Displaying publications 601 - 620 of 3507 in total

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  1. Fulltext Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia
    Veera Singham G, Othman AS, Lee CY
    PLoS One, 2017;12(11):e0186690.
    PMID: 29186140 DOI: 10.1371/journal.pone.0186690
    Dispersal of soil-dwelling organisms via the repeatedly exposed Sunda shelf through much of the Pleistocene in Southeast Asia has not been studied extensively, especially for invertebrates. Here we investigated the phylogeography of an endemic termite species, Macrotermes gilvus (Hagen), to elucidate the spatiotemporal dynamics of dispersal routes of terrestrial fauna in Pleistocene Southeast Asia. We sampled 213 termite colonies from 66 localities throughout the region. Independently inherited microsatellites and mtDNA markers were used to infer the phylogeographic framework of M. gilvus. Discrete phylogeographic analysis and molecular dating based on fossil calibration were used to infer the dynamics of M. gilvus dispersal in time and space across Southeast Asia. We found that the termite dispersal events were consistently dated within the Pleistocene time frame. The dispersal pattern was multidirectional, radiating eastwards and southwards out of Indochina, which was identified as the origin for dispersal events. We found no direct dispersal events between Sumatra and Borneo despite the presence of a terrestrial connection between them during the Pleistocene. Instead, central Java served as an important link allowing termite colonies to be established in Borneo and Sumatra. Our findings support the hypothesis of a north-south dispersal corridor in Southeast Asia and suggest the presence of alternative dispersal routes across Sundaland during the Pleistocene. For the first time, we also propose that a west-east dispersal through over-water rafting likely occurred across the Pleistocene South China Sea. We found at least two independent entry routes for terrestrial species to infiltrate Sumatra and Borneo at different times.
    Matched MeSH terms: DNA, Mitochondrial/genetics
  2. Comprehensive multi-locus phylogeny of Old World tree frogs (Anura: Rhacophoridae) reveals taxonomic uncertainties and potential cases of over- and underestimation of species diversity
    Chan KO, Grismer LL, Brown RM
    Mol Phylogenet Evol, 2018 10;127:1010-1019.
    PMID: 30030179 DOI: 10.1016/j.ympev.2018.07.005
    The family Rhacophoridae is one of the most diverse amphibian families in Asia, for which taxonomic understanding is rapidly-expanding, with new species being described steadily, and at increasingly finer genetic resolution. Distance-based methods frequently have been used to justify or at least to bolster the recognition of new species, particularly in complexes of "cryptic" species where obvious morphological differentiation does not accompany speciation. However, there is no universally-accepted threshold to distinguish intra- from interspecific genetic divergence. Moreover, indiscriminant use of divergence thresholds to delimit species can result in over- or underestimation of species diversity. To explore the range of variation in application of divergence scales, and to provide a family-wide assessment of species-level diversity in Old-World treefrogs (family Rhacophoridae), we assembled the most comprehensive multi-locus phylogeny to date, including all 18 genera and approximately 247 described species (∼60% coverage). We then used the Automatic Barcode Gap Discovery (ABGD) method to obtain different species-delimitation schemes over a range of prior intraspecific divergence limits to assess the consistency of divergence thresholds used to demarcate current species boundaries. The species-rich phylogeny was able to identify a number of taxonomic errors, namely the incorrect generic placement of Chiromantis inexpectatus, which we now move to the genus Feihyla, and the specific identity of Rhacophorus bipunctatus from Peninsular Malaysia, which we tentatively reassign to R. rhodopus. The ABGD analysis demonstrated overlap between intra- and interspecific divergence limits: genetic thresholds used in some studies to synonymize taxa have frequently been used in other studies to justify the recognition of new species. This analysis also highlighted numerous groups that could potentially be split or lumped, which we earmark for future examination. Our large-scale and en bloc approach to species-level phylogenetic systematics contributes to the resolution of taxonomic uncertainties, reveals possible new species, and identifies numerous groups that require critical examination. Overall, we demonstrate that the taxonomy and evolutionary history of Old-World tree frogs are far from resolved, stable or adequately characterized at the level of genus, species, and/or population.
    Matched MeSH terms: DNA Barcoding, Taxonomic/methods
  3. Contribution of transposable elements in the plant's genome
    Sahebi M, Hanafi MM, van Wijnen AJ, Rice D, Rafii MY, Azizi P, et al.
    Gene, 2018 Jul 30;665:155-166.
    PMID: 29684486 DOI: 10.1016/j.gene.2018.04.050
    Plants maintain extensive growth flexibility under different environmental conditions, allowing them to continuously and rapidly adapt to alterations in their environment. A large portion of many plant genomes consists of transposable elements (TEs) that create new genetic variations within plant species. Different types of mutations may be created by TEs in plants. Many TEs can avoid the host's defense mechanisms and survive alterations in transposition activity, internal sequence and target site. Thus, plant genomes are expected to utilize a variety of mechanisms to tolerate TEs that are near or within genes. TEs affect the expression of not only nearby genes but also unlinked inserted genes. TEs can create new promoters, leading to novel expression patterns or alternative coding regions to generate alternate transcripts in plant species. TEs can also provide novel cis-acting regulatory elements that act as enhancers or inserts within original enhancers that are required for transcription. Thus, the regulation of plant gene expression is strongly managed by the insertion of TEs into nearby genes. TEs can also lead to chromatin modifications and thereby affect gene expression in plants. TEs are able to generate new genes and modify existing gene structures by duplicating, mobilizing and recombining gene fragments. They can also facilitate cellular functions by sharing their transposase-coding regions. Hence, TE insertions can not only act as simple mutagens but can also alter the elementary functions of the plant genome. Here, we review recent discoveries concerning the contribution of TEs to gene expression in plant genomes and discuss the different mechanisms by which TEs can affect plant gene expression and reduce host defense mechanisms.
    Matched MeSH terms: DNA Transposable Elements/physiology*
  4. Fulltext Epigenome-wide association study of adiposity and future risk of obesity-related diseases
    Campanella G, Gunter MJ, Polidoro S, Krogh V, Palli D, Panico S, et al.
    Int J Obes (Lond), 2018 Dec;42(12):2022-2035.
    PMID: 29713043 DOI: 10.1038/s41366-018-0064-7
    BACKGROUND: Obesity is an established risk factor for several common chronic diseases such as breast and colorectal cancer, metabolic and cardiovascular diseases; however, the biological basis for these relationships is not fully understood. To explore the association of obesity with these conditions, we investigated peripheral blood leucocyte (PBL) DNA methylation markers for adiposity and their contribution to risk of incident breast and colorectal cancer and myocardial infarction.

    METHODS: DNA methylation profiles (Illumina Infinium® HumanMethylation450 BeadChip) from 1941 individuals from four population-based European cohorts were analysed in relation to body mass index, waist circumference, waist-hip and waist-height ratio within a meta-analytical framework. In a subset of these individuals, data on genome-wide gene expression level, biomarkers of glucose and lipid metabolism were also available. Validation of methylation markers associated with all adiposity measures was performed in 358 individuals. Finally, we investigated the association of obesity-related methylation marks with breast, colorectal cancer and myocardial infarction within relevant subsets of the discovery population.

    RESULTS: We identified 40 CpG loci with methylation levels associated with at least one adiposity measure. Of these, one CpG locus (cg06500161) in ABCG1 was associated with all four adiposity measures (P = 9.07×10-8 to 3.27×10-18) and lower transcriptional activity of the full-length isoform of ABCG1 (P = 6.00×10-7), higher triglyceride levels (P = 5.37×10-9) and higher triglycerides-to-HDL cholesterol ratio (P = 1.03×10-10). Of the 40 informative and obesity-related CpG loci, two (in IL2RB and FGF18) were significantly associated with colorectal cancer (inversely, P DNA methylation patterns, may be an intermediate biomarker at the intersection of obesity and obesity-related diseases, and could offer clues as to underlying biological mechanisms.

    Matched MeSH terms: DNA Methylation/genetics*
  5. Diatom Nitzschia navis-varingica (Bacillariophyceae) and its domoic acid production from the mangrove environments of Malaysia
    Tan SN, Teng ST, Lim HC, Kotaki Y, Bates SS, Leaw CP, et al.
    Harmful Algae, 2016 12;60:139-149.
    PMID: 28073557 DOI: 10.1016/j.hal.2016.11.003
    The distribution of the toxic pennate diatom Nitzschia was investigated at four mangrove areas along the coastal brackish waters of Peninsular Malaysia. Eighty-two strains of N. navis-varingica were isolated and established, and their identity confirmed morphologically and molecularly. Frustule morphological characteristics of the strains examined are identical to previously identified N. navis-varingica, but with a sightly higher density of the number of areolae per 1μm (4-7 areolae). Both LSU and ITS rDNAs phylogenetic trees clustered all strains in the N. navis-varingica clade, with high sequence homogeneity in the LSU rDNA (0-0.3%), while the intraspecific divergences in the ITS2 data set reached up to 7.4%. Domoic acid (DA) and its geometrical isomers, isodomoic A (IA) and isodomoic B (IB), were detected in cultures of N. navis-varingica by FMOC-LC-FLD, and subsequently confirmed by LC-MS/MS, with selected ion monitoring (SIM) and multiple reaction monitoring (MRM) runs. DA contents ranged between 0.37 and 11.06pgcell-1. This study demonstrated that the toxigenic euryhaline diatom N. navis-varingica is widely distributed in Malaysian mangrove swamps, suggesting the risk of amnesic shellfish poisoning and the possibility of DA contamination in the mangrove-related fisheries products.
    Matched MeSH terms: DNA, Ribosomal/genetics
  6. Fulltext MGMT and SPOCK2 Promoter Methylation in diffuse large B-Cell Lymphoma: a study in two tertiary health centres in the East Coast of Malaysia
    Norafiza Zainuddin, Lailatul Jalilah Mohd Ridah, Aqilah Nabihah Omar, Norlelawati A. Talib, Naznin Muhammad, Faezahtul Arbaeyah Hussain
    Jurnal Sains Kesihatan Malaysia, 2017;15(2):77-82.
    MyJurnal
    MGMT (O6
    -Methylguanine-DNA Methyltransferase) suppresses tumor development by removing alkyl adduct, while
    SPOCK2 (SPARC/Osteonectin CWCV and Kazal-like domains proteoglycan) abolishes the inhibition of membrane-type
    matrix metalloproteinases (MT-MMP) which leads to angiogenesis. Hence, MGMT methylation may initiate malignant cells
    transformation. In contrast, SPOCK2 methylation is hypothesized not to be a common event in diffuse large B-cell lymphoma
    (DLBCL). In this study, we examined the methylation status of MGMT and SPOCK2 in DLBCL as in Malaysia the information
    is extremely lacking. A total of 88 formalin-fixed paraffin-embedded tissue of patients diagnosed with DLBCL from the
    year 2006 to 2013 were retrieved from Hospital Universiti Sains Malaysia, Kelantan and Hospital Tengku Ampuan Afzan,
    Pahang. Methylation-specific polymerase chain reaction (MSP) was used to examine the methylation status of both genes.
    Interestingly, methylation of MGMT was detected in all the 88 DLBCL samples, whereas SPOCK2 was found to be methylated
    in 83 of 88 (94.3%) DLBCL cases. Our study showed a remarkably high percentage of promoter methylation of both
    MGMT and SPOCK2 genes. Our finding also negates initial expectation that SPOCK2 methylation would be an uncommon
    event in the majority of DLBCL cases. This study has shown a very high percentage of promoter methylation of MGMT and
    SPOCK2 in the DLBCL cases studied by MSP, using archival lymphoma tissues. Nonetheless, additional research is needed
    to quantitatively evaluate MGMT and SPOCK2 methylation, and to analyse gene expression and/or protein expression in
    order to further understand the role of MGMT and SPOCK2 methylation in the pathogenesis of DLBCL.
    Matched MeSH terms: DNA; O(6)-Methylguanine-DNA Methyltransferase
  7. Fulltext HLA-B*15:02 screening in epileptic patients using a high resolution melting-real time PCR (HRM-QPCR) method
    Zam Zureena Mohd Rani, Nor Azian Abdul Murad, Saberi Saimun, Sri Noraima Othman, Rahman Jamal, Sue-Mian Then, et al.
    Neurology Asia, 2018;23(2):137-144.
    MyJurnal
    Background: The HLA-B*15:02 polymorphism in epileptic patients is known to be associated with carbamazepine-induced Stevens-Johnson syndrome (SJS). The prevalence of HLA-B*15:02 polymorphism seemed to be ethnic-specific with a higher frequency of HLA-B*15:02 in Asian compared to the Europeans. This study was performed to determine the frequency of the HLA-B*15:02 polymorphism in epileptic patients at the Chancellor Tuanku Muhriz Hospital-UKM Medical Centre (HCTM-UKMMC) using high resolution melting-real time PCR (HRM-QPCR) method.
    Methods: We performed a fast and effective in-house high resolution melting-real time polymerase chain reaction method and compared it with the conventional multiplex-PCR method. The specificity and sensitivity of each test were also determined using DNA from saliva.
    Results: Using the conventional multiplexPCR approach for screening, 25 out of 64 (39.1%) epileptic patients were positive for HLA-B*15:02. However, using the HRM-QPCR technique, 24/64 (37.5%) of the patients were positive. The one patient who tested positive by the multiplex-PCR but negative using the HRM-QPCR turned out to be negative by DNA sequencing. The HRM-QPCR and DNA sequencing showed 100% sensitivity and specificity. The multiplex-PCR showed 100% sensitivity and 98.4% specificity compared to both HRM-QPCR and DNA sequencing. The HRM-QPCR is also more cost-effective (DNA sequencing
    Matched MeSH terms: DNA; Sequence Analysis, DNA
  8. Fulltext Development and validation of high resolution melting assays for high-throughput screening of BDNF rs6265 and DAT1 rs40184
    Asraa Faris, Hadri Hadi Md Yusof, Shahidee Zainal Abidin, Omar Habib, Cheah, Pike-See, Stanslas, Johnson, et al.
    Malaysian Journal of Medicine and Health Sciences, 2018;14(101):64-71.
    MyJurnal
    Introduction: One of the commonly used techniques for mutation screening is High Resolution Melting (HRM) analysis. HRM is a post PCR method that relies on the detection of the fluorescent signals acquired due to the release of DNA intercalated dyes upon the melting of dsDNA to ssDNA. The method is simple, inexpensive and does not require post PCR-handling, making it suitable for high throughput screening. Methods: This study aimed to develop and validate HRM technique for the screening of two disease-associated single nucleotide polymorphisms (SNPs) namely BDNF rs6265 and DAT1 rs40184 using a total of 30 gDNA samples. The obtained results were confirmed and validated by sequencing. Results: HRM analysis showed that the predicted genotypes of BDNF rs6265 and DAT1 rs40184 among all the gDNA samples were in 100% concordance with the sequencing results, making it an accurate and sensitive method for the detection of SNPs. Conclusions: The application of HRM can accurately determine the genotype of BDNF rs6265 and DAT1 rs40184 SNPs, making it a promising tool for rapid and high-throughput screening of targeted SNPs in a large population study.
    Matched MeSH terms: DNA; DNA, Single-Stranded
  9. Fulltext Authenticity Testing and Detection of Eurycoma longifolia in Commercial Herbal Products Using Bar-High Resolution Melting Analysis
    Fadzil NF, Wagiran A, Mohd Salleh F, Abdullah S, Mohd Izham NH
    Genes (Basel), 2018 Aug 12;9(8).
    PMID: 30103564 DOI: 10.3390/genes9080408
    The present study demonstrated High Resolution Melting (HRM) analysis combined with DNA barcode (Bar-HRM) as a fast and highly sensitive technique for detecting adulterants in Eurycoma longifolia commercial herbal products. Targeting the DNA barcoding of the chloroplastic region-ribulose biphosphate carboxylase large chain (rbcL) and the nuclear ribosomal region- internal transcribed spacer 2 (ITS2), PCR amplification and HRM analysis using saturated Eva green dye as the source of fluorescence signals, was accomplished by employing a real-time cycler. The results were further validated by sequencing to identify unknown sequence from Genbank database and to generate phylogenetic tree using neighbour joint (NJ) analysis. Both of the DNA markers exhibited a distinguishable melting temperature and shape of the normalised curve between the reference and the adulterants. In the case of species identification, ITS2 was more successful in differentiating between species. Additionally, detection of admixture sample containing small traces of targeted E. longifolia DNA (w/v) can be detected as low as 5% for rbcL and less than 1% for ITS2, proving the sensitivity and versatility of the HRM analysis. In conclusion, the Bar-HRM analysis is a fast and reliable technique that can effectively detect adulterants in herbal products. Therefore, this will be beneficial for regulatory agencies in order to regulate food safety issues.
    Matched MeSH terms: DNA; DNA Barcoding, Taxonomic
  10. An Outbreak of Leaf Spot Caused by Stemphylium solani on Eggplant in Malaysia
    Nasehi A, Kadir JB, Esfahani MN, Mahmodi F, Ghadirian H, Ashtiani FA, et al.
    Plant Dis, 2013 May;97(5):689.
    PMID: 30722195 DOI: 10.1094/PDIS-10-12-0901-PDN
    In 2011, a severe gray leaf spot was observed on eggplant (Solanum melongena) in major eggplant growing areas in Malaysia, including the Pahang, Johor, and Selangor states. Disease incidence was >70% in severely infected areas of about 150 ha of eggplant greenhouses and fields examined. Symptoms initially appeared as small (1 to 5 mm diameter), brownish-black specks with concentric circles on the lower leaves. The specks then coalesced and developed into greyish-brown, necrotic lesions, which also appeared on the upper leaves. Eventually, the leaves senesced and were shed. Tissue cut from the edges of leaf spots were surface-sterilized in 1% NaOCl for 2 min, rinsed in sterilized water, dried, and incubated on potato dextrose agar (PDA). Fungal colonies were greyish green to light brown, and produced a yellow pigment. Single, muriform, brown, oblong conidia formed at the terminal end of each conidiophore, were each 21.6 to 45.6 μm long and 11.5 to 21.6 μm wide, and contained 2 to 7 transverse and 1 to 4 longitudinal septa. The conidiophores were tan to light brown and ≤220 μm long. Based on these morphological criteria, 25 isolates of the fungus were identified as Stemphylium solani (1). To produce conidia in culture, 7-day-old single-conidial cultures were established on potato carrot agar (PCA) and V8 juice agar media under an 8-h/16-h light/dark photoperiod at 25°C (4). Further confirmation of the identification was obtained by molecular characterization in which fungal DNA was extracted and the internal transcribed spacer (ITS) region of ribosomal DNA amplified using primers ITS5 and ITS4 (2), followed by direct sequencing. A BLAST search in the NCBI database revealed that the sequence was 99% identical with published ITS sequences for two isolates of S. solani (Accession Nos. AF203451 and HQ840713). The amplified ITS region was deposited in GenBank (JQ736023). Pathogenicity testing of a representative isolate was performed on detached, 45-day-old eggplant leaves of the cv. 125066-X under laboratory conditions. Four fully expanded leaves (one wounded and two non-wounded leaflets/leaf) were placed on moist filter paper in petri dishes, and each leaflet inoculated with a 20-μl drop of a conidial suspension containing 1 × 105 conidia/ml in sterilized, distilled water (3). The leaves were wounded by applying pressure to leaf blades with the serrated edge of forceps. Four control leaves were inoculated similarly with sterilized, distilled water. Inoculated leaves were incubated in humid chambers at 25°C with 95% RH and a 12-h photoperiod. After 7 days, symptoms similar to those observed in the original fields developed on both wounded and non-wounded inoculated leaves, but not on control leaves, and S. solani was reisolated consistently from the symptoms using the same method as the original isolations. Control leaves remained asymptomatic and the fungus was not isolated from these leaves. The pathogenicity testing was repeated with similar results. To our knowledge, this is the first report of S. solani on eggplant in Malaysia. References: (1) B. S. Kim et al. Plant Pathol. J. 20:85, 2004. (2) Y. R. Mehta et al. Curr. Microbiol. 44:323, 2002. (3) B. M. Pryor and T. J. Michailides. Phytopathology 92:406, 2002. (4) E. G. Simmons. CBS Biodiv. Series 6:775, 2007.
    Matched MeSH terms: DNA, Fungal; DNA, Ribosomal
  11. First Report of Gray Leaf Spot on Pepper Caused by Stemphylium solani in Malaysia
    Nasehi A, Kadir JB, Abidin MAZ, Wong MY, Ashtiani FA
    Plant Dis, 2012 Aug;96(8):1227.
    PMID: 30727084 DOI: 10.1094/PDIS-03-12-0262-PDN
    Symptoms of gray leaf spot were first observed in June 2011 on pepper (Capsicum annuum) plants cultivated in the Cameron Highlands and Johor State, the two main regions of pepper production in Malaysia (about 1,000 ha). Disease incidence exceeded 70% in severely infected fields and greenhouses. Symptoms initially appeared as tiny (average 1.3 mm in diameter), round, orange-brown spots on the leaves, with the center of each spot turning gray to white as the disease developed, and the margin of each spot remaining dark brown. A fungus was isolated consistently from the lesions using sections of symptomatic leaf tissue surface-sterilized in 1% NaOCl for 2 min, rinsed in sterile water, dried, and plated onto PDA and V8 agar media (3). After 7 days, the fungal colonies were gray, dematiaceous conidia had formed at the end of long conidiophores (19.2 to 33.6 × 12.0 to 21.6 μm), and the conidia typically had two to six transverse and one to four longitudinal septa. Fifteen isolates were identified as Stemphylium solani on the basis of morphological criteria described by Kim et al. (3). The universal primers ITS5 and ITS4 were used to amplify the internal transcribed spacer region (ITS1, 5.8, and ITS2) of ribosomal DNA (rDNA) of a representative isolate (2). A 570 bp fragment was amplified, purified, sequenced, and identified as S. solani using a BLAST search with 100% identity to the published ITS sequence of an S. solani isolate in GenBank (1). The sequence was deposited in GenBank (Accession No. JQ736024). Pathogenicity of the fungal isolate was tested by inoculating healthy pepper leaves of cv. 152177-A. A 20-μl drop of conidial suspension (105 spores/ml) was used to inoculate each of four detached, 45-day-old pepper leaves placed on moist filter papers in petri dishes (4). Four control leaves were inoculated similarly with sterilized, distilled water. The leaves were incubated at 25°C at 95% relative humidity for 7 days. Gray leaf spot symptoms similar to those observed on the original pepper plants began to develop on leaves inoculated with the fungus after 3 days, and S. solani was consistently reisolated from the leaves. Control leaves did not develop symptoms and the fungus was not reisolated from these leaves. Pathogenicity testing was repeated with the same results. To our knowledge, this is the first report of S. solani causing gray leaf spot on pepper in Malaysia. References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997. (2) M. P. S. Camara et al. Mycologia 94:660, 2002. (3) B. S. Kim et al. Plant Pathol. J. 15:348, 1999. (4) B. M. Pryor and T. J. Michailides. Phytopathology 92:406, 2002.
    Matched MeSH terms: DNA, Ribosomal; DNA Primers
  12. Human Papillomavirus E6 biosensing: Current progression on early detection strategies for cervical Cancer
    Parmin NA, Hashim U, Gopinath SCB, Nadzirah S, Rejali Z, Afzan A, et al.
    Int J Biol Macromol, 2019 Apr 01;126:877-890.
    PMID: 30597241 DOI: 10.1016/j.ijbiomac.2018.12.235
    Prognosis of early cancer detection becomes one of the tremendous issues in the medical health system. Medical debates among specialist doctor and researcher in therapeutic approaches became a hot concern for cervix cancer deficiencies early screening, risk factors cross-reaction, portability device, rapid and free labeling system. The electrical biosensing based system showed credibility in higher specificity and selectivity due to hybridization of DNA duplex between analyte target and DNA probes. Electrical DNA sensor for cervix cancer has attracted too many attentions to researcher notification based on high performance, easy to handle, rapid system and possible to miniaturize. This review explores the current progression and future insignificant for HPV E6 genobiosensing for early Detection Strategies of Cervical Cancer.
    Matched MeSH terms: DNA; DNA Probes
  13. First Report of Pseudoperonospora cubensis Causing Downy Mildew of Trichosanthes cucumerina in Malaysia
    Salati M, Wong MY, Sariah M, Nik Masdek H
    Plant Dis, 2010 May;94(5):642.
    PMID: 30754434 DOI: 10.1094/PDIS-94-5-0642A
    In December 2008, infected leaves of Trichosanthes cucumerina were observed on commercial cucurbit farms located in Pontian, Johor (south of West Malaysia). Bright yellow and small necrotic lesions were observed on the adaxial surface of the leaves, whereas sporangiophores were observed on pale yellowish brown-to-brown lesions on the abaxial surface. The length and width of the sporangia ranged from 19 to 36 μm (28.6) and 11 to 23 μm (17.6), respectively. The length of the sporangiophores ranged from 310 to 450 μm, with an average length of 380 μm. The pathogen was identified as Pseudoperonospora cubensis on the basis of the morphological criteria described by Palti and Cohen (2). To confirm the morphological findings, DNA was extracted from symptomatic tissue and the internal transcribed spacer (ITS) region was PCR amplified using primers ITS5-P2 and ITS4 (3). The appropriate-sized amplicon was gel excised and column purified and then submitted for direct sequencing. The resulting 802 bp amplified ITS region was 100% identical to published P. cubensis sequences (GenBank Accession Nos. EU876603, EU876584, and AY198306). This sequence was deposited with NCBI GenBank under the Accession No. GU233293. In this study, pathogenicity tests were conducted using detached leaf disc assays (1) and a P. cubensis isolate obtained from T. cucumerina. For this purpose, leaf discs were excised from 6- to 8-week-old leaves of T. cucumerina using a 20-mm cork borer. Five leaf discs were placed with their abaxial surface facing upward on moist filter paper in petri dishes. Each of four leaf discs was inoculated with four 10-μl droplets of a 1 × 105 per ml sporangial suspension, whereas the fifth disc was inoculated with water droplets and served as a control. Three replications were completed. The leaf discs were placed in darkness at 14 ± 2°C for 24 h and subsequently incubated with a 12-h photoperiod. After 10 days, sporulation was observed on the sporangia-inoculated leaf discs with similar morphological features to the initial field samples. To our knowledge, this is the first report of P. cubensis causing downy mildew of T. cucumerina in Malaysia. References: (1) A. Lebeda and M. P. Widrlechner. J. Plant Dis. Prot. 110:337, 2003. (2) J. Palti and Y. Cohen. Phytoparasitica 8:109, 1980. (3) H. Voglmayr and O. Constantinescu. Mycol. Res. 112:487, 2008.
    Matched MeSH terms: DNA; DNA Primers
  14. Voltammetric determination of human papillomavirus 16 DNA by using interdigitated electrodes modified with titanium dioxide nanoparticles
    Parmin NA, Hashim U, Gopinath SCB, Nadzirah S, Rejali Z, Afzan A, et al.
    Mikrochim Acta, 2019 05 08;186(6):336.
    PMID: 31069542 DOI: 10.1007/s00604-019-3445-2
    A gene sensor for rapid detection of the Human Papillomavirus 16 (HPV 16) which is associated with the appearance of cervical cancer was developed. The assay is based on voltammetric determination of HPV 16 DNA by using interdigitated electrodes modified with titanium dioxide nanoparticles. Titanium dioxide nanoparticles (NPs) were used to modify a semiconductor-based interdigitated electrode (IDE). The surface of the NPs was then functionalized with a commercial 24-mer oligomer DNA probe for HPV 16 that was modified at the 5' end with a carboxyl group. If the probe interacts with the HPV 16 ssDNA, the current, best measured at a working voltage of 1.0 V, increases. The gene sensor has has a ∼ 0.1 fM limit of detection which is comparable to other sensors. The dielectric voltammetry analysis was carried out from 0 V to 1 V. The electrochemical sensitivity of the IDE is 2.5 × 10-5 μA·μM-1·cm-2. Graphical abstract Schematic of an interdigitated electrode (IDE) modified with titanium dioxide nanoparticles for voltammetric determination of HPV 16 DNA by using an appropriate DNA probe.
    Matched MeSH terms: DNA, Single-Stranded; DNA Probes
  15. Fulltext Combinatorial Cytotoxic Effects of Gelam Honey and 5-Fluorouracil against Human Adenocarcinoma Colon Cancer HT-29 Cells In Vitro
    T-Johari SAT, Hashim F, Ismail WI, Ali AM
    Int J Cell Biol, 2019;2019:3059687.
    PMID: 30923553 DOI: 10.1155/2019/3059687
    Combination of natural products with chemodrugs is becoming a trend in discovering new therapeutics approach for enhancing the cancer treatment process. In the present study, we aimed to investigate the cytotoxic and apoptosis induction of Gelam honey (GH) combined with or without 5-Fluorouracil (5-FU) on HT-29 cells. The cell viability was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay to assess cytotoxicity. Morphological changes and apoptosis were determined by the inverted microscope, Annexin V-FITC, and DNA fragmentation via flow cytometric analysis, respectively. Our results demonstrate that combined treatment revealed a remarkable and concentration-dependent cytotoxic effect on HT-29 cells in comparison with GH and 5-FU alone. Flow cytometry analysis showed that early apoptosis event was more pronounced in combined treatment. In addition, compared to 5-FU alone, apoptosis of HT-29 cells treated with combinations of GH and 5-FU demonstrated increasing percentages of fragmented DNA. Our results suggest that GH has a synergistic cytotoxic effect with 5-FU in HT-29 cell lines in vitro. Although the actions of the molecular mechanisms are not yet clear, the results reveal that the combination of GH and 5-FU could have the potential as a therapeutic agent.
    Matched MeSH terms: DNA; DNA Fragmentation
  16. Acrylic-based genosensor utilizing metal salphen labeling approach for reflectometric dengue virus detection
    Mazlan NF, Tan LL, Karim NHA, Heng LY, Jamaluddin ND, Yusof NYM, et al.
    Talanta, 2019 Jun 01;198:358-370.
    PMID: 30876573 DOI: 10.1016/j.talanta.2019.02.036
    An optical genosensor based on Schiff base complex (Zn2+ salphen) DNA label and acrylic microspheres (AMs) as polymer support of the capturing DNA probe (cpDNA) was developed for dengue virus serotype 2 (DEN-2) detection via reflectance spectrophotometric method. The solid-state optical DNA biosensor showed high selectivity and specificity up to one-base mismatch in the target DNA sequence owing to the salphen chemical structure that is rich in localized electrons, and allowed π-π stacking interaction between stacked base pairs of double-stranded DNA (dsDNA). The reflectometric DNA microsensor demonstrated a broad linear detection range towards DEN-2 DNA from 1 × 10-15 M to 1 × 10-3 M with a low limit of detection (LOD) obtained at 1.21 × 10-16 M. The DNA biosensor gave reproducible optical response with a satisfactory relative standard deviation (RSD) at 3.1%, (n = 3), and the reflectance response was stable even after four regeneration cycles of the DNA biosensor. The optical genosensor was proven comparable with standard reverse transcription polymerase chain reaction (RT-PCR) in detecting DEN-2 genome acquired from clinical samples of serum, urine and saliva of dengue virus infected patients under informed consent. The developed reflectometric DNA biosensor is advantageous in offering an early DEN-2 diagnosis, when fever symptom started to manifest in patient.
    Matched MeSH terms: DNA Probes/chemistry
  17. Who is biting you? DNA barcodes reveal cryptic diversity in human-biting black flies (Diptera: Simuliidae)
    Jomkumsing P, Tangkawanit U, Wongpakam K, Pramual P
    Acta Trop, 2019 Aug;196:22-29.
    PMID: 31059708 DOI: 10.1016/j.actatropica.2019.05.001
    Black flies (Simuliidae) are important biting insects and vectors of diseases agents of humans and livestock. Thus, understanding the taxonomy and biodiversity of these insects is crucial for control and management of these diseases. In this study, we used mitochondrial cytochrome c oxidase I sequences to examine genetic diversity of three human-biting and possible vector black fly taxa; the Simulium asakoae species-complex, S. chamlongi and S. nigrogilvum. High levels of genetic diversity (>3.5% intraspecific genetic divergence) were found in all three taxa. Phylogenetic analyses indicated that the S. asakoae complex can be divided into seven groups with the largest group consisting of specimens from Thailand, Malaysia and Myanmar. This group most likely represents true S. asakoae. The remaining haplotypes formed groups with conspecific haplotypes or with other closely related species. Among these groups, one including S. monglaense and another including S. myanmarense suggest that certain specimens identified as S. asakoae most likely belong to those species. Therefore, they constitute new locality records for Thailand and also represent new records of anthropophily. Members of S. chamlongi are not monophyletic as its clade also included S. hackeri. A median joining network revealed strong geographic associations of the haplotypes of S. nigrogilvum suggesting limitation of gene flow. Because this species occurs mainly in high elevation habitats, low land areas could present a barrier to gene flow.
    Matched MeSH terms: DNA Barcoding, Taxonomic*
  18. 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*
  19. Dual panel multiplex PCR assay for rapid detection of medically important fungi and resistant species of candida and aspergillus
    Jacinta Santhanam, Mohd Hanif Jainlabdin, Ang LC, Tzar Mohd Nizam
    Sains Malaysiana, 2018;47:489-498.
    Invasive fungal infections (IFIs) have risen dramatically in recent years among high risk immunocompromised patients.
    Rapid detection of fungal pathogens is crucial to timely and accurate antifungal therapy. Two multiplex polymerase
    chain reaction (PCR) assays were developed to detect major fungal species that cause invasive infections and identify
    resistant species. Genus specific primers for Candida, Aspergillus, Fusarium and species specific primers for Candida
    glabrata, Candida krusei and Aspergillus terreus which are known to be clinically resistant species, were designed from
    the internal transcribed spacer (ITS) regions of ribosomal ribonucleic acid (rRNA) gene complex. Both assays were
    performed simultaneously to promote rapid detection of fungal isolates based on distinct amplicon sizes. Inclusion of the
    universal fungal primers ITS 1 and ITS 4 in the genus specific assay produced a second amplicon for each isolate which
    served to confirm the detection of a fungal target. The limit of detection for the genus specific assay was 1 nanogram
    (ng) deoxyribonucleic acid (DNA) for Aspergillus fumigatus and Candida albicans, 0.1 ng DNA for Fusarium solani, while
    the species-specific assay detected 0.1 ng DNA of A. terreus and 10 picogram (pg) DNA of C. krusei and C. glabrata. The
    multiplex PCR assays, apart from universal detection of any fungal target, are able to detect clinically important fungi
    and differentiate resistant species rapidly and accurately, which can contribute to timely implementation of effective
    antifungal regime.
    Matched MeSH terms: DNA; DNA Primers
  20. 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*
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