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Search Results: 1 - 10 of 1079 matches for " ROFINA YASMIN OTHMAN "
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Bioinformatics in molecular immunology laboratories demonstrated: Modeling an anti-CMV scFv antibody
Chua Kek Heng,Rofina Yasmin Othman
Bioinformation , 2006,
Abstract: A scFv (single chain variable fragment) antibody clone from anti-CMV (anti-cucumber mosaic virus) was successfully constructed from immunized mouse and the DNA sequence was submitted to GenBank (AY337618 and AY337619). The expression of a 32 kDa recombinant antibody in bacteria was verified using ELISA (enzyme-linked immunoassay) and western blot. However, elucidation of specific anti-CMV scFv function requires detailed and time consuming immuno-assays. Alternatively, useful functional information on anti-CMV scFV antibody can be obtained using available Bioinformatics tools and techniques without performing tedious assays. Here, we use the commonly used Bioinformatics tools and databases such as BLAST (basic local alignment search tool), GenBank, PDB (protein databank), KABAT numbering, SWISS-MODEL and Insight II to gain specific functional insights into anti-CMV scFv.
In vitro Direct Shoot Organogenesis and Regeneration of Plantlets from Leaf Explants of Sentang (Azadirachta excelsa)
Chin Chiew Foan,Rofina Yasmin Othman
Biotechnology , 2006,
Abstract: A micropropagation protocol for the production of Azadirachta excelsa plantlets was developed through the formation of shoots using leaf cuttings. Leaf cuttings cultured on Murashige and Skoog (MS) medium supplemented with 2 mg L-1 benzylaminopurine (BAP), .2 mg L-1 kinetin and 6 mg L-1 adenine sulphate produced an average of 5 shoot primordias per leaf cutting. Twenty five percent of these shoot primordias formed shoots with true leaves when cultured on MS medium supplemented with 1 mg L-1 BAP and 12.5 mg L-1 magnesium sulphate. One hundred percent of these shoots formed roots when transferred onto medium supplemented with 10 mg L-1 α-naphthaleneacetic acid (NAA).
Development of a Single Chain Variable Fragment Antibody Combinatorial Library Through a Simple Three Fragment Ligation Strategy
Chua Kek Heng,Rofina Yasmin Othman
Journal of Biological Sciences , 2007,
Abstract: A strategy to construct a single chain variable fragment antibody combinatorial library was carried out through three fragment ligation using self-designed primers. Sequence information of antibody variable heavy and light fragments was used to design 2 sets of primers with the appropriate restriction endonuclease sites to facilitate the clone construction. This alternative approach allows construction of single chain variable fragment (scFv) phage display library through a simple three-fragment ligation process and allows inclusion of any desired detection marker at the same time.
CHARACTERIZATION OF MALAYSIAN WILD BANANAS BASED ON ANTHOCYANINS
MUHAMMAD ASIF JAVED,MAK . CHAI,ROFINA YASMIN OTHMAN
BIOTROPIA : the Southeast Asian Journal of Tropical Biology , 2001,
Abstract: The male buds of 16 Musa species (Musaceae) populations were investigated by HPLC for the occurrence of anthocyanins. The investigation was based on the presence of 6 anthocyanins. The 16 Musa samples could be classified into three distinct species i.e. Musa acuminata, Musa violascens and Musa balbisiana. Musa acuminata could be divided into two subspecies : malaccensis (lowland) and tmncata (highland) according to their constituents and content of major anthocyanins. No variation was observed in the composition of the anthocyanins of Kedah type ssp. siamea and Selangor types ssp. malaccensis. The classification of M. acuminata into two subspecies based on anthocyanin data further supported the current taxonomic grouping of the species.
MORPHOLOGICAL CHARACTERIZATION OF MALAYSIAN WILD BANANA MUSA ACUMINATA
MUHAMMAD ASIF JAVED,MAK CHAI,ROFINA YASMIN OTHMAN
BIOTROPIA : the Southeast Asian Journal of Tropical Biology , 2002,
Abstract: Fourteen populations of Musa acuminata ranging from populations in the lowlands of northern (ssp. siamea) to central Malaysian region (ssp. malaccensis) and highland banana (ssp. truncata) were characterized based on chromosome number and 46 morphological characters. A large amount of variation was observed within the populations. However, only highland bananas appeared morphologically distinct. Lowland populations both from northern and central Malaysia were found to be overlapping and no distinguishing pattern was observed. The morphological characters found variable within these populations were related to developmental changes and mutations. The results ob tained in this study were not revolutionary. However, the survey of a large number of characters treated with multivariate techniques further sharpened the existing groupings of the Musa acuminata subspecies.
PLOJDY ANALYSIS AND DNA CONTENT OF MUTANT BANANA
ABDELGADIR RAYIS SHADIA,ROFINA YASMIN OTHMAN,MAK CHAI
BIOTROPIA : the Southeast Asian Journal of Tropical Biology , 2002,
Abstract: Mutagens cause random changes in the nuclear DNA or cytoplasmic organelles, resulting in gene, chromosomal or genomic mutations and hence, create variability. In this study, flow cytometry (FCM) was used to determine ploidy levels and DNA content in gamma-irradiated variants of mutated Pisang Berangan (cv. Intan, AAA) - a local banana genotype. Induced variants such as shor t plant stature (stunted growth), late flowering plants (late maturity) and abnormalities in bunch characters were selected to stud y possible changes at the DNA level. The study showed that DNA content of mutated plants differed from non-irradiated control and that irradiation had the most effect at high doses (40 and 60 Gy). The increase of DNA content in 20 Gy and 30 Gy treated plants was not more than that of the control plants. The values of genomic DNA content of gamma-irra diation variants decreased as the dose of irradiation increased from 20 to 60 Gy, indicating that the high dose of gamma-irradiation had a significant effect on the genome of the plants. The analysis further showed that phenotypic variation due to mutagenesis was reflected in the DNA content of the plants. The results also showed that ploidy levels were not affected by gamma-irradiation even at high doses.
Virus-Specific Read-Through Codon Preference Affects Infectivity of Chimeric Cucumber Green Mottle Mosaic Viruses Displaying a Dengue Virus Epitope
Pak-Guan Teoh,Aik-Seng Ooi,Sazaly AbuBakar,Rofina Yasmin Othman
Journal of Biomedicine and Biotechnology , 2009, DOI: 10.1155/2009/781712
Abstract: A Cucumber green mottle mosaic virus (CGMMV) was used to present a truncated dengue virus type 2 envelope (E) protein binding region from amino acids 379 to 423 (EB4). The EB4 gene was inserted at the terminal end of the CGMMV coat protein (CP) open reading frame (ORF). Read-through sequences of TMV or CGMMV, CAA-UAG-CAA-UUA, or AAA-UAG-CAA-UUA were, respectively, inserted in between the CP and the EB4 genes. The chimeric clones, pRT, pRG, and pCG
Direct Cloning Approach for Expression of an Anti-cucumber Mosaic Virus Single-chain Variable Fragment in Plant
Chua Kek Heng,Norzulaani Khalid,Jennifer A. Harikrishna,Rofina Yasmin Othman
Biotechnology , 2005,
Abstract: An anti Cucumber Mosaic Virus (anti-CMV) single chain variable fragment (scFv) was constructed into a plant expression vector using self-designed primers. Initially, sequence information of the scFv was obtained through automated sequencing. Based on the sequence information, two primers with appropriate restriction endonuclease sites were designed to facilitate the clone construction. This technique allows insertion of the desired gene to replace the GUS second exon in pCAMBIA 1301, without the need to form a complete cassette including promoter and termination signal prior to cloning into the vector. After insertion of the construct into the plant system through Agroinfection, the foreign protein, anti-CMV scFv antibody was expressed in tobacco plants.
Biopanning for Banana streak virus Binding Peptide by Phage Display Peptide Library
Chua Kek Heng,Suzita Mohd Noor,Tan Siok Yee,Rofina Yasmin Othman
Journal of Biological Sciences , 2007,
Abstract: Banana streak virus (BSV) is a plant virus that can potentially cause serious problems for banana cultivation, compounded by difficulties in properly diagnosing the infection and identifying the virus itself. In this study, we identified a peptide that can bind to BSV and potentially be developed as a cost effective detection reagent. To select a binding peptide against BSV, biopanning by way of utilising the phage display peptide library was the method used. Three rounds of biopanning successfully yielded a peptide, VVVGSLVVARLR., that bound selectively to BSV.
In-Depth Tanscriptomic Analysis on Giant Freshwater Prawns
Maizatul Izzah Mohd-Shamsudin, Yi Kang, Zhao Lili, Tian Tian Tan, Qi Bin Kwong, Hang Liu, Guojie Zhang, Rofina Yasmin Othman, Subha Bhassu
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0060839
Abstract: Gene discovery in the Malaysian giant freshwater prawn (Macrobrachium rosenbergii) has been limited to small scale data collection, despite great interest in various research fields related to the commercial significance of this species. Next generation sequencing technologies that have been developed recently and enabled whole transcriptome sequencing (RNA-seq), have allowed generation of large scale functional genomics data sets in a shorter time than was previously possible. Using this technology, transcriptome sequencing of three tissue types: hepatopancreas, gill and muscle, has been undertaken to generate functional genomics data for M. rosenbergii at a massive scale. De novo assembly of 75-bp paired end Ilumina reads has generated 102,230 unigenes. Sequence homology search and in silico prediction have identified known and novel protein coding candidate genes (~24%), non-coding RNA, and repetitive elements in the transcriptome. Potential markers consisting of simple sequence repeats associated with known protein coding genes have been successfully identified. Using KEGG pathway enrichment, differentially expressed genes in different tissues were systematically represented. The functions of gill and hepatopancreas in the context of neuroactive regulation, metabolism, reproduction, environmental stress and disease responses are described and support relevant experimental studies conducted previously in M. rosenbergii and other crustaceans. This large scale gene discovery represents the most extensive transcriptome data for freshwater prawn. Comparison with model organisms has paved the path to address the possible conserved biological entities shared between vertebrates and crustaceans. The functional genomics resources generated from this study provide the basis for constructing hypotheses for future molecular research in the freshwater shrimp.
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