Displaying publications 81 - 100 of 1097 in total

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  1. Ernieenor FCL, NorJaiza MJ, Fadillah A, Canedy J, Mariana A
    Exp Appl Acarol, 2021 May;84(1):171-182.
    PMID: 33826009 DOI: 10.1007/s10493-021-00609-3
    Orientia tsutsugamushi is the causative agent of scrub typhus vectored by larval stages of trombiculid mites (chiggers) that occur in most tropical regions of Southeast Asia. A total of 242 chiggers extracted from eight small mammals captured from a positive scrub typhus locality in Kelantan, Malaysia, were screened for the presence of O. tsutsugamushi. The chiggers were grouped in 16 pools for extraction of DNA prior to screening of O. tsutsugamushi based on the nucleotide sequence of 56-kDa type specific antigen (TSA) gene using nested polymerase chain reaction. Two species of on-host chiggers were identified, the one, Leptotrombidium deliense, much more dominant (94.8%) than the other, Ascoshoengastia sp. (5.2%). The pathogen was detected in two pools (12.5%) of L. deliense recovered from Rattus rattus and Tupaia sp. The 56-kDa TSA gene sequence analysis revealed the O. tsutsugamushi harboured in those chiggers were Karp prototype strain with high similarity (99.3%). Findings of this study strongly supported the existence of scrub typhus infections in certain parts of Malaysia which agrees with previous local reports. Moreover, this study highlighted the pressing need of a large-scale close observation of O. tsutsugamushi DNA sequences from chiggers that can probably be collected from other positive scrub typhus localities to precisely provide the distribution and prevalence of this zoonotic pathogen.
    Matched MeSH terms: Genotype
  2. Teh CSJ, Yap PSX, Zulkefli NJ, Subramaniam P, Sit PS, Kong ZX, et al.
    Transbound Emerg Dis, 2021 Jan 27.
    PMID: 33506647 DOI: 10.1111/tbed.14005
    Burkholderia pseudomallei, a Gram-negative bacterial pathogen that causes melioidosis, is of public health importance in endemic areas including Malaysia. An investigation of the molecular epidemiology links of B. pseudomallei would contribute to better understanding of the clonal relationships, transmission dynamics and evolutionary change. Multi-locus sequence typing (MLST) of 45 clinical B. pseudomallei isolates collected from sporadic meliodosis cases in Malaysia was performed. In addition, a total of 449 B. pseudomallei Malaysian strains submitted to the MLST database from 1964 until 2019 were included in the temporal analysis to determine the endemic sequence types (STs), emergence and re-emergence of ST(s). In addition, strain-specific distribution was evaluated using BURST tool. Genotyping of 45 clinical strains were resolved into 12 STs and the majority were affiliated with ST46 (n=11) and ST1342 (n=7). Concomitantly, ST46 was the most prevalent ST in Malaysia which first reported in 1964. All the Malaysian B. pseudomallei strains were resolved into 76 different STs with 36 of them uniquely present only in Malaysia. ST1342 was most closely related to ST1034, in which both STs were unique to Malaysia and first isolated from soil samples in Pahang, a state in Malaysia. The present study revealed a high diversity of B. pseudomallei in Malaysia. Localised evolution giving rise to the emergence of new STs was observed, suggesting that host and environmental factors play a crucial role in the evolutionary changes of B. pseudomallei.
    Matched MeSH terms: Genotype
  3. Jani J, Abu Bakar SF, Mustapha ZA, Ling CK, Teo R, Ahmed K
    Microbiol Resour Announc, 2020 Jan 09;9(2).
    PMID: 31919173 DOI: 10.1128/MRA.01322-19
    This is a report on the whole-genome sequence of Mycobacterium tuberculosis strain SBH163, which was isolated from a patient in the Malaysian Borneo state of Sabah. This report provides insight into the molecular characteristics of an M. tuberculosis Beijing genotype strain related to strains from Russia and South Africa.
    Matched MeSH terms: Genotype
  4. Lau WC, Rafii MY, Ismail MR, Puteh A, Latif MA, Ramli A
    Front Plant Sci, 2015;6:832.
    PMID: 26528304 DOI: 10.3389/fpls.2015.00832
    After yield, quality is one of the most important aspects of rice breeding. Preference for rice quality varies among cultures and regions; therefore, rice breeders have to tailor the quality according to the preferences of local consumers. Rice quality assessment requires routine chemical analysis procedures. The advancement of molecular marker technology has revolutionized the strategy in breeding programs. The availability of rice genome sequences and the use of forward and reverse genetics approaches facilitate gene discovery and the deciphering of gene functions. A well-characterized gene is the basis for the development of functional markers, which play an important role in plant genotyping and, in particular, marker-assisted breeding. In addition, functional markers offer advantages that counteract the limitations of random DNA markers. Some functional markers have been applied in marker-assisted breeding programs and have successfully improved rice quality to meet local consumers' preferences. Although functional markers offer a plethora of advantages over random genetic markers, the development and application of functional markers should be conducted with care. The decreasing cost of sequencing will enable more functional markers for rice quality improvement to be developed, and application of these markers in rice quality breeding programs is highly anticipated.
    Matched MeSH terms: Genotype
  5. Aldoghachi, Asraa Faris, Cheah, Pike-See, Normala Ibrahim, Lye, Munn Sann, Ling, King-Hwa
    MyJurnal
    Major depressive disorder (MDD) is a serious mental illness with a multifactorial aetiology that was shown to influence behaviour and affect cognition. Previous research has favoured the involvement of dopamine in the aetiology of the disorder, and since one of the critical regulators of the dopamine levels and activity in the brain is DAT1, the present study investigated the association of a single nucleotide polymorphism in the DAT1gene (rs40184) and MDD in the Malaysian population. A total of 300cases and 300 matched controls were recruited from four Klang valley hospitals and were screened for DAT1rs40184 using high resolution melting assays. The allele and genotype frequencies were analysed by using Chi-square. Hardy Weinberg equilibrium for the distribution of alleles and genotypes was tested by using Chi-square. Determination of the association between rs40184 and MDD was achieved by conditional logistic regression using SPSS. In the present study, no significant association was obtained between DAT1and MDD in the Malaysianpopulation.
    Matched MeSH terms: Genotype
  6. Angelopoulou E, Paudel YN, Papageorgiou SG, Piperi C
    ACS Chem Neurosci, 2021 08 04;12(15):2749-2764.
    PMID: 34275270 DOI: 10.1021/acschemneuro.1c00295
    Alzheimer's disease (AD) is the most common neurodegenerative disorder with obscure pathogenesis and no disease-modifying therapy to date. AD is multifactorial disease that develops from the complex interplay of genetic factors and environmental exposures. The E4 allele of the gene encoding apolipoprotein E (APOE) is the most common genetic risk factor for AD, whereas the E2 allele acts in a protective manner. A growing amount of epidemiological evidence suggests that several lifestyle habits and environmental factors may interact with APOE alleles to synergistically affect the risk of AD development. Among them, physical exercise, dietary habits including fat intake and ketogenic diet, higher education, traumatic brain injury, cigarette smoking, coffee consumption, alcohol intake, and exposure to pesticides and sunlight have gained increasing attention. Although the current evidence is inconsistent, it seems that younger APOE4 carriers in preclinical stages may benefit mostly from preventive lifestyle interventions, whereas older APOE4 noncarriers with dementia may show the most pronounced effects. The large discrepancies between the epidemiological studies may be attributed to differences in the sample sizes, the demographic characteristics of the participants, including age and sex, the methodological design, and potential related exposures and comorbidities as possible cofounding factors. In this Review, we aim to discuss available evidence of the prominent APOE genotype-environment interactions in regard to cognitive decline with a focus on AD, providing an overview of the current landscape in this field and suggesting future directions.
    Matched MeSH terms: Genotype
  7. Samsir SA, Bunawan H, Yen CC, Noor NM
    Data Brief, 2016 Sep;8:1438-42.
    PMID: 27617279 DOI: 10.1016/j.dib.2016.08.016
    In this dataset, we present 15 Simple Sequence Repeat (SSR) markers with the motifs (AC)n, (GA)n, and (AC)n(AG)n using a ISSR-Suppression-PCR technique in order to discriminate Garcinia mangostana from diverse geographical origins in Peninsular Malaysia. A few loci showed differences between 3 and 6 bp in allele size, indicating that there are some polymorphisms between individuals correlating to the number of SSR repeats that may be useful for differentiate of genotypes. Collectively, these data show that the ISSR-Suppression-PCR is a valuable method to illustrate genetic variation of selected G. mangostana in Malaysia.
    Matched MeSH terms: Genotype
  8. Haque M, Islam SMS, Subramaniam S
    3 Biotech, 2017 May;7(1):63.
    PMID: 28452013 DOI: 10.1007/s13205-017-0675-z
    An efficient callus induction and plant regeneration system has been developed using salt and heat as pre-treatment factors for three barley genotypes viz. BB-3, BB-6 and BHL-18. Different concentrations of NaCl (1.5, 2.5, 3.5, 4.5, 5.5 and 6.5 g/L) were used and its effects were determined on the basis of the viability of callus (CV), plant regeneration (PR), relative growth rate (RGR) and tolerance index (TI). The BB-6 showed highest performance on tolerance based on CV (14.72%), PR (7.69%), RGR (0.91%) and TI (0.42%) at 6.5 g/L NaCl. Various NaCl concentrations displayed significantly differences at P 
    Matched MeSH terms: Genotype
  9. Lind CE, Kilian A, Benzie JAH
    Anim. Genet., 2017 Jun;48(3):362-364.
    PMID: 28094451 DOI: 10.1111/age.12536
    The development of genomic markers is described for Nile tilapia, Oreochromis niloticus, using the Diversity Arrays Technology (DArT) genotype-by-sequencing platform. A total of 13 215 single nucleotide polymorphism (SNP) markers and 12 490 silicoDArT (dominant) markers were identified from broodstock of two selective breeding programs [Genetically Improved Farmed Tilapia (GIFT) strain from Malaysia and the Abbassa strain from Egypt]. Over 10 000 SNPs were polymorphic in either strain, and 2985 and 3087 showed strain-specific polymorphisms for the GIFT and Abbassa strains respectively. We demonstrate the potential utility of these markers for rapid genomic screening and use in breeding programs.
    Matched MeSH terms: Genotype
  10. Zaidah AR, Mohammad NI, Suraiya S, Harun A
    PMID: 28473912 DOI: 10.1186/s13756-017-0200-5
    BACKGROUND: Infections by multidrug-resistant gram-negative bacteria (MDR-GNB) have been continuously growing and pose challenge to health institution globally. Carbapenem-resistant Enterobacteriacea (CRE) was identified as one of the MDR-GNB which has limited treatment options and higher mortality compared to those of sensitive strains. We report an increased burden of CRE fecal carriage at a hospital in the North-eastern region of Malaysia.

    METHODS: A retrospective descriptive study from August 2013 to December 2015 was conducted in the Medical Microbiology & Parasitology laboratory of Hospital Universiti Sains Malaysia, which is a tertiary teaching hospital with more than 700 beds. This hospital treats patients with various medical and surgical conditions. Suspected CRE from any clinical specimens received by the laboratory was identified and confirmed using standard protocols. Polymerase chain reaction (PCR) assay was performed to determine the genotype.

    RESULTS: Altogether, 8306 Enterobacteriaceae was isolated from various clinical specimens during the study period and 477/8306 (5.74%) were CRE. Majority of the isolated CRE were Klebsiella [408/477, (85.5%)], of which Klebsiella pneumoniae was the predominant species, 388/408 (95%). CRE were mainly isolated from rectal swab (screening), 235/477 (49.3%); urine, 76/477 (15.9%); blood, 46/477 (9.6%) and about 7.1% from tracheal aspirate. One hundred and thirty-six isolates were subjected to genotype determination and., 112/136 (82.4%) showed positive detection of New Delhi metallo-β-lactamase 1 (NDM-1) gene (blaNDM1).

    CONCLUSION: The study noted a high numbers of CRE isolated especially from rectal swabs. Active screening results in significant cost pressures and therefore should be revisited and revised, especially in low resource settings.

    Matched MeSH terms: Genotype
  11. Syafawati WU, Zefarina Z, Zafarina Z, Hassan MN, Norazmi MN, Panneerchelvam S, et al.
    Immunohematology, 2016 Dec;32(4):143-160.
    PMID: 28257229
    Matched MeSH terms: Genotype
  12. Asmah Awal, Nazatul Asikin Muda
    MyJurnal
    In this paper, a micropropagation protocol of sugar palm (Arenga pinnata Wurmb Merr) through callogenesis and somatic embryogenesis was examined. Callus induction frequency and somatic embryogenesis response were dependent on plant growth regulators (PGRs) and genotype. Semi-compact and compact embryogenic calluses were induced from excised immature zygotic embryo (IZE) cultured on semi-solid MS (Murashige & Skoog, 1962) medium supplemented with various concentration and combination of 2,4-dichlorophenoxyacetic acid (2,4-D) and 6-benzyl aminopurine acid (BAP). MS medium supplemented with 0.4 mg/L 2,4-D and 0.5 mg/L BAP was found optimum to induce 100% rate of embryogenic calluses and maximum degree of callus formation after 8 and 12 weeks of culture. The incorporation of increased sucrose concentration (60.0 g/L) and 2.0 g/L casein hydrolysate (CH) to the culture medium with similar PGRs composition enhanced the induction of globular somatic embryos (SEs), while addition of silver nitrate (AgNO3) produced SEs of different stages. SEs maturated in MS medium containing 1.0 mg/L BAP and 1.0 mg/L naphthalene-acetic acid (NAA) formed cotyledon-stage embryos. Clonal roots regeneration was obtained on half-strength MS devoid of PGRs after 4 months of culture. Frequent subcultures increased embryogenesis rate favourably.
    Matched MeSH terms: Genotype
  13. Nor Yusliza Kamaruddin, Shamsiah Abdullah
    MyJurnal
    This study looked at mutagenic effectiveness of gamma rays d on two varieties of Zingiber officinale Roscoe: Bentong and Tanjung Sepat. The rhizomes were exposed to different doses (0, 5, 7, 9, 11, 13 and 15 Gy) using Caesium-137 as source of the gamma rays. The effect of different gamma doses on the crude fibre composition of irradiated ginger was studied and genetic variability was assessed using molecular marker technique, RAPD. Findings showed different doses of gamma rays could induce variability in these two ginger varieties and the effect was found to be variety-dependent. Bentong variety irradiated with 9 Gy recorded 8.53% of crude fibre composition while Tanjung Sepat irradiated ginger with 5 Gy recorded 8.70% of crude fibre which gave the lowest composition compared with other irradiated ginger. A total of nine different arbitrary decamers were used as primers to amplify DNA from mutant plant material to assess their polymorphism level of ginger mutant lines. Polymorphism of all mutant lines was 97.62% indicating that there were significant changes in genetic sequences in irradiated ginger genotypes.
    Matched MeSH terms: Genotype
  14. Tariq Elhashim, M. Imad Mustafa Mahmud, Nasser Amjad, Norra Harun, Imad M. Alani
    MyJurnal
    Introduction: H. pylori BabA is an outer membrane protein that mediates bacterial adherence to the gastric
    epithelium, triggers several pathways during the course of infection, and thus contributes to the disease
    development. Considering the variability in the presence of BabA coding gene (babA2) among H. pylori
    clinical strains, the aim of this study was to assess the relationship between the genotype status of H. pylori
    babA2 and the severity of clinical and histopathological outcomes. Methods: Gastric mucosal biopsy
    specimens were collected from 30 CLO test-positive patients, 16 with gastritis and 14 with peptic ulcer
    disease. Polymerase chain reaction was carried out to detect the presence of H. pylori-specific glmM gene
    and BabA coding gene (babA2). Histopathological examination was performed to evaluate the severity of H.
    pylori-associated gastric disease according to the Updated Sydney Classification System. Results: The glmM
    and babA2 genes were present in 100% and 86.7% of the tested H. pylori strains, respectively. Although
    higher degrees of inflammatory activity and H. pylori density were noted in babA2-positive biopsy
    specimens, there was no statistically significant association between babA2 genotype status and the severity
    of gastric disease. Conclusion: The babA2 genotype status of H. pylori may not be considered as a sole
    marker for determining the infection outcomes.
    Matched MeSH terms: Genotype
  15. Tee YK, Balasundram SK, Ding P, M Hanif AH, Bariah K
    J Sci Food Agric, 2019 Mar 15;99(4):1700-1708.
    PMID: 30206959 DOI: 10.1002/jsfa.9359
    BACKGROUND: A series of fluorescence indices (anthocyanin, flavonol, chlorophyll and nitrogen balance) were deployed to detect the pigments and colourless flavonoids in cacao pods of three commercial cacao (Theobroma cacao L.) genotypes (QH1003, KKM22 and MCBC1) using a fast and non-destructive multiparametric fluorescence sensor. The aim was to determine optimum harvest periods (either 4 or 5 months after pod emergence) of commercial cacao based on fluorescence indices of cacao development and bean quality.

    RESULTS: As pod developed, cacao exhibited a rise with the peak of flavonol occurring at months 4 and 5 after pod maturity was initiated while nitrogen balance showed a decreasing trend during maturity. Cacao pods contained high chlorophyll as they developed but chlorophyll content declined significantly on pods that ripened at month 5.

    CONCLUSION: Cacao pods harvested at months 4 and 5 can be considered as commercially-ready as the beans have developed good quality and comply with the Malaysian standard on cacao bean specification. Thus, cacao pods can be harvested earlier when they reach maturity at month 4 after pod emergence to avoid germinated beans and over fermentation in ripe pods harvested at month 5. © 2018 Society of Chemical Industry.

    Matched MeSH terms: Genotype
  16. Mohd Aizat Zain, Nor Zuraida Zainal, Sharmilla Kanagasundram, Zahurin Mohamed
    Neuroscience Research Notes, 2018;1(1):11-20.
    MyJurnal
    Genetic hereditary has been implicated in bipolar disorder pathogenesis. The PDLIM5 and HTR2A genes have been investigated for its association with bipolar disorder in various populations, however, the results have been conflicting. In this study, we investigate the association between bipolar disorder and the two genes of interest, PDLIM5 and HTR2A genes. We recruited 253 bipolar disorder patients (75 Malays, 104 Chinese, and 74 Indians) and 505 control individuals (198 Malays, 155 Chinese, and 152 Indians) from three ethnic groups within Malaysian population. We genotyped for 3 SNPs of the PDLIM5 (rs2433320, rs2433322 and rs2438146) and 3 SNPs of the HTR2A (rs6313, rs2070040 and rs6311). Significant associations between bipolar disorder and each of the 3 SNPs of PDLIM5 in Malays, Indians and pooled samples. However, only rs2438146 remains significant in the Malays as co-dominant (T/T vs. C/C, p=0.004, OR=0.128, 95%CI=0.031-0.524) and recessive genetic models (T/T vs. C/T+C/C, p=0.003, OR=0.122, 95%CI=0.030-0.494) after applying conservative Bonferroni correction. Haplotype analysis of 3 SNPs of PDLIM5 also showed a significant association with bipolar disorder. No association was observed between bipolar disorder and each of the 3 SNPs of HTR2A in any of the ethnicities. We conclude that PDLIM5 polymorphisms are associated with bipolar disorder in the pooled analysis. After stratification to different ethnic groups, the association remains significant in the Malay and Indian groups. The association is also supported by the significant association in haplotype analysis of PDLIM5. We also conclude there is no association between the HTR2A polymorphisms in the Malaysian population.
    Matched MeSH terms: Genotype
  17. Sinding MS, Gopalakrishan S, Vieira FG, Samaniego Castruita JA, Raundrup K, Heide Jørgensen MP, et al.
    PLoS Genet, 2018 11;14(11):e1007745.
    PMID: 30419012 DOI: 10.1371/journal.pgen.1007745
    North America is currently home to a number of grey wolf (Canis lupus) and wolf-like canid populations, including the coyote (Canis latrans) and the taxonomically controversial red, Eastern timber and Great Lakes wolves. We explored their population structure and regional gene flow using a dataset of 40 full genome sequences that represent the extant diversity of North American wolves and wolf-like canid populations. This included 15 new genomes (13 North American grey wolves, 1 red wolf and 1 Eastern timber/Great Lakes wolf), ranging from 0.4 to 15x coverage. In addition to providing full genome support for the previously proposed coyote-wolf admixture origin for the taxonomically controversial red, Eastern timber and Great Lakes wolves, the discriminatory power offered by our dataset suggests all North American grey wolves, including the Mexican form, are monophyletic, and thus share a common ancestor to the exclusion of all other wolves. Furthermore, we identify three distinct populations in the high arctic, one being a previously unidentified "Polar wolf" population endemic to Ellesmere Island and Greenland. Genetic diversity analyses reveal particularly high inbreeding and low heterozygosity in these Polar wolves, consistent with long-term isolation from the other North American wolves.
    Matched MeSH terms: Genotype
  18. Hanafiah A, Lopes BS
    Infect Genet Evol, 2020 Mar;78:104135.
    PMID: 31837482 DOI: 10.1016/j.meegid.2019.104135
    Helicobacter pylori is the most predominant bacterium in almost 50% of the world's population and colonization causes a persistent inflammatory response leading to chronic gastritis. It shows high genetic diversity and individuals generally harbour a distinct bacterial population. With the advancement of whole-genome sequencing technology, new H. pylori subpopulations have been identified that show admixture between various H. pylori strains. Genotypic variation of H. pylori may be related to the presence of virulence factors among strains and is associated with different outcomes of infection in different individuals. This review summarizes the genetic diversity in H. pylori strain populations and its virulence characteristics responsible for variable outcomes in different ethnic groups.
    Matched MeSH terms: Genotype
  19. Gunter NV, Yap BJM, Chua CLL, Yap WH
    Front Genet, 2019;10:395.
    PMID: 31130981 DOI: 10.3389/fgene.2019.00395
    Psoriasis is multifactorial disease with complex genetic predisposition. Recent advances in genetics and genomics analyses have provided many insights into the relationship between specific genetic predisposition and the immunopathological mechanisms driving psoriasis manifestation. Novel approaches which utilize array-based genotyping technologies such as genome-wide association studies and bioinformatics tools for transcriptomics analysis have identified single nucleotide polymorphisms, genes and pathways that are associated with psoriasis. The discovery of these psoriasis-associated susceptibility loci, autoimmune targets and altered signaling pathways have provided opportunities to bridge the gap of knowledge from sequence to consequence, allowing new therapeutic strategies for the treatment of psoriasis to be developed. Here, we discuss recent advances in the field by highlighting how immune functions associated with psoriasis susceptibility loci may contribute to disease pathogenesis in different populations. Understanding the genetic variations in psoriasis and how these may influence the immunological pathways to cause disease will contribute to the efforts in developing novel and targeted personalized therapies for psoriasis patients.
    Matched MeSH terms: Genotype
  20. Fazeli-Nasab B, Sayyed RZ, Farsi M, Ansari S, El-Enshasy HA
    Physiol Mol Biol Plants, 2020 Jan;26(1):107-117.
    PMID: 32158124 DOI: 10.1007/s12298-019-00732-x
    Mango (Mangifera indica) is one of the most important tropical fruits in the world. Twenty-two genotypes of native mangoes from different regions of southern Iran (Hormozgan and Kerman) were collected and analyzed for the ribosomal genes. GC content was found to be 55.5%. Fu and Li's D* test statistic (0.437), Fu and Li's F* test statistic (0.500) and Tajima's D (1.801) were positive and nonsignificant. A total of 769 positions were identified (319 with insertion or deletion including 250 polymorphic and 69 monomorphic loci; 450 loci without any insertion or deletion including 35 Singletons and 22 haplotypes). Nucleotide diversity of 0.309 and a high genetic differentiation including Chi square of 79.8; P value of 0.3605 and df value of 76 was observed among mango genotypes studied. The numerical value of the ratio dN/dS (0.45) indicated a pure selection in the examined gene and the absence of any key changes. Cluster analysis differentiated the mango used in this research (M. indica L.) into two genotypes but could not differentiate their geographical locations. The results of this study indicated that a high genetic distance exists between HajiGholam (Manojan) and Arbabi (Rodan) genotypes and showed higher genetic diversity in mango of Rodan region. Results of present study suggested that for successful breeding, the genotypes of Rodan region mango especially Arbabi mango can be used as a gene donor and ITS can be a suitable tool for genetic evaluations of inter and intra species.
    Matched MeSH terms: Genotype
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