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Oligonucleotide fingerprint analysis of strains of Getah virus isolated in Japan and Malaysia

Morita K, Igarashi A

J Gen Virol, 1984 Nov;65 ( Pt 11):1899-908.
PMID: 6094708

Eighteen strains of Getah virus isolated from mosquitoes, swine and horses in Japan (1956 to 1981), and one strain isolated in Malaysia (1955), were analysed by RNase T1-resistant oligonucleotide fingerprinting. All fingerprints showed a poly(A) tract. The fingerprint pattern of the Malaysian strain was quite different from those of the Japanese strains. Although most of the recent Japanese isolates shared many large oligonucleotide spots in common, the patterns were not identical even among the strains obtained in one locality in the same year. These results suggest that the Getah virus genome undergoes mutation rather frequently. However, there is a tendency for the isolates of the same year to show greater similarity. The fingerprint patterns of certain host-dependent temperature-sensitive (ts) mutants differed from that of the parental strain. Also, there were some differences in large oligonucleotide spots between strain JaNAr12380M isolated in suckling mouse brain (SMB) and strain JaNAr12380A isolated in C6/36 cells, despite the fact that both strains were derived from the same wild mosquito homogenate. In addition, many host-dependent ts mutants were present in strain JaNAr12380A, whereas no such mutants were observed in strain JaNAr12380M. It is concluded that there is considerable variation in the strains of Getah virus infecting mosquitoes in the wild, and also that the variants or mutants present in mosquitoes might be subject to selection during viral multiplication in the mammalian host.

Matched MeSH terms: Alphavirus/genetics*; RNA, Viral/genetics*
Nucleotide sequences of the nonstructural protein NS1 gene of three dengue-2 viruses, M1, M2 and M3, isolated in Malaysia from patients with dengue haemorrhagic fever, dengue shock syndrome and dengue fever, respectively

Fong MY, Koh CL, Samuel S, Pang T, Lam SK

Nucleic Acids Res, 1990 Mar 25;18(6):1642.
PMID: 2139210
Matched MeSH terms: Dengue Virus/genetics*; Viral Core Proteins/genetics*
Biochemical characteristics of glucose-6-phosphate dehydrogenase variants among the Malays of Singapore with report of a new non-deficient (GdSingapore) and three deficient variants

Saha N, Hong SH, Wong HA, Jeyaseelan K, Tay JS

Jinrui Idengaku Zasshi, 1991 Dec;36(4):307-12.
PMID: 1811096 DOI: 10.1007/BF01883603

Biochemical characteristics of one non-deficient fast G6PD variant (GdSingapore) and six different deficient variants (three new, two Mahidol, one each of Indonesian and Mediterranean) were studied among the Malays of Singapore. The GdSingapore variant had normal enzyme activity (82%) and fast electrophoretic mobilities (140% in TEB buffer, 160% in phosphate and 140% in Tris-HCl buffer systems respectively). This variant is further characterized by normal Km for G6P; utilization of analogues (Gal6P, 2dG6P; dAmNADP), heat stability and pH optimum. The other six deficient G6PD variants had normal electrophoretic mobility in TEB buffer with enzyme activities ranging from 1 to 12% of GdB+. The biochemical characteristics identity them to be 2 Mahidol, 1 Indonesian and 1 Mediterranean variants and three new deficient variants.

Matched MeSH terms: Glucosephosphate Dehydrogenase/genetics*; Glucosephosphate Dehydrogenase Deficiency/genetics*
Genetic polymorphism of the vitamin D-binding protein (DBP) in crab-eating macaques (Macaca fascicularis)

Tanaka H, Kawamoto Y, Terao K

J Med Primatol, 1991 May;20(3):126-32.
PMID: 1895332

Vitamin D-binding protein (DBP) of crab-eating macaques (Macaca fascicularis) was examined by means of three electrophoretic methods. DBP phenotypes were observed to be one or two bands in each method. All of DBP molecular variants could be detected by the simultaneous typing with these three methods. Family analysis suggested that DBP variants followed the mode of autosomal codominant inheritance. A total of 17 phenotypes governed by at least 11 alleles were observed in the populations of Malaysia, Indonesia, and the Philippines. The genetic variability was high in Malaysian and Indonesian populations but low in the Philippine population.

Matched MeSH terms: Macaca fascicularis/genetics*; Vitamin D-Binding Protein/genetics*
Population genetic analysis of host seeking and resting behaviors in the malaria vector, Anopheles balabacensis (Diptera: Culicidae)

Hii JL, Chew M, Sang VY, Munstermann LE, Tan SG, Panyim S, et al.

J Med Entomol, 1991 Sep;28(5):675-84.
PMID: 1682492

During the intermonsoon period from mid-September to mid-October 1986, wild-caught Anopheles balabacensis Baisas females were marked and released in a host-choice experiment. Association between capture and recapture of marked mosquitoes from human and bovid hosts and blood meal host identification of recaptured females were determined on a daily basis. Although the mark-recapture and blood meal data indicated behavioral heterogeneity between buffalo and human biters, restriction endonuclease fragment length polymorphism analysis revealed no differences in repeat sequence profiles. Doubly-marked recaptures strongly indicated a "learning" component involved in a separate host preference experiment. In a "habitat loyalty" experiment conducted in January 1987, females of An. balabacensis preferentially returned to the resting sites (indoor surfaces and exit traps) where they were first caught. Of nine isozyme loci found to be polymorphic, the genotypic frequencies of Esterase-3 and Isocitrate dehydrogenase-3 were different in "faithfully" endophilic and exophilic subpopulations. Genetic heterozygosity, as determined by polyacrylamide gel electrophoresis, was greater in exophilic than endophilic population components. These results confirm that genetic and learning components can significantly influence house resting and host seeking behavior and may contribute to local epidemiological patterns of malaria transmission observed in Sabah, Malaysia.

Matched MeSH terms: Anopheles/genetics*; Insect Vectors/genetics*
Genetic variation of Japanese encephalitis virus in nature

Chen WR, Tesh RB, Rico-Hesse R

J Gen Virol, 1990 Dec;71 ( Pt 12):2915-22.
PMID: 2273391

Forty-six strains of Japanese encephalitis (JE) virus from a variety of geographic areas in Asia were examined by primer-extension sequencing of the RNA template. A 240 nucleotide sequence from the pre-M gene region was selected for study because it provided sufficient information for determining genetic relationships among the virus isolates. Using 12% divergence as a cutoff point for virus relationships, the 46 isolates fell into three distinct genotypic groups. One genotypic group consisted of JE virus isolates from northern Thailand and Cambodia. A second group was composed of isolates from southern Thailand, Malaysia, Sarawak and Indonesia. The remainder of the isolates, from Japan, China, Taiwan, the Philippines, Sri Lanka, India and Nepal, made up a third group. The implications of these findings in relation to the epidemiology of JE are discussed. Results of this study demonstrate that the comparison of short nucleotide sequences can provide insight into JE virus evolution, transmission and, possibly, pathogenesis.

Matched MeSH terms: Encephalitis Virus, Japanese/genetics*; RNA, Viral/genetics*
Fulltext Nucleotide and encoded amino acid sequences of the capsid protein gene of three dengue-2 viruses isolated in Malaysia from patients with dengue haemorrhagic fever, dengue shock syndrome or dengue fever

Samuel S, Koh CL, Pang T, Lam SK

Nucleic Acids Res, 1990 Apr 11;18(7):1904.
PMID: 2336373
Matched MeSH terms: Dengue Virus/genetics*; Viral Structural Proteins/genetics*
Kin-structured migration: causes and consequences

Fix AG

Am J Hum Biol, 2004 Jul-Aug;16(4):387-94.
PMID: 15214057

Migration among local populations classically has been seen as the principal process retarding genetic microdifferentiation. However, as Sewall Wright pointed out long ago, migration may also act as a random differentiating force. In fact, when migrants comprise a biological kin group, migration may be considered a component of genetic drift. The causes of kin-structured migration (KSM) lie in the common, if not universal, tendency for kin to associate and cooperate. However, similar to genetic drift, KSM has its greatest effect in smaller populations and is most apparent in low-density fission-fusion societies such as the Yanomamo of South America and the Semai of Malaysia, and less salient in higher density, low-mobility populations such as those of the New Guinea Highlands. The evolutionary consequences of KSM begin with increased genetic variation among populations. Such intergroup variation provides a basis for group selection. The origin of larger-scale geographic differentiation can arise from kin-structured migrant groups colonizing new regions. Waves of colonizing kin-structured founder groups may produce gene frequency clines, mimicking demic diffusion and natural selection. Finally, because kin structuring reduces the effective size of a population, it may be speculated that the extremely small effective size inferred for ancestral populations of Homo sapiens may be an artifact of kin-structured demographically larger populations.

Matched MeSH terms: Hemoglobin E/genetics; Genetic Variation/genetics*
Fulltext Immunohistochemical localization of RET rearrangements in a Malaysian papillary thyroid carcinoma population

Omar E, Othman NH

Med J Malaysia, 2003 Aug;58(3):461-2.
PMID: 14750392
Matched MeSH terms: Oncogene Proteins/genetics*; Receptor Protein-Tyrosine Kinases/genetics*
Quantitative trait loci in Anopheles gambiae controlling the encapsulation response against Plasmodium cynomolgi Ceylon

Zheng L, Wang S, Romans P, Zhao H, Luna C, Benedict MQ

BMC Genet, 2003 Oct 24;4:16.
PMID: 14577840

Anopheles gambiae females are the world's most successful vectors of human malaria. However, a fraction of these mosquitoes is refractory to Plasmodium development. L3-5, a laboratory selected refractory strain, encapsulates transforming ookinetes/early oocysts of a wide variety of Plasmodium species. Previous studies on these mosquitoes showed that one major (Pen1) and two minor (Pen2, Pen3) autosomal dominant quantitative trait loci (QTLs) control the melanotic encapsulation response against P. cynomolgi B, a simian malaria originating in Malaysia.

Matched MeSH terms: Anopheles/genetics*; Insect Vectors/genetics*
Haemoglobin S in Malays and Indians: association of Hb CoSp and Hb S in a Malay family

Saidi HT, Duraisamy G

Trop Geogr Med, 1978 Mar;30(1):103-8.
PMID: 675819

Four cases of Hb S were seen between Jan. 1976 and June 1976; three of them were newly discovered while the fourth was previously diagnosed. Out of the four cases, two were Malays and the other Indians. The family members of one Malay case were investigated. Six members had Hb S and three had Hb CoSp. Association of Hb CoSp and Hb S was seen in two of the members. Clinically they were healthy.

Matched MeSH terms: Anemia, Sickle Cell/genetics*; Sickle Cell Trait/genetics*
Immunogenetic aspects of nasopharyngeal carcinoma: I. Differences in HL-A antigen profiles between patients and control groups

Simons MJ, Wee GB, Day NE, Morris PJ, Shanmugaratnam K, De-Thé GB

Int J Cancer, 1974 Jan 15;13(1):122-34.
PMID: 4131857
Matched MeSH terms: Carcinoma/genetics; Immunogenetics; Nasopharyngeal Neoplasms/genetics
Fulltext Association of MMP-9 gene polymorphisms with nephrolithiasis patients

Mehde AA, Mehdi WA, Yusof F, Raus RA, Zainal Abidin ZA, Ghazali H, et al.

J Clin Lab Anal, 2018 Jan;32(1).
PMID: 28205286 DOI: 10.1002/jcla.22173

BACKGROUND: Nephrolithiasis is one of the causes which lead to chronic kidney disease (CKD). Matrix metalloproteinases (MMPs) are endopeptidases degrading extracellular matrix which correlate with the pathogenesis of atherosclerosis. The current study was designed to analyze the association of (R279Q, C1562T) polymorphism of MMP-9 with nephrolithiasis patients.
METHODS: Genotyping of MMP-9/R279Q and of MMP-9/C1562T polymorphism were carried out by PCR-based restriction digestion method. Serum level of MMP-9, oxidative stress marker, MDA, and uric acid were measured in patients and control.
RESULTS: Allele frequencies of the MMP-9/C1562T polymorphism for C and T allele were 71.25% and 28.75% in patients, 87.08% and 12.92% in control respectively. The homozygote TT was more frequent in the nephrolithiasis patients group, while T allele frequency was significantly higher in the nephrolithiasis patients group than in the control group. The patients with CT and TT genotype showed a significant increase in serum MMP-9, Total Oxidant Status (TOS), Oxidative Stress Index (OSI), Malondialdehyde (MDA), and uric acid when compared to CC genotype in patients with nephrolithiasis. The R279Q polymorphism site with regard to the relationship with nephrolithiasis was not significant.
CONCLUSION: The result indicates that patients with TT genotype had an increased risk of stones. Also, the results demonstrate that TT allele of the C1562T polymorphism in the MMP-9gene is related with an increase of oxidative stress in nephrolithiasis patients and may possibly impose a risk for cardiovascular diseases in patients with TT genotype of MMP-9.

Matched MeSH terms: Matrix Metalloproteinase 9/genetics*; Nephrolithiasis/genetics*
Fulltext Issues in identifying germ tube positive yeasts by conventional methods

Yazdanpanah A, Khaithir TM

J Clin Lab Anal, 2014 Jan;28(1):1-9.
PMID: 24375729 DOI: 10.1002/jcla.21635

Candida speciation is vital for epidemiology and management of candidiasis. Nonmolecular conventional methods often fail to identify closely related germ tube positive yeasts from clinical specimens. The present study was conducted to identify these yeasts and to highlight issues in conventional versus molecular methods of identification. A total of 98 germ tube positive yeasts from high vaginal swabs were studied over a 12-month period. Isolates were examined with various methods including growth at 42 °C and 45 °C on Sabouraud dextrose agar (SDA), color development on CHROMagar Candida medium, chlamydospore production on corn meal agar at 25 °C, carbohydrate assimilation using ID 32C system, and polymerase chain reaction using a single pair of primers targeting the hyphal wall protein 1 (Hwp1) gene. Of all the isolates studied, 97 were molecularly confirmed as C. albicans and one isolate was identified as C. dubliniensis. No C. africana was detected in this study. The molecular method used in our study was an accurate and useful tool for discriminating C. albicans, C. dubliniensis, and C. africana. The conventional methods, however, were less accurate and riddled with many issues that will be discussed in further details.

Matched MeSH terms: Candida/genetics; DNA, Fungal/genetics
FOXRED1 silencing in mice: a possible animal model for Leigh syndrome

Salama M, El-Desouky S, Alsayed A, El-Hussiny M, Moustafa A, Taalab Y, et al.

Metab Brain Dis, 2019 02;34(1):367-372.
PMID: 30392038 DOI: 10.1007/s11011-018-0334-z

Leigh syndrome (LS) is one of the most puzzling mitochondrial disorders, which is also known as subacute necrotizing encephalopathy. It has an incidence of 1 in 77,000 live births worldwide with poor prognosis. Currently, there is a poor understanding of the underlying pathophysiological mechanisms of the disease without any available effective treatment. Hence, the inevitability for developing suitable animal and cellular models needed for the development of successful new therapeutic modalities. In this short report, we blocked FOXRED1 gene with small interfering RNA (siRNA) using C57bl/6 mice. Results showed neurobehavioral changes in the injected mice along with parallel degeneration in corpus striatum and sparing of the substantia nigra similar to what happen in Leigh syndrome cases. FOXRED1 blockage could serve as a new animal model for Leigh syndrome due to defective CI, which echoes damage to corpus striatum and affection of the central dopaminergic system in this disease. Further preclinical studies are required to validate this model.

Matched MeSH terms: Leigh Disease/genetics*; Molecular Chaperones/genetics*
Prevalence and ethnic differences of autosomal-dominant cerebellar ataxia in Singapore

Zhao Y, Tan EK, Law HY, Yoon CS, Wong MC, Ng I

Clin Genet, 2002 Dec;62(6):478-81.
PMID: 12485197

We report the prevalence and ethnic differences of autosomal-dominant cerebellar ataxia (ADCA) in Singapore. Amongst 204 patients with ataxia who underwent genetic testing for dentatorubral-pallidoluysian atrophy (DRPLA) and for spinocerebellar ataxias (SCA) 1, 2, 3, 6, 7, 8, 10 and 12, 58 (28.4%) patients from 36 families tested positive. SCA 3 was identified in 31 (53.4%) patients from 15 families, SCA 2 in 17 (29.3%) patients from 12 families and SCA 1 in four (6.9%) patients from four families. Other SCA subtypes were rare. SCA 2 was the only subtype identified amongst ethnic Malay and ethnic Indian families. The estimated prevalence of ADCA in Singaporean families was at least 1 : 27,000. Based on the history and ancestry of Singaporeans, our study supported a founder effect for specific SCA subtypes and the association of ethnicity-specific SCA subtypes. Our findings suggest that SCA 2 is relatively common amongst the Malay race and that priority testing for SCA 3 and SCA 2 for ethnic Chinese, and SCA 2 for ethnic Malay, may be cost effective and relevant for the region.

Matched MeSH terms: Cerebellar Ataxia/genetics*; Ethnic Groups/genetics*
Disruption of MAPK1 expression in the ERK signalling pathway and the RUNX1‑RUNX1T1 fusion gene attenuate the differentiation and proliferation and induces the growth arrest in t(8;21) leukaemia cells

Bashanfer SAA, Saleem M, Heidenreich O, Moses EJ, Yusoff NM

Oncol Rep, 2019 Mar;41(3):2027-2040.
PMID: 30569130 DOI: 10.3892/or.2018.6926

The t(8;21) translocation is one of the most frequent chromosome abnormalities associated with acute myeloid leukaemia (AML). This abberation deregulates numerous molecular pathways including the ERK signalling pathway among others. Therefore, the aim of the present study was to investigate the gene expression patterns following siRNA‑mediated suppression of RUNX1‑RUNX1T1 and MAPK1 in Kasumi‑1 and SKNO‑1 cells and to determine the differentially expressed genes in enriched biological pathways. BeadChip microarray and gene ontology analysis revealed that RUNX1‑RUNX1T1 and MAPK1 suppression reduced the proliferation rate of the t(8;21) cells with deregulated expression of several classical positive regulator genes that are otherwise known to enhance cell proliferation. RUNX1‑RUNX1T1 suppression exerted an anti‑apoptotic effect through the overexpression of BCL2, BIRC3 and CFLAR genes, while MAPK1 suppression induced apopotosis in t(8;21) cells by the apoptotic mitochondrial changes stimulated by the activity of upregulated TP53 and TNFSF10, and downregulated JUN gene. RUNX1‑RUNX1T1 suppression supported myeloid differentiation by the differential expression of CEBPA, CEBPE, ID2, JMJD6, IKZF1, CBFB, KIT and CDK6, while MAPK1 depletion inhibited the differentiation of t(8;21) cells by elevated expression of ADA and downregulation of JUN. RUNX1‑RUNX1T1 and MAPK1 depletion induced cell cycle arrest at the G0/G1 phase. Accumulation of cells in the G1 phase was largely the result of downregulated expression of TBRG4, CCNE2, FOXO4, CDK6, ING4, IL8, MAD2L1 and CCNG2 in the case of RUNX1‑RUNX1T1 depletion and increased expression of RASSF1, FBXO6, DADD45A and P53 in the case of MAPK1 depletion. Taken together, the current results demonstrate that MAPK1 promotes myeloid cell proliferation and differentiation simultaneously by cell cycle progression while suppresing apoptosis.

Matched MeSH terms: Cell Differentiation/genetics; Chromosomes, Human, Pair 21/genetics; Chromosomes, Human, Pair 8/genetics; Leukemia, Myeloid, Acute/genetics*; Oncogene Proteins, Fusion/genetics*; Apoptosis/genetics; Mitogen-Activated Protein Kinase 1/genetics*; MAP Kinase Signaling System/genetics*; Cell Proliferation/genetics; Core Binding Factor Alpha 2 Subunit/genetics*; G1 Phase Cell Cycle Checkpoints/genetics
Fulltext Investigation of the microbial communities colonizing prepainted steel used for roofing and walling

Huynh TT, Jamil I, Pianegonda NA, Blanksby SJ, Barker PJ, Manefield M, et al.

Microbiologyopen, 2017 04;6(2).
PMID: 27998037 DOI: 10.1002/mbo3.425

Microbial colonization of prepainted steel, commonly used in roofing applications, impacts their aesthetics, durability, and functionality. Understanding the relevant organisms and the mechanisms by which colonization occurs would provide valuable information that can be subsequently used to design fouling prevention strategies. Here, next-generation sequencing and microbial community finger printing (T-RFLP) were used to study the community composition of microbes colonizing prepainted steel roofing materials at Burrawang, Australia and Kapar, Malaysia over a 52-week period. Community diversity was low and was dominated by Bacillus spp., cyanobacteria, actinobacteria, Cladosporium sp., Epicoccum nigrum, and Teratosphaeriaceae sp. Cultivation-based methods isolated approximately 20 different fungi and bacteria, some of which, such as E. nigrum and Cladosporium sp., were represented in the community sequence data. Fluorescence in situ hybridization imaging showed that fungi were the most dominant organisms present. Analysis of the sequence and T-RFLP data indicated that the microbial communities differed significantly between locations and changed significantly over time. The study demonstrates the utility of molecular ecology tools to identify and characterize microbial communities associated with the fouling of painted steel surfaces and ultimately can enable the targeted development of control strategies based on the dominant species responsible for fouling.

Matched MeSH terms: DNA, Bacterial/genetics; Polymorphism, Restriction Fragment Length/genetics
Insecticidal activity and expression of cytochrome P450 family 4 genes in Aedes albopictus after exposure to pyrethroid mosquito coils

Avicor SW, Wajidi MF, El-Garj FM, Jaal Z, Yahaya ZS

Protein J, 2014 Oct;33(5):457-64.
PMID: 25199940 DOI: 10.1007/s10930-014-9580-z

Mosquito coils are insecticides commonly used for protection against mosquitoes due to their toxic effects on mosquito populations. These effects on mosquitoes could induce the expression of metabolic enzymes in exposed populations as a counteractive measure. Cytochrome P450 family 4 (CYP4) are metabolic enzymes associated with a wide range of biological activities including insecticide resistance. In this study, the efficacies of three commercial mosquito coils with different pyrethroid active ingredients were assessed and their potential to induce the expression of CYP4 genes in Aedes albopictus analyzed by real-time quantitative PCR. Coils containing 0.3 % D-allethrin and 0.005 % metofluthrin exacted profound toxic effects on Ae. albopictus, inducing high mortalities (≥90 %) compared to the 0.2 % D-allethrin reference coil. CYP4H42 and CYP4H43 expressions were significantly higher in 0.3 % D-allethrin treated mosquitoes compared to the other treated populations. Short-term (KT50) exposure to mosquito coils induced significantly higher expression of both genes in 0.005 % metofluthrin exposed mosquitoes. These results suggest the evaluated products provided better protection than the reference coil; however, they also induced the expression of metabolic genes which could impact negatively on personal protection against mosquito.

Matched MeSH terms: Aedes/genetics; Cytochrome P-450 Enzyme System/genetics
Fulltext Diversity of Streptomyces spp. from mangrove forest of Sarawak (Malaysia) and screening of their antioxidant and cytotoxic activities

Law JW, Chan KG, He YW, Khan TM, Ab Mutalib NS, Goh BH, et al.

Sci Rep, 2019 12 03;9(1):15262.
PMID: 31792235 DOI: 10.1038/s41598-019-51622-x

Streptomycetes have been the center of attraction within scientific community owing to their capability to produce various bioactive compounds, for instance, with different antimicrobial, anticancer, and antioxidant properties. The search for novel Streptomyces spp. from underexplored area such as mangrove environment has been gaining attention since these microorganisms could produce pharmaceutically important metabolites. The aim of this study is to discover the diversity of Streptomyces spp. from mangrove in Sarawak and their bioactive potentials - in relation to antioxidant and cytotoxic activities. A total of 88 Streptomyces isolates were successfully recovered from the mangrove soil in Kuching, state of Sarawak, Malaysia. Phylogenetic analysis of all the isolates and their closely related type strains using 16S rRNA gene sequences resulted in 7 major clades in the phylogenetic tree reconstructed based on neighbour-joining algorithm. Of the 88 isolates, 18 isolates could be considered as potentially novel species according to the 16S rRNA gene sequence and phylogenetic analyses. Preliminary bioactivity screening conducted on the potential novel Streptomyces isolates revealed significant antioxidant activity and notable cytotoxic effect against tested colon cancer cell lines (HCT-116, HT-29, Caco-2, and SW480), with greater cytotoxicity towards SW480 and HT-29 cells. This study highlighted that the Sarawak mangrove environment is a rich reservoir containing streptomycetes that could produce novel secondary metabolites with antioxidant and cytotoxic activities.

Matched MeSH terms: RNA, Ribosomal, 16S/genetics; Streptomyces/genetics

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