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  1. Fulltext Effect of acute gamma irradiation on Curcuma alismatifolia varieties and detection of DNA polymorphism through SSR marker
    Taheri S, Abdullah TL, Ahmad Z, Abdullah NA
    Biomed Res Int, 2014;2014:631813.
    PMID: 24719878 DOI: 10.1155/2014/631813
    The effects of eight different doses (0, 10, 20, 25, 35, 40, 60, and 100 Gy) of acute gamma irradiation on 44 (three varieties of Curcuma alismatifolia: Chiang Mai Red, Sweet Pink, Kimono Pink, and one Curcuma hybrid (Doi Tung 554) individual plants were investigated. Radiation sensitivity tests revealed that the LD50 values of the varieties were achieved at 21 Gy for Chiang Mai Red, 23 Gy for Sweet Pink, 25 Gy for Kimono Pink, and 28 Gy for Doi Tung 554. From the analysis of variance (ANOVA), significant variations were observed for vegetative traits, flowering development, and rhizome characteristics among the four varieties of Curcuma alismatifolia and dose levels as well as the dose × variety interaction. In irradiated plants, the leaf length, leaf width, inflorescence length, the number of true flowers, the number of pink bracts, number of shoots, plant height, rhizome size, number of storage roots, and number of new rhizomes decreased significantly (P < 0.05) as the radiation dose increased. The cophenetic correlation coefficient (CCC) between genetic dissimilarity matrix estimated from the morphological characters and the UPGMA clustering method was r = 0.93, showing a proof fit. In terms of genetic variation among the acutely irradiated samples, the number of presumed alleles revealed by simple sequence repeats ranged from two to seven alleles with a mean value of 3.1, 4.5, and 5.3 alleles per locus for radiation doses of 0, 10, and 20 Gy, respectively. The average values of the effective number of alleles, Nei's gene diversity, and Shannon's information index were 2.5-3.2, 0.51-0.66, and 0.9-1.3, respectively. The constructed dendrogram grouped the entities into seven clusters. Principal component analysis (PCA) supported the clustering results. Consequently, it was concluded that irradiation with optimum doses of gamma rays efficiently induces mutations in Curcuma alismatifolia varieties.
    Matched MeSH terms: DNA, Plant/genetics*
  2. Fulltext A novel rare copy number variant of the ABCF1 gene identified among dengue fever patients from Peninsular Malaysia
    Hoh BP, Sam SS, Umi SH, Mahiran M, Nik Khairudin NY, Rafidah Hanim S, et al.
    Genet. Mol. Res., 2014;13(1):980-5.
    PMID: 24634119 DOI: 10.4238/2014.February.19.9
    Copy number variation (CNV) is a form of genetic variation in addition to single nucleotide polymorphisms. The significance of CNV in the manifestation of a number of diseases is only recently receiving considerable attention. We genotyped 163 dengue patients from Peninsular Malaysia for genes possibly linked to dengue infection using quantitative real-time PCR. Here, we report a serendipitous discovery of a novel rare CNV of the ABCF1 gene among the dengue patients. Among these patients, two had a gain of 1 copy (CN = 3) and one had lost 1 copy (CN = 1), indicating that a rare CNV of the ABCF1 gene was detected among dengue patients from Peninsular Malaysia. Although the gene is suspected to regulate inflammatory responses and pathogen-induced cytokine storm, its relevance to dengue requires further investigation.
    Matched MeSH terms: DNA Copy Number Variations*
  3. Genomic DNA copy number alterations from precursor oral lesions to oral squamous cell carcinoma
    Salahshourifar I, Vincent-Chong VK, Kallarakkal TG, Zain RB
    Oral Oncol, 2014 May;50(5):404-12.
    PMID: 24613650 DOI: 10.1016/j.oraloncology.2014.02.005
    Oral cancer is a multifactorial disease in which both environmental and genetic factors contribute to the aetiopathogenesis. Oral cancer is the sixth most common cancer worldwide with a higher incidence among Melanesian and South Asian countries. More than 90% of oral cancers are oral squamous cell carcinoma (OSCC). The present study aimed to determine common genomic copy number alterations (CNAs) and their frequency by including 12 studies that have been conducted on OSCCs using array comparative genomic hybridization (aCGH). In addition, we reviewed the literature dealing with CNAs that drive oral precursor lesions to the invasive tumors. Results showed a sequential accumulation of genetic changes from oral precursor lesions to invasive tumors. With the disease progression, accumulation of genetic changes increases in terms of frequency, type and size of the abnormalities, even on different regions of the same chromosome. Gains in 3q (36.5%), 5p (23%), 7p (21%), 8q (47%), 11q (45%), 20q (31%) and losses in 3p (37%), 8p (18%), 9p (10%) and 18q (11%) were the most common observations among those studies. However, losses are less frequent than gains but it appears that they might be the primary clonal events in causing oral cancer.
    Matched MeSH terms: DNA Copy Number Variations*
  4. Phenotypic screening and molecular analysis of blast resistance in fragrant rice for marker assisted selection
    Khan MA, Sen PP, Bhuiyan R, Kabir E, Chowdhury AK, Fukuta Y, et al.
    C. R. Biol., 2014 May;337(5):318-24.
    PMID: 24841958 DOI: 10.1016/j.crvi.2014.02.007
    Experiments were conducted to identify blast-resistant fragrant genotypes for the development of a durable blast-resistant rice variety during years 2012-2013. The results indicate that out of 140 test materials including 114 fragrant germplasms, 25 differential varieties (DVs) harbouring 23 blast-resistant genes, only 16 fragrant rice germplasms showed comparatively better performance against a virulent isolate of blast disease. The reaction pattern of single-spore isolate of Magnaporthe oryzae to differential varieties showed that Pish, Pi9, Pita-2 and Pita are the effective blast-resistant genes against the tested blast isolates in Bangladesh. The DNA markers profiles of selected 16 rice germplasms indicated that genotype Chinigura contained Pish, Pi9 and Pita genes; on the other hand, both BRRI dhan50 and Bawaibhog contained Pish and Pita genes in their genetic background. Genotypes Jirakatari, BR5, and Gopalbhog possessed Pish gene, while Uknimodhu, Deshikatari, Radhunipagol, Kalijira (3), Chinikanai each contained the Pita gene only. There are some materials that did not contain any target gene(s) in their genetic background, but proved resistant in pathogenicity tests. This information provided valuable genetic information for breeders to develop durable blast-resistant fragrant or aromatic rice varieties in Bangladesh.
    Matched MeSH terms: DNA, Plant/genetics
  5. Fulltext Inherited Anti-Thrombin Deficiency in A Malay-Malaysian Family: A Missense Mutation at Nucleotide g.13267C>A aka anti-thrombin Budapest 5 (p.Pro439Thr) of the SERPINC 1 gene
    Norlelawati AT, Rusmawati I, Naznin M, Nur Nadia O, Rizqan Aizzani R, Noraziana AW
    Med J Malaysia, 2014 Feb;69(1):27-30.
    PMID: 24814625 MyJurnal
    OBJECTIVE: Inherited anti-thrombin deficiency is an autosomal dominant disorder which is associated with increased risk for venous thromboembolism (VTE). This condition is very rare in Malaysia and there has been no documented report. Thus, the aim of the present study is to investigate the type of an inherited anti-thrombin deficiency mutation in a 25-year-old Malay woman who presented with deep vein thrombosis in her first pregnancy.

    METHODS: DNA was extracted from the patient's blood sample and buccal mucosal swabs from family members. Polymerase chain reaction(PCR) assays were designed to cover all seven exons of the serpin peptidase inhibitor, clade C (antithrombin), member 1 (SERPINC1) gene; and the products were subjected to DNA sequencing. Sequences were referred to NCBI Reference Sequence: NG_012462.1.

    RESULTS: A heterozygous substitution mutation at nucleotide position 13267 (CCT->ACT) was identified in the patient and two other family members, giving a possible change of codon 439 (Pro→Thr) also known as anti-thrombin Budapest 5. The genotype was absent in 90 healthy controls.

    CONCLUSION: The study revealed a heterozygous antithrombin Budapest 5 mutation in SERPINC 1 giving rise to a possible anti-thrombin deficiency in a Malay-Malaysian family.
    Matched MeSH terms: DNA; Sequence Analysis, DNA
  6. Fulltext Quorum sensing activity of Hafnia alvei isolated from packed food
    Tan JY, Yin WF, Chan KG
    Sensors (Basel), 2014 Apr 14;14(4):6788-96.
    PMID: 24736131 DOI: 10.3390/s140406788
    Quorum sensing (QS) is a mechanism adopted by bacteria to regulate expression of genes according to population density. N-acylhomoserine lactones (AHLs) are a type of QS signalling molecules commonly found in Gram-negative bacteria which have been reported to play a role in microbial spoilage of foods and pathogenesis. In this study, we isolated an AHL-producing Hafnia alvei strain (FB1) from spherical fish pastes. Analysis via high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS) on extracts from the spent supernatant of H. alvei FB1 revealed the existence of two short chain AHLs: N-(3-oxohexanoyl) homoserine lactone (3-oxo-C6-HSL) and N-(3-oxo- octanoyl) homoserine lactone (3-oxo-C8-HSL). To our knowledge, this is the first report of the production of AHLs, especially 3-oxo-C8-HSL, by H. alvei.
    Matched MeSH terms: DNA, Ribosomal/genetics
  7. Fulltext Efficient oil palm total RNA extraction with a total RNA extraction kit
    Habib SH, Saud HM, Kausar H
    Genet. Mol. Res., 2014;13(2):2359-67.
    PMID: 24781991 DOI: 10.4238/2014.April.3.8
    Oil palm tissues are rich in polyphenols, polysaccharides and secondary metabolites; these can co-precipitate with RNA, causing problems for downstream applications. We compared two different methods (one conventional and a kit-based method - Easy-Blue(TM) Total RNA Extraction Kit) to isolate total RNA from leaves, roots and shoot apical meristems of tissue culture derived truncated leaf syndrome somaclonal oil palm seedlings. The quality and quantity of total RNA were compared through spectrophotometry and formaldehyde gel electrophoresis. The specificity and applicability of the protocols were evaluated for downstream applications, including cDNA synthesis and RT-PCR analysis. We found that the conventional method gave higher yields of RNA but took longer, and it was contaminated with genomic DNA. This method required extra genomic DNA removal steps that further reduced the RNA yield. The kit-based method, on the other hand, produced good yields as well as well as good quality RNA, within a very short period of time from a small amount of starting material. Moreover, the RNA from the kit-based method was more suitable for synthesizing cDNA and RT-PCR amplification than the conventional method. Therefore, we conclude that the Easy-BlueTM Total RNA Extraction Kit method is suitable and superior for isolation of total RNA from oil palm leaf, root and shoot apical meristem.
    Matched MeSH terms: DNA, Complementary/genetics*
  8. Potential halophilic cellulases for in situ enzymatic saccharification of ionic liquids pretreated lignocelluloses
    Gunny AA, Arbain D, Edwin Gumba R, Jong BC, Jamal P
    Bioresour Technol, 2014 Mar;155:177-81.
    PMID: 24457303 DOI: 10.1016/j.biortech.2013.12.101
    Ionic liquids (ILs) have been used as an alternative green solvent for lignocelluloses pretreatment. However, being a salt, ILs exhibit an inhibitory effect on cellulases activity, thus making the subsequent saccharification inefficient. The aim of the present study is to produce salt-tolerant cellulases, with the rationale that the enzyme also tolerant to the presence of ILs. The enzyme was produced from a locally isolated halophilic strain and was characterized and assessed for its tolerance to different types of ionic liquids. The results showed that halophilic cellulases produced from Aspergillus terreus UniMAP AA-6 exhibited higher tolerance to ILs and enhanced thermo stability in the presence of high saline conditions.
    Matched MeSH terms: DNA Primers/genetics
  9. Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol
    Cheng KK, Lee BS, Masuda T, Ito T, Ikeda K, Hirayama A, et al.
    Nat Commun, 2014;5:3233.
    PMID: 24481126 DOI: 10.1038/ncomms4233
    Comparative whole-genome sequencing enables the identification of specific mutations during adaptation of bacteria to new environments and allelic replacement can establish their causality. However, the mechanisms of action are hard to decipher and little has been achieved for epistatic mutations, especially at the metabolic level. Here we show that a strain of Escherichia coli carrying mutations in the rpoC and glpK genes, derived from adaptation in glycerol, uses two distinct metabolic strategies to gain growth advantage. A 27-bp deletion in the rpoC gene first increases metabolic efficiency. Then, a point mutation in the glpK gene promotes growth by improving glycerol utilization but results in increased carbon wasting as overflow metabolism. In a strain carrying both mutations, these contrasting carbon/energy saving and wasting mechanisms work together to give an 89% increase in growth rate. This study provides insight into metabolic reprogramming during adaptive laboratory evolution for fast cellular growth.
    Matched MeSH terms: DNA-Directed RNA Polymerases/genetics*
  10. Identification and characterization of RAPD-SCAR markers linked to glyphosate-susceptible and -resistant biotypes of Eleusine indica (L.) Gaertn
    Cha TS, Anne-Marie K, Chuah TS
    Mol Biol Rep, 2014 Feb;41(2):823-31.
    PMID: 24374894 DOI: 10.1007/s11033-013-2922-7
    Eleusine indica is one of the most common weed species found in agricultural land worldwide. Although herbicide-glyphosate provides good control of the weed, its frequent uses has led to abundant reported cases of resistance. Hence, the development of genetic markers for quick detection of glyphosate-resistance in E. indica population is imperative for the control and management of the weed. In this study, a total of 14 specific random amplified polymorphic DNA (RAPD) markers were identified and two of the markers, namely S4R727 and S26R6976 were further sequence characterized. Sequence alignment revealed that marker S4R727 showing a 12-bp nucleotides deletion in resistant biotypes, while marker S26R6976 contained a 167-bp nucleotides insertion in the resistant biotypes. Based on these sequence differences, three pairs of new sequence characterized amplified region (SCAR) primers were developed. The specificity of these primer pairs were further validated with genomic DNA extracted from ten individual plants of one glyphosate-susceptible and five glyphosate-resistant (R2, R4, R6, R8 and R11) populations. The resulting RAPD-SCAR markers provided the basis for assessing genetic diversity between glyphosate-susceptible and -resistant E. indica biotypes, as well for the identification of genetic locus link to glyphosate-resistance event in the species.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique/methods*
  11. Mitochondrial DNA diversity of mud crab Scylla olivacea (Portunidae) in Peninsular Malaysia: a preliminary assessment
    Rosly HA, Nor SA, Yahya K, Naim DM
    Mol Biol Rep, 2013 Nov;40(11):6407-18.
    PMID: 24062076 DOI: 10.1007/s11033-013-2755-4
    A primary factor in population management and wildlife conservation is the delineation of population units derived from descriptions of population genetic structure. Yet, predicting factors that influence the patterns of gene flow in a population particularly at landscape scales remains a major challenge in evolutionary biology. Here we report a population genetic study of the mud crab Scylla olivacea examined based on a 542 bp segment of the mitochondrial DNA cytochrome c oxidase I gene among 91 individuals from six localities in the west and east coast of Peninsular Malaysia. In total 55 unique haplotypes were distinguished with 45 private haplotypes and a single common haplotype shared among all populations studied. The other ten haplotypes were shared among various populations. The sharing of this haplotype reflects the connection of the mangrove areas between east and west coast of Peninsular Malaysia. High haplotype diversity (h = 0.968 ± 0.021; mean ± SD) and low nucleotide diversity (π = 0.120 ± 0.015; mean ± SD) were displayed, which may be indicative of genetic bottleneck events. No significant phylogenetic lineages were recognized using neighbour-joining and maximum parsimony methods. Hierarchical AMOVA analysis indicated that 99.33 % of the genetic variation was contained within populations and 0.67 % occurred among populations, suggesting no geographical patterning among populations studied, supported by F st test. Mismatch distribution analysis showed that the observed distribution of the pairwise mutation differences among haplotypes was multimodal, which is not concordant with a sudden range expansion scenario. However, neutrality tests showed non-significant negative values suggesting that the populations studied may have experienced past population growth, but the expansion may have been restricted to separate local areas that resulted in the non-significant negative Fu's Fs and Tajima's D value. Overall, this present preliminary study was able to be a reference on the phylogenetic relationships and assessment of genetic structure of Scylla sp. in Malaysia.
    Matched MeSH terms: DNA, Mitochondrial/genetics*
  12. Fulltext Cytotoxicity and genotoxicity assessment of Euphorbia hirta in MCF-7 cell line model using comet assay
    Ping KY, Darah I, Chen Y, Sasidharan S
    Asian Pac J Trop Biomed, 2013 Sep;3(9):692-6.
    PMID: 23998008 DOI: 10.1016/S2221-1691(13)60140-9
    To evaluate the cytotoxicity and genotoxicity activity of Euphorbia hirta (E. hirta) in MCF-7 cell line model using comet assay.
    Matched MeSH terms: DNA Damage*
  13. Fulltext Genetic assemblage of Sarcocystis spp. in Malaysian snakes
    Lau YL, Chang PY, Subramaniam V, Ng YH, Mahmud R, Ahmad AF, et al.
    Parasit Vectors, 2013 Sep 09;6(1):257.
    PMID: 24010903 DOI: 10.1186/1756-3305-6-257
    BACKGROUND: Sarcocystis species are protozoan parasites with a wide host range including snakes. Although there were several reports of Sarcocytis species in snakes, their distribution and prevalence are still not fully explored.

    METHODS: In this study, fecal specimens of several snake species in Malaysia were examined for the presence of Sarcocystis by PCR of 18S rDNA sequence. Microscopy examination of the fecal specimens for sporocysts was not carried as it was difficult to determine the species of the infecting Sarcocystis.

    RESULTS: Of the 28 snake fecal specimens, 7 were positive by PCR. BLASTn and phylogenetic analyses of the amplified 18S rDNA sequences revealed the snakes were infected with either S. nesbitti, S. singaporensis, S. zuoi or undefined Sarcocystis species.

    CONCLUSION: This study is the first to report Sarcocystis infection in a cobra, and S. nesbitti in a reticulated python.

    Matched MeSH terms: DNA, Protozoan/genetics
  14. Fulltext Assessment of genotoxicity and cytotoxicity of standardized aqueous extract from leaves of Erythroxylum cuneatum in human HepG2 and WRL68 cells line
    Wesam RK, Ghanya AN, Mizaton HH, Ilham M, Aishah A
    Asian Pac J Trop Med, 2013 Oct;6(10):811-6.
    PMID: 23870471 DOI: 10.1016/S1995-7645(13)60143-1
    OBJECTIVE: To investigate the cytotoxicity and the genotoxicity of standardized aqueous of dry leaves of Erythroxylum cuneatum (E. cuneatum) in human HepG2 and WRL68 cells.

    METHODS: The cytotoxicity of E. cuneatum extract was evaluated by both MTS and LDH assays. Genotoxicity study on E. cuneatum extract was assessed by the single cell gel electrophoresis (comet assay). The protective effect of E. cuneatum against menadione-induced cytotoxicity was also investigated.

    RESULTS: Results from this study showed that E. cuneatum extract exhibited cytotoxic activities towards the cells with IC50 value of (125±12) and (125±14) μg/mL for HepG2 and WRL68 cells respectively, after 72 h incubation period as determined by MTS assay. LDH leakage was detected at (251±19) and (199.5±12.0) μg/mL for HepG2 and WRL68 respectively. Genotoxicity study results showed that treatment with E. cuneatum up to 1 mg/mL did not cause obvious DNA damage in WRL68 and HepG2 cells. Addition of E. cunaetum did not show significant protection towards menadione in WRL68 and HepG2 Cells.

    CONCLUSIONS: E. cuneatum standardized aqueous extract might be developed in order to establish new pharmacological possibilities for its application.

    Matched MeSH terms: DNA Damage/drug effects
  15. Fulltext Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification
    Teoh BT, Sam SS, Tan KK, Johari J, Danlami MB, Hooi PS, et al.
    BMC Infect Dis, 2013;13:387.
    PMID: 23964963 DOI: 10.1186/1471-2334-13-387
    BACKGROUND: Early and rapid detection of dengue virus (DENV) infection during the febrile period is crucial for proper patient management and prevention of disease spread. An easy to perform and highly sensitive method is needed for routine implementation especially in the resource-limited rural healthcare settings where dengue is endemic.
    METHODS: A single-tube reverse transcription-loop-mediated isothermal amplification (RT-LAMP) assay with a set of nine primers was developed for the detection of all four DENV serotypes and their different genotypes. The sensitivity and specificity of the RT-LAMP were evaluated. The clinical applicability of RT-LAMP assay for detection of DENV RNA was assessed in a total of 305 sera of clinically-suspected dengue patients. The test results of RT-LAMP were statistically compared to those of quantitative reverse transcription-polymerase chain reaction (qRT-PCR), IgM- and IgG-capture enzyme-linked immunosorbent assays (ELISA).
    RESULTS: Acute DENV infection was confirmed in 171 samples (n = 305); 43.3% (74/171) and 46.8% (80/171) of the samples were positive for DENV using RT-LAMP and qRT-PCR, respectively. The combination of RT-LAMP with the dengue IgM and IgG ELISA increased detection of acute DENV infection to 97.7% (167/171), in comparison to only 70.8% (121/171) when dengue IgM and IgG ELISA alone were used. The RT-LAMP assays showed high concordance (κ = 0.939) with the qRT-PCR. The RT-LAMP assay detected up to 10 copies of virus RNA within an hour but 100% reproducibility (12/12) was achieved with 100 copies. There was no cross reactivity of RT-LAMP with other closely related arboviruses.
    CONCLUSION: The RT-LAMP assay developed in this study is sensitive, specific and simple to perform. The assay improved the detection of dengue when used in combination with serological methods.
    Matched MeSH terms: DNA Primers/genetics
  16. Detection of Neospora caninum DNA in semen of experimental infected rams with no evidence of horizontal transmission in ewes
    Syed-Hussain SS, Howe L, Pomroy WE, West DM, Smith SL, Williamson NB
    Vet Parasitol, 2013 Nov 8;197(3-4):534-42.
    PMID: 23819894 DOI: 10.1016/j.vetpar.2013.06.002
    Recent reports from New Zealand indicate Neospora caninum has a possible role in causing abortions in sheep. Transmission of N. caninum via semen has been documented in cattle. This study aimed to investigate if horizontal transmission through semen was also possible in sheep. Initially, 6-month old crossbred ram lambs (n=32), seronegative to N. caninum, were divided into 4 equal groups. Group 1 remained uninoculated whilst the remainder were inoculated with N. caninum tachyzoites intravenously as follows: Group 2 - 50 tachyzoites; Group 3 - 10(3) tachyzoites; Group 4 - 10(7) tachyzoites. Semen samples were collected weekly for 8 weeks for the detection of N. caninum DNA and quantified using quantitative PCR (qPCR). Plasma collected 1 month post-inoculation was subjected to ELISA (IDEXX Chekit) and Western blot. At 2 weeks post-infection, three rams from Group 1 (uninoculated) and three rams from Group 4 (10(7)tachyzoites/ml) were mated with two groups of 16 ewes over two oestrus cycles. Ewe sera collected 1 and 2 months post-mating were tested for seroconversion by ELISA and Western blot. All experimentally infected rams seroconverted by 1 month with ELISA S/P% values ranging from 11% to 36.5% in Group 2, 12-39.5% in Group 3 and 40-81% in Group 4. However, none of the ewes mated with the experimentally infected rams seroconverted. For the Western blot, responses towards immunodominant antigens (IDAs) were observed in ram sera directed against proteins at 10, 17, 21, 25-29, 30, 31, 33 and 37 kDa. Rams in Group 2, 3 and 4 were noted to have at least 3 IDAs present. None of the ewes showed any of the 8 prominent IDAs except for the one at 21 kDa which was seen in 30 out of 32 ewes in both groups. N. caninum DNA was detected intermittently in the ram's semen up to 5 weeks post-inoculation with the concentrations ranging from that equivalent to 1-889 tachyzoites per ml of semen. Low concentrations of N. caninum DNA were also detected in the brain tissue of two rams (Groups 1 and 4). These results suggest that although N. caninum DNA can be found in the semen of experimentally infected rams, the transmission of N. caninum via natural mating is an unlikely event.
    Matched MeSH terms: DNA, Protozoan/isolation & purification*
  17. Inheritance studies of SSR and ISSR molecular markers and phylogenetic relationship of rice genotypes resistant to tungro virus
    Latif MA, Rahman MM, Ali ME, Ashkani S, Rafii MY
    C. R. Biol., 2013 Mar;336(3):125-33.
    PMID: 23643394 DOI: 10.1016/j.crvi.2012.12.002
    Multivariate analyses were performed using 13 morphological traits and 13 molecular markers (10 SSRs and three ISSRs) to assess the phylogenetic relationship among tungro resistant genotypes. For morphological traits, the genotypes were grouped into six clusters, according to D(2) statistic and Canonical vector analysis. Plant height, days to flowering, days to maturity, panicle length, number of spikelet per panicle, number of unfilled grain per panicle and yield were important contributors to genetic divergence in 14 rice genotypes. Based on Nei's genetic distance for molecular studies, seven clusters were formed among the tungro resistant and susceptible genotypes. Mantel's test revealed a significant correlation (r = 0.834*) between the morphological and molecular data. To develop high yielding tungro resistant varieties based on both morphological and molecular analyses, crosses could be made with susceptible (BR10 and BR11) genotypes with low yielding but highly resistant genotypes, Sonahidemota, Kumragoir, Nakuchimota, Khaiyamota, Khairymota and Kachamota. The chi-square analysis for seven alleles (RM11, RM17, RM20, RM23, RM80, RM108 and RM531) of SSR and five loci (RY1, MR1, MR2, MR4 and GF5) of three ISSR markers in F2 population of cross, BR11×Sonahidemota, showed a good fit to the expected segregation ratio (1:2:1) for a single gene model.
    Matched MeSH terms: DNA, Plant/genetics
  18. Fulltext Vancomycin-resistant Enterococcus faecium of multi locus sequence type 18 in Malaysia
    Poh LW, Rukman AW, Cheah YK, Norital Z, Nazri AM, Mariana NS
    Med J Malaysia, 2012 Dec;67(6):639-40.
    PMID: 23770967 MyJurnal
    Vancomycin-resistant Enterococcus faecium (VREF) in human infections mostly belong to the high-risk, epidemic, clonal complex-17 (CC17) group. Treatment limitation and high conjugation frequency makes it dominant in hospitals worldwide. We investigated positive cultures by Pulse-field gel electrophoresis (PFGE), multi locus sequence typing (MLST). DNA of two strains (A2 and C) appeared to be clonally related by PFGE. Three strains were of ST 18 type (A1, B and C) and strain A2 is of a new ST 596. This ST 18 type strain found in our study is crucial and is believed to be the first in Malaysia.
    Matched MeSH terms: DNA, Bacterial/genetics
  19. First molecular identification of Entamoeba moshkovskii in Malaysia
    Anuar TS, Al-Mekhlafi HM, Ghani MK, Azreen SN, Salleh FM, Ghazali N, et al.
    Parasitology, 2012 Oct;139(12):1521-5.
    PMID: 22939193 DOI: 10.1017/S0031182012001485
    Entamoeba moshkovskii and Entamoeba dispar are microscopically indistinguishable from the pathogenic species Entamoeba histolytica. Although sporadic cases of human infection with E. moshkovskii have been reported, the amoeba is still considered primarily as a free-living amoeba. A cross-sectional study was carried out among Orang Asli communities in 3 different states of Peninsular Malaysia. Fecal samples were examined by formalin-ether sedimentation and trichrome staining techniques and then single-round PCR assay was used to detect E. moshkovskii. Out of 500 fecal samples examined microscopically, 93 (18·6%) samples were positive for E. histolytica/E. dispar/E. moshkovskii complex cysts and/or trophozoites. PCR products were detected in 106 fecal samples. E. moshkovskii isolates were detected in 13 (12·3%) fecal samples. Of the 13 E. moshkovskii-positive samples, 5 were of single isolation of E. moshkovskii, 6 were also positive for E. dispar, and only 2 samples were positive for E. dispar and E. histolytica. Moreover, 3 E. moshkovskii-positive samples were collected from symptomatic individuals while the remaining 10 samples were from asymptomatic subjects. This is the first report on the identification of E. moshkovskii in Malaysia. Further studies are needed to confirm the pathogenicity of E. moshkovskii infection and determine the epidemiology among Orang Asli communities in Malaysia.
    Matched MeSH terms: DNA, Protozoan/genetics
  20. Enhancing the efficiency of polymerase chain reaction using graphene nanoflakes
    Abdul Khaliq R, Kafafy R, Salleh HM, Faris WF
    Nanotechnology, 2012 Nov 16;23(45):455106.
    PMID: 23085573 DOI: 10.1088/0957-4484/23/45/455106
    The effect of the recently developed graphene nanoflakes (GNFs) on the polymerase chain reaction (PCR) has been investigated in this paper. The rationale behind the use of GNFs is their unique physical and thermal properties. Experiments show that GNFs can enhance the thermal conductivity of base fluids and results also revealed that GNFs are a potential enhancer of PCR efficiency; moreover, the PCR enhancements are strongly dependent on GNF concentration. It was found that GNFs yield DNA product equivalent to positive control with up to 65% reduction in the PCR cycles. It was also observed that the PCR yield is dependent on the GNF size, wherein the surface area increases and augments thermal conductivity. Computational fluid dynamics (CFD) simulations were performed to analyze the heat transfer through the PCR tube model in the presence and absence of GNFs. The results suggest that the superior thermal conductivity effect of GNFs may be the main cause of the PCR enhancement.
    Matched MeSH terms: DNA/analysis
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