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Fulltext Forensic parameter and paternity testing of tpa-25 element in elantan-Malay and Jawa-Malay

Nurul Syafika Muslimin, Nur Hilwani Ismail, Farida Zuraina Mohd Yusof

Pertanika Journal of Science & Technology, 2019;27(4):1575-1588.
MyJurnal

Malays consist of multi sub-ethnic group believed to have different ancestral origins based on their migrations centuries ago. The DNA profiling for every individual in Malaysia is not recorded, making Malaysia lacking in genetic data of its own citizens. This research aimed to study the geographic-ancestry origin of two Malay sub-ethnic population; Kelantan- Malay and Jawa-Malay by looking into the variation of TPA-25 insertion in each population. It specifically studied on several areas of Peninsular Malaysia in the region of Kelantan, Selangor and Johor as the representative of main areas with high percentage of Kelantan- Malay and Jawa-Malay populations. All the data were obtained from an application of TPA-PCR method, forensic parameter (F-statistic) and survey questionnaire that polled genetically on their ancestry origin in each sub-ethnic population. The research showed that population with high percentage of heterozygous allele (Tt) of TPA-25 insertion was likely to have high possibility of genetic drift occurrence. Jawa- Malay showed the highest percentage of heterozygous allele (Tt) with approximately 48% of the population. The FIS value of Kelantan-Malay and Jawa-Malay populations were recorded positive with the values of 0.678 and 0.366 respectively. Moreover, the FIT value recorded was 0.535 which suggested that these two populations were deficits of heterozygotes.
Association between dialysis dose and biochemical blood parameters

Nur Zakiah Mohd Saat, Sazlina Kamaralzaman, Farida Zuraina Mohd Yusoff, Norshafarina Shaari

Sains Malaysiana, 2011;40.

The end stage renal disease (ESRD) patients requires hemodialysis to survive. Efficacy of the treatment is determined by evaluation of minimal dialysis dose (Kt/V) which is 1.2. A cross sectional study was conducted among patients that undergo hemodialysis in a dialysis centre in Kuala Lumpur, Malaysia. The objectives of the study were to determine the association between dialysis dose and demographic factors and assessed the association between biochemical blood parameter and the demographic factors. The biochemical blood parameters were serum albumin, creatinine, cholesterol and hemoglobin. Result showed that all Indians and 54% of Chinese patients achieved the required dialysis dose. However only 29% of Malay patients attained the effective dialysis dose. More women patients accomplished the dialysis dose of at least 1.2 compared to men patients with odd ratio of 11.24. All the biochemical blood parameters were independent of the demographic factors. However, the cholesterol level was associated significantly with gender (p<0.05). In conclusion, the study found the biochemical blood parameter and dialysis dose were not influenced by the demographic factors.
Fulltext Analysing population structure of Elaeis oleifera germplasm using model-based approach programme STRUCTURE

Wan Nurhayati Wan Hanaf, Farida Zuraina Mohd Yusof, Rajinder Singh, Ahmad Kushairi Din, Rajanaidu Nookiah, Maizura Ithnin

Scientific Research Journal, 2017;14(1):54-63.
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Elaeis oleifera serves as a source of genetic foundation in oil palm improvement programme, as it possess several interesting agronomic traits such as slow growth, higher oil unsaturation and disease resistance. Malaysian Palm Oil Board (MPOB) has developed a collection of simple sequence repeats (SSRs) from Elaeis oleifera genome (E. oleifera-gSSRs). A total of 21 polymoprhic SSR markers were evaluated in the attempt to assess the population structure of E. oleifera populations. The appropriate common ancestry (K) value was determined to be seven from the likelihood scores. The profile from STRUCTURE analysis indicates considerable sharing of genetic components among E. oleifera population with an exception for Population 01 from Columbia and Population 02 from Costa Rica. The present study provides information on population structure of MPOB E. oleifera collection via model-based method for germplasm conservation and utilisation in breeding programmes.
Quantification of hsp70 gene expression and determination of capacitation status of magnetically separated cryopreserved bovine spermatozoa at different thawing temperature and time

Syarifah Faezah Syed Mohamad, Nur Hilwan Ismail, Farida Zuraina, Mohd Yusof, Siti Fatimah Ibrahim, Farah Hanan Fathihah Jaafar, et al.

Sains Malaysiana, 2018;47:1101-1108.

The role of heat shock protein in reproduction is widely known as a molecular chaperone in aiding and repairing protein
formation when stress occurred. The present objectives were to evaluate the effect of different thawing temperature and
time on the expression of HSP70 gene expression and the capacitation status in cryopreserved bovine spermatozoa. Briefly,
fresh ejaculates were obtained from three different adult bulls. The semen then underwent a sperm washing technique
known as Magnetic Activated Cell Sorting System (MACS) and later on, cryopreserved. The sperm- containing straws
were then thawed at five different thawing temperatures and time post-cryostorage; 20°C for 13 s, 37°C for 30 s, 40°C
for 7 s, 60°C for 6 s and 80°C for 5 s. The RNA was extracted from each of the sperm’s pellets and converted to cDNA
prior to the qPCR process. Capacitation status was then determined by means of CTC assay. The results showed that after
the process of amplification, there is a significant different of HSP70 gene expression in MACS process samples when the
thawing process was performed at 37°C for 30 s, with p<0.05. Furthermore, the CTC assay also showed that thawing at
the same temperature gave less capacitated spermatozoa with p<0.05. As a conclusion, MACS yield spermatozoa with a
better expression of HSP70 gene and less capacitated spermatozoa when thawing was done at 37°C for 30 s.
Fulltext Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines

Mohd Yussup SS, Marzukhi M, Md-Zain BM, Mamat K, Mohd Yusof FZ

Evol Bioinform Online, 2017;13:1176934317735318.
PMID: 29085238 DOI: 10.1177/1176934317735318

The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.
Fulltext Pathogenic nsSNPs that increase the risks of cancers among the Orang Asli and Malays

Khoruddin NA, Noorizhab MN, Teh LK, Mohd Yusof FZ, Salleh MZ

Sci Rep, 2021 Aug 09;11(1):16158.
PMID: 34373545 DOI: 10.1038/s41598-021-95618-y

Single-nucleotide polymorphisms (SNPs) are the most common genetic variations for various complex human diseases, including cancers. Genome-wide association studies (GWAS) have identified numerous SNPs that increase cancer risks, such as breast cancer, colorectal cancer, and leukemia. These SNPs were cataloged for scientific use. However, GWAS are often conducted on certain populations in which the Orang Asli and Malays were not included. Therefore, we have developed a bioinformatic pipeline to mine the whole-genome sequence databases of the Orang Asli and Malays to determine the presence of pathogenic SNPs that might increase the risks of cancers among them. Five different in silico tools, SIFT, PROVEAN, Poly-Phen-2, Condel, and PANTHER, were used to predict and assess the functional impacts of the SNPs. Out of the 80 cancer-related nsSNPs from the GWAS dataset, 52 nsSNPs were found among the Orang Asli and Malays. They were further analyzed using the bioinformatic pipeline to identify the pathogenic variants. Three nsSNPs; rs1126809 (TYR), rs10936600 (LRRC34), and rs757978 (FARP2), were found as the most damaging cancer pathogenic variants. These mutations alter the protein interface and change the allosteric sites of the respective proteins. As TYR, LRRC34, and FARP2 genes play important roles in numerous cellular processes such as cell proliferation, differentiation, growth, and cell survival; therefore, any impairment on the protein function could be involved in the development of cancer. rs1126809, rs10936600, and rs757978 are the important pathogenic variants that increase the risks of cancers among the Orang Asli and Malays. The roles and impacts of these variants in cancers will require further investigations using in vitro cancer models.
Fulltext Diversified lineages and drug-resistance profiles of clinical isolates of Mycobacterium tuberculosis complex in Malaysia

Noorizhab Fakhruzzaman MN, Abidin NZ, Aziz ZA, Lim WF, Richard JJ, Noorliza MN, et al.

Int J Mycobacteriol, 2019 12 4;8(4):320-328.
PMID: 31793500 DOI: 10.4103/ijmy.ijmy_144_19

Background: Tuberculosis (TB) is still a major health problem in Malaysia with thousands of cases reported yearly. This is further burdened with the emergence of multidrug-resistant TB (MDR-TB). Whole-genome sequencing (WGS) provides high-resolution molecular epidemiological data for the accurate determination of Mycobacterium tuberculosis complex (MTBC) lineages and prediction of the drug-resistance patterns. This study aimed to investigate the diversity of MTBC in Malaysia in terms of lineage and drug-resistance patterns of the clinical MTBC isolates using WGS approach.
Methods: The genomes of 24 MTBC isolated from sputum and pus samples were sequenced. The phenotypic drug susceptibility testing (DST) of the isolates was determined for ten anti-TB drugs. Bioinformatic analysis comprising genome assembly and annotation and single-nucleotide polymorphism (SNP) analysis in genes associated with resistance to the ten anti-TB drugs were done on each sequenced genome.
Results: The draft assemblies covered an average of 97% of the expected genome size. Eleven isolates were aligned to the Indo-Oceanic lineage, eight were East-Asian lineage, three were East African-Indian lineage, and one was of Euro-American and Bovis lineages, respectively. Twelve of the 24 MTBC isolates were phenotypically MDR M. tuberculosis: one is polyresistance and another one is monoresistance. Twenty-six SNPs across nine genes associated with resistance toward ten anti-TB drugs were detected where some of the mutations were found in isolates that were previously reported as pan-susceptible using DST. A haplotype consisting of 65 variants was also found among the MTBC isolates with drug-resistance traits.
Conclusions: This study is the first effort done in Malaysia to utilize 24 genomes of the local clinical MTBC isolates. The high-resolution molecular epidemiological data obtained provide valuable insights into the mechanistic and epidemiological qualities of TB within the vicinity of Southeast Asia.
Fulltext Stress, Anxiety and Depression among a Cohort of Health Sciences Undergraduate Students: The Prevalence and Risk Factors

Fauzi MF, Anuar TS, Teh LK, Lim WF, James RJ, Ahmad R, et al.

Int J Environ Res Public Health, 2021 03 22;18(6).
PMID: 33809939 DOI: 10.3390/ijerph18063269

Stress, anxiety, and depression (SAD) have a negative impact on the learning and academic performance of university students. Hence, this study aimed to determine the prevalence, as well as the risk factors associated with SAD among a cohort of students pursuing undergraduate degree courses in health sciences. This is part of the strategy in building a healthy nation. A questionnaire containing socio-demographic factors and the short version of Depression, Anxiety, and Stress Scale-21 (DASS-21) was used to assess the likelihood of psychological distress. Logistic regression analysis was conducted to determine the risk factors of SAD. In total, 449 students completed the questionnaire (93.9% response rate). Of these, 65% had stress, 85.1% had anxiety and 51.4% had depression. Most cases of stress (74.6%) and depression (66.2%) were of normal-to-mild level, while 74.6% of them showed moderate-to-extremely severe anxiety. There was a statistically significant association between stress score and the year of study. In the regression analysis, poor sleep quality and fatigue were risk factors of anxiety and depression, whereas low-grade fever and frequent headaches were risk factors for stress and anxiety. Stress, anxiety, and depression scores were significantly higher among students studying medical imaging. A substantial proportion of health science students are suffering from SAD. This study recommends screening and close monitoring of the above-mentioned predictors and the formulation of comprehensive intervention strategies for students with SAD.