Subha Bhassu
University of Malaya, Malaysia, Genetics and Molecular Biology, Faculty Member
- I have aspiration to to do good, be good and see good in anything I do and embark.edit
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The exciting discovery of the semiconducting-like properties of deoxyribonucleic acid (DNA) and its potential applications in molecular genetics and diagnostics in recent times has resulted in a paradigm shift in biophysics research.... more
The exciting discovery of the semiconducting-like properties of deoxyribonucleic acid (DNA) and its potential applications in molecular genetics and diagnostics in recent times has resulted in a paradigm shift in biophysics research. Recent studies in our laboratory provide a platform towards detecting charge transfer mechanism and understanding the electronic properties of DNA based on the sequence-specific electronic response, which can be applied as an alternative to identify or detect DNA. In this study, we demonstrate a novel method for identification of DNA from different shrimp viruses and bacteria using electronic properties of DNA obtained from both negative and positive bias regions in current-voltage (I-V) profiles. Characteristic electronic properties were calculated and used for quantification and further understanding in the identification process. Aquaculture in shrimp industry is a fast-growing food sector throughout the world. However, shrimp culture in many Asian c...
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Malaysian giant prawn, Macrobrachium rosenbergii (de Man, 1879), is an important crustacean aquaculture candidate globally cultured chiefly in hot climates and seasonally in temperate zones. Although the first hatchery for artificial... more
Malaysian giant prawn, Macrobrachium rosenbergii (de Man, 1879), is an important crustacean aquaculture candidate globally cultured chiefly in hot climates and seasonally in temperate zones. Although the first hatchery for artificial production of the species was established in Malaysia in 1984, however, its genetic improvement program has just started recently. This study was executed as a part of this improvement project to evaluate morphometric growth related traits of four populations collected from the Western Coast of Peninsular Malaysia and their progenies. The results of the study disclosed significant differences among these populations for all traits that were considered; with Kedah population showing significant (p<.05) superiority over the rest. Within the eight successfully cohort progeny families produced, Kedah progeny group was the heaviest at the same level of significance as that of parental groups. Fixed effects of family, sex and their interactions showed high...
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An 11-year-old boy living in Otsu City, Shiga Prefecture, Kansai Region, Western Honshu, Japan had zoonotic onchocercosis. The patient developed a painful swelling on the little finger of his left hand. The worm detected in the excised... more
An 11-year-old boy living in Otsu City, Shiga Prefecture, Kansai Region, Western Honshu, Japan had zoonotic onchocercosis. The patient developed a painful swelling on the little finger of his left hand. The worm detected in the excised mass had external transverse ridges but did not have inner striae in the cuticle. On the basis of the parasite's histopathological characteristics, the causative agent was identified as a female Onchocerca dewittei japonica (Spirurida: Onchocercidae). The species of the filarial parasite was confirmed by sequencing the cox1 gene of the parasite. The Japanese wild boar Sus scrofa leucomystax is a definitive host for O. dewittei japonica, which is then transmitted by blackflies as the vector to humans. The current case described occurred in the Kansai Region, Western Honshu, where such infections were previously not reported.
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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... more
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 molecule...
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The genetic structure of the locally threatened cyprinid Osteochilus melanopleurus, collected from four locations (Gerik, Manong, Bernam and Kahang) in Peninsular Malaysia River systems, was assessed based on partial sequences of the... more
The genetic structure of the locally threatened cyprinid Osteochilus melanopleurus, collected from four locations (Gerik, Manong, Bernam and Kahang) in Peninsular Malaysia River systems, was assessed based on partial sequences of the control region (D-loop) mitochondrial DNA. A partial D-loop of 364 base pair gene was extracted from 88 individuals through PCR amplification and direct sequencing. The results show that haplo-type diversity (hd ¼ 0.7956e0.9485) was high, with low nucleotide (p ¼ 0.0045e0.0080) variation for each of the populations examined. A molecular variance analysis (AMOVA) revealed few differences between the four populations. A Tajima D test and Fu Fs test were used to investigate the neutrality of each population, revealing that the all examined populations might experience recent population expansion or the bottleneck effect. A phylogeny tree and mismatch distribution analysis provided further evidence that three of four populations had recently expanded, as well as indicating that the Kahang population had in contrast remained stable. Overall, this study concludes that the populations of O. melanopleurus distributed throughout the river systems of Peninsular Malaysia probably originated from a single ancestral source during the last glaciation period, and should therefore be treated as a single evolutionary unit in any conservation efforts.
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Dystrophin, an essential protein functional in the maintenance of muscle structural integrity is known to be responsible for muscle deterioration during white spot syndrome virus (WSSV) infection among prawn species. Previous studies have... more
Dystrophin, an essential protein functional in the maintenance of muscle structural integrity is known to be responsible for muscle deterioration during white spot syndrome virus (WSSV) infection among prawn species. Previous studies have shown the upregulation of dystrophin protein in Macrobrachium rosenbergii (the giant freshwater prawn) upon white spot syndrome virus (WSSV) infection. The literature has also suggested the important role of calcium ion alterations in causing such muscle diseases. Thus, the interest of this study lies within the linkage between dystrophin functioning, intracellular calcium and white spot syndrome virus (WSSV) infection condition. In this study, the dystrophin gene from M. rosenbergii (MrDys) was first characterised followed by the characterization of dystrophin gene from a closely related shrimp species, Penaeus monodon (PmDys). Dystrophin sequences from different phyla were then used for evolutionary comparison through BLAST analysis, conserved do...
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ABSTRACT Small Crocidurinae shrews (weight &lt;8 g) from Southeast Asia have been poorly studied to date, mainly because of the difficulty to catch them and the concomitant paucity of reference specimens available in museums. Hence... more
ABSTRACT Small Crocidurinae shrews (weight &lt;8 g) from Southeast Asia have been poorly studied to date, mainly because of the difficulty to catch them and the concomitant paucity of reference specimens available in museums. Hence their systematics is still debated, and most small Crocidura shrews from Sundaland are assigned to the monticola species complex. Here, we report a study based on a survey of shrews caught with large pitfalls set on forest floors in Peninsular Malaysia. Morphometric analyses based on 14 skull measurements showed that these shrews tend to be larger with increasing altitude, but showed otherwise no consistent variation. When compared to museum specimens of the monticola species complex sampled in the Sundaland (total: 77 specimens), the Malay shrews tend also to be larger than those living on Kalimantan (Borneo) and Sumatra. All are, however, morphologically distinct from the other species, C. maxi, found in eastern Java and on the Lesser Sundas. Molecular analyses of a subset of these small shrews and based on a mitochondrial (cytochrome b) and a nuclear gene (Apolipoprotein B) suggest that samples from the central region of Peninsular Malaysia (Bukit Rengit and Ulu Gombak) genetically differ from other Malaysian populations (by about 7% K2P distance at the cyt b gene) and are more closely related to some samples from Sumatra and Borneo. These differences did not correlate with the altitudinal variation evidenced from the morphological analysis. Reference sequences from the terra typica of monticola and maxi (both species were originally described from Java) are however needed to determine if these unexpected genetic differences warrant additional taxonomic subdivision within the Sundaland.
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Aroma and cooked kernel elongation are the most important quality traits of aromatic rice, which differentiate the highly valued aromatic rice from the other rice types. Previous studies on genetic analysis have shown that genes/QTLs for... more
Aroma and cooked kernel elongation are the most important quality traits of aromatic rice, which differentiate the highly valued aromatic rice from the other rice types. Previous studies on genetic analysis have shown that genes/QTLs for these two traits are linked. In the present study, it tried to evaluate the expression of aroma, kernel elongation and their association in 55 fine rice genotypes in the tropical environment of Malaysia. Highest percentage of elongation ratio was observed in Genotype E2 followed by E11, Gharib, E6, ...
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Prawns of the genus Macrobrachium Bate, 1868 (Crustacea: Palaemonidae) are a highly diverse group of decopod crustaceans found in circumtropical marine-, estuarine- and freshwaters. At present, wild stocks have been used to cultivate... more
Prawns of the genus Macrobrachium Bate, 1868 (Crustacea: Palaemonidae) are a highly diverse group of decopod crustaceans found in circumtropical marine-, estuarine- and freshwaters. At present, wild stocks have been used to cultivate commercial cultures in many areas in Malaysia. Such repeated harvesting from wild stocks, however, will eventually lead to extinction and loss of genetic diversity. Therefore, it is important to know the genetic make up of these wild stocks in order to manage the populations for conservation and breeding purposes. In the present study, a novel method known as Random Amplified Microsatellites (RAMS) was used to develop single locus microsatellite markers. A total of 13 microsatellite regions were detected. The findings of this study showed a successful detection of the microsatellite sequences in M. rosenbergii using RAMS. This study will be continued to identify more clones that contain microsatellite sequences and to design the forward and reverse prim...
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Malaysian arowana (dragonfish; Scleropages formosus) is an ancient osteoglossid fish from southeast Asia. Due to the high demand of the ornamental fish trade and because of habitat loss, the species is close to extinction. We isolated and... more
Malaysian arowana (dragonfish; Scleropages formosus) is an ancient osteoglossid fish from southeast Asia. Due to the high demand of the ornamental fish trade and because of habitat loss, the species is close to extinction. We isolated and characterized 10 polymorphic microsatellites of this species, using 5'-anchored PCR. The number of alleles at the 10 microsatellite loci ranged from 2 to 28, with a mean of 7.8/locus. The observed heterozygosity ranged from 0.03 to 0.93 (mean: 0.39), whereas the expected heterozygosity ranged from 0.03 to 0.94 (mean: 0.46). Seven microsatellites deviated from Hardy-Weinberg equilibrium, and three conformed to Hardy-Weinberg equilibrium and were in linkage equilibrium. These 10 novel microsatellites should facilitate studies of genetic diversity and population structure of arowana to help plan actions for the conservation of the indigenous Malaysian arowana.
Research Interests: Genetics()
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In this study, we reported a full length of catalase gene (designated as MrCat), identified from the transcriptome database of freshwater prawn Macrobrachium rosenbergii. The complete gene sequence of the MrCat is 2504 base pairs in... more
In this study, we reported a full length of catalase gene (designated as MrCat), identified from the transcriptome database of freshwater prawn Macrobrachium rosenbergii. The complete gene sequence of the MrCat is 2504 base pairs in length, and encodes 516 amino acids. The MrCat protein contains three domains such as catalase 1 (catalase proximal heme-ligand signature) at 350-358, catalase 2 (catalase proximal active site signature) at 60-76 and catalase 3 (catalase family profile) at 20-499. The mRNA expressions of MrCat in healthy and the infectious hypodermal and hematopoietic necrosis virus (IHHNV) challenged M. rosenbergii were examined using quantitative real time polymerase chain reaction (qRT-PCR). The MrCat is highly expressed in digestive tract and all the other tissues (walking leg, gills, muscle, hemocyte, hepatopancreas, pleopods, brain and eye stalk) of M. rosenbergii taken for analysis. The expression is strongly up-regulated in digestive tract after IHHNV challenge. ...
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The population structure of Probarbus jullieni from Malaysia and Thailand stocks was based on seven microsatellite primers and truss network measurements. Truss morphometric measurements were made on Temoleh, Probarbus jullieni to... more
The population structure of Probarbus jullieni from Malaysia and Thailand stocks was based on seven microsatellite primers and truss network measurements. Truss morphometric measurements were made on Temoleh, Probarbus jullieni to demonstrate the degree of speciation that can be induced by both biotic and abiotic conditions and contribute to the definition of different stocks of Probarbus sp. At the momment
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A novel mannose binding lily type lectin-3 gene, OfLTL-3, identified from rock bream (Oplegnathus fasciatus) cDNA library was cloned, expressed and characterized. OfLTL-3 encodes a polypeptide of 114 amino acids with a calculated... more
A novel mannose binding lily type lectin-3 gene, OfLTL-3, identified from rock bream (Oplegnathus fasciatus) cDNA library was cloned, expressed and characterized. OfLTL-3 encodes a polypeptide of 114 amino acids with a calculated molecular mass of 13kDa. The deduced amino acid sequence of OfLTL-3 displayed all conserved features. There was a high similarity and close phylogenetic relationship that OfLTL-3 shared
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Lectins may function as pattern-recognition receptors (PRRs) and play important roles in immune responses. In this study, a novel galectin-1 (designated OfGLec-1) gene was identified from rock bream, Oplegnathus fasciatus, cDNA library.... more
Lectins may function as pattern-recognition receptors (PRRs) and play important roles in immune responses. In this study, a novel galectin-1 (designated OfGLec-1) gene was identified from rock bream, Oplegnathus fasciatus, cDNA library. The complete cDNA sequence of the OfGLec-1 gene is 993 base pairs in length, and encodes 135 amino acids. OfGLec-1 shares a highly conserved carbohydrate recognition domain with
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Arginine kinase-1 (MrAK-1) was sequenced from the freshwater prawn Macrobrachium rosenbergii using Illumina Solexa Genome Analyzer Technique. MrAK-1 consisted of 1068 bp nucleotide encoded 355 polypeptide with an estimated molecular mass... more
Arginine kinase-1 (MrAK-1) was sequenced from the freshwater prawn Macrobrachium rosenbergii using Illumina Solexa Genome Analyzer Technique. MrAK-1 consisted of 1068 bp nucleotide encoded 355 polypeptide with an estimated molecular mass of 40 kDa. MrAK-1 sequence contains a potential ATP:guanido phosphotransferases active domain site. The deduced amino acid sequence of MrAK-1 was compared with other 7 homologous arginine kinase (AK) and showed
Research Interests: Zoology, Immune response, Kinetics, Gene expression, Energy Metabolism, and 16 morePhylogeny, Sequence alignment, Escherichia coli, Animals, Polymerase Chain Reaction, Muscles, Fisheries Sciences, Molecular cloning, Energy Production, Palaemonidae, Enzyme activity, Molecular Mass, Veterinary Sciences, Amino Acid Sequence, Fish and Shellfish Diseases, and Nucleotides
Seven single-locus dinucleotide microsatellite markers were developed to characterize an economically important sport fish and food fish in Malaysia and in Southeast Asia. They were obtained by using a rapid method namely the 5′-anchored... more
Seven single-locus dinucleotide microsatellite markers were developed to characterize an economically important sport fish and food fish in Malaysia and in Southeast Asia. They were obtained by using a rapid method namely the 5′-anchored PCR enrichment protocol. The specific primers were designed to flank the repeat sequences and these were subsequently used to characterize 120 unrelated fish from Malaysia and
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Research Interests: Zoology, Immune response, Computational Biology, Gene expression, Aedes aegypti, and 18 morePhylogeny, Animals, Fisheries Sciences, Pan troglodytes, Palaemonidae, Phylogenetic Tree, Molecular Mass, Veterinary Sciences, Species Specificity, Amino Acid Sequence, Base Sequence, Gene Expression Analysis, Ixodes scapularis, Fish and Shellfish Diseases, Nucleotides, Hepatopancreas, Gene Expression Regulation, and Gene expression profiling(Phylogeny, Animals, Fisheries Sciences, Pan troglodytes, Palaemonidae, Phylogenetic Tree, Molecular Mass, Veterinary Sciences, Species Specificity, Amino Acid Sequence, Base Sequence, Gene Expression Analysis, Ixodes scapularis, Fish and Shellfish Diseases, Nucleotides, Hepatopancreas, Gene Expression Regulation, and Gene expression profiling)
(Phylogeny, Animals, Fisheries Sciences, Pan troglodytes, Palaemonidae, Phylogenetic Tree, Molecular Mass, Veterinary Sciences, Species Specificity, Amino Acid Sequence, Base Sequence, Gene Expression Analysis, Ixodes scapularis, Fish and Shellfish Diseases, Nucleotides, Hepatopancreas, Gene Expression Regulation, and Gene expression profiling)