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Articles by J. Ismail
Total Records ( 5 ) for J. Ismail
  B.L. Tchin , W.S. Ho , S.L. Pang and J. Ismail
  Candidate-gene-based association study which involves the identification of causative Single Nucleotide Polymorphisms (SNPs) for excellent traits has been proposed as a promising approach to dissect complex traits in forest trees. Hence, the goal of this study was to identify the genetic association among SNPs from Cinnamate 4-Hydroxylase (C4H) and Cinnamyl Alcohol Dehydrogenase (CAD) genes and an array of wood properties namely, specific gravity, wood density, fiber-length, cell wall thickness and microfibril angle from Acacia mangium Superbulk trees. Sequence variations within these two genes in 12 A. mangium Superbulk trees were examined and wood properties were measured. The data obtained was tested using General Linear Model (GLM) within TASSEL software. Two SNPs were identified in the exon of C4H, of which all the SNPs caused nonsynonymous mutations whereas five SNPs were identified in the CAD exons along with one deletion mutation. In addition, two SNPs were also identified in the CAD introns. Variation in these two lignin biosynthesis genes might change the structural, functional or biochemical properties of the enzyme being produced, and therefore possibly lead to changes in phenotypic characteristic of the trees. The genetic association study also revealed that SNPs in CAD gene do associate with the wood density, specific gravity and cell wall thickness (p<0.05). However, no significant results were obtained for SNPs in C4H gene with wood properties studied. Thickening of cell wall is affected by the arrangement of biopolymer aggregates which comprise of cellulose, hemicellulose and lignin. Results indicated that SNP in CAD gene might alter the lignin biosynthesis and thus lead to changes in phenotypic characteristics of the trees. Overall, the study has demonstrated that SNP is very useful in association genetic study to identify Quantitative Trait Nucleotide (QTN) which then leads to Gene-assisted Selection (GAS) in the tree breeding programme.
  B.L. Tchin , W.S. Ho , S.L. Pang and J. Ismail
  Association genetics study is a powerful approach to detect the potential genetic variants (i.e., SNPs) underlying the common and complex adaptive traits. Once the quantitative trait nucleotides are identified, such powerful approach provides significant advantages to the forest industry. Hence, attempts were made to discover SNPs from Neolamarckia cadamba partial C4H (3,538 bp) and CAD (2,354 bp) DNA sequences and further associate those SNPs with basic wood density. Overlapping primers were designed in flanking the partial C4H and CAD DNA from 12 N. cadamba trees. The amplified DNA fragments were sequenced and the basic wood density measurements were determined for each tree. The sequence variation analyses revealed that there were 60 and 32 SNPs detected in the partial C4H and CAD DNA sequences, respectively. Those SNPs were distributed throughout the exon, intron, 5’-UTR and 3’-UTR regions. The total nucleotide diversities were π = 0.00302 and θW = 0.00412. The synonymous mutations (π = 0.00983; θW = 0.01210) were more common than nonsynonymous mutations (π = 0.00045; θw = 0.00089) for both C4H and CAD genes. LD declined linearly over short distance at the loci examined. Association genetics study also revealed that 4 and 6 SNPs from C4H and CAD genes, respectively were in significant associations with basic wood density of N. cadamba (p<0.05). The genetic variation identified by the SNP markers, once validated, will facilitate the selection of N. cadamba parental lines or seedlings with optimal quality through Gene-assisted Selection (GAS) approach.
  C.S. Sipaut , N. Ahmad , R. Adnan , I.Ab. Rahman , M.A. Bakar , J. Ismail and C.K. Chee
  Modified fumed silica-epoxy nanocomposites were obtained by refluxing epoxy molecule with fumed silica using imidazole as catalyst. The modified fumed silica was then used as filler in epoxy resin with amine as curing agent. The properties of the surface modified silica and their effect as fillers in bulk epoxy composite were characterized by Fourier Transform Infrared spectroscopy (FTIR), Proton Nuclear Magnetic Resonance Spectroscopy (1H-NMR), Thermogravimetri Analysis (TGA), Differential Scanning Calorimeter (DSC), Coefficient of Thermal Expansion (CTE), Tensile testing, Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray spectrometry (EDX). From FTIR, 1H-NMR and TGA analysis, it was found that the epoxy resin was chemically bonded onto silica surface. From the DSC and CTE analysis, the addition of modified silica filler in the composite matrix highly influences thermal properties. This new synthesis filler shows higher glass transition temperature and more stable CTE data compared to unmodified filler when introduce into composite matrix. The tensile properties of composite matrix with and without the addition of filler show no significant difference in their tensile properties. SEM-EDX analysis show modified fillers have better adhesion with composite matrix compared to unmodified filler.
  S.Y. Tiong , W.S. Ho , S.L. Pang and J. Ismail
  A detailed study was carried out to discover single nucleotide polymorphisms (SNPs) from Neolamarckia cadamba partial XTH (~1283bp) and CesA (778bp) DNA sequences and further associates those SNPs with basic wood density. Primers were designed in flanking the partial XTH and CesA genes from 15 N. cadamba trees. The amplified DNA fragments were sequenced and the basic wood density measurements were determined for each tree. The sequence variation analyses revealed that 34 SNPs (2.65% occurrence) and 3 SNPs (0.39% occurrence) were found in 15 partial genomic DNA sequences of NcXTH1 and NcCesA1, respectively. All the SNPs were discovered in both exon and intron regions. NcXTH1 examined sites showed higher nucleotide diversities of π = 0.00402 and θw = 8.919 when compared to NcCesA1 (π = 0.00127; θw = 0.9226). The LD decayed slowly with distance of polymorphic sites in a linear pattern with the mean R2 value of 0.000687. Association genetics study showed that 2 SNPs from NcXTH1 genes were significantly associated with basic wood density (p<0.05) of N. cadamba. Once the gene-associated SNP markers in NcXTH1 genes are validated, it could be potentially used as a tool in Gene-Assisted Selection (GAS) of N. cadamba trees. This study has also demonstrated that the candidate-gene based association genetics is a powerful approach to dissect complex adaptive traits for organism lacking a genome sequence or reference genomic resources.
  M.K. Abu Hena , S.M.S. Kohinoor , M.A.M. Siddique , J. Ismail , M.H. Idris and S.M.N. Amin
  Macrobenthos in coastal environment that play a significant role in the food web. It could also use as a good indicator of aquatic ecosystem health. The abundance and composition of macrobenthos in Bakkhali channel system, Cox’s Bazar were conducted in relation to the soil parameters. Samples were collected using Ekman Berge bottom grab from five different stations of Bakkhali channel. Macrobenthos were comprised of five major groups namely Polychaeta (9.96-30.31%), Oligochaeta (3.68-59.707%), Crustacea (0.02-58.40%), Bivalvia (1.40-82.09%) and Gastropoda (0.08-4.25%). Total number of macrobenthos was higher at station I (9000 individuals m-2) and station II (8517 individuals m-2) compared to other stations. Shannon diversity index among the stations ranged from 0.65-1.04. Soil pH and soil moisture ranged from 6.1-6.4 and 23.44-31.29%, respectively. The highest organic carbon concentration was observed at station I (2.11%) and lowest at station III (1.40%). Maximum fraction of sand by weight was found at stations II (81.88%) and III (87.88) while the highest fraction of clay (21.52%) and silt (8.0%) were recorded in station I. It was observed that benthic bivalves were positively correlated (r = 0.891, p>0.05) with silt fraction of the sediments.
 
 
 
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