete urea, transitioning to cutaneous and later branchial ammonia excretion. In zebrafish, ammonia excretion involves rhesus glycoproteins Rhbg and Rhcgb in keratinocytes and ionocytes, but the developmental moment they appear in the gill remains unclear. Potential redundancy between Rhbg and Rhcgb in ammonia excretion is also not fully investigated, nor is the difference in response to low pH. We hypothesized that rhesus glycoproteins are partially redundant, and that they differ in their response to low pH as ammonia excretion enables ionocytes to exchange Na+ and H+ (Rh-NHE-metabolon). We predicted that a loss of rhbg or rhcgb induces compensatory responses. We characterized the transition from urea to branchial ammonia excretion from 0 to 8 days-post fertilization (dpf) and the response to pH 5.0 on the expression and localization of rhesus glycoproteins in control zebrafish and rhbg or rhcgb-crispants. Effects of high external ammonia (HEA, 500 M NH4Cl) and 10 mM HEPES-buffering were further characterized in rhcgb-crispants. Rhag and Rhbg appeared in the gill at 5 dpf, while Rhcgb appeared at 6 dpf. A loss of rhbg or rhcgb did not impact baseline N-excretion, illustrating that zebrafish can maintain ammonia excretion without the full complement of rhesus glycoproteins. We observed no compensatory increase in rhesus glycoproteins, but expression of the transporter hippocampus-abundant transcript 1b increased. HEA-exposed rhcgb-crispants switched to urea as primary nitrogen waste. Together, these findings underline the plasticity of the larval in dealing with nitrogenous waste.

Excessive alcohol intake is frequently associated with hypertriglyceridemia, a condition that increases the risk of severe complications including acute pancreatitis and cardiovascular disease. The very low-density lipoprotein (VLDL) receptor (VLDLR) promotes uptake of apoE-containing VLDL particles by peripheral tissues and plays an important role in maintaining plasma triglyceride (TG) homeostasis. Brown adipose tissue (BAT) is a major metabolic organ that contributes to circulating lipid clearance during thermogenic activation. It was reported that cold-induced thermogenesis upregulates VLDLR expression in BAT and reduces plasma TG via VLDL uptake. However, whether BAT VLDLR-mediated VLDL uptake regulates alcohol-induced hypertriglyceridemia remains unknown. Here, we generated BAT-specific fatty acid synthase (FASN) knockout mice (FASNBKO) and subjected them to binge and acute-on-chronic alcohol feeding paradigms. We found that BAT FASN deficiency enhanced thermogenic function and promoted VLDL uptake, resulting in attenuation of alcohol-induced elevations in plasma TG. Consistent with these findings, pharmacological inhibition of FASN by TVB3664 treatment in differentiated brown adipocytes (bADs) increased thermogenic gene expression and VLDL uptake under both control and alcohol-exposed conditions. In addition, FASNBKO mice were protected from alcohol-induced hepatic steatosis, which was accompanied by increased hepatic AMP-activated-protein kinase (AMPK) activation and enhanced {beta}-oxidation. Furthermore, FASNBKO mice exhibited upregulated FGF21 mRNA expression in the BAT and elevated circulating FGF21 levels. Similarly, TVB3664-treated differentiated bADs showed higher FGF21 expression and increased FGF21 content in culture medium. Taken together, these findings identify the important role of brown adipocyte FASN in regulating thermogenic function and TG homeostasis during alcohol exposure and suggest that enhancing thermogenic lipid utilization in BAT may represent a potential therapeutic strategy for mitigating alcohol-associated increases in plasma TG and hepatic fat accumulation.

Sepsis mimics resemble sepsis clinically but may require different treatments. We evaluated whether inflammatory protein profiles could distinguish these conditions in a retrospective case-control study using 4 prospective Japanese cohorts. The study included 34 adults with sepsis and 46 with sepsis mimics. We measured 92 proteins using Olink, assessed between-group differences with false discovery rate (FDR) adjustment, and evaluated 3 prediction models using repeated nested cross-validation. No protein met the FDR threshold; the lowest FDR-adjusted P value was 0.345. The primary elastic-net model had an area under the receiver operating characteristic curve of 0.442 (95% confidence interval, 0.315-0.574), based on cross-validation predictions averaged for each participant. Random forest and gradient boosting also showed no clear evidence of discrimination above chance. Confidence intervals included chance performance in both the all-serum and quality-control-Pass sensitivity analyses. In this cohort, a single measurement of an inflammation-focused protein panel showed limited discrimination between sepsis and sepsis mimics. Integration with clinical information and longitudinal measurements warrants further investigation.

Largemouth bass (Micropterus salmoides) is a globally significant freshwater aquaculture species known for its rapid growth, high-quality flesh, and excellent nutritional value. Given the increasing incidence of hypoxia in its aquaculture setting, understanding the molecular mechanisms underlying gill adaptation to hypoxic stress is critical for improving resilience in this species. To achieve this, we employed full-length transcript sequencing using PacBio Iso-Seq and high-throughput Illumina RNA-seq to construct a comprehensive transcriptome profile. Histological analyses revealed apparent structural alterations in gill tissues under hypoxic stress (dissolved oxygen: 2.0 +/- 0.5 mg/L, duration: 96 h), including curved and swollen gill filaments, apoptosis, and epithelial cell vacuolation. Comparative transcriptomic analysis revealed pronounced shifts in the expression of genes involved in energy metabolism, angiogenesis, immune responses, cell proliferation, and apoptosis. Notably, the down-regulation of genes associated with cell cycle and proliferation suggests that M. salmoides may conserve energy by suppressing cell division under hypoxic conditions. In contrast, the increased expression of apoptosis-related genes, including Caspase 7, indicates that apoptosis may play a protective role to maintain tissue homeostasis under hypoxia. Furthermore, the suppression of chemokine-mediated immune pathways implies that hypoxia redirects energy toward essential metabolic processes at the cost of local immune responses. GO and KEGG enrichment analyses identified TNF- and chemokine-mediated signaling pathways as key regulators for tissue homeostasis and adaptive responses to hypoxic stress. These findings enhance our understanding of the mechanisms underlying hypoxia adaptation and provide valuable genetic resources for breeding strategies aimed at enhancing hypoxia tolerance in M. salmoides.

Melittin, a potent amphipathic cationic peptide derived from bee venom, exhibits broad-spectrum antineoplastic efficacy, notably against cervical carcinoma. Despite its established therapeutic potential, the global transcriptional reprogramming orchestrating its acute multi-pathway cytotoxicity remains incompletely understood. To bridge this knowledge gap, we generated the first comprehensive, untargeted RNA-seq dataset profiling the acute phase of melittin-induced cell death in murine cervical carcinoma U14 cells (exposed to 4 g/mL melittin for 20 minutes) alongside untreated controls. Utilizing deep sequencing and rigorous bioinformatics workflows, we quantified genome-wide mRNA abundances and mapped a distinct transcriptomic shift, identifying 254 significantly differentially expressed genes, comprising 158 up- and 96 down-regulated transcripts. Validated by stringent quality control metrics, exceptional genomic mapping rates, and comprehensive functional annotations via the GO and KEGG databases, this high-resolution transcriptomic resource provides a systems-level map of early molecular alterations. All raw and processed sequencing data are publicly available. This transcriptomic resource provides a valuable foundation for elucidating the acute regulatory networks underlying melittin-induced anti-cervical cancer effects. DatasetThe dataset can be accessed through the NGDC website by searching with the BioProject accession number PRJCA068439. Reviewers may use this link for anonymous access during the review process. Direct URL to data: Genome Sequence Archive-CNCB-NGDC

Cross-beaks are deemed a threat to poultry health, productivity, and animal welfare. Nevertheless, due to sporadic cases, heterogeneity of gene loci and incomplete dominance, the molecular mechanism of cross-beak formation, especially the degree of cross, is not yet clear. Thus, we screen key genes and reveal the possible phenotypic formation mechanism of cross-beak by comparison with different degrees of deformity in Huiyang Bearded chickens by compare whole-genome resequencing-based variant analysis. Comparative analysis between cross-beak and normal-beaked chickens identified differential variants in several candidate genes, including CDH11, CTNNAL1, NRXN3, NRXN1, CDH5, SDC3, and DHFR. Genes harboring these variants were enriched in pathways related to cell adhesion molecules and metabolic processes, with functional annotations involving cell-cell adhesion and neural crest cell migration. Comparative analysis between chickens with severe and slight cross-beak deformities identified additional candidate genes, including MRPL21, NSUN2, DDX55, GNB3, and NFKB2. These genes were associated with enriched terms and pathways related to focal adhesion, amyotrophic lateral sclerosis, steroid 7 -hydroxylase activity, and skin-barrier establishment. These findings provide a preliminary catalogue of genetic variants and candidate genes for future functional studies of cross-beak development and severity in chickens.

Global aquaculture has grown significantly, but to maintain current consumption, supply must double over the next 20 years. Here, we characterised the digestive and absorptive capacities in the intestines of three commercially important, farmed fish species with varying natural diets: Nile tilapia (Oreochromis niloticus), common carp (Cyprinus carpio ), and rainbow trout (Oncorhynchus mykiss). Disaccharidase activity (maltase, sucrase) and sodium-dependent D-glucose absorption were highest in Nile tilapia, followed by common carp, and lowest in rainbow trout. We found regional intestinal differences in disaccharidase activity and SGLT1 expression in the three species. Aminopeptidase A (APA) and aminopeptidase N (APN) activities were typically highest in Nile tilapia. Intestinal expression of the neutral amino acid transporter B0AT1 was approx. double in tilapia and carp compared to trout. We also assessed common carp, zebrafish and Rainbow trout's digestion profile when fed low-carbohydrate/high protein and high-carbohydrate/low-protein diets. Common carp and zebrafish adapted to high-carbohydrate diets by up-regulating both digestive enzymes and SGLT1. Common carp increased SGLT1 protein abundance 2.7-fold in the foregut and 4.6-fold in the hindgut. Rainbow trout increased disaccharidase activity but not SGLT1 expression in response to a high-carbohydrate diet. Both Rainbow trout and common carp down-regulated their APN activity but upregulated their B0AT1 expression 2-fold in response to increased dietary protein. These physiological limitations are critical considerations for formulating sustainable plant-based aquafeeds.

Rationale: Plasma proteins are used as biomarkers of inflammation and injury in acute respiratory distress syndrome (ARDS). Whether they vary with body size before ARDS is not well established. Objectives: To determine whether ARDS biomarkers vary with body mass index in adults without acute illness. Methods: We analyzed 8,680 ambulatory adults in the All of Us Research Program with proteomics covering 5,420 protein assays. We grouped 35 proteins associated with ARDS risk or mortality into five compartments by the pathophysiological role assigned in a published systematic review, registered in advance. We modeled body mass index as a restricted cubic spline and reported the difference in each protein between 35 and 25 kg/m2 in standard deviations, adjusted for age, sex, smoking, thirteen chronic conditions and ten genetic principal components. Each estimate was ranked against all 5,420 protein assays. Results: Median age was 50 years, and median body mass index was 27.2 kg/m2. Associations with body mass index across all assays were predominantly positive with a median of 0.065 standard deviations. All four epithelial proteins were lower at higher body mass index, each below at least 92% of assays. Soluble receptor for advanced glycation end products was lower by 0.350 standard deviations and surfactant protein A2, surfactant protein D and club cell secretory protein 16 were lower by 0.081 to 0.084 standard deviations. Interleukin-6 and E-selectin were 0.534 and 0.465 standard deviations higher, above 99% of assays. Differences across body mass index extended to lung enriched proteins outside the prespecified panel. Compartments accounted for 49% of the variance in the 35 protein estimates, against 10% under random reassignment (P < 0.001). At fixed body mass index, type 2 diabetes, hypertension and dyslipidemia showed smaller differences in ARDS biomarkers and were not associated with lower epithelial proteins. Conclusions: Plasma proteins used as biomarkers of inflammation and injury in ARDS vary with body size even in the absence of acute illness. Differences during ARDS may not be attributable to injury alone and may be misinterpreted in patients with obesity due to antecedent variation.

Postmenopausal women are vulnerable to metabolic dysfunction. Compelling evidence suggests this is because they lack the protective effects of estrogens. We have shown that circulating estrogens regulate daily eating and activity rhythms in female mice and protect them from obesity and metabolic dysfunction. However, few studies have investigated whether postmenopausal women have disrupted eating and sleep-activity rhythms that could contribute to metabolic dysfunction. The purpose of this cross-sectional study was to investigate the relationship between sleep and eating rhythms and metabolic risk in postmenopausal women with overweight or obesity. Seven days of sleep and food intake behavior data were collected from postmenopausal women with overweight or obesity. Sleep timing was assessed using wrist-worn actigraphy and sleep logs. First and last calorie intake times were collected daily using text messaging. Visceral adipose tissue (DXA), insulin resistance (Matsuda index), blood pressure, and triglycerides were analyzed as markers of metabolic risk. In 122 postmenopausal women (mean {+/-} SD: 58.1 {+/-} 3.6 yr, 33.2 {+/-} 5.2 kg/m2 BMI), we found that later sleep onset was associated with greater visceral adipose tissue (p=0.0007), but not insulin resistance, blood pressure, or triglycerides. Next, we used a random forest model to quantify the relative contributions of sleep and meal timing variables to predict visceral adipose tissue. The top predictors of visceral adipose tissue were time of sleep onset, sleep duration, and time of last caloric intake. These data suggest that interventions that advance sleep onset may reduce metabolic risk in postmenopausal women.