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.
DNA microarray technology has permitted large scale parallel analysis of gene expression of several diseases, including cancers. Real-time PCR has become a well-established procedure for
quantifying levels of gene expression. We evaluated Real-Time PCR to validate differentially expressed genes identified by DNA arrays. Gene expression of three different grade of transitional cell carcinoma (TCC) of human bladder cancer was determined using microarray slide containing cancer-related genes. Data obtained were sorted according based on the ratios between Cy3 and Cy5 dyes used and revealed 119, 235 and 183 differentially expressed genes in TCC WHO Grades I, II and III, respectively. Real-time PCR used SYBR Green-1 dye detection to validate relative change in gene expression. Real- Time PCR confirmed the change in gene expression of 17 of 28 (75%) genes identified by microarray. Real-Time PCR also suggest that genes identified by microarray with two or higher fold change cannot be eliminated as false nor be accepted as true without validation. Real-Time PCR based on SYBR Green- 1 is well-suited to validate DNA array results because it is quantitative, rapid and requires less RNA compared to the conventional assays.
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.
Genome Wide Association (GWA) Studies of complex diseases represents a new paradigm in the
post-genomic era. Since then, the eld of human genetics has been revolutionized by the GWA Studies approach (Yang and Hibberd 2009). Adding to this, the completion of human genome sequence had enabled a systemic identi cation of genetic loci that determines
the etiology of complex diseases.
Cancer of the cervix is caused by micro-organisms called Human Papilloma Virus (HPV). This virus is only transmitted to women from their partners/spouses through sexual intercourse. In Malaysia, cancer of the cervix is the second most common cancer among females after breast cancer. The incidence is 21.5 per 100,000 population, with incidence among the Chinese being highest at 33.6 per 100,000 and among Malays the lowest being 12.6 per 100,000. For the past twenty years or so the Annual Reports of Ministry of Health recorded an average of 2500 new cases per year. Cancer of the cervix is preventable. The precursor cancer cells can be easily detected provided the women do regular screening tests called Pap Smear. In nearly all cases this cancer arises from the transformation
zone of the cervix. This is the zone in the cervical mucosa in which the epithelium abruptly changes from hardy squamous epithelium of the ectocervix to the fragile columnar epithelium of the endocervix.
Cervical cancer is the first solid tumour to be shown directly induced by virus. HPV is found in virtually all cervical carcinomas and their precursors.
This study was part of the larger studies to isolate and characterize gene related to flowering in teak. This study isolated differentially expressed genes of teak flowering tissues. One of the genes encodes plant protein kinases highly homologous to the AtSK-II of Arabidopsis GSK3/SHAGGY subfamily. The gene was named as Tectona grandis SHAGGY kinase (Tg-SK). The protein sequence of this gene contained the characteristic catalytic domain of GSK-3/SHAGGY protein kinase. The gene also shows the same genomic organization of 11 introns and 12 exons. Although the size of the introns varies, the positions of exon/intron boundaries are very similar to AtSK-II. The discovery of this gene in teak, which is a forest tree species, supports the hypothesis, which suggested the gene is found in all eukaryotes.
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.
Since the early 1950’s, Singapore is internationally known as the guppy-breeding centre. At least 40 different colour varieties of guppies are cultured in Singapore, with each farm specialising in 10 to 15 varieties. These fancy varieties have been developed by skilful farmers through intensive and continual selective breeding. Genes controlling background body pigmentation such as albino (a), blond (b), gold (g) and blue (r) are autosomally inherited and recessive to their wild-type alleles which produce drab olive-brown background coloration. Colour patterns which are superimposed onto wild-type background coloration are due to genes located on the sex chromosomes. These
sex-linked colour genes are dominant and sex-limited to males as their expression requires male hormones. Y-linked colour pattern genes carried by males are inherited only along the paternal line while X-linked genes are present in both sexes. Among the guppy varieties produced locally, only two Y-linked genes, Ssb and Sst, that control snakeskin tail and body patterns, respectively, have been found in varieties with snakeskin-like reticulations. Single colour genes that are both X- and Y-linked produce red (Rdt), blue (Blt), green (Grt), black (Bt) and variegated (Var) patterns
on the caudal fin. The black caudal-peduncle of the Tuxedo variety is the result of Bcp, a gene that is both X- and Ylinked. Different combinations of colour pattern genes and background pigmentation genes as well as interactions among them give rise to various colour phenotypes. For
instance, the inclusion of Bcp in Snakeskin varieties causes black reticulations on the tail fin to be replaced by large, coarse black spots. Neon coloration is produced by interactions between the Ln (light turquoise) gene with Blt, Rdt and Bcp.
Molecular techniques involving the application of DNA based molecular markers for the conservation and management of endemic and endangered species have assumed significance as
genome sequencing projects have generated an extensive database which can be mined for informative genomic regions. Scientific approaches towards conservation involve several stages, which encompass determination of appropriate genomic regions for characterization, design and testing of specific molecular markers, screening of multiple populations and statistical treatment and
interpretation of data. Population data can be utilized to develop controlled breeding and relocation programs aimed at ensuring that genetic diversity within populations of endangered species is
sustained within the context of an overall conservation program. The information derived as a result of this approach can be applied to establish a scientific and legal framework for the conservation of endemic species. Species specific genomic markers can be applied to enforce the implementation of CITES within the guidelines of a national biodiversity conservation policy.
The Malaysian fish production is about 1.5 million metric tonnes and 86.9% of this comes from the marine sector and 13.1% from the inland sector. This included fish production by capture and culture. (DOF, 2002). Fisheries genetic resources need to have a value in terms of economic, ecological and social uses and they need to characterized. This is the mandate to FAO and it is also necessary for fisheries management and aquaculture development. The vast aquatic diversity that exists in Malaysia consist of numerous taxa of marine and freshwater fishes, crustaceans, mollusks, plants and animals. These figures could be an underestimate to the actual figure. The levels of genetic diversity includes ecosystems, communities, population, genotypes and individual genes. A knowledge of the genetic background of a species and its population structure is essential for its management, breeding and conservation programmes in fisheries. Problems like how to choose the right candidates for breeding, identifiying and monitoring lines, families and individuals, monitoring and control of inbreeding, inheritance of simple traits and genetic improvement through selection for favourable gene and gene combinations can potentially be answered through the use of molecular markers in the management of fisheries genetic resources.
Smaller family size and advancing parental age have increased the demand for prenatal diagnosis.
Prenatal cytogenetic diagnoses currently used, such as amniocentesis and chorionic villus
sampling, are usually not preferred by the expectant couples due to the risk imposed on the mother and child. High false positive rates (5%) of current non-invasive screening methods, such as serum analysts or ultrasound, cause a large number of unnecessary invasive practices to be performed, which apart from the associated risk, place considerable psychological distress on the couples
involved (Wald et al., 1999). (Copied from article).
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).
Telomerase has become important in molecular genetics since its discovery in 1984. The study of telomere in ciliate Tetrahymena thermophilia since 4 decades ago has led to the discovery of telomerase that was discovered by Elizabeth Blackburn and her postgraduate student, Carol Widney Greider in 1984. Later in 2009, Jack William Szostak together with Greider and Blackburn were awarded the Nobel Prize in Physiology or Medicine for their discovery. (Copied from article).
Resistance to anti-HER2 targeted therapy imposes a crucial limitation to the successful treatment of HER2 positive breast cancer. The expression of HER4 and its prognostic value is controversial in breast cancer. The role of HER4 in trastuzumab treatment and resistance in HER2-positive breast cancer has been recently studied. HER4 activation, cleavage and nuclear translocation have been demonstrated mediate trastuzumab resistance in HER2 positive breast cancer. In addition, nuclear HER4 is suggested could be a novel predictive and prognostic biomarker in HER2 positive breast cancer patients. Understanding the role of HER4 may offer useful insights to cancer treatment in HER2-positive breast cancer and other cancers.
The blood of the Painted Storks (Mycteria leucocephala) and the Milky Storks (M. cinerea) from Malaysia were collected
invasively from the breeding site. The blood was dropped on to FTA® cards and stored at room temperature. DNA was isolated from
the FTA® cards through a modification of the Wizard DNA Purification kit (Promega) procedure and PCR was performed with 11 pairs
of microsatellite primers of the American Wood Stork (M. americana). The collection of a drop of blood onto the card is superior to the
usual practice of collecting about five ml of blood into a vacuum tube as it causes fewer traumas to these sensitive birds. Moreover, this
collection procedure can be adopted for use in various wild animal species which are usually found in the remote areas of Malaysia as
the sample collection cards can be transported back to the laboratory at room temperature. Our procedure allows the typing of several
molecular genetic markers from just a drop of blood collected in the field and stored at room temperature alleviating the need for storage
in expensive deep freezers or liquid nitrogen tanks.
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.
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.
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 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.