Suhaimi Napis

Influence of silver nitrate (ethylene inhibitor) on cucumber in vitro shoot regeneration

The effect of addition of silver nitrate (AgNO3) on organogenesis of proximal and distal cotyledon and hypocotyl explants of five cucumber (Cucumis sativus L.) cultivars was investigated. Distal cotyledon and hypocotyl were unresponsive while only poor shoot regeneration was observed in proximal cotyledon and hypocotyl explants of all cucumber cultivars. The addition of different concentrations of AgNO3 (10, 30 and 50 µM) to the medium, however, induced shoot regeneration in distal cotyledon except Suyo Long cultivar and effectively increased shoot regeneration response as well as the number of shoots per explant in proximal cotyledon and hypocotyl of all cucumber cultivars.

Overexpression of monodehydroascorbate reductase from a mangrove plant (AeMDHAR) confers salt tolerance on rice.

Monodehydroascorbate reductase (MDHAR), an important enzyme of the ascorbate-glutathione cycle, is involved in salt tolerance of plants through scavenging of reactive oxygen species (ROS). In this study, a cDNA encoding MDHAR from the mangrove plant Acanthus ebracteatus was introduced into rice to examine its role in salt tolerance. Three stable transgenic lines (MT22, MT24 and MT25) overexpressing AeMDHAR were selected in vitro using hygromycin and confirmed by PCR, quantitative reverse-transcription (qRT) PCR and enzyme assay. The transgenic line MT24 was predicted to possess a single copy of the transgene while the other two transgenic lines were predicted to have multiple transgene integrations. The AeMDHAR transcripts were detected only in transgenic rice lines but not in untransformed rice. The abundance of AeMDHAR transcripts in transgenic lines MT22 and MT25 was approximately 2.75 times the amount found in MT24. The transgenic rice lines overexpressing AeMDHAR showed a significant increase in MDHAR enzyme activity compared to untransformed plants under both NaCl and control conditions. All transgenic lines showed better yield attributes such as a higher tiller number and increased 1000-grain weight compared to non-transgenics. They also showed tolerance to salt at germination and seedling stages. The transgenic line MT24, which harbors a single copy of AeMDHAR, displayed a lower rate of sterility, a higher number of tillers and longer panicle compared to untransformed plants when subjected to salt stress.

Bio-Mirror project for public bio-data distribution

Timely worldwide distribution of biosequence and bioinformatics data depends on high performance networking and advances in Internet transport methods. The Bio-Mirror project focuses on providing up-to-date distribution of this rapidly growing and changing data. It offers FTP, Web and Rsync access to many high-volume databanks from several sites around the world. Experiments with data grids and other methods offer future improvements in biology data distribution.

Studies on the genetic variation of the green unicellular alga Haematococcus pluvialis (Chlorophyceae) obtained from different geographical locations using ISSR and RAPD molecular marker.

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.

Bioinformatics in Malaysia: Hope, Initiative, Effort, Reality, and Challenges

The published articles in PLoS Computational Biology on the development of computational biology research in Mexico, Brazil, Cuba, Costa Rica, and Thailand have inspired us to report on the development of bioinformatics activities in Malaysia. Rapid progress in molecular biology research and biotechnology in Malaysia has created sufficient demand for bioinformatics in Malaysia. Although bioinformatics in Malaysia started in the early 1990s, the initial focus on the development of the biotechnology industry has curtailed the early gains and overshadowed the systematic development of bioinformatics in Malaysia, which currently lacks in human capital development, research, and commercialization. However, government initiatives have been devised to develop the necessary national bioinformatics network and human resource development programs and to provide the necessary infrastructure, connectivity, and resources for bioinformatics. Stakeholders are experiencing reorientation and consolidating existing strengths to align with the global trends in bioinformatics. This exercise is expected to reinvigorate the bioinformatics industry in Malaysia. Tapping into niche expertise and resources such as biodiversity and coupling it with the existing biotechnology infrastructure will help to create sustainable development momentum for the future. An initiative arose from several senior scientists across local universities in Malaysia to promote this new scientific discipline in the country.

Sequence Analysis and Potentials of the Native RbcS Promoter in the Development of an Alternative Eukaryotic Expression System Using Green Microalga Ankistrodesmus convolutus

The availability of highly active homologous promoters is critical in the development of a transformation system and improvement of the transformation efficiency. To facilitate transformation of green microalga Ankistrodesmus convolutus which is considered as a potential candidate for many biotechnological applications, a highly-expressed native promoter sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (AcRbcS) has been used to drive the expression of β-glucuronidase (gusA) gene in this microalga. Besides the determination of the transcription start site by 5′-RACE, sequence analysis revealed that AcRbcS promoter contained consensus TATA-box and several putative cis-acting elements, including some representative light-regulatory elements (e.g., G-box, Sp1 motif and SORLIP2), which confer light responsiveness in plants, and several potential conserved motifs (e.g., CAGAC-motif, YCCYTGG-motifs and CACCACA-motif), which may be involved in light responsiveness of RbcS gene in green microalgae. Using AcRbcS promoter::gusA translational fusion, it was demonstrated that this promoter could function as a light-regulated promoter in transgenic A. convolutus, which suggested that the isolated AcRbcS promoter was a full and active promoter sequence that contained all cis-elements required for developmental and light-mediated control of gene expression, and this promoter can be used to drive the expression of heterologous genes in A. convolutus. This achievement therefore advances the development of A. convolutus as an alternative expression system for the production of recombinant proteins. This is the first report on development of gene manipulation system for unicellular green alga A. convolutus.

A Novel Transcript of Oil Palm (Elaeis guineensis Jacq.), Eg707, is Specifically Upregulated in Tissues Related to Totipotency

In this study, we report the molecular characterization of clone Eg707 isolated from cell suspension culture of the oil palm. The deduced polypeptide of clone Eg707 is highly similar to an unknown protein from Arabidopsis thaliana. The presence of an Ald-Xan-dh-C2 superfamily domain in the deduced protein sequence suggested that Eg707 protein might be involved in abscisic acid biosynthesis. Eg707 might be present as a single copy gene in the oil palm genome. This gene is highly expressed in tissue cultured materials compared to vegetative and reproductive tissues, suggesting a role of this gene during oil palm somatic embryogenesis or at the early stages of embryo development. Expression analysis of Eg707 by RNA in situ hybridization showed that Eg707 transcripts were present throughout somatic embryo development starting from proembryo formation at the embryogenic callus stages till the maturing embryo stages. Since proembryo formation within the embryogenic callus is one of the first key factors in oil palm somatic embryo development, it is suggested that Eg707 could be used as a reliable molecular marker for detecting early stage of oil palm somatic embryogenesis.

Efficiency of ligation-mediated PCR and TAIL-PCR methods for isolation of RbcS promoter sequences from green microalga Ankistrodesmus convolutus

Isolation of promoter sequences from known gene sequences is a tedious task in genome-related research. An efficient method of obtaining the promoter sequences is necessary in order to successfully use targeted promoters for genetic manipulations. Here, efficiency and usefulness of two PCR-based methods, namely: ligation-mediated PCR and thermal asymmetric interlaced (TAIL) PCR, for isolation of promoter sequences of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (RbcS) gene from green microalga Ankistrodesmus convolutus (A. convolutus) were evaluated. The results showed that the amplification efficiency of TAIL-PCR was higher than that of the ligation-mediated PCR method, i.e. the amplified promoter fragments of 1.2 and 0.8 kb in length or promoter sequences of 813 and 606 bp (after eliminating the unreadable sequences). The use of TAIL-PCR described here presents a low cost and efficient strategy for the isolation of promoter sequences of known genes, especially in GC-rich regions, and species with little or no available genome information such as A. convolutus.

Improvement of digital mammogram images using histogram equalization, histogram stretching and median filter

Breast cancer is one of the most important diseases in females worldwide. According to the Malaysian Oncological Society, about 4% of women who are 40 years old and above are involved have breast cancer. Masses and microcalcifications are two important signs of breast cancer diagnosis on mammography. Enhancement techniques, i.e. histogram equalization, histogram stretching and median filters, were used to provide better visualization for radiologists in order to help early detection of breast abnormalities. In this research 60 digital mammogram images which includes 20 normal and 40 confirmed diagnosed cancerous cases were selected and manipulated using the mentioned techniques. The original and manipulated images were scored by three expert radiologists. Results showed that the selected methods have a positive significant effect on image quality.

Knowledge Management system architecture in agricultural industries environment

Knowledge Management (KM) has emerged as the hottest topic in the entire global world of business. Its contributions toward the successful of the organizations are currently been proved and saluted. The power of KM as a system is no longer possesses any limitations. In fact, many KM system practitioners have claimed it as the most desired and demanded energizer to the organizations today, as the role it plays is absolutely important. The role of KM system could be determined by looking on technicalities issues, challenges and opportunities of how to make sure that the right knowledge could be disseminated to the right people at the right time for any purposes. Besides that, KM also could be looked on how the processes involved in gathering and storing the knowledge in the proper placing and formating it as well to be able to access or use when it is needed. While, the agriculture-based industries environment which deal with business of plantation, forestries, and animals, including soil cultivation, crop and livestock management as well as many other activities which have a lot of potential to promote knowledge sharing among its community of practice (CoP) in term of best practice and lesson learnt. This paper analyzes the concept and the system architecture of KM in the agriculture-based industries and discusses various aspects in terms of its technicalities of KM system (KMS) as well as issues, challenges and opportunities involved in this field that will help CoP to increase their productivity and quality as well as to gain return on investment (ROI).