Search Results (279)

Objectives: Sillago japonica is a commercially important marine fish species in the Northwestern Pacific, and understanding its genetic diversity and population structure is crucial for germplasm resource conservation and elucidating population evolution mechanisms. This study specifically aimed to systematically explore the genetic diversity and population structure of S. japonica across five geographic regions (DJW, YSW, ST, ZS, and RS) in its distribution range. Methods: A total of 50 S. japonica individuals from the five geographic regions were analyzed using high-throughput mitochondrial genome sequencing data. We identified single nucleotide polymorphisms (SNPs) and insertion-deletion (InDel) loci, followed by comprehensive population genetic analyses including phylogenetic tree construction, principal component analysis (PCA), ADMIXTURE analysis, and calculation of genetic differentiation indices (Fst) and genetic diversity parameters. Results: A total of 2966 SNPs and 414 insertion-deletion loci were identified. Phylogenetic tree topology, PCA, and ADMIXTURE 1.3.0 analysis consistently showed low genetic differentiation among the five populations, a pattern supported by low pairwise Fst values ranging from 0.00047 to 0.05589, indicating extensive gene flow across regions. Genetic diversity parameters varied slightly among populations: observed heterozygosity (0.00001–0.00528), expected heterozygosity (0.04552–0.07311), percentages of polymorphic loci (19.41–30.36%), and nucleotide diversity (0.04792–0.07697). Conclusions: The low genetic differentiation and diversity observed in S. japonica populations may result from the combined effects of historical bottleneck-induced gene pool reduction and extensive gene flow. These findings provide essential theoretical support for formulating targeted conservation strategies for S. japonica germplasm resources and further studies on its population evolution mechanisms. Full article

Myopathies and muscular dystrophies are a diverse group of rare or ultra-rare diseases that significantly impact patients’ quality of life and pose major challenges for diagnosis and treatment. Despite their heterogeneity, many share common molecular mechanisms, particularly involving sarcomeric dysfunction, impaired autophagy, and disrupted gene expression. This review explores the genetic and pathophysiological foundations of major myopathy subtypes, including cardiomyopathies, metabolic and mitochondrial myopathies, congenital and distal myopathies, myofibrillar myopathies, inflammatory myopathies, and muscular dystrophies. Special emphasis is placed on the role of autophagy dysregulation in disease progression, as well as its therapeutic potential. We discuss emerging diagnostic approaches, such as whole-exome sequencing, advanced imaging, and muscle biopsy, alongside therapeutic strategies, including physiotherapy, supplementation, autophagy modulators, and gene therapies. Gene therapy methods, such as adeno-associated virus (AAV) vectors, CRISPR-Cas9, and antisense oligonucleotide, are evaluated for their promise and limitations. The review also highlights the potential of drug repurposing and artificial intelligence tools in advancing diagnostics and personalized treatment. By identifying shared molecular targets, particularly in autophagy and proteostasis networks, we propose unified therapeutic strategies across multiple myopathy subtypes. Finally, we discuss international research collaborations and rare disease programs that are driving innovation in this evolving field. Full article

Identifying the diversity of wildlife hosts for malaria parasites in wildlife is crucial for understanding transmission dynamics in endemic regions where humans, vectors, and wildlife heavily overlap. We examined the presence of Plasmodium parasites in free-ranging ring-tailed coatis (Nasua nasua, n = 44) and nine-banded armadillos (Dasypus novemcinctus, n = 66) from an Indigenous community in the Peruvian Amazon. Nested PCR targeting the mitochondrial cytb gene detected Plasmodium spp. DNA in two coatis (4.7%). Sequencing revealed one lineage identical to Plasmodium vivax/P. simium and another to P. malariae/P. brasilianum. A subset of samples was reanalyzed using cox3-based PCR and sequencing in an independent laboratory, confirming P. malariae/P. brasilianum in one coati. No infections were observed in armadillos. These results indicate that coatis in the wild may host diverse Plasmodiidae parasites and that coatis may even carry Plasmodium spp., likely as incidental hosts. Expanding surveillance to additional non-primate mammals will help clarify their role in sylvatic malaria ecology and evaluate potential zoonotic risks. Full article

As the laying cycle is prolonged, the egg albumen quality exhibits a declining trend. A Haugh unit (HU) is a standard measure of the albumen quality, which reflects viscosity and freshness. During the late laying period, the HU not only decreased significantly, but also exhibited greater variability among individuals. The magnum, as the primary site of albumen synthesis, plays a central role in this process; however, the mechanisms by which it regulates the albumen quality remain unclear. To address this, we obtained genomic and transcriptomic data from 254 individuals, along with single-cell RNA sequencing (scRNA-seq) data of the magnum tissue. Genome-wide association studies (GWAS) across five laying stages (66, 72, 80, 90, and 100 weeks of age) identified 77 HU-associated single-nucleotide polymorphisms (SNPs). Expression quantitative trait locus (eQTL) mapping linked these variants to the expression of 12 genes in magnum tissue. In addition, transcriptomic analysis using linear regression and random forest models identified 259 genes that significantly correlated with the HU. Single-cell RNA sequencing further revealed two key cell types, plasma cells and a subset of epithelial cells, marked by ADAMTSL1 and OVAL, which are functionally relevant to the HU. Through integrated Transcriptome-Wide Association Study (TWAS) and Summary-data-based Mendelian Randomization (SMR) analyses, we identified four robust regulators of the albumen quality: CISD1, NQO2, SLC22A23, and CMTM6. These genes are functionally involved in mitochondrial function, antioxidant defense, and membrane transport. Overall, our findings uncovered the genetic and cellular mechanisms underlying age-related decline in the albumen quality and identified potential targets for improving the egg quality in aging flocks. Full article

Polyphagous fruit fly (Diptera: Tephritidae) pests from the Pacific Islands pose a biosecurity risk to New Zealand, a country free from pest fruit flies. Among them, Bactrocera facialis, B. passiflorae, B. kirki, and B. distincta are sympatric species commonly intercepted at immature stages at the border. However, current mitochondrial cytochrome oxidase I (COI) barcode data lack sufficient variation for a confident identification of the above four species. To address this, we generated COI barcode data for 403 fruit fly individuals including these four species and an additional 17 related fruit fly species. A phylogenetic analysis of the COI sequences of B. facialis revealed two genetically distinct populations, one closely related to B. passiflorae. Complete mitochondrial genomes were explored, identifying minor fixed differences in Cytochrome b (CYTB), NADH dehydrogenase 2 (ND2), and ATP synthase membrane subunit 6 (ATP6) genes. Based on sequence data for COI, ND2, and ATP6 genes, a multiplex real-time PCR assay has been developed and validated for the four target species. Each assay demonstrated high specificity, with no cross-reactions, and sensitivity as low as 10 copies/μL of the target DNA. This study shows that the developed assays enable the rapid and reliable identification of the target fruit fly species, supporting global biosecurity efforts. Full article

Preeclampsia (PE) is a leading cause of maternal and fetal morbidity that affects 2–8% of pregnancies worldwide, driven by placental dysfunction and systemic inflammation. Growth arrest-specific protein 6 (Gas6) and its receptor AXL play pivotal roles in PE pathogenesis, promoting trophoblast impairment and vascular dysregulation. This study investigated the transcriptomic reversal effects of AXL Receptor Tyrosine Kinase (AXL) inhibition in a Gas6-induced rat model of PE using RNA sequencing (RNA-seq). Pregnant rats were administered Gas6 to induce PE-like symptoms such as hypertension and proteinuria; a subset also received the AXL inhibitor R428. RNA-seq of placental tissues revealed 2331 differentially expressed genes (DEGs) in Gas6-AXLi versus Gas6 (1277 upregulated, 1054 downregulated). Protein–protein interaction networks and Gene Ontology enrichment highlighted upregulated mitochondrial functions, including electron transport chain components (e.g., NDUFC2, COX5A), suggesting enhanced energy metabolism. In the secondary analysis that compared Gas6 to Control, Gas6-upregulated extracellular matrix proteins (e.g., COL4A1, LAMC1) linked to fibrosis were reversed by AXL inhibition, indicating ameliorated placental remodeling. AXL inhibition activated compensatory pathways beyond Gas6 blockade, unveiling novel mechanisms for PE resolution. These findings position AXL inhibitors as promising therapeutics, offering insights into mitochondrial and fibrotic targets to mitigate this enigmatic disorder. Full article

Background/Objectives: Male infertility is a major health concern with a complex etiopathology, yet a substantial proportion of cases remain idiopathic. Mitochondrial dysfunction and non-coding RNA (ncRNA) deregulation have both been implicated in impaired spermatogenesis, but their interplay remains poorly understood. This study aimed to identify infertility-specific variants in ncRNAs that affect mitochondrial dynamics and homeostasis and to explore their roles. Methods: Whole-genome sequencing (WGS) was performed on genomic DNA samples from teratozoospermic, asthenozoospermic, oligozoospermic, and normozoospermic men. Variants uniquely present in infertile individuals and mapped to ncRNAs that affect mitochondrial dynamics were selected and prioritized using bioinformatics tools. An independent transcriptomic validation was conducted using RNA-sequencing data from testicular biopsies of men with non-obstructive azoospermia (NOA) to determine whether the ncRNAs harboring WGS-derived variants were transcriptionally altered. Results: We identified several infertility-specific variants located in lncRNAs known to interact with mitochondrial regulators, including GAS5, HOTAIR, PVT1, MEG3, and CDKN2B-AS1. Transcriptomic analysis confirmed significant deregulation of these lncRNAs in azoospermic testicular samples. Bioinformatic analysis also implicated the disruption of lncRNA–miRNA–mitochondria networks, potentially contributing to mitochondrial membrane potential loss, elevated reactive oxygen species (ROS) production, impaired mitophagy, and germ cell apoptosis. Conclusions: Our integrative genomic and transcriptomic analysis highlights lncRNA–mitochondrial gene interactions as a novel regulatory layer in male infertility, while the identified lncRNAs hold promise as biomarkers and therapeutic targets. However, future functional studies are warranted to elucidate their mechanistic roles and potential for clinical translation in reproductive medicine. Full article

Effective species identification is crucial for the conservation and management of marine mammals, particularly in regions such as the Mediterranean Sea, where several cetacean populations are endangered or vulnerable. In this study, we developed and validated a High-Resolution Melting (HRM) analysis protocol for the rapid, cost-effective, and reliable identification of the four representative marine cetacean species that occur in the Mediterranean Sea: the bottlenose dolphin (Tursiops truncatus), the striped dolphin (Stenella coeruleoalba), the sperm whale (Physeter macrocephalus), and the fin whale (Balaenoptera physalus). Species-specific primers targeting mitochondrial DNA regions (cytochrome b and D-loop) were designed to generate distinct melting profiles. The protocol was tested on both tissue and fecal samples, demonstrating high sensitivity, reproducibility, and discrimination power. The results confirmed the robustness of the method, with melting curve profiles clearly distinguishing the target species and achieving a success rate > 95% in identifying unknown samples. The use of HRM offers several advantages over traditional sequencing methods, including reduced cost, speed, portability, and suitability for degraded samples, such as those from the stranded individuals. This approach provides a valuable tool for non-invasive genetic surveys and real-time species monitoring, contributing to more effective conservation strategies for cetaceans and enforcement of regulations against illegal trade. Full article

Background: Oxidative stress is a critical factor contributing to male infertility, impairing spermatogonial stem cells (SSCs) and disrupting normal spermatogenesis. This study aimed to isolate and characterize human SSCs and to investigate oxidative stress-related gene expression, protein interaction networks, and developmental trajectories involved in SSC function. Methods: SSCs were enriched from human orchiectomy samples using CD49f-based magnetic-activated cell sorting (MACS) and laminin-binding matrix selection. Enriched cultures were assessed through morphological criteria and immunocytochemistry using VASA and SSEA4. Transcriptomic profiling was performed using microarray and single-cell RNA sequencing (scRNA-seq) to identify oxidative stress-related genes. Bioinformatic analyses included STRING-based protein–protein interaction (PPI) networks, FunRich enrichment, weighted gene co-expression network analysis (WGCNA), and predictive modeling using machine learning algorithms. Results: The enriched SSC populations displayed characteristic morphology, positive germline marker expression, and minimal fibroblast contamination. Microarray analysis revealed six significantly upregulated oxidative stress-related genes in SSCs—including CYB5R3 and NDUFA10—and three downregulated genes, such as TXN and SQLE, compared to fibroblasts. PPI and functional enrichment analyses highlighted tightly clustered gene networks involved in mitochondrial function, redox balance, and spermatogenesis. scRNA-seq data further confirmed stage-specific expression of antioxidant genes during spermatogenic differentiation, particularly in late germ cell stages. Among the machine learning models tested, logistic regression demonstrated the highest predictive accuracy for antioxidant gene expression, with an area under the curve (AUC) of 0.741. Protein oxidation was implicated as a major mechanism of oxidative damage, affecting sperm motility, metabolism, and acrosome integrity. Conclusion: This study identifies key oxidative stress-related genes and pathways in human SSCs that may regulate spermatogenesis and impact sperm function. These findings offer potential targets for future functional validation and therapeutic interventions, including antioxidant-based strategies to improve male fertility outcomes. Full article

Due to their clinical heterogeneity, nonspecific symptoms, and the limitations of existing biomarkers and imaging modalities, metabolic brain diseases (MBDs), such as mitochondrial encephalopathies, lysosomal storage disorders, and glucose metabolism syndromes, pose significant diagnostic challenges. This review examines the growing potential of cell-free DNA (cfDNA) derived from cerebrospinal fluid (CSF) epigenetic profiling as a dynamic, cell-type-specific, minimally invasive biomarker approach for MBD diagnosis and monitoring. We review important technological platforms and their use in identifying CNS-specific DNA methylation patterns indicative of neuronal injury, neuroinflammation, and metabolic reprogramming, including cfMeDIP-seq, enzymatic methyl sequencing (EM-seq), and targeted bisulfite sequencing. By synthesizing current findings across disorders such as MELAS, Niemann–Pick disease, Gaucher disease, GLUT1 deficiency syndrome, and diabetes-associated cognitive decline, we highlight the superior diagnostic and prognostic resolution offered by CSF cfDNA methylation signatures relative to conventional CSF markers or neuroimaging. We also address technical limitations, interpretive challenges, and translational barriers to clinical implementation. Ultimately, this review explores CSF cfDNA epigenetic analysis as a liquid biopsy modality. The central objective is to assess whether epigenetic profiling of CSF-derived cfDNA can serve as a reliable and clinically actionable biomarker for improving the diagnosis and longitudinal monitoring of metabolic brain diseases. Full article

Oncolytic virotherapy is a rapidly evolving approach to cancer treatment. Our group previously designed VV-GMCSF-Lact, a recombinant oncolytic vaccinia virus targeting solid tumors including gliomas. In this study, we used single-cell RNA sequencing to compare transcriptional responses in human glioma cells, non-malignant brain cells, and immortalized glioblastoma U87 MG cells following infection with this oncolytic virus. We found that proneural glioblastoma cells and microglia-like cells from patient-derived glioma cultures were the most susceptible to VV-GMCSF-Lact. Increased expressions of histones, translational regulators, and ribosomal proteins positively correlated with viral load at the transcript level. Furthermore, higher viral loads were accompanied by a large-scale downregulation of genes involved in mitochondrial translation, metabolism, and oxidative phosphorylation. Levels of early vaccinia virus transcripts are also positively correlated with infection intensity, suggesting that the fate of cells is determined at the early stage of infection. Full article

Background/Objectives: The treatment of multiple myeloma (MM) remains a challenge, as almost all patients will eventually relapse. Proteasome inhibitors are a cornerstone in the management of MM. Unfortunately, validated biomarkers predicting drug response are largely missing. Therefore, we aimed to identify genes associated with drug resistance or sensitization to proteasome inhibitors. Methods: We performed genome-wide CRISPR-Cas9 knockout (KO) screens in human KMS-28-BM myeloma cells to identify genetic determinants associated with resistance or sensitization to proteasome inhibitors. Results: We show that KO of KLF13 and PSMC4 induces drug resistance, while NUDCD2, OSER1 and HERC1 KO cause drug sensitization. Subsequently, we focused on top sensitization hit, NUDCD2, which acts as a co-chaperone of Hsp90 to regulate the LIS1/dynein complex. RNA sequencing showed downregulation of genes involved in the ERAD pathway and in ER-associated ubiquitin-dependent protein catabolic processes in both untreated and carfilzomib-treated NUDCD2 KO cells, suggesting that NUDCD2 depletion alters protein degradation. Furthermore, bortezomib-treated NUDCD2 KO cells showed a decreased expression of genes that have a function in oxidative phosphorylation and the mitochondrial membrane, such as Carnitine Palmitoyltransferase 1A (CPT1A). CPT1A catalyzes the uptake of long chain fatty acids into mitochondria. Mitochondrial lipid metabolism has recently been reported as a possible therapeutic target for MM drug sensitivity. Conclusions: These results contribute to the search for therapeutic targets that can sensitize MM patients to proteasome inhibitors. Full article

Background: The family Buprestidae is one of the largest families in Coleoptera; however, the number of reported mitochondrial genomes for this family is limited. Methods: In this study, mitogenomes of Chrysobothris violacea, C. shirakii, Buprestis fairmairei, and Phaenops yin were sequenced, assembled, and annotated. The mitogenomes of Chrysobothris, Phaenops, and Buprestis are reported for the first time. Results: The mitogenomes of Chrysobothris violacea, C. shirakii, and Phaenops yin are complete, while the mitogenome of Buprestis fairmairei is partial, lacking trnV and 12S genes. The AT-skew of these four mitogenomes is positive (0.02–0.09). Among the protein-coding genes, the Ka/Ks ratio for cox1 is the lowest (0.05), and the nucleotide diversity for nd6 is the highest. Conclusions: The phylogenetic trees based on mitogenome sequences suggest that the target genus Chrysobothris is sister to Phaenops, and the target genus Buprestis is sister to (Melanophila + (Chrysobothris + Phaenops)) clade. The results of this study will provide mitogenomic data for further research on the mitogenome and phylogeny of Buprestidae. Full article

Hippophae rhamnoides subsp. sinensis is extensively found in China, where the annual precipitation ranges from 400 to 800 mm. It is the most dominant species in natural sea buckthorn forests and the primary cultivar for artificial ecological plantations. Additionally, it exhibits significant nutritional and medicinal value, making it a renowned eco-economic tree species. Despite extensive research into its ecological functions and health benefits, the mitochondrial genome of this widespread species has not yet been published, and knowledge of the mitochondrial genome is crucial for understanding plant environmental adaptation, evolution, and maternal inheritance. Therefore, the complete mitochondrial genome was successfully assembled by aligning third-generation sequencing data to the reference genome sequence using the Illumina NovaSeq 6000 platform and Nanopore Prometh ION technologies. Additionally, the gene structure, composition, repeat sequences, codon usage bias, homologous fragments, and phylogeny-related indicators were also analyzed. The results showed that the length of the mitochondrial genome is 454,489 bp, containing 30 tRNA genes, three rRNA genes, 40 PCGs, and two pseudogenes. A total of 411 C-to-U RNA editing sites were identified in 33 protein-coding genes (PCGs), with higher frequencies observed in ccmFn, ccmB, nad5, ccmC, nad2, and nad7 genes. Moreover, 31 chloroplast-derived fragments were detected, accounting for 11.86% of the mitochondrial genome length. The ccmB, nad4L, and nad7 genes related to energy metabolism exhibited positive selection pressure. The mitochondrial genome sequence similarity between H. rhamnoides subsp. sinensis and H. tibetana or H. salicifolia was 99.34% and 99.40%, respectively. Fifteen shared gene clusters were identified between H. rhamnoides subsp. sinensis and H. tibetana. Phylogenetically, the Rosales order showed close relationships with Fagales, Fabales, Malpighiales, and Celastrales. These findings provide fundamental data for exploring the widespread distribution of H. rhamnoides subsp. sinensis and offer theoretical support for understanding the evolutionary mechanisms within the Hippophae genus and the selection of molecular breeding targets. Full article

Background: Colorectal cancer (CRC) is a prevalent global malignancy with particularly challenging treatment outcomes in advanced stages. Oxaliplatin (OXA) is a frontline chemotherapeutic agent for CRC. However, 15% to 50% of stage III patients experience recurrence due to drug resistance. Elucidating the molecular mechanisms underlying OXA resistance is, therefore, crucial for improving CRC prognosis. The role of DIRAS1, a RAS superfamily member with reported tumor-suppressive functions in various cancers, remains poorly defined in CRC. Methods: The effects of DIRAS1 on CRC cell proliferation and migration were evaluated using MTT, wound healing, and colony formation assays. Stable cell lines with knockdown or overexpression of DIRAS1 and PHB1 were established via plasmid and lentiviral systems. Drug sensitivity to OXA was assessed through cytotoxicity assays and IC₅₀ determination. Clinical relevance was validated through immunohistochemical analysis of CRC tissue samples. Transcriptomic sequencing was performed to explore downstream regulatory mechanisms. Results: DIRAS1 expression was positively correlated with OXA resistance and was significantly upregulated following prolonged chemotherapy exposure. Silencing DIRAS1 reduced the IC₅₀ of OXA in vitro and increased tumor sensitivity to OXA in vivo. Transcriptome analysis identified PHB1 as a downstream effector of DIRAS1. Functional studies revealed that PHB1 contributes to chemoresistance by maintaining mitochondrial stability. Conclusions: This study identifies DIRAS1 as a key contributor to OXA resistance in CRC by modulating PHB1 expression and mitochondrial function. Targeting the DIRAS1–PHB1 axis may offer a novel therapeutic strategy to overcome chemoresistance in CRC. Full article