Search Results (3,787)

Analysis of the genetic diversity of natural populations of economically valuable plants is important for conservation and selection strategies. In this study, the genetic diversity of 11 natural populations of Hippophae rhamnoides L.—sea buckthorn from different regions of Kazakhstan—was studied using Inter-Primer Binding Site Polymorphism (iPBS) markers based on conserved sequences of tRNA primer-binding sites (PBSs) that initiate retrotransposon replication. Universal PBS primers yielded reproducible and informative amplicons, forming unique profiles for each sample. Analysis of molecular variance showed that 60% of the total genetic variation was due to intrapopulation differences and 40% was due to interpopulation differentiation. The highest genetic diversity was found in the Shetlasty and Tersayryk sea buckthorn populations, whereas the Karatal and Topkain populations were characterised by minimal values, although unique alleles were observed in the latter population, indicating possible adaptation to local environmental conditions or genetic isolation. Principal coordinate analysis, UPGMA clustering, and Bayesian structure analysis (K = 4) confirmed geographical structuring. This study provides insights into the genetic structure of sea buckthorn populations in Kazakhstan and demonstrates the effectiveness of iPBS markers for assessing intraspecific diversity. The obtained results provide a basis for the conversation of H. rhamnoides gene pool and underscore the need for both in situ conservation of genetically rich populations and ex situ protection of vulnerable groups. Full article

Genome sequencing has possibly been the greatest step in the development of advanced tools for animal genetic improvement: knowledge of gene sequences and use of haplotype markers for productivity traits can provide important improvements in yield production and optimisation of reproductive program. Next-generation and, more recently, third-generation sequencing techniques enormously increased the ability to produce sequences from single individuals and increased the interest in exome or whole-genome sequencing as an alternative to SNP chips in breeding programs as these techniques allowed for the capture of a wider range of variations, including characterisation of rare variants, structural variations, and copy number changes. Here, we present a procedure, based on fast de novo assembly and a scaffolding step, to quickly build an almost complete genome starting from long reads obtained in a single sequencing run. The procedure, applied to sequences from five water buffaloes, was able to independently build, for each individual, an almost complete high-quality genome with highly continuous chromosome sequences; in most cases, over 90% of the length of the reference chromosome was covered by less than ten long contigs. Unlike other pipelines based on slower assemblers or which require many sequencing data, in 1–2 days, the proposed procedure can go from a single run to continuous genome assembly, supporting fast analysis of large chromosome structures, potentially useful for improving animal breeding and productivity. Full article

Sugars function as essential signaling molecules and metabolic substrates in plant growth, development, yield formation, and fruit quality. The aril of litchi (Litchi chinensis Sonn.) accumulates high levels of hexoses, primarily glucose and fructose; however, the molecular mechanisms underlying this process remain poorly characterized. This study aimed to systematically identify the monosaccharide transporter (MST) gene family in litchi and elucidate its role in aril sugar accumulation. Through a comprehensive analysis of the litchi genome, we identified a total of 45 LcMST genes, which were classified into seven distinct subfamilies: STP, ERD6L, PLT, INT, pGlcT, TMT, and VGT. Analysis of gene structure and conserved motifs revealed notable conservation among members within the same subfamily. Collinearity and gene duplication analyses suggested that the LcMST family expanded through both tandem and whole-genome duplication events, a process primarily governed by purifying selection. Expression profiling across diverse tissues demonstrated that LcMST genes exhibit distinct tissue-specific expression patterns. During fruit development in the hexose-dominant cultivar ‘Tianshuili’, the expression of the tonoplast monosaccharide transporter gene LcTMT1 exhibited a significant positive correlation with the accumulation of fructose, glucose, and total sugars. Heterologous functional complementation assays in yeast confirmed the ability of LcTMT1 to transport both glucose and fructose. In conclusion, this study presents the first genome-wide identification and characterization of the MST gene family in litchi, and identifies LcTMT1 as a key contributor of hexose accumulation in the aril. These findings establish a foundation for elucidating the molecular mechanisms of sugar accumulation in litchi fruit and for guiding future genetic improvement of fruit quality. Full article

High-speed solid rotor induction motors (HS-SRIMs) are favored for their robust structure but suffer from significant eddy current losses at high speeds, leading to efficiency reduction and thermal challenges. This study establishes a comprehensive multi-objective optimization framework to address this issue. The eddy current loss characteristics are first investigated using finite element analysis (FEA), focusing on the impact of key parameters like air gap length and rotor slotting. A sensitivity analysis quantifies their influence on motor performance. Subsequently, the Non-dominated Sorting Genetic Algorithm II (NSGA-II) is employed for multi-objective optimization, aiming to minimize eddy current loss while maximizing efficiency and electromagnetic torque. The optimization results demonstrate a significant improvement: a reduction in eddy current loss of 59.8%, an increase in efficiency of 17.2%, and a boost in output torque of 50.8%. Coupled electromagnetic–thermal simulations further validate a substantial decrease in operating temperatures. The proposed method provides an effective design approach for high-performance HS-SRIMs. Full article

The Blackspot Seabream, Pagellus bogaraveo, is a commercially valuable species widely distributed in the northeastern Atlantic and Mediterranean. Its biology makes it vulnerable to overfishing, but its population structure and ontogenetic migration strategy remain unclear. Building on previous work based on microsatellite markers, we expanded the investigation by analysing the mitochondrial Control Region (CR) to complement nuclear data. We analysed 199 specimens from 13 sites and combined the new CR sequences with 129 published records to achieve the broadest coverage in terms of biogeographic and genetic data. We calculated genetic diversity and performed AMOVA, pairwise ΦST comparisons, and multivariate analyses. Eighty-eight haplotypes were identified, showing high haplotype diversity (Hd = 0.767–0.945) and moderate nucleotide diversity (π = 0.0026–0.0054). Most genetic variation occurred within populations, and overall analyses indicated genetic homogeneity. However, pairwise analysis and AMOVA confirmed significant differentiation of the Azores population. These results confirm extensive genetic connectivity throughout the Atlantic–Mediterranean range of P. bogaraveo, likely due to a combination of large larval dispersal and a common spawning migration strategy, but identify the Azores as a genetically distinct unit. This highlights the need to consider both large-scale connectivity and local divergence in fisheries management. Full article

The tokay gecko (Gekko gecko) is a widely distributed lizard species in Southeast Asia, with significant importance in traditional medicine and the pet trade. Previous studies using mitochondrial DNA sequences revealed extensive genetic variation across its range, indicating the presence of distinct evolutionary lineages. In this study, we assessed the nuclear genetic variation and phylogenetic pattern of G. gecko using the recombination activating gene 1 (RAG1). We analyzed 105 RAG1 sequences from 16 localities across Thailand, Laos, and Cambodia, along with additional sequences from GenBank. Sequence analysis revealed 20 variable sites and 20 haplotypes (TgR1–TgR20). Haplotype network and phylogenetic analyses revealed strong regional structuring and at least three distinct evolutionary lineages (A–C), supported by the species delimitation test (PTP). Both red- and black-spotted morphs were present in different clades, indicating that external coloration does not correspond to genetic differentiation at this locus. Our results support the presence of distinct evolutionary lineages in G. gecko and emphasize the importance of integrative taxonomy for accurate species delimitation. These findings have implications for conservation, sustainable management, and regulation of international trade in this commercially exploited species. Full article

Background/Objectives: Lower-grade gliomas, particularly IDH-mutant astrocytomas, represent a distinct molecular subtype with unique therapeutic challenges. Whole-genome sequencing (WGS) plays a crucial role in uncovering genetic alterations that drive glioma pathogenesis and therapeutic resistance. This study identifies and evaluates a novel GATA2 p.Arg396Trp mutation in a clinical sample of lower-grade glioma, assessing its structural impact and implications for drug binding. Methods: A WHO Grade II astrocytoma specimen from a 33-year-old female patient was analyzed using WGS with Oxford Nanopore sequencing, followed by comprehensive bioinformatics processing to identify genomic variants. The GATA2 p.Arg396Trp mutation was evaluated using protein modeling, structural analysis, and pathogenicity prediction tools. Drug affinity analysis was conducted using molecular docking simulations to assess the computational impact of the mutation on drug binding. Results: The GATA2 p.Arg396Trp mutation was identified as a computationally predicted pathogenic variant, potentially disrupting protein interactions within critical functional domains. Structural analysis revealed altered binding dynamics with key anti-neoplastic agents, suggesting potential implications for therapeutic response. These findings represent computational predictions requiring experimental validation. Conclusions: Our preliminary findings suggest a potential role of the GATA2 p.Arg396Trp mutation in lower-grade glioma pathogenesis. The mutation predicted impact on transcriptional regulation and drug affinity suggests GATA2 as a possible biomarker candidate. Extensive experimental validation in larger patient cohorts is needed to establish clinical relevance and explore targeted therapeutic strategies. Full article

ATPase family AAA domain-containing protein 2 (ATAD2) has been recognized as a key oncogene that regulates chromatin remodeling, transcription, and cancer progression. As a member of the bromodomain (BRD) family, ATAD2 plays a crucial role in epigenetic modifications and is associated with multiple malignancies. Despite being considered an undruggable target in the past, crystallography and computational modeling have significantly accelerated ATAD2 drug discovery and development. This review provides a comprehensive overview of the structural features, functional roles, and biological significance of ATAD2, particularly in the context of cancer. We present an in-depth overview of different molecular strategies reported in the literature to suppress ATAD2 expression, including genetic and pharmacological approaches, and discuss their mechanistic and therapeutic implications. Particular emphasis is given to recent efforts in developing small-molecule inhibitors, detailing their binding interactions, therapeutic potential, and challenges in clinical translation. In addition, we performed alanine scanning calculations on molecular dynamics (MD)-simulated trajectories derived from protein–ligand complexes based on X-ray co-crystal structures containing three distinct ligands with different binding modes. This analysis provided critical insights into the binding interface of BRD-ATAD2, enhancing our understanding of its ligand interactions. Furthermore, we examine the emerging roles of ATAD2 in mediating resistance to cancer therapies, underscoring its potential as a target for overcoming drug resistance. By integrating structural insights, mechanistic studies, drug discovery efforts, and the challenges of developing ATAD2-targeted cancer therapies, this review emphasizes the need for further research to optimize ATAD2 inhibition strategies and explore its full therapeutic potential in oncology. Full article

Angulyagra polyzonata is a significant freshwater snail species in southern China. However, its wild resources have sharply declined due to overfishing. To assess the current status of germplasm resources in the Guangxi region, during this study, we first successfully developed nine pairs of primers that enable the amplification of highly polymorphic microsatellite markers (SSRs) with trinucleotide and tetranucleotide repeat sequences (PIC values ranging from 0.662 to 0.861) using transcriptomic data. Then, these designed primers were tested and applied for the genetic investigation of selected wild populations of the species. Finally, a genetic diversity analysis was conducted based on 12 wild populations (360 individuals) in Guangxi. After 798,244 SSR loci were screened out via high-throughput sequencing, the results showed that dinucleotide repeats accounted for the highest proportion (47.64%), mainly consisting of (AC/GT)n repeat units. Among the SSR loci in A. polyzonata, microsatellite loci with 5 to 20+ repeats are the most abundant. All nine selected and tested SSR loci significantly deviated from Hardy–Weinberg equilibrium (p < 0.001) and had heterozygote deficiency (average inbreeding coefficient of F = 0.390), indicating widespread inbreeding. The fixation index among populations was high (average Fst = 0.175), with 73% of the genetic variation occurring within populations and 27% between populations. Gene flow (Nm) was generally restricted (most population pairs had Nm < 1), with the (Tiandeng) TD and (Long’an) LA populations showing the smallest differentiation (Fst = 0.017), and the (Qinnan) QN and (Yinhai) YH populations showing the greatest differentiation (Fst = 0.409). UPGMA clustering and structure analysis (K = 2) divided the 12 populations into two subgroups. Overall, our research suggests that the genetic diversity of the wild population of A. polyzonata in the Guangxi region has declined. Thus, prioritizing the protection of highly genetically diverse populations, such as the LA population, is urgently needed. This study provides a scientific basis for the protection and sustainable utilization of A. polyzonata resources in Guangxi. Full article

Studies of the genetic diversity of ‘Candidatus Liberibacter asiaticus’ strains based on housekeeping genes have been unsuccessful. The increasing availability of complete genome sequences of several strains from different countries has allowed the identification of regions having greater variability, which have been successfully implemented for the bacterium characterization, including microsatellites, genes of prophage origin, and miniature transposable elements with inverted-repeats (MITEs). In the present work, the genetic structure of 147 ‘Ca. L. asiaticus’ strains from nine provinces of Cuba were investigated using two polymorphic regions, consisting of typing for prophages and MITEs. The results showed an important level of coexistence of type 1 and 2 prophages in the Cuban strains, while the type 3 prophage was not detected. Likewise, a high rate of co-occurrence of both types of MITEs (MCLas-A and -B) was also observed. However, the MITE MCLas-A was detected only in its empty form. The double-locus analysis allowed the identification of eight genotypes. Out of these, seven genotypes were present in the Western region, which constitutes the region with the highest genetic variability. This is the first report of a genetic characterization of Cuban strains of ‘Ca. L. asiaticus’ with polymorphic markers in orchards growing in commercial citrus regions. Full article

Background: Fragile X Syndrome (FXS) is the most common monogenic cause of autism spectrum disorders, and is characterized by the excessive immature excitatory synapses in cortical neurons, leading to excitatory/inhibitory imbalance and core autistic behaviors. This synaptic pathology has been attributed to dysregulated levels of synaptic proteins, including CYFIP2: a key regulator of synaptic structure and plasticity. However, the mechanism underlying the increased CYFIP2 protein level in FXS neurons remains unclear. Neurons abundantly secrete extracellular vesicles (EVs) enriched with bioactive cargos (proteins and miRNAs). Objectives: the goal of this research is to identify whether EV-dependent secretion plays important roles in regulating the intracellular CYFIP2 protein level in WT and FXS neurons. Methods and Results: our proteomic analysis reveals that CYFIP2 protein is packaged in EVs released by mouse cortical neurons. Pharmacological and genetic blockades of neuronal EV release significantly elevated intracellular CYFIP2 levels by 78 ± 14% and 168 ± 39%, respectively. Glutamate-evoked EV release significantly reduced the CYFIP2 level by 24 ± 2%. Neurons from Fmr1 KO mice, an FXS model, secreted significantly less EVs (46 ± 5%) than the wild type, and showed significantly elevated CYFIP2 (by 155 ± 31%). Evoking EV release in FXS neurons significantly lowered the intracellular CYFIP2 (by 53 ± 6%). Conclusions: these findings identify an EV-secretion-dependent mechanism that controls neuronal CYFIP2 level, implicating EV-mediated export in the regulation of synaptic protein homeostasis, synaptic remodeling, and FXS-associated synaptic deficits. Full article

This study investigates the species composition and distribution of blackflies (Diptera: Simuliidae) in Kazakhstan, with a focus on two species newly recorded for the country: Simulium murmanum (Enderlein, 1935) and Simulium reptans (Linnaeus, 1758). The presence of S. murmanum in Kazakhstan is reported for the first time, supported by morphological and molecular genetic analyses. Diagnostic features of the larva, pupa, and adult stages are described in detail, including the structure and coloration of the larval head capsule, pupal cocoon, and genitalia of both sexes. Habitat preferences and pupal substrate attachment patterns are illustrated, with observations on variations in cocoon branching across different flow regimes. Species identification was conducted using the morphological keys of Rubtsov and Yankovsky, and taxonomic classification was confirmed using the framework proposed by Adler. Molecular confirmation of S. murmanum was performed via DNA analysis. The species was found to be restricted to the foothill regions of East Kazakhstan, suggesting a distribution closely associated with the Altai mountain systems and adjacent regions in Mongolia and China. Unlike its status as a dominant hematophagous species in parts of Russia, S. murmanum has not demonstrated biting activity in Kazakhstan, Mongolia, or China. Additionally, the study provides the first records of S. reptans within the fauna of Kazakhstan, initially identified in the Irtysh River (Pavlodar Region). Subsequent sampling conducted in June 2024 revealed a continuous distribution of S. reptans along the Irtysh River through to the mountain streams of East Kazakhstan. The species was found in mountainous, foothill, and lowland environments, highlighting its wide ecological plasticity. Full article

The present study investigated the impact of genetic engineering strategies to produce a cell-free xylanase for applications in the baking industry. The xynA1 gene from the nonpathogenic bacterium Caulobacter vibrioides was integrated into the pAS22 vector with a xylose-inducible promoter and introduced back into the bacteria, resulting in the creation of the BS-xynA1. This construct exhibited substantial secreted xylanase 1 (XynA1) activity, reaching 17.22 U/mL, and a specific activity of 278.64 U/mg after an 18 h growth period with 0.3% (v/v) xylose plus 0.2% (w/v) corn straw. RT-qPCR analysis confirmed that higher xylanase activity in C. vibrioides cells was correlated with increased transcription of the xynA1 gene in the induction medium. Moreover, BS-xynA1 cells coexpress other enzymes, including xylanase 2 (XynA2), cellulase, pectinase, α-amylase, β-glucosidase, β-xylosidase, and α-L-arabinosidase, at low levels (≤2 U/mL). In vitro comparison of cell-free xylanases from BS-xynA1 with three commercially available xylanase-containing mixtures commonly utilized in baking protocols revealed its superior specific activity (163.4 U/mg) across a broad temperature range (30–100 °C), with optimal performance at 50 °C. In practical baking tests, the addition of cell-free XynA1 led to a reduction in dough kneading time and increase in bread height compared to those of the control. Notably, the incorporation of XynA1 resulted in enhanced alveolar structure formation within the bread crumb. Specifically, the following changes were observed in the mass parameters compared to those of the control: an increase in extensibility, elasticity, and deformation energy, and subsequent improvements in strength. Additionally, XynA1 addition led to a reduction in toughness and toughness/elasticity index, indicating a reduction in the mass stiffness of the enzyme-treated bread. To date, this is the first successful application of recombinant XynA1 from C. vibrioides in biotechnological processes related to baking, underscoring the potential and prospects in the food industry. Full article

This study introduces a novel approach to optimizing geometric tolerances on freeform surfaces, specifically turbine blades, by leveraging a global tolerance framework. Unlike traditional methods that rely on multiple local tolerances, this research proposes a unified model to streamline design complexity while maintaining functional integrity and cost efficiency. A turbine blade, reconstructed from 3D-scanned point cloud data, serves as the basis for this investigation. The reconstructed geometry was analyzed to define deviation distributions, followed by the application of a global tolerance model. Using genetic algorithms, the tolerances were optimized to balance manufacturing costs and performance penalties. Results demonstrate a substantial simplification in quality control processes, with a reduction in manufacturing costs by up to 20%, while preserving aerodynamic and structural performance. The study highlights the potential of global tolerance strategies to transform tolerance allocation in industries such as aerospace and energy, where freeform surfaces are prevalent. The integration of optimization techniques and advanced surface analysis offers a forward-looking perspective on enhancing manufacturing precision and efficiency. Full article

Advancements in genomic technologies have transformed prenatal genetic testing, offering more accurate, comprehensive, and noninvasive approaches to reproductive care. This review provides an in-depth overview of current methodologies and emerging innovations, including expanded carrier screening (ECS), cell-free DNA (cfDNA) testing, chromosomal microarray analysis (CMA), and sequencing-based diagnostics. We highlight how next-generation sequencing (NGS) technologies have revolutionized carrier screening and fetal genome analysis, enabling detection of a broad spectrum of genetic conditions. The clinical implementation of cfDNA has expanded from common aneuploidies to include copy number variants (CNVs), and single-gene disorders. Diagnostic testing has similarly evolved, with genome sequencing outperforming traditional CMA and exome sequencing through its ability to detect both sequence and structural variants in a single assay. Emerging tools such as optical genome mapping, RNA sequencing, and long-read sequencing further enhance diagnostic yield and variant interpretation. This review summarizes major technological advancements, assesses their clinical utility and limitations, and outlines future directions in prenatal genomics. Full article