Search Results (2,263)

Platax teira is a marine fish species with both ornamental and economic value, but it faces challenges in aquaculture due to environmental stress and disease. Genetic research on P. teira has been limited due to the limitations of the partially incomplete reference genome and the lack of a complete transcriptome. In this study, we utilized PacBio SMRT sequencing to generate a full-length transcriptome for P. teira, obtaining 39,770 isoforms, including 32,265 known gene-related transcripts and 4730 novel transcripts from 3455 new genes. All novel genes were annotated, and enrichment analysis revealed significant associations between immune-related pathways, such as cAMP, MAPK, PI3K-Akt, and Wnt. We also identified 14,398 alternative splicing events, 2754 alternative polyadenylation events, 42,250 SSRs, 1569 transcription factors, and 2067 long non-coding RNAs. Additionally, protein–protein interaction (PPI) analysis of immune-related pathways predicted chemokines as key immune factors among novel genes. Domain prediction analysis highlighted the diverse functional potential of immune factors such as NLRC3, tyrosine kinase 2, and A2M in different alternative splicing events. Overall, the characterization of the full-length transcriptome dataset of P. teira lays the foundation for further studies on its genetic analysis and immune regulation. Full article

Environmental pollution is becoming increasingly unpredictable over time due to its complexity, given the number of new chemicals produced annually and the constantly changing environmental conditions. Regulation has yet to keep pace with the rapid changes posed by chemical mixtures, especially in the Global South. Understanding the potential outcomes of co-exposure to multiple compounds can be challenging, even for professionals with a background in sustainability and mixture toxicity, due to the complexity of the issue. Some tools have been developed to tackle this uncertainty like the Species Sensitivity Distribution curve (SSD), the Adverse Outcome Pathways (AOP), and the Mixture Assessment Factor (MAF). This study aims to bridge the gap between knowledge generated in the field of mixture toxicity and regulatory practices by proposing sustainable management practices at the local scale, particularly for countries in the Global South. The proposed framework is called GlORIES and comprises the following measures. The first proposed step is to describe the chemicals used in industries or identified in existing environmental studies and/or monitoring campaigns on a watershed basis. Having a watchlist of compounds and organisms present in the region, and by generating a regionalized SSD, it is possible to use models such as AOPs to try to predict which compounds could potentially interact and thus generate a correcting factor, such as a MAF. A MAF could then be incorporated into regulations to further protect the environment by reducing the concentration of the compound in the mixture. Including local communities in reporting human and environmental health alterations could be a key to identifying the possible harmful emissions. It is proposed that watershed management committees be established to integrate all stakeholders and promote workshops organized by academia, industry, regulatory agencies, and civil society, leveraging existing structures to conserve energy in the process. The proposed framework can improve the sustainability of the process and the knowledge flow from academia to regulatory bodies, increasing the efficacy of the chosen water quality thresholds by adapting to real-life scenarios. Full article

Through binding to complementary mRNAs, microRNAs (miRNAs) mediate gene silencing. The stability and half-life of microRNAs are controlled by two isoforms of the RNA-binding protein Roquin. This study aimed at identifying the role of Roquin to miRNA-dependent regulation of the transcriptome in the post-ischemic heart. Both Roquin isoforms are highly conserved between rats and humans and constitutively expressed in cardiomyocytes. In both cell species, hypoxia induces a down-regulation of Roquin-1 and Roquin-2. An integrative miRNA-and-mRNA analysis (MMIA) identified miR-23b-5p as a potential interaction partner of Roquins. The open data bank TargetScan8.0 suggests that the transcription factor ZBTB20 is a potential target of miR-23b-5p. The level of expression of ZBTB20 correlated with the functional recovery of rat hearts after myocardial infarction. Moreover, the down-regulation of Roquin-2 in AC16 cells by siRNA under normoxic conditions was associated with an up-regulation of miR-23b-5p and a down-regulation of ZBTB20. Furthermore, in the case of hypoxia-dependent down-regulation of Roquin, the subsequent down-regulation of ZBTB20 was reversed with the help of an antagomir against miR-23b-5p. In conclusion, hypoxia-induced down-regulation of the two Roquin isoforms was associated with an increased stability of miR-23b-5p, a Roquin-2-dependent miRNA, which subsequently led to silencing of the transcription factor ZBTB20. Full article

This study investigates the distribution patterns, interspecific relationships, and community stability mechanisms of phytoplankton functional groups, aiming to elucidate the ecological processes that drive phytoplankton communities in aquatic ecosystems of arid regions. We conducted seasonal sampling from 2023 to 2024 at four auxiliary reservoirs in the Tarim River Basin, namely Shangyou Reservoir (SY), Shengli Reservoir (SL), Duolang Reservoir (DL), and Xinjingzi Reservoir (XJZ). In recent years, researchers have grouped phytoplankton into functional groups based on their shared morphological, physiological, and ecological characteristics—with these three types of traits serving as the core criteria for distinguishing different functional groups. A total of 18 functional groups were identified from the phytoplankton collected across four seasons, among which eight (A, D, H1, L0, M, MP, P, and S1) are dominant. Redundancy Analysis (RDA) indicated that environmental factors such as pH, electrical conductivity (COND), and dissolved oxygen (DO) are key driving factors affecting phytoplankton functional groups. Interspecific association analysis showed that the phytoplankton communities in DL, SL, and XJZ reservoirs were dominated by positive associations, reflecting stable community structures that are less prone to drastic fluctuations under stable environmental conditions. In contrast, the SY Reservoir was dominated by negative associations, indicating that it is in the early stage of succession with an unstable community. This may be related to intense human disturbance to the reservoir and its role in replenishing the Tarim River, which leads to significant water level fluctuations. The results of the Chi-square test and Pearson correlation analysis showed consistent trends but also differences: constrained by the requirement for continuous normal distribution, Pearson correlation analysis identified more pairs of negative associations, reflecting its limitations in analysing clumped-distributed species. Random forest models further indicated that functional groups M, MP, L0, and S1 are the main positive drivers of interspecific relationships. Among them, the increase in S1 can promote the growth of functional groups dominated by Navicula sp. and Chroococcus sp. by reducing resource competition. Conversely, the expansion of functional group H1 inhibits other groups, which is related to its adaptive strategy of resisting photo-oxidation in eutrophic environments. This study reveals the patterns of interspecific interactions and stability mechanisms of phytoplankton functional groups in arid-region reservoirs, providing a scientific basis for the management and conservation of aquatic ecosystems in similar extreme environments. Full article

MicroRNAs (miRNAs) are key post-transcriptional regulators of plant development and stress responses, with many being conserved across diverse plant lineages. In this study, we investigated the expression profiles of miRNAs and their corresponding target genes in Arachis stenosperma, a wild peanut relative that exhibits robust resistance to root-knot nematodes (RKN). Small RNA sequencing of nematode-infected roots identified 107 miRNA loci, of which 93 corresponded to conserved miRNA families and 14 represented novel candidates, designated as miRNOVO. Among these, 18 miRNAs belonging to 11 conserved families were identified as differentially expressed (DEMs). Notably, miR399 and miR319 showed the highest upregulation (logFC = 4.25 and 4.20), while miR393 and miR477 were the most downregulated (logFC = −0.83 and −0.79). Integrated analysis of miRNA and transcriptome data revealed several regulatory interactions involving key defense-related genes. These included NLR genes targeted by miR393 and miR477, hormone signaling components such as the auxin response factor ARF8 targeted by miR167, and the growth regulator GRF2 targeted by miR396. Additionally, miR408 was predicted to target laccase3, a gene involved in the oxidation of phenolic compounds, lignin biosynthesis, copper homeostasis and defense responses. Remarkably, four immune receptor genes belonging to the nucleotide-binding site leucine-rich repeat (NLR) family displayed inverse expression patterns relative to their regulatory miRNAs, suggesting miRNA-mediated post-transcriptional control during the early stages of nematode infection. These findings reveal both conserved and species-specific miRNA–mRNA modules associated with nematode resistance in A. stenosperma, highlighting promising targets for developing RKN-tolerant peanut cultivars through miRNA-based strategies. Full article

The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome–host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress. Full article

Cleaning stations on seamounts play a crucial ecological role in the health and behavior of marine megafauna, yet interspecific interactions at these sites remain understudied. This study investigates potential hierarchical dynamics between reef manta rays (Mobula alfredi) and pelagic thresher sharks (Alopias pelagicus) at two cleaning stations atop a seamount in the Philippines. Using over 960 h of autonomous video recordings across 119 survey days, we examined species-specific site preferences, visitation types, and behavioral responses to interspecific encounters. Results indicate that, while manta rays used both stations equally, thresher sharks showed a strong preference for the deeper, sloped station. Interruptions during cleaning suggest a hierarchy: all manta-to-shark interactions resulted in thresher sharks vacating the station prematurely, possibly before completing cleaning. In contrast, manta–manta interactions showed more balanced outcomes, with no significant impact on cleaning duration. Shark presence decreased as the flow speed intensified and was lowest during high tide, suggesting that sharks’ decision to clean may be dictated by factors affecting the effectiveness of the cleaning process. These findings also suggest that manta rays may outcompete thresher sharks for access to cleaning services. Understanding such interspecific dynamics is vital for effective marine habitat management and the conservation of vulnerable pelagic species. Full article

Photosystem I (PSI) is a photosynthetic protein–pigment complex that, upon photoexcitation, transfers electrons to ferredoxin, facilitating the production of NADPH. Isolated PSI reaction centers (RCs) have also been used in hybrid systems to reduce protons and produce ‘biohydrogen’. This review article examines how various cyanobacteria with similar photosynthetic machinery utilize different wavelengths of light to execute photosynthetic electron transport through PSI. Key factors, such as, the structure of the electron transfer cofactors, the protein environment surrounding the primary donor pigments and hydrogen-bonding interactions with the surrounding protein matrix are analyzed to understand their roles in maintaining efficient electron transfer when it is driven using photons of different energies. We compare PSI complexes with known atomic structures from four species of cyanobacteria, Thermosynechococcus elongatus, Acaryochloris marina, Halomicronema hongdechloris, and Fischerella thermalis. T. elongatus is typical of most oxygenic photosynthetic organisms in that it requires visible light and uses only chlorophyll a (Chl a) in PSI. In contrast, H. hongdechloris and F. thermalis are photoacclimating species capable of producing Chl f and Chl d that use red light when little visible light is available. A. marina, on the other hand, is adapted to red light conditions and consistently utilizes Chl d as its primary photosynthetic pigment, maintaining a stable pigment composition. Here, we explore the structural and functional differences between the PSI RCs of these organisms and the impact of these differences on electron transport. The structural differences in the cofactors influence both the absorption wavelengths of the cofactors and the energy levels of the intermediate states of electron transfer. An analysis of the surrounding protein shows how it has been adapted and underscores the interplay between the pigment structure, protein environment, and hydrogen bonding networks in tuning the efficiency and adaptability of photosynthetic mechanisms across different species of cyanobacteria. Full article

Most traits of assimilative branches (ABs) present large spatial and interspecific differences; however, it is still unclear how small-scale soil heterogeneity influences nutrient traits in ABs under the same climatic conditions. The AB samples of Ephedra przewalskii (EP; small-sized), Calligonum mongolicum (CM; medium-sized), and Haloxylon persicum (HP; large-sized), as well as soil samples, were collected at three sites (north, middle, and south; within 65 km) in the southeastern Gurbantunggut Desert, China. The interspecific and inter-site differences in C:N:P:K stoichiometry and the relationships with soil properties were discussed. From north to south, soil nutrients and biocrust development improved, whereas coarse sand proportion decreased. Species and site markedly influenced ABs’ stoichiometry, with a significant interaction. At the species level, each stoichiometric trait differed among species. CM exhibited the lowest C:P and N:P, whereas HP had the highest N:P. At the site level, N:P and C:P of EP and CM increased from north to south, whereas HP changed unclearly. CM and HP had higher N–P scaling exponents, EP and CM exhibited a higher K allocation rate, resulting in the co-limitation of N and P for all species. The overall stoichiometric homeostasis ranked as follows: HP > CM > EP. The three shrubs were dispersed among each other in an ordination diagram based on nutrient metrics, with different distribution patterns. The nutrient traits in the ABs of EP and CM, rather than HP, were markedly correlated with most soil factors. Local-scale soil variation indeed influenced the nutrient strategies of desert shrubs; plant size might be another important factor. Full article

Venomous snakes constitute ecologically significant and medically relevant organisms due to the risks associated with their bites, which frequently result in secondary infections. The oral microbiota of these reptiles plays a crucial role in the pathogenesis of such infections; however, its diversity and clinical implications remain insufficiently characterized. This is the first comprehensive review to systematically trace the methodological evolution in snake oral microbiota research, documenting the paradigm shift from traditional culture-dependent techniques to advanced culture-independent approaches, including next-generation sequencing and metagenomics. Our analysis uniquely demonstrates the transformative impact of these technological advances on bacterial diversity identification and antimicrobial resistance gene detection in venomous species. Environmental factors, captivity conditions, and venom composition significantly influence microbial community structure and resistance profiles. These intricate interactions are essential for improving clinical management of snakebite infections, informing empirical antibiotic therapy protocols, and guiding antivenom production strategies. Additionally, the potential of snake oral microbiota as a source of novel bioactive compounds represents an emerging area of bioprospecting research. This review uniquely bridges microbiology, venomics, and clinical medicine, demonstrating the necessity for integrative, multidisciplinary approaches to fully elucidate the ecological and biomedical significance of oral microbial communities in venomous snakes. Full article

The structure and assembly mechanism of wild animal gut microbiota represent persistent research hotspots. Among, the impact of geographic factors on the bacterial co-occurrence network characteristics and assembly mechanism of the gut microbiome remains unclear. Therefore, this study analyzed the gut microbiome of Niviventer confucianus and Apodemus agrarius from Anhui and Hubei provinces. The same alpha diversity pattern was found in the gut microbiome of species from the same region. The gut microbiome of the two rodent species in Anhui region exhibited “small world” characteristics, such as nodes with more local connections to allow interaction information (such as metabolites) to rapidly spread throughout the entire microbial community. In addition, dispersal limitations and heterogeneous selection accounted for higher proportions of the gut microbiome in the rodents from the Anhui and Hubei regions, respectively. The higher proportion of heterogeneous selection may exacerbate selection pressure in the Hubei region. Multiple regression on distance matrices analysis revealed that geographic region exerted a limited but significant influence (0 < R² < 0.2, * p < 0.05) on the gut microbiome, surpassing the effects of host phylogeny, gender, and weight. Nevertheless, the roles of regional factors—such as environmental microbes, pollutants, and diet—remain unexamined, and their potential as key drivers of microbiota variation in these rodents warrants further investigation. Full article

Chlamydia trachomatis (CT) remains the most commonly reported bacterial sexually transmitted infection (STI) globally, with particularly high incidence among adolescents and young adults. In Europe, CT cases have continued to rise over the past decade, despite ongoing public health efforts in prevention and screening. Screening coverage, however, remains inconsistent across countries. CT infections are often asymptomatic, especially in women, yet can lead to serious CT-related reproductive complications if left untreated, including pelvic inflammatory disease (PID), tubal factor infertility, and ectopic pregnancy. Emerging evidence highlights the cervicovaginal microbiota as a key factor influencing susceptibility to STIs, including CT infection, its progression, and associated outcomes. A Lactobacillus-dominated microbiota, particularly L. crispatus, is well-known to be a protective factor against CT acquisition, whereas vaginal dysbiosis, characterized by a depletion of these species and an overgrowth of anaerobes, such as Gardnerella vaginalis, Atopobium vaginae, and Prevotella spp., has been linked to increased CT acquisition risk, reduced immune control, and impaired infection resolution. Interaction between microbial communities and host immunity may modulate whether CT infections spontaneously clear, persist, or progress into pathological conditions. This review explores the natural history of CT genital infection in women, emphasizing the role of cervicovaginal dysbiosis in disease progression and reproductive sequelae. By integrating current knowledge about resident cervicovaginal microbes, host-microbe interaction, and CT-related reproductive outcomes, we discuss how microbiota-targeted strategies, including probiotic or microbiome-modulating strategies, may complement current CT prevention, diagnosis, and treatment approaches. Full article

Nanoplastics are pervasive contaminants that adversely affect male reproductive function, yet the molecular basis of polystyrene nanoplastic (PS-NP) toxicity in immature testes and effective preventive strategies remain unclear. Here, male mice (postnatal days 22–35, PND 22–35) and TM3 Leydig cells were exposed to graded PS-NPs, followed by transcriptomic profiling to identify differentially expressed genes (DEGs). Candidate therapeutics were prioritized using Connectivity Map (CMap) analysis and molecular docking, and protein interactions were examined by co-immunoprecipitation (Co-IP). PS-NPs accumulated in immature testes, eliciting excessive reactive oxygen species (ROS) and activation of NF-κB. These events coincided with the downregulation of steroidogenic enzymes (CYP11A1 and StAR) and disruption of testicular microarchitecture. In TM3 cells, PS-NPs suppressed testosterone synthesis in a concentration-dependent manner; this effect was fully reversed by pretreatment with N-acetylcysteine (NAC) or Bay 11-7082. Co-IP demonstrated p65–steroidogenic factor-1 (SF-1) binding consistent with formation of a transcriptional repressor complex targeting steroidogenic genes. CMap and docking analyses nominated parthenolide (PTL) as a candidate inhibitor of NF-κB nuclear translocation (predicted binding affinity, −6.585 kcal/mol), and PTL mitigated PS-NP-induced impairment of testosterone synthesis in vitro. Collectively, these data indicate that PS-NPs disrupt testosterone biosynthesis in immature testes through the ROS/NF-κB/p65–SF-1 axis, while PTL emerges as a candidate small molecule to counter nanoplastic-associated reproductive toxicity. These findings underscore translational relevance and support future evaluation under chronic low-dose exposure conditions, including in vivo validation of PTL efficacy, pharmacokinetics, and safety. Full article

The efficient removal of natural organic matter (NOM) through a coagulation process is crucial for improving the quality of drinking water. Recent studies have focused on the interaction between NOM and coagulants during the floc formation and aging process. Therefore, based on the relevant literature from the past few decades, this review focuses on changes in floc activity during floc formation and aging at a molecular level. It systematically clarifies the mechanisms and factors influencing floc formation and aging and summarizes the characterization techniques for NOM and flocs. Notably, the interaction between NOM and coagulant flocs is determined by the presence of carboxyl groups and hydroxyl groups on NOM and hydroxyl groups (η-OH) and water molecules (η-OH₂) on coagulant flocs. Aging involves the transformation of coagulant species and an increase in floc crystallinity, which leads to the absorption or release of organic matter. Although numerous analytical techniques currently offer new insights into the interaction between coagulants and NOM, in situ characterization techniques remain limited. This review provides a theoretical foundation for the full life cycle assessment of NOM in coagulation processes, which is of great significance for advancing drinking water technologies and achieving carbon neutrality goals. Full article

Urban agglomerations in plateau regions often face severe landscape fragmentation and cross-boundary ecological pressures, highlighting the need for coordinated eco-logical planning for sustainable urban development. We coupled species–landscape interactions and multi-ecological services to construct sustainable ecological security patterns (ESPs) and establish a collaborative optimization framework. Specifically, we integrated MaxEnt-derived habit suitability with InVEST-based ecosystem services to identify ecological sources (ESs) and analysis the environmental impacts on species distribution. Based on this, we built a multi-factor resistance surface and employed circuit theory to extract ecological corridors (ECs) and critical nodes (pinch points and barrier points). Then, we quantitatively compared two simulated scenarios (barrier points restoration and stepping stone augmentation) to assess the spatial priority of ecological nodes. We identified 48 ESs (26,410.48 km², mainly distributed in Chuxiong, Yuxi, Honghe, and Kunming), 115 ECs (2670.02 km, with a west-dense and east-sparse spatial pattern), 43 pinch points, and 39 barrier points. Scenario simulation shows that repairing 39 barrier nodes increases network connectivity by an average of 33.52% and global network efficiency by 19.44%, whereas adding steeping stones yields improvements of 20.09% and 5.56%, respectively, indicating that barrier-node restoration produces larger contribution in both connectivity and efficiency at the global scale. Leveraging EN construction and scenario simulation, we developed an ESP-based sustainable framework for collaborative optimization in plateau urban agglomerations. The framework specifies agglomeration-specific coordination pathways, which are expected to provide a transferable blueprint for biodiversity conservation, ecosystem optimization, and sustainable development. Full article