Yahya Mat Arip

Microbiological Quality of Catfish (Clarias Gariepinus) and Tilapia (Tilapia Mossambica) Obtained from Wet Markets and Ponds in Malaysia

The aim of this study was to determine the microbiological quality in catfish (Clarias gariepinus) and tilapia (Tilapia mossambica) obtained from wet markets and ponds in Malaysia. A total of 108 samples (32 catfish, 32 tilapia, and 44 water samples) were obtained from nine wet markets and eight ponds in Penang, Malaysia. The feed in fish ponds were chicken offal, spoiled eggs and commercial fish feed. Using standard procedures, aerobic plate counts (APC), coliform, fecal coliform including E. coli were performed. A total 31/32 of catfish and 31/32 of tilapia exceeded the recommended microbiological standard for the APC. E. coli was less than 3 MPN/g for all catfish and tilapia samples. Temperature and pH of water ponds ranged from 26 to 27.5oC and 6 to 6.8, respectively. Homemade feed using chicken offal and spoiled egg may contribute to the microbiological quality in fish. This highlights the importance of feed in aquaculture system.

Complete Genome Sequence of Proteus mirabilis Phage pPM_01 Isolated from Raw Sewage

Objectives: Phage pPM_01 was previously isolated from a raw sewage treatment facility located in Batu Maung, Penang, Malaysia, and it was highly lytic against Proteus mirabilis, which causes urinary tract infections in humans. In this paper, we characterize the biology and complete genome sequence of the phage. Methods and Results: Transmission electron microscopy revealed phage pPM_01 to be a siphovirus (the first reported virus to infect P. mirabilis), with its complete genome sequence successfully determined. The genome was sequenced using Illumina technology and the reads obtained were assembled using CLC Genomic Workbench v.7.0.3. The whole genome contains a total of 58,546 bp of linear double-stranded DNA with a G+C content of 46.9%. Seventy putative genes were identified and annotated using various bioinformatics tools including RAST, Geneious v.R7, National Center for Biotechnology Information (NCBI) BLAST, and tRNAscan-SE-v1.3 Search. Functional clusters of related potential genes were defined (structural, lytic, packaging, replication, modification, and modulatory). The whole genome sequence showed a low similarity to known phages (i.e., Enterobacter phage Enc34 and Enterobacteria phage Chi). Host range determination and SDS-PAGE analysis were also performed. Conclusions: The inability to lysogenize a host, the absence of endotoxin genes in the annotated genome, and the lytic behavior suggest phage pPM_01 as a possible safe biological candidate to control P. mirabilis infection.

PCR assembly of synthetic human erythropoietin gene

Electronic Journal of Biotechnology ISSN: 0717-3458 Vol.12 No.3, Issue of July 15, 2009

Genome Organization of Escherichia Phage YD-2008.s: A New Entry to Siphoviridae Family

Malaysia is one of the countries that are loaded with mega biodiversity which includes microbial communities. Phages constitute the major component in the microbial communities and yet the numbers of discovered phages are just a minute fraction of its population in the biosphere. Taking into account of a huge numbers of waiting to be discovered phages, a new bacteriophage designated as Escherichia phage YD-2008.s was successfully isolated using Escherichia coli ATCC 11303 as the host. Phage YD-2008.s poses icosahedral head measured at 57nm in diameter with a long non-contractile flexible tail measured at 107nm; proving the phage as one of the members of Siphoviridae family under the order of Caudovirales. Genomic sequence analyses revealed phage YD-2008.s genome as linear dsDNA of 44,613 base pairs with 54.6% G+C content. Sixty-two open reading frames (ORFs) were identified on phage YD-2008.s full genome, using bioinformatics annotation software; Rapid Annotation using Subsystem Technology (RAST). Among the ORFs, twenty-eight of them code for functional proteins. Thirty two are classified as hypothetical proteins and there are two unidentified proteins. Even though majority of the coded putative proteins have high amino acids similarities to phages from the genus Hk578likevirus of the Siphoviridae family, yet phage YD-2008.s stands with its’ own distinctiveness. Therefore, this is another new finding to Siphoviridae family as well as to the growing list of viruses in International Committee on Taxonomy of Viruses (ICTV) database.