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Fulltext mRNA expression of EgCHI1, EgCHI2, and EgCHI3 in oil palm leaves (Elaeis guineesis Jacq.) after treatment with Ganoderma boninense pat. and Trichoderma harzianum Rifai

Naher L, Tan SG, Ho CL, Yusuf UK, Ahmad SH, Abdullah F

ScientificWorldJournal, 2012;2012:647504.
PMID: 22919345 DOI: 10.1100/2012/647504

Basal stem rot (BSR) disease caused by the fungus Ganoderma boninense is the most serious disease affecting the oil palm; this is because the disease escapes the early disease detection. The biocontrol agent Trichoderma harzianum can protect the disease only at the early stage of the disease. In the present study, the expression levels of three oil palm (Elaeis guineensis Jacq.) chitinases encoding EgCHI1, EgCHI2, and EgCHI3 at 2, 5, and 8 weeks inoculation were measured in oil palm leaves from plants treated with G. boninense or T. harzianum alone or both.
Virus-like particles of Macrobrachium rosenbergii nodavirus produced in bacteria

Goh ZH, Tan SG, Bhassu S, Tan WS

J Virol Methods, 2011 Jul;175(1):74-9.
PMID: 21536072 DOI: 10.1016/j.jviromet.2011.04.021

Macrobrachium rosenbergii nodavirus (MrNv) infects giant freshwater prawns and causes white tail disease (WTD). The coding region of the capsid protein of MrNv was amplified with RT-PCR and cloned into the pTrcHis2-TOPO vector. The recombinant plasmid was introduced into Escherichia coli and protein expression was induced with IPTG. SDS-PAGE showed that the recombinant protein containing the His-tag and myc epitope has a molecular mass of about 46 kDa and it was detected by the anti-His antibody in Western blotting. The protein was purified using immobilized metal affinity chromatography (IMAC) and transmission electron microscopic analysis revealed that the recombinant protein assembled into virus-like particles (VLPs) with a diameter of about 30±3 nm. The size of the particles was confirmed by dynamic light scattering. Nucleic acids were extracted from the VLPs and treatment with nucleases showed that they were mainly RNA molecules. This is the first report describing the production of MrNv capsid protein in bacteria and its assembly into VLPs.
Virus-like particle of Macrobrachium rosenbergii nodavirus produced in Spodoptera frugiperda (Sf9) cells is distinctive from that produced in Escherichia coli

Kueh CL, Yong CY, Masoomi Dezfooli S, Bhassu S, Tan SG, Tan WS

Biotechnol Prog, 2017 Mar;33(2):549-557.
PMID: 27860432 DOI: 10.1002/btpr.2409

Macrobrachium rosenbergii nodavirus (MrNV) is a virus native to giant freshwater prawn. Recombinant MrNV capsid protein has been produced in Escherichia coli, which self-assembled into virus-like particles (VLPs). However, this recombinant protein is unstable, degrading and forming heterogenous VLPs. In this study, MrNV capsid protein was produced in insect Spodoptera frugiperda (Sf9) cells through a baculovirus system. Dynamic light scattering (DLS) and transmission electron microscopy (TEM) revealed that the recombinant protein produced by the insect cells self-assembled into highly stable, homogenous VLPs each of approximately 40 nm in diameter. Enzyme-linked immunosorbent assay (ELISA) showed that the VLPs produced in Sf9 cells were highly antigenic and comparable to those produced in E. coli. In addition, the Sf9 produced VLPs were highly stable across a wide pH range (2-12). Interestingly, the Sf9 produced VLPs contained DNA of approximately 48 kilo base pairs and RNA molecules. This study is the first report on the production and characterization of MrNV VLPs produced in a eukaryotic system. The MrNV VLPs produced in Sf9 cells were about 10 nm bigger and had a uniform morphology compared with the VLPs produced in E. coli. The insect cell production system provides a good source of MrNV VLPs for structural and immunological studies as well as for host-pathogen interaction studies. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:549-557, 2017.
Transferrin C subtyping in Malaysians and in Indonesians from North Sumatra

Tan SG, Gan YY, Asuan K

Hum Genet, 1982;60(4):369-70.
PMID: 7106773

Malays, Chinese, and Indians from Peninsular Malaysia; Ibans and Bidayuh from Sarawak State; Kadazans from Sabah State, Northern Borneo; and Bataks, Minangkabau, and Javanese from North Sumatra, Indonesia, were subtyped for transferrin C by polyacrylamide gel isoelectric focusing. All nine populations studied are polymorphic for two alleles, TfCl and TfC2, TfC3 was polymorphic in six populations and present as a rare variant in the other three. The frequency of TfC1 ranged from 0.855 in Bidayuh to 0.711 in Javanese, that of TfC2 from 0.231 in Indians to 0.113 in Bidayuh, and that of TfC3 from 0.030 in Javanese and Chinese to 0.008 in Bidayuh. TfDchi is polymorphic in all the populations that we studied except in Minangkabau, in whom it is present as a rare variant, and in Indians, in whom it is absent.
Toxicities and tolerances of Cd, Cu, Pb and Zn in a primary producer (Isochrysis galbana) and in a primary consumer (Perna viridis)

Yap CK, Ismail A, Omar H, Tan SG

Environ Int, 2004 Feb;29(8):1097-104.
PMID: 14680893

Studies on toxicities and tolerances of cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn) in the brown alga Isochrysis galbana and in the green-lipped mussel Perna viridis were conducted by short-term bioassays using endpoints growth production and mortality, respectively. The 5-day EC(50) and 24-h LC(50) of these heavy metals were determined in the brown alga and mussel, respectively. The EC(50) values calculated for the alga were 0.74 mg/l for Cd, 0.91 mg/l for Cu, 1.40 mg/l for Pb and 0.60 mg/l for Zn. The LC(50) values for the mussels were 1.53 mg/l for Cd, 0.25 mg/l for Cu, 4.12 mg/l for Pb and 3.20 mg/l for Zn. These LC(50) values were within the concentration ranges as reported by other authors who used P. viridis as the test organism. Based on these EC(50) and LC(50) values, the alga was most sensitive to Zn, followed by Cd, Cu and Pb while the mussel was most sensitive to Cu, followed by Cd, Zn and Pb. Differences in the trophic levels, metal handling strategies, biology and ecology of the primary producer (brown alga) and the primary consumer (mussel) are believed to be the plausible causes for the different toxicities and tolerances of the metals studied.
Tolerance and biosorption of copper (Cu) and lead (Pb) by filamentous fungi isolated from a freshwater ecosystem

Iskandar NL, Zainudin NA, Tan SG

J Environ Sci (China), 2011;23(5):824-30.
PMID: 21790056

Filamentous fungi are able to accumulate significant amount of metals from their environment. The potential of fungal biomass as agents for biosorption of heavy metals from contaminated sediments is currently receiving attention. In the present study, a total of 41 isolates of filamentous fungi obtained from the sediment of the Langat River, Selangor, Malaysia were screened for their tolerance and uptake capability of copper (Cu) and lead (Pb). The isolates were identified as Aspergillus niger, A. fumigatus, Trichoderma asperellum, Penicillium simplicissimum and P. janthinellum. A. niger and P. simplicissimum, were able to survive at 1000 mg/L of Cu(II) concentration on Potato Dextrose Agar (PDA) while for Pb, only A. niger survived at 5000 mg/L concentration. The results showed that A. niger, P. simplicissimum and T. asperellum have a better uptake capacity for Pb compared to Cu and the findings indicated promising biosorption of Cu and Pb by these filamentous fungi from aqueous solution. The present study was also determined the maximum removal of Cu(II) and Pb(II) that was performed by A. niger. The metal removal which occurred at Cu(II) 200 mg/L was (20.910 +/- 0.581) mg/g and at 250 mg/L of Pb(II) was (54.046 +/- 0.328) mg/g.
Fulltext The promising future of chia, Salvia hispanica L

Mohd Ali N, Yeap SK, Ho WY, Beh BK, Tan SW, Tan SG

J Biomed Biotechnol, 2012;2012:171956.
PMID: 23251075 DOI: 10.1155/2012/171956

With increasing public health awareness worldwide, demand for functional food with multiple health benefits has also increased. The use of medicinal food from folk medicine to prevent diseases such as diabetes, obesity, and cardiovascular problems is now gaining momentum among the public. Seed from Salvia hispanica L. or more commonly known as chia is a traditional food in central and southern America. Currently, it is widely consumed for various health benefits especially in maintaining healthy serum lipid level. This effect is contributed by the presence of phenolic acid and omega 3/6 oil in the chia seed. Although the presence of active ingredients in chia seed warrants its health benefits, however, the safety and efficacy of this medicinal food or natural product need to be validated by scientific research. In vivo and clinical studies on the safety and efficacy of chia seed are still limited. This paper covers the up-to-date research on the identified active ingredients, methods for oil extraction, and in vivo and human trials on the health benefit of chia seed, and its current market potential.
The genetic structure of Oreochromis spp. (Tilapia) populations in Malaysia as revealed by microsatellite DNA analysis

Bhassu S, Yusoff K, Panandam JM, Embong WK, Oyyan S, Tan SG

Biochem Genet, 2004 Aug;42(7-8):217-29.
PMID: 15487586

The genetic make-up of five populations of Oreochromis spp. was examined by microsatellite analysis. Eleven polymorphic microsatellite loci showed significant departures from the Hardy-Weinberg equilibrium. The mean heterozygosity ranged from 0.6280 to 0.7040 for each population. The genetic distance values showed a clear separation between O. niloticus and O. mossambicus. The differentiation of the O. niloticus populations was then tested with various genetic measures, which are based on both the Infinite Allele and the Stepwise Mutation models. All these measures grouped the populations similarly.
Fulltext The first Malay database toward the ethnic-specific target molecular variation

Halim-Fikri H, Etemad A, Abdul Latif AZ, Merican AF, Baig AA, Annuar AA, et al.

BMC Res Notes, 2015;8:176.
PMID: 25925844 DOI: 10.1186/s13104-015-1123-y

The Malaysian Node of the Human Variome Project (MyHVP) is one of the eighteen official Human Variome Project (HVP) country-specific nodes. Since its inception in 9(th) October 2010, MyHVP has attracted the significant number of Malaysian clinicians and researchers to participate and contribute their data to this project. MyHVP also act as the center of coordination for genotypic and phenotypic variation studies of the Malaysian population. A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of Malaysian ethnic groups. This ethnic-specific database is called the Malaysian Node of the Human Variome Project database (MyHVPDb).
Fulltext The effects of different velogenic NDV infections on the chicken bursa of Fabricius

Kristeen-Teo YW, Yeap SK, Tan SW, Omar AR, Ideris A, Tan SG, et al.

BMC Vet Res, 2017 May 31;13(1):151.
PMID: 28569155 DOI: 10.1186/s12917-017-1071-y

BACKGROUND: Virulent Newcastle disease virus (NDV) was reported to cause rapid depletion of chicken bursa of Fabricius. Severe pathological condition of the organ is commonly associated with high levels of virus replication, intense inflammatory response and also the degree of apoptosis. In this study, the responses of chicken bursa of Fabricius infected with two different strains of velogenic NDV, namely AF2240 and IBS002, were investigated by observing cell population changes, oxidative stress, viral replication and cytokine expression in the organ. Subsequently, apoptosis of enriched bursal IgM+ cells was determined to help us elucidate possible host pathogen relationships between the chicken bursa of Fabricius and NDV infection.
RESULTS: The depletion of IgM+ cells and infiltration of macrophages were observed to be higher in bursa infected with AF2240 as compared to IBS002. In line with the increment of the macrophage population, higher nitric oxide (NO) and malondialdehyde (MDA) contents which indicated higher oxidative stress were also detected in bursa infected with NDV AF2240. In addition, higher pro-inflammatory cytokines and chemokine gene expression such as chicken CXCLi2, IL-18 and IFN-γ were observed in AF2240 infected bursa. Depletion of IgM+ cells was further confirmed with increased cell death and apoptosis of the cells in AF2240 infected bursa as compared to IBS002. However, it was found that the viral load for NDV strain IBS002 was comparatively higher than AF2240 although the magnitude of the pro- inflammatory cytokines expression and cell apoptosis was lower than AF2240.
CONCLUSION: The results of our study demonstrated that infection of NDV strains AF2240 and IBS002 caused apoptosis in bursa IgM+ cells and its severity was associated with increased expression of pro-inflammatory cytokines/chemokine, macrophage infiltration and oxidative stress as the infection duration was prolonged. However, of the two viruses, we observed that NDV AF2240 induced a greater magnitude of apoptosis in chicken bursa IgM+ cells in comparison to IBS002. This might be due to the high level of oxidative stress and inflammatory cytokines/chemokine as well as lower IL10 expression which subsequently led to a high rate of apoptosis in the chicken bursa of Fabricius although the detected viral load of AF2240 was lower than IBS002.
Telescopium telescopium as potential biomonitors of Cu, Zn, and Pb for the tropical intertidal area

Yap CK, Noorhaidah A, Azlan A, Nor Azwady AA, Ismail A, Ismail AR, et al.

Ecotoxicol Environ Saf, 2009 Feb;72(2):496-506.
PMID: 18243309 DOI: 10.1016/j.ecoenv.2007.12.005

The distributions of Cu, Zn, and Pb concentrations in the selected soft tissues (foot, cephalic tentacle, mantle, muscle, gill, digestive caecum, and remaining soft tissues) and shells of the mud-flat snail Telescopium telescopium were determined in snails from eight geographical sites in the south-western intertidal area of Peninsular Malaysia. Generally, the digestive caecum compared with other selected soft tissues, accumulated higher concentration of Zn (214.35+/-14.56 microg/g dry weight), indicating that the digestive caecum has higher affinity for the essential Zn to bind to metallothionein. The shell demonstrated higher concentrations of Pb (41.23+/-1.20 microg/g dry weight) when compared to the selected soft tissues except gill from Kuala Sg. Ayam (95.76+/-5.32 microg/g dry weight). The use of different soft tissues also can solve the problem of defecation to reduce error in interpreting the bioavailability of heavy metals in the intertidal area.
Fulltext Studies on the genetic variation of the green unicellular alga Haematococcus pluvialis (Chlorophyceae) obtained from different geographical locations using ISSR and RAPD molecular marker

Mostafa N, Omar H, Tan SG, Napis S

Molecules, 2011 Mar 22;16(3):2599-608.
PMID: 21441863 DOI: 10.3390/molecules16032599

Haematococcus pluvialis (Flotow) is a unicellular green alga, which is considered to be the best astaxanthin-producing organism. Molecular markers are suitable tools for the purpose of finding out genetic variations in organisms; however there have been no studies conducted on ISSR or RAPD molecular markers for this organism. The DNA of 10 different strains of H. pluvialis (four strains from Iran, two strains from Finland, one strain from Switzerland and three strains from the USA) was extracted. A genetic similarity study was carried out using 14 ISSR and 12 RAPD primers. Moreover, the molecular weights of the bands produced ranged from 0.14 to 3.4 Kb. The PCA and dendrogram clustered the H. pluvialis strains into various groups according to their geographical origin. The lowest genetic similarity was between the Iran2 and USA2 strains (0.08) and the highest genetic similarity was between Finland1 and Finland2 (0.64). The maximum numbers of bands produced by the ISSR and RAPD primers were 35 and 6 bands, respectively. The results showed that ISSR and RAPD markers are useful for genetic diversity studies of Haematococcus as they showed geographical discrimination.
Similarities and differences of metal distributions in the tissues of molluscs by using multivariate analyses

Yap CK, Edward FB, Tan SG

Environ Monit Assess, 2010 Jun;165(1-4):39-53.
PMID: 19452255 DOI: 10.1007/s10661-009-0925-6

Multivariate analysis including correlation, multiple stepwise linear regression, and cluster analyses were applied to investigate the heavy metal concentrations (Cd, Cu, Fe, Ni, Pb, and Zn) in the different parts of bivalves and gastropods. It was also aimed to distinguish statistically the differences between the marine bivalves and the gastropods with regards to the accumulation of heavy metals in the different tissues. The different parts of four species of bivalves and four species of gastropods were obtained and analyzed for heavy metals. The multivariate analyses were then applied on the data. From the multivariate analyses conducted, there were correlations found between the soft tissues of bivalves and gastropods, but none was found between the shells and the soft tissues of most of the molluscs (except for Cerithidea obtusa and Puglina cochlidium). The significant correlations (P < 0.05) found between the soft tissues were further complemented by the multiple stepwise linear regressions where heavy metals in the total soft tissues were influenced by the accumulation in the different types of soft tissues. The present study found that the distributions of heavy metals in the different parts of molluscs were related to their feeding habits and living habitats. The statistical approaches proposed in this study are recommended for use in biomonitoring studies, since multivariate analyses can reduce the cost and time involved in identifying an effective tissue to monitor the heavy metal(s) bioavailability and contamination in tropical coastal waters.
Fulltext Segregation and genetic linkage analyses of river catfish, Mystus nemurus, based on microsatellite markers

Hoh BP, Siraj SS, Tan SG, Yusoff K

Genet. Mol. Res., 2013;12(3):2578-93.
PMID: 23479146 DOI: 10.4238/2013.February.28.1

The river catfish Mystus nemurus is an important fresh water species for aquaculture in Malaysia. We report the first genetic linkage map of M. nemurus based on segregation analysis and a linkage map using newly developed microsatellite markers of M. nemurus. A total of 70 of the newly developed polymorphic DNA microsatellite markers were analyzed on pedigrees generated using a pseudo-testcross strategy from 2 mapping families. In the first mapping family, 100 offspring were produced from randomly selected dams of the same populations; dams of the second family were selected from 2 different populations, and this family had 50 offspring. Thirty-one of the 70 markers segregated according to the Mendelian segregation ratio. Linkage analysis revealed that 17 microsatellite markers belonging to 7 linkage groups were obtained at a logarithm of the odds score of 1.2 spanning 584 cM by the Kosambi mapping function, whereas the other 14 remained unlinked. The results from this study will act as primer to a more extensive genetic mapping study aimed towards identifying genetic loci involved in determining economically important traits.
Salivary peroxidase, Pm, and Ph protein polymorphisms in Malasians.

Noraini I, Tan SG, Gan YY, Teng YS

Hum Genet, 1980;56(2):205-7.
PMID: 7450777

Three human saliva genetic markers, namely, salivary peroxidase (SAPX), Pm, and Ph proteins, were investigated in the three major ethnic groups of Malaysia: Malays, Chinese, and Indians. For Pm, the allelic frequencies of Pm+ for Malays, Chinese, and Indians are 0.385 +/- 0.030, 0.282 +/- 0.026, and 0.289 +/- 0.026 respectively. For Ph, the allelic frequencies of Ph+ are 0.082 +/- 0.016 for Malays, 0.109 +/- 0.017 for Chinese, and 0.062 +/- 0.013 for Indians. For SAPX, the allelic frequencies of SAPX1 in Malays, Chinese, and Indians are 0.762 +/- 0.027, 0.755 +/- 0.027, and 0.723 +/- 0.026 respectively.
Saliva acid phosphatases in Malaysians: report of a new variant

Tan SG, Teng YS

Hum. Hered., 1979;29(1):61-3.
PMID: 761925

A total of 640 Malaysians, 355 of Malay, 155 of Chinese, and 130 of Indian ancestries have been examined for saliva acid phosphatases. The three ethnic groups were polymorphic for saliva acid phosphatase A (Sap-A) and saliva acid phosphatase (B (Sap-B). The gene frequencies were: Sap-A, Malays: A = 0.469, A' = 0.001, A degrees = 0.530; Chinese: A = 0.436, A' = 0.010, A degrees = 0.555; Indians: A = 0.533, A' = 0.012, A degrees = 0.456. For Sap-B, Malays: B = 0.925, B degrees = 0.075; Chinese: B = 0.797, B1 = 0.016, B degrees = 0.187; Indians: B 0.752, B degrees = 0.248. Phenotype ABB1 is described.
Saliva acid phosphatases and amylase in Senoi and aboriginal Malays and superoxide dismutase in various racial groups of Peninsular Malaysia

Tan SG, Teng YS

Jinrui Idengaku Zasshi, 1978 Jun;23(2):133-8.
PMID: 691834
SSR mining in oil palm EST database: application in oil palm germplasm diversity studies

Ting NC, Zaki NM, Rosli R, Low ET, Ithnin M, Cheah SC, et al.

J Genet, 2010 Aug;89(2):135-45.
PMID: 20861564

This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group (45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT (7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification.
Red cell glyoxalase I and placental soluble aconitase polymorphisms in the three major ethnic groups of Malaysia

Teng YS, Tan SG, Ng T, Lopez CG

Jinrui Idengaku Zasshi, 1978 Sep;23(3):211-5.
PMID: 732016
Fulltext Recycling of superfine resolution agarose gel

Seng TY, Singh R, Faridah QZ, Tan SG, Alwee SS

Genet. Mol. Res., 2013;12(3):2360-7.
PMID: 23546970 DOI: 10.4238/2013.March.11.1

Genetic markers are now routinely used in a wide range of applications, from forensic DNA analysis to marker-assisted plant and animal breeding. The usual practice in such work is to extract the DNA, prime the markers of interest, and sift them out by electrically driving them through an appropriate matrix, usually a gel. The gels, made from polyacrylamide or agarose, are of high cost, limiting their greater applications in molecular marker work, especially in developing countries where such technology has great potential. Trials using superfine resolution (SFR) agarose for SSR marker screening showed that it is capable of resolving SSR loci and can be reused up to 14 times, thus greatly reducing the cost of each gel run. Furthermore, for certain applications, low concentrations of agarose sufficed and switching to lithium borate buffer, instead of the conventional Tris-borate-ethylenediaminetetraacetic acid buffer, will further save time and cost. The 2.5% gel was prepared following the Agarose SFR(TM) manual by adding 2.5 g agarose powder into 100 mL 1X lithium borate buffer in a 250-mL flask with rapid stirring. Two midigels (105 x 83 mm, 17 wells) or 4 minigels (50 x 83 mm, 8 wells), 4 mm thickness can be prepared from 100 mL gel solution. A total of 1680 PCR products amplified using 140 SSR markers from oil palm DNA samples were tested in this study using SFR recycled gel. As average, the gel can be recycled 8 times with good resolution, but can be recycled up to 14 times before the resolutions get blurred.

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