Search Results (1,805)

Eel populations are globally threatened by overfishing and illegal trade, making accurate species identification essential for resource conservation and regulatory enforcement. Conventional molecular identification methods are generally applied in the laboratory, with limited rapid on-site application. This study developed a field-deployable assay to identify the Japanese eel (Anguilla japonica), by incorporating multienzyme isothermal rapid amplification (MIRA) technology with a visually readable lateral flow assay (LFA). Species-specific primers targeting a 286 bp region within the mitochondrial genome of A. japonica were designed and labeled with fluorescein amidite and biotin, respectively. The performance of the MIRA-LFA was validated by assessing its specificity against four other major eel species and its analytical sensitivity, i.e., limit of detection (LoD), under optimized temperature and reaction-time conditions. The MIRA-LFA demonstrated 100% specificity, generating a positive signal only for A. japonica, with no cross-reactivity. A clear visual result was obtained within 10 min at the optimal reaction temperature of 39 °C. Under these optimal conditions, the assay showed a high sensitivity, with an LoD of 0.1 ng/μL of genomic DNA. The proposed assay is an effective tool for the rapid, specific, and sensitive identification of A. japonica. The ability to obtain fast, equipment-free visual results makes this assay an ideal point-of-care testing solution to combat seafood fraud and support the sustainable management of this economically important and vulnerable species. Full article

Treatment-resistant schizophrenia (TRS) affects up to one in three individuals with schizophrenia and is associated with a significant clinical, social, and economic burden. Different from treatment-responsive forms, TRS appears to involve other biological mechanisms extending beyond dopaminergic dysfunctions. This review outlines current knowledge on the molecular and cellular basis of TRS, focusing on alterations in glutamate signaling, imbalances between excitatory and inhibitory activity, disruptions in D-amino acid metabolism, and evidence of neuroinflammation, oxidative stress, and mitochondrial or endoplasmic reticulum dysfunction. Data from genomics, proteomics, metabolomics, preclinical models, and postmortem studies suggest that TRS may have a peculiar neurobiological substrate. Further, multimodal brain imaging studies reveal differences in brain structure, white matter integrity, and network connectivity when compared to treatment-responsive individuals. Altogether, these findings support a shift from the traditional dopamine hypothesis toward a more comprehensive model that includes multiple immune, metabolic, and synaptic factors. Understanding the possible interplay of these complex mechanisms may lead to the identification of potential biomarkers that may help to predict antipsychotic response, as well as the development of more targeted treatments. Early recognition and a deeper biological insight into TRS are essential for improving care and guiding personalized therapeutic strategies. Full article

Mitochondrial genomes are powerful tools for taxonomic delimitation and species identification, yet they remain scarce for Chironomidae (Diptera). In this study, we assembled and annotated 63 new mitochondrial genomes, encompassing 63 species within 39 genera in Orthocladiinae sensu lato (including Prodiamesinae and Orthocladiinae) and Chironominae by whole-genome sequencing, marking the first report of mitochondrial genome data for the Xiaomyini. Comparative analyses revealed structural variation, including transfer RNA gene rearrangements, along with strong nucleotide composition bias, codon usage patterns, and gene-specific selection pressure differences. Distinct evolutionary dynamics were detected among protein-coding genes, ribosomal RNAs, transfer RNAs, and the control region. Heterogeneity analyses and phylogenetic analyses showed that amino acid datasets perform better for basal branch of Orthocladiinae relationships, although the resolution within non-basal branches of Orthocladiinae remains limited. By substantially increasing both the number and taxonomic breadth of mitochondrial genomes in Chironomidae, this study delivers a vital foundation for future multi-marker phylogenetic reconstruction, taxonomic revision, and rapid species identification, with direct applications to biodiversity conservation and freshwater ecosystem monitoring. Full article

Feed efficiency is a key economic trait that affects the cost of production in broiler farming. Reducing broiler feed costs contributes to reducing excessive feed consumption and increasing the productivity of broiler breeding. Therefore, identifying genetic regions associated with feed efficiency is crucial for broiler breeding. In this study, we performed genome-wide association (GWAS) analyses of feed conversion ratio (FCR) and residual feed intake (RFI) traits for four growth cycles (72–81, 81–89, 89–113, and 113–120 days of age) using 55K single-nucleotide microarray genotypic data of 4493 Wenchang chickens from two generations. In the single-trait GWAS, a total of 59 SNPs were identified, and 36 genes were annotated within the ±50 kb regions surrounding candidate loci (including ABCC6, CLDN10, DGKB, EXT2, FOXO1, IFT140, JAG2, among others. These candidate loci explained 1.4–7.0% of the phenotypic variance explained, and applying a filtering criterion that required a deleteriousness score greater than 8, one locus-Gallus gallus chromosome (GGA) 5:3550350 (chCADD score = 12.51524) was located within intron 3 of ANOX3. In the FCR and RFI traits in the longitudinal GWAS (LONG-GWAS) model, 80 SNPs and 191 SNPs were identified, respectively, and a total of 43 genes and 121 genes were annotated. A total of 33 candidate loci were screened by combining the locus deleteriousness scores, and 25 candidate genes were annotated within the upper and lower 50 kb ranges. Through KEGG signaling pathway analysis, it was found that the candidate genes were highly enriched mainly in autophagy, mitochondrial phagocytosis, and other pathways. In conclusion, the SNPs and potential genes identified in this study will be helpful for chicken breeding and provide fundamental data for the genetic basis of chicken feed efficiency-related traits. Full article

Background: Oral cancer remains a significant global health concern due to its high incidence and mortality, as highlighted by GLOBOCAN 2022, and is characterized by poor survival rates despite available therapies. Therefore, there is an imperative need for developing novel therapeutic targets for this disease. Methods: This study investigates the oncogenic role of mortalin in oral cancer. We have used The Cancer Genome Atlas (TCGA) dataset, samples from North Eastern Region of India and tissue microarray to examine the expression of this gene/protein in patient samples. siRNA related knock down studies were carried out to determine the role of mortalin on oral cancer cell proliferation, survival, metastases, EMT, autophagy etc. Results: Analysis of TCGA dataset revealed increased mortalin expression in head and neck squamous cell carcinoma (HNSCC), which correlated with tumor grade and stage, and was associated with diminished overall survival. These findings were validated in oral cancer patient tissue samples obtained from the North East Region of India and oral cancer cell lines. Functional assays showed that mortalin knockdown via siRNA reduced cancer cell proliferation, migration, invasion, and angiogenesis while inducing apoptosis, disrupting mitochondrial membrane potential, and modulating autophagy. These effects were linked to altered expression of regulatory molecules, including p53, p21WAF1, cyclins, caspases, MMPs, Survivin, and components of the Akt/mTOR pathway, thereby alleviating key hallmarks of oral cancer. Conclusion: Collectively, these data support mortalin as a potential therapeutic target for oral cancer and warrant further studies for the development of mortalin-targeting drugs in both laboratory and clinical settings. Full article

Alterations in the mitochondrial genome (mtDNA) have been shown to be key in cancer development and could be useful as biomarkers for diagnosis, prognosis, and treatment. To identify mtDNA variants associated with breast cancer, we analyzed the whole mtDNA sequence from paired tissues (tumor–peripheral blood) of women with this malignancy and from peripheral blood samples of healthy women. The mtDNA mutational landscape, heteroplasmy levels of the variants, and mitochondrial ancestry were established. Comparative analysis between cases and controls revealed significant differences in the number and location of variants, as well as in the heteroplasmy levels. Cases showed higher mutation number in MT-ND5, tRNAs, and rRNAs genes; increased proportion of missense variants; and elevated mtDNA content, than controls. Notably, a high blood mtDNA mutational burden (OR = 3.83, CI: 1.89–7.95, p = 5.3 × 10⁻⁵) and five mtDNA variants showed association with the risk of breast cancer. Furthermore, a low tumor mutational burden (HR = 7.82, CI: 1.0–63.6, p = 0.05) and the haplogroup L (HR = 12.16, CI: 2.0–72.8, p = 0.0062) were associated with decreased overall and disease-free survival, respectively. Our study adds evidence of the potential usefulness of mtDNA variants as risk and prognosis biomarkers for breast cancer. Full article

Mycoplasma bovis (M. bovis) adheres to host cells and persists intracellularly, causing chronic inflammation and significant economic losses in the cattle industry. The role of host cell apoptosis in this host–pathogen interaction remains unclear. This study isolated and identified the M. bovis Xinjiang strain XJ01 from diseased cattle in China. XJ01 exhibited typical “fried egg” colony morphology, distinct biochemical characteristics, and a 1.02 Mb genome (29.33% GC content) encoding 939 genes, including 93 unique genes. Functional analysis under optimal infection conditions (MOI = 1000, 24 h) revealed that XJ01 induced significant apoptosis and reduced viability in bovine macrophages (BoMac). This was accompanied by mitochondrial homeostasis disruption, characterized by increased Bax expression and suppressed Bcl-2 levels. Transcriptome analysis identified 9926 differentially expressed genes. KEGG pathway enrichment indicated significant activation of apoptosis and P53 signaling pathways, with Gadd45 and XIAP identified as key regulators. Mechanistic validation demonstrated that Gadd45 overexpression or XIAP knockdown enhanced Bax expression, inhibited Bcl-2, increased apoptosis rates, and consequently significantly reduced intracellular bacterial load at 24 h post-infection. Conversely, suppressing Gadd45 or overexpressing XIAP promoted pathogen survival. Collectively, this study reveals that M. bovis XJ01 activates host stress signaling to upregulate Gadd45 and suppress XIAP, thereby triggering mitochondrial apoptosis as a mechanism to eliminate intracellular bacteria—illustrating a self-limiting antibacterial mechanism. Full article

Background: Traditional morphology-based classification of the Oriental Plover (Anarhynchus veredus) is inconsistent with molecular evidence, underscoring the necessity of incorporating molecular data to elucidate its evolutionary relationships within Charadriidae. Methods: Here, we present the first complete mitochondrial genome of A. veredus by Illumina NovaSeq Sequencing and explore its evolutionary implications within Charadriidae. Results: The mitogenome spans 16,886 bp and exhibits conserved structural features typical of Charadriidae, including gene order, overlapping coding regions, and intergenic spacers. Nucleotide composition analysis revealed a GC content of 44.3%, aligning with other Charadriidae species (44.5–45.8%), and hierarchical GC distribution across rRNA, tRNA, and protein-coding genes (PCGs) reflects structural and functional optimization. Evolutionary rate heterogeneity was observed among PCGs, with ATP8 and ND6 showing accelerated substitution rates (Ka/Ks = 0.1748 and 0.1352) and COX2 under strong purifying selection (Ka/Ks = 0.0678). Notably, a conserved translational frameshift in ND3 (position 174) was identified. Phylogenetic analyses (ML/NJ) of 88 Charadriiformes species recovered robust topologies, confirming that the division of Charadriidae into four monophyletic clades (Pluvialis, Vanellus, Charadrius, and Anarhynchus) and supporting the reclassification of A. veredus under Anarhynchus. Conclusions: This study resolves the systematic position of A. veredus and highlights the interplay between conserved mitochondrial architecture and lineage-specific adaptations in shaping shorebird evolution. Full article

Clonorchis sinensis, a parasitic liver fluke, is the primary aetiological agent of clonorchiasis, a disease predominantly characterized by liver-related clinical manifestations. Currently, research on the complete mitochondrial (mt) genome of local C. sinensis populations remains inadequate. Thus, in this study, we sequenced and annotated the mt genome of fish-borne C. sinensis (Cs-c2) from Changchun, Jilin Province, China, a strain not previously described. This mt genome is 14,136 bp in length and harbours 12 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a single control region (CR). We constructed a maximum likelihood (ML) phylogenetic tree using concatenated ND5, ND6, and ND1 from protein-coding genes (PCGs) of the C. sinensis mitochondrial genome (mt genome). This tree more clearly differentiated C. sinensis strains from three geographical regions (China, Russia, and South Korea) and distinguished Opisthorchiidae from two closely related families (Fasciolidae and Dicrocoeliidae). Additionally, we constructed an ML phylogenetic tree using concatenated ND4, ND5, ND1, ND2, and COX1 from the PCGs of digenean (Digenea) mt genomes. This approach—utilizing multiple high-resolution PCGs with evolutionary rates distinct from those of the mt genome—yielded robust clustering for multiple suborders and 13 families within Digenea and provided new molecular evidence for intergeneric relationships within the suborder Plagiorchiata of Digenea. These findings serve as important references for future research on the differentiation of closely related geographical strains of digeneans, as well as for studies on molecular taxonomy and population genetics. Full article

Suruga fundicola, one of the few known deep-dwelling gobies, is found in Japan, South Korea, and China. Owing to the limited availability of specimens, little is known about its mitogenome characterization, phylogenetic relationship, and adaptive evolution. In this study, we sequenced four complete mitogenomes using the DNBSEQ platform and Sanger sequencing. The mitogenomes in length ranged from 17,138 to 17,352 bp, primarily due to the variation in the number of long tandem repeat (LTR) sequences within variable region 3 (VR3). Although the gene composition and arrangement of the S. fundicola mitogenome are largely consistent with those of other gobies, we identified an expansion of the ND2 gene (78 bp), and an unexpected noncoding region (NC, 35 bp) located between the ND2 and tRNA^trp genes. To further investigate the variation in VR3, we sequenced this region in all nineteen individuals with the Sanger sequencing method. We detected eight distinct LTR types, containing one–three mutation sites, which formed ten different VR3 patterns. Most VR3 patterns (14/19) consisted of a single type of pure LTR, while the remaining five exhibited heterogeneous patterns composed of two different LTRs. Notably, in LTR types T1 and T3, which co-occur in heterogeneous patterns P1 and P9, we found their respective pure patterns (P2–3 and P7). Recombination provides a better, more plausible mechanism for generating the heterogeneity patterns than slipped-strand mispairing, which better explains the homogeneous LTR expansions. These findings provide evidence of recombination in the control region of a vertebrate mitogenome. A phylogenetic analysis confirmed that S. fundicola has a close relationship with Am. hexanema and C. stigmatias. Compared to five shallow-water species of the AcanthogobiusGroup, the deep-dwelling goby S. fundicola was found to be under stronger purifying selection. Within its mitochondrial protein-coding genes (PCGs), ND2 and ND6 genes were subject to stronger purifying selection than the others. Additionally, four genes showed signs of selection sites with high credibility (one in ATP6, ND3, and ND4; eight in ND2). This study provides valuable genomic resources for S. fundicola and enhances our understanding of the phylogenetic relationship, mitogenome recombination, and adaptive evolution of the goby. Full article

Background/Objectives: Circulating cell-free DNA (cfDNA) consists of genomic DNA (cf-nDNA) and mitochondrial DNA (cf-mtDNA) fragments released from cells primarily through apoptosis and necrosis. In healthy individuals, the main source of cfDNA is apoptosis, whereas in cancer patients, necrosis predominates. Considering that in vitro cfDNA models are valuable research tools, this study presents an in vitro characterization of cf-mtDNA patterns released into the culture medium by four human cell lines: normal dermal fibroblasts (Hs27), induced pluripotent stem cells (iPSCs), melanoma cells (BMel), and prostate cancer cells (PC3). Furthermore, as fetal bovine serum (FBS)—a widely used supplement in cell culture media—has been shown to contain bovine cfDNA, species-specific primers were employed to eliminate potential artifacts arising from this contamination in in vitro experiments. Methods: Fragmentation analysis of cf-mtDNA was conducted by amplifying the human MT-CYB gene and the D-loop region in four cell lines using species-specific primers. Two indices, Q and λ, were employed to quantify fragmentation. Results: These indices reveal that cancer cells exhibit the highest degree of fragmentation compared to fibroblasts, whereas stem cells show the lowest degree of fragmentation. This study identified species-specific primers for the human and bovine MT-CYB gene, confirming the presence of bovine cf-mtDNA in cell culture media supplemented with FBS. Conclusions: in vitro cellular models are useful for studying the mechanisms of cfDNA release and fragmentation; designed primers provide a reliable tool for assessing contamination across different growth time points minimizing interference errors and non-specific amplifications. Full article

The present study characterizes the complete mitochondrial genome of Potamotrygon leopoldi, commonly referred to as the “white blotched stingray”, a member of the Potamotrygonidae family that are a group of stingrays that live exclusively in freshwater environments. Potamotrygon leopoldi, endemic to the Xingu River in the Amazon region, are exploited by commercial fisheries for food and commonly exploited by the ornamental industry, and this has a significant impact on the populations. Here, newly assembled PacBio long-read sequencing assesses the complete mitogenome of P. leopoldi and performs a comparative investigation into the evolutionary connections to other extant taxa of elasmobranchs. The mitogenome has 17,504 bp, containing 13 protein-coding, 22 tRNA, and 2 rRNA genes. The mitogenome comprises A: 32.32%, T: 24.41%, C: 12.84%, and G: 30.42%, with an AT content of 56.73%. The values of AT and GC skewness were 0.13 and −0.40, respectively. Our phylogenetic analyses with mitogenome sequences of 40 elasmobranch species support the monophyly for the Potamotrygonidae family and indicate a close relationship to the Dasyatidae family and a sister relationship with Potamotrygon orbignyi and Potamotrygon falkneri. We also detected various amino acid sites in positive selection exclusively in P. leopoldi. This extensive comparative mitogenomic investigation offers novel and significant insights into the evolutionary lineage of neotropical freshwater stingrays and their closely related taxa. It is an indispensable resource for facilitating ongoing and prospective investigations into the molecular evolution of elasmobranchs. Full article

Proceroplatus (Keroplatidae: Keroplatinae) is a distinct keroplatid group comprising 39 described species. These species are found worldwide, but none had previously been reported in China prior to this study. In this paper, Proceroplatus is recorded for the first time from China, along with two new species: P. dapanshanussp. n. and P. biemarginatussp. n., which were collected from the southern region. Here, a worldwide distribution map of this genus is presented by species, including the new ones. Images and detailed morphological descriptions are provided for each new species, accompanied by molecular identification based on the standard mitochondrial cytochrome oxidase subunit I (COI) gene. To clarify the mitogenomic characteristics of Proceroplatus, the well-assembled and annotated mitogenome of P. dapanshanus was obtained and described in detail. The comparative analyses and phylogenetic tree indicate that the mitogenomic evolution of keroplatids is relatively conserved and influenced not only by mutation pressure but also by natural selection and other factors. Full article

The Naozhou stock of large yellow croakers (Larimichthys crocea) exhibits unique phenotypic traits and high genetic diversity, making it a valuable resource for selective breeding and genetic conservation in aquaculture. Despite its importance, simple sequence repeat (SSR) markers have not been developed for this stock, which limits efforts in genetic evaluation, breeding optimization, and sustainable utilization of this commercially important species. In this study, 195,263 SSRs were identified from the genome of the Naozhou stock of large yellow croaker, covering a total length of 16,578,990 bp with a density of 288 bp/Mb. Dinucleotide repeats were the most common, with the AC motif being the most prevalent. The frequency of SSR markers ranged from 245.63 to 346.60 per Mb. A total of 30 primer pairs were synthesized, of which 28 pairs (93.3%) successfully amplified clear and reproducible bands in PCR assays. Among these, 28 SSR markers exhibited distinct and reproducible bands following gel electrophoresis. For eight SSR loci, the number of alleles (Na) ranged from 4 to 22 (mean = 11.375), while the effective number of alleles (Ne) ranged from 1.5401 to 10.4727 (mean = 5.6475). The assembled mitochondrial genome (mtDNA) was 16,467 bp in length and comprised 37 genes, including 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The total sequence length of the PCGs was 11,431 bp, accounting for 69.4% of the mtDNA. A large portion of the PCGs (5) used incomplete stop codons (e.g., nad2, nad3, cox2), while others used TAA stop codons (e.g., nad6, nad5, TrnT). The mtDNA encoded a total of 3808 codons, with UAA showing the highest relative synonymous codon usage value. The SSR markers and mtDNA data generated in this study provide valuable tools for future genetic breeding and genomic research on the Naozhou stock of large yellow croakers. Full article

Biomolecular condensates (BCs), formed through liquid–liquid phase separation (LLPS), are membraneless compartments that dynamically regulate key cellular processes. Beyond their canonical roles in energy metabolism and apoptosis, Mitochondria harbor distinct BCs, including mitochondrial RNA granules (MRGs), nucleoids, and degradasomes, that coordinate RNA processing, genome maintenance, and protein homeostasis. These structures rely heavily on proteins with intrinsically disordered regions (IDRs), which facilitate the transient and multivalent interactions necessary for LLPS. In this review, we explore the composition and function of mitochondrial BCs and their emerging involvement in neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Amyotrophic lateral sclerosis, and Huntington’s disease. We provide computational evidence identifying IDR-containing proteins within the mitochondrial proteome and demonstrate their enrichment in BC-related functions. Many of these proteins are also implicated in mitochondrial stress responses, apoptosis, and pathways associated with neurodegeneration. Moreover, the evolutionary conservation of phase-separating proteins from bacteria to mitochondria underscores the ancient origin of LLPS-mediated compartmentalization. Comparative analysis reveals functional parallels between mitochondrial and prokaryotic IDPs, supporting the use of bacterial models to study mitochondrial condensates. Overall, this review underscores the critical role of mitochondrial BCs in health and disease and highlights the potential of targeting LLPS mechanisms in the development of therapeutic strategies. Full article