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Molecular characterization of a Toxocara variant from cats in Kuala Lumpur, Malaysia

Zhu XQ, Jacobs DE, Chilton NB, Sani RA, Cheng NA, Gasser RB

Parasitology, 1998 Aug;117 ( Pt 2):155-64.
PMID: 9778638

The ascaridoid nematode of cats from Kuala Lumpur, Malaysia, previously identified morphologically as Toxocara canis, was characterized using a molecular approach. The nuclear ribosomal DNA (rDNA) region spanning the first internal transcribed spacer (ITS-1), the 5.8S gene and the second internal transcribed spacer (ITS-2) was amplified and sequenced. The sequences for the parasite from Malaysian cats were compared with those for T. canis and T. cati. The sequence data showed that this taxon was genetically more similar to T. cati than to T. canis in the ITS-1, 5.8S and ITS-2. Differences in the ITS-1 and ITS-2 sequences between the taxa (9.4-26.1%) were markedly higher than variation between samples within T. canis and T. cati (0-2.9%). The sequence data demonstrate that the parasite from Malaysian cats is neither T. canis nor T. cati and indicate that it is a distinct species. Based on these data, PCR-linked restriction fragment length polymorphism (RFLP) and single-strand conformation polymorphism (SSCP) methods were employed for the unequivocal differentiation of the Toxocara variant from T. canis and T. cati. These methods should provide valuable tools for studying the life-cycle, transmission pattern(s) and zoonotic potential of this parasite.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Genomic variations among wildtype and mutant strains of pseudorabies virus

Zeenathul NA, Mohd-Azmi ML, Ali AS, Aini I, Sheik-Omar AR, Abdul-Rahim AM, et al.

Rev. Argent. Microbiol., 2002 Jan-Mar;34(1):7-14.
PMID: 11942085

Both wild-type virulent and mutant strains of pseudorabies virus (PrV) were used in this study. Mutants used were derived from the plaque purified strain PrVmAIP. A total of six drug resistant mutants, three bromodeoxyuridine (BUdR) resistant and three iododeoxyuridine (IUdR) resistant, respectively, were isolated and passaged in chicken embryo fibroblast (CEF) cells. The DNA of these PrVs were compared with the wild-type isolates by means of the restriction fragment pattern (RFP) findings produced with Bam HI, Kpn I, Hind III and Bgl II restriction enzymes (RE). Compared to the wild-type PrVs (PrV-VBA1-parental strain of PrVmAIP; PrV-VBA2; PrV-VBA3), the RFP of PrVmAIP showed the presence of mutations within the RE sites studied. Both PrV-VBA1 and PrV-VBA2 appeared to be closely related but their RFPs differed from PrV-VBA3. Significant differences either in the number, size or migrations of the DNA fragments could also be detected in the BUdR resistant strains. Even though different features of cytopathic effect (GPE) were observed in the IUdR resistant PrVs, the RFP findings remained identical. The PrVs studied showed considerable differences from the reference PrV (PrV-CD).

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Fulltext Distribution of Candida in the oral cavity and its differentiation based on the internally transcribed spacer (ITS) regions of rDNA

Zahir RA, Himratul-Aznita WH

Yeast, 2013 Jan;30(1):13-23.
PMID: 23208647 DOI: 10.1002/yea.2937

This study aimed to determine the distribution of Candida species in the oral cavity and differentiate the species based on PCR amplification, including HinfI and MspI digestion, in order to assess the effectiveness of using the rDNA region for species identification. Samples from saliva as well as palate, tongue and cheek mucosa surfaces were collected from 45 individuals, consisting of three groups: periodontal disease patients; denture-wearers; and the control group. The samples were serially diluted, spread on BHI and YPD agar plates and scored for colony-forming units (CFUs). Fifteen random candidal colonies were isolated and subjected to genomic DNA extraction, based on glass beads disruption. Four primers were used to amplify regions in the rDNA, and the ITSI-5.8S-ITSII PCR product was digested by HinfI and MspI restriction enzymes. The microbial loads on all sites of the denture-wearers were found to be significantly higher than control, while in the periodontal disease group only the microbial loads on the tongue were significantly higher than control. Meanwhile, there was no significant difference at other sites. The restriction fragment lengths of the clinical samples were compared to those of seven control species, allowing the differentiation of all seven species and the identification of 14 species from the clinical samples. The MspI restriction digest was not able to distinguish between C. albicans and C. dubliniensis, whereas the HinfI digest could not distinguish between C. tropicalis and C. parapsilosis. It was concluded that PCR-RFLP of the candidal rDNA region has potential for species identification. This study demonstrates the potential use of candidal rDNA as a means for identifying Candida species, based on genotype. The results also indicate the possibility of constructing genetic probes that target specific restriction fragments in the ITSI-5.8S-ITSII region, enabling swift and precise identification of Candida species.

Matched MeSH terms: Polymorphism, Restriction Fragment Length*
Polymorphisms of cell cycle regulator genes CCND1 G870A and TP53 C215G: Association with colorectal cancer susceptibility risk in a Malaysian population

Zahary MN, Ahmad Aizat AA, Kaur G, Yeong Yeh L, Mazuwin M, Ankathil R

Oncol Lett, 2015 Nov;10(5):3216-3222.
PMID: 26722315

Colorectal cancer (CRC) occurs as a more common sporadic form and a less common familial form. Our earlier analysis of germline mutations of mismatch repair genes confirmed only 32% of familial CRC cases as Lynch syndrome cases. It was hypothesized that the remaining familial aggregation may be 'polygenic' due to single nucleotide polymorphisms (SNPs) of low penetrance genes involved in cancer predisposition pathways, such as cell cycle regulation and apoptosis pathways. The current case-control study involving 104 CRC patients (52 sporadic and 52 familial) and 104 normal healthy controls investigated the contribution of the SNPs cyclin D1 (CCND1) G870A and tumor protein p53 (TP53) C215G in modulating familial and sporadic CRC susceptibility risk. DNA was extracted from peripheral blood and the polymorphisms were genotyped by employing a polymerase chain reaction-restriction fragment length polymorphism method. The association between these polymorphisms and CRC susceptibility risk was calculated using a binary logistic regression analysis and deriving odds ratios (ORs). The A/A variant genotype of CCND1 and G/G variant genotype of TP53 exhibited a significantly greater association with the risk of sporadic CRC [CCND1: OR, 3.471; 95% confidence interval (CI), 1.443-8.350; P=0.005. TP53: OR, 2.829; CI, 1.119-7.152; P=0.026] as well as familial CRC susceptibility (CCND1: OR, 3.086; CI, 1.270-7.497; P=0.019. TP53: OR, 3.048; CI, 1.147-8.097; P=0.030). The results suggest a potential role of the SNPs CCND1 G870A and TP53 C215G in the modulation of sporadic and familial CRC susceptibility risk.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Genotyping and characterization of Toxoplasma gondii strain isolated from pigs in Hubei province, central China

Xia NB, Lu Y, Zhao PF, Wang CF, Li YY, Tan L, et al.

Trop Biomed, 2020 Jun 01;37(2):489-498.
PMID: 33612818

Toxoplasma gondii, a ubiquitous pathogen that infects nearly all warm-blooded animals and humans, can cause severe complications to the infected people and animals as well as serious economic losses and social problems. Here, one local strain (TgPIG-WH1) was isolated from an aborted pig fetus, and the genotype of this strain was identified as ToxoDB #3 by the PCR RFLP typing method using 10 molecular markers (SAG1, SAG2, alternative SAG2, SAG3, BTUB, GRA6, L358, PK1, C22-8, C29-2 and Apico). A comparison of the virulence of this isolate with other strains in both mice and piglets showed that TgPIG-WH1 was less virulent than type 1 strain RH and type 2 strain ME49 in mice, and caused similar symptoms to those of ME49 such as fever in piglets. Additionally, in piglet infection with both strains, the TgPIG-WH1 caused a higher IgG response and more severe pathological damages than ME49. Furthermore, TgPIG-WH1 caused one death in the 5 infected piglets, whereas ME49 did not, suggesting the higher virulence of TgPIG-WH1 than ME49 during piglet infection. Experimental infections indicate that the virulence of TgPIG-WH1 relative to ME49 is weaker in mice, but higher in pigs. This is probably the first report regarding a ToxoDB #3 strain from pigs in Hubei, China. These data will facilitate the understanding of genetic diversity of Toxoplasma strains in China as well as the prevention and control of porcine toxoplasmosis in the local region.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Molecular identification of house dust mites and storage mites

Wong SF, Chong AL, Mak JW, Tan J, Ling SJ, Ho TM

Exp Appl Acarol, 2011 Oct;55(2):123-33.
PMID: 21468750 DOI: 10.1007/s10493-011-9460-6

Mites are known causes of allergic diseases. Currently, identification of mites based on morphology is difficult if only one mite is isolated from a (dust) sample, or when only one gender is found, or when the specimen is not intact especially with the loss of the legs. The purpose of this study was to use polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) of the ITS2 gene, to complement the morphological data for the identification of mites to the species level. For this, six species were cultured: Dermatophagoides pteronyssinus, D. farinae, Blomia tropicalis, Tyrophagus putrescentiae, Aleuroglyphus ovatus and Glycycometus malaysiensis. Genomic DNA of the mites was extracted, quantified, amplified and digested individually with restriction enzymes. Hinf I and Ple I differentiated the restriction patterns of D. pteronyssinus and D. farinae. Bfa I and Alu I enzymes differentiated B. tropicalis and G. malaysiensis. Ple I enzyme was useful for the differentiation between T. putrescentiae and A. ovatus. Bfa I was useful for the differentiation of G. malaysiensis from the rest of the species. In conclusion, different species of mites can be differentiated using PCR-RFLP of ITS2 region. With the established PCR-RFLP method in this study, identification of these mites to the species level is possible even if complete and intact adult specimens of both sexes are not available. As no study to date has reported PCR-RFLP method for the identification of domestic mites, the established method should be validated for the identification of other species of mites that were not included in this study.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Randomly amplified polymorphic DNA typing: a useful tool for rapid epidemiological typing of Klebsiella pneumoniae

Wong NA, Linton CJ, Jalal H, Millar MR

Epidemiol Infect, 1994 Dec;113(3):445-54.
PMID: 7995354

Discriminatory typing methods are invaluable in the investigation of outbreaks of infectious diseases. Single primers were used to generate randomly amplified polymorphic DNA (RAPD) profiles from Klebsiella pneumoniae isolates of various serotype and K. pneumoniae isolates from cases of sepsis at a Malaysian hospital and two English hospitals. RAPD profiles of acceptable reproducibility, a maximum of three minor band variations, were produced using a rapid DNA extraction method. RAPD typing of K. pneumoniae was shown to be as discriminatory as restriction fragment length polymorphism analysis using pulsed field gel electrophoresis yet quicker and less costly. The findings suggest that RAPD typing may be a useful tool for the epidemiological typing of K. pneumoniae.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Analysis of fliC variation among clinical isolates of Burkholderia cepacia

Winstanley C, Hales BA, Morgan JAW, Gallagher MJ, Puthucheary SD, CISSé MF, et al.

J Med Microbiol, 1999 Jul;48(7):657-662.
PMID: 10403416 DOI: 10.1099/00222615-48-7-657

PCR and restriction fragment length polymorphism (RFLP) typing of flagellin genes (fliC) from 57 clinical isolates of Burkholderia cepacia indicated that only type 11 flagellins were present. Twenty-two isolates previously identified as the epidemic UK cystic fibrosis strain were indistinguishable by this method, as were 11 isolates from a pseudo-outbreak in Senegal. Other clinical isolates, including 19 from disparate sources in Malaysia, were separated into nine fliC RFLP groups, exhibiting a large degree of divergence. When isolates were indistinguishable by fliC genotyping, their similarity was confirmed by whole genome macro-restriction analysis with pulsed-field gel electrophoresis following XbaI digestion. The variation in fliC sequences of B. cepacia was far greater than that with B. pseudomallei, supporting the view that 'B. cepacia', as currently defined, may comprise several different genomic species.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Haplotype analysis of leptin gene polymorphisms in obesity among Malays in Terengganu, Malaysia population

Wan Rohani WT, Aryati A, Amiratul Athirah S

Med J Malaysia, 2018 10;73(5):281-285.
PMID: 30350805 MyJurnal

INTRODUCTION: The prevalence of overweight and obesity has developed the critical global threat which leads to metabolic risks and mortality. A Leptin hormone that regulates the food intake as well as food expenditure is encoded by Leptin gene. The gene has shown a pivotal role in obesity pathogenesis. This study was sought to determine the SNPs and haplotype association of the Leptin gene that were assigned as G2548A, H1328080, and A19G with obesity among Malays in Terengganu, Malaysia.
METHODOLOGY: This study comprised of 249 participants (148 overweight/ obese as a case group and 101 lean participants as controls). The PCR-RFLP technique was performed to distinguish the genotype distribution of Leptin gene polymorphisms. The allele and genotype frequencies were assessed for single and haplotype analyses.
RESULT: Single association analysis of G2548A (P=0.74), A19G (P=0.38), and H1328080 (P=0.56) polymorphisms yielded no statistically significant association. However, haplotype association analysis showed a suggestive indication of AAG haplotype (G2548A, H1328080, and A19G sequence) with susceptibility effect towards obesity predisposition [P=0.002, OR=8.897 (1.59-9.78)].
CONCLUSION: This data on single and haplotype might disclose the preliminary exposure and pave the way for the obesity development with an evidence of revealed susceptibility to obesity.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Association of solute carrier family 2, member 9 (SLC2A9) genetic variant rs3733591 with gout in a Malay sample set

Wan Rohani WT, Mahfudzah A, Nazihah MY, Tan HL, Wan Syamimee WG, Amanda Jane PG, et al.

Med J Malaysia, 2018 10;73(5):307-310.
PMID: 30350810 MyJurnal

INTRODUCTION: Gout is one of the most common inflammatory arthritis in Malaysia. It is due to persistent hyperuricemia that leads to the formation and deposition of intra- and periarticular monosodium urate crystals either due to excessive production or insufficient excretion of uric acid. Incidence and prevalence of gout is increasing worldwide, with a higher rate among men compared to women. Malay is the largest ethnic group in Malaysia, followed by Chinese and Indian. SLC2A9 is a renal urate transporter that controls renal uric acid excretion and genetic variants in SLC2A9 are associated with the risk of gout in several populations. This study aimed to test if the SLC2A9 variant (R265H, rs3733591) is also associated with gout among Malays in Malaysia.
METHODOLOGY: A total of 89 patients with gouty arthritis and 100 normal subjects who consented and were recruited in this study. The serum urate and creatinine were measured. The SNP genotyping was performed using PCR-RFLP method for rs3733591 and BST 1236 was used as a restriction enzyme to cut the targeted amplicons.
RESULT: SLC2A9 variant was associated with gout, p-value of 0.007, OR=4.713 [95%CI 1.530-14.513], however this association was not significant after adjustment for age and gender with p=0.465 (OR=1.950; 95%CI[0.325-11.718]).
CONCLUSION: Our data suggest that the genetic variant of SLC2A9 may contribute to the susceptibility of gout among Malays in Malaysia.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Distribution and haplotype associations of XPD Lys751Gln, XRCC1 Arg280His and XRCC1 Arg399Gln polymorphisms with nasopharyngeal carcinoma in the Malaysian population

Visuvanathan S, Chong PP, Yap YY, Lim CC, Tan MK, Lye MS

Asian Pac J Cancer Prev, 2014;15(6):2747-51.
PMID: 24761895

BACKGROUND: DNA repair pathways play a crucial role in maintaining the human genome. Previous studies associated DNA repair gene polymorphisms (XPD Lys751Gln, XRCC1 Arg280His and XRCC1 Arg399Gln) with nasopharyngeal carcinoma. These non-synonymous polymorphisms may alter DNA repair capacity and thus increase or decrease susceptibility. The present study aimed to determine the genotype distribution of XPD codon 751, XRCC1 codon 280 and codon 399 polymorphisms and haplotype associations among NPC cases and controls in the Malaysian population.
MATERIALS AND METHODS: We selected 157 NPC cases and 136 controls from two hospitals in Kuala Lumpur, Malaysia for this study. The polymorphisms studied were genotyped by PCR-RFLP assay and allele and genotype frequencies, haplotype and linkage disequilibrium were determined using SNPstat software.
RESULTS: For the XPD Lys751Gln polymorphism, the frequency of the Lys allele was higher in cases than in controls (94.5% versus 85.0%). For the XRCC1 Arg280His polymorphism, the frequency of Arg allele was 90.0% and 89.0% in cases and controls, respectively and for XRCC1 Arg399Gln the frequency of the Arg allele was 72.0% and 72.8% in cases and controls respectively. All three polymorphisms were in linkage disequilibrium. The odds ratio from haplotype analysis for these three polymorphisms and their association with NPC was 1.93 (95%CI: 0.90-4.16) for haplotype CGC vs AGC allele combinations. The global haplotype association with NPC gave a p-value of 0.054.
CONCLUSIONS: Our study provides an estimate of allele and genotype frequencies of XRCC1Arg280His, XRCC1 Arg399Gln and XPD Lys751Gln polymorphisms in the Malaysian population and showed no association with nasopharyngeal cancer.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Fulltext Analysis of human bradykinin receptor gene and endothelial nitric oxide synthase gene polymorphisms in end-stage renal disease among malaysians

Vasudevan R, Ismail P, Jaafar N, Mohamad N, Etemad E, Wan Aliaa W, et al.

Balkan J. Med. Genet., 2014 Jun;17(1):37-40.
PMID: 25741213 DOI: 10.2478/bjmg-2014-0023

The aim of this study was to determine the association of the c.894G>T; p.Glu298Asp polymorphism and the variable number tandem repeat (VNTR) polymorphism of the endothelial nitric oxide synthase (eNOS) gene and c.181C>T polymorphism of the bradykinin type 2 receptor gene (B2R) in Malaysian end-stage renal disease (ESRD) subjects. A total of 150 ESRD patients were recruited from the National Kidney Foundation's (NKF)dialysis centers in Malaysia and compared with 150 normal healthy individuals. Genomic DNA was extracted from buccal cells of all the subjects. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was carried out to amplify the products and the restricted fragments were separated by agarose gel electrophoresis. Statistical analyses were carried out using software where a level of p <0.05 was considered to be statistically significant. The genotypic and allelic frequencies of the B2R gene (c.181C>T, 4b/a) and eNOS gene (c.894G>T) polymorphisms were not statistically significant (p >0.05) when compared to the control subjects. The B2R and eNOS gene polymorphisms may not be considered as genetic susceptibility markers for Malaysian ESRD subjects.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
HLA-DR2 haplotypic diversity in populations of South-East Asia, northern China, Melanesia and Australian aborigines using PCR-RFLP for DRB1, DRB5, DQA1 and DQB1. A novel DRB1 allele: DRB1*16022

Trejaut J, Bhatia K, Greville WD, Hu KR, Duraisamy G, Nuchprayoon C, et al.

Eur. J. Immunogenet., 1996 Dec;23(6):437-49.
PMID: 8971541

The polymorphism of the human leucocyte antigen HLA-DR2 and the heterogeneity of HLA-DR2 class II-related haplotypes (HLA-DRB1-DRB5-DQA1-DQB1) were investigated in four populations of east and south-east Asia (SEA) and five Melanesian populations using TaqI restriction fragment length polymorphism (RFLP) analysis, and the polymerase chain reaction (PCR) amplification-based techniques PCR-RFLP and sequence-specific oligonucleotide (SSO) typing. The haplotype DRB1*1502-DRB5*0101-DQA1*0102-DQB1*0601 was common in Malaysians, Javanese, Thursday Islanders, Madang, Goroka and the Australian Aborigines, while DRB1*16021-DRB5*0101-DQA1*0102-DQB1*0502 was common in the Thai and Thursday Islanders. DRB1*1501-DRB5*0101-DQA1*0102-DQB1*0602 was present at a high frequency in Northern Chinese, Goroka, Watut and Australian Aborigines. The study describes four rare or unusual haplotypes: HLA-DRB1*1501-DRB5*0101-DQA1*0101-DQB1*0601, DRB1*1502-DRB5*0101-DQA1*0101-DQB1*0502, DRB1*1502-DRB5*0102-DQA1* 0102-DQB1*0502 and DRB1*1501-DRB5*0101-DQA1*0101/2-DQB1*0503; the latter two were confirmed by segregation in two Javanese families. A new DR2 allele, initially detected by PCR-RFLP and confirmed by DNA sequencing as DRB1*16022 (previously designated DRB1*16Madang), was seen in a Madang individual. A new HLA-DR2 TaqI RFLP subtype, locally designated as DR15U, is also described. This RFLP subtype segregated in a Javanese family and correlated with a typically SEA haplotype, DRB1*1502-DRB5*0102-DQA1*0101-DQB1*0501. The allele HLA-DR16Thai, determined by TaqI DRB RFLP, was found by PCR-RFLP and SSO typing to correlate with a unique SEA haplotype, HLA-DRB1*16021-DRB5*0101-DQA1*0102-DQB1*0502, and was observed in the Thai, Malaysian, Thursday Islander, Javanese and Northern Chinese populations.

Matched MeSH terms: Polymorphism, Restriction Fragment Length*
Fulltext The effects of polymorphisms in 7 candidate genes on resistance to Salmonella Enteritidis in native chickens

Tohidi R, Idris IB, Malar Panandam J, Hair Bejo M

Poult Sci, 2013 Apr;92(4):900-9.
PMID: 23472012 DOI: 10.3382/ps.2012-02797

Salmonella enterica serovar Enteritidis infection is a common concern in poultry production for its negative effects on growth as well as food safety for humans. Identification of molecular markers that are linked to resistance to Salmonella Enteritidis may lead to appropriate solutions to control Salmonella infection in chickens. This study investigated the association of candidate genes with resistance to Salmonella Enteritidis in young chickens. Two native breeds of Malaysian chickens, namely, Village Chickens and Red Junglefowl, were evaluated for bacterial colonization after Salmonella Enteritidis inoculation. Seven candidate genes were selected on the basis of their physiological role in immune response, as determined by prior studies in other genetic lines: natural resistance-associated protein 1 (NRAMP1), transforming growth factor β3 (TGFβ3), transforming growth factor β4 (TGFβ4), inhibitor of apoptosis protein 1 (IAP1), caspase 1 (CASP1), lipopolysaccharide-induced tumor necrosis factor (TNF) α factor (LITAF), and TNF-related apoptosis-inducing ligand (TRAIL). Polymerase chain reaction-RFLP was used to identify polymorphisms in the candidate genes; all genes exhibited polymorphisms in at least one breed. The NRAMP1-SacI polymorphism correlated with the differences in Salmonella Enteritidis load in the cecum (P = 0.002) and spleen (P = 0.01) of Village Chickens. Polymorphisms in the restriction sites of TGFβ3-BsrI, TGFβ4-MboII, and TRAIL-StyI were associated with Salmonella Enteritidis burden in the cecum, spleen, and liver of Village Chickens and Red Junglefowl (P < 0.05). These results indicate that the NRAMP1, TGFβ3, TGFβ4, and TRAIL genes are potential candidates for use in selection programs for increasing genetic resistance against Salmonella Enteritidis in native Malaysian chickens.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
The effects of polymorphisms in IL-2, IFN-γ, TGF-β2, IgL, TLR-4, MD-2, and iNOS genes on resistance to Salmonella enteritidis in indigenous chickens

Tohidi R, Idris IB, Panandam JM, Bejo MH

Avian Pathol, 2012 Dec;41(6):605-12.
PMID: 23237374 DOI: 10.1080/03079457.2012.739680

Salmonella Enteritidis is a major cause of food poisoning worldwide, and poultry products are the main source of S. Enteritidis contamination for humans. Among the numerous strategies for disease control, improving genetic resistance to S. Enteritidis has been the most effective approach. We investigated the association between S. Enteritidis burden in the caecum, spleen, and liver of young indigenous chickens and seven candidate genes, selected on the basis of their critical roles in immunological functions. The genes included those encoding interleukin 2 (IL-2), interferon-γ (IFN-γ), transforming growth factor β2 (TGF-β2), immunoglobulin light chain (IgL), toll-like receptor 4 (TLR-4), myeloid differentiation protein 2 (MD-2), and inducible nitric oxide synthase (iNOS). Two Malaysian indigenous chicken breeds were used as sustainable genetic sources of alleles that are resistant to salmonellosis. The polymerase chain reaction restriction fragment-length polymorphism technique was used to genotype the candidate genes. Three different genotypes were observed in all of the candidate genes, except for MD-2. All of the candidate genes showed the Hardy-Weinberg equilibrium for the two populations. The IL-2-MnlI polymorphism was associated with S. Enteritidis burden in the caecum and spleen. The TGF-β2-RsaI, TLR-4-Sau 96I, and iNOS-AluI polymorphisms were associated with the caecum S. Enteritidis load. The other candidate genes were not associated with S. Enteritidis load in any organ. The results indicate that the IL-2, TGF-β2, TLR-4, and iNOS genes are potential candidates for use in selection programmes for increasing genetic resistance against S. Enteritidis in Malaysian indigenous chickens.

Matched MeSH terms: Polymorphism, Restriction Fragment Length/genetics*
Fulltext High density SNP and SSR-based genetic maps of two independent oil palm hybrids

Ting NC, Jansen J, Mayes S, Massawe F, Sambanthamurthi R, Ooi LC, et al.

BMC Genomics, 2014;15:309.
PMID: 24767304 DOI: 10.1186/1471-2164-15-309

Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Fulltext Identification of QTLs associated with callogenesis and embryogenesis in oil palm using genetic linkage maps improved with SSR markers

Ting NC, Jansen J, Nagappan J, Ishak Z, Chin CW, Tan SG, et al.

PLoS One, 2013;8(1):e53076.
PMID: 23382832 DOI: 10.1371/journal.pone.0053076

Clonal reproduction of oil palm by means of tissue culture is a very inefficient process. Tissue culturability is known to be genotype dependent with some genotypes being more amenable to tissue culture than others. In this study, genetic linkage maps enriched with simple sequence repeat (SSR) markers were developed for dura (ENL48) and pisifera (ML161), the two fruit forms of oil palm, Elaeis guineensis. The SSR markers were mapped onto earlier reported parental maps based on amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers. The new linkage map of ENL48 contains 148 markers (33 AFLPs, 38 RFLPs and 77 SSRs) in 23 linkage groups (LGs), covering a total map length of 798.0 cM. The ML161 map contains 240 markers (50 AFLPs, 71 RFLPs and 119 SSRs) in 24 LGs covering a total of 1,328.1 cM. Using the improved maps, two quantitative trait loci (QTLs) associated with tissue culturability were identified each for callusing rate and embryogenesis rate. A QTL for callogenesis was identified in LGD4b of ENL48 and explained 17.5% of the phenotypic variation. For embryogenesis rate, a QTL was detected on LGP16b in ML161 and explained 20.1% of the variation. This study is the first attempt to identify QTL associated with tissue culture amenity in oil palm which is an important step towards understanding the molecular processes underlying clonal regeneration of oil palm.

Matched MeSH terms: Polymorphism, Restriction Fragment Length/genetics
STK15 Phe31Ile and Val57Ile polymorphisms increase the risk of gastrointestinal cancer

TianXin Lai, Eric Tzyy Jiann Chong, Ping-Chin Lee, Jitt Aun Chuah, Kek Heng Chua

Sains Malaysiana, 2018;47:141-148.

STK15 is a serine/threonine kinase that regulates chromosomal segregation during mitosis. Single nucleotide polymorphisms (SNPs) in this gene, Phe31Ile (rs2273535) and Val57Ile (rs1047972), are inconsistently associated with gastrointestinal cancer (GIC) across different populations. However, this association is unclear in Malaysian population. Therefore, this study investigated the association of STK15 Phe31Ile and Val57Ile polymorphisms to GIC risk in Malaysia. Genomic DNA was extracted from 185 GIC patients and 1110 healthy controls and was subjected to polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis. SNPs were further confirmed using sequencing. We found that the 31Phe allele and 31Phe/Phe genotype in the Phe31Ile SNP significantly increased GIC risk in Malaysian population, particularly in gastric cancer (p<0.017). The combined analysis for both SNPs also increased the risk of GIC in this study. Etiological factors such as age, gender and ethnicity were not associated with GIC in the population. This is the first study to report the association of STK15 Phe31Ile and Val57Ile SNPs with an increased risk of GIC in Malaysians; the 31Phe allele is exclusively associated with the risk of gastric cancer. In addition, GIC incidences among Malaysians have significantly shifted to a younger age (<50 years).

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Epidemiologic analysis of sporadic Salmonella typhi isolates and those from outbreaks by pulsed-field gel electrophoresis

Thong KL, Cheong YM, Puthucheary S, Koh CL, Pang T

J Clin Microbiol, 1994 May;32(5):1135-41.
PMID: 7914202

Pulsed-field gel electrophoresis (PFGE) was used to compare and analyze 158 isolates of Salmonella typhi from five well-defined outbreaks of typhoid fever in Malaysia and also isolates involved in sporadic cases of typhoid fever occurring during the same period. Digestion of chromosomal DNAs from these S. typhi isolates with the restriction endonucleases XbaI (5'-TCTAGA-3'), SpeI (5'-ACTAGT-3'), and AvrII (5'-CCTAGG-3') and then PFGE produced restriction endonuclease analysis (REA) patterns consisting of 11 to 24 DNA fragments ranging in size from 20 to 630 kbp. Analysis of the REA patterns generated by PFGE after digestion with XbaI and SpeI indicated that the S. typhi isolates obtained from sporadic cases of infection were much more heterogeneous (at least 13 different REA patterns were detected; Dice coefficient, between 0.73 and 1.0) than those obtained during outbreaks of typhoid fever. The clonal nature and the close genetic identities of isolates from outbreaks in Alor Setar, Penang, Kota Kinabalu, Johor Bahru, and Kota Bahru were suggested by the fact that only a limited number of REA patterns, which mostly differed by only a single band, were detected (one to four patterns; Dice coefficient, between 0.82 and 1.0), although a different pattern was associated with each of these outbreaks. Comparison of REA patterns with ribotyping for 18 S. typhi isolates involved in sporadic cases of infection showed a good correlation, in that 72% of the isolates were in the same group. There was no clear correlation of phage types with a specific REA pattern. We conclude that PFGE of s. typhi chromosomal DNA digested with infrequently cutting restriction endonucleases is a useful method for comparing and differentiating S. typhi isolates for epidemiological purposes.

Matched MeSH terms: Polymorphism, Restriction Fragment Length
Molecular analysis of environmental and human isolates of Salmonella typhi

Thong KL, Cordano AM, Yassin RM, Pang T

Appl Environ Microbiol, 1996 Jan;62(1):271-4.
PMID: 8572705

Molecular characterization of a total of 54 isolates of Salmonella typhi from Santiago, Chile, was performed by pulsed-field gel electrophoresis (PFGE) after digestion of chromosomal DNA with three restriction endonucleases: XbaI (5'-TCTAGA-3'), AvrII (5'-CCTAGG-3'), and SpeI (5'-ACTAGT-3'). Thirteen of the 54 isolates were obtained from environmental sources (sewage and river water), and the rest were isolates from clinical cases of typhoid fever. Considerable genetic diversity was detected among the human isolates obtained in 1994, as evidenced by the presence of 14 to 19 different PFGE patterns among 20 human isolates, with F (coefficient of similarity) values ranging from 0.69 to 1.0 (XbaI), 0.61 to 1.0 (AvrII), and 0.70 to 1.0 (SpeI). A total of eight phage types were detected among these 20 isolates, with 50% possessing the E1 or 46 phage type. There was no correlation between PFGE pattern and phage types. Similar diversity was seen among 21 isolates obtained in 1983, with 17 to 19 PFGE patterns detected and F values of 0.56 to 1.0 (XbaI), 0.55 to 1.0 (AvrII), and 0.67 to 1.0 (SpeI). Comparison of these two groups of human isolates obtained 11 years apart indicated that certain molecular types of S. typhi are shared and are able to persist for considerable periods. A similar degree of genetic diversity was also detected among the environmental isolates of S. typhi, for which 10 to 12 different PFGE patterns were detected among the 13 isolates analyzed, with F values ranging from 0.56 to 1.0 (XbaI), 0.52 to 1.0 (AvrII), and 0.69 to 1.0 (SpeI). Certain molecular types present among the environmental isolates of S. typhi were also found among the human isolates from the same time period, providing evidence for the epidemiological link between environmental reservoirs and human infection.

Matched MeSH terms: Polymorphism, Restriction Fragment Length*

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