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  1. A genetic similarity algorithm for searching the Gene Ontology terms and annotating anonymous protein sequences
    Othman RM, Deris S, Illias RM
    J Biomed Inform, 2008 Feb;41(1):65-81.
    PMID: 17681495
    A genetic similarity algorithm is introduced in this study to find a group of semantically similar Gene Ontology terms. The genetic similarity algorithm combines semantic similarity measure algorithm with parallel genetic algorithm. The semantic similarity measure algorithm is used to compute the similitude strength between the Gene Ontology terms. Then, the parallel genetic algorithm is employed to perform batch retrieval and to accelerate the search in large search space of the Gene Ontology graph. The genetic similarity algorithm is implemented in the Gene Ontology browser named basic UTMGO to overcome the weaknesses of the existing Gene Ontology browsers which use a conventional approach based on keyword matching. To show the applicability of the basic UTMGO, we extend its structure to develop a Gene Ontology -based protein sequence annotation tool named extended UTMGO. The objective of developing the extended UTMGO is to provide a simple and practical tool that is capable of producing better results and requires a reasonable amount of running time with low computing cost specifically for offline usage. The computational results and comparison with other related tools are presented to show the effectiveness of the proposed algorithm and tools.
  2. Fulltext CYP11B2 gene polymorphism among coronary heart disease patients and blood donors in Malaysia
    Normaznah Y, Azizah MR, Kuak SH, Rosli MA
    Malays J Pathol, 2015 Apr;37(1):45-7.
    PMID: 25890613 MyJurnal
    Various previous studies have reported the implication of CYP11B2 gene polymorphism in the pathophysiology of cardiovascular diseases. In particular, the -344T/C polymorphism, which is located at a putative binding site for the steroidogenic transcription factor (SF-1) has been associated with essential hypertension, left ventricular dilation and coronary heart disease. In the present study, we aim to determine the allele and genotype frequencies of the CYP11B2 gene in patients with clinical manifestation of coronary heart disease and confirmed by angiography and blood donors and to calculate the association of the gene polymorphism with CHD. A total of 79 DNA from patients with coronary heart disease admitted to the National Heart Institute and 84 healthy blood donors have been genotyped using polymerase chain reaction technique followed by restriction enzyme digestion (RFLP). Results of the study demonstrated that out of 79 for the patients, 40 were homozygous T, 10 were homozygous C and 29 were heterozygous TC. The frequencies of genotype TT, CC and TC for patients were 0.5, 0.13 and 0.36 respectively. The frequencies of allele T and C in patients were 0.68 and 0.31 respectively. While for the blood donors, 40 subjects were of homozygous T, 7 were homozygous C and 37 were heterozygous TC. The genotype frequencies for the TT, CC and TC were 0.47, 0.08 and 0.44 respectively. The frequency of the allele T was 0.69 and allele C was 0.3. Chi-Square analysis showed that there was no significant difference in the genotype and C allele frequencies between the CHD patients and the blood donors. Our study suggests that there is lack of association between -344T/C polymorphism of CYP11B2 gene and coronary heart disease.
  3. Enhanced secretory production of hemolysin-mediated cyclodextrin glucanotransferase in Escherichia coli by random mutagenesis of the ABC transporter system
    Low KO, Mahadi NM, Abdul Rahim R, Rabu A, Abu Bakar FD, Abdul Murad AM, et al.
    J Biotechnol, 2010 Dec;150(4):453-9.
    PMID: 20959127 DOI: 10.1016/j.jbiotec.2010.10.001
    The hemolysin transport system was found to mediate the release of cyclodextrin glucanotransferase (CGTase) into the extracellular medium when it was fused to the C-terminal 61 amino acids of HlyA (HlyAs(61)). To produce an improved-secretion variant, the hly components (hlyAs, hlyB and hlyD) were engineered by directed evolution using error-prone PCR. Hly mutants were screened on solid LB-starch plate for halo zone larger than the parent strain. Through screening of about 1 × 10(4) Escherichia coli BL21(DE3) transformants, we succeeded in isolating five mutants that showed a 35-217% increase in the secretion level of CGTase-HlyAs(61) relative to the wild-type strain. The mutation sites of each mutant were located at HlyB, primarily along the transmembrane domain, implying that the corresponding region was important for the improved secretion of the target protein. In this study we describe the finding of novel site(s) of HlyB responsible for enhancing secretion of CGTase in E. coli.
  4. Fulltext Cellobiohydrolase B of Aspergillus niger over-expressed in Pichia pastoris stimulates hydrolysis of oil palm empty fruit bunches
    Woon JS, Mackeen MM, Illias RM, Mahadi NM, Broughton WJ, Murad AMA, et al.
    PeerJ, 2017;5:e3909.
    PMID: 29038760 DOI: 10.7717/peerj.3909
    BACKGROUND: Aspergillus niger, along with many other lignocellulolytic fungi, has been widely used as a commercial workhorse for cellulase production. A fungal cellulase system generally includes three major classes of enzymes i.e., β-glucosidases, endoglucanases and cellobiohydrolases. Cellobiohydrolases (CBH) are vital to the degradation of crystalline cellulose present in lignocellulosic biomass. However, A. niger naturally secretes low levels of CBH. Hence, recombinant production of A. niger CBH is desirable to increase CBH production yield and also to allow biochemical characterisation of the recombinant CBH from A. niger.

    METHODS: In this study, the gene encoding a cellobiohydrolase B (cbhB) from A. niger ATCC 10574 was cloned and expressed in the methylotrophic yeast Pichia pastoris X-33. The recombinant CBHB was purified and characterised to study its biochemical and kinetic characteristics. To evaluate the potential of CBHB in assisting biomass conversion, CBHB was supplemented into a commercial cellulase preparation (Cellic(®) CTec2) and was used to hydrolyse oil palm empty fruit bunch (OPEFB), one of the most abundant lignocellulosic waste from the palm oil industry. To attain maximum saccharification, enzyme loadings were optimised by response surface methodology and the optimum point was validated experimentally. Hydrolysed OPEFB samples were analysed using attenuated total reflectance FTIR spectroscopy (ATR-FTIR) to screen for any compositional changes upon enzymatic treatment.

    RESULTS: Recombinant CBHB was over-expressed as a hyperglycosylated protein attached to N-glycans. CBHB was enzymatically active towards soluble substrates such as 4-methylumbelliferyl-β-D-cellobioside (MUC), p-nitrophenyl-cellobioside (pNPC) and p-nitrophenyl-cellobiotrioside (pNPG3) but was not active towards crystalline substrates like Avicel(®) and Sigmacell cellulose. Characterisation of purified CBHB using MUC as the model substrate revealed that optimum catalysis occurred at 50 °C and pH 4 but the enzyme was stable between pH 3 to 10 and 30 to 80 °C. Although CBHB on its own was unable to digest crystalline substrates, supplementation of CBHB (0.37%) with Cellic(®) CTec2 (30%) increased saccharification of OPEFB by 27%. Compositional analyses of the treated OPEFB samples revealed that CBHB supplementation reduced peak intensities of both crystalline cellulose Iα and Iβ in the treated OPEFB samples.

    DISCUSSION: Since CBHB alone was inactive against crystalline cellulose, these data suggested that it might work synergistically with other components of Cellic(®) CTec2. CBHB supplements were desirable as they further increased hydrolysis of OPEFB when the performance of Cellic(®) CTec2 was theoretically capped at an enzyme loading of 34% in this study. Hence, A. niger CBHB was identified as a potential supplementary enzyme for the enzymatic hydrolysis of OPEFB.

  5. Fulltext Optimization of a continuous hybrid impeller mixer via computational fluid dynamics
    Othman N, Kamarudin SK, Takriff MS, Rosli MI, Engku Chik EM, Meor Adnan MA
    ScientificWorldJournal, 2014;2014:619474.
    PMID: 25170524 DOI: 10.1155/2014/619474
    This paper presents the preliminary steps required for conducting experiments to obtain the optimal operating conditions of a hybrid impeller mixer and to determine the residence time distribution (RTD) using computational fluid dynamics (CFD). In this paper, impeller speed and clearance parameters are examined. The hybrid impeller mixer consists of a single Rushton turbine mounted above a single pitched blade turbine (PBT). Four impeller speeds, 50, 100, 150, and 200 rpm, and four impeller clearances, 25, 50, 75, and 100 mm, were the operation variables used in this study. CFD was utilized to initially screen the parameter ranges to reduce the number of actual experiments needed. Afterward, the residence time distribution (RTD) was determined using the respective parameters. Finally, the Fluent-predicted RTD and the experimentally measured RTD were compared. The CFD investigations revealed that an impeller speed of 50 rpm and an impeller clearance of 25 mm were not viable for experimental investigations and were thus eliminated from further analyses. The determination of RTD using a k-ε turbulence model was performed using CFD techniques. The multiple reference frame (MRF) was implemented and a steady state was initially achieved followed by a transient condition for RTD determination.
  6. Fulltext Optimization of integrated impeller mixer via radiotracer experiments
    Othman N, Kamarudin SK, Takriff MS, Rosli MI, Engku Chik EM, Adnan MA
    ScientificWorldJournal, 2014;2014:242658.
    PMID: 24741344 DOI: 10.1155/2014/242658
    Radiotracer experiments are carried out in order to determine the mean residence time (MRT) as well as percentage of dead zone, V dead (%), in an integrated mixer consisting of Rushton and pitched blade turbine (PBT). Conventionally, optimization was performed by varying one parameter and others were held constant (OFAT) which lead to enormous number of experiments. Thus, in this study, a 4-factor 3-level Taguchi L9 orthogonal array was introduced to obtain an accurate optimization of mixing efficiency with minimal number of experiments. This paper describes the optimal conditions of four process parameters, namely, impeller speed, impeller clearance, type of impeller, and sampling time, in obtaining MRT and V dead (%) using radiotracer experiments. The optimum conditions for the experiments were 100 rpm impeller speed, 50 mm impeller clearance, Type A mixer, and 900 s sampling time to reach optimization.
  7. Fulltext Optimization of PCR conditions to amplify Cyt b, COI and 12S rRNA gene fragments of Malayan gaur (Bos gaurus hubbacki) mtDNA
    Rosli MK, Zamzuriada AS, Syed-Shabthar SM, Mahani MC, Abas-Mazni O, Md-Zain BM
    Genet. Mol. Res., 2011;10(4):2554-68.
    PMID: 22033937 DOI: 10.4238/2011.October.19.2
    PCR has been extensively used for amplification of DNA sequences. We conducted a study to obtain the best amplification conditions for cytochrome b (Cyt b), cytochrome c oxidase I (COI) and 12S rRNA (12S) gene fragments of Malayan gaur mtDNA. DNA from seven Malayan gaur samples were extracted for PCR amplification. Various trials and combinations were tested to determine the best conditions of PCR mixture and profile to obtain the best PCR products for sequencing purposes. Four selected target factors for enhancing PCR, annealing temperature, concentration of primer pairs, amount of Taq polymerase, and PCR cycle duration, were optimized by keeping the amount of DNA template (50 ng/μL) and concentration of PCR buffer (1X), MgCl(2) (2.5 mM) and dNTP mixture (200 μM each) constant. All genes were successfully amplified, giving the correct fragment lengths, as assigned for both forward and reverse primers. The optimal conditions were determined to be: 0.1 μM primers for Cyt b and COI, 0.3 μM primers for 12S, 1 U Taq polymerase for all genes, 30 s of both denaturation and annealing cycles for Cyt b, 1 min of both stages for 12S and COI and annealing temperature of 58.4 ° C for Cyt b, 56.1 ° C for 12S and 51.3 ° C for COI. PCR products obtained under these conditions produced excellent DNA sequences.
  8. Fulltext The foundation of NCVD PCI Registry: the Malaysia's first multi-centre interventional cardiology project
    Liew HB, Rosli MA, Wan Azman WA, Robaayah Z, Sim KH, NCVD PCI investigators
    Med J Malaysia, 2008 Sep;63 Suppl C:41-4.
    PMID: 19230246
    The National Cardiovascular Database for Percutaneous Coronary Intervention (NCVD PCI) Registry is the first multicentre interventional cardiology project, involving the main cardiac centres in the country. The ultimate goal of NCVD PCI is to provide a contemporary appraisal of PCI in Malaysia. This article introduces the foundation, the aims, methodology, database collection and preliminary results of the first six-month database.
  9. Bilateral ophthalmic vein thrombosis secondary to nasal furunculosis
    Rohana AR, Rosli MK, Nik Rizal NY, Shatriah I, Wan Hazabbah WH
    Orbit, 2008;27(3):215-7.
    PMID: 18569833 DOI: 10.1080/01676830802009754
    We were presented with a teenage female who developed superior ophthalmic vein thrombosis and cavernous sinus thrombophlebitis after a 1-week history of a single acne-like lesion or furuncle at the anterior tip of the nose. She was managed aggressively with heparin and intravenous antibiotic. Signs and symptoms improved after 2 weeks of treatment, and she was discharged with an anticoagulant.
  10. Fulltext Comparison of energy and protein adequacy between closed and open enteral nutrition system in critically-ill adult patients [Abstract]
    Zheng YL, Norafizah MN, Rosli MS, Marlina MN, Maslina M, Nora Nurlinda Z, et al.
    Borneo Journal of Medical Sciences, 2019;2(101):17-18.
    MyJurnal
    Introduction: Critically-ill patients are commonly fed with EN via open system (OS) or closed system (CS). Several studies showed that patients on CS had received greater volume of EN compared to OS.
    Objective: As there was no study conducted in Malaysia, hence this study is conducted to compare the energy and protein adequacy of both systems.
    Methodology: This cohort prospective study was conducted in GICU (OS) and NICU/NHDW (CS) in Hospital Kuala Lumpur. Patients aged ≥18 years and fed by feeding pump in OS were included. Patients who were moribund or not given EN were excluded. Patients’ demographic data and disease severity score were collected on day 1 in ICU and followed for 5 days until decease or discharge. Adequacy was determined by percentage of energy/protein received from requirements.
    Results: Fifty-five patients were included (25 OS and 30 CS) with mean aged 45.41±17.46 years old, 78.2% male and 65.5% Malay. The mean SAPS II, SOFA score and ICU LOS were 46.47±10.65, 8.60±3.64 and 9.24±7.91 days respectively. The ICU mortality was 20%. EN was started about 2.56±2.89 days after ICU admission and the mean adequacy of energy was 74.56±32.23%, while protein adequacy was and 69.15±35.78%. Compared with the CS, OS were significantly older than CS (51 years old vs 42.5 years old; p=0.035) and had a higher SOFA score (10 vs 7.5; p= 0.014). No difference in ICU LOS and mortality between group were found. Energy (45.64% vs 96.71%; p<0.001) and protein adequacy (38.78% vs 94.12%; p<0.001) were significantly higher in the CS than the OS.
    Conclusion: CS as compared with OS may improve nutritional adequacy as CS delivered more 108% energy and 141% protein than OS. The difference in adequacy might be attributed to these factors; feeding method used in the system, patients’ characteristics and condition rather than the feeding system itself.
    Keywords: enteral nutrition, critically-ill patients, open system, closed system, adequacy
  11. Fulltext Management of rhinosinusitis in adults in primary care
    Husain S, Amilia HH, Rosli MN, Zahedi FD, Sachlin IS, Development Group Clinical Practice Guidelines Management of Rhinosinusitis in Adolescents & Adults
    Malays Fam Physician, 2018;13(1):28-33.
    PMID: 29796207 MyJurnal
    Rhinosinusitis is a common health problem encountered in primary care. It is due to mucosal inflammation of the nose and paranasal sinuses. Less than 2% of the cases are associated with bacterial infections. Diagnosis is based on clinical symptoms and supported by nasal endoscopy and imaging studies. Intranasal corticosteroids and normal saline irrigation are important treatments. Antibiotics are seldom indicated.
  12. Numerical analysis of flow distribution behavior in a proton exchange membrane fuel cell
    Lim BH, Majlan EH, Daud WRW, Rosli MI, Husaini T
    Heliyon, 2018 Oct;4(10):e00845.
    PMID: 30338304 DOI: 10.1016/j.heliyon.2018.e00845
    The flow distribution of a proton exchange membrane fuel cell within a manifold plays an important role on its performance. This study presents a numerical analysis of the flow distribution behavior within different manifold configurations. A two-dimensional model with 75 cells was employed to study the flow behavior. The variation in the stoichiometry and number of cells was also studied. Three different flow configurations were considered with different numbers of flow inlets and outlets. The flow characteristics, such as the pressure and velocity variations in the manifold and cells, were measured to determine the effects of the different flow configurations. The results indicated that the double inlet/outlet configuration had the best flow distribution when using 75 cells. Moreover, increasing the stoichiometry resulted in a better flow distribution to the cells in a stack.
  13. Evaluation of home medication review for patients with type 2 diabetes mellitus by community pharmacists: a randomised controlled trial
    Rosli MR, Neoh CF, Wu DB, Hassan NW, Mahmud M, Rahimi A, et al.
    Pharm Pract (Granada), 2021 09 09;19(3):2397.
    PMID: 34621450 DOI: 10.18549/PharmPract.2021.3.2397
    Background: Successful diabetes treatment requires commitment and understanding of disease management by the patients.

    Objective: This trial aimed to evaluate the programme effectiveness of home medication review by community pharmacists (HMR-CP) in optimising diabetes care and reducing medication wastage.

    Methods: A randomised controlled trial was conducted on 166 patients with Type 2 Diabetes Mellitus (T2DM) who were randomly assigned to the intervention or control groups. The intervention group received HMR-CP at 0-month, 3-month, and 6-month. The primary outcome was haemoglobin A1c (HbA1c) while clinical outcomes, anthropometric data, and humanistic outcomes were the secondary outcomes. For the intervention group, drug-related problems (DRP) were classified according to the Pharmaceutical Care Network Europe Foundation (PCNE). Medication adherence was determined based on the Pill Counting Adherence Ratio (PCAR). The cost of medication wastage was calculated based on the total missed dose by the T2DM patients multiplied by the cost of medication. General linear model and generalised estimating equations were used to compare data across the different time-points within and between the groups, respectively.

    Results: No significant difference was observed in the demographic and anthropometric data at baseline between the two groups except for fasting blood glucose (FBG). There was a significant reduction in the HbA1c (-0.91%) and FBG (-1.62mmol/L) over the study period (p<0.05). A similar observation was noted in diastolic blood pressure (DBP) and total cholesterol (TC) but not in high-density lipoprotein (HDL), and anthropometric parameters. Both utility value and Michigan Diabetes Knowledge Test (MDKT) scores increased significantly over time. As for the intervention group, significant changes in PCAR (p<0.001) and the number of DRP (p<0.001) were noted.

    Conclusions: HMR-CP significantly improved the glycaemic control, QoL, medication adherence, and knowledge of T2DM patients as well as reduced the number of DRP and cost of medication wastage. However, the impact of HMR-CP on certain clinical and anthropometric parameters remains inconclusive and further investigation is warranted.

  14. Spherical nanocrystalline cellulose (NCC) from oil palm empty fruit bunch pulp via ultrasound assisted hydrolysis
    Zianor Azrina ZA, Beg MDH, Rosli MY, Ramli R, Junadi N, Alam AKMM
    Carbohydr Polym, 2017 Apr 15;162:115-120.
    PMID: 28224888 DOI: 10.1016/j.carbpol.2017.01.035
    Nanocrystalline cellulose (NCC) was isolated from oil palm empty fruit bunch pulp (EFBP) using ultrasound assisted acid hydrolysis. The obtained NCC was analysed using FESEM, XRD, FTIR, and TGA, and compared with raw empty fruit bunch fibre (REFB), empty fruit bunch pulp (EFBP), and treated empty fruit bunch pulp (TEFBP). Based on FESEM analysis, it was found that NCC has a spherical shaped after acid hydrolysis with the assistance of ultrasound. This situation was different compared to previous studies that obtained rod-like shaped of NCC. Furthermore, the crystallinity of NCC is higher compared to REFB and EFBP. According to thermal stability, the NCC obtained shows remarkable sign of high thermal stability compared to REFB and EFBP.
  15. Fulltext Crystal structure of 2-amino-pyridinium 6-chloro-nicotinate
    Jasmine NJ, Rajam A, Muthiah PT, Stanley N, Razak IA, Rosli MM
    Acta Crystallogr E Crystallogr Commun, 2015 Sep 01;71(Pt 9):o655-6.
    PMID: 26396888 DOI: 10.1107/S2056989015014796
    In the title salt, C5H7N(+)·C6H3ClNO(-), the 2-amino-pyri-din-ium cation inter-acts with the carboxyl-ate group of the 6-chloro-nicotinate anion through a pair of independent N-H⋯O hydrogen bonds, forming an R 2 (2)(8) ring motif. In the crystal, these dimeric units are connected further via N-H⋯O hydrogen bonds, forming chains along [001]. In addition, weak C-H⋯N and C-H⋯O hydrogen bonds, together with weak π-π inter-actions, with centroid-centroid distances of 3.6560 (5) and 3.6295 (5) Å, connect the chains, forming a two-dimensional network parallel to (100).
  16. Fulltext Phylogenetic relationships of Malayan gaur with other species of the genus Bos based on cytochrome b gene DNA sequences
    Rosli MK, Zakaria SS, Syed-Shabthar SM, Zainal ZZ, Shukor MN, Mahani MC, et al.
    Genet. Mol. Res., 2011;10(1):482-93.
    PMID: 21476194 DOI: 10.4238/vol10-1gmr1002
    The Malayan gaur (Bos gaurus hubbacki) is one of the three subspecies of gaurs that can be found in Malaysia. We examined the phylogenetic relationships of this subspecies with other species of the genus Bos (B. javanicus, B. indicus, B. taurus, and B. grunniens). The sequence of a key gene, cytochrome b, was compared among 20 Bos species and the bongo antelope, used as an outgroup. Phylogenetic reconstruction was employed using neighbor joining and maximum parsimony in PAUP and Bayesian inference in MrBayes 3.1. All tree topologies indicated that the Malayan gaur is in its own monophyletic clade, distinct from other species of the genus Bos. We also found significant branching differences in the tree topologies between wild and domestic cattle.
  17. Updates in the management of Dyslipidaemia in the high and very high risk individual for CV risk reduction
    Jeyamalar R, Wan Azman WA, Nawawi H, Choo GH, Ng WK, Rosli MA, et al.
    Med J Malaysia, 2018 06;73(3):154-162.
    PMID: 29962499 MyJurnal
    Cardiovascular disease (CVD) has been the main cause of mortality and an important cause of morbidity in Malaysia for several years. To reduce global cardiovascular (CV) risk in the population, primary preventive strategies need to be implemented. Hypercholesterolaemia is one of the major risk factors for CVD. This paper is an expert review on the management of hypercholesterolemia focusing on high and very high risk individuals. In low and Intermediate risk individuals, therapeutic lifestyle changes (TLC) and a healthy lifestyle alone may suffice. In high and very high risk individuals, drug therapy in conjunction with TLC are necessary to achieve the target LDL-C levels which have been shown to slow down progression and sometimes even result in regression of atherosclerotic plaques. Statins are first-line drugs because they have been shown in numerous randomized controlled trials to be effective in reducing CV events and to be safe. In some high risk individuals, despite maximally tolerated statin therapy, target Low Density Lipoprotein Cholesterol (LDL-C) levels are not achieved. These include those with familial hypercholesterolaemia and statin intolerance. This paper discusses non-statin therapies, such as ezetimibe and the newer Proprotein convertase subtilisin/kexin type 9 Inhibitors (PCSK9-i).
  18. Fulltext A new subspecies identification and population study of the Asian small-clawed otter (Aonyx cinereus) in Malay Peninsula and southern Thailand based on fecal DNA method
    Rosli MK, Syed-Shabthar SM, Abdul-Patah P, Abdul-Samad Z, Abdul SN, Burhanuddin MN, et al.
    ScientificWorldJournal, 2014;2014:457350.
    PMID: 24715812 DOI: 10.1155/2014/457350
    Three species of otter can be found throughout Malay Peninsula: Aonyx cinereus, Lutra sumatrana, and Lutrogale perspicillata. In this study, we focused on the A. cinereus population that ranges from the southern and the east coast to the northern regions of Malay Peninsula up to southern Thailand to review the relationships between the populations based on the mitochondrial D-loop region. Forty-eight samples from six populations were recognized as Johor, Perak, Terengganu, Kelantan, Ranong, and Thale Noi. Among the 48 samples, 33 were identified as A. cinereus, seven as L. sumatrana, and eight as L. perspicillata. Phylogenetically, two subclades formed for A. cinereus. The first subclade grouped all Malay Peninsula samples except for samples from Kelantan, and the second subclade grouped Kelantan samples with Thai sample. Genetic distance analysis supported the close relationships between Thai and Kelantan samples compared to the samples from Terengganu and the other Malaysian states. A minimum-spanning network showed that Kelantan and Thailand formed a haplogroup distinct from the other populations. Our results show that Thai subspecies A. cinereus may have migrated to Kelantan from Thai mainland. We also suggest the classification of a new subspecies from Malay Peninsula, the small-clawed otter named A. cinereus kecilensis.
  19. Fulltext Species identification of Malayan Gaur, Kedah-Kelantan and Bali cattle using polymerase chain reaction-restricted fragment length polymorphism
    Romaino SM, Fazly-Ann ZA, Loo SS, Hafiz MM, Hafiz MD, Iswadi MI, et al.
    Genet. Mol. Res., 2014;13(1):406-14.
    PMID: 24535867 DOI: 10.4238/2014.January.21.8
    Mitochondrial DNA (mtDNA) is a useful genetic marker that can be used for species identification. The cytochrome b (Cyt b) gene is a suitable mtDNA candidate gene for use in phylogenetic analyses due to its sequence variability, which makes it appropriate for comparisons at the subspecies, species, and genus levels. This study was conducted to develop a rapid molecular method for species identification of Malayan gaur (Bos gaurus hubbacki), Kedah-Kelantan (KK) (Bos indicus), and Bali (Bos javanicus) cattle in Malaysia. DNA was extracted from blood samples of 8 Malayan gaurs, 30 KK, and 28 Bali cattle. A set of both specific and universal primers for the Cyt b gene were used in PCR amplification. DNA sequences obtained were then analyzed using BioEdit and Restriction Mapper softwares. The PCR products obtained from Cyt b gene amplification were then subjected to restriction enzyme digestion. The amplification, using both specific and universal primers, produced a 154- and a 603-bp fragment, respectively, in all three species. Two restriction enzymes, NlaIV and SspI, were used to obtain specific restriction profiles that allowed direct identification of Malayan gaur, KK, and Bali cattle. Our findings indicate that all three species can be identified separately using a combination of universal primers and the restriction enzyme SspI.
  20. The molecular phylogenetic signature of Bali cattle revealed by maternal and paternal markers
    Syed-Shabthar SM, Rosli MK, Mohd-Zin NA, Romaino SM, Fazly-Ann ZA, Mahani MC, et al.
    Mol Biol Rep, 2013 Aug;40(8):5165-76.
    PMID: 23686165 DOI: 10.1007/s11033-013-2619-y
    Bali cattle is a domestic cattle breed that can be found in Malaysia. It is a domestic cattle that was purely derived from a domestication event in Banteng (Bos javanicus) around 3,500 BC in Indonesia. This research was conducted to portray the phylogenetic relationships of the Bali cattle with other cattle species in Malaysia based on maternal and paternal lineage. We analyzed the cytochrome c oxidase I (COI) mitochondrial gene and SRY of Y chromosome obtained from five species of the Bos genus (B. javanicus, Bos gaurus, Bos indicus, Bos taurus, and Bos grunniens). The water buffalo (Bubalus bubalis) was used as an outgroup. The phylogenetic relationships were observed by employing several algorithms: Neighbor-Joining (PAUP version 4.0), Maximum parsimony (PAUP version 4.0) and Bayesian inference (MrBayes 3.1). Results from the maternal data showed that the Bali cattle formed a monophyletic clade, and together with the B. gaurus clade formed a wild cattle clade. Results were supported by high bootstrap and posterior probability values together with genetic distance data. For the paternal lineage, the sequence variation is low (with parsimony informative characters: 2/660) resulting an unresolved Neighbor-Joining tree. However, Bali cattle and other domestic cattle appear in two monophyletic clades distinct from yak, gaur and selembu. This study expresses the potential of the COI gene in portraying the phylogenetic relationships between several Bos species which is important for conservation efforts especially in decision making since cattle is highly bred and hybrid breeds are often formed. Genetic conservation for this high quality beef cattle breed is important by maintaining its genetic characters to prevent extinction or even decreased the genetic quality.
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