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PubMed2025

Stepping out of the dark: how metabolomics shed light on fungal biology.

Metabolomics, a critical tool for analyzing small-molecule metabolites, integrates with genomics, transcriptomics, and proteomics to provide a systems-level understanding of fungal biology. By mapping metabolic networks, it elucidates regulatory mechanisms driving physiological and ecological adaptations. In fungal pathogenesis, metabolomics reveals host-pathogen dynamics, identifying virulence factors like gliotoxin in Aspergillus fumigatus and metabolic shifts, such as glyoxylate cycle upregulation in Candida albicans. Ecologically, it highlights fungal responses to abiotic stressors, including osmolyte production like trehalose, enhancing survival in extreme environments. These insights highlight metabolomics' role in decoding fungal persistence and niche colonization. In drug discovery, it aids target identification by profiling biosynthetic pathways, supporting novel antifungal and nanostructured therapy development. Combined with multi-omics, metabolomics advances insights into fungal pathogenesis, ecological interactions, and therapeutic innovation, offering translational potential for addressing antifungal resistance and improving treatment outcomes for fungal infections. Its progress shed light on complex fungal molecular profiles, advancing discovery and innovation in fungal biology.

Metabolomics↗
PubMed1976

Ultrastructural basis for alveolar-capillary permeability to protein.

The intravenous injection into mice of small volumes (less than 0.1 ml) of peroxidatic enzymes of molecular weight of 40 000 daltons or greater results in little if any penetration of these probe molecules into endothelial junctions. The injection of cytochrome c (12 000 daltons), on the other hand, results in the localization of this tracer in some but not all endothelial junctions. When horseradish peroxidase (EC 1.11.1.7) is injected in a large volume of saline (0.5 ml), reaction product is present in endothelial junctions and basement membrane, but is prevented from entering the alveolar space by zonulae occludentes between epithelial cells. These experiments indicate that although endothelial junctions, under physiological conditions, are largely impermeable to molecules the size of horseradish peroxidase, and presumably most serum proteins, they are labile and susceptible to stretching if intravascular pressure is increased. Freeze-fracture studies show that pulmonary capillary endothelial junctions are composed of one or at the most two strands which show areas of discontinuity. Epithelial junctions, by contrast, are composed of a continuous, complex network of anastomosing fibres. These observations confirm physiological experiments which indicate that it is the pulmonary epithelium rather than the endothelium which determines the permeability properties of the alveolar-capillary membrane to lipid-insoluble molecules. Bidirectional pinocytic transport is an additional mechanism whereby lipid-insoluble molecules are transported across both endothelial and epithelial layers. The relative contribution of this transport mechanism to the total amount transported remains to be established.

Animals↗
PubMed1978

Endogenous pain control mechanisms: review and hypothesis.

The anatomy, physiology, and pharmacology of an intrinsic neural network that monitors and modulates the activity of pain-transmitting neurons is reviewed. This system can be activated by opiate administration or by electrical stimulation of discrete brainstem sites. Evidence is presented that its pain-suppressing action is mediated in part by endogenous opiatelike compounds (endorphins). This pain suppression system is organized at three levels of the neuraxis: midbrain, medulla, and spinal cord. Activation of neurons in the midbrain periaqueductal gray matter (by electrical stimulation, opiates, and possibly psychological factors) excites neurons of the rostral medulla, some of which contain serotonin. The medullary neurons, in turn, project to and specifically inhibit the firing of trigeminal and spinal pain-transmission neurons. As part of a negative feedback loop, the output of the pain transmission neurons, i.e., pain itself, is an important factor in activating the pain-suppression system. A neural model which incorporates the experimental findings is proposed, and the clinical implications of the model are discussed.

Analgesia↗
PubMed2026

Comparative analysis of conserved non-coding elements identifies gene regulatory networks rewired during the water-to-land transition in vertebrates.

The conquest of land by vertebrates has been a pivotal moment in evolutionary history. Adapting to the new habitats necessitated numerous changes in vertebrate anatomy and physiology, creating an enduring imprint on the developmental gene regulatory networks (GRNs) of tetrapods. The increase of high-quality genomic resources over the past decade has made it possible to study the genomic legacy of the water-to-land transition. While much attention has been given to the highly conserved non-coding elements (CNEs) of the genome that share high levels of similarity across evolutionarily diverged clades, recent evidence suggests that perhaps comparable attention should be given to "missing" CNE-s, conserved sequence patches present in extant stem gnathostomes and actinopterygian fishes that have become undetectable in tetrapods during the adaptation to terrestrial life, whether through true sequence loss or divergence beyond alignability. These sequences could help us reveal the relaxation of certain developmental constraints, related to the aquatic lifestyle, that made reaching new adaptive peaks in the developmental landscape possible. In this paper, we search for such CNEs and characterize them in comparison with pan-Gnathostome CNEs, using the zebrafish (Danio rerio) genome as a reference. Our results suggest that the rewiring of developmental networks related to pigmentation and muscle structure formation has left the largest genomic imprint. We also find that components of canonical Wnt and Hedgehog signalling, are enriched among CNEs retained in fish.

cis-regulatory evolution↗
PubMed2026

Listening forward: emerging roles of bioacoustics in ecology, evolution, and conservation.

Bioacoustics is increasingly shifting from a mostly descriptive pursuit to one that can anticipate ecological change. Recent innovations-from autonomous recording units and edge-computing sensors to speech-inspired feature extraction and machine-learning techniques like transfer learning, unsupervised discovery, and explainable AI-are transforming the study of animal communication. These advances let us work at scales previously difficult to imagine. Automated species recognition, individual identification, and even tracking cultural evolution over decades are now within reach. Entire ecosystem soundscapes can be mapped with unprecedented resolution. Looking ahead, global listening networks, adaptive acoustic indices, and live biodiversity dashboards seem increasingly realistic. We may soon build digital models that simulate communication networks under future scenarios. Closer integration with genomics, physiology, and robotics could link vocal traits to their genetic, physiological, and ecological drivers. Challenges remain, including data governance, acoustic privacy, and equitable access to the planet's sonic heritage. Bioacoustics may be on the way to becoming a predictive, integrative science - one particularly well suited to monitoring, interpreting, and helping safeguard life's communication systems in a rapidly changing world.

Animals↗
PubMed2026

Evolutionary constraints and regulatory plasticity shape host specialization in the Magnaporthe oryzae species complex.

Rice blast caused by Magnaporthe oryzae threatens global rice production, and wheat blast emergence highlights the pathogen's capacity for host shifts. Although numerous studies have described M. oryzae genome organization and infection mechanisms, critical questions remain regarding the evolutionary drivers of stable host specialization. Importantly, the blast pathogen comprises a species complex of genetically differentiated, host-adapted lineages rather than single homogeneous species. To address this knowledge gap, we integrate evidence from evolutionary genomics, transcriptomics, and metabolomics to develop the "Constrained Plasticity" framework. We argue that host adaptation arises from three interacting layers: genomic scaffolding (including epigenetic and noncoding RNA regulation), regulatory networks (enabling transcriptional plasticity), and metabolic compatibility (determining physiological success). This systems-level perspective explains the long-term stability of host-adapted lineages and the rare breakdowns resulting in host shifts, such as wheat blast. This framework generates testable predictions for pathogen emergence and provides a roadmap for developing lineage-aware resistance strategies.

Oryza↗
PubMed2004

Calcium sensors and their interacting protein kinases: genomics of the Arabidopsis and rice CBL-CIPK signaling networks.

Calcium signals mediate a multitude of plant responses to external stimuli and regulate a wide range of physiological processes. Calcium-binding proteins, like calcineurin B-like (CBL) proteins, represent important relays in plant calcium signaling. These proteins form a complex network with their target kinases being the CBL-interacting protein kinases (CIPKs). Here, we present a comparative genomics analysis of the full complement of CBLs and CIPKs in Arabidopsis and rice (Oryza sativa). We confirm the expression and transcript composition of the 10 CBLs and 25 CIPKs encoded in the Arabidopsis genome. Our identification of 10 CBLs and 30 CIPKs from rice indicates a similar complexity of this signaling network in both species. An analysis of the genomic evolution suggests that the extant number of gene family members largely results from segmental duplications. A phylogenetic comparison of protein sequences and intron positions indicates an early diversification of separate branches within both gene families. These branches may represent proteins with different functions. Protein interaction analyses and expression studies of closely related family members suggest that even recently duplicated representatives may fulfill different functions. This work provides a basis for a defined further functional dissection of this important plant-specific signaling system.

Amino Acid Sequence↗
PubMed2025

Genotype by Environment Interactions in Gene Regulation Underlie the Response to Soil Drying in the Model Grass Brachypodium distachyon.

Gene expression is a quantitative trait under the control of genetic and environmental factors and their interaction, so-called genotype and environment (G × E). Understanding the mechanisms driving G × E is fundamental for ensuring stable crop performance across environments and for predicting the response of natural populations to climate change. Gene expression is regulated through complex molecular networks, yet the interactions between genotype and environment in gene regulation are rarely considered, particularly at the genome scale. Current frameworks and experimental designs often lack power to explicitly test network rewiring or to systematically compare regulatory networks. Here, we leverage a highly replicated RNA-sequencing dataset to model genome-scale gene expression variation between two natural accessions of the model grass Brachypodium distachyon and their response to soil drying. We first identified genotypic, environmental, and G × E effects on physiological, metabolic, and gene expression traits. We identify patterns of conservation-or variation-in gene coexpression networks and link these coexpression features to physiological traits. We further develop predictions of gene-gene interactions using causal inference and screen for interactions specific to-or with higher affinity in-a single genotype, treatment, or their interaction, G × E. Our analyses identify variation in candidate gene regulatory networks that may shape the evolution of environmental response in B. distachyon. We highlight the environmentally dependent regulatory control of several metabolic traits shown previously to play a role in drought acclimation. The framework presented here provides a scalable approach for more complex comparisons, particularly with the growing availability of large datasets from technologies such as single-cell transcriptomics.

Brachypodium↗
PubMed2025

Genomics control of biostimulant-induced stress tolerance and crop yield enhancement.

Biostimulants are changing modern agriculture, as they have the potential to secure healthy and sustainable food production while preserving the environment. They have two main biological effects: growth promotion and stress protection. Both effects can lead to enhancement of the yield and improvement of the marketable grade of the produce in crops, without compromising crop quality. Their use increased exponentially in the past decade, as they are highly efficient, ecologically friendly (non-toxic, biodegradable), and applicable to all major crops. While exponential data on the physiological mechanisms of stress protection is accumulating in recent years, the information as to how biostimulants act at the molecular level is still rather limited. Here we review the growing evidence of the biostimulants role in stress protection and yield enhancement of crops, as well as the recent transcriptomic and metabolomic data, which indicate biostimulants' molecular mode of action. In particular, we outline the role of genes encoding signaling components, plant hormones (abscisic acid, brassinosteroids, and ethylene), genes encoding transcription factors from ERF, WRKY, NAC, and MYB families, and genes related to growth, photosynthesis, and stress response. Finally, we describe strategies to study the genetic and genomics control of biostimulants mode of action, with foci on stress tolerance and yield enhancement. In Arabidopsis, established systems for biostimulants-induced protection against drought and oxidative stress will allow both forward and reverse genetics approaches to identify key genes from the biostimulants network. Mutations in such genes compromise the stress-protective effect of biostimulants. In major crops such as pepper and tomato, large Genome Wide Association Studies (GWAS) panels can be utilized to study crops responses to biostimulants in terms of drought tolerance, fruit qualities, and yield in order to pinpoint genes controlling biostimulants-induced stress protection and yield enhancement. The combination of these approaches allows identification and verification of important genes involved in the pathways of biostimulant-induced stress protection and yield enhancement, as well as deciphering parts of the intricate biostimulant-signaling network.

Crops, Agricultural↗
PubMed1979

Photoreceptor coupling in retina of the toad, Bufo marinus. I. Anatomy.

1. Red rod photoreceptors in the toad retina, which are known to be physiologically coupled, were examined for interreceptor contacts. 2. A dense network of large gap junctions was found between the inner segments of red rods, this being the only specialized site of contact that was observed between rods. Each red rod contacts an average of about four neighboring red rods with a junctional area of approximately 0.75 micrometer2. From freeze-fracture micrographs, the density of junctional particles was found to be 5 X 10(3)/micrometer2. 3. The large gap junctions were found only to connect red rods to each other in agreement with physiological data. Only small focal gap junctions were seen between red rods and cones and no junctions were observed between red and green rods. 4. It is concluded that these gap junctions are the site of coupling between the red rods and that the coupling is electrical.

Animals↗
PubMed1978

Requirement for matching T cell and B cell subsets in secondary anti-hapten antibody responses.

The in vitro secondary anti-hapten response to trinitrophenylated keyhole limpet hemocyanin (TNP-KLH) has been investigated using B and T cells from the same or a pool of identically primed syngeneic individuals. The optimum antibody response obtained from B cells of any given animal was seen when the same individual's T cells were used as a helper cell source. This individual preference was lost if secondary challenge in culture was made with TNP on a heterologous carrier, with the helper cells obtained from suitably primed individuals or a pool thereof. These data are interpreted in terms of a network theory for the regulation of immune responses under physiological conditions.

Animals↗
PubMed2026

Proteome-wide structural and interaction analysis using cross-linking mass spectrometry and its applications.

Deciphering the mechanisms of protein-protein interactions (PPIs) and protein structural changes within the native cellular environment is crucial for advancing drug discovery. In vivo chemical cross-linking coupled with mass spectrometry (XL-MS) captures weak, transient, and higher-order interactions that are often dysregulated under altered physiological conditions and remain challenging to detect using conventional methods. Applications of in vivo XL-MS range from targeted mapping of PPIs to large-scale identification of interactome networks within the cells. The integration of quantitative approaches further facilitates comparison across different physiological conditions. The recent incorporation of machine learning (ML) tools into XL-MS workflows is transforming the depth and efficiency of this technology. AI-driven algorithms now enable more accurate identification of cross-linked peptides and the mapping of interaction topologies. Furthermore, the synergistic coupling of in vivo XL-MS data with AI-assisted structural modeling platforms such as AlphaFold allows dynamic and high-throughput prediction of protein networks. This review discusses the broader applications of in vivo XL-MS in complex biological samples, ranging from organelles and cells to whole tissues, and highlights how AI integration is expanding structural biology toward a systems-level understanding of proteome architecture.

Mass Spectrometry↗
PubMed1975

Physiological properties of vertebrate nerve cells in tissue culture.

Vertebrate neurons in tissue culture are providing us with a new model system for studying the complex events which occur during neuronal differentiation, synaptogenesis, and neural network formation. It is already apparent that dissociated embryo neurons are capable of differentiating both morphologically and physiologically along predetermined lines in the absence of external influences. These neurons can form new connections with one another but retain some specificity in their selections. Both simple and complex neural networks can be seen. At the present time, the development of the invitro model system is just being explored. The potential value of a system of this kind at a variety of investigative levels should be appreciated. Questions of a fundamental nature in neurobiology, such as how synapses form, what rules govern such interaction, how cells recognize one another, and the nature of the basic two-, three-, or four-cell circuits that comprise the more complex neurons tissue can be approached with this system. Studies of the neurons and synapses themselves can lead to a more basic understanding of vertebrate nervous system functioning. The development of certain pathophysiological processes and the effects of neuroactive drugs on vertebrate neurons may be studied at the cellular level. Finally, the basic mechanism of some genetic abnormalities which produce abnormal nervous structure and function may be more easily determined in a simplified in vitro model than in the intact central nervous system. The value of any model is not inherent in the elegance of the model itseld, but only in its ability to suggest answers to fundamental questions about the system being modeled. Many fundamental questions about brain mechanisms in mental retardation remain unanswered. Perhaps some day the model of nerve cells in tissue culture will bring us closer to the answers to these questions.

Animals↗
PubMed2026

Instrumented Walkway Gait Analysis Predicts Fallers in Neurological Disorders: Identifying Digital Biomarkers for Balance Monitoring.

Assessing balance is crucial in neurological rehabilitation, yet while wearable sensors enable real-world monitoring, identifying reliable digital biomarkers remains challenging. This study utilized a high-fidelity instrumented walkway to determine which gait parameters best predict balance impairment, providing robust targets for future wearable applications. We analyzed 49 steady-state gait metrics from 140 individuals with diverse neurological conditions. Using statistical analysis and machine learning, we evaluated these parameters against objective force plate sway scores and clinical fall-history labels. Group analysis identified 16 parameters significantly distinguishing fallers from non-fallers, and a neural network classified fallers with an area under the curve of 0.75. Across all analytical approaches, overall gait variability, e.g., Stride Width S.D. and the Gait Variability Index, emerged as a universal predictor of balance impairment and fall risk. Furthermore, while traditional linear models emphasized spatial postural control, machine learning classification uniquely identified inter-limb asymmetry as a premier driver of fall prediction. These findings indicate that instrumented gait analysis effectively identifies digital biomarkers for balance deficits. Isolating these specific metrics provides a clear blueprint for meaningful metrics required for continuous objective monitoring and future development of personalized, adaptive rehabilitation strategies.

Humans↗
PubMed1979

Cortical circulation of long bones.

Intravascular injections of India ink in the femora of adult dogs revealed the existence of two distinct vascular systems in the cortex. One courses through the entire thickness of the cortex and is a regular, longitudinal network of uniform capillaries which is in continuity with the periosteal and endosteal networks. Once the haversian systems form a second network appears, radiating from the bone marrow. That system, primarily transverse, anastomoses in the haversian canals with the capillaries of the first system. Therefore, the merging of the two networks occurs primarily in the middle layer of the cortex. The direction of the arterial blood flow in the mature animal is predominantly centrifugal, while the venous drainage is centripetal. In the immature animal, the contribution of the periosteal network is much greater. Because the two cortical systems are profusely anastomosed with each other and with the periosteal and endosteal circulatory networks, the blood can flow in either direction, depending on physiological conditions.

Animals↗
PubMed2026

Comparative transcriptomic and physiological analyses uncover key regulatory pathways associated with drought tolerance in wheat.

Drought severely limits wheat yield, yet its molecular basis remains incompletely understood. We compared a drought-tolerant line (A25) and a drought-sensitive line (A8) under water deficit across three developmental stages using physiological assays and transcriptomics. A25 exhibited stronger osmotic adjustment and antioxidant defense, with higher proline accumulation and enhanced activities of ascorbate peroxidase, catalase, and other ROS-scavenging enzymes. RNA-seq revealed distinct drought-responsive expression patterns, with differentially expressed genes enriched in MAPK signaling and ABA-dependent pathways. ABA-responsive genes were more abundant and strongly induced in A25, suggesting enhanced ABA signal transduction as a key mechanism. Weighted gene co-expression network analysis identified a drought-associated purple module positively correlated with physiological resistance, from which six hub genes (MAPKKK17, Avr9/Cf-9, RPPL1, RGA1, UBC28, AGPs5) were highlighted as potential regulators. Collectively, coordinated activation of ABA signaling and MAPK cascades, mediated by these hub genes, underlies the robust drought tolerance of A25, providing promising molecular targets for wheat breeding and improvement.

Triticum↗
PubMed2026

Deciphering differential mRNA and lncRNA expression profiles in response to PEG simulated drought stress in cucumber (Cucumis sativus L.).

Cucumber (Cucumis sativus L.), a vital fruit vegetable of the Cucurbitaceae family, originated in India ∼ 3000 years ago. It is widely used in the culinary, therapeutic, and cosmetic sectors. Cucumber cultivation is significantly impacted by drought stress, especially in arid and semi-arid regions. This study investigates the molecular response to drought using two contrasting cucumber lines: WBC-23-2 (drought-tolerant) and DGPC-59 (drought-sensitive). Drought was simulated using polyethylene glycol (PEG), and effects on physiological and biochemical traits were evaluated. The tolerant line exhibited reduced leaf wilting and higher relative water content (RWC). Based on these physiological markers, transcriptomic profiling was employed to identify the underlying regulatory networks. Analysis identified 4,736 DEGs, suggesting that the tolerant line's superior resilience is driven by preferential activation of genes involved in photosynthesis and glutathione metabolism. Conversely, the sensitive genotype showed enrichment in organonitrogen compound catabolism and water deprivation response. This divergence is further reflected in the regulation of 155 transcription factors (TFs) across various families, indicating distinct regulatory architectures between the two lines. Additionally, 774 drought-responsive long non-coding RNAs (lncRNAs) were identified, acting via cis, trans, and competing endogenous RNA (ceRNA) mechanisms to modulate gene expression. Key candidate genes associated with drought tolerance included WAT1-related protein At5g64700, thaumatin-like protein, berberine bridge enzyme-like 18, probable WRKY transcription factor, and pathogenesis-related protein 1. This study reveals a complex regulatory network of mRNAs, lncRNAs, and TFs underlying drought response and provides a valuable foundation for breeding drought-resilient cucumber cultivars. A web-based genomic resource, CsDTDb, has been developed and made publicly available to facilitate future functional genomics studies related to drought tolerance in cucumber.

DEGs↗
PubMed2026

Research progress on multi-mechanism analysis and protection strategies of ovarian aging and fertility decline.

Age-related fertility decline is an increasingly important challenge in reproductive medicine, driven largely by progressive ovarian aging. The aging ovary undergoes functional deterioration characterized by reduced ovarian reserve and declining oocyte quality, ultimately limiting female reproductive lifespan. Although multiple molecular and cellular processes associated with ovarian aging have been identified, these mechanisms are often discussed independently, limiting an integrated understanding of how they interact within the ovary. In this review, we propose an ovary-centered, multi-mechanistic framework to organize current evidence on ovarian aging and fertility decline. We discuss how genomic instability, telomere attrition, mitochondrial dysfunction, oxidative stress, chronic cellular stress responses, and alterations in ovarian signaling and microenvironmental homeostasis collectively contribute to follicle depletion and impaired oocyte competence. Particular emphasis is placed on signaling pathways involved in follicle activation and stress adaptation, including PI3K/AKT/mTOR, FOXO3, Hippo, and AMPK-Sirtuin networks, while acknowledging that many mechanistic relationships remain incompletely defined in physiological ovarian aging. Building on this integrative perspective, we further evaluate mechanism-oriented intervention strategies, including mitigation of cellular stress, metabolic and signaling modulation, optimization of the ovarian microenvironment, established fertility preservation technologies, and emerging exploratory approaches. By integrating current mechanistic and translational evidence, this review provides a conceptual framework for understanding ovarian aging and highlights future directions for evidence-based fertility preservation and reproductive health management in the context of aging.

Humans↗