Displaying publications 1 - 20 of 773 in total

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  1. Oladosu Y, Rafii MY, Magaji U, Abdullah N, Miah G, Chukwu SC, et al.
    Biomed Res Int, 2018;2018:8936767.
    PMID: 30105259 DOI: 10.1155/2018/8936767
    The associations among yield-related traits and the pattern of influence on rice grain yield were investigated. This evaluation is important to determine the direct and indirect effects of various traits on yield to determine selection criteria for higher grain yield. Fifteen rice genotypes were evaluated under tropical condition at five locations in two planting seasons. The experiment was laid out in a randomized complete block design with three replications across the locations. Data were collected on vegetative and yield components traits. The pooled data based on the analysis of variance revealed that there were significant differences (p < 0.001) among the fifteen genotypes for all the characters studied except for panicle length and 100-grain weight. Highly significant and positive correlations at phenotypic level were observed in grain weight per hill (0.796), filled grains per panicle (0.702), panicles per hill (0.632), and tillers per hill (0.712) with yield per hectare, while moderate positive correlations were observed in flag leaf length to width ratio (0.348), days to flowering (0.412), and days to maturity (0.544). By contrast, unfilled grains per panicle (-0.225) and plant height (-0.342) had a negative significant association with yield per hectare. Filled grains per panicle (0.491) exhibited the maximum positive direct effect on yield followed by grain weight per hill (0.449), while unfilled grain per panicle (-0.144) had a negative direct effect. The maximum indirect effect on yield per hectare was recorded by the tillers per hill through the panicles per hill. Therefore, tillers per hill, filled grains per panicle, and grain weight per hill could be used as selection criteria for improving grain yield in rice.
    Matched MeSH terms: Genotype*
  2. Harun A
    Malays J Med Sci, ;21(6):1-2.
    PMID: 25897275
    The emergence of fungal species as opportunistic pathogens has warranted further studies on their pathogenicity, epidemiology, and transmissibility. Fungal genotyping has been employed to study the genetic relatedness within the organism, in order to obtain answers to epidemiological questions (such as in outbreak confirmation) as well as to provide basis for the improvement for patients care. Various fungal genotyping methods have been previously published, which can be chosen depending on the intended use and the capability of individual laboratory.
    Matched MeSH terms: Genotype
  3. Siti Yazmin Zahari Sham, Nor Aini Umar, Khalidah Mazlan
    MyJurnal
    With advancement in genetic studies, familial phaeochromocytoma (PCC) and paraganglioma (PGL)
    are increasingly being recognized. Characteristically, correlations exist between genotypes and clinical
    and biochemical phenotypes. We report a phaeochromocytoma in a young patient with intriguing family
    histories, raising the possibility of his being a familial case.
    Matched MeSH terms: Genotype
  4. AR Siti Nurul Fazlin, H Hairul Aini, HM Hadzri, MM Mohammed Imad
    MyJurnal
    Hepatitis C virus (HCV) genotyping is very important for the clinical management of HCV-infected patients. The aim of this study was to determine the genotypes of HCV-infected patients and to identify their risk factors and comorbidities.
    Matched MeSH terms: Genotype
  5. Ahmad F, Hanafi MM, Hakim MA, Rafii MY, Arolu IW, Akmar Abdullah SN
    PLoS ONE, 2015;10(9):e0138246.
    PMID: 26393807 DOI: 10.1371/journal.pone.0138246
    Coloured rice genotypes have greater nutritious value and consumer demand for these varieties is now greater than ever. The documentation of these genotypes is important for the improvement of the rice plant. In this study, 42 coloured rice genotypes were selected for determination of their genetic divergence using 25 simple sequence repeat (SSR) primers and 15 agro-morphological traits. Twenty-one out of the 25 SSR primers showed distinct, reproducible polymorphism. A dendrogram constructed using the SSR primers clustered the 42 coloured rice genotypes into 7 groups. Further, principle component analysis showed 75.28% of total variations were explained by the first-three components. All agro-morphological traits showed significant difference at the (p≤0.05) and (p≤0.01) levels. From the dendrogram constructed using the agro-morphological traits, all the genotypes were clustered into four distinct groups. Pearson's correlation coefficient showed that among the 15 agro-morphological traits, the yield contributing factor had positive correlation with the number of tillers, number of panicles, and panicle length. The heritability of the 15 traits ranged from 17.68 to 99.69%. Yield per plant and harvest index showed the highest value for both heritability and genetic advance. The information on the molecular and agro-morphological traits can be used in rice breeding programmes to improve nutritional value and produce higher yields.
    Matched MeSH terms: Genotype*
  6. Soon YY, Junaidi I, Kumarasamy V, Chem YK, Juliana R, Chua KB
    Med. J. Malaysia, 2007 Aug;62(3):214-7.
    PMID: 18246910 MyJurnal
    Since its isolation in Tanzania in 1953, chikungunya virus has caused periodic outbreaks in both tropical Africa and Asia. In the last decade, the virus has shown not only increased activity but has expanded its geographical locations, thus classical delineation of various genotypes of chikungunya virus to specific geographic locales no longer holds true. Rapid mass movement of people and the constant presence of the right vectors in this region could have contributed to the change in virus ecology. This paper documents the first detection of chikungunya virus of Central/East genotype in Malaysia from a patient who was most likely infected with the virus during her visit to India. Without good Aedes vector measures, only time will tell whether this genotype rather than the existing endemic genotype will subsequently cause the next chikungunya outbreak in Malaysia.
    Matched MeSH terms: Genotype*
  7. Zuridah H
    Med. J. Malaysia, 2012 Oct;67(5):548.
    PMID: 23770884
    Matched MeSH terms: Genotype
  8. Hazwani Ahmad Yusof, Rabinderjeet Singh, Zainuddin Zafarina, Kieron Rooney, Ahmad Munir Che Muhamed
    MyJurnal
    The purpose of this study was to examine the effect of the ACE I/D gene polymorphism on athletic status and physical performance of well-trained Malaysian athletes. The distribution of ACE I/D gene polymorphism among 180 well trained athletes was compared with 180 sedentary controls. 20 meter Yo-Yo intermittent recovery and leg strength tests were used to measure maximal oxygen consumption (VO2max) and leg strength value of athletes with different ACE I/D genotype, respectively. Chi-Square and one way ANOVA tests were used for data analysis. The II and DD genotype were more prevalent among the endurance athletes and the strength/ power athletes compared to the other groups, respectively (p=0.00). The VO2max was not significantly associated with ACE genotype in athlete (p=0.828). However, athletes with the DD genotype had recorded a greater result for leg strength (113.8 ± 36.2) than those with the II (96.2 ± 28.0) and the ID (112.2 ± 33.5) genotype (p=0.047). This study supports the notion that ACE I/D gene polymorphism might be a genetic factor associated with athletic status and strength performance among the Malaysian population. Future studies with more representation of endurance athletes might able to detect the association between I allele and endurance performance.
    Matched MeSH terms: Genotype
  9. Tan, Y.F., Haresh, K.K., Chai, L.C., Son R.
    MyJurnal
    A study to determine the antibiotic sensitivity pattern and genotyping using RAPD-PCR was performed on 50 C. jejuni isolated from sushi retailed in different supermarkets. With less than half of the isolates susceptible to the antibiotics tested, resistant to two or more antibiotics were observed in most of the isolates. The banding patterns obtained from RAPD-PCR revealed that no predominant clone exists and the bacterial population is rather diverse. Hence, the resistance of the C. jejuni to different classes of antibiotic as well as their diverse genotypes suggests that these C. jejuni isolates were generated from different sources in the contaminated supermarkets where sushi were retailed. Our data showed that C. jejuni can be an important reservoir for resistance genes and that study with comprehensive collections of samples are urgently required to establish better measures to reduce or eliminate the risk from antibiotic resistant and pathogenic bacteria originating from minimally processed ready-to-eat food.
    Matched MeSH terms: Genotype
  10. Yamamoto T, Tsuda Y, Mori GM, Cruz MV, Shinmura Y, Wee AK, et al.
    Appl Plant Sci, 2016 Sep;4(9).
    PMID: 27672519 DOI: 10.3732/apps.1600042
    PREMISE OF THE STUDY: Twenty-seven nuclear microsatellite markers were developed for the mangrove fern, Acrostichum aureum (Pteridaceae), to investigate the genetic structure and demographic history of the only pantropical mangrove plant.

    METHODS AND RESULTS: Fifty-six A. aureum individuals from three populations were sampled and genotyped to characterize the 27 loci. The number of alleles and expected heterozygosity ranged from one to 15 and 0.000 to 0.893, respectively. Across the 26 polymorphic loci, the Malaysian population showed much higher levels of polymorphism compared to the other two populations in Guam and Brazil. Cross-amplification tests in the other two species from the genus determined that seven and six loci were amplifiable in A. danaeifolium and A. speciosum, respectively.

    CONCLUSIONS: The 26 polymorphic microsatellite markers will be useful for future studies investigating the genetic structure and demographic history of of A. aureum, which has the widest distributional range of all mangrove plants.

    Matched MeSH terms: Genotype
  11. Chew EGY, Liany H, Tan LCS, Au WL, Prakash KM, Annuar AA, et al.
    Neurobiol. Aging, 2019 Feb;74:235.e1-235.e4.
    PMID: 30337193 DOI: 10.1016/j.neurobiolaging.2018.09.013
    Recent whole-exome sequencing studies in European patients with Parkinson's disease (PD) have identified potential risk variants across 33 novel PD candidate genes. We aim to determine if these reported candidate genes are similarly implicated in Asians by assessing common, rare, and novel nonsynonymous coding variants by sequencing all 33 genes in 198 Chinese samples and genotyping coding variants in an independent set of 9756 Chinese samples. We carried out further targeted sequencing of CD36 in an additional 576 Chinese and Korean samples. We found that only 8 of 43 reported risk variants were polymorphic in our Chinese samples. We identified several heterozygotes for rare loss-of-function mutations, including the reported CD36 p.Gln74Ter variant, in both cases and controls. We also observed 2 potential compound heterozygotes among PD cases for rare loss-of-function mutations in CD36 and SSPO. The other reported variants were common in East Asians and not associated with PD, completely absent, or only found in controls. Therefore, the 33 reported candidate genes and associated variants are unlikely to confer significant PD risk in the East Asian population.
    Matched MeSH terms: Genotype
  12. 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
  13. Low TY, Mohtar MA, Ang MY, Jamal R
    Proteomics, 2018 Nov 15.
    PMID: 30431238 DOI: 10.1002/pmic.201800235
    Understanding the relationship between genotypes and phenotypes is essential to disentangle biological mechanisms and to unravel the molecular basis of diseases. Genes and proteins are closely linked in biological systems. However, genomics and proteomics have developed separately into two distinct disciplines whereby crosstalk among scientists from the two domains is limited and this constrains the integration of both fields into a single data modality of useful information. The emerging field of proteogenomics attempts to address this by building bridges between the two disciplines. In this review, how genomics and transcriptomics data in different formats can be utilized to assist proteogenomics application is briefly discussed. Subsequently, a much larger part of this review focuses on proteogenomics research articles that are published in the last five years that answer two important questions. First, how proteogenomics can be applied to tackle biological problems is discussed, covering genome annotation and precision medicine. Second, the latest developments in analytical technologies for data acquisition and the bioinformatics tools to interpret and visualize proteogenomics data are covered.
    Matched MeSH terms: Genotype
  14. Tan TK, Low VL, Ng WH, Ibrahim J, Wang D, Tan CH, et al.
    Parasitol. Int., 2019 Apr;69:110-113.
    PMID: 30590124 DOI: 10.1016/j.parint.2018.12.007
    This report describes the detection of zoonotic Cryptosporidium muris, C. parvum subgenotype IIa and Giardia duodenalis genotype B in urban rodents in Malaysia. A rare occurrence of C. meleagridis was also reported suggesting a role of rodents in mechanical transmission of this pathogen. Utilization of DNA sequencing and subtyping analysis confirmed the presence of zoonotic C. parvum subtypes IIaA17G2R1 and IIaA16G3R1 for the first time in rodents.
    Matched MeSH terms: Genotype
  15. Filho JAF, de Brito LS, Leão AP, Alves AA, Formighieri EF, Júnior MTS
    Bioinform Biol Insights, 2017;11:1177932217702388.
    PMID: 28469420 DOI: 10.1177/1177932217702388
    Transposable elements (TEs) are mobile genetic elements present in almost all eukaryotic genomes. Due to their typical patterns of repetition, discovery, and characterization, they demand analysis by various bioinformatics software. Probably, as a result of the need for a complex analysis, many genomes publicly available do not have these elements annotated yet. In this study, a de novo and homology-based identification of TEs and microsatellites was performed using genomic data from 3 palm species: Elaeis oleifera (American oil palm, v.1, Embrapa, unpublished; v.8, Malaysian Palm Oil Board [MPOB], public), Elaeis guineensis (African oil palm, v.5, MPOB, public), and Phoenix dactylifera (date palm). The estimated total coverage of TEs was 50.96% (523 572 kb) and 42.31% (593 463 kb), 39.41% (605 015 kb), and 33.67% (187 361 kb), respectively. A total of 155 726 microsatellite loci were identified in the genomes of oil and date palms. This is the first detailed description of repeats in the genomes of oil and date palms. A relatively high diversity and abundance of TEs were found in the genomes, opening a range of further opportunities for applied research in these genera. The development of molecular markers (mainly simple sequence repeat), which may be immediately applied in breeding programs of those species to support the selection of superior genotypes and to enhance knowledge of the genetic structure of the breeding and natural populations, is the most notable opportunity.
    Matched MeSH terms: Genotype
  16. 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
  17. Apalasamy YD, Mohamed Z
    Hum. Genet., 2015 Apr;134(4):361-74.
    PMID: 25687726 DOI: 10.1007/s00439-015-1533-x
    Obesity is a complex and multifactorial disease that occurs as a result of the interaction between "obesogenic" environmental factors and genetic components. Although the genetic component of obesity is clear from the heritability studies, the genetic basis remains largely elusive. Successes have been achieved in identifying the causal genes for monogenic obesity using animal models and linkage studies, but these approaches are not fruitful for polygenic obesity. The developments of genome-wide association approach have brought breakthrough discovery of genetic variants for polygenic obesity where tens of new susceptibility loci were identified. However, the common SNPs only accounted for a proportion of heritability. The arrival of NGS technologies and completion of 1000 Genomes Project have brought other new methods to dissect the genetic architecture of obesity, for example, the use of exome genotyping arrays and deep sequencing of candidate loci identified from GWAS to study rare variants. In this review, we summarize and discuss the developments of these genetic approaches in human obesity.
    Matched MeSH terms: Genotype
  18. Hama-Ali EO, Alwee SS, Tan SG, Panandam JM, Ling HC, Namasivayam P, et al.
    Mol. Biol. Rep., 2015 May;42(5):917-25.
    PMID: 25399079 DOI: 10.1007/s11033-014-3829-7
    Oil palm breeding has been progressing very well in Southeast Asia, especially in Malaysia and Indonesia. Despite this progress, there are still problems due to the difficulty of controlled crossing in oil palm. Contaminated/illegitimate progeny has appeared in some breeding programs; late and failure of detection by the traditional method causes a waste of time and labor. The use of molecular markers improves the integrity of breeding programs in perennial crops such as oil palm. Four half-sib families with a total of 200 progeny were used in this study. Thirty polymorphic single locus DNA microsatellites markers were typed to identify the illegitimate individuals and to obtain the correct parental and progeny assignments by using the CERVUS and COLONY programs. Three illegitimate palms (1.5%) were found, and 16 loci proved to be sufficient for sibship assignments without parental genotypes by using the COLONY program. The pairwise-likelihood score (PLS) method was better for half-sib family assignments than the full likelihood (FL) method.
    Matched MeSH terms: Genotype
  19. Voon K, Ng QM, Yu M, Wang LF, Chua KB
    PMID: 23077814
    Viruses in the family Picornaviridae are classified into nine genera. Within the family Picornaviridae, two species: Encephalomyocarditis virus and Theilovirus, are listed under the genus Cardiovirus. A novel Theilovirus, Saffold virus (SAFV), was first reported in 2007. Since then, numerous SAFV isolates have been detected around the world and genetic recombinations have been reported among them. In 2009, SAFV-Penang was isolated from a febrile child with influenza-like illness in Malaysia. SAFV-Penang is a genotype 3 SAFV. In this study we investigated the genome features of SAFV-Penang to exclude the possibility it is a recombinant variant. SAFV-Penang was found not to be a recombinant variant but to have three unique non-synonymous substitutions, alanine [A689], lysine [K708] and isoleucine [I724] in the VP1 protein.
    Matched MeSH terms: Genotype
  20. Sahebzadeh N, Mardan M, Ali AM, Tan SG, Adam NA, Lau WH
    PLoS ONE, 2012;7(7):e41020.
    PMID: 22911733 DOI: 10.1371/journal.pone.0041020
    Knowledge on the population of genetic structure and ecological behaviour of Apis dorsata from Peninsular Malaysia is needed for effective management and conservation of this species since unsustainable whole solitary low nest cutting for product harvesting is the current common practice here. The analysis of 15 single locus DNA microsatellite markers on samples from 20 solitary nests of A. dorsata showed that while these markers were polymorphic, high intracolonial relatedness existed. Furthermore, in general, slightly negative values of intercolony relatedness (R) among the nests of A. dorsata were found. However, positive values of mean intercolony relatedness were observed between 54 pairs of nests out of 190 possible combinations. The R values among nest pairs 3-4 and 3-5 was higher than 0.50 showing that their queens were half siblings, whereas nest pair 19-20 showed relatedness of 0.95 indicating that the same queen was sampled. The results that we obtained could not conclusively support the hypothesis of this study that the honey hunters in Marang district of Malaysia repeatedly harvest the same nest located at a different site and at a different time during the same honey harvesting season. However, our finding of an appreciable level of intercolonial relatedness between several pairs of nests in this pioneer study indicated that a comprehensive study with a larger sample size of solitary nests found throughout the region would be necessary to provide concrete proof for this novel idea.
    Matched MeSH terms: Genotype
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