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  1. Fulltext Experimental and theoretical investigation of sensing parameters in carbon nanotube-based DNA sensor
    Nouri M, Meshginqalam B, Sahihazar MM, Sheydaie Pour Dizaji R, Ahmadi MT, Ismail R
    IET Nanobiotechnol, 2018 Dec;12(8):1125-1129.
    PMID: 30964025 DOI: 10.1049/iet-nbt.2018.5068
    Nowadays, sensitive biosensors with high selectivity, lower costs and short response time are required for detection of DNA. The most preferred materials in DNA sensor designing are nanomaterials such as carbon and Au nanoparticles, because of their very high surface area and biocompatibility which lead to performance and sensitivity improvements in DNA sensors. Carbon nanomaterials such as carbon nanotubes (CNTs) can be considered as a suitable DNA sensor platform due to their high surface-to-volume ratio, favourable electronic properties and fast electron transfer rate. Therefore, in this study, the CNTs which are synthesised by pulsed AC arc discharge method on a high-density polyethylene substrate are used as conducting channels in a chemiresistor for the electrochemical detection of double stranded DNA. Moreover, the response of the proposed sensor is investigated experimentally and analytically in different temperatures, which confirm good agreement between the presented model and experimental data.
    Matched MeSH terms: DNA/analysis*
  2. 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*
  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. Fulltext Genetic diversity and phylogeographic patterns of the peacock jewel-damselfly, Rhinocypha fenestrella (Rambur, 1842)
    Noorhidayah M, Azrizal-Wahid N, Low VL, Yusoff NR
    PLoS One, 2024;19(4):e0301392.
    PMID: 38578719 DOI: 10.1371/journal.pone.0301392
    Despite is known to have widespread distribution and the most active species of the family Chlorocyphidae, the molecular data of Rhinocypha fenestrella (Rambur, 1842) are relatively scarce. The present study is the first that examined the genetic diversity and phylogeographic pattern of the peacock jewel-damselfly R. fenestrella by sequencing the cytochrome C oxidase I (cox1) and 16S rRNA gene regions from 147 individuals representing eight populations in Malaysia. A total of 26 and 10 unique haplotypes were revealed by the cox1 and 16S rRNA genes, respectively, and 32 haplotypes were recovered by the concatenated sequences of cox1+16S. Analyses indicated that haplotype AB2 was the most frequent and the most widespread haplotype in Malaysia while haplotype AB1 was suggested as the common ancestor haplotype of the R. fenestrella that may arose from the Negeri Sembilan as discovered from cox1+16S haplotype network analysis. Overall haplotype and nucleotide diversities of the concatenated sequences were Hd = 0.8937 and Pi = 0.0028, respectively, with great genetic differentiation (FST = 0.6387) and low gene flow (Nm = 0.14). Population from Pahang presented the highest genetic diversity (Hd = 0.8889, Pi = 0.0022, Nh = 9), whereas Kedah population demonstrated the lowest diversity (Hd = 0.2842, Pi = 0.0003, Nh = 4). The concatenated sequences of cox1+16S showed genetic divergence ranging from 0.09% to 0.97%, whereas the genetic divergence for cox1 and 16S rRNA genes were 0.16% to 1.63% and 0.01% to 0.75% respectively. This study provides for the first-time insights on the intraspecific genetic diversity, phylogeographic pattern and ancestral haplotype of Rhinocypha fenestrella. The understanding of molecular data especially phylogeographic pattern can enhance the knowledge about insect origin, their diversity, and capability to disperse in particular environments.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  5. In vitro and in vivo evaluation of the antimicrobial, antioxidant, cytotoxic, hemolytic activities and in silico POM/DFT/DNA-binding and pharmacokinetic analyses of new sulfonamide bearing thiazolidin-4-ones
    Hassan SA, Aziz DM, Abdullah MN, Bhat AR, Dongre RS, Hadda TB, et al.
    J Biomol Struct Dyn, 2024 Apr;42(7):3747-3763.
    PMID: 37402503 DOI: 10.1080/07391102.2023.2226713
    In this work, Schiff bases and Thiazolidin-4-ones, were synthesized using Sonication and Microwave techniques, respectively. The Schiff base derivatives (3a-b) were synthesized via the reaction of Sulfathiazole (1) with benzaldehyde derivatives (2a-b), followed by the synthesis of 4-thiazoledinone (4a-b) derivatives by cyclizing the synthesized Schiff bases through thioglycholic acid. All the synthesized compounds were characterized by spectroscopic techniques such as FT IR, NMR and HRMS. The synthesized compounds were tested for their in vitro antimicrobial and antioxidant and in vivo cytotoxicity and hemolysis ability. The synthesized compounds displayed better antimicrobial and antioxidant activity and low toxicity in comparison to reference drugs and negative controls, respectively. The hemolysis test revealed the compounds exhibit lower hemolytic effects and hemolytic values are comparatively low and the safety of compounds is in comparison with standard drugs. Theoretical calculations were carried out by using the molecular operating environment (MOE) and Gaussian computing software and observations were in good agreement with the in vitro and in vivo biological activities. Petra/Osiris/Molinspiration (POM) results indicate the presence of three combined antibacterial, antiviral and antitumor pharmacophore sites. The molecular docking revealed the significant binding affinities and non-bonding interactions between the compounds and Erwinia Chrysanthemi (PDB ID: 1SHK). The molecular dynamics simulation under in silico physiological conditions revealed a stable conformation and binding pattern in a stimulating environment. HighlightsNew series of Thaiazolidin-4-one derivatives have been synthesized.Sonication and microwave techniques are used.Antimicrobial, Antioxidant, cytotoxicity, and hemolysis activities were observed for all synthesized compounds.Molecular Docking and DFT/POM analyses have been predicted.Communicated by Ramaswamy H. Sarma.
    Matched MeSH terms: DNA/chemistry
  6. Molecular epidemiology of tuberculosis in Malaysia
    Dale JW, Nor RM, Ramayah S, Tang TH, Zainuddin ZF
    J Clin Microbiol, 1999 May;37(5):1265-8.
    PMID: 10203468
    Molecular typing with IS6110 was applied to Mycobacterium tuberculosis isolates from all parts of Malaysia. The degree of clustering increased with patient age, suggesting that reactivation may contribute to clustering. Identical banding patterns were also obtained for isolates from widely separate regions. Therefore, the use of clustering as a measure of recent transmission must be treated with caution. Strains related to the Beijing family were common in Peninsular Malaysia but were less common in Sabah and Sarawak, while a distinct group of strains comprised nearly 40% of isolates from East Malaysia but such strains were rare in Peninsular Malaysia. Single-copy strains, common in South and Southeastern Asia, constituted nearly 20% of isolates from the peninsula but were virtually absent in East Malaysia. The marked geographical difference in the prevailing strains indicates not only a restricted dissemination of M. tuberculosis but also a considerable degree of stability in the banding patterns.
    Matched MeSH terms: DNA Transposable Elements*
  7. Mismatch repair genes expression defects & association with clinicopathological characteristics in colorectal carcinoma
    Kaur G, Masoud A, Raihan N, Radzi M, Khamizar W, Kam LS
    Indian J Med Res, 2011 Aug;134:186-92.
    PMID: 21911971
    DNA mismatch repair gene (MMR) abnormalities are seen in 95 per cent of hereditary nonpolyposis colorectal cancer (HNPCC) and 10-15 per cent of sporadic colorectal cancers. There are no data on MMR abnormalities in Malaysian colorectal cancer patients. This study was aimed to determine the frequency of abnormal MMR gene protein expression in colorectal carcinoma in Northern Peninsular Malaysia using immunohistochemistry.
    Matched MeSH terms: DNA-Binding Proteins/metabolism*; DNA Repair Enzymes/metabolism*; MutS DNA Mismatch-Binding Protein/metabolism; DNA Mismatch Repair/genetics*
  8. Fulltext Forensic DNA Profiling: Autosomal Short Tandem Repeat as a Prominent Marker in Crime Investigation
    Nwawuba Stanley U, Mohammed Khadija A, Bukola AT, Omusi Precious I, Ayevbuomwan Davidson E
    Malays J Med Sci, 2020 Jul;27(4):22-35.
    PMID: 32863743 DOI: 10.21315/mjms2020.27.4.3
    Short tandem repeat (STR) typing continues to be the primary workhorse in forensic DNA profiling. Therefore, the present review discusses the prominent role of STR marker in criminal justice system. All over the world, deoxyribonucleic acid (DNA) profiling provides evidence that may be used to convict criminals, as an irrefutable proof of wrongful convictions, invaluable links to the actual perpetrators of crimes, and could also deter some offenders from committing more serious offences. Clearly, DNA profiling tools have also aided forensic scientists to re-evaluate old cases that were considered closed as a result of inadequate evidence. In carrying out this review, a comprehensive electronic literature search using PubMed, ScienceDirect, Google Scholar and Google Search were used, and all works meeting the subject matter were considered, including reviews, retrospective studies, observational studies and original articles. Case reports presented here, further demonstrates the crucial role of forensic DNA profiling in mitigating and providing compelling evidence for the resolution of crimes. For case report 1, there was a 100% match between the DNA recovered from the items found in the crime scene, and the suspect's DNA sample collected via buccal swab following 15 STR loci examination. Case report 2 further highlights the indispensable contribution of DNA database in solving crime. Therefore, it has become very necessary for developing countries like Nigeria to develop a national DNA database and make policies and legislatures that will further expand and enable the practice of forensic genetics, particularly DNA profiling.
    Matched MeSH terms: DNA; DNA Fingerprinting
  9. 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
  10. Fulltext Duplex TaqMan Hydrolysis Probe-Based Molecular Assay for Simultaneous Detection and Differentiation of Burkholderia pseudomallei and Leptospira spp. DNA
    Mohd Ali MR, Lih Huey L, Foo PC, Goay YX, Ismail AS, Mustaffa KMF, et al.
    Biomed Res Int, 2019;2019:9451791.
    PMID: 31355287 DOI: 10.1155/2019/9451791
    Melioidosis and leptospirosis, caused by two different bacteria, Burkholderia pseudomallei and Leptospira spp., are potentially fatal infections that share a very similar spectrum of clinical features and cause significant mortality and morbidity in humans and livestock. Early detection is important for better clinical consequences. To our knowledge, there is no diagnostic tool available to simultaneously detect and differentiate melioidosis and leptospirosis in humans and animals. In this study, we described a duplex TaqMan probe-based qPCR for the detection of B. pseudomallei and Leptospira spp. DNA. The performance of the assay was evaluated on 20 B. pseudomallei isolates, 23 Leptospira strains, and 39 other microorganisms, as well as two sets of serially diluted reference strains. The duplex qPCR assay was able to detect 0.02 pg (~ 4 copies) Leptospira spp. DNA and 0.2 pg (~ 25.6 copies) B. pseudomallei DNA. No undesired amplification was observed in other microorganisms. In conclusion, the duplex qPCR assay was sensitive and specific for the detection of B. pseudomallei & Leptospira spp. DNA and is suitable for further analytical and clinical evaluation.
    Matched MeSH terms: DNA, Bacterial/genetics*
  11. Fulltext Impact of RNA Virus Evolution on Quasispecies Formation and Virulence
    Mandary MB, Masomian M, Poh CL
    Int J Mol Sci, 2019 Sep 19;20(18).
    PMID: 31546962 DOI: 10.3390/ijms20184657
    RNA viruses are known to replicate by low fidelity polymerases and have high mutation rates whereby the resulting virus population tends to exist as a distribution of mutants. In this review, we aim to explore how genetic events such as spontaneous mutations could alter the genomic organization of RNA viruses in such a way that they impact virus replications and plaque morphology. The phenomenon of quasispecies within a viral population is also discussed to reflect virulence and its implications for RNA viruses. An understanding of how such events occur will provide further evidence about whether there are molecular determinants for plaque morphology of RNA viruses or whether different plaque phenotypes arise due to the presence of quasispecies within a population. Ultimately this review gives an insight into whether the intrinsically high error rates due to the low fidelity of RNA polymerases is responsible for the variation in plaque morphology and diversity in virulence. This can be a useful tool in characterizing mechanisms that facilitate virus adaptation and evolution.
    Matched MeSH terms: DNA-Directed RNA Polymerases/genetics*
  12. Fulltext Nodosilinea signiensis sp. nov. (Leptolyngbyaceae, Synechococcales), a new terrestrial cyanobacterium isolated from mats collected on Signy Island, South Orkney Islands, Antarctica
    Radzi R, Muangmai N, Broady P, Wan Omar WM, Lavoue S, Convey P, et al.
    PLoS One, 2019;14(11):e0224395.
    PMID: 31682631 DOI: 10.1371/journal.pone.0224395
    Terrestrial cyanobacteria are very diverse and widely distributed in Antarctica, where they can form macroscopically visible biofilms on the surfaces of soils and rocks, and on benthic surfaces in fresh waters. We recently isolated several terrestrial cyanobacteria from soils collected on Signy Island, South Orkney Islands, Antarctica. Among them, we found a novel species of Nodosilinea, named here as Nodosilinea signiensis sp. nov. This new species is morphologically and genetically distinct from other described species. Morphological examination indicated that the new species is differentiated from others in the genus by cell size, cell shape, filament attenuation, sheath morphology and granulation. 16S rDNA phylogenetic analyses clearly confirmed that N. signiensis belongs to the genus Nodosilinea, but that it is genetically distinct from other known species of Nodosilinea. The D1-D1´ helix of the 16S-23S ITS region of the new species was also different from previously described Nodosilinea species. This is the first detailed characterization of a member of the genus Nodosilinea from Antarctica as well as being a newly described species.
    Matched MeSH terms: DNA, Bacterial/isolation & purification
  13. 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
  14. 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
  15. Development of a T7 RNA polymerase expressing cell line using lentivirus vectors for the recovery of recombinant Newcastle disease virus
    Yeong MY, Cheow PS, Abdullah S, Song AA, Lei-Rossmann J, Tan TK, et al.
    J Virol Methods, 2021 05;291:114099.
    PMID: 33592218 DOI: 10.1016/j.jviromet.2021.114099
    The development of a T7 RNA polymerase (T7 RNAP) expressing cell line i.e. BSR T7/5 cells marks an improvement of reverse genetics for the recovery of recombinant Newcastle disease virus (rNDV). BSR T7/5 is developed by transient transfection of plasmid encoding T7 RNAP gene for rNDV rescue. However, the gene expression decreases gradually over multiple passages and eventually hinders the rescue of rNDV. To address this issue, lentiviral vector was used to develop T7 RNAP-expressing HEK293-TA (HEK293-TA-Lv-T7) and SW620 (SW620-Lv-T7) cell lines, evidenced by the expression of T7 RNAP after subsequent 20 passages. rNDV was rescued successfully using HEK293-TA-Lv-T7 clones (R1D3, R1D8, R5B9) and SW620-Lv-T7 clones (R1C11, R3C5) by reverse transfection, yielding comparable virus rescue efficiency and virus titres to that of BSR T7/5. This study provides new tools for rNDV rescue and insights into cell line development and virology by reverse genetics.
    Matched MeSH terms: DNA-Directed RNA Polymerases/genetics
  16. 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*
  17. Fulltext Identification of Brucella spp. isolated from human brucellosis in Malaysia using high-resolution melt (HRM) analysis
    Mohamed Zahidi J, Bee Yong T, Hashim R, Mohd Noor A, Hamzah SH, Ahmad N
    Diagn Microbiol Infect Dis, 2015 Apr;81(4):227-33.
    PMID: 25641125 DOI: 10.1016/j.diagmicrobio.2014.12.012
    Molecular approaches have been investigated to overcome difficulties in identification and differentiation of Brucella spp. using conventional phenotypic methods. In this study, high-resolution melt (HRM) analysis was used for rapid identification and differentiation of members of Brucella genus. A total of 41 Brucella spp. isolates from human brucellosis were subjected to HRM analysis using 4 sets of primers, which identified 40 isolates as Brucella melitensis and 1 as Brucella canis. The technique utilized low DNA concentration and was highly reproducible. The assay is shown to be a useful diagnostic tool, which can rapidly differentiate Brucella up to species level.
    Matched MeSH terms: DNA, Bacterial/genetics; DNA Primers/genetics
  18. Fulltext The use of protein-DNA, chromatin immunoprecipitation, and transcriptome arrays to describe transcriptional circuits in the dehydrated male rat hypothalamus
    Qiu J, Kleineidam A, Gouraud S, Yao ST, Greenwood M, Hoe SZ, et al.
    Endocrinology, 2014 Nov;155(11):4380-90.
    PMID: 25144923 DOI: 10.1210/en.2014-1448
    The supraoptic nucleus (SON) of the hypothalamus is responsible for maintaining osmotic stability in mammals through its elaboration of the antidiuretic hormone arginine vasopressin. Upon dehydration, the SON undergoes a function-related plasticity, which includes remodeling of morphology, electrical properties, and biosynthetic activity. This process occurs alongside alterations in steady state transcript levels, which might be mediated by changes in the activity of transcription factors. In order to identify which transcription factors might be involved in changing patterns of gene expression, an Affymetrix protein-DNA array analysis was carried out. Nuclear extracts of SON from dehydrated and control male rats were analyzed for binding to the 345 consensus DNA transcription factor binding sequences of the array. Statistical analysis revealed significant changes in binding to 26 consensus elements, of which EMSA confirmed increased binding to signal transducer and activator of transcription (Stat) 1/Stat3, cellular Myelocytomatosis virus-like cellular proto-oncogene (c-Myc)-Myc-associated factor X (Max), and pre-B cell leukemia transcription factor 1 sequences after dehydration. Focusing on c-Myc and Max, we used quantitative PCR to confirm previous transcriptomic analysis that had suggested an increase in c-Myc, but not Max, mRNA levels in the SON after dehydration, and we demonstrated c-Myc- and Max-like immunoreactivities in SON arginine vasopressin-expressing cells. Finally, by comparing new data obtained from Roche-NimbleGen chromatin immunoprecipitation arrays with previously published transcriptomic data, we have identified putative c-Myc target genes whose expression changes in the SON after dehydration. These include known c-Myc targets, such as the Slc7a5 gene, which encodes the L-type amino acid transporter 1, ribosomal protein L24, histone deactylase 2, and the Rat sarcoma proto-oncogene (Ras)-related nuclear GTPase.
    Matched MeSH terms: DNA/metabolism; DNA-Binding Proteins/metabolism
  19. Fulltext Comparison of cytotoxicity and genotoxicity of 4-hydroxytamoxifen in combination with Tualang honey in MCF-7 and MCF-10A cells
    Yaacob NS, Ismail NF
    BMC Complement Altern Med, 2014;14:106.
    PMID: 24646375 DOI: 10.1186/1472-6882-14-106
    The Malaysian Tualang honey (TH) is not only cytotoxic to human breast cancer cell lines but it has recently been reported to promote the anticancer activity induced by tamoxifen in MCF-7 and MDA-MB-231 cells suggesting its potential as an adjuvant for the chemotherapeutic agent. However, tamoxifen produces adverse effects that could be due to its ability to induce cellular DNA damage. Therefore, the study is undertaken to determine the possible modulation of the activity of 4-hydroxytamoxifen (OHT), an active metabolite of tamoxifen, by TH in non-cancerous epithelial cell line, MCF-10A, in comparison with MCF-7 cells.
    Matched MeSH terms: DNA Damage*; DNA Repair/drug effects*
  20. Haplotype-habitat associations of Coptotermes gestroi (Termitoidae: Rhinotermitidae) from mitochondrial DNA genes
    Cheng S, Thinagaran D, Mohanna SZ, Noh NA
    Environ Entomol, 2014 Aug;43(4):1105-16.
    PMID: 24915136 DOI: 10.1603/EN13318
    Coptotermes gestroi (Wasmann) or the Asian subterranean termite is a serious structural pest in urban settlements in Southeast Asia that has been introduced to other parts of the world through human commerce. Although mitochondrial DNA markers were previously used to shed light on the dispersal history of the Asian subterranean termite, there were limited attempts to analyze or include populations of the termite found in the wild in Southeast Asia. In this study, we analyzed the 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase subunit 1 (cox1) genes of Asian subterranean termite colonies found in mangrove swamps, beach forests, plantations, and buildings in semi-urban and urban areas to determine the relationship between colonies found in the wild and the urban habitat, and to investigate the possibility of different ecotypes of the termite in Peninsular Malaysia. Our findings show that the 16S rRNA haplotypes recovered from this study clustered into eastern, western, and southern populations of the termite, while the cox1 haplotypes were often specific to an area or site. The 16S rRNA and cox1 genes or haplotypes showed that the most abundant haplotype occupied a wide range of environments or habitats. In addition, the cox1 tree showed evidence of historical biogeography where basal haplotypes inhabited a wide range of habitats, while apical haplotypes were restricted to mangrove swamps and beach forests. Information on the haplotype-habitat association of C. gestroi will enable the prediction of habitats that may harbor or be at risk of invasion in areas where they have been introduced.
    Matched MeSH terms: DNA, Mitochondrial/genetics; DNA, Mitochondrial/metabolism; Sequence Analysis, DNA
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