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  1. Fulltext Cloning of gene encoding yeast alcohol dehydrogenase 1 (YADH 1) in Escherichia coli TOP10 for biocatalysis
    Mohd Rezuan M Aspar, Rashidah Abdul Rahim, Mohamad Hekarl Uzir
    Pertanika Journal of Science & Technology, 2011;19(2):423-430.
    MyJurnal
    Yeast producing alcohol dehydrogenase 1 (YADH 1) enzyme has been used as a biocatalyst for the synthesis of an optically active flavouring compound known as citronellol. However, the slow growth of yeast (Saccharomyces cerevisiae) has deterred the progress of biotransformation. The main purpose of this work is to clone the genes producing YADH1 enzyme from yeast into a faster growing bacteria, Escherichia coli. Initially, the sequence of the gene encoding this protein has been identified in the S. cerevisiae Genome Databases (SGD). The so-called Yadh1 gene sequence is located from coordinate 159548 to 160594 on chromosome XV of yeast. Based on this information, two primer sequences (Forward and Reverse) were constructed. Each of these primers will bind to either end of the Yadh1 gene. The Yadh1 gene was then amplified using Polymerase Chain Reaction (PCR) technique. The amplified Yadh 1 gene was successfully cloned into a cloning vector, TOPO TA plasmid. This plasmid also contains a gene which confers resistance to ampicillin. This recombinant
    plasmid was then inserted into Escherichia coli TOP 10 using heat shock protocol at 42oC. Finally, the cloned bacteria containing the recombinant TOPO TA plasmid harbouring Yadh1 gene was able to grow on Luria Bertani (LB) media supplied with antibiotic.
    Matched MeSH terms: DNA Primers
  2. Fulltext Thalassaemia screening among healthy blood donors in Hospital Tengku Ampuan Rahimah, Klang
    Irmi Elfina, R., Ezalia, E., Elizabeth, G., Wan Hayati, M.Y, Norhanim, A., Wahidah, A., et al.
    Medicine & Health, 2014;9(1):44-52.
    MyJurnal
    Thalassaemia screening programme has been conducted in Malaysia since 2004. The aim of the programme was to reduce the burden of the disease by identifying thalassaemia carriers. However, the response towards the screening activities was unsatisfactory as there was lack of public awareness against the importance of thalassaemia screening. An alternative approach is to screen blood donors. The purpose of this study was to observe the prevalence of thalassaemia carriers among healthy blood donors. Seven hundred and thirty eight healthy blood donors were screened in Hospital Tengku Ampuan Rahimah, Klang from July to September 2010 using cation-exchange high performance liquid chromatography (HPLC). Cases with haemoglobin variants were further analyzed by gel electrophoresis at alkaline pH. Result shows that the blood donors consisted of 413 Malays (56%), 162 Indians (22%), 148 Chinese (20%) and 15 others (2%). There were 19 (2.6%) individuals with haemoglobin E trait, six (0.8%) with co-inheritance of haemoglobin E and αα- thalassaemia and five (0.7%) with β-thalassaemia trait. Haemoglobin Constant Spring and haemoglobin A2 prime were observed in two (0.3%); and Haemoglobin Lepore and alpha chain variant in one (0.2%). αα-thalassaemia and normal haemoglobin A2 β-thalassaemia could not be excluded in 190 cases (26%), as they required deoxyribonucleic acid (DNA) studies for identification. Thalassaemia screening in blood donors is more feasible and effective. Therefore, a wider scale population screening including blood donors could benefit the existing thalassaemia screening programme in Malaysia.
    Matched MeSH terms: DNA
  3. Fulltext A Demonstration Of The Polymerase Chain Reaction Technique In Class Teaching
    Yusof, R., Abdul Rahman, P.S., Rahim, Z.H.A.
    Ann Dent, 1999;6(1):-.
    MyJurnal
    The application of PCR technique in genetic screening was demonstrated using the genetic materials from buccal cells of the students in the class. Two factors were taken into consideration when designing the experiments. The DNA region to be amplified should not be associated with any disease state. This is to eliminate any emotional and ethical problems associated with the experiments. In this practical, the presence and absence of a 38 bp sequence in the intron of COLIA2 gene were studied. The students were also shown on how to analyse the presence of homozygous and heterozygous alleles and the genetic variations that might be observed in the different ethnic groups of students. Another factor was the time taken to complete the experiment. Our experience showed that this experiment would take at least six hours to obtain and analyse the results. It is therefore suitable to be used in class teaching.
    Matched MeSH terms: DNA
  4. Fulltext Beta thalassaemia mutations in Malays: a simplified cost-effective strategy to identify the mutations
    George, E., Teh, L.K., Rosli, R., Lai, M.I., Tan, J.A.M.A.
    Malaysian Journal of Medicine and Health Sciences, 2012;8(1):45-53.
    MyJurnal
    Beta (β)- thalassaemia is a public health problem in Malaysia. The carrier rate is estimated to be 4.5% by micro-mapping studies particularly among Malays who comprise 53.5% of the population in Malaysia. The common diagnostic method in Malaysia for mutation detection is by amplification refractory mutation system (ARMS). It allows single mutation detection in each reaction but is labour intensive and time consuming when many mutations need to be identified. The purpose of this study was to develop a diagnostic tool for effective mutation detection of beta thalassaemia in Malay patients and compare its efficacy with ARMS-PCR, the current method in use. Methods: Reverse dot blot hybridization (RDBH) technique was incorporated in the development of two strip assays [RDBH-Strip M(6) and RDBH-Strip C(6)] to identify common beta thalassaemia mutations in the Malays. The panels of selected mutations were based on the mutation frequencies in Malaysia reported in previous studies. RDBH-Strip M(6) was applied as step 1 and RDBH-Strip C(6) was applied as step 2 for unidentified mutations. The strips were validated with the gold standard method, ARMS- PCR. Results: One hundred and thirty seven Malay patients with 274 alleles were studied. In Step 1 mutation detection, 238 alleles (86.9%) were identified in 119 of patients by RDBH-Strip M(6). Step 2 resulted in a further detection of 20 alleles in another 10 patients by RDBH-Strip C(6). The combination of both strips resulted in the identification of 258 alleles in 129 (94.6%) of 137 Malay patients. The strip assays were 100% sensitive and specific when compared with ARMS-PCR method. Conclusion: Two strip assays utilising the RDBH technique were developed to identify common β-thalassaemia mutations in Malays. The RDBH Strip M(6) identified 86.9% of the mutations and the RDBH-Strip C (6) detected further 7.3% alleles. This two step strategy was found to be rapid and cost effective for the direct diagnosis of β-thalassaemia mutations in the Malays. The remaining unidentified mutations would require DNA sequencing. It can serve as a specific molecular diagnostic tool for effective diagnosis of
    β-thalassaemia mutations in this ethnic group.
    Matched MeSH terms: Sequence Analysis, DNA
  5. Fulltext Detection of human herpesvirus 6 (HHV-6) in saliva of healthy adults in Malaysia
    Choo, H.L., Shoji, Y., Leong, C.O.
    Malaysian Journal of Medicine and Health Sciences, 2012;8(2):55-64.
    MyJurnal
    Human herpesvirus-6 (HHV-6) levels have been considered as markers for various diseases. The aim of this study was to evaluate the prevalence of HHV-6 infection in healthy adults in Malaysia. Methods: The level of HHV-6 in saliva was investigated in 36 healthy adults, age 19 to 23 years, at Kuala Lumpur, Malaysia using variant-specific TaqmanTM quantitative real-time PCR (qPCR). Results: The amount of HHV-6 DNA in the saliva of healthy adults ranged from negative to 10,000 HHV-6 genomes/ml of saliva (median, 360 genomes/ml of saliva). Of the 36 samples tested, 30 (83%) contained HHV-6 DNA. HHV-6B was the only variant detected in the saliva of all the positive cases. Conclusions: The detection of HHV-6 DNA in saliva by real-time PCR assay provides a sensitive and specific quantitation of HHV-6. Our pilot study suggests the wide prevalence of HHV-6 in saliva from
    healthy adults.
    Matched MeSH terms: DNA, Viral
  6. Fulltext Iatrogenic (‘clinician-induced’) damage incurred by human sperm during infertility treatment: postgraduate research and collaborative developments between the universities of Malaya and Oxford
    Yelumalai, S., Jones, C., Coward, K.
    JUMMEC, 2013;16(2):1-6.
    MyJurnal
    Assisted Reproductive Technology (ART) is a suite of laboratory techniques designed to rescue infertile phenotypes. While ART has led to the birth of 5 million ART babies worldwide, success rates rarely exceed 40%. One potential factor for this could be iatrogenic (‘clinician-induced’) damage to critical sperm proteins, such as phospholipase C zeta (PLCζ) and protamine, which are fundamental for oocyte activation and sperm DNA integrity, respectively. This report describes how we have begun to investigate the adverse effects of ART techniques upon these key sperm proteins. We also describe the pathway taken by Miss Suseela Yelumalai to acquire a scholarship from the Malaysian Government and her postgraduate experience at the University of Oxford. We introduce the facilities and learning opportunities available at the Institute of Reproductive Sciences (IRS) which houses Dr Kevin Coward’s research laboratory, and finally, highlight the potential for collaborative development between the Universities of Oxford and Malaya.
    Matched MeSH terms: DNA
  7. Fulltext Epigenetics, mental health and transgenerational epigenetic effects
    Lake, H., Pridmore, S.
    Malaysian Journal of Psychiatry, 2014;23(1):89-100.
    MyJurnal
    Objective: to review the field of epigenetics, and present basic and recent material that may be of interest to clinical psychiatrists. We include basic molecular mechanism, a consideration of findings related to mental disorders, evidence of sustained effects, and the evidence for and implications of transgenerational epigenetic modifications. Method: we examined all the available papers for the last five years identified by PubMed using the words ‘epigenetics’ and ‘epigenetics psychiatry’, and the available leading specialized textbooks. Results: we report on molecular mechanisms including DNA and histone modifications, and non-coding RNAs. While some modifications are short-lived, others are life-long. Depression, suicide, schizophrenia, PTSD, borderline personality disorder and drug addiction are among the conditions for which epigenetic involvement has been proposed. Transgenerational epigenetics enables the environmental experience of one generation to be non-genetically inherited by subsequent generations. This has been molecularly demonstrated in laboratory animals and epidemically suggested in humans. Conclusions: epigenetics provides a new way of understanding human behavior and points to potential therapies for mental disorders. Should it transpire that transgenerational epigenetic modifications apply with force in humans as they do to laboratory animals, this will emphasize the need for cultural shift, safe societies with ample opportunities.
    Matched MeSH terms: DNA
  8. Fulltext Pyrosequencing-based quantitative evaluation of P16 methylation in diffuse large b-cell lymphoma
    Mohd. Ridah L.J., Ismail A., A. Talib N., Muhammad N., Hussain F.A., Zainuddin N.
    Journal of Biomedical and Clinical Sciences, 2016;1(1):12-17.
    MyJurnal
    Introduction: Methylation of promoter region of p16 leading to gene silencing has been implicated ina wide range of malignancies including lymphomas. In diffuse large B cell lymphoma (DLBCL) particularly, a varying percentage of epigenetic inactivation of p16 promoter region was observed ranging from 16 -54%. However, quantitative analysis of p16 promoter methylation in DLBCL has not been extensively studied in Malaysia. Objective: This study aims to quantitatively analyse p16 methylation in DLBCL samples using pyrosequencing technique. Methods: Genomic DNA was extracted from 16 formalin-fixed paraffin-embedded lymphoma tissue blocks from patients diagnosed with DLBCL. Samples were retrieved from Hospital Tengku Ampuan Afzan, Pahang and Hospital Universiti Sains Malaysia, Kelantan. Primers were designed to amplify bisulfite-treated DNA targeting p16 promoter region. Methylation status of 7 CpG sites was determined by pyrosequencing. Results: All the 16 samples studied showed promoter methylation of p16. The range of mean methylation percentage was between 18 to 81%. Conclusion: The present study has successfully measured the level of methylation of p16 in all 7 CpG sites despite the limitation in sample size. Since p16 methylation is a common event in our series of DLBCL cases, it is worth including a larger sample size in future studies to increase the chance of finding a significant correlation with clinical parameters.
    Matched MeSH terms: DNA
  9. Metal-Polydopamine Framework as an Effective Fluorescent Quencher for Highly Sensitive Detection of Hg(II) and Ag(I) Ions through Exonuclease III Activity
    Ravikumar A, Panneerselvam P, Morad N
    ACS Appl Mater Interfaces, 2018 Jun 20;10(24):20550-20558.
    PMID: 29792319 DOI: 10.1021/acsami.8b05041
    In this paper, we propose a metal-polydopamine (MPDA) framework with a specific molecular probe which appears to be the most promising approach to a strong fluorescence quencher. The MPDA framework quenching ability toward various organic fluorophore such as aminoethylcoumarin acetate, 6-carboxyfluorescein (FAM), carboxyteramethylrhodamine, and Cy5 are used to establish a fluorescent biosensor that can selectively recognize Hg2+ and Ag+ ions. The fluorescent quenching efficiency was sufficient to achieve more than 96%. The MPDA framework also exhibits different affinities with ssDNA and dsDNA. In addition, the FAM-labeled ssDNA was adsorbed onto the MPDA framework, based on their interaction with the complex formed between MPDA frameworks/ssDNA taken as a sensing platform. By taking advantage of this sensor, highly sensitive and selective determination of Hg2+ and Ag+ ions is achieved through exonuclease III signal amplification activity. The detection limits of Hg2+ and Ag+ achieved to be 1.3 and 34 pM, respectively, were compared to co-existing metal ions and graphene oxide-based sensors. Furthermore, the potential applications of this study establish the highly sensitive fluorescence detection targets in environmental and biological fields.
    Matched MeSH terms: DNA, Single-Stranded
  10. Characterization of Simulium (Simulium) hackeri Edwards (Diptera: Simuliidae) from Malaysia: Morphological description of the pupa and larva, and DNA barcoding
    Ya'cob Z, Takaoka H, Low VL, Sofian-Azirun M
    Acta Trop, 2018 Sep;185:110-114.
    PMID: 29709632 DOI: 10.1016/j.actatropica.2018.04.029
    Simulium (Simulium) hackeri Edwards, 1928 of the Simulium variegatum species-group from Malaysia was described initially based on the female specimen from Cameron Highlands, Pahang. In the present study, the pupa and larva of this species are described for the first time. Their morphological characters resemble those of the Simulium variegatum species-group by having six gill filaments per side, abdomen with dorsal spine-combs at least on segments 7 and 8, cocoon with wall-pocket shaped and with or without an anterodorsal projection. Postgenal cleft of the larva medium-sized, rarely small, ventral papillae small or absent. The DNA barcode of this species is also reported herein.
    Matched MeSH terms: DNA Barcoding, Taxonomic
  11. Fulltext Developing new primers for molecular identification of plasmodium spp. recorded in Sabah
    Chua, T.H., Stanis, C.S., Song, B.K., Lau, Y.L., Jelip, P., Lau, T.Y.
    Borneo Journal of Medical Sciences, 2015;9(1):3-10.
    MyJurnal
    Malaria is a major public health problem in tropical and subtropical areas, caused by five
    species of Plasmodium (P. falciparum, P. vivax, P. malariae, P. ovale andP. knowlesi) and is the leading cause of morbidity and mortality worldwide. We have developed molecular markers for three genes viz, Cytb, dhfr and Msp-1 gene and designed a protocol for rapid molecular diagnostics of the four malaria parasites prevalent in Southeast Asia. The new primers were used on the blood
    samples containing Plasmodium parasites by conventional PCR. The result was compared with
    the nested PCR of Singh et al. (2004) and the microscopy method. The result shows that the new
    set of primers had successfully amplified all four human malaria parasite species. These primers
    were 100% sensitive and more specific than microscopy and PCR identification using these
    primers was faster than the nested PCR. These alternative primers should provide powerful and
    rapid molecular diagnostic method for detecting Plasmodium species as well as providing reliable
    data for epidemiology study. These primers have the potential to be combined and used in
    multiplex PCR.
    Matched MeSH terms: DNA Primers
  12. Fulltext Evaluation of heterozygous Hb E and its interaction with deletional alpha thalassaemia in Kelantan
    Nur Hidayah Muhamad Yasin, Majdan Ramli, Ilunihayati Ibrahim, Rosnah Bahar, Noraesah Mahmud, Siti Shahrum Muhamed Said, et al.
    Journal of Biomedical and Clinical Sciences, 2017;2(202):35-37.
    MyJurnal
    Haemoglobin E (Hb E) is a variant of structurally abnormal haemoglobin that can be found very commonly in the Asian countries particularly the Southeast Asian [1]. [H1] Alpha thalassaemia is a red cell disorder which is caused by deletion or mutation of one or more of the four alpha globin genes leading to absence or decrease in production of alpha globin peptides [2]. This disorder is far more common in South East Asian regions and in Malaysia itself, and the gene frequency is about 4.1% [2]. The interactions of Hb E and alpha thalassaemia are evident in Kelantan which is bordered by southern Thailand. Using capillary electrophoresis (CE), a reduction of Hb E level is noticed as compared to Hb E heterozygotes. DNA analysis should be done to determine the presence of concurrent alpha thalassaemia variant. This study was done to evaluate haematological parameters using automated blood counters, morphology of red cells, Hb separation and quantitation of Hb fractions using CE and molecular analysis for alpha thalassemia. The study also aimed to discover cut off point of Hb E level in heterozygous Hb E patients with concurrent deletional alpha thalassaemia by CE.
    Matched MeSH terms: DNA
  13. Enhanced phagocytosis of Aggregatibacter actinomycetemcomitans cells by macrophages activated by a probiotic Lactobacillus strain
    Jaffar N, Okinaga T, Nishihara T, Maeda T
    J Dairy Sci, 2018 Jul;101(7):5789-5798.
    PMID: 29680655 DOI: 10.3168/jds.2017-14355
    The activation of phagocytosis is one important approach to clearing pathogenic cells in a host. This study evaluated the ability of probiotic lactobacilli to induce phagocytic activity as well as the clearance of a periodontal pathogen, Aggregatibacter actinomycetemcomitans. First, the activation of phagocytosis was found by using lyophilized dead cells. Probiotic Lactobacillus strains significantly enhanced the phagocytic activity of macrophage cells, indicating that the probiotic lactobacilli have a remarkable ability to stimulate the macrophages. Essentially, 3 Lactobacillus strains tested did not have any critical toxic effect on the murine macrophage, and Lactobacillus johnsonii NBRC 13952 showed the least cytotoxic effect on the RAW264.7 macrophages. The expression of classically activated macrophage markers, IL-1β, and cluster of differentiation 80 increased by L. johnsonii NBRC 13952; however, there was no significant difference for IL-18. The highest phagocytic activity by macrophages was found in a condition in which the macrophage activated by L. johnsonii NBRC 13952 functions to kill the cells of A. actinomycetemcomitans. Correlating with the result, a high amount of hypodiploid DNA (SubG1) was detected from the macrophage cells stimulated by L. johnsonii NBRC 13952. Taken together, the results suggest that macrophages activated by the Lactobacillus strain can facilitate the phagocytosis of A. actinomycetemcomitans cells by linking with enhanced apoptotic activities. In conclusion, L. johnsonii NBRC 13952 has a certain role in activating the RAW264.7 macrophages, thereby counteracting the infection of A. actinomycetemcomitans.
    Matched MeSH terms: DNA
  14. The use of transgenic parasites in malaria vaccine research
    Othman AS, Marin-Mogollon C, Salman AM, Franke-Fayard BM, Janse CJ, Khan SM
    Expert Rev Vaccines, 2017 Jul;16(7):1-13.
    PMID: 28525963 DOI: 10.1080/14760584.2017.1333426
    INTRODUCTION: Transgenic malaria parasites expressing foreign genes, for example fluorescent and luminescent proteins, are used extensively to interrogate parasite biology and host-parasite interactions associated with malaria pathology. Increasingly transgenic parasites are also exploited to advance malaria vaccine development. Areas covered: We review how transgenic malaria parasites are used, in vitro and in vivo, to determine protective efficacy of different antigens and vaccination strategies and to determine immunological correlates of protection. We describe how chimeric rodent parasites expressing P. falciparum or P. vivax antigens are being used to directly evaluate and rank order human malaria vaccines before their advancement to clinical testing. In addition, we describe how transgenic human and rodent parasites are used to develop and evaluate live (genetically) attenuated vaccines. Expert commentary: Transgenic rodent and human malaria parasites are being used to both identify vaccine candidate antigens and to evaluate both sub-unit and whole organism vaccines before they are advanced into clinical testing. Transgenic parasites combined with in vivo pre-clinical testing models (e.g. mice) are used to evaluate vaccine safety, potency and the durability of protection as well as to uncover critical protective immune responses and to refine vaccination strategies.
    Matched MeSH terms: Vaccines, DNA/genetics; Vaccines, DNA/immunology; Vaccines, DNA/therapeutic use
  15. Analysis of the genetic structure of the Malay population: Ancestry-informative marker SNPs in the Malay of Peninsular Malaysia
    Yahya P, Sulong S, Harun A, Wan Isa H, Ab Rajab NS, Wangkumhang P, et al.
    Forensic Sci Int Genet, 2017 09;30:152-159.
    PMID: 28743033 DOI: 10.1016/j.fsigen.2017.07.005
    Malay, the main ethnic group in Peninsular Malaysia, is represented by various sub-ethnic groups such as Melayu Banjar, Melayu Bugis, Melayu Champa, Melayu Java, Melayu Kedah Melayu Kelantan, Melayu Minang and Melayu Patani. Using data retrieved from the MyHVP (Malaysian Human Variome Project) database, a total of 135 individuals from these sub-ethnic groups were profiled using the Affymetrix GeneChip Mapping Xba 50-K single nucleotide polymorphism (SNP) array to identify SNPs that were ancestry-informative markers (AIMs) for Malays of Peninsular Malaysia. Prior to selecting the AIMs, the genetic structure of Malays was explored with reference to 11 other populations obtained from the Pan-Asian SNP Consortium database using principal component analysis (PCA) and ADMIXTURE. Iterative pruning principal component analysis (ipPCA) was further used to identify sub-groups of Malays. Subsequently, we constructed an AIMs panel for Malays using the informativeness for assignment (In) of genetic markers, and the K-nearest neighbor classifier (KNN) was used to teach the classification models. A model of 250 SNPs ranked by In, correctly classified Malay individuals with an accuracy of up to 90%. The identified panel of SNPs could be utilized as a panel of AIMs to ascertain the specific ancestry of Malays, which may be useful in disease association studies, biomedical research or forensic investigation purposes.
    Matched MeSH terms: DNA Fingerprinting
  16. Fulltext Effects of Physiochemical Factors on Prokaryotic Biodiversity in Malaysian Circumneutral Hot Springs
    Chan CS, Chan KG, Ee R, Hong KW, Urbieta MS, Donati ER, et al.
    Front Microbiol, 2017;8:1252.
    PMID: 28729863 DOI: 10.3389/fmicb.2017.01252
    Malaysia has a great number of hot springs, especially along the flank of the Banjaran Titiwangsa mountain range. Biological studies of the Malaysian hot springs are rare because of the lack of comprehensive information on their microbial communities. In this study, we report a cultivation-independent census to describe microbial communities in six hot springs. The Ulu Slim (US), Sungai Klah (SK), Dusun Tua (DT), Sungai Serai (SS), Semenyih (SE), and Ayer Hangat (AH) hot springs exhibit circumneutral pH with temperatures ranging from 43°C to 90°C. Genomic DNA was extracted from environmental samples and the V3-V4 hypervariable regions of 16S rRNA genes were amplified, sequenced, and analyzed. High-throughput sequencing analysis showed that microbial richness was high in all samples as indicated by the detection of 6,334-26,244 operational taxonomy units. In total, 59, 61, 72, 73, 65, and 52 bacterial phyla were identified in the US, SK, DT, SS, SE, and AH hot springs, respectively. Generally, Firmicutes and Proteobacteria dominated the bacterial communities in all hot springs. Archaeal communities mainly consisted of Crenarchaeota, Euryarchaeota, and Parvarchaeota. In beta diversity analysis, the hot spring microbial memberships were clustered primarily on the basis of temperature and salinity. Canonical correlation analysis to assess the relationship between the microbial communities and physicochemical variables revealed that diversity patterns were best explained by a combination of physicochemical variables, rather than by individual abiotic variables such as temperature and salinity.
    Matched MeSH terms: DNA
  17. Fulltext Integrative taxonomy of a new and highly-diverse genus of onchidiid slugs from the Coral Triangle (Gastropoda, Pulmonata, Onchidiidae)
    Goulding TC, Khalil M, Tan SH, Dayrat B
    Zookeys, 2018.
    PMID: 29896045 DOI: 10.3897/zookeys.763.21252
    A new genus of onchidiid slugs, Wallaconchis Goulding & Dayrat, gen. n., is described, including ten species. Five species were previously described but known only from the type material: Wallaconchis ater (Lesson, 1830), W. graniferum (Semper, 1880), W. nangkauriense (Plate, 1893), W. buetschlii (Stantschinsky, 1907), and W. gracile (Stantschinsky, 1907), all of which were originally classified in Onchidium Buchannan, 1800. Many new records are provided for these five species, which greatly expand their known geographic distributions. Five species are new: Wallaconchis achleitneri Goulding, sp. n., W. comendadori Goulding & Dayrat, sp. n., W. melanesiensis Goulding & Dayrat, sp. n., W. sinanui Goulding & Dayrat, sp. n., and W. uncinus Goulding & Dayrat, sp. n. Nine of the ten Wallaconchis species are found in the Coral Triangle (eastern Indonesia and the Philippines). Sympatry is high, with up to six species found on the island of Bohol (Philippines) and eight species overlapping in northern Sulawesi (Indonesia). Wallaconchis is distinguished from other onchidiids by its bright dorsal colors (red, yellow, orange) but those are extremely variable and not useful for specific identification. Internally, the reproductive system can be used to identify all Wallaconchis species. The copulatory organs of Wallaconchis species are especially diverse compared to other onchidiid genera, and the possible role of reproductive incompatibility in species diversification is discussed. All specimens examined were freshly collected for the purpose of a worldwide revision of the Onchidiidae Rafinesque, 1815. The species are well delineated using DNA sequences and comparative anatomy. Mitochondrial DNA analysis yields thirteen molecular units separated by a large barcode gap, while nuclear DNA yields nine units. By integrating nuclear DNA and mitochondrial DNA with morphology, ten species are recognized. The natural history of each species (e.g., the microhabitat where they are found) is also documented. Nomenclature is addressed thoroughly (the types of all onchidiid species were examined, lectotypes were designated when needed, nomina dubia are discussed). Morphological characters, transitions to new microhabitats, and diversification processes are discussed in the context of a robust molecular phylogeny.
    Matched MeSH terms: DNA, Mitochondrial
  18. Fulltext Avian polyomavirus: a recent update
    Padzil, F., Mariatulqabtiah, A. R., Abu, J.
    Jurnal Veterinar Malaysia, 2017;29(2):9-13.
    MyJurnal
    Avian polyomavirus disease is among the most common viral diseases of domesticated exotic birds as such in psittacine families. Caused by avian polyomavirus (APV) which possess a circular, double-stranded DNA which encodes for major structural virus protein 1 (VP1) and minor structural proteins VP2, VP3 and VP4, the disease is also known as Budgerigar fledgling disease polyomavirus (BFPyV), Papovavirus, and Psittacine polyomavirus. Infections from APV may lead to cutaneous haemorrhage, abdominal distension, feather abnormalities and even death. The APV virus has a broad avian host range and is known to cause acute chronic disease in several psittacine birds such as parrot, cockatoo, macaw, and budgerigar. The current status of APV epidemiology globally has not been fully recorded. Only the studies of the virus and disease caused within several countries are used as references, and few were done together with detection of beak and feather disease virus. Despite the common occurrence of APV among bird breeders in Malaysia, a very limited study has been done to evaluate the prevalence status of APV in Malaysia. In this review, we wish to disseminate knowledge, particularly to pet owners and bird breeders, on APV characterisations, its updated occurrence worldwide and prevention strategies. This information may be useful to trigger in depth study on the epidemiology of disease and better management practises among breeders.
    Matched MeSH terms: DNA
  19. Fulltext Acute ophthalmic artery occlusion in decompression illness with underlying anterior cerebral artery A1 segment hypoplasia
    Omar AR, Ibrahim M, Hussein A
    Diving Hyperb Med, 2018 Jun 30;48(2):112-113.
    PMID: 29888385 DOI: 10.28920/dhm48.2.112-113
    A diver presented with total loss of vision in the left eye and right hemiparesis following a routine no-stop scuba dive to 20 metres' depth. A diagnosis of decompression illness (DCI) with acute ophthalmic artery air embolism and left carotid artery insult causing acute anterior circulatory ischaemia was made. He underwent seven hyperbaric treatments leading to a full recovery. Magnetic resonance angiography revealed an underlying left anterior cerebral artery A1 segment hypoplasia. Making a prompt diagnosis and early hyperbaric oxygen treatment are crucial to halt further tissue damage from ischaemia in central nervous system DCI. In this case, the finding of a left A1 anterior cerebral artery segment hypoplasia variant may have increased the severity of DCI due to deficient collateral circulation.
    Matched MeSH terms: Random Amplified Polymorphic DNA Technique
  20. Fulltext Diversity and natural selection on the thrombospondin-related adhesive protein (TRAP) gene of Plasmodium knowlesi in Malaysia
    Ahmed MA, Lau YL, Quan FS
    Malar J, 2018 Jul 27;17(1):274.
    PMID: 30053885 DOI: 10.1186/s12936-018-2423-1
    BACKGROUND: Plasmodium knowlesi a parasite of the macaques is currently the most common cause of human malaria in Malaysia. The thrombospondin-related adhesive protein (TRAP) gene is pre-erythrocytic stage antigen. It is a well-characterized vaccine candidate in Plasmodium vivax and Plasmodium falciparum, however, no study has been done in the orthologous gene of P. knowlesi. This study investigates nucleotide diversity, haplotypes, natural selection and population differentiation of full-length pktrap genes in clinical samples from Malaysia.

    METHODS: Forty full-length pktrap sequences from clinical isolates of Malaysia along with the reference H-strain were downloaded from published databases. Genetic diversity, polymorphism, haplotype and natural selection were determined using DnaSP 5.10 software. McDonald-Kreitman test was conducted using P. vivax and Plasmodium coatneyi as ortholog sequence in DnaSP 5.10 software. Population genetic differentiation index (FST) of parasite populations was determined using Arlequin v3.5. Phylogenetic relationships between trap ortholog genes were determined using MEGA 5.0 software.

    RESULTS: Comparison of 40 full-length pktrap sequences along with the H-strain identified 74 SNPs (53 non-synonymous and 21 synonymous substitutions) resulting in 29 haplotypes. Analysis of the full-length gene showed that the nucleotide diversity was lower compared to its nearest ortholog pvtrap. Domain-wise analysis indicated that the proline/asparagine rich region had higher nucleotide diversity compared to the von Willebrand factor domain and the thrombospondin-type-1 domain. McDonald-Kreitman test identified that the ratio of the number of nonsynonymous to synonymous polymorphic sites within P. knowlesi was significantly higher than that of the number of nonsynonymous to synonymous fixed sites between P. knowlesi and P. vivax. The von Willebrand factor domain also indicated balancing selection using MK test, however, it did not give significant results when tested with P. coatneyi as an outgroup. Phylogenetic analysis of full-length genes identified three distinct sub-clusters of P. knowlesi, one originating from Peninsular Malaysia and two originating from Malaysian Borneo. High population differentiation values was observed within samples from Peninsular Malaysia and Malaysian Borneo.

    CONCLUSIONS: This study is the first to report on the genetic diversity and natural selection of full-length pktrap. Low level of genetic diversity was found across the full-length gene of pktrap. Balancing selection of the von Willebrand factor domain indicated that TRAP could be a target in inducing immune response against P. knowlesi infections. However, higher number of samples would be necessary to further confirm the findings.

    Matched MeSH terms: Sequence Analysis, DNA
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