搜索结果：Physiological genomics

Fertility limits productivity in cattle and camels. Bovine fertility genomics is advanced, but determinants of fertility in camels remain poorly defined. Advances in long-read assemblies, transcriptomics, multi-omics, and biotechnology provide opportunities to resolve species-specific mechanisms and improve assisted reproductive technologies (ART). This review synthesizes genomic, molecular, endocrine, and biotechnological evidence to evaluate ART and precision breeding strategies. A structured search (2010-2025) across databases retrieved studies reporting molecular, genetic, physiological, or ART evidence related to fertility, enabling cross-species comparisons. Study quality and relevance were appraised, and findings were synthesized narratively with emphasis on translational relevance for breeding and herd management. In cattle, FSHR, LHCGR, IGF1, LEP/LEPR, BMP15, and GDF9 show consistent support from genome-wide association studies (GWAS), transcriptomics, and functional assays. In camels, preliminary evidence implicates FSHR, LHCGR, STAR, CYP19A1, BMP15, GDF9, and ESR1. The hypothalamic-pituitary-gonadal axis, gonadotropin signaling, PI3K-AKT and TGF-β cascades, steroidogenesis, epigenetic regulation, and oocyte-derived factors. Comparative analysis indicates conserved genes but distinct features of induced ovulation, seasonality, and endocrine control in camels. Emerging tools-long-read assemblies, RNA-seq, single-cell omics, CRISPR, and AI-based prediction-are promising. Assisted Reproductive Technologies (IVF/ICSI, OPU-IVEP, embryo grading, hormonal synchronization) is well established in cattle but still developing in camels. We conclude that cattle fertility genomics is robust, whereas camel genomics remain fragmented. Integrating genomic data, reproductive physiology, and ART can accelerate genetic gain. Priorities include camel SNP arrays (genome-wide SNP genotyping platforms), multi-omics datasets, improved ART outcomes, Artificial Intelligence/Machine Learning phenotyping and prediction, supported by coordinated regional and international collaborations to enhance reproductive management in arid systems.

Sunflower (Helianthus annuus L.), an important oilseed crop, is often used as a pioneer species for improving saline-alkali soils. However, the molecular mechanisms underlying sunflower seedling responses to combined saline-alkali stress remain unclear. This study aimed to elucidate the molecular basis of saline-alkali tolerance at the seedling stage by comparing physiological and transcriptomic responses between tolerant and sensitive sunflower hybrids. The saline-alkali tolerant hybrid K-27 and the sensitive hybrid K-7 were used as experimental materials. Root samples were collected at 0, 3, 12, 24, 48, and 96 h after exposure to combined saline-alkali stress (0.5% NaCl + Na2CO3, adjusted to pH 9.0). Physiological parameters, including antioxidant enzyme activities, osmolyte contents, ion concentrations, membrane damage levels, and cell wall components, were measured, followed by transcriptome sequencing analysis. Phenotypic analysis showed that the root length inhibition rate and fresh weight loss rate of K-27 were significantly lower than those of K-7, indicating stronger tolerance. Physiological analysis revealed that K-27 exhibited an inducible antioxidant enzyme response pattern. In addition, K-27 achieved osmotic adjustment through sustained proline accumulation (peaking at 12 h and remaining significantly higher than that of K-7 at 96 h) and exhibited higher basal levels of lignin and hemicellulose. Transcriptome analysis showed that the number of upregulated genes in K-27 was consistently higher than in K-7 at all time points, with 5,283 genes upregulated as early as 3 h after stress exposure. Venn analysis identified 44 core differentially expressed genes (cDEGs) shared between the two genotypes, which were mainly enriched in auxin biosynthesis regulation, phenylpropanoid biosynthesis, and glutathione metabolism. Among them, the benzoic acid carboxyl methyltransferase gene (BAMT) was continuously upregulated in K-27 but persistently downregulated in K-7. In addition, five other genes (encoding fatty aldehyde dehydrogenase, pectin methylesterase inhibitor, glutathione S-transferase, INPP5E, and HXXXD-type acyltransferase) exhibited significantly higher expression levels in K-27. K-27 tolerates combined saline-alkali stress through coordinated multi-layered response mechanisms, including inducible antioxidant defense, maintenance of ion homeostasis, sustained osmotic adjustment, and activation of the phenylpropanoid metabolic pathway. Candidate genes such as BAMT may provide potential targets for molecular breeding of saline-alkali tolerant sunflower, although their functions require further experimental validation.

Hibernation/brumation represents an important physiological adaptation for animals to cope with seasonal environmental changes. Field observations suggested increased gallbladder weight in the Five-pacer viper (Deinagkistrodon acutus) during brumation, and our quantitative measurements confirmed this increase together with bile acid accumulation. By integrating a multi-omic approach, this study elucidates the regulatory mechanisms of bile acid accumulation in the gallbladder during brumation. Results showed that taurocholic acid (TCA) and taurodeoxycholic acid (TDCA) were the major components in the gallbladder of the brumation-like group, with significantly elevated concentrations of bile acids, whereas bile acid concentrations in serum and intestinal contents were markedly reduced, indicating suppression of the enterohepatic circulation and consequent accumulation of bile acids in the gallbladder. Hepatic transcriptomic analysis revealed significant downregulation of bile acid synthesis and regulatory genes in brumation-like snakes. In contrast, the alternative synthesis pathway gene sterol 27-hydroxylase (CYP27A1) and some transporter genes were slightly upregulated. Further, some modification genes and regulatory genes showed no significant differences between active and brumation-like states. Gut microbiota analysis demonstrated Akkermansia muciniphila, Bacteroides fragilis, and Citrobacter freundii were more enriched in the active group, which were common microbes related to bile acid metabolism, and the correlation analysis confirmed this relationship. Taken together, these findings indicate that the "physiological bile acid accumulation" observed in snakes during brumation-like state is jointly driven by suppressed hepatic synthesis, reduced enterohepatic circulation, and remodeled microbial community structure. The study provides novel comparative physiological insights into extreme metabolic homeostasis in animals.

Cowpea (Vigna unguiculata (L.) Walp.) is a climate-resilient grain legume that contributes to nutritional and food safety in a variety of production regions around the world; however, many of these regions are becoming more vulnerable to climate-driven flooding and waterlogging, endangering productivity and seed quality. In this study, we used RNA-seq to assess transcriptional responses to waterlogging in different cowpea genotypes during the vegetative, flowering, and maturity stages. Using measured phenotypic/physiological, biochemical, yield, and seed-quality traits, RNA-seq expression profiles were combined with differential expression analysis, KEGG pathway enrichment/Pathview mapping, transcription factor profiling, weighted gene co-expression network analysis (WGCNA), and XGBoost-based machine-learning prediction. The tolerant genotype UCR369 demonstrated stronger physiological recovery and more dynamic transcriptional adjustment than EpicSelect.4, whereas flowering and maturity exhibited the clearest divergence in waterlogging responses, which were strongly stage- and genotype-dependent. Waterlogging caused stage-dependent alterations to soluble sugars, phenolics, flavonoids and seed-quality traits while decreasing pigment status, gas exchange, chlorophyll fluorescence, membrane stability, and yield components. Pathway analysis revealed four prominent response axes: phenylpropanoid biosynthesis, flavonoid/isoflavonoid biosynthesis, starch and sucrose metabolism, and cutin/suberin/wax biosynthesis. KEGG pathway and Pathview analyses revealed activation of antioxidant and wall-associated phenolic metabolism, carbohydrate reallocation, and surface-lipid/barrier remodelling in UCR369, with a stronger integration of these responses, particularly during flowering and maturation. Transcription factor expression dynamics exhibited stage-specific activation of the MYB, bHLH, ERF/AP2, WRKY, HD-ZIP, and HSF families, which is compatible with redox buffering, hormone-linked stress signalling, and membrane/cuticle protection. WGCNA detected 35 co-expression modules, with the top five modules as the most closely linked to phenolics/starch, sucrose, plastid/pigment functions, and membrane stability. These transcriptome-scale patterns were condensed by XGBoost into a compact collection of trait-linked predictors, with the strongest cross-layer support centred on LTP3, CER1/CER22, and CASPL1D1 for cuticle/barrier remodelling, NIA2/NR2, ICL, and SAG12 for carbohydrate and redox reprogramming, HSP21 for plastid protection, and ACS6 for ethylene-associated stress signalling. Additional recurrent predictors, such as Vigun07g271600 and Vigun08g155100, point to cytochrome P450 and HSP20-related stress-protective activities. These findings establish a trait-anchored, systems-level framework for cowpea waterlogging tolerance, as well as biologically grounded targets for marker development, functional validation, and breeding in waterlogging-prone regions.

Real-time physiological state awareness is central to next-generation wearable computing, yet most existing electrophysiological signal acquisition platforms remain limited to single-modality sensing, high component cost, or bulky form factors that hinder everyday deployment. Here, we present a compact, low-cost wearable platform for simultaneous electroencephalography (EEG), electromyography (EMG), and electrocardiography (ECG) acquisition. The system integrates an analog front-end, a microcontroller, and a Bluetooth wireless link on a compact single-board platform (5.6 × 3.8 cm, approximately 12.8 g with the selected lithium-polymer battery installed), with an estimated bill-of-materials cost of 67.40 USD. Experimental validation across three healthy subjects, with the ECG channel additionally benchmarked against a commercial clinical-grade ambulatory ECG recorder, demonstrates that the platform captures ECG waveforms with recognizable P-QRS-T morphology under controlled recording conditions, supports reliable R-peak detection and heart rate estimation, records stable resting-state EEG spectral features, and distinguishes EMG activation from resting baseline in both time-domain amplitude and time-frequency structure. Leveraging the real-time wireless data link between the wearable hardware and a PC-hosted MATLAB environment, we further explore application-oriented signal processing scenarios. As an offline algorithm-pipeline compatibility demonstration, a CNN-based seizure detection pipeline is applied to the Bonn EEG benchmark for five-class epileptic state classification, achieving 86.60% mean classification accuracy. The proposed system offers a scalable and affordable foundation for wearable human-state-aware interaction, with potential applications in clinical monitoring, rehabilitation, and brain-computer interfaces.

Extraocular muscles (EOM) display distinct physiological and pathological characteristics compared with limb skeletal muscles. To define the molecular basis of these differences, we performed single-nucleus RNA sequencing on EOM and quadriceps femoris muscle (QFM) from Macaca fascicularis. Transcriptomic profiling revealed distinct cell type compositions, with EOM enriched in fast-twitch fibers (2 A/2×), fibro-adipogenic progenitors, and neural-associated cells. EOM myonuclei expressed genes involved in synaptic transmission and axon development, whereas QFM myofibers were enriched for oxidative phosphorylation and glycolysis pathways. EOM uniquely expressed diverse myosin isoforms, including MYH13 and MYH4, supporting specialized contractile function. Disease-associated genes showed differential expression between the two muscle types, suggesting distinct susceptibilities. Intercellular communication analysis further revealed neuromuscular and regenerative signaling dominance in EOM, contrasting with immune and metabolic signaling in QFM. Together, these findings provide a comprehensive molecular framework for understanding EOM specialization and disease vulnerability.

Sudden cardiac death (SCD) in athletes often represents the first manifestation of an underlying inherited cardiovascular disorder exposed by adrenergic stress, altered calcium cycling, mechanical loading, and metabolic demand during intense exercise. This review focuses on the molecular architecture that links genotype to arrhythmogenic phenotype in athletes, emphasizing sarcomeric force generation and energetic inefficiency in hypertrophic cardiomyopathy, desmosomal failure and Hippo/Wnt/transforming growth factor-beta (TGF-β) signaling in arrhythmogenic cardiomyopathy, and ion-channel and calcium/calmodulin-dependent protein kinase II (CaMKII)calcium handling abnormalities in inherited channelopathies. This review further examines how exercise-induced physiological remodeling intersects with these pathways through insulin-like growth factor-1 (IGF-1)/phosphoinositide 3-kinase (PI3K)/ protein kinase B (AKT) signaling, mitochondrial biogenesis, oxidative stress, inflammatory signaling, and epigenetic regulation. Attention is given to the molecular basis of genotype-positive/phenotype-negative states, variable penetrance, and exercise-mediated disease expression. Finally, the integration of molecular biology with genomic data, polygenic risk, and emerging digital phenotyping is discussed to refine mechanism-based risk stratification and identify future therapeutic targets for prevention of SCD in athletes.

Understanding how age and sex influence molecular and physiological changes is essential for studying endangered species, particularly Père David's deer, which is extinct in the wild. In this study, multi-omics analyses were performed to investigate transcriptomic, metabolomic, and proteomic dynamics in male and female Père David's deer across different developmental stages under captive conditions. The results revealed sex- and stage-specific molecular trajectories, with males showing enhanced ion metabolism during early life and females exhibiting increased lipid metabolism during the subadult stage. A substantial proportion of differentially abundant metabolites and differentially expressed proteins were associated with immune and inflammatory processes. Transcriptome-based age estimation indicated that individuals at the Fawn stage exhibited younger transcriptomic profiles, and enrichment analysis of highly weighted genes highlighted immune-related pathways. In addition, transcriptomic deconvolution analysis revealed coordinated alterations in innate and adaptive immune cell populations during development. These findings provide a comprehensive multi-omics characterization of molecular and immune dynamics in captive Père David's deer and improve understanding of developmental and sex-associated biological variation in this endangered species.

Background/Objectives: NPF proteins are important transporters that mediate nitrate uptake, nutrient allocation, and abiotic stress responses in plants. However, the evolutionary patterns of the NPF gene family in grasses remain largely unclear. This study aimed to clarify the evolutionary expansion and stress response characteristics of NPF genes in Poaceae. Methods: A comprehensive comparative genomic analysis was conducted across nine representative Poaceae species and Arabidopsis thaliana. Multiple analytical approaches were used, including gene family identification, phylogenetic classification, collinearity analysis, Ka/Ks calculation, cis-element prediction, protein interaction analysis, and RNA-seq expression verification. Results: A total of 1109 NPF genes were identified with substantial variation in gene copy number among species, particularly the remarkable expansion observed in hexaploid Triticum aestivum. Phylogenetic analysis classified grass NPF proteins into eight major subfamilies, while collinearity analyses revealed that whole-genome duplication and segmental duplication were the primary drivers of NPF expansion. Most duplicated gene pairs exhibited Ka/Ks values below 1, indicating strong purifying selection during evolution. Promoter analyses identified abundant stress- and hormone-responsive cis-elements, especially in Triticeae species. In addition, protein-protein interaction and RNA-seq analyses suggested potential functional associations among NPF genes and revealed expression variation under low-temperature treatments in rice and wheat. Conclusions: Collectively, this study objectively clarifies the evolutionary expansion, functional conservation, and potential stress-responsive diversification of the NPF gene family in grasses. These findings provide straightforward and reliable insights for further evolutionary and functional research on the NPF gene family in Poaceae.

The criteria for distinguishing between association and causation in studies of genes and function are clarified. Genomic association scores alone cannot satisfy those criteria, which is why treatment of common diseases has not benefitted from the cures expected when the Human Genome Project was launched. Instead, causal understanding of function and disease requires detailed experimental data at the relevant levels of organization in the organism, from which quantitative physiological modelling then enables causal processes to be measured accurately. They can then be compared with association scores. An example shows how this process works in the heart and how that work led to the identification of a useful medication. Another major field of clinical importance is the nervous system, because nervous diseases were also expected to yield to genomics-driven discoveries of genetic cures. That expectation also has not been fulfilled. It is now necessary to investigate causation at functional physiological levels of organization in order to develop strategies that can identify cures for multifactorial diseases.

Human bronchial organoids represent a highly advanced 3D cell culture model system that reflects complex features of the airway epithelium, including structure, developmental aspects, tissue-specific functions and heterogeneous cell-cell interactions. Thus, they serve as an ideal model to study physiological differentiation and activation processes of the bronchial epithelial cells, as well as pathophysiological mechanisms of lower airway diseases. We have established, refined and validated a series of protocols for the generation, perpetuation and characterization of human bronchial lung organoids based on somatic cells derived from surgical lung tissue samples as well as from primary bronchial epithelial cells which may be obtained from healthy and diseased donors. Such organoids are cultured in an extracellular matrix gel with a serum-free medium containing a precisely adjusted growth factor cocktail. This maintains the balance between the self-renewal and differentiation capacities of the local progenitor cells, allowing the long-term culture of organoids if specific splitting and dilution as well as freezing/thawing procedures are carried out regularly and appropriately. Here we provide these detailed protocols to enable researchers to apply the organoid technology and to generate highly comparable and complementary data. Furthermore, we present several examples for the detailed characterization and analysis of human bronchial organoids, such as gene-level expression analysis, covering single cell RNA sequencing, as well as imaging and metabolic activity-based assays.

Zebrafish (Danio rerio) is a powerful vertebrate model organism with strong genetic and physiological similarity to humans, yet its use in large-scale transcriptomic research remains constrained by incomplete gene annotations, inefficient ribodepletion methods, and limited transcript-level resolution. To tackle these challenges, we applied CapTrap-seq, a platform-agnostic long-read RNA sequencing approach combining cap-trapping with oligo(dT) priming to selectively capture 5'-capped, full-length transcripts, to zebrafish developmental stages and adult tissues. We further introduce a size-selection step that substantially improves recovery of longer RNA molecules without compromising quantitative accuracy. Benchmarking against the template-switching oligo (TSO) approach demonstrated that CapTrap-seq enables accurate and reproducible transcript reconstruction in a non-mammalian system without requiring external ribodepletion or validation resources. Comparative analysis across multiple long-read catalogues showed that CapTrap-seq detected the largest number of biologically and clinically relevant genes, including oxidative phosphorylation, cardiac, and Online Mendelian Inheritance in Man (OMIM) disease genes, while revealing extensive isoform diversity absent from current annotations. Analysis of the carmn and dancr lncRNA loci further demonstrated the ability to resolve complex splicing landscapes, uncovering novel full-length isoforms with distinct domain architectures not represented in existing zebrafish reference annotations. CapTrap-seq thus emerges as a robust, genome-agnostic framework for high-quality transcriptome characterisation in zebrafish and other under-annotated species, with broad implications for functional genomics and translational research.

Despite current multimodal therapies for glioblastoma (GBM), its prognosis remains grim. Thus, a tremendous need exists to identify new genetic drivers that may serve as potential therapeutic targets in glioblastoma (GBM). We describe an in vivo overexpression screening strategy to identify drivers of glioblastoma where we have leveraged TCGA datasets to conduct a functional genomics screen of prioritized open reading frames (ORFs) that are overexpressed and/or amplified in GBM. To interrogate these potential drivers within a more relevant physiological context, the screening was accomplished in vivo in an orthotopic patient-derived glioma stem-like cell (GSC) model. Among 5 positive "hits" from the screen, Cellular Communication Network factor 4 (CCN4) was prioritized for further evaluation. Our functional analyses demonstrated that CCN4 overexpression drives tumor growth in multiple GBM models. Depletion of CCN4 reduced growth in vitro and in vivo and markedly decreased colony formation with the growth phenotype restored upon ectopic expression of CCN4. Structural functional analysis of CCN4 was also conducted. We believe that this screening strategy can serve as a platform for further identification and validation of drivers of GBM.

Tissue function emerges from coordinated interactions among diverse cell populations, whereas disruption of these interactions can lead to dysfunction. Recent advances in single-cell and spatial genomics have not only cataloged cellular diversity but also revealed how tissues are organized as dynamic multicellular ecosystems. Moving beyond descriptive cell atlases toward functional, system-level representations represents a major frontier in tissue biology. In this review, we outline conceptual and methodological frameworks for dissecting multicellular coordination, highlight recurrent multicellular ecosystems across physiological and pathological contexts, and explore translational opportunities such as patient stratification, therapeutic reprogramming, and regenerative strategies. Viewing tissues through an ecosystem lens provides a unifying framework that links cellular diversity to emergent tissue function and informs strategies for disease intervention.

Polyploidy results in genome redundancy and drives ecological diversification in freshwater fishes, yet the genomic architecture and adaptive significance of recent polyploidization in high-altitude ecosystems remain poorly understood. Herein, after determining genome size and karyotype, we tackle the long-standing challenge of resolving highly similar homologous chromosomes in autopolyploid vertebrates. By integrating long-read sequencing, Hi-C scaffolding, and haplotype-specific phasing, we assemble a haplotype-resolved genome of the autotetraploid Schizothorax nukiangensis, comprising 100 chromosomes grouped into 25 homologous sets, with a genome size of 3.59 Gb per cell. Evidence consistently supports its autotetraploid origin, with a lineage-specific polyploidization event dated to ~0.68 million years ago. Comparative genomics reveals substantial expansions of gene families in innate immunity, redox regulation, and transposon activity, suggesting genome remodeling might have contributed to adaptation in hypoxic, pathogen-rich, and fast-flowing mountain rivers. Population genomics across three elevational zones reveal subtle yet significant structure and identify candidate genes under selection related to skeletal development, immune defense, and ciliary function, consistent with adaptation to the torrents or rapids in fast-moving rivers characteristic of steep mountain ranges. Transcriptomic profiling further shows altitude-associated upregulation of genes related to immune responses and oxidative stress mitigation, which is consistent with other reported schizothoracines, highlighting convergent molecular strategies for altitude adaptation. Collectively, these demonstrate that recent autotetraploidization, coupled with gene family innovation and homeolog-specific expression divergence, has facilitated the ecological success of S. nukiangensis in extreme environments of the Salween River. This work provides important insights into the genomic imprints underlying adaptation in high-altitude freshwater vertebrates.

In this study, we optimized cryopreservation and hypothermic storage protocols for the European eel (Anguilla anguilla) spermatogonial stem cells (SSCs). As the European eel is listed as a critically endangered fish species on the IUCN red list, there is a strong need to develop and advance ex situ conservation strategies beyond the current conservation measures. Cryopreservation of SSCs was done through freezing and vitrification of testicular tissue pieces. Freezing was optimized through five sequential experiments and has yielded SSC post-thaw viability above 50%. The physiological competence of frozen/thawed cells was tested by transplanting donor-derived testicular cells into sterilized common carp larvae. After two months, gonads of 32% of the recipients displayed a positive fluorescent signal indicating that frozen/thawed cells retained physiological competence. Needle-immersed vitrification was optimized by testing different equilibration and vitrification solutions. SSCs displayed viability rates above 70% after protocol optimization. Hypothermic storage experiments displayed that storage of isolated testicular cells is more favorable than storing testicular tissue pieces, and that there was no significant reduction of SSC viability for 6 days when storing them in testicular cell suspension. Results obtained in this study are the first validated protocols for SSC preservation in the European eel and present the foundation for biobanking and future development of surrogate-based ex situ conservation programs for this and phylogenetically-related eel species.

Viruses are abundant and ecologically important in soils, yet the persistence and production dynamics of extracellular virions remain poorly understood. We applied genome-resolved stable isotope probing viromics (SIP-viromics), combining H218O labeling with viral metagenomics, to track virion turnover in seasonally dry grassland soils following rewetting. We identified 354 viral populations (vOTUs) using individual-sample and combined virome assemblies. Only 22% of vOTUs exhibited significant 18O enrichment, indicating active replication and new virion production during the 1-week incubation; the majority (78%) persisted without detectable replication, consistent with a viral seed bank. Active vOTUs accounted for 4.76-5.15% of total virions per gram of soil, with viral loads ranging from 3.15 × 1010 to 6.59 × 1010 virions per gram. Probabilistic and deterministic sensitivity analyses spanning viral DNA fraction and genome length reinforced that persistent virions represented the majority of the extracellular viral pool post-wet-up, regardless of parameter assumptions. Host predictions linked both active and persistent vOTUs primarily to Actinomycetota and Pseudomonadota-bacterial groups known to rapidly resuscitate following rewetting-suggesting that some viruses exhibit rapid turnover, while others persist over longer timescales, forming a stable viral pool capable of reinitiating infections during favorable conditions. These results demonstrate that SIP-viromics can distinguish newly produced from persistent virions and reveal predicted host-associated, lineage-level patterns consistent with lytic infection and virion production. Our findings advance understanding of soil virus-host interactions and highlight the ecological role of persistent virions as a genetic reservoir contributing to microbial turnover and biogeochemical cycling following environmental disturbance.IMPORTANCESoil viruses influence microbial survival, nutrient cycling, and ecosystem recovery after environmental disturbance, yet it remains difficult to determine which viruses are newly produced versus those persisting in the environment. By integrating H218O stable isotope probing with viromics, this study introduces SIP-viromics, a framework that directly distinguishes newly produced from persistent extracellular virions in situ. Unlike conventional viromics, which primarily catalogs viral diversity, SIP-viromics enables quantification of active viral replication and persistence. Following rewetting of a seasonally dry grassland soil, most virions persisted without detectable replication, while only a small subset became active. Active viruses were primarily associated with bacterial groups known to rapidly recover after wet-up, linking viral activity to host physiological responses. These findings show that soil viruses can persist as stable reservoirs of genetic material while retaining the potential to rapidly reactivate under favorable conditions.

Sleep and dietary behavior are deeply conserved biological processes that co-evolved under ecological pressures shaping human anatomy, metabolism, immunity, cognition, and life history strategies. Major transitions in human dietary ecology, including plant-dominant hominin foraging, increased meat consumption, control of fire and cooking, agricultural domestication, industrialization, and postindustrial globalization, restructured nutrient intake, pathogen exposure, microbial ecology, metabolic demands, and temporal organization of behavior. Emerging evidence from evolutionary genomics, chronobiology, neuroendocrinology, and microbiome science indicates that sleep-feeding interactions represent a conserved adaptive regulatory module optimized for fluctuating energy availability and strong photoperiodic entrainment. Modern environments characterized by widespread availability of highly palatable, energy-dense foods rich in refined carbohydrates, added sugars, and multiple industrial additives, together with artificial light at night, continuous caloric access, sedentary behavior, and psychosocial stress produce a profound evolutionary mismatch destabilizing circadian-metabolic homeostasis. This mismatch is characterized by circadian disruption, temporal misalignment of feeding and sleep behaviors, and, in many populations, insufficient sleep duration. Within this conceptual landscape, the emerging framework of "evolutionary chrononutrition" proposes that metabolic health and sleep integrity depend not only on what humans eat, but critically on when food is consumed in relation to endogenous circadian architecture shaped across deep evolutionary time. This review synthesizes anthropological, physiological, and molecular evidence to develop an integrative evolutionary framework linking sleep and diet to contemporary cardiometabolic, neurodegenerative, inflammatory, and psychiatric disorders, with particular emphasis on how each major dietary transition plausibly altered sleep duration, architecture, circadian timing, neuroendocrine regulation, and the temporal alignment between feeding behavior and biological rhythms.

Algae represent one of the most metabolically diverse and ecologically significant groups of photosynthetic organisms, contributing fundamentally to global biogeochemical cycles while offering major potential for biotechnology applications such as biofuels, nutraceuticals, wastewater remediation, and carbon capture. However, the complexity of algal metabolism, driven by evolutionary diversity, compartmentalized cellular organization, and strong environmental coupling, makes predictive understanding of their physiology challenging. In recent years, systems biology approaches combining omics technologies, genome-scale metabolic models, and data-driven methods have begun to transform algal research from descriptive studies toward predictive frameworks. This review summarizes the current state of algal systems biology, highlighting advances in genomics, transcriptomics, proteomics, and metabolomics that enable mechanistic insights into metabolic regulation and environmental adaptation. We discuss the development, curation, and application of algal GEMs across diverse lineages, emphasizing their role in predicting metabolic flux distributions, nutrient utilization, and lipid biosynthesis. In parallel, machine learning and artificial intelligence approaches have emerged to model algal growth and cultivation performance from large physiological datasets. Finally, we discuss emerging hybrid modeling strategies that integrate mechanistic metabolic networks with data-driven predictions, outlining how these frameworks can enable next-generation predictive algal biotechnology and guide rational design of cultivation and metabolic engineering strategies.