Complete mitochondrial genome of six Cheilinusundulatus (Napoleon Wrasse): an endangeredmarine fish species from Sabah, Malaysia

We report here the complete mitochondrial (mt) genomes of six individuals of Cheilinus undulatus (Napoleon Wrasse), an endangered marine fish species. The six mt DNA sequences had an average size of 17,000 kb and encoded 22 tRNA, two sRNA, 13 highly conserved protein coding genes and a control region. The polymorphic variation (control region) in these six individuals suggests their potential use as a specific marker for phylogeographic conservation. Moreover, the sequence polymorphism within the control region (D-loop) suggests that this locus can be applied for phylogenetic studies

Genotyping of Salmonella spp. on the basis of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)

Aims: The CRISPR locus in Salmonella genome is comprised of three main components which are the (CRISPR-associated) cas genes, an AT-rich leader sequence and the CRISPR array. The length of CRISPR array is determined by the number of spacers within it and varies not only among different organisms but also varies among the bacterial serotypes and strains. This present study aimed at determining if the CRISPR array in Salmonella spp. could be applied to establish a correlation between serogroup type and the fingerprint generated by CRISPR typing. Methodology and results: A total of 30 Salmonella samples were obtained from the Veterinary Diagnostic Laboratory, Kota Kinabalu, Sabah. Salmonella serogroup was determined using the slide agglutination test. Four different serogroups were identified which were serogroup B, C, D, and E. Deoxyribonucleic acid (DNA) was extracted and polymerase chain reaction (PCR) was performed using primers which were designed to amplify the CRISPR array in Salmonella genome. Our results indicate that there is a positive correlation between serogroup results obtained using slide agglutination test and the profile generated by CRISPR typing. Conclusion, significance and impact of study: CRISPR typing has the potential to be applied for the genotyping of Salmonella bacteria

Amalan kualiti MOOC Malaysia

Dasar e-Pembelajaran Negara (DePAN) untuk Pengajian Tinggi Awam dan Swasta (IPTA & IPTS) telah dilancarkan pada 16 April 2011 oleh YAB Menteri Pengajian Tinggi. Dasar ini dibangunkan khusus untuk menyokong Pelan Strategik Pendidikan Tinggi Negara (PSPTN) untuk menyediakan satu kerangka e-Pembelajaran berkualiti bertujuan membangunkan modal insan bertaraf dunia melalui penggunaan teknologi maklumat dan komunikasi. DePAN mempunyai lima tunggak iaitu Infrastruktur, Struktur Organisasi, Kurikulum dan e- Kandungan, Perkembangan Profesional dan Pembudayaan. Setiap tunggak ini pula mempunyai bidang fokus dan juga aktiviti yang perlu dilaksanakan mengikut tiga fasa pelaksanaan, iaitu Fasa Awal (2011-2012), Fasa Pelaksanaan (2013 - 2014) dan Fasa Matang (2015)

Genetic Identification and Mass Propagation of Economically Important Seaweeds

Seaweeds are a primary source of hydrocolloids, which can be processed into various food additives, cosmetics, and pharmaceuticals. The inability of current commercial seaweed farming projects to meet industrial demands is underscored by a plethora of challenges, which include the lack of high-quality germplasm with the desired cultural characteristics. This chapter describes the current trends in commercial seaweed production and the potential technological advances in production methods and genetic selection strategies, which can be applied to raise the productivity of seaweed farms. Molecular markers have become increasingly relevant to the selection of a diverse range of wild varieties for domestication, and this augurs well for strain identification. The development of high-density linkage maps based on molecular markers offers an avenue for the implementation of molecular breeding strategies based on quantitative trait loci (QTLs). Concurrently, productivity of existing varieties can be enhanced by the analysis of exogenous factors known to affect the growth and survival of tissue-cultured seedlings. The application of photobioreactors for tissue culture is another important development, which will be digressed upon. In addition to this, quality control which focuses on the comparison of chemical and physical qualities of the tissue-cultured and conventional cultivated seaweeds will become increasingly relevant to the development of industry standards for sustainable seaweed production to fulfill the increasing demands of seaweed-related industries

Quantitative real-time PCR for determination of Transgene in Callus of Jatropha curcas

Jatropha curcas is an important plant belonging to the family Euphorbiaceae which is a potential candidate for biofuel production. Genetic transformation protocol for J. curcas callus mediated by Agrobacterium tumefaciens were optimized using a pCAMBIA1303 plasmid which carries green fluorescent protein (GFP) gene as a reporter. Results obtained were based on the highest percentage of GFP expression which was observed three days post-transformation. Immersion of callus into 1×105 cfu ml-1 (OD600nm 0.6) of A. tumefaciens LBA4404 with addition of 300 µM of acetosyringone for 45 min, two days of pre-culture and three days of co-cultivation periods were determined to be ideal for J. curcas callus transformation. Putative transformants were selected in the presence of 25 mg/l hygromycin. Surviving calli were transferred into proliferation media (MS with 1 mg/l NAA and 1 mg/l BAP) to proliferate the callus for further molecular analyses and to confirm the presence of the target GFP transgene in the putative transformants. Polymerase chain reaction (PCR) was carried out using a 35S specific primer pair confirmed the presence of the 454 bp of 35S promoter region from the transformed callus. Quantitative real-time PCR (qRT-PCR) was carried out to demonstrate the integration and copy number of the 35S promoter in the putative tranformants. The 35S promoter gene (178 bp) as a target gene and J. curcas actin gene (179 bp) which functions as reference gene was designed to detect the positive transformants and control sample in real-time PCR reaction analysis. The results indicated that the actin specific PCR product was present in both the control and transformed calli, however the 35S PCR product was found only in the positive transformants. The similarity in CT values confirmed that both the genes were present as single copy thus confirming a single integration event

Characterization of the pscC (Type III secretion) gene of Pseudomonas aeruginosa (PA01) and assessment of immunogenicity of pscC protein in rats

Proteins associated with the bacterial membrane can be recruited for application as antigens for the development of vaccines. This preliminary study was directed towards evaluating the antigenic properties of the Pseudomonas aeruginosa (PA01) pscC protein which is a component of the Type III secretion system. Gene specific primers were designed to isolate the pscC gene which was isolated, ligated onto the multiple cloning site of vector pGS21(a), cloned and expressed in Escherichia coli (BL21). The molecular weight of the expressed pscC protein was determined by SDS-PAGE (10% sodium dodecyl sulphate-polyacrylamide gel electrophoresis) and was found to be around 57 KDa and purified by the size exclusion chromatography. Finally, the purified pscC protein was injected subcutaneously into adult Sprague Dawley rats with a range of concentrations (50, 100 and 150 microgram per rat) respectively. Recombinant pscC antigen induced a specific humoral immune response against the antigen, which was validated by Enzyme-linked immunosorbent assay (ELISA). The results concluded that anti-pscC antibody was elicited in the animal model

Gene expression in the biosynthesis of Paralytic Shellfish Poisoning (PSP) toxins in dinoflagellates: a mini review

Some dinoflagellates are known to synthesize saxitoxin (STX), a potent neurotoxin that causes severe paralytic shellfish poisoning (PSP). In addition, several freshwater species of cyanobacteria also synthesize the same toxin with the same biosynthetic pathway and genes responsible. This review focuses on the gene expression involved in the biosynthesis pathway of PSP toxins in dinoflagellates. The expression of the PSP biosynthetic genes have been identified in certain cyanobacteria and the dinoflagellate Alexandrium sp. with eight genes involved viz. sxtA, sxtB, sxtD, sxtG, sxtH/T, sxtI, sxtS and sxtU. sxtA, a unique starting gene, and sxtG, the second “core” gene appearing in the biosynthesis of PSP toxins are found in both cyanobacteria and Alexandrium sp. Three theories have been proposed to explain the origin of PSP toxin in dinoflagellates: I) the genes are produced by bacteria associated with the dinoflagellates, II) independent evolution III) horizontal gene transfer between cyanobacteria and dinoflagellates. Useful information regarding the expression and function of genes involved in the STX biosynthesis pathway provides an understanding of toxin production and possible mitigation and public health management of STX poisoning

A metagenomic study of bacterial communities associated with the saxitoxin producing dinoflagellate, Pyrodinium bahamense var. Compressum

Aim: A number of reports have implicated the role of the symbiotic bacterial communities associated with toxic dinoflagellates in the biosynthesis of saxitoxin during harmful algal blooms (HABs). However, the exact mechanisms by which the bacteria facilitate toxin production remain inconclusive. The toxic dinoflagellate, Pyrodinium bahamense var. compressum, is the causative organism responsible for paralytic shellfish poisoning in the coastal waters of Sabah, and it is caused by the consumption of filter-feeding shellfish contaminated with the neurotoxin, saxitoxin. The present study aimed at characterizing the species diversity of symbiotic bacteria occurring within a monoalgal culture of P. bahamense var. compressum. Methodology and results: The total bacterial DNA was amplified using paired-end 16S community sequencing on the Illumina platform, targeting the V3–V4 region of the 16S ribosomal RNA gene. Bacteria were classified into 20 classes, 43 orders, 60 families, and 105 genera. A total of 10 phyla were present, where the major phylum was Proteobacteria (69.5%). The major genera were Pseudoruegeria (32%), Roseibium (16%), Hyphomonas (16%), Phaeobacter (7%), Lutimaribacter (5%) and Methylophaga (5%). This study showed that the previous method of assessing microbial diversity occurring in P. bahamense var. compressum has underestimated the actual species diversity. Conclusion, significance and impact of study: The high-throughput sequencing of the 16S metagenomes revealed hitherto unreported bacterial taxa associated with P. bahamense var. compressum. The findings of the present work will pave the way for further studies aimed at isolating and characterizing symbiotic bacteria that are likely to be associated with the biosynthesis of toxins

Inhibition and Substrate Specificity Properties of FKBP22 from a Psychrotrophic Bacterium, Shewanella sp. SIB1

SIB1 FKBP22 is a peptidyl prolyl cis–trans isomerase (PPIase) member from a psychrotrophic bacterium, Shewanella sp. SIB1, consisting of N- and C-domains responsible for dimerization and catalytic PPIase activity, respectively. This protein was assumed to be involved in cold adaptation of SIB1 cells through its dual activity of PPIase activity and chaperone like function. Nevertheless, the catalytic inhibition by FK506 and its substrate specificity remain unknown. Besides, ability of SIB1 FKBP22 to inhibit phosphatase activity of calcinuerin is also interesting to be studied since it may reflect wider cellular functions of SIB1 FKBP22. In this study, we found that wild type (WT) SIB1 FKBP22 bound to FK506 with IC50 of 77.55 nM. This value is comparable to that of monomeric mutants (NNC-FKBP22, C-domain+ and V37R/L41R mutants), yet significantly higher than that of active site mutant (R142A). In addition, WT SIB1 FKBP22 and monomeric variants were found to prefer hydrophobic residues preceding proline. Meanwhile, R142A mutant has wider preferences on bulkier hydrophobic residues due to increasing hydrophobicity and binding pocket space. Surprisingly, in the absence of FK506, SIB1 FKBP22 and its variants inhibited, with the exception of N-domain, calcineurin phosphatase activity, albeit low. The inhibition of SIB1 FKBP22 by FK506 is dramatically increased in the presence of FK506. Altogether, we proposed that local structure at substrate binding pocket of C-domain plays crucial role for the binding of FK506 and peptide substrate preferences. In addition, C-domain is essential for inhibition, while dimerization state is important for optimum inhibition through efficient binding to calcineurin