Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, ...using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Tualang honey (TH) is a Malaysian multifloral jungle honey. In recent years, there has been a marked increase in the number of studies published in medical databases regarding its potential health ...benefits. The study aimed to investigate the effect of TH against
and
.
The effect of TH on both bacteria was investigated using MIC, MBC, growth curve, time-kill curve, scanning electron microscopy (SEM) and RT-qPCR.
The MIC of TH against
and
was 18.5% (w/v) and 13% (w/v) respectively and MBC was 25% (w/v) for both bacteria. Spectrophotometric readings of at least 90% inhibition yielded MIC
values of TH, 18.5% (w/v) and 15% (w/v) for
and
respectively. A time-kill curve demonstrated a bactericidal with a 4-log reduction estimated within 8 hours. Using SEM, loss of structural integrity and marked changes in cell shape were observed. RT-qPCR analysis showed that TH reduced the pattern of gene expression in both bacteria, with a trend toward reduced expression of the virulence genes of interest.
This study suggests that TH could potentially be used as an alternative therapeutic agent for microbial infection particularly against these two organisms.
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Pseudomonas aeruginosa
and
Streptococcus pyogenes
are the most common pathogens to humans and are able to form a biofilm following ineffective precautionary approach. Biofilm is defined as a ...surface-attached community of bacterium embedded in an extracellular matrix which leads to tremendous problems in the environment, among humans and animals. This study aims to investigate the ability of
P. aeruginosa
and
S. pyogenes
to form biofilms in 96-well plate before further study in antibiofilm will be done. Initially, the 96-well plate was added with 100 μl of overnight
P. aeruginosa
culture with optical density (OD) 0.1 and
S. pyogenes
culture with OD 0.05. The cultures were incubated for 7 days at 37 °C to justify the formation of biofilm. Subsequently, stained blue biofilm was detached from the plate by using 95% ethanol. Biofilms were finally measured using a micro plate reader at 570 nm and were classified based on the adherence strength formula.
P. aeruginosa
and
S. pyogenes
biofilms strongly adhered to the plates on days three, four, five and six. Interestingly on day three, biofilms showed the highest formation. However, moderate biofilm formation onto the plates by both
P. aeruginosa
and
S. pyogenes
were observed on day two, but non-adherence was observed on days one and seven. Day three is the optimum cultivation period for
P. aeruginosa
and
S. pyogenes
to switch into a strong biofilm in microtiter plate and could be beneficial for antibiofilm experiments.
The dopamine D2 receptor gene (DRD2) plays a role in many diseases such as schizophrenia, Parkinson's disease, and addictive behaviour. Methods currently available for the detection of DRD2 ...polymorphisms are costly and cannot detect all 8 polymorphisms of our research interest simultaneously (Val96Ala, Leu141Leu, Val154Ile, Pro310Ser, Ser311Cys, TaqI A, A-241G, and -141C Ins/Del). Therefore, we developed a nested multiplex polymerase chain reaction (PCR) for simultaneous detection of these polymorphisms.
Genomic DNA was extracted from blood using standardised methods. Primers specific at the 3'-end for the polymorphic sites were designed. A two-step PCR method was developed. In the first PCR, a region from exon 3 to 4, exon 7, the promoter region, and the 3'-region of DRD2 were specifically amplified. The products were subsequently used as templates in the second PCR. Sequencing was performed to validate the test results.
Specific bands corresponding to the amplified product of interest were obtained. The method was reproducible and specific when used to genotype patients with schizophrenia. The amplified sequences showed 100% homology to the DRD2 sequence.
The method was found to be simple, rapid, specific, and reproducible for the simultaneous detection of the DRD2 polymorphisms.
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Polymorphisms in the genes of G-protein subunit beta 3 (GNB3); rs5443, tryptophan hydroxylase 1 (TPH1); rs211105 and rs4537731, tryptophan hydroxylase 2 (TPH2); rs4570625 and sodium voltage-gated ...channel alpha subunit 5 (SCN5A); rs1805124, have known to cause the abnormalities in the gastrointestinal tract that are implicated to irritable bowel syndrome (IBS) predisposition. Upfront genetic polymorphism genotyping in IBS-related gene polymorphisms will help to intervene and guide the decision-making in the management of IBS patients. This study aimed to develop a genotyping method to detect the respective polymorphisms using nested allele-specific multiplex polymerase chain reaction (NASM-PCR). A combination of nested and allele-specific multiplex PCR method was developed to determine the five single nucleotide polymorphisms (SNPs) mentioned. Annealing temperature, annealing and extension times, and the concentrations of MgCl2, primers, and DNA samples were optimized in the PCR. Sanger sequencing was performed to validate the genotyping results. NASM-PCR for IBS-related gene polymorphisms were successfully developed. DNA bands which correspond to the genes and SNPs have shown 100% homologous with the gene database. The developed method of NASM-PCR was reproducible and specific to be used for determining the respective polymorphisms of IBS. Notably, the described method can easily be integrated into other laboratories for population study or clinical use.
Aim: Irritable bowel syndrome (IBS) defined by chronic or recurrent abdominal pain or discomfort and changes in bowel habits, is the most common functional gastrointestinal disorder. Studies proved ...that polymorphisms in the genes were one of the key roles in the underlying IBS. This study aimed to investigate the genotypes and allele frequencies of the IBS-associated single nucleotide polymorphism (SNP) from the genes GNB3 (rs54443) and SCN5A (rs8015124) in unrelated, healthy Malays of Malaysia.
Material and Methods: The genomic DNA of 404 subjects was set to nested, multiplex, and allele-specific PCR to determine the aforementioned SNPs. The PCR results were validated through the Sanger sequencing analysis.
Results: Malays possessed a slightly higher frequency of wild (C) than mutant (T) alleles in the rs5443 with 56.3 vs 43.7%. However, the frequencies of the alleles were equivalent in the subset of Malay females (C-50%, T-50%). For rs1805124, only 18.6% of Malays carried the mutant allele G with less than 10 subjects being homozygous mutant GG carriers. Concurrently, the Hardy-Weinberg equilibrium of the SNPs in the study was not deviated.
Conclusion: IBS is a common gastrointestinal problem that has significantly reduced the life quality of oneself and become an economic burden to societies. Though the mutant alleles were rather low, the IBS-associated polymorphisms, rs5443 and rs1805124 were noted to be commonly present in the Malays. Further research on the local IBS patients is recommended to affirm the association of rs5443 and rs1805124 polymorphisms and the syndrome.
Amaç: Kronik veya tekrarlayan karın ağrısı veya rahatsızlığı ve bağırsak alışkanlıklarında değişiklik ile tanımlanan irritabl bağırsak sendromu (irritable bowel syndrome, IBS), en sık görülen fonksiyonel gastrointestinal bozukluktur. Çalışmalar, genlerdeki polimorfizmlerin, IBS'de altta yatan anahtar rollerden biri olduğunu kanıtlamıştır. Bu çalışmada, Malezya'nın ilişkisiz, sağlıklı Malaylarında, GNB3 (rs54443) ve SCN5A (rs8015124) genlerinden, IBS ile ilişkili tek nükleotid polimorfizminin (single nucleotide polymorphism, SNP) genotiplerinin ve alel frekanslarının araştırılması amaçlanmıştır.
Gereç ve Yöntemler: Toplam 404 katılımcının genomik DNA'sı, yukarıda belirtilen SNP'leri belirlemek için yuvalanmış, multipleks ve alele özgü polimeraz zincir reaksiyonu (polymerase chain reaction, PCR) ile analiz edildi. PCR sonuçları, Sanger sıralama analizi ile doğrulandı.
Bulgular: Malaylar, rs5443'te %56,3’e karşı %43,7 ile mutant (T) alellerinden biraz daha yüksek bir yabanıl (C) alel frekansına sahipti. Bununla birlikte, alellerin frekansları Malay kadınlar alt grubunda eşitti (C-%50, T-%50). rs1805124 için, Malayların sadece %18,6'sı mutant alel G'yi taşıyordu ve 10'dan az katılımcı homozigot mutant GG taşıyıcılarıydı. Aynı zamanda, çalışmadaki SNP Hardy-Weinberg dengesinden de sapmamıştı.
Sonuç: İBS, kişinin yaşam kalitesini önemli ölçüde düşüren ve toplumlara ekonomik yük haline gelen yaygın bir gastrointestinal sorunudur. Mutant alellerin oldukça düşük olmasına rağmen, IBS ile ilişkili polimorfizmlerin, rs5443 ve rs1805124'ün Malaylarda yaygın olarak bulunduğu kaydedildi. rs5443 ve rs1805124 polimorfizmleri ile sendromun ilişkisini doğrulamak için yerel IBS hastaları üzerinde daha fazla araştırma yapılması önerilir.
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Peroxisome proliferator-activated receptor Ɣ2 (PPARƔ2) gene Pro12Ala polymorphism has been extensively studied in relation to obesity and its associated metabolic complications but the results were ...inconclusive. This study aimed to identify the genotypic and allelic frequencies of PPARƔ2 gene and its association with anthropometric measurements, lipid profiles and the susceptibility for obesity in Malay subjects.
This cross-sectional, comparative study involved 217 subjects (94 obese and 123 non-obese as controls). Anthropometric and lipid profiles were measured. Genotyping was performed by allele-specific PCR. Comparisons were made between the genotypes and the association of PPARƔ2 Pro12Ala polymorphism with obesity was evaluated. The Pro12Pro, Pro12Ala and Ala12Ala genotypic frequencies were significantly different between groups (88.3%/11.7%/0.0% vs. 97.6%/2.4%/0.0% respectively, P=0.006).The Ala12 allele was more frequent in obese than the non-obese (5.9% vs. 1.1%, P=0.007). Ala12 carriers were associated with higher BMI (P=0.016), BF% (P=0.019) and a trend towards higher BAI (P=0.055) than the non-carriers. Besides age, high level of triglycerides and LDL-cholesterol, Ala12 allele (Adjusted OR=5.46, 95% CI=1.27–23.40; P=0.022) were regarded as independent risk factors for obesity.
This study indicates that the PPARƔ2 gene Pro12Ala polymorphism predisposes to obesity in Malay subjects and Ala12 allele could predict alterations in adipocyte and lipid metabolism among them. Age, triglycerides, LDL-cholesterol and Ala12 allele conferred to increased risk for obesity in this ethnicity.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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