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  1. Fulltext Persistent DNA Methylation Changes across the First Year of Life and Prenatal NO2 Exposure in a Canadian Prospective Birth Study
    Lee S, Sbihi H, MacIsaac JL, Balshaw R, Ambalavanan A, Subbarao P, et al.
    Environ Health Perspect, 2024 Apr;132(4):47004.
    PMID: 38573328 DOI: 10.1289/EHP13034
    BACKGROUND: Evidence suggests that prenatal air pollution exposure alters DNA methylation (DNAm), which could go on to affect long-term health. It remains unclear whether DNAm alterations present at birth persist through early life. Identifying persistent DNAm changes would provide greater insight into the molecular mechanisms contributing to the association of prenatal air pollution exposure with atopic diseases.

    OBJECTIVES: This study investigated DNAm differences associated with prenatal nitrogen dioxide (NO2) exposure (a surrogate measure of traffic-related air pollution) at birth and 1 y of age and examined their role in atopic disease. We focused on regions showing persistent DNAm differences from birth to 1 y of age and regions uniquely associated with postnatal NO2 exposure.

    METHODS: Microarrays measured DNAm at birth and at 1 y of age for an atopy-enriched subset of Canadian Health Infant Longitudinal Development (CHILD) study participants. Individual and regional DNAm differences associated with prenatal NO2 (n=128) were identified, and their persistence at age 1 y were investigated using linear mixed effects models (n=124). Postnatal-specific DNAm differences (n=125) were isolated, and their association with NO2 in the first year of life was examined. Causal mediation investigated whether DNAm differences mediated associations between NO2 and age 1 y atopy or wheeze. Analyses were repeated using biological sex-stratified data.

    RESULTS: At birth (n=128), 18 regions of DNAm were associated with NO2, with several annotated to HOX genes. Some of these regions were specifically identified in males (n=73), but not females (n=55). The effect of prenatal NO2 across CpGs within altered regions persisted at 1 y of age. No significant mediation effects were identified. Sex-stratified analyses identified postnatal-specific DNAm alterations.

    DISCUSSION: Regional cord blood DNAm differences associated with prenatal NO2 persisted through at least the first year of life in CHILD participants. Some differences may represent sex-specific alterations, but replication in larger cohorts is needed. The early postnatal period remained a sensitive window to DNAm perturbations. https://doi.org/10.1289/EHP13034.

    Matched MeSH terms: DNA Methylation*
  2. Dietary Plant Metabolites Induced Epigenetic Modification as a Novel Strategy for the Management of Prostate Cancer
    Singh V, Shirbhate E, Kore R, Mishra A, Johariya V, Veerasamy R, et al.
    Mini Rev Med Chem, 2024;24(15):1409-1426.
    PMID: 38385496 DOI: 10.2174/0113895575283895240207065454
    Prostate cancer is a widespread malignancy among men, with a substantial global impact on morbidity and mortality. Despite advances in conventional therapies, the need for innovative and less toxic treatments remains a priority. Emerging evidence suggests that dietary plant metabolites possess epigenetic-modifying properties, making them attractive candidates for prostate cancer treatment. The present work reviews the epigenetic effects of dietary plant metabolites in the context of prostate cancer therapy. We first outline the key epigenetic mechanisms involved in prostate cancer pathogenesis, including histone modifications, DNA methylation, and miRNA or Long Noncoding RNA (lncRNA) dysregulation. Next, we delve into the vast array of dietary plant metabolites that have demonstrated promising anti-cancer effects through epigenetic regulation. Resveratrol, minerals, isothiocyanates, curcumin, tea polyphenols, soy isoflavones and phytoestrogens, garlic compounds, anthocyanins, lycopene, and indoles are among the most extensively studied compounds. These plant-derived bioactive compounds have been shown to influence DNA methylation patterns, histone modifications, and microRNA expression, thereby altering the gene expression allied with prostate cancer progression, cell proliferation, and apoptosis. We also explore preclinical and clinical studies investigating the efficacy of dietary plant metabolites as standalone treatments or in combination with traditional treatments for people with prostate cancer. The present work highlights the potential of dietary plant metabolites as epigenetic modulators to treat prostate cancer. Continued research in this field may pave the way for personalized and precision medicine approaches, moving us closer to the goal of improved prostate cancer management.
    Matched MeSH terms: DNA Methylation/drug effects
  3. Environmental DNA metabarcoding of freshwater fish in Malaysian tropical rivers using short-read nanopore sequencing as a potential biomonitoring tool
    Munian K, Ramli FF, Othman N, Mahyudin NAA, Sariyati NH, Abdullah-Fauzi NAF, et al.
    Mol Ecol Resour, 2024 May;24(4):e13936.
    PMID: 38419264 DOI: 10.1111/1755-0998.13936
    The approach of combining cost-effective nanopore sequencing and emerging environmental DNA (eDNA) metabarcoding could prove to be a promising tool for biodiversity documentation, especially in Malaysia. Given the substantial funding constraints in recent years, especially in relation to the country's biodiversity, many researchers have been limited to conduct restricted research without extended monitoring periods, potentially hindering comprehensive surveys and could compromise the conservation efforts. Therefore, the present study aimed to evaluate the application of eDNA metabarcoding on freshwater fish using short reads generated through nanopore sequencing. This assessment focused on species detection in three selected rivers within the Endau Rompin Landscape in Malaysia. Additionally, the study compared levels of species detection between eDNA metabarcoding and conventional sampling methods, examined the effectiveness of primer choice, and applied both metabarcoding and shotgun sequencing to the eDNA approach. We successfully identified a total of 22 and 71 species with an identification threshold of >97% and >90%, respectively, through the MinION platform. The eDNA metabarcoding approach detected over 13% more freshwater fish species than when the conventional method was used. Notably, the distinction in freshwater fish detection between eDNA primers for 12S rRNA and cytochrome oxidase I was insignificant. The cost for eDNA metabarcoding proved to be more effective compared to conventional sampling with cost reduction at 33.4%. With favourable cost-effectiveness and increased species detection, eDNA metabarcoding could complement existing methods, enhance holistic diversity documentation for targeted habitats and facilitate effective conservation planning.
    Matched MeSH terms: DNA Barcoding, Taxonomic/methods
  4. Preclinical Development of a Novel Epitope-based DNA Vaccine Candidate against SARS-CoV-2 and Evaluation of Immunogenicity in BALB/c Mice
    Khalid K, Lim HX, Anwar A, Tan SH, Hwang JS, Ong SK, et al.
    AAPS PharmSciTech, 2024 Mar 12;25(3):60.
    PMID: 38472523 DOI: 10.1208/s12249-024-02778-x
    The protective efficacies of current licensed vaccines against COVID-19 have significantly reduced as a result of SARS-CoV-2 variants of concern (VOCs) which carried multiple mutations in the Spike (S) protein. Considering that these vaccines were developed based on the S protein of the original SARS-CoV-2 Wuhan strain, we designed a recombinant plasmid DNA vaccine based on highly conserved and immunogenic B and T cell epitopes against SARS-CoV-2 Wuhan strain and the Omicron VOC. Literature mining and bioinformatics were used to identify 6 immunogenic peptides from conserved regions of the SARS-CoV-2 S and membrane (M) proteins. Nucleotide sequences encoding these peptides representing highly conserved B and T cell epitopes were cloned into a pVAX1 vector to form the pVAX1/S2-6EHGFP recombinant DNA plasmid vaccine. The DNA vaccine was intranasally or intramuscularly administered to BALB/c mice and evaluations of humoral and cellular immune responses were performed. The intramuscular administration of pVAX1/S2-6EHGFP was associated with a significantly higher percentage of CD8+ T cells expressing IFN-γ when compared with the empty vector and PBS controls. Intramuscular or intranasal administrations of pVAX1/S2-6EHGFP resulted in robust IgG antibody responses. Sera from mice intramuscularly immunized with pVAX1/S2-6EHGFP were found to elicit neutralizing antibodies capable of SARS-CoV-2 Omicron variant with the ACE2 cell surface receptor. This study demonstrated that the DNA vaccine construct encoding highly conserved immunogenic B and T cell epitopes was capable of eliciting potent humoral and cellular immune responses in mice.
    Matched MeSH terms: Vaccines, DNA*
  5. Construction of 13-locus X-STR multiplex PCR system that reinforces Argus X-12 kit discrimination capacity: Application to the Malay population
    Minaguchi K, Samejima M, Nambiar P, Kaneko Y, Ochiai E, Kakimoto Y, et al.
    Leg Med (Tokyo), 2024 Sep;70:102463.
    PMID: 38823287 DOI: 10.1016/j.legalmed.2024.102463
    Closely linked groups of markers on the X chromosome are very useful for testing complex kinship relationships involving X-STR transmission. The Argus X-12 kit, a unique commercially available kit, can obtain haplotypes of 4 linkage groups (LGs) consisting of 3 markers. Although many population data have been reported for forensic purposes, differences in discrimination ability exist between LG1 and LG2, 3, and 4 in East Asian populations, and the data of this kit would become more useful if the discrimination ability of the latter groups were increased. Therefore, for matches found using this kit for some linkage group data, then to increase the identification ability, we additionally introduced 13 X-STR loci and established a method allowing comparison using data from 25 loci. The 13X-STRs add two locus data to each of LG2, 3, and 4, and also add two closely linked group (CLG) data between LG2 and 3 and LG3 and 4 in one multiplex PCR. Assessment of this method for a Malay population for which data by Argus X-12 had already been reported showed that the frequencies of distinct haplotypes in LG2, 3, and 4 were increased by 33.0-42.6 %, and frequencies of unique haplotypes increased by 45.4-59.2 %. The respective haplotype diversity values of the additional 3-locus and 4-locus CLGs were 0.9838 and 0.9939, which helps to improve discriminatory power and to predict recombination locations on the X chromosome. Although we have been testing these loci with Japanese subjects, this system would also be useful for the Malay population.
    Matched MeSH terms: DNA Fingerprinting/methods
  6. Fulltext Epigenetic Biomarkers and the Wnt/β-Catenin Pathway in Opisthorchis viverrini-associated Cholangiocarcinoma: A Scoping Review on Therapeutic Opportunities
    Kafle A, Suttiprapa S, Muhammad M, Tenorio JCB, Mahato RK, Sahimin N, et al.
    PLoS Negl Trop Dis, 2024 Sep;18(9):e0012477.
    PMID: 39236081 DOI: 10.1371/journal.pntd.0012477
    BACKGROUND: Epigenetic modifications, such as DNA methylation and histone modifications, are pivotal in regulating gene expression pathways related to inflammation and cancer. While there is substantial research on epigenetic markers in cholangiocarcinoma (CCA), Opisthorchis viverrini-induced cholangiocarcinoma (Ov-CCA) is overlooked as a neglected tropical disease (NTD) with limited representation in the literature. Considering the distinct etiological agent, pathogenic mechanisms, and pathological manifestations, epigenetic research plays a pivotal role in uncovering markers and potential targets related to the cancer-promoting and morbidity-inducing liver fluke parasite prevalent in the Great Mekong Subregion (GMS). Emerging studies highlight a predominant hypermethylation phenotype in Opisthorchis viverrini (O. viverrini) tumor tissues, underscoring the significance of abnormal DNA methylation and histone modifications in genes and their promoters as reliable targets for Ov-CCA.

    PRINCIPAL FINDINGS: Relevant published literature was identified by searching major electronic databases using targeted search queries. This process retrieved a total of 81 peer-reviewed research articles deemed eligible for inclusion, as they partially or fully met the pre-defined selection criteria. These eligible articles underwent a qualitative synthesis and were included in the scoping review. Within these, 11 studies specifically explored Ov-CCA tissues to investigate potential epigenetic biomarkers and therapeutic targets. This subset of 11 articles provided a foundation for exploring the applications of epigenetics-based therapies and biomarkers for Ov-CCA. These articles delved into various epigenetic modifications, including DNA methylation and histone modifications, and examined genes with aberrant epigenetic changes linked to deregulated signalling pathways in Ov-CCA progression.

    CONCLUSIONS: This review identified epigenetic changes and Wnt/β-catenin pathway deregulation as key drivers in Ov-CCA pathogenesis. Promoter hypermethylation of specific genes suggests potential diagnostic biomarkers and dysregulation of Wnt/β-catenin-modulating genes contributes to pathway activation in Ov-CCA progression. Reversible epigenetic changes offer opportunities for dynamic disease monitoring and targeted interventions. Therefore, this study underscores the importance of these epigenetic modifications in Ov-CCA development, suggesting novel therapeutic targets within disrupted signalling networks. However, additional validation is crucial for translating these novel insights into clinically applicable strategies, enhancing personalised Ov-CCA management approaches.

    Matched MeSH terms: DNA Methylation*
  7. Fulltext Long-read sequencing and genome assembly of natural history collection samples and challenging specimens
    Bein B, Chrysostomakis I, Arantes LS, Brown T, Gerheim C, Schell T, et al.
    Genome Biol, 2025 Feb 10;26(1):25.
    PMID: 39930463 DOI: 10.1186/s13059-025-03487-9
    Museum collections harbor millions of samples, largely unutilized for long-read sequencing. Here, we use ethanol-preserved samples containing kilobase-sized DNA to show that amplification-free protocols can yield contiguous genome assemblies. Additionally, using a modified amplification-based protocol, employing an alternative polymerase to overcome PCR bias, we assemble the 3.1 Gb maned sloth genome, surpassing the previous 500 Mb protocol size limit. Our protocol also improves assemblies of other difficult-to-sequence molluscs and arthropods, including millimeter-sized organisms. By highlighting collections as valuable sample resources and facilitating genome assembly of tiny and challenging organisms, our study advances efforts to obtain reference genomes of all eukaryotes.
    Matched MeSH terms: Sequence Analysis, DNA/methods
  8. Fulltext Genetic characterization and phylogenetic analysis of common house crows (Corvus splendens)
    Khan MA, Latif M, Mansha M, Hussain T, Bin Jardan YA, Metouekel A, et al.
    Sci Rep, 2025 Feb 10;15(1):4871.
    PMID: 39929864 DOI: 10.1038/s41598-025-85207-8
    The Common House Crow (Corvus splendens) exhibits remarkable ecological adaptability, enabling its rapid expansion across continents. However, despite its wide distribution, there is a need for genetic studies to clarify its evolutionary history and population structure. This research employs DNA barcoding, focusing on the mitochondrial gene cytochrome oxidase subunit I (Cox1), which is effective for species identification and phylogenetic analysis. Blood samples were collected from 70 C. splendens specimens across seven cities in Punjab, Pakistan: Lahore, Kasur, Sialkot, Narowal, Pakpattan, Gujranwala, and Bahawalpur. Genomic DNA extraction was performed, and a partial sequence of the COX1 gene was amplified using PCR techniques. Sequencing of the Cox1 marker from 10 randomly selected specimens revealed nine distinct genetic variants. Interspecific analysis positioned our C. splendens sequences alongside various Corvus species available in GenBank, while intraspecific analysis identified a total of 15 genetic variants. These variants showed nucleotide identity rates ranging from 98.7 to 99.8%, with genetic distances between 0.002 and 0.013. The analysis indicated that the C. splendens group consists of a single heterogeneous clade with variants from multiple countries, including Pakistan, Tanzania, Nepal, South Africa, Malaysia, Sri Lanka, Bangladesh, Kenya, Australia, and Singapore. This study significantly enhances our understanding of genetic diversity and evolutionary relationships within C. splendens populations, highlighting the necessity of genetic research to inform conservation strategies. Further research employing advanced molecular techniques and broader geographic sampling is essential to assess the genetic diversity and population dynamics of this adaptable species.
    Matched MeSH terms: DNA Barcoding, Taxonomic/methods
  9. E-Cigarette effects on oral health: A molecular perspective
    Ganapathy V, Jaganathan R, Chinnaiyan M, Chengizkhan G, Sadhasivam B, Manyanga J, et al.
    Food Chem Toxicol, 2025 Feb;196:115216.
    PMID: 39736445 DOI: 10.1016/j.fct.2024.115216
    Electronic cigarettes (e-cigarettes) have emerged as a potential alternative to traditional smoking and may aid in tobacco harm reduction and smoking cessation. E-cigarette use has notably increased, especially among young non-tobacco users, raising concerns due to the unknown long-term health effects. The oral cavity is the first and one of the most crucial anatomical sites for the deposition of e-cigarette aerosols. E-cigarette aerosols contain nicotine, flavors, volatile organic compounds, heavy metals, carcinogens, and other hazardous substances. These aerosols impact the oral cavity, disrupting host-microbial interactions and triggering gingivitis and systemic diseases. Furthermore, oral inflammation and periodontitis can be caused by proinflammatory cytokines induced by e-cigarette aerosols. The toxic components of e-cigarette aerosols increase the cellular reactive oxygen species (ROS) levels, reduce antioxidant capacity, increase DNA damage, and disrupt repair processes, which may further contribute to harmful effects on oral epithelum, leading to inflammatory and pre-malignant oral epithelial lesions. In this review, we analyze the toxicological properties of compounds in e-cigarette aerosols, exploring their cytotoxic, genotoxic, and inflammatory effects on oral health and delving into the underlying molecular mechanisms. Further research is essential to understand the impact of e-cigarettes on oral health and make informed regulatory decisions based on reliable scientific evidence.
    Matched MeSH terms: DNA Damage/drug effects
  10. Chiari malformation type 1 with combined nuclear PAX1 and DKK1 genes and mitochondrial D-loop variants: a case report
    Rosdi SNM, Omar S, Ghazali MM, Ghani ARI, Yusoff AAM
    Croat Med J, 2025 Feb 28;66(1):56-61.
    PMID: 40047162
    Chiari malformation type 1 (CM 1) is a rare and complex neurological condition. This congenital condition affects the lower posterior fossa, where the brain connects to the spinal cord. Although the exact cause of CM 1 remains unclear, genetic predisposition plays a considerable role in structural defects of the cerebellum. Here, we report on a 15-year-old female patient with CM 1 who exhibited both nuclear and mitochondrial genetic variants, a combination that has not been previously described. We identified a silent mutation in exon 2 (c. 556 G>A, p. Lys185=) of PAX1 and a DKK1 variant in intron 3 (548-3 t>C) in the nuclear DNA. We also screened the D-loop region of mitochondrial DNA as it exhibits a higher susceptibility to mutations than other mitochondrial DNA regions. Several hotspot variants were revealed, including those in positions 303-309 and 16519 (t>C), as well as some variants that had not been documented in MITOMAP. Our findings highlight the potential role of genetic alterations in D-loop in CM 1.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  11. Detection of Leptospira in environmental samples of wet markets and paddy fields in Penang, Malaysia
    Ling BL, Tay ZE, Philip N
    Trop Biomed, 2025 Mar 01;42(1):51-57.
    PMID: 40163404 DOI: 10.47665/tb.42.1.009
    Leptospirosis, caused by the Leptospira spp., is endemic in humid subtropical and tropical climates. Several environmental settings can harbour the survival of Leptospira; hence, continuous surveillance of the high-risk areas is critical. This study was conducted to detect the presence of Leptospira in wet markets and paddy fields in Penang, Malaysia. A total of 62 soil and water samples were collected aseptically from three wet markets and two paddy fields. The samples were cultured twice on the sampling day and after two weeks of storage in the dark at ambient temperature. All environmental samples and positive cultures were subjected to deoxyribonucleic acid (DNA) extraction and polymerase chain reaction (PCR) targeting 16S rRNA, lipL32 and rrs genes. 16S rRNA-positive samples were further sent for sequencing. Of 62 samples, 21 (21/62, 33.9%) tested positive via culture and PCR. Wet markets significantly had a higher detection rate of leptospires (29%) than paddy fields (4.8%). Four Leptospira species (L. selangorensis, L. dzoumogneensis, L. mtsangambouensis, and L. meyeri) were identified in wet markets and three (L. meyeri, L. wolffii, and L. kmetyi) in paddy fields. Storing the environmental samples for two weeks before isolation yielded a higher positivity (11/14) than culturing samples on the sampling day (6/14). The presence of Leptospira in the environment of wet markets and paddy fields in Penang although primarily intermediate and saprophyte indicates the crucial need to implement preventive measures to prevent the possibility of leptospirosis infection among the workers.
    Matched MeSH terms: DNA, Bacterial/genetics
  12. Fulltext Epigenetic changes driven by environmental pollutants in lung carcinogenesis: a comprehensive review
    Zhang A, Luo X, Li Y, Yan L, Lai X, Yang Q, et al.
    Front Public Health, 2024;12:1420933.
    PMID: 39440184 DOI: 10.3389/fpubh.2024.1420933
    Lung cancer remains the leading cause of cancer-related mortality globally, with environmental pollutants identified as significant risk factors, especially for nonsmokers. The intersection of these pollutants with epigenetic mechanisms has emerged as a critical area of interest for understanding the etiology and progression of lung cancer. Epigenetic changes, including DNA methylation, histone modifications, and non-coding RNAs, can induce alterations in gene expression without affecting the DNA sequence and are influenced by environmental factors, contributing to the transformation of normal cells into malignant cells. This review assessed the literature on the influence of environmental pollutants on lung cancer epigenetics. A comprehensive search across databases such as PubMed, Web of Science, Cochrane Library, and Embase yielded 3,254 publications, with 22 high-quality papers included for in-depth analysis. These studies demonstrated the role of epigenetic markers, such as DNA methylation patterns of genes like F2RL3 and AHRR and alterations in the miRNA expression profiles, as potential biomarkers for lung cancer diagnosis and treatment. The review highlights the need to expand research beyond homogenous adult male groups typically found in high-risk occupational environments to broader population demographics. Such diversification can reduce biases and enhance the relevance of findings to various clinical contexts, fostering the development of personalized preventive and therapeutic measures. In conclusion, our findings underscore the potential of innovative epigenetic therapies, such as DNA demethylating drugs and histone modification agents, to counter environmental toxins' carcinogenic effects. The growing interest in miRNA therapies and studies aiming to correct aberrant methylation patterns indicate significant strides toward better lung cancer management and a healthier future for global communities.
    Matched MeSH terms: DNA Methylation*
  13. Epidemiology of rumen fluke infection in selected buffalo farms in perak, malaysia: prevalence, molecular species identification, and associated risk factors
    Tookhy NA, Isa NM, Rahaman YA, Ahmad NI, Sharma RSK, Idris LH, et al.
    Parasitol Res, 2024 Apr 30;123(5):199.
    PMID: 38687367 DOI: 10.1007/s00436-024-08219-9
    Rumen flukes cause heavy economic losses in the ruminant industry worldwide, especially in tropical and subtropical countries. This study estimated the prevalence of rumen flukes in buffaloes, identified the species diversity, and determined risk factors associated with rumen fluke prevalence in Perak, Peninsular Malaysia. A cross-sectional study was conducted, and 321 faecal samples were collected from six buffalo farms. A structured questionnaire was developed, and farmers were interviewed to obtain information regarding risk factors associated with rumen fluke infection. The faecal samples were examined using sedimentation and Flukefinder® techniques. Genomic DNA was extracted from the fluke eggs recovered using the Flukefinder® method, and the internal transcribed spacer 2 (ITS2) fragment was amplified and sequenced to facilitate species identification. The results showed that the overall prevalence of rumen fluke across the sampled farms was 40.2% (129/321). Three rumen fluke species were identified, namely, Fischoederius elongatus, F. cobboldi, and Orthocoelium streptocoelium. Several management factors had a significant association (P 
    Matched MeSH terms: DNA, Helminth/genetics
  14. Fulltext Molecular diagnosis of 405 individuals with autism spectrum disorder
    Miyake N, Tsurusaki Y, Fukai R, Kushima I, Okamoto N, Ohashi K, et al.
    Eur J Hum Genet, 2024 Dec;32(12):1551-1558.
    PMID: 36973392 DOI: 10.1038/s41431-023-01335-7
    Autism spectrum disorder (ASD) is caused by combined genetic and environmental factors. Genetic heritability in ASD is estimated as 60-90%, and genetic investigations have revealed many monogenic factors. We analyzed 405 patients with ASD using family-based exome sequencing to detect disease-causing single-nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variations (CNVs) for molecular diagnoses. All candidate variants were validated by Sanger sequencing or quantitative polymerase chain reaction and were evaluated using the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines for molecular diagnosis. We identified 55 disease-causing SNVs/indels in 53 affected individuals and 13 disease-causing CNVs in 13 affected individuals, achieving a molecular diagnosis in 66 of 405 affected individuals (16.3%). Among the 55 disease-causing SNVs/indels, 51 occurred de novo, 2 were compound heterozygous (in one patient), and 2 were X-linked hemizygous variants inherited from unaffected mothers. The molecular diagnosis rate in females was significantly higher than that in males. We analyzed affected sibling cases of 24 quads and 2 quintets, but only one pair of siblings shared an identical pathogenic variant. Notably, there was a higher molecular diagnostic rate in simplex cases than in multiplex families. Our simulation indicated that the diagnostic yield is increasing by 0.63% (range 0-2.5%) per year. Based on our simple simulation, diagnostic yield is improving over time. Thus, periodical reevaluation of ES data should be strongly encouraged in undiagnosed ASD patients.
    Matched MeSH terms: DNA Copy Number Variations*
  15. Next generation sequencing yields the complete mitochondrial genome of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae)
    Shen KN, Chang CW, Loh KH, Chen CH, Hsiao CD
    Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4118-4119.
    PMID: 25600747
    In this study, the complete mitogenome sequence of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae) has been sequenced by next-generation sequencing method. The length of the assembled mitogenome is 16,615 bp, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Clarion angelfish is 28.3% for A, 29.3% for C, 16.5% for G, 25.9% for T and show 85% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Clarion angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.
    Matched MeSH terms: DNA, Mitochondrial/genetics; Sequence Analysis, DNA/methods
  16. Fulltext Genetic diversity of Haemonchus contortus isolated from sympatric wild blue sheep (Pseudois nayaur) and sheep in Helan Mountains, China
    Shen DD, Wang JF, Zhang DY, Peng ZW, Yang TY, Wang ZD, et al.
    Parasit Vectors, 2017 Sep 19;10(1):437.
    PMID: 28927469 DOI: 10.1186/s13071-017-2377-0
    BACKGROUND: Haemonchus contortus is known among parasitic nematodes as one of the major veterinary pathogens of small ruminants and results in great economic losses worldwide. Human activities, such as the sympatric grazing of wild with domestic animals, may place susceptible wildlife hosts at risk of increased prevalence and infection intensity with this common small ruminant parasite. Studies on phylogenetic factors of H. contortus should assist in defining the amount of the impact of anthropogenic factors on the extent of sharing of agents such as this nematode between domestic animals and wildlife.

    METHODS: H. contortus specimens (n = 57) were isolated from wild blue sheep (Pseudois nayaur) inhabiting Helan Mountains (HM), China and additional H. contortus specimens (n = 20) were isolated from domestic sheep that were grazed near the natural habitat of the blue sheep. Complete ITS2 (second internal transcribed spacer) sequences and partial sequences of the nad4 (nicotinamide dehydrogenase subunit 4 gene) gene were amplified to determine the sequence variations and population genetic diversities between these two populations. Also, 142 nad4 haplotype sequences of H. contortus from seven other geographical regions of China were retrieved from database to further examine the H. contortus population structure.

    RESULTS: Sequence analysis revealed 10 genotypes (ITS2) and 73 haplotypes (nad4) among the 77 specimens, with nucleotide diversities of 0.007 and 0.021, respectively, similar to previous studies in other countries, such as Pakistan, Malaysia and Yemen. Phylogenetic analyses (BI, MP, NJ) of nad4 sequences showed that there were no noticeable boundaries among H. contortus populations from different geographical origin and population genetic analyses revealed that most of the variation (94.21%) occurred within H. contortus populations. All phylogenetic analyses indicated that there was little genetic differentiation but a high degree of gene flow among the H. contortus populations among wild blue sheep and domestic ruminants in China.

    CONCLUSIONS: The current work is the first genetic characterization of H. contortus isolated from wild blue sheep in the Helan Mountains region. The results revealed a low genetic differentiation and high degree of gene flow between the H. contortus populations from sympatric wild blue sheep and domestic sheep, indicating regular cross-infection between the sympatrically reared ruminants.

    Matched MeSH terms: Sequence Analysis, DNA; DNA, Helminth/genetics*; DNA, Ribosomal Spacer
  17. Fulltext Genome-wide mosaicism in divergence between zoonotic malaria parasite subpopulations with separate sympatric transmission cycles
    Divis PCS, Duffy CW, Kadir KA, Singh B, Conway DJ
    Mol Ecol, 2018 02;27(4):860-870.
    PMID: 29292549 DOI: 10.1111/mec.14477
    Plasmodium knowlesi is a significant cause of human malaria transmitted as a zoonosis from macaque reservoir hosts in South-East Asia. Microsatellite genotyping has indicated that human infections in Malaysian Borneo are an admixture of two highly divergent sympatric parasite subpopulations that are, respectively, associated with long-tailed macaques (Cluster 1) and pig-tailed macaques (Cluster 2). Whole-genome sequences of clinical isolates subsequently confirmed the separate clusters, although fewer of the less common Cluster 2 type were sequenced. Here, to analyse population structure and genomic divergence in subpopulation samples of comparable depth, genome sequences were generated from 21 new clinical infections identified as Cluster 2 by microsatellite analysis, yielding a cumulative sample size for this subpopulation similar to that for Cluster 1. Profound heterogeneity in the level of intercluster divergence was distributed across the genome, with long contiguous chromosomal blocks having high or low divergence. Different mitochondrial genome clades were associated with the two major subpopulations, but limited exchange of haplotypes from one to the other was evident, as was also the case for the maternally inherited apicoplast genome. These findings indicate deep divergence of the two sympatric P. knowlesi subpopulations, with introgression likely to have occurred recently. There is no evidence yet of specific adaptation at any introgressed locus, but the recombinant mosaic types offer enhanced diversity on which selection may operate in a currently changing landscape and human environment. Loci responsible for maintaining genetic isolation of the sympatric subpopulations need to be identified in the chromosomal regions showing fixed differences.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Protozoan/genetics
  18. Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy
    Poli A, Romano I, Mastascusa V, Buono L, Orlando P, Nicolaus B, et al.
    Antonie Van Leeuwenhoek, 2018 Jul;111(7):1105-1115.
    PMID: 29299771 DOI: 10.1007/s10482-017-1013-5
    Strain Corallo1T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1T. A draft genome sequence of strain Corallo1T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1T are C16:1, n-C16:0 and C18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1T (= DSM 27495T = CIP 110630T).
    Matched MeSH terms: DNA, Bacterial/genetics; DNA, Ribosomal/genetics
  19. Fulltext Optical DNA Biosensor Based on Square-Planar Ethyl Piperidine Substituted Nickel(II) Salphen Complex for Dengue Virus Detection
    Ariffin EY, Tan LL, Abd Karim NH, Yook Heng L
    Sensors (Basel), 2018 Apr 12;18(4).
    PMID: 29649118 DOI: 10.3390/s18041173
    A sensitive and selective optical DNA biosensor was developed for dengue virus detection based on novel square-planar piperidine side chain-functionalized N,N'-bis-4-(hydroxysalicylidene)-phenylenediamine-nickel(II), which was able to intercalate via nucleobase stacking within DNA and be functionalized as an optical DNA hybridization marker. 3-Aminopropyltriethoxysilane (APTS)-modified porous silica nanospheres (PSiNs), was synthesized with a facile mini-emulsion method to act as a high capacity DNA carrier matrix. The Schiff base salphen complexes-labelled probe to target nucleic acid on the PSiNs renders a colour change of the DNA biosensor to a yellow background colour, which could be quantified via a reflectance transduction method. The reflectometric DNA biosensor demonstrated a wide linear response range to target DNA over the concentration range of 1.0 × 10-16-1.0 × 10-10 M (R² = 0.9879) with an ultralow limit of detection (LOD) at 0.2 aM. The optical DNA biosensor response was stable and maintainable at 92.8% of its initial response for up to seven days of storage duration with a response time of 90 min. The reflectance DNA biosensor obtained promising recovery values of close to 100% for the detection of spiked synthetic dengue virus serotypes 2 (DENV-2) DNA concentration in non-invasive human samples, indicating the high accuracy of the proposed DNA analytical method for early diagnosis of all potential infectious diseases or pathological genotypes.
    Matched MeSH terms: DNA
  20. Fulltext Epigenetic changes of DRD2 gene in Pathogenesis of Schizophrenia
    Nour El Huda Abd Rahim, Mohd Nabil Fikri Rahim, Norsidah Ku Zaifah, Hanisah Mohd Noor, Kartini Abdullah, Norlelawati A. Talib
    International Medical Journal Malaysia, 2017;16(11):3-3.
    MyJurnal
    The dopamine hypothesis has earlier dominated the theories for the
    development of schizophrenia based on the early pharmacologic evidence. The
    antipsychotic drugs, among others, is thought to interfere with the function of the
    dopamine D2 receptor (DRD2) resulting in clinical improvement. Accumulating evidence
    suggest the role of epigenetic mechanisms in the pathophysiology of schizophrenia.
    Despite this, specific evidence linking the DRD2 DNA methylation with schizophrenia is
    insufficient mainly due to the poor accessibility and limited brain samples. Of late, new
    data has suggested the global impact of DNA methylation in the development of
    schizophrenia, thus methylation in the peripheral blood could infer changes in the brain.
    The aim of this study was to assess the DRD2 DNA methylation in the peripheral blood of
    schizophrenia.
    Matched MeSH terms: DNA Methylation
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