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  1. Mustafa MF, Fakurazi S, Abdullah MA, Maniam S
    Genes (Basel), 2020 02 12;11(2).
    PMID: 32059522 DOI: 10.3390/genes11020192
    Mitochondria are best known for their role in energy production, and they are the only mammalian organelles that contain their own genomes. The mitochondrial genome mutation rate is reported to be 10-17 times higher compared to nuclear genomes as a result of oxidative damage caused by reactive oxygen species during oxidative phosphorylation. Pathogenic mitochondrial DNA mutations result in mitochondrial DNA disorders, which are among the most common inherited human diseases. Interventions of mitochondrial DNA disorders involve either the transfer of viable isolated mitochondria to recipient cells or genetically modifying the mitochondrial genome to improve therapeutic outcome. This review outlines the common mitochondrial DNA disorders and the key advances in the past decade necessary to improve the current knowledge on mitochondrial disease intervention. Although it is now 31 years since the first description of patients with pathogenic mitochondrial DNA was reported, the treatment for mitochondrial disease is often inadequate and mostly palliative. Advancements in diagnostic technology improved the molecular diagnosis of previously unresolved cases, and they provide new insight into the pathogenesis and genetic changes in mitochondrial DNA diseases.
    Matched MeSH terms: DNA, Mitochondrial
  2. Yusoh NA, Leong SW, Chia SL, Harun SN, Rahman MBA, Vallis KA, et al.
    ACS Chem Biol, 2020 Feb 21;15(2):378-387.
    PMID: 31898884 DOI: 10.1021/acschembio.9b00843
    There is a need to improve and extend the use of clinically approved poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi), including for BRCA wild-type triple-negative breast cancer (TNBC). The demonstration that ruthenium(II) polypyridyl complex (RPC) metallointercalators can rapidly stall DNA replication fork progression provides the rationale for their combination alongside DNA damage response (DDR) inhibitors to achieve synergism in cancer cells. The aim of the present study was to evaluate use of the multi-intercalator [Ru(dppz)2(PIP)]2+ (dppz = dipyrido[3,2-a:2',3'-c]phenazine, PIP = (2-(phenyl)imidazo[4,5-f][1,10]phenanthroline, Ru-PIP) alongside the PARPi olaparib and NU1025. Cell proliferation and clonogenic survival assays indicated a synergistic relationship between Ru-PIP and olaparib in MDA-MB-231 TNBC and MCF7 human breast cancer cells. Strikingly, low dose Ru-PIP renders both cell lines hypersensitive to olaparib, with a >300-fold increase in olaparib potency in TNBC, the largest nongenetic PARPi enhancement effect described to date. A negligible impact on the viability of normal human fibroblasts was observed for any combination tested. Increased levels of DNA double-strand break (DSB) damage and olaparib abrogation of Ru-PIP-activated pChk1 signaling are consistent with PARPi-facilitated collapse of Ru-PIP-associated stalled replication forks. This results in enhanced G2/M cell-cycle arrest, apoptosis, and decreased cell motility for the combination treatment compared to single-agent conditions. This work establishes that an RPC metallointercalator can be combined with PARPi for potent synergy in BRCA-proficient breast cancer cells, including TNBC.
    Matched MeSH terms: DNA/drug effects; DNA Breaks, Double-Stranded/drug effects
  3. Etebari K, Filipović I, Rašić G, Devine GJ, Tsatsia H, Furlong MJ
    Virus Res, 2020 03;278:197864.
    PMID: 31945420 DOI: 10.1016/j.virusres.2020.197864
    Oryctes rhinoceros nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNV infection in O. rhinoceros from Solomon Islands and used Oxford Nanopore Technologies (ONT) long-read sequencing to determine the full length of the virus genomic sequence isolated from an individual belonging to a mitochondrial lineage (CRB-G) that was previously reported as resistant to OrNV. The complete circular genome of the virus consisted of 125,917 nucleotides, 1.698 bp shorter than the originally-described full genome sequence of Ma07 strain from Malaysia. We found 130 out of 139 previously annotated ORFs (seven contained interrupted/non-coding sequences, two were identified as duplicated versions of the existing genes), as well as a putatively inverted regions containing four genes. These results demonstrate the usefulness of a long-read sequencing technology for resolving potential structural variations when describing new virus isolates. While the Solomon Islands isolate exhibited 99.41 % nucleotide sequence identity with the originally described strain, we found several genes, including a core gene (vlf-1), that contained multiple amino acid insertions and/or deletions as putative polymorphisms of large effect. Our complete annotated genome sequence of a newly found isolate in Solomon Islands provides a valuable resource to help elucidate the mechanisms that compromise the efficacy of OrNV as a biocontrol agent against the coconut rhinoceros beetle.
    Matched MeSH terms: Sequence Analysis, DNA
  4. Sekhar Goud EVS, Kannan R, Rao UK, Joshua E, Tavaraja R, Jain Y
    J Pharm Bioallied Sci, 2019 Nov;11(Suppl 3):S523-S529.
    PMID: 31920269 DOI: 10.4103/jpbs.JPBS_260_18
    Aims and Objective: The aim of this study was to identify the presence of Helicobacter pylori in saliva of patients with and without gastritis by polymerase chain reaction (PCR) method.

    Materials and Methods: The study comprised 20 patients in Group I presenting with various symptoms of gastritis and 10 asymptomatic subjects in Group II. The intestinal endoscopy antral biopsies were collected from 20 symptomatic patients with gastroduodenal disorders. The saliva specimens were taken from all patients before endoscopy. PCR was performed using genomic DNA, isolated from the saliva and the biopsies of the patients as the template to detect the presence of the 16S ribosomal RNA gene in H. pylori.

    Results: In Group I, 10 (50%) cases of clinical gastritis were positive for H. pylori by endoscopy biopsy and 10 (50%) were negative. Of the 10 endoscopy biopsy positive cases for H. pylori, eight were PCR positive in saliva and two were negative. Of the 10 endoscopy biopsy negative cases, three were PCR positive for H. pylori in saliva and seven were negative. In Groups II, four were symptomatic for gastritis and six were negative. Of the six gastritis negative cases, three were PCR positive, four were gastritis positive, and three were PCR positive. Sensitivity and specificity of PCR were found to be 80% and 70%, respectively. The positive predictive and negative predictive values of PCR in saliva were 72.7% and 77.7%, respectively.

    Conclusion: PCR analysis of saliva may be handy in identification of H. pylori and serves as a noninvasive technique to diagnose and monitor the prognosis.

    Matched MeSH terms: DNA
  5. Omar, S., Mohd Zainudin, N.A.I., Azman, N., Jessie-Bay, J.X.
    Jurnal Veterinar Malaysia, 2019;31(1):34-37.
    MyJurnal
    This report documents a case of 5-month old intact male German Shepherd dog diagnosed with pythiosis on its left forelimb. This is the first ever reported case of pythiosis presented at the University Veterinary Teaching Hospital (UVH), Universiti Putra Malaysia and may be the first ever reported incidence in Malaysia with a complaint of a chronic non-healing wound. The case became complicated as the dog was concurrently infected with a mixed bacterial infection and the identified bacteria were resistant towards a number of antibiotics tested. The antibiotic that was determined to be sensitive was only able to act on certain bacteria and not to the others. The journey of getting to the final diagnosis was almost impossible if we had not tried different media preparation: with and without Dermasel supplement; and through molecular approach using amplification at ITS region followed by DNA sequence analysis. The unwarranted lack during the diagnosis process of this incidence has made us more aware of the presence of Pythium insidiosum in Malaysia and plan for a more strategize ways of diagnosing the suspected fungus at laboratory setting in future. The objective of this paper is to share our experience and reflection on the diagnosis of the rare incidence of pythiosis present in Malaysia.
    Matched MeSH terms: Sequence Analysis, DNA
  6. Jani J, Mustapha ZA, Ling CK, Hui ASM, Teo R, Ahmed K
    Data Brief, 2020 Dec;33:106388.
    PMID: 33102655 DOI: 10.1016/j.dib.2020.106388
    In 2019, 10 million new cases of tuberculosis have been reported worldwide. Our data reports genetic analyses of a Mycobacterium tuberculosis strain SBH321 isolated from a 31-year-old female with pulmonary tuberculosis. The genomic DNA of the strain was extracted from pure culture and subjected to sequencing using Illumina platform. M. tuberculosis strain SBH321 consists of 4,374,895 bp with G+C content of 65.59%. The comparative analysis by SNP-based phylogenetic analysis using maximum-likelihood method showed that our strain belonging to sublineage of the Ural family of Europe-America-Africa lineage (Lineage 4) and clustered with M. tuberculosis strain OFXR-4 from Taiwan. The whole genome sequence is deposited at DDBJ/ENA/GenBank under the accession WCJH00000000 (SRR10230353).
    Matched MeSH terms: DNA
  7. Jazli Aziz, Zamri Radzi, Rathna Devi Vaithilingam, Mohammad Tariqur Rahman
    MyJurnal
    Introduction: While sharing a common causal link, both rheumatoid arthritis (RA) and periodontitis (PD) manifest similar inflammatory responses. With the progression of severity, both diseases result in bone loss. Hence, Ca and Zn, as structural components of the bones, are expected to be altered in saliva and serum in PD and RA respectively. Zinc and calcium concentrations have been studied previously in patients with PD or RA, with PD patients exhibiting increased salivary Ca and decreased Zn concentrations in serum, while RA patients have been reported to express low plasma concentrations of both Zn and Ca. The aim of this study is to evaluate the saliva and serum levels of Ca and Zn in PD patients with or without RA. Methods: Serum and saliva samples were collected from 82 patients from the Faculty of Dentistry, University of Malaya and the University Malaya Medical Centre rheumatoid clinic. Patients were grouped according to their periodontal health and RA status (healthy n=21; PD n=21; RA n=21; RAPD n=19). Results: Zinc concentration in serum was significantly higher (p
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  8. Bande F, Arshad SS, Bejo MH, Omar AR, Moeini H, Khadkodaei S, et al.
    Microb Pathog, 2020 Dec;149:104560.
    PMID: 33068733 DOI: 10.1016/j.micpath.2020.104560
    Infectious Bronchitis (IB) is an economically important avian disease that considerably threatens the global poultry industry. This is partly, as a result of its negative consequences on egg production, weight gain as well as mortality rate.The disease is caused by a constantly evolving avian infectious bronchitis virus whose isolates are classified into several serotypes and genotypes that demonstrate little or no cross protection. In order to curb the menace of the disease therefore, broad based vaccines are urgently needed. The aim of this study was to develop a recombinant DNA vaccine candidate for improved protection of avian infectious bronchitis in poultry. Using bioinformatics and molecular cloning procedures, sets of monovalent and bivalent DNA vaccine constructs were developed based on the S1 glycoprotein from classical and variants IBV strains namely, M41 and CR88 respectively. The candidate vaccine was then encapsulated with a chitosan and saponin formulated nanoparticle for enhanced immunogenicity and protective capacity. RT-PCR assay and IFAT were used to confirm the transcriptional and translational expression of the encoded proteins respectively, while ELISA and Flow-cytometry were used to evaluate the immunogenicity of the candidate vaccine following immunization of various SPF chicken groups (A-F). Furthermore, histopathological changes and virus shedding were determined by quantitative realtime PCR assay and lesion scoring procedure respectively following challenge of various subgroups with respective wild-type IBV viruses. Results obtained from this study showed that, groups vaccinated with a bivalent DNA vaccine construct (pBudCR88-S1/M41-S1) had a significant increase in anti-IBV antibodies, CD3+ and CD8+ T-cells responses as compared to non-vaccinated groups. Likewise, the bivalent vaccine candidate significantly decreased the oropharyngeal and cloacal virus shedding (p < 0.05) compared to non-vaccinated control. Chickens immunized with the bivalent vaccine also exhibited milder clinical signs as well as low tracheal and kidney lesion scores following virus challenge when compared to control groups. Collectively, the present study demonstrated that bivalent DNA vaccine co-expressing dual S1 glycoprotein induced strong immune responses capable of protecting chickens against infection with both M41 and CR88 IBV strains. Moreso, it was evident that encapsulation of the vaccine with chitosan-saponin nanoparticle further enhanced immune responses and abrogates the need for multiple booster administration of vaccine. Therefore, the bivalent DNA vaccine could serve as efficient and effective alternative strategy for the control of IB in poultry.
    Matched MeSH terms: Vaccines, DNA/genetics; Vaccines, DNA/immunology*; Vaccines, DNA/chemistry
  9. Yusof WNSW, Abdullah H
    Trop Life Sci Res, 2020 Apr;31(1):69-84.
    PMID: 32963712 DOI: 10.21315/tlsr2020.31.1.5
    Conventional and modern cancer treatment were reported to manifest adverse effects to the patients. More researches were conducted to search for selective cytotoxic agent of plant natural product on cancer cells. The presences of wide range phytochemicals in Quercus infectoria (QI) extract have been implicated with the cytotoxic effect against various types of cancer cell which remain undiscovered. This present study aimed to evaluate cytotoxic effect of QI extracts on selected human cancer cells and then, the most potent extract was further analysed for general phytochemical constituents. QI galls were extracted successively with n-hexane, ethyl acetate and methanol yielded three main extracts; n-hexane (QIH), ethyl acetate (QIEA) and methanol (QIM), respectively. The most potent extract was qualitatively analysed for the present of tannin, alkaloids, glycosides, saponins, terpenoids, flavonoids and phenolic compounds. Next, the extracts were tested to determine the cytotoxic activity against cervical cancer cells (HeLa), breast cancer cells (MDA-MB-231) and liver cancer cells (Hep G2) using MTT assay. Cytotoxic activity of QI extracts against normal fibroblast (L929) cell line was also evaluated to determine the cytoselective property. Meanwhile, DMSO-treated cells served as negative control while cisplatin-treated cells served as positive control. The most potent extract then chosen to be further investigated for DNA fragmentation as hallmark of apoptosis using Hoechst staining. Qualitative phytochemical analysis revealed the presence of tannin, alkaloids, glycosides, saponins, terpenoids, flavonoids and phenolic compounds. QIEA extract exhibited the most potent cytotoxic activity against HeLa cells with (IC50 value = 6.33 ± 0.33 μg/mL) and showed cytoselective property against L929 cells. DNA fragmentation revealed QIEA induced apoptosis in the treated cells. The richness of phytochemical constituents in QIEA extract might contribute to the potency of cytotoxic activity towards HeLa cells.
    Matched MeSH terms: DNA Fragmentation
  10. Venkatramanan M, Sankar Ganesh P, Senthil R, Akshay J, Veera Ravi A, Langeswaran K, et al.
    ACS Omega, 2020 Oct 13;5(40):25605-25616.
    PMID: 33073086 DOI: 10.1021/acsomega.0c02483
    Chromobacterium violaceum (C. violaceum) is a Gram-negative, rod-shaped facultatively anaerobic bacterium implicated with recalcitrant human infections. Here, we evaluated the anti-QS and antibiofilm activities of ethyl acetate extracts of Passiflora edulis (P. edulis) on the likely inactivation of acyl-homoserine lactone (AHL)-regulated molecules in C. violaceum both by in vitro and in silico analyses. Our investigations showed that the sub-MIC levels were 2, 1, and 0.5 mg/mL, and the concentrations showed a marked reduction in violacein pigment production by 75.8, 64.6, and 35.2%. AHL quantification showed 72.5, 52.2, and 35.9% inhibitions, inhibitions of EPS production (72.8, 36.5, and 25.9%), and reductions in biofilm formation (90.7, 69.4, and 51.8%) as compared to a control. Light microscopy and CLSM analysis revealed dramatic reduction in the treated biofilm group as compared to the control. GC-MS analysis showed 20 major peaks whose chemical structures were docked as the CviR ligand. The highest docking score was observed for hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester bonds in the active site of CviR with a binding energy of -8.825 kcal/mol. Together, we found that hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester remarkably interacted with CviR to inhibit the QS system. Hence, we concluded that hexadecanoic acid, 2-hydroxy-1-(hydroxymethyl) ethyl ester of P. edulis could likely be evaluated for treating C. violaceum infections.
    Matched MeSH terms: Sequence Analysis, DNA
  11. Melinda, Mei Lin Lau, Edmund, Sim Ui Hang
    MyJurnal
    Association between the expression of ribosomal protein (RP) genes and cancer is widely known. More specifically, the extra-ribosomal functions of RPs have been linked to carcinogenesis. The ribosomal protein gene, eL14 has been reported to be associated with malignancy of the colorectum, albeit of mechanism yet unclear. Its expression in cells derived from different tissue origin of colorectal carcinoma (CRC) has never been explored. Therefore, this study aims to comparatively analyse the expression pattern of eL14 between two different CRC cell lines (DLD-1 and HCT116). It involved a conventional gene expression analysis, the Reverse-Transcriptase PCR (RT-PCR) assays. Products of RT-PCR assay were resolved via an agarose gel electrophoresis method, and band intensities of amplicons were documented and quantified using TotalLab Quant software. We observed differential expression patterns of eL14 between DLD-1 and HCT116 cells, but statistical analysis revealed insignificant differences. Therefore, the relevance of eL14 as a biomarker to distinguish between different colorectal cancer cells is suggestive but not conclusive.
    Matched MeSH terms: DNA-Directed RNA Polymerases
  12. Mossanen-Parsi A, Parisi D, Browne-Marke N, Bharudin I, Connell SR, Mayans O, et al.
    Mol Microbiol, 2020 Oct 12.
    PMID: 33047379 DOI: 10.1111/mmi.14613
    The role of post-transcriptional RNA modification is of growing interest. One example is the addition of non-templated uridine residues to the 3´ end of transcripts. In mammalian systems uridylation is integral to cell cycle control of histone mRNA levels. This regulatory mechanism is dependent on the nonsense mediated decay (NMD) component, Upf1, which promotes histone mRNA uridylation and degradation in response to the arrest of DNA synthesis. We have identified a similar system in Aspergillus nidulans, where Upf1 is required for the regulation of histone mRNA levels. However, other NMD components are also implicated, distinguishing it from the mammalian system. As in human cells, 3´ uridylation of histone mRNA is induced upon replication arrest. Disruption of this 3´ tagging has a significant but limited effect on histone transcript regulation, consistent with multiple mechanisms acting to regulate mRNA levels. Interestingly, 3´ end degraded transcripts are also subject to re-adenylation. Both mRNA pyrimidine tagging and re-adenylation are dependent on the same terminal-nucleotidyltransferases, CutA and CutB, and we show this is consistent with the in vitro activities of both enzymes. Based on these data we argue that mRNA 3´ tagging has diverse and distinct roles associated with transcript degradation, functionality and regulation.
    Matched MeSH terms: DNA
  13. Venkatachalam K, Vinayagam R, Arokia Vijaya Anand M, Isa NM, Ponnaiyan R
    Toxicol Res (Camb), 2020 Feb;9(1):2-18.
    PMID: 32440334 DOI: 10.1093/toxres/tfaa004
    1,2-dimethylhydrazine (DMH) is a member in the class of hydrazines, strong DNA alkylating agent, naturally present in cycads. DMH is widely used as a carcinogen to induce colon cancer in animal models. Exploration of DMH-induced colon carcinogenesis in rodent models provides the knowledge to perceive the biochemical, molecular, and histological mechanisms of different stages of colon carcinogenesis. The procarcinogen DMH, after a series of metabolic reactions, finally reaches the colon, there produces the ultimate carcinogen and reactive oxygen species (ROS), which further alkylate the DNA and initiate the development of colon carcinogenesis. The preneolpastic lesions and histopathological observations of DMH-induced colon tumors may provide typical understanding about the disease in rodents and humans. In addition, this review discusses about the action of biotransformation and antioxidant enzymes involved in DMH intoxication. This understanding is essential to accurately identify and interpret alterations that occur in the colonic mucosa when evaluating natural or pharmacological compounds in DMH-induced animal colon carcinogenesis.
    Matched MeSH terms: DNA
  14. Aminuddin A, Ng PY, Leong CO, Chua EW
    Sci Rep, 2020 May 12;10(1):7885.
    PMID: 32398775 DOI: 10.1038/s41598-020-64664-3
    Cisplatin is the first-line chemotherapeutic agent for the treatment of oral squamous cell carcinoma (OSCC). However, the intrinsic or acquired resistance against cisplatin remains a major obstacle to treatment efficacy in OSCC. Recently, mitochondrial DNA (mtDNA) alterations have been reported in a variety of cancers. However, the role of mtDNA alterations in OSCC has not been comprehensively studied. In this study, we evaluated the correlation between mtDNA alterations (mtDNA content, point mutations, large-scale deletions, and methylation status) and cisplatin sensitivity using two OSCC cell lines, namely SAS and H103, and stem cell-like tumour spheres derived from SAS. By microarray analysis, we found that the tumour spheres profited from aberrant lipid and glucose metabolism and became resistant to cisplatin. By qPCR analysis, we found that the cells with less mtDNA were less responsive to cisplatin (H103 and the tumour spheres). Based on the findings, we theorised that the metabolic changes in the tumour spheres probably resulted in mtDNA depletion, as the cells suppressed mitochondrial respiration and switched to an alternative mode of energy production, i.e. glycolysis. Then, to ascertain the origin of the variation in mtDNA content, we used MinION, a nanopore sequencer, to sequence the mitochondrial genomes of H103, SAS, and the tumour spheres. We found that the lower cisplatin sensitivity of H103 could have been caused by a constellation of genetic and epigenetic changes in its mitochondrial genome. Future work may look into how changes in mtDNA translate into an impact on cell function and therefore cisplatin response.
    Matched MeSH terms: DNA, Mitochondrial/drug effects*; DNA, Mitochondrial/genetics; DNA, Mitochondrial/metabolism
  15. Mat Nanyan NSB, Takagi H
    Front Genet, 2020;11:438.
    PMID: 32411186 DOI: 10.3389/fgene.2020.00438
    Overexpression of MSN2, which is the transcription factor gene in response to stress, is well-known to increase the tolerance of the yeast Saccharomyces cerevisiae cells to a wide variety of environmental stresses. Recent studies have found that the Msn2 is a feasible potential mediator of proline homeostasis in yeast. This result is based on the finding that overexpression of the MSN2 gene exacerbates the cytotoxicity of yeast to various amino acid analogs whose uptake is increased by the active amino acid permeases localized on the plasma membrane as a result of a dysfunctional deubiquitination process. Increased understanding of the cellular responses induced by the Msn2-mediated proline incorporation will provide better comprehension of how cells respond to and counteract to different kinds of stimuli and will also contribute to the breeding of industrial yeast strains with increased productivity.
    Matched MeSH terms: DNA-Binding Proteins
  16. Mohd Izham NZ, Yusoff HM, Ul Haq Bhat I, Endo T, Fukumura H, Kwon E, et al.
    Data Brief, 2020 Jun;30:105568.
    PMID: 32368595 DOI: 10.1016/j.dib.2020.105568
    The structural investigation of synthesized compounds can be carried out by various spectroscopic techniques. It is an important prospect in order to elucidate the structure of the desired products before being further utilized. The preparation of new p-nitro stilbene Schiff base derivatives as an electrochemical DNA potential spacer was synthesized using (E)-4-(4-nitrostyryl)aniline from Heck reaction with aldehydes in ethanolic solution. The data presented here in this article contains FTIR, UV-Vis and 1H and 13C NMR of (E)-4-(4-nitrostyryl)aniline and nitrostyryl aniline derivatives.
    Matched MeSH terms: DNA, Intergenic
  17. Md Naim D, Kamal NZM, Mahboob S
    Saudi J Biol Sci, 2020 Mar;27(3):953-967.
    PMID: 32127775 DOI: 10.1016/j.sjbs.2020.01.021
    The population genetics study is crucial as it helps in understanding the epidemiological aspects of dengue and help improving a vector control measures. This research aims to investigate the population genetics structure of two common species of Aedes mosquitoes in Penang; Aedes aegypti and Aedes albopictus using Cytochrome Oxidase I (COI) mitochondrial DNA (mtDNA) marker. Molecular investigations were derived from 440 bp and 418 bp mtDNA COI on 125 and 334 larvae of Aedes aegypti and Aedes albopictus respectively, from 32 locations in Penang. All samples were employed in the BLASTn for species identification. The haplotype diversity, nucleotide diversity, neutrality test and mismatch distribution analysis were conducted in DnaSP version 5.10.1. AMOVA analysis was conducted in ARLEQUIN version 3.5 and the phylogenetic reconstructions based on maximum likelihood (ML) and neighbor-joining (NJ) methods were implemented in MEGA X. The relationships among haplotypes were further tested by creating a minimum spanning tree using Network version 4.6.1. All samples were genetically identified and clustered into six distinct species. Among the species, Ae. albopictus was the most abundant (67.2%), followed by Ae. aegypti (25.2%) and the rest were counted for Culex sp. and Toxorhynchites sp. Both Ae. aegypti and Ae. albopictus show low nucleotide diversity (π) and high haplotype diversity (h), while the neutrality test shows a negative value in most of the population for both species. There are a total of 39 and 64 haplotypes recorded for Ae. aegypti and Ae. albopictus respectively. AMOVA analysis revealed that most of the variation occurred within population for both species. Mismatch distribution analysis showed bimodal characteristic of population differentiation for Ae. aegypti but Ae. albopictus showed unimodal characteristics of population differentiation. Genetic distance based on Tamura-Nei parameter showed low genetic divergent within population and high genetic divergent among population for both species. The maximum likelihood tree showed no obvious pattern of population genetic structure for both Ae. aegypti and Ae. albopictus from Penang and a moderate to high bootstrap values has supported this conclusion. The minimum spanning network for Ae. aegypti and Ae. albopictus showed five and three dominant haplotypes respectively, which indicates a mixture of haplotypes from the regions analysed. This study revealed that there is no population genetic structure exhibited by both Ae. aegypti and Ae. albopictus in Penang. Mutation has occurred rapidly in both species and this will be challenging in controlling the populations. However, further analysis needed to confirm this statement.
    Matched MeSH terms: DNA, Mitochondrial
  18. Hart T, Tang WY, Mansoor SAB, Chio MTW, Barkham T
    BMC Infect Dis, 2020 Apr 28;20(1):314.
    PMID: 32345231 DOI: 10.1186/s12879-020-05019-1
    BACKGROUND: Mycoplasma genitalium is an emerging sexually transmitted infection, with increasing rates of resistance to fluroquinolones and macrolides, the recommended treatments. Despite this, M. genitalium is not part of routine screening for Sexually Transmitted Infections (STIs) in many countries and the prevalence of infection and patterns of disease remain to be determined in many populations. Such data is of particular importance in light of the reported rise in antibiotic resistance in M. genitalium isolates.

    METHODS: Urine and urethral swab samples were collected from the primary public sexual health clinic in Singapore and tested for C. trachomatis (CT) or N. gonorrhoeae (NG) infection and for the presence of M. genitalium. Antibiotic resistance in M. genitalium strains detected was determined by screening for genomic mutations associated with macrolide and fluroquinolone resistance.

    RESULTS: We report the results of a study into M. genitalium prevalence at the national sexual health clinic in Singapore. M. genitalium was heavily associated with CT infection (8.1% of cases), but present in only of 2.4% in CT negative cases and not independently linked to NG infection. Furthermore, we found high rates of resistance mutations to both macrolides (25%) and fluoroquinolones (37.5%) with a majority of resistant strains being dual-resistant. Resistance mutations were only found in strains from patients with CT co-infection.

    CONCLUSIONS: Our results support targeted screening of CT positive patients for M. genitalium as a cost-effective strategy to reduce the incidence of M. genitalium in the absence of comprehensive routine screening. The high rate of dual resistance also highlights the need to ensure the availability of alternative antibiotics for the treatment of multi-drug resistant M. genitalium isolates.

    Matched MeSH terms: DNA, Bacterial/genetics; DNA, Bacterial/metabolism; Sequence Analysis, DNA
  19. Kofi AE, Hakim HM, Khan HO, Ismail SA, Ghansah A, Haslindawaty ARN, et al.
    Data Brief, 2020 Aug;31:105746.
    PMID: 32490095 DOI: 10.1016/j.dib.2020.105746
    Short tandem repeat (STR) loci are widely used as genetic marker for ancestral and forensic analyses. The latter application includes for paternity testing and DNA profiling of samples collected from scenes of crime and suspects. This survey provides the first dataset for 21 STR loci across the Akan population in Ghana by genotyping of 109 unrelated healthy individuals using Investigator 24plex kit. None of the STR loci screened deviated from Hardy-Weinberg equilibrium after applying Bonferroni correction. Overall, 224 unique alleles were observed with allele frequencies ranging from 0.005 to 0.518. The combined match probability, combined power of exclusion and combined power discrimination were 1 in 4.07 × 10-25, 0.999999999 and 1, respectively. Principal coordinate analysis carried out using 21 STR allele frequency data mapped the Akans with Nigerian subpopulation groups (Hausa, Igbo and Yoruba), but separated from Thais of Thailand, Chechen of Jordan and Tijuana of Mexico.
    Matched MeSH terms: DNA Fingerprinting
  20. Emrizal R, Nor Muhammad NA
    PeerJ, 2020;8:e9019.
    PMID: 32617187 DOI: 10.7717/peerj.9019
    Porphyromonas gingivalis is one of the major bacteria that causes periodontitis. Chronic periodontitis is a severe form of periodontal disease that ultimately leads to tooth loss. Virulence factors that contribute to periodontitis are secreted by Type IX Secretion System (T9SS). There are aspects of T9SS protein components that have yet to be characterised. Thus, the aim of this study is to investigate the phylogenetic relationship between members of 20 T9SS component protein families. The Bayesian Inference (BI) trees for 19 T9SS protein components exhibit monophyletic clades for all major classes under Bacteroidetes with strong support for the monophyletic clades or its subclades that is consistent with phylogeny exhibited by the constructed BI tree of 16S rRNA. The BI tree of PorR is different from the 19 BI trees of T9SS protein components as it does not exhibit monophyletic clades for all major classes under Bacteroidetes. There is strong support for the phylogeny exhibited by the BI tree of PorR which deviates from the phylogeny based on 16S rRNA. Hence, it is possible that the porR gene is subjected to horizontal transfer as it is known that virulence factor genes could be horizontally transferred. Seven genes (porR included) that are involved in the biosynthesis of A-LPS are found to be flanked by insertion sequences (IS5 family transposons). Therefore, the intervening DNA segment that contains the porR gene might be transposed and subjected to conjugative transfer. Thus, the seven genes can be co-transferred via horizontal gene transfer. The BI tree of UgdA does not exhibit monophyletic clades for all major classes under Bacteroidetes which is similar to the BI tree of PorR (both are a part of the seven genes). Both BI trees also exhibit similar topology as the four identified clusters with strong support and have similar relative positions to each other in both BI trees. This reinforces the possibility that porR and the other six genes might be horizontally transferred. Other than the BI tree of PorR, the 19 other BI trees of T9SS protein components also exhibit evidence of horizontal gene transfer. However, their genes might undergo horizontal gene transfer less frequently compared to porR because the intervening DNA segment that contains porR is easily exchanged between bacteria under Bacteroidetes due to the presence of insertion sequences (IS5 family transposons) that flank it. In conclusion, this study can provide a better understanding about the phylogeny of T9SS protein components.
    Matched MeSH terms: DNA Transposable Elements
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