In Malaysia, harmful algal blooms often occur along the coastal waters of west Sabah, where one of the causative organisms is the toxin-producing dinoflagellate, Pyrodinium bahamense var. compressum. A total of five P. bahamense var. compressum isolates were obtained from four locations and were cultured in f/2 medium. A Polymerase Chain Reaction (PCR) based technique was developed and used to screen for the presence of the dinoflagellate, P. bahamense var. compressum. A dinoflagellate-specific primer pair was designed based on sequences of P. bahamense var. compressum to amplify the 18S small subunit ribosomal DNA (rDNA) sequences. The rDNA of the P. bahamense var. compressum isolates were obtained. A species-specific primer pair was designed to target a 600 bp rDNA sequence of the target dinoflagellate. The primer pair targeting P. bahamense var. compressum did not yield any product with the fifteen algae cultures used as negative controls, but only amplified the rDNA of P. bahamense var. compressum cultures. The PCR method for identification of P. bahamense var. compressum was also applied on twenty field samples collected with plankton net. P. bahamense var. compressum cells were detected by PCR in five field samples and were confirmed by direct sequencing. From this study, a species-specific primer pair was obtained to identify the target species, P. bahamense var. compressum, among the natural complex communities of seawater.
In the human genome, point variations are most common (Nachman & Crowell, 2000) and well understood. These variations, when existing in more than 1% of the population, is referred to as
Single Nucleotide Polymorphism (SNP) and can fall in the coding region of a gene, non coding region or intergenic regions.
Known as ‘belangkas’ in Malaysia, horseshoe crabs have been used by locals for food, bait and as fertilizer. Currently, these ancient mariners are gaining a lot of attention as the amoebocyte from their blood are harvested by the biomedical industry for use to detect human pathogens in patients, injectable drugs and intravenous devices.
Microsatellite markers associated with blast resistance genes were used to study the polymorphism and genetic relationship among 20 Malaysian upland rice and four varieties from the
International Rice Research Institute (IRRI) Collection. Among the 11 microsatellite markers used, 10 were polymorphic (90.91%). Only RM313 showed monomorphic pattern. The genetic distances
ranged from 0 to 0.833. The lowest genetic distance was found between Ambas and Babayau. The highest genetic distance was found between Kedinga and Gulfmont. The average genetic
distance is 0.478. A dendrogram generated using genetic distance classified all 24 rice samples into 15 clusters. However, there were no well defined groupings. Further research is needed to verify the existence of the blast resistance genes among these Malaysian upland rice samples.
Avian Influenza viruses belonging to the Orthomyxoviridae family are enveloped viruses with segmented negative sense RNA genome surrounded by a helical symmetry capsid. Influenza viruses, especially the highly pathogenic avian influenza virus (HPAI) such as H5 or H7 subtype are the most important pathogens for the poultry industry in recent times. The haemagglutinin protein and neuraminidase, serves as the target for the immune response of the host. Due to recurrent genetic reassortments between avian and human influenza viruses, global pandemics may emerge and the naive human immunity could not withstand pressure by the novel hybrid virus. The emergence of genetic engineering technology provided the industry with new methods of manufacturing diagnostics tools and vaccines. After extraction of RNA from the cell culture of strain influenza A/Chicken/Malaysia/2004(H5N1) of AIV, the viral RNA was converted to cDNA by a specific primer. The cDNA was amplified by the polymerase chain reaction (PCR) and analyzed
by agarose gel electrophoresis. The intact PCR product of full length haemagglutinin gene was cloned in TO POTM TA Cloning vector. The full-length HA-encoding gene of H5N1 AIV was subcloned into a pPICZA vector. After successful ligation, the constructed plasmid was transformed into E.coli.Top10, Plasmid DNA from transformed bacteria was extracted in white colony and positive clones were confirmed by restriction digestion with Sacl and Not1 restriction enzymes, colony PCR screening and nucleotide sequencing. Construction of a recombinant pPICZA/H5HA plasmid containing the full length haemagglutinin gene was achieved as a first step
towards the expression in Pichia pastoris.
The world’s biodiversity is not distributed uniformly throughout the globe. Some areas such as the tropical rainforests, seas and coral reefs teem with the varieties of life whereas others such as some deserts and polar regions are almost devoid of them (Gaston, 2000). Malaysia, with her tropical jungles and seas, is rich with biodiversity. She is fortunate to have had eminent pioneers such as Ridley (1967), Corner (1972), Soepadmo (1972) and Whitmore (1983) to study her flora and Medway (1968) and Lim (1991) to study her fauna taxonomy. Other pioneers in Malaysian biology included Berry, Dhaliwal and Mohsin. These pioneers are then ably followed by workers such as Latiff, Kiew, Go, Khoo, Davidson, Saberi, Omar, Jambari, Idris, Zekri, Teo, Marziah, Tan, Mukherjee, Shapor, Yusoff, Azmi and many others studying the various subdisciplines of biology. In addition to the more obvious large plants and animals, microorganisms and aquatic organisms had not been neglected either. Workers such as Nawawi, Verghese, Ho and Faridah are known
for their work on fungi while Fatimah, Phang, Japar and Anton had studied algae, seaweeds, diatoms and seagrasses. However, some of these workers have now either retired or are soon going to attain retirement age and the worrying part is that there are not many younger
workers keen to pursue research in taxonomy and biosystematics, a prerequisite to further studies in ecology, genetics, biotechnology which in turn are prerequisites for rational conservation, management and sustainable utilization of our rich biological resources. With each passing day species are becoming extinct sometimes without us even knowing that they had ever existed. Even in a developed country such as the USA, one third of her plant and animal species are at risk of extinction (McCann, 2000). Hence, taxonomic and biosystematic studies of our plants, animals and microbes whether terrestrial or aquatic, freshwater and marine, should be priority areas. So should studies on their reproductive biology, life cycles, physiology, feeding habits, migration patterns, predators and their sensitivities to environmental changes.
Spinal muscular atrophy (SMA), a leading genetic cause of death in childhood, is caused by deletion of the SMN1 gene, located at chromosome 5q13. The molecular pathogenesis, which results in motor neuron degeneration within the anterior horn of spinal cord, is a focus of debate among scientists. The unique nature of the duplicative 5q chromosomal region provides considerable yet challenging opportunity for disease correction as well as complication in performing molecular diagnosis and understanding the molecular pathogenesis. This article reviewed recent findings in the molecular pathogenesis of SMA as well as the research advances in the molecular diagnosis and therapeutic approaches.
Never in the history of modern Malaysia, the general population at all levels are being threatened by food security. Food becoming less available and more expensive. Many factors, both long- and short-term, have contributed to the shortage. At a global level, available data seems to indicate that we have been consuming more than what we produce. Then came the shortfall in global rice production caused by the impact of climate change such as the widespread drought in India and China in 2002, typhoons in the Philippines in 2006, and the major flooding in Bangladesh in 2007. This was followed by the returns of pests such as planthoppers, and the various virus diseases transmitted particularly at regions with growing seasons having abnormally higher temperatures caused by climate change. Since the crisis started, scientists particularly breeders all over the world were requested to strengthen and upgrade the breeding program and facilities for the development of new varieties with increased tolerance to drought, flooding, and salinity as well resistant to insects and diseases. An important pre-requisite for such activities is the free flow of plant genetic resources for food and agriculture (pgrfa). The adoption of the Convention on Biological Diversity (CBD) has drastically slowed down the movement of many plant genetic resources and this has threatened the future supply of food. The International Treaty on Plant Genetic Resource for Food and Agriculture (ITPGRFA or the Treaty) is a global reaction to the rising tide of measures taken by many governments as a result CBD to extend their sovereign control over genetic resources. Many countries felt that those measures are inappropriate for food and agricultural crop genetic resources. The Treaty on the other hand recognizes that access and benefit sharing for agricultural biodiversity must be treated differently from the way it is generally treated under CBD. This paper discusses some of the key points and provisions from the treaty and some issues arising from its negotiation and future implementation in Malaysia.
Electrophoresis is a crucial step for the studies of proteins, allozymes, DNAs and RNAs. Two commonly used electrophoresis systems are agarose gel and polyacrylmide gel. Agarose gel is frequently used for DNAs and RNAs studies whereas polyacrylmide gel is widely used for the studies of other macromolecules such as proteins, allozymes (isozymes), DNAs and RNAs. The banding patterns of the gels, rather than the numbers of bands appearing on the gels are important for scoring in fingerprinting, footprinting and in population genetic studies.
Targeted therapies for cancer are designed to inhibit speci c cellular changes or signals required for tumour cells to proliferate, survive, promote angiogenesis and metastasize. Examples include trastuzumab (a monoclonal antibody that targets the human epidermal growth factor receptor 2 [HER2]), imatinib ( a small molecule inhibitor of bcl-abr, an oncogenic kinase) and cetuximab ( a monoclonal antibody that binds to the extracellular domain of the epidermal growth factor receptor [EGFR]).
There is a need to set up a germplasm resource centre or gene bank in Sabah to keep the collections of varieties of locally cultivated crops, especially rice. This is necessary to prevent genetic loss caused by the infrastructure development in the state of Sabah especially when Sabah is known for her rich genetic resources for food and agriculture. This gene bank will play an important role in the conservation of genetic resources especially for future rice crop improvement and development. These collections are known to carry useful gene(s) for crop improvement such as aroma, taste, resistance to insect pests and diseases, and tolerance to abiotic stress. Decades ago, a set of local landrace rice collection were made and conserved at International Rice Research Institute (IRRI) and Malaysia Agriculture Research and Development Institute (MARDI). Besides IRRI and MARDI, local farmers also play an important role as conservationist. Therefore, this study has been carried out to re ne the status of the current genetic diversity in local rice farming. From January 2009 to February 2010, 108 samples were collected from Tuaran and Kota Belud districts. Preliminary observation of 19 samples found that
there is a high genetic diversity based on seed morphology alone. Variations in the characteristics were detected in awn, apiculus, lemma and palea, sterile lemma and seed coat. Length and width of seeds were measured and calculated for ratio to estimate the shapes of the seeds. The weight of 100 grains ranged from 1.42 to 3.19 g. However, further studies on morphology evaluation, disease screening, and molecular evaluation are needed to be compared with the existing data. In addition, genetic erosion, migration, and drift also need to be studied due to high seed exchanges among the local farmers.
This paper describes the first reported attempt to isolate DNA sequences containing repeat motifs in Eurycoma longifolia and Orthosiphon stamineus. A library enriched for genomic repeat motifs was developed using novel oligonucleotides designed with inosine residues incorporated at predetermined positions. A total of eight and twelve specific molecular markers were developed for O. stamineus and E. longifolia respectively. These markers have a potential application in estimating population diversity levels and QTL mapping in these two medicinal plants, which are widely used in the Malaysian herbal industry.
The telomere and telomerase hypothesis of aging and cancer is based on the findings that most human tumors have telomerase activity while almost all normal human somatic cells do not. Telomeres are nucleoprotein structure that located 100-300 kb from the end of linear eukaryotic chromosomes (Blackburn et al, 2001; Yoo & Robinson, 2000). Human telomeres consist of thousand repetitive sequences TTAGGG with ranging from 5 to 20 kb (Figure 1) (Martin, 2002). In human cell, there are 92 telomeres which have several functions including protecting chromosome ends, to maintain chromosome stability, serve as an attachment point to the nuclear matrix and also involve in the cell replication.
The Gamma Green House (GGH) is a chronic irradiation facility located at MINT Tech Park, Nuclear Malaysia, Jalan Dengkil. GGH is used for induction of mutation in plants and other biological samples with low dose radiation over period of time depending on the nature and sensitivity of the plant species. Gamma Greenhouse facility at Malaysian Nuclear Agency comprises an open topped
irradiation area consisting of circular green house with 30 meters radius, control room and irradiator with interlock system. The irradiation source is a REVISS RSL6050 double encapsulated 800 Ci 137Cs (half-life 30.1 years for 137Cs) pencils and allowed to be exposed only when the entire 300 m diameter site is free from personnel. The irradiator system is secured by a sophisticated interlock system, which only allows the source to be exposed when all the prerequisite safety conditions are met, and automatically returns the source to the safe
storage position if any safety device is compromised.
Sanger sequencing has been the major method in directly sequencing DNA, and has dominated the DNA sequencing market for nearly past 30 years (Varshney et al., 2009). Along with PCR, we cannot underestimate how important this technology has been to research in various elds of molecular biology. It has revolutionized genetics by allowing us to gain unprecedented insights into the
workings of different organisms.
Orofacial clefts are one of the most common congenital malformations among newborns. The two main types of oral clefts are cleft lip with or without cleft (CLP) and cleft palate alone (CP). Cleft is an abnormal ssure in an anatomical structure that is normally fused. Cleft lip is the congenital failure of the maxillary and medial nasal processes to fuse, forming a ssure in the lip. Cleft palate is the congenital failure of the palate to fuse properly, forming a ssure in the roof of the mouth (Mossey, 2009).clefts are one of the most common congenital malformations among newborns. The two main types of oral clefts are cleft lip with or without cleft (CLP) and cleft palate alone (CP). Cleft is an abnormal ssure in an anatomical structure that is normally fused. Cleft lip is the congenital failure of the maxillary and medial nasal processes to fuse, forming a ssure in the lip. Cleft palate is the congenital failure of the palate to fuse properly, forming a ssure in the roof of the mouth (Mossey, 2009).
The splicing of the pre-mRNA is one of the most essential and one of the several processes that characterized the exponential enrichment of proteomic diversity in higher eukaryotic organisms (Black, 2000, Graveley, 2001). For the splicing process, the introns must be removed and this is accurately carried out by an assembly of spliceosome
Malaysia, with her tropical jungles, mangroves and seas, is blessed with riches in biodiversity, being one of the twelve megabiodiversity countries on earth. Genetics has contributed substantially to the success of our country's agricultural production especially of rubber and palm oil. Hence, it should play a pivotal role in helping Malaysia fulfill her responsibility to identify, characterize and sustainably utilize her numerous indigenous bioresources for the benefit of humanity.
Animal species identification is one of the important fields in forensic science. Unlike human forensics which makes use of DNA fingerprinting techniques to identify individuals of the same species - humans, animal forensic species identification is much more complicated as it involves the ability to identify and distinguish between hundreds to thousands of species when the material evidence is only a trace of animal tissue without the presence of any visual physical morphology. It is even more difficult when the specimen is an unknown and no reference material is available. Animal species identification is not only important for the prevention of wildlife crimes for the purpose of wildlife protection and conservation but it is also becoming more and more significant in food safety issues especially for the meat industry. Owing to the demand and the necessity of providing such services for regulation and enforcement in the context of environmental protection, food safety and biosafety, the Department of Chemistry (DOC)
Malaysia has initiated the use of DNA techniques employing the most widely used genetic markers as part of its scientific solution for animal species identification.
Two isolates of brown root disease fungi were obtained from diseased roots of sentang (Azadirachta excelsa). Morphological characters from macroscopic and microscopic studies suggested that both isolates were from the same genus namely Phellinus noxius and Phellinus sp. Cloning and sequencing of ITS region were conducted to investigate further the variation between the two species at
molecular level. PCR-amplified ITS regions were cloned in pCR2.1 and sequenced. DNA sequences sized 723bp and 710bp were obtained for Phellinus noxius and Phellinus sp respectively. Comparison between the two sequences showed 98% similarity where three nucleotide substitutions and three insertion/deletion regions were found sized 8bp, 2bp and 3bp respectively.