Search Results (102)

Drought severely limits crop yield every year, making it critical to clarify the genetic basis of drought tolerance for breeding of improved varieties. As drought tolerance is a complex quantitative trait, we analyzed three phenotypic groups: (1) agronomic traits under well-watered (WW) and water-deficit (WD) conditions, (2) stress tolerance indices of these traits, and (3) phenotypic plasticity, using a multi-parent doubled haploid (DH) population assessed in multi-environment trials. Genome-wide association studies (GWAS) identified 130, 171, and 71 quantitative trait loci (QTL) for the three groups of phenotypes, respectively. Only one QTL was shared among all trait groups, 25 between stress indices and agronomic traits, while the majority of QTL were specific to their group. Functional annotation of candidate genes revealed distinct pathways of the three phenotypic groups. Candidate genes under WD conditions were enriched for stress response and epigenetic regulation, while under WW conditions for protein synthesis and transport, RNA metabolism, and developmental regulation. Stress tolerance indices were enriched for transport of amino/organic acids, epigenetic regulation, and stress response, whereas plasticity showed enrichment for environmental adaptability. Transcriptome analysis of 26 potential candidate genes showed tissue-specific drought responses in leaves, ears, and tassels. Collectively, these results indicated both shared and independent genetic mechanisms underlying drought tolerance, providing novel insights into the complex phenotypes related to drought tolerance and guiding further strategies for molecular breeding in maize. Full article

Bovine viral diarrhea (BVD) is caused by bovine viral diarrhea virus (BVDV), a member of the genus Pestivirus and in the family Flaviviridae. According to some studies, the disease incurs USD 1.5–2.5 billion per year and USD 0.50 to USD 687.80 per cow loss in beef and dairy farms, respectively. Using vaccines is among the strategies to prevent the disease. However, complete protection requires vaccines that target both the humoral and cellular immune responses of the adaptive immune system. A comprehensive literature review was made to provide insights into the interaction of BVDV with host immunity, vaccine applications, and the limitation of the currently available vaccines, as well as explore strategies used to advance the vaccines. BVDV causes immunosuppression by interfering with the innate and adaptive immune systems in a manner that is species and biotype-dependent. Interferon production, apoptosis, neutrophil activity, and antigen-processing and presenting cells are significantly affected during the viral infection. Despite maternal antibodies (MatAbs) being crucial to protect calves from early-age infection, a higher level of MatAbs are counterproductive during the immunization of calves. There are numerous inactivated or modified BVDV vaccines, most of which are made of cytopathic BVDV 1 and 2 and the BVDV 1a subgenotypes. Furthermore, subunit, marker, DNA and mRNA vaccines are made predominantly from E2, E^rns, and NS₃ proteins of the virus in combination with modern adjuvants, although the vaccines have not yet been licensed for use and are in the experimental stage. The existing BVDV vaccines target the humoral immune system, which never gives the full picture of protection without the involvement of the cell-mediated immune system. Several limitations were associated with conventional and next-generation vaccines that reduce BVDV vaccine efficiency. In general, providing complete protection against BVDV is very complex, which requires a multi-pronged approach to study factors affecting vaccine efficacy and strategies needed to improve vaccine efficacy and safety. Full article

Understanding the molecular mechanisms of cellobiohydrolase I (CBHI), a key enzyme in cellulase complexes, is crucial for developing efficient enzymes for the degradation of lignocellulosic biomasses (LCB). Building on our previous discovery that Chaetomium thermophilum CBHI (C-CBH) exhibits significantly higher specific activity than Trichoderma reesei CBHI (T-CBH), systematic domain-swapping experiments were conducted to elucidate the structural determinants of catalytic efficiency in CBHI. Herein, the carbohydrate-binding modules (CBM) of the CBHIs from Trichoderma reesei (T-CBH) and Chaetomium thermophilum (C-CBH) were interchanged and to obtain two chimeric mutants TC-CBH and CT-CBH. These four CBHs were expressed in T. reesei, and the enzyme properties were analyzed. Comparative characterization revealed that while module exchange preserved native temperature/pH adaptability, it significantly altered substrate specificity and catalytic performance. The CT-CBH variant was identified as the most efficient biocatalyst, exhibiting four key advantages over T-CBH: (1) protein expression levels that far exceed those of T-CBH, (2) specific activity enhanced by 2.6-fold (734.5 U/μM vs. 282.5 U/μM on MU-cellobiose), (3) superior degradation capacities for filter paper (1.6-fold) and xylan, and (4) improved binding affinity for crystalline cellulose. These findings establish cross-species domain engineering as a viable strategy for creating high-performance cellulases, providing both mechanistic insights and practical solutions for lignocellulose degradation. Full article

The evolution of SARS-CoV-2, particularly the emergence of Omicron variants, has raised questions regarding changes in its binding affinity to the human angiotensin-converting enzyme 2 receptor (hACE2). Understanding the impact of mutations on the interaction between the receptor-binding domain (RBD) of the spike protein and hACE2 is critical for evaluating viral transmissibility, immune evasion, and the efficacy of therapeutic strategies. Here, we used molecular dynamics (MD) simulations and binding energy calculations to investigate the structural and energetic differences between the hACE2- RBD complexes of wild-type (WT), Delta, and Omicron subvariants. Our results indicate that the Delta and the first Omicron variants showed the highest and the second-highest binding energy among the variants studied. Furthermore, while Omicron variants exhibit increased structural stability and altered electrostatic potential at the hACE2–RBD interface when compared to the ancestral WT, their binding strength to hACE2 does not consistently increase with viral evolution. Moreover, newer Omicron subvariants like JN.1 exhibit a bimodal conformational strategy, alternating between a high-affinity state for hACE2 and a low-affinity state, which could potentially facilitate immune evasion. These findings suggest that, in addition to enhanced hACE2 binding affinity, other factors, such as immune evasion and structural adaptability, shape SARS-CoV-2 evolution. Full article

The two multi-subunit complexes, Polycomb Repressive Complex 1 and 2 (PRC1/2), act synergistically during development to maintain the gene silencing state among different species. In contrast with mammals and Drosophila melanogaster, the enzyme activities and components of the PRC1 complex in plants are not fully conserved. In addition, the mutual recruitment of PRC1 and PRC2 in plants differs from that observed in mammals and Drosophila. Polycomb Group (PcG) proteins and their catalytic activity play an indispensable role in transcriptional regulation, developmental processes, and the maintenance of cellular identity. In plants, PRC1 and PRC2 deposit H2Aub and H3K27me3, respectively, and also play an important role in influencing three-dimensional (3D) chromatin structure. With the development of high-throughput sequencing techniques and computational biology, remarkable progress has been made in the field of plant 3D chromatin structure, and PcG has been found to be involved in the epigenetic regulation of gene expression by mediating the formation of 3D chromatin structures. At the same time, some genetic evidence indicates that PcG enables plants to better adapt to and resist a wide range of stresses by dynamically regulating gene expression. In the following review, we focus on the recruitment relationship between PRC1 and PRC2, the crucial role of PcG enzyme activity, the effect of PcG on 3D chromatin structure, and the vital role of PcG in environmental stress in plants. Full article

Nitrogen, an indispensable macronutrient, significantly affects the appearance, quality, and yield of grapes (Vitis vinifera). Adequate nitrate uptake and intracellular transport, facilitated primarily by nitrate transport (NRT) proteins, are crucial for maintaining nutritional balance. However, there are no reports on the NRT gene family in grapes. In this study, we identified 53 Nitrate Transporter 1/Peptide Transporter Family (NPF), 3 nitrate transporter 2 family (NRT2), and 1 Nitrate Assimilation-Related 2 (NAR2) genes in the grapevine Pinot Noir PN40024 genome. A comprehensive analysis of these gene families, including their physicochemical properties, structural organization, chromosomal distribution, collinearity, cis-acting element distribution, and phylogenetic relationships, revealed the rich diversity and evolutionary conservation of the grapevine Nitrate Transporter (NRT) genes. Furthermore, the expression profiles of VvNRTs in different tissues demonstrated that the NRT genes possess spatio-temporal expression specificity. The expression patterns of the NRT genes were examined by transcriptome sequencing in grapevines across various tissues under nitrogen-deficiency conditions. The expression patterns in grapevine leaves under nitrogen-deficiency conditions showed upregulation of the VvNPF2.3 gene in conditions of nitrogen deficiency. This upregulation was strongly associated with a 62.2% reduction in indole-3-acetic acid (IAA) levels and a 21.3% increase in hydrogen peroxide (H₂O₂) levels, suggesting a complex regulatory response to nitrogen-induced stress. These findings emphasize the potential involvement of NRT genes in the adaptive reaction to nitrogen deficiency and set the stage for future investigations into the molecular mechanisms of nitrogen transportation in grapevines. Full article

Exercise plays a crucial role in maintaining metabolic health, enhancing muscle function, and improving insulin sensitivity, thereby preventing metabolic diseases such as type 2 diabetes. Emerging evidence highlights the significance of the cystathionine γ-lyase (CSE)/hydrogen sulfide (H₂S) signaling pathway as a pivotal regulator in the molecular and physiological adaptations induced by exercise. This review comprehensively examines the biosynthesis and metabolism of H₂S, its distribution in different muscle tissues, and the mechanisms by which CSE/H₂S influences muscle contraction, repair, and protein synthesis. Additionally, it explores how CSE/H₂S modulates insulin signaling pathways, glucose uptake, and lipid metabolism, thereby enhancing insulin sensitivity. The potential of H₂S donors as exercise supplements is also discussed, highlighting their ability to improve exercise performance and metabolic health. Current research advancements, including the application of multi-omics approaches, are reviewed to provide a deeper understanding of the complex molecular networks involved. Furthermore, the challenges and future directions in CSE/H₂S research are addressed, emphasizing the need for further mechanistic studies and clinical applications. This review underscores the therapeutic potential of targeting the CSE/H₂S pathway to optimize the benefits of exercise and improve metabolic health. Full article

Background. Antibiotic-resistant (AR) bacteria pose an increasing threat to public health, but the dynamics of antibiotic resistance gene (ARG) spread in complex microbial communities are poorly understood. Conjugation is a predominant direct cell-to-cell mechanism for the horizontal gene transfer (HGT) of ARGs. We hypothesized that commensal Escherichia coli donor strains would mediate the conjugative transfer of ARGs to phylogenetically distinct bacteria without antibiotic selection pressure in gastrointestinal tracts of mice carrying a human-derived microbiota with undetectable levels of E. coli. Our objective was to identify a mouse model to study the factors regulating AR transfer by conjugation in the gut. Methods. Two donor E. coli strains were engineered to carry chromosomally encoded red fluorescent protein, and an ARG- and green fluorescent protein (GFP)-encoding broad host range RP4 conjugative plasmid. Mice were orally gavaged with two donor strains (1) E. coli MG1655 or (2) human-derived mouse-adapted E. coli LM715-1 and their colonization assessed by culture over time. Fluorescence-activated cell sorting (FACS) and 16S rDNA sequencing were performed to trace plasmid spread to the microbiota. Results. E. coli LM715-1 colonized mice for ten days, while E. coli MG1655 was not recovered after 72 h. Bacterial cells from fecal samples on days 1 and 3 post inoculation were sorted by FACS. Samples from mice given donor E. coli LM715-1 showed an increase in cells expressing green but not red fluorescence compared to pre-inoculation samples. 16S rRNA gene sequencing analysis of FACS GFP positive cells showed that bacterial families Lachnospiraceae, Clostridiaceae, Pseudomonadaceae, Rhodanobacteraceae, Erysipelotrichaceae, Oscillospiraceae, and Butyricicoccaceae were the primary recipients of the RP4 plasmid. Conclusions. Results show this ARG-bearing conjugative RP4 plasmid spread to diverse human gut bacterial taxa within a live animal where they persisted. These fluorescent marker strategies and human-derived microbiota transplanted mice provided a tractable model for investigating the dynamic spread of ARGs within gut microbiota and could be applied rigorously to varied microbiotas to understand conditions facilitating their spread. Full article

In drug development, drug-target affinity (DTA) prediction is a key indicator for assessing the drug’s efficacy and safety. Despite significant progress in deep learning-based affinity prediction approaches in recent years, there are still limitations in capturing the complex interactions between drugs and target receptors. To address this issue, a dynamic heterogeneous graph prediction model, DynHeter-DTA, is proposed in this paper, which fully leverages the complex relationships between drug–drug, protein–protein, and drug–protein interactions, allowing the model to adaptively learn the optimal graph structures. Specifically, (1) in the data processing layer, to better utilize the similarities and interactions between drugs and proteins, the model dynamically adjusts the connection strengths between drug–drug, protein–protein, and drug–protein pairs, constructing a variable heterogeneous graph structure, which significantly improves the model’s expressive power and generalization performance; (2) in the model design layer, considering that the quantity of protein nodes significantly exceeds that of drug nodes, an approach leveraging Graph Isomorphism Networks (GIN) and Self-Attention Graph Pooling (SAGPooling) is proposed to enhance prediction efficiency and accuracy. Comprehensive experiments on the Davis, KIBA, and Human public datasets demonstrate that DynHeter-DTA exceeds the performance of previous models in drug-target interaction forecasting, providing an innovative solution for drug-target affinity prediction. Full article

Cyanobacterial cytochrome c6 (Cyt c6) is crucial for electron transfer between the cytochrome b6f complex and photosystem I (PSI), playing a key role in photosynthesis and enhancing adaptation to extreme environments. This study investigates the high-resolution crystal structures of Cyt c6 from Synechococcus elongatus PCC 7942 and Synechocystis PCC 6803, focusing on its dimerization mechanisms and functional implications for photosynthesis. Cyt c6 was expressed in Escherichia coli using a dual-plasmid co-expression system and characterized in both oxidized and reduced states. X-ray crystallography revealed three distinct crystal forms, with asymmetric units containing 2, 4, or 12 molecules, all of which consist of repeating dimeric structures. Structural comparisons across species indicated that dimerization predominantly occurs through hydrophobic interactions within a conserved motif around the heme crevice, despite notable variations in dimer positioning. We propose that the dimerization of Cyt c6 enhances structural stability, optimizes electron transfer kinetics, and protects the protein from oxidative damage. Furthermore, we used AlphaFold3 to predict the structure of the PSI-Cyt c6 complex, revealing specific interactions that may facilitate efficient electron transfer. These findings provide new insights into the functional role of Cyt c6 dimerization and its contribution to improving cyanobacterial photosynthetic electron transport. Full article

Background/Objectives: Endometriosis is a painful chronic condition in which the endometrium grows outside the uterus. The epithelial–mesenchymal transition (EMT) is critical to endometriosis progression, where cells lose epithelial traits and gain invasiveness. Methods: This study investigates the effects of phoenixin-14 (PNX-14), a neuropeptide found at reduced levels in endometriosis patients, on the expression of two molecular EMT markers, CDH1 (E-cadherin) and THBS2 (thrombospondin 2), as well as cell viability in the endometriosis-derived 12Z cell line. Cells were treated with physiological (0.2 nM) and endometriosis-relevant (0.05 nM) concentrations of PNX-14. Gene expression was analyzed using RT-qPCR, while protein localization was assessed by immunocytochemistry. Cell viability was measured using an XTT assay. Results: THBS2 gene expression was significantly decreased, and CDH1 remained unchanged in cells stimulated by 0.05 nM PNX-14. Immunolocalization indicates a weaker THBS2 and CDH1 protein immunosignal reaction for 0.05 nM PNX-14. PNX-14 treatment also exhibited a biphasic effect on cell viability. Lower concentration initially decreased viability at 48 h but then significantly increased it at 72 h. This increase coincided with the decrease in THBS2 expression, suggesting a potential link between PNX-14, THBS2, and cell viability. Conclusions: A negative correlation between cell viability and the expression of both EMT markers further highlights their possible involvement in the survival and adaptability of ectopic epithelial cells. Our findings suggest a complex interplay between PNX-14, EMT markers, and cell viability in ectopic epithelial cells. PNX-14’s ability to modulate these factors warrants further investigation to elucidate its role in endometriosis. Full article

Background: Dysregulated cellular metabolism is known to be associated with drug resistance in cancer treatment. Methods: In this study, we investigated the impact of cellular adaptation to lactic acidosis on intracellular energy metabolism and sensitivity to docetaxel in prostate carcinoma (PC) cells. The effects of curcumin and the role of hexokinase 2 (HK2) in this process were also examined. Results: PC-3AcT and DU145AcT cells that preadapted to lactic acid displayed increased growth behavior, increased dependence on glycolysis, and reduced sensitivity to docetaxel compared to parental PC-3 and DU145 cells. Molecular analyses revealed activation of the c-Raf/MEK/ERK pathway, upregulation of cyclin D1, cyclin B1, and p-cdc2Thr161, and increased levels and activities of key regulatory enzymes in glycolysis, including HK2, in lactate-acclimated cells. HK2 knockdown resulted in decreased cell growth and glycolytic activity, decreased levels of complexes I–V in the mitochondrial electron transport chain, loss of mitochondrial membrane potential, and depletion of intracellular ATP, ultimately leading to cell death. In a xenograft animal model, curcumin combined with docetaxel reduced tumor size and weight, induced downregulation of glycolytic enzymes, and stimulated the upregulation of apoptotic and necroptotic proteins. This was consistent with the in vitro results from 2D monolayer and 3D spheroid cultures, suggesting that the efficacy of curcumin is not affected by docetaxel. Conclusions: Overall, our findings suggest that metabolic plasticity through enhanced glycolysis observed in lactate-acclimated PC cells may be one of the underlying causes of docetaxel resistance, and targeting glycolysis by curcumin may provide potential for drug development that could improve treatment outcomes in PC patients. Full article

Background: The anterior cingulate cortex (ACC) is known for its involvement in various regulatory functions, including in the central control of feeding. Activation of local elements of the central glucose-monitoring (GM) neuronal network appears to be indispensable in these regulatory processes. Destruction of these type 2 glucose transporter protein (GLUT2)-equipped chemosensory cells results in multiple feeding-associated functional alterations. Methods: In order to examine this complex symptomatology, (1) dopamine sensitivity was studied in laboratory rats by means of the single-neuron-recording multibarreled microelectrophoretic technique, and (2) after local bilateral microinjection of the selective type 2 glucose transporter proteindemolishing streptozotocin (STZ), open-field, elevated plus maze, two-bottle and taste reactivity tests were performed. Results: A high proportion of the anterior cingulate cortical neurons changed their firing rate in response to microelectrophoretic administration of D-glucose, thus verifying them as local elements of the central glucose-monitoring network. Approximately 20% of the recorded cells displayed activity changes in response to microelectrophoretic application of dopamine, and almost 50% of the glucose-monitoring units here proved to be dopamine-sensitive. Moreover, taste stimulation experiments revealed even higher (80%) gustatory sensitivity dominance of these chemosensory cells. The anterior cingulate cortical STZ microinjections resulted in extensive behavioral and taste-associated functional deficits. Conclusions: The present findings provided evidence for the selective loss of glucose-monitoring neurons in the anterior cingulate cortex leading to motivated behavioral and gustatory alterations. This complex dataset also underlines the varied significance of the type 2 glucose transporter protein-equipped, dopamine-sensitive glucose-monitoring neurons as potential therapeutic targets. These units appear to be indispensable in adaptive control mechanisms of the homeostatic–motivational–emotional–cognitive balance for the overall well-being of the organism. Full article

The CRISPR-Cas system functions as an adaptive immune mechanism in archaea and bacteria, providing defense against the invasion of foreign nucleic acids. Most CRISPR-Cas systems are classified into class 1 or class 2, with further subdivision into several subtypes. The primary distinction between class 1 and class 2 systems lies in the assembly of their effector modules. In class 1 systems, the effector complex consists of multiple proteins with distinct functions, whereas in class 2 systems, the effector is associated with a single protein. Class 1 systems account for approximately 90% of the CRISPR-Cas repertoire and are categorized into three types (type I, type IV, and type III) and 12 subtypes. To date, various CRISPR-Cas systems have been widely employed in the field of genetic engineering as essential tools and techniques for genome editing. Type I CRISPR-Cas systems remain a valuable resource for developing sophisticated application tools. This review provides a comprehensive review of the characteristics, mechanisms of action, and applications of class 1 type I CRISPR-Cas systems, as well as transposon-associated systems, offering effective approaches and insights for future research on the mechanisms of action, as well as the subsequent development and application of type I CRISPR-Cas systems. Full article

This study aimed to explore the effects of different incubation temperatures on ruminal fermentation and rumen microorganisms and determine the appropriate protein and energy levels to enhance microbial protein synthesis using an in vitro system. Rumen inoculum was collected from two fistulated Holstein heifers (trial 1: BW: 652.3 kg ± 25.2; trial 2: BW: 683.3 kg ± 30.2) and assessed using a closed-batch culture system. The experimental model employed a 2 × 5 factorial arrangement using incubation temperatures set to 39 and 41 °C, with protein levels set to 12.0, 13.5, 15.0, 16.5, and 18.0% of DM in trial 1 or with energy levels set to 2.4, 2.5, 2.6, 2.7, and 2.8 Mcal/kg of DM in trial 2. The data were analyzed using the MIXED procedure. The results showed increased (p < 0.05) NH₃-N concentrations and total volatile fatty acids (TVFAs) with higher incubation temperatures, while the liquid-associated bacterial (LAB) amounts decreased (p < 0.05) in trials 1 and 2. The interaction between the energy level and incubation temperature affected (p < 0.05) the LAB protein levels in trial 2. Higher protein levels led to increased (p < 0.05) NH₃-N and acetate concentrations, but it decreased (p < 0.05) the propionate percentage. Conversely, higher energy levels decreased (p < 0.05) the amount of acetate and increased the propionate concentration, altering the acetate-to-propionate ratio. However, no interaction involving TVFA and LAB was observed between the incubation temperature and the protein or energy levels. Changes in the NH₃-N, TVFAs, and LAB protein amounts were observed under different incubation temperatures and energy levels. In conclusion, these findings provide insight into the metabolic adaptation under different ruminal temperatures and the impacts of dietary adjustments on rumen fermentation and microbial activity. However, there are limitations to replicating the complex physiological responses that occur within the whole body solely through in vitro experiments. Full article