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Choy Leong Hew

Publications and source records attributed to Choy Leong Hew.

8 recordsLinked to original sources
PubMed2006

Identification and characterization of NleI, a new non-LEE-encoded effector of enteropathogenic Escherichia coli (EPEC).

Enteropathogenic Escherichia coli (EPEC), a major gastrointestinal pathogen, causes infantile diarrhea in many developing countries. EPEC is an attaching and effacing (A/E) pathogen that utilizes a LEE-encoded type III secretion system (TTSS) to deliver effector proteins into host cells. These effectors have been identified as potential virulence factors in A/E pathogens including EPEC, enterohemorrhagic E. coli (EHEC) and Citrobacter rodentium (CR). We used a proteomics approach to identify a new non-LEE-encoded effector, NleI, from the EPEC sepL and sepD mutants. The nleI gene, located in a prophage-associated island with nleBCD, is also present in EHEC and CR but not in E. coli K-12. In EPEC, the transcription of nleI was increased upon sepD inactivation but remained unaffected in ler and sepL mutants. We demonstrated that NleI is secreted and translocated into HeLa cells in a TTSS-dependent manner and that the CesT chaperone is required for efficient NleI translocation. Nevertheless, under overexpression conditions, the first 20 amino acids of NleI are sufficient to support both secretion and translocation. After translocation, NleI can be detected in the cytoplasmic and membrane of HeLa cells.

Blotting, Western↗
PubMed2006

SPLASH: systematic proteomics laboratory analysis and storage hub.

In the field of proteomics, the increasing difficulty to unify the data format, due to the different platforms/instrumentation and laboratory documentation systems, greatly hinders experimental data verification, exchange, and comparison. Therefore, it is essential to establish standard formats for every necessary aspect of proteomics data. One of the recently published data models is the proteomics experiment data repository [Taylor, C. F., Paton, N. W., Garwood, K. L., Kirby, P. D. et al., Nat. Biotechnol. 2003, 21, 247-254]. Compliant with this format, we developed the systematic proteomics laboratory analysis and storage hub (SPLASH) database system as an informatics infrastructure to support proteomics studies. It consists of three modules and provides proteomics researchers a common platform to store, manage, search, analyze, and exchange their data. (i) Data maintenance includes experimental data entry and update, uploading of experimental results in batch mode, and data exchange in the original PEDRo format. (ii) The data search module provides several means to search the database, to view either the protein information or the differential expression display by clicking on a gel image. (iii) The data mining module contains tools that perform biochemical pathway, statistics-associated gene ontology, and other comparative analyses for all the sample sets to interpret its biological meaning. These features make SPLASH a practical and powerful tool for the proteomics community.

Database Management Systems↗
PubMed2006

Proteomic analysis of protein profiles during early development of the zebrafish, Danio rerio.

In the present study, profiles of protein expression were examined during early development of zebrafish, an increasingly popular experimental model in vertebrate development and human diseases. By 2-DE, an initial increase in protein spots from 6 h post-fertilization (hpf) to 8-10 hpf was observed. There was no dramatic change in protein profiles up to 18 hpf, but significant changes occurred in subsequent stages. Interestingly, 49% of the proteins detected at 6 hpf remained detectable by 1 week of age. To map the protein expression patterns in 2-D gels, MALDI-TOF/TOF MS was employed to identify selected protein spots from early embryos. 108 protein spots were found to match known proteins and they were derived from 55 distinct genes. Interestingly, 11 (20%) of them produced multiple protein isoforms or distinct cleavage products. Although deyolked embryos were used in the analysis, a large number of vitellogenin derivatives remained prominently present in the embryos. Other than these, most of the identified proteins are cytosolic, cytoskeletal and nuclear proteins, which are involved in diversified functions such as metabolism, cytoskeleton, translation, protein degradation, etc. Some of the proteins with interesting temporal expression profiles during development are further discussed.

Animals↗
PubMed2006

Temporal and differential gene expression of Singapore grouper iridovirus.

Singapore grouper iridovirus (SGIV), an iridovirus in the genus Ranavirus, is a major pathogen that results in significant economic losses in grouper aquaculture. To investigate further its infective mechanisms, for the first time, a viral DNA microarray was generated for the SGIV genome to measure the expression of its predicted open reading frames simultaneously in vitro. By using the viral DNA microarray, the temporal gene expression of SGIV was characterized and the DNA microarray data were consistent with the results of real-time RT-PCR studies. Furthermore, different-stage viral genes (i.e. immediate-early, early and late genes) of SGIV were uncovered by combining drug treatments and DNA microarray studies. These results should offer important insights into the replication and pathogenesis of iridoviruses.

Animals↗
PubMed2004

Identification of structural proteins from shrimp white spot syndrome virus (WSSV) by 2DE-MS.

White spot syndrome virus (WSSV) is a major shrimp pathogen that also infects many other species of crustaceans. Its 305-kb double-stranded DNA genome has the capacity to encode 181 presumptive proteins. In an attempt to identify the viral proteins from the 181 theoretical proteins, proteins of the purified WSSV were separated by two-dimensional electrophoresis (2-DE). More than 60 protein spots were revealed, as detected by silver staining, from which 12 viral proteins were identified by mass spectrometry. In total, 25 WSSV proteins, including those reported in one of our earlier studies (Huang et al., Mol Cell Proteomics 2002;1:223-231), were revealed by this proteomic approach, and their corresponding genes were further confirmed by reverse transcription-polymerase chain reaction (RT-PCR). Two of them were characterized to be WSSV envelope proteins using immuno-electron microscopy. Our study showed that the proteomic approach is a powerful method for discovering the viral structural proteins and their corresponding genes.

Animals↗
PubMed2004

Functional genomics analysis of Singapore grouper iridovirus: complete sequence determination and proteomic analysis.

Here we report the complete genome sequence of Singapore grouper iridovirus (SGIV). Sequencing of the random shotgun and restriction endonuclease genomic libraries showed that the entire SGIV genome consists of 140,131 nucleotide bp. One hundred sixty-two open reading frames (ORFs) from the sense and antisense DNA strands, coding for lengths varying from 41 to 1,268 amino acids, were identified. Computer-assisted analyses of the deduced amino acid sequences revealed that 77 of the ORFs exhibited homologies to known virus genes, 23 of which matched functional iridovirus proteins. Forty-two putative conserved domains or signatures were detected in the National Center for Biotechnology Information CD-Search database and PROSITE database. An assortment of enzyme activities involved in DNA replication, transcription, nucleotide metabolism, cell signaling, etc., were identified. Viruses were cultured on a cell line derived from the embryonated egg of the grouper Epinephelus tauvina, isolated, and purified by sucrose gradient ultracentrifugation. The protein extract from the purified virions was analyzed by polyacrylamide gel electrophoresis followed by in-gel digestion of protein bands. Matrix-assisted laser desorption ionization-time of flight mass spectrometry and database searching led to identification of 26 proteins. Twenty of these represented novel or previously unidentified genes, which were further confirmed by reverse transcription-PCR (RT-PCR) and DNA sequencing of their respective RT-PCR products.

Animals↗
PubMed2003

Ice nucleation inhibition: mechanism of antifreeze by antifreeze protein.

The effect of antifreeze protein type III (one type of fish antifreeze protein) on ice crystallization was examined quantitatively based on a "micro-sized ice nucleation" technique. It was found for the first time that antifreeze proteins can inhibit the ice nucleation process by adsorbing onto both the surfaces of ice nuclei and dust particles. This leads to an increase of the ice nucleation barrier and the desolvation kink kinetics barrier, respectively. Based on the latest nucleation model, the increases in the ice nucleation barrier and the kink kinetics barrier were measured. This enables us to quantitatively examine the antifreeze mechanism of antifreeze proteins for the first time.

Antifreeze Proteins↗