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.
Hibernation is characterized by repeated torpor-arousal cycles during which profound physiological suppression occurs, but its effect on memory retention remains controversial. This may be partly due to the fact that most previous studies have focused on obligatory hibernators, often examining only single species, which can limit comparability between studies. We investigated whether facultative hibernation affects memory retention in two closely related species: the Mongolian hamster (Allocricetulus curtatus) and Eversmann’s hamster (Allocricetulus eversmanni), whose hibernation is characterized by short torpor bouts lasting up to 48 h. Animals were trained in the operant conditioning and spatial maze tasks before hibernation and retested after a three-month hibernation period. We found no significant effect of hibernation on general memory retention or species-specific differences in the operant conditioning task. In the spatial maze task, overall performance of the Firth penalized logistic regression model was not significant (p = 0.054), however, a species x hibernation interaction effect was significant, indicating hibernation affected spatial memory retention differently in the two studied species, with a positive effect in Mongolian hamsters and a likely different (negative or missing) effect in Eversmann’s hamsters. These results suggest that the effect of hibernation on memory retention can be task-dependent and can vary between species with similar torpor-arousal patterns under the same environmental conditions for hibernation.
Salvia is a chemically rich and pharmacologically diverse genus within the Lamiaceae family, widely recognized for its antimicrobial, antioxidant, anti-inflammatory, and other therapeutic effects. With the recent trend toward natural products, the economic importance of this genus is also steadily increasing. One reason for the economic importance of the genus Salvia is that its secondary metabolites possess pharmaceutical or nutraceutical properties. Its long-standing use in traditional medicine emphasizes its relevance for modern drug discovery. However, conventional propagation of many Salvia species is limited by slow growth rates, habitat degradation, and overharvesting. Therefore, in vitro tissue culture has become an essential tool for sustainable use, propagation, conservation, and enhancement of valuable metabolites. Integrating data on micropropagation techniques with biological activity studies enables a comprehensive understanding of the genus’s medicinal and biotechnological potential. This review assesses recent developments in research on in vitro methods for sage to facilitate the in vitro clonal propagation of Salvia species—which are of significance to various industries—and to determine their phytochemical profiles and evaluate their biological activity.
Glomalin-related soil proteins (GRSP) are operationally defined soil fractions associated with arbuscular mycorrhizal fungi (AMF) and are widely studied for their contributions to soil structure, carbon dynamics, and ecosystem functioning. Since its discovery, GRSP has attracted considerable attention because of its association with soil aggregation, carbon stabilization, and ecosystem sustainability. Glomalin, has been associated with various soil attributes, including the stability of soil aggregates, the size of soil carbon and nitrogen reservoirs, the sequestration of heavy metals, and the mitigation of diverse plant stresses. While GRSP concentrations in soil have often been correlated with AMF biomass measured through alternative (microscopic) methods, the chemical composition of GRSP extracted from soil remains intricate and not fully understood. This complexity arises from the nonspecific nature of its extraction and purification processes, as well as the diverse array of analytical techniques employed thus far to evaluate it. Current evidence suggests that GRSP contributes to soil organic carbon stabilization primarily through its association with soil aggregates. In this review, we endeavor to synthesize and explore various facets of glomalin, encompassing its composition, production mechanisms, soil-related functions, recalcitrant properties, and its potential role in the sequestration and stabilization of soil carbon.
Euryhaline cichlid Etroplus suratensis (Pearl spot), was found to exhibit strong acclimatization efficiency in brackish water (BW, 18 ppt), fresh water (FW, 0 ppt) as well as in sea water (SW, 36 ppt) condition throughout their life cycle. This capability makes it to be considered as a suitable euryhaline teleost model for investigating and understanding the effect of salinity challenges in fishes. Here, we investigated the effect of salinity on the gills of E. suratensis acclimated to different salinity conditions using Suppression Subtractive Hybridization (SSH) and Real Time PCR (qPCR). The Rapid amplification of cDNA ends (RACE) technique was used to obtain complete coding sequences (CDSs) from the selected EST’s obtained through SSH. The findings revealed the increased expression of isocitrate dehydrogenase (IDH) when E. suratensis were exposed to higher salinities. Thus the study highlights the role of IDH in salinity adaptation by contributing to cellular energy homeostasis and enhancing antioxidant defence through ROS scavenging during oxidative stress. The derived complete CDS was used to deduce its amino acid sequences, which were used to construct a phylogenetic tree and protein model to obtain secondary and tertiary structure information of IDH. The present study is the first of its kind in characterising and studying the expression analysis of IDH derived from E. suratensis at varying salinities.
The increasing challenges, posed by plant biotic and abiotic stress, significantly impact agroecosystems, particularly in the context of rapid global climate change. Phytohormones function as critical chemical messengers, enabling plants to endure these stresses through a complex regulatory framework, thereby playing an essential role in plant survival. Recent research has increasingly underscored the significance of abscisic acid (ABA), in facilitating a prominent role under adverse conditions within plants. ABA has been shown to engage with major phytohormones, such as gibberellins (GAs), ethylene (ET), auxin, and cytokinins (CKs). It also interacts with several plant growth regulators (PGRs) and endogenous signaling compounds like brassinosteroids (BRs), strigolactones (SLs), nitric oxide (NO), salicylic acid (SA), melatonin (Mel), jasmonic acid (JA), polyamines (PAs), hydrogen sulfide (H2S) and with secondary messengers like calcium ions. These interactions facilitate the equilibrium of resource allocation between plant growth and defense responses under suboptimal conditions. A thorough understanding of the intricate interrelationships among these phytohormones and PGRs under prevailing hostile environment, characterized by both synergistic and antagonistic actions, remains largely lacking. This exhaustive review elucidates the processes of ABA biosynthesis, metabolism, and its signal transduction pathways. Moreover, it sheds light on the complex crosstalk networks that exist among ABA, other phytohormones, PGRs and calcium in the face of various stress conditions, highlighting their pivotal roles in enhancing plant plasticity. The comprehensive insights presented in this review provide a molecular understanding of the phytohormonal pathways involved in improving environmental stress tolerance in plants and may serve as a foundational blueprint for developing precise strategies aimed at engineering climate-resilient crop cultivars.
Rice (Oryza sativa L.) is an important staple crop in global food security and highly vulnerable to chilling stress, which greatly affects growth, development, and yield. The conventional breeding methods for enhancing chilling tolerance face numerous problems due to the polygenic nature of chilling tolerance and genetic complexities. The present review discusses the use of CRISPR-Cas genome editing technologies as an accurate and effective approach to increasing chilling tolerance in rice. We initially describe the physiological effects of chilling stress, such as membrane fluidity impairment, inhibition of photosynthesis, nutrient imbalance, and oxidative injury, and summarize major molecular pathways and genetic materials involved in chilling tolerance. The review then outlines the recent developments in CRISPR-Cas systems, including the modes of delivery (Agrobacterium-mediated transformation, protoplast transfection, and ribonucleoprotein techniques) and how they apply to rice genome editing. The precise examination of CRISPR-based functional genomics has shown that cold-responsive genes (OsMYB30, OsWRKY76, OsAnn3, OsPRP1, and OsKASI-2) are selectively manipulated, thus contributing to a clearer understanding of their functional roles in stress signaling, membrane stability, and antioxidant defense. Moreover, we also discuss recent CRISPR strategies, including multiplex editing, transcriptional reprogramming (CRISPRa/i), and omics-guided fine-tuning of gene networks. Synthesizing latest advancements, current review establishes a conceptual framework to overcome translational challenges in CRISPR-mediated improvement of complex traits in oilseed crops, through integrating the pivotal aspects of genotype-specific delivery, multi-gene network design, field validation, and the evolving regulatory landscape. The review concludes with a reflection of gaps in research and future opportunities, with a discussion on how integrated CRISPR technologies can be used to enhance the development of climate-resistant rice varieties.
Nile tilapia culture faces significant challenges due to early maturation and uncontrolled reproduction, leading to stunted growth and overpopulation. The primary solution is producing all-male populations or sterile fish. While the synthetic androgen 17α-methyltestosterone has been the industry standard for hormonal sex reversal for decades, environmental and consumer safety concerns, including potential carcinogenicity, have driven the search for sustainable alternatives. This critical review examines the full spectrum of approaches for producing monosex male tilapia, encompassing traditional methods (manual sexing, hybridization), hormonal treatments (synthetic steroids, aromatase inhibitors), biodegradable options (plant extracts like Tribulus terrestris and Basella alba, animal by-products such as cattle and carp testes), and novel genetic strategies (YY male technology, genome editing). We highlight innovative biodegradable programs and discuss how nanoparticle-mediated drug delivery can enhance therapeutic efficacy. Furthermore, we explore how genome editing technologies like CRISPR-Cas9 offer groundbreaking potential for understanding and controlling sex determination systems. Finally, we critically evaluate these methods based on effectiveness, cost, scalability, and sustainability to guide future research and the development of more environmentally responsible practices for the tilapia aquaculture industry.
Young edible seedlings of herbs and vegetables, commonly referred to as microgreens, have become nutrient-dense crops, ideally adapted to controlled environment agriculture (CEA). Their short growth cycle, minimal input requirements, and compatibility with both soil and soilless systems make them ideal candidates for weather-resilient and urban crop productions. Unlike previous reviews focusing either on nutrient composition or cultivation practices, the present review uniquely brings together nutritional optimization, agronomical innovations, and postharvest sustainability within CEA framework. The objective is to critically assess the interrelation among environmental management, growth strategies, and nutritional modulation to shape microgreen yield, quality, and resilience. Species from the key families such as Brassicaceae, Amaranthaceae, and Apiaceae have 2–3 times higher levels of vitamins (A, C, E, K) and phenolic-based antioxidant compounds compared to their mature counterparts. Innovations in management of the light spectra, nutrient solution formulation, and substrates have offered precise control over biomass and phytochemical composition. Nevertheless, gaps still exist in genotype-based nutritional response, microbial safety, shelf-life extension, and sustainability. The inclusion of AI-based environment control, biofortification, and environment-friendly packaging will provide nutritional consistency and reduced postharvest losses. By correlating the agronomical management with the nutritional sciences, the present synthesis highlights the potential of microgreens as functional foods to provide sustainable diets alongside global food security.
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.
Informatics technologies are transforming biodiversity conservation by enabling large-scale data analysis, predictive modelling, and real-time monitoring in the face of anthropogenic climate change. This study presents a bibliometric analysis of global research on the application of informatics tools − such as machine learning, remote sensing, geographic information systems, and big data analytics − to biodiversity conservation and anthropogenic climate change. Using the Scopus database, we analysed 643 publications from 1993 to 2024 to identify research trends, collaboration networks, and emerging thematic areas. The results reveal a rapid increase in publications over the last decade, with developed countries and China leading research output, while contributions from Africa remain limited. Keyword co-occurrence analysis highlights key research themes, including species distribution modelling, climate change impacts, conservation technology, and ecological informatics. Co-authorship network mapping underscores the interdisciplinary and collaborative nature of biodiversity informatics and anthropogenic climate change research. This bibliometric review provides a quantitative synthesis of knowledge production in this field, offering insights into dominant research trajectories and identifying gaps in geographic representation and thematic coverage. Overall, the review reveals a large but geographically skewed scientific footprint whose future value depends on closing gaps in data-poor, biodiversity-rich regions and explicitly linking biodiversity informatics outputs to climate-resilient policy and practice. The findings inform future research and policy efforts aimed at leveraging informatics technologies for effective and inclusive biodiversity conservation strategies in a changing climate. This study is FAIR-aligned and accompanied by openly shared data and materials with ISO-aligned, machine-readable metadata.
Securing a sustainable global food supply for the future necessitates a paradigm shift towards technologies that amplify biological potential while minimizing environmental harm, a goal that can be achieved through the controlled generation of reactive oxygen and nitrogen species (RONS) by non‑thermal plasma. This interdisciplinary review synthesizes current knowledge on plasma‑based approaches, a rapidly advancing interdisciplinary frontier converging physics, chemistry, and biology, to fundamentally enhance plant nutrient acquisition and performance. We elucidate how reactive oxygen and nitrogen species (RONS), generated by non-thermal plasma (NTP) or delivered via plasma-activated water (PAW), act as potent biochemical signals and physical agents. These trigger a cascade of responses from seed coat etching and hormonal modulation to profound root system remodeling that collectively boost the plant's innate nutrient foraging capacity. We critically evaluate evidence for improved uptake of essential macro- and micronutrients linked to increased biomass and yield across diverse species. Practical applications in seed priming, soil amendment, and foliar sprays are explored as pathways to reduce dependency on conventional fertilizers. However, to transition this promise into reality, we discuss the critical hurdles of scalability, protocol standardization, and regulatory frameworks. We conclude that plasma technology represents more than an incremental improvement; it is a transformative tool that can inform choices for sustainable agricultural intensification. By unlocking plant physiological potential, it offers a tangible pathway to align agricultural productivity with the urgent goals of planetary health, making it a pivotal area of research for biological sciences.
The aims of this study were determining monthly and annual litterfall mass, turnover rates, and the relationship between the litterfall of some tree components (needles, branches, bark, and miscellaneous) and various stand parameters in in afforested coastal sand dunes; nutrient- and water-poor ecosystems, having scarce research. The study was conducted on Stone pine (Pinus pinea L.) and Maritime pine (Pinus pinaster Aiton) afforestation in a coastal sand dune on the Black Sea coast of Istanbul. The total annual litterfall was calculated as 4332 kg/ha/year for P. pinea and 4275 kg/ha/year for P. pinaster. Among the total annual litterfall, the needle litterfall accounted for 81
This study aimed to explore the potential effects of bee venom (BV) and cold exposure (CE) on behavioral and physiological alterations induced by a high-fat diet (HFD) in rats. Three-week-old male Sprague-Dawley rats were assigned to seven groups: Control, CE, BV, HFD, HFD+CE, HFD+BV and HFD+CE+BV. Anxiety- and depression-like behaviors were evaluated using the open field, elevated plus maze and forced swim tests. HFD increased anxiety and depression like behaviors, whereas BV administration alleviated these alterations. HFD also elevated plasma triglycerides, total cholesterol, LDL, glucose, insulin and leptin levels while reducing HDL concentrations. BV treatment improved these metabolic parameters. Histological analysis revealed enlarged adipocyte diameters in both white (WAT) and brown (BAT) adipose tissues in HFD-fed rats, which were reduced following BV administration. Moreover, BV enhanced UCP-1 gene expression in BAT and WAT, particularly under CE conditions, suggesting increased thermogenic activity. These findings indicate that BV may exert beneficial effects on HFD-induced metabolic dysfunctions and behavioural alterations, possibly through modulation of adipose tissue function and thermogenesis. The combination of BV and CE may represent a potential therapeutic approach for managing obesity associated physiological and behavioral disorders.
The growing threat of antibiotic resistance underscores the urgent need to investigate alternative antimicrobial agents, including bacteriocins or bacteriocins like peptides. The purpose of the present work was to isolate and characterize bacteria from sheep milk that produce antibacterial substances. A strain identified as Mammaliicoccus sciuri 1SH was isolated and its extracellular peptides were extracted and partially purified by ethyl acetate. Sodium dodecyl sulphate poly acrylamide gel electrophoresis (SDS-PAGE) analysis revealed a substance with a molecular weight of about 70 kDa. Activity was characterized across varying pH (2.5–8.5) and temperature (25–80 °C) ranges, demonstrating optimal activity between 25–37 °C and pH 6.5–7.4. Enzyme treatment with pepsin and pancreatin significantly reduced the activity, confirming its proteinaceous nature. The antibacterial substance demonstrated antibacterial activity against 26 clinical isolates of Escherichia coli, with minimum inhibitory concentration (MIC) values ranging from 1.125–70 µg/mL and minimum bactericidal concentration (MBC) 6.5–75 µg/mL. Growth kinetic tests demonstrated that growth of Escherichia. coli was suppressed in a dose-dependent way. Mechanistic studies revealed that the peptide induces DNA and protein leakage, indicating membrane disruption as a potential mode of action. Furthermore, the peptide demonstrated significant anti-oxidant activity (IC50: 13.5 μg/mL) and anti-inflammatory properties (IC50: 11 μg/mL). Fourier Transform Infra-Red (FT-IR) analysis identified key functional groups associated with the peptide. This study marks the first characterization and partial purification of a peptide derived from M. sciuri isolated from sheep milk, underscoring its potential as a promising antimicrobial agent with additional functional attributes.
Soil salinization and drought, exacerbated by climate change, pose a significant threat to global crop productivity, yet the response of weeds, which are key competitors in agro-ecosystems, remains underexplored. This study aimed to evaluate the morphological, physiological, and biochemical responses and stress tolerance of five dominant summer weed species (Dactyloctenium aegyptium, Echinochloa crus-galli, Setaria viridis, Trianthema portulacastrum, and Amaranthus viridis) under salinity (8.0 dS m⁻1) and drought (50.0
The salt-tolerant genes (STGs) play important roles in protecting plants against salt stress. Although various types of STGs have been systematically characterized in plant species, the key genes (KGs) regulating salt stress tolerance in rice (Oryza sativa L.) remain elusive. This study focused on the identification and characterization of the members of STGs in rice through integrated bioinformatic and molecular approaches, including chromosomal location, physicochemical characteristics, protein–protein interaction, and expression profiles of the identified genes. A total of 164 differentially expressed genes (DEGs) were systematically identified as responsive to salt tolerance and sorted out potential 12 kg (OsHSP20.2, OsGFP2, OsBBTI2, OsEN20.6, OsUBC17, OsACD5, OsPEAB5, OsDP11, OsDFP5, OsWD40.7, OsEP11.1, and OsGRAM12) through the CytoHubba algorithms analysis. Physicochemical characterization indicated substantial variation among KGs, including genomic sequences (824–4051 bp), amino acid length (148–659 aa), molecular weight (16.39–71.35 kDa), and isoelectric point (4.66–10.37). Protein–protein interaction (PPI) network prediction indicated intricate functional associations among key STGs. Gene Ontology (GO) enrichment analysis revealed that the KGs are involved in numerous biological processes and molecular functions. Moreover, gene homology results revealed that KGs have multiple relationships with other plant species. Co-expression network analysis revealed that 12 kg are potentially involved in the regulatory mechanisms underlying the biological process. Relative gene expression through the comparative threshold (ΔΔCT) of qRT-PCR revealed that the KGs are salt-induced and may play crucial roles in rice responses to salt stress. Tissue-specific expression patterns revealed that the KGs significantly altered expression levels across different tissues and under stress. This systematic investigation demonstrated that the 12 identified genes may play roles in the development of salt-tolerant rice varieties.
Beetle genetics is becoming increasingly important in research on agricultural ecosystems, not only from a basic biological perspective but also for practical applications in pest management, biodiversity, and agroecosystem sustainability. Our study analyzed the genetic variability of beetle populations (Harpalus rufipes and Silpha obscura) under two types of agricultural management systems—organic and conventional—using RAPD markers. Out of six tested markers (OPB 5, OPB 8, OPB 11, OPB 12, OPB 14, and OPB 18), three markers (OPB 11, OPB 14, and OPB 18) demonstrated clear genetic differentiation between beetle samples collected from organically and conventionally cultivated wheat. The results of DNA fingerprinting and t-SNE analysis confirmed the formation of two genetic clusters corresponding to the management type. Jaccard similarity coefficient values indicated moderate to strong genetic similarity within individual management systems, while similarity between systems was weaker. These findings suggest that agronomic practices influence the genetic structure of beetle populations, likely due to ecological and anthropogenic factors such as pesticide use and landscape modification. The study emphasizes the importance of molecular markers in assessing population-level responses to agroecosystem management and their contribution to sustainable agriculture.
Lentil (Lens culinaris Medik.) is an important edible legume widely cultivated worldwide. Various abiotic stress factors cause significant challenges to lentils’ productivity. Among these factors, salt stress adversely affects plant growth and development, resulting in yield losses. In this study, the effects of salt stress (150 mM) on phenotypic traits such as physiological measurements, leaf color traits, relative electrolyte leakage and visual evaluation were initially evaluated in twelve lentil cultivars. Significant reductions in root and shoot weight, root and shoot length, and leaf color traits were observed under salt stress. Subsequently, the effects of different GA3 doses (control, 50 µM, 100 µM, and 200 µM) on the bioactive and enzymatic traits of lentil were investigated under varying levels of salt stress (control, 75 mM, and 150 mM) in the most salt-sensitive lentil cultivar. Application of different GA3 doses to the lentil cultivar grown under salt stress increased chlorophyll a content, total carotenoid content, total phenolic content, total flavonoid content, total soluble protein content, DPPH and CUPRAC compared to the control group. Enzyme activity analyses also revealed that GA3 treatments statistically influenced catalase (CAT) and ascorbate peroxidase (APX) activities, playing a crucial role in the plant's defense mechanisms against salt stress. Principal component analysis (PCA) revealed that PC1 and PC2 components explained 65.40
De novo mutations (DNMs), which arise in the offspring and are absent in the parents, are increasingly studied in farm animals with the advent of whole-genome sequencing (WGS). Variant calling after genome sequencing is a crucial step in modern genomics, and its accuracy directly influences subsequent genetic analyses, which are vital not only in breeding and human healthcare but also in functional genomic research. Yet, using only families with trios neglects the important shared information in the family and leads to an inaccurate determination of DNMs. Here, we show that using inheritance-based Whole Genome Sequencing (WGS) data analysis on a larger family is an effective way to identify DNMs in offspring accurately, and we present the first such study in rabbits.
