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PubMedDate not supplied

Bioinformatics and food allergens.

Bioinformatics can play an important role in developing improved technology for the detection and characterization of food allergens. However, the full realization of this potential will depend on the development of allergen-specific databases as well as improved methods for data mining within these databases. Examples of existing allergen databases and analysis tools are described, as are the most important issues that need to be addressed in the next stage of database development.

Allergens↗

PubMed2005

Selection of choriocarcinoma-associated genes using bioinformatics.

OBJECTIVE: To analyze the data of gene expression profiles of choriocarcinoma and screen for choriocarcinoma- related genes. METHODS: Human cDNA expression microarray containing 4 096 genes was used to study the gene expression profiles in specimens of complete hydatidiform moles (n=3) and choriocarcinomas (n=3), with normal placental villi serving as the control group. The candidate genes with similar expression profiles were identified by hierarchical cluster analysis, and their expressions in normal and neoplastic tissues analyzed by electronic Northern analysis and other bioinformatics methods. Three selected genes were analyzed by beta-actin semiquantitative reverse transcriptase-PCR to confirm the data. RESULTS: A total of 52 coexpressed candidate genes were identified from the gene expression data derived from the choriocarcinoma specimens, of which 19 genes were selected as choriocarcinoma-related genes by further cluster analysis, such as dynamin (L07807), katanin p60 (AF056022), zinc finger protein ZNF184 (U6656), calmodulin (U12022), carboxypeptidase M (BC022276), calcineurin-binding protein cabin 1 (NM_012295) and transducin-like enhancer protein TLE1(M99435). CONCLUSION: The identification of choriocarcinoma-related genes by cluster analysis provides new clues for seeking the key genes associated with the progression and metastasis of choriocarcinoma.

Choriocarcinoma↗

PubMed2004

Public sphere and the sustainability of the bioinformatics promise.

The literature about genomics and bioinformatics achievements in high-impact journals such as Nature and Science has raised disproportionate expectations amongst the general public about fast and revolutionary drugs and breakthroughs in biomedicine. However, the yield obtained by database mining activities has been modest, as reported in the February 2001 issues of these journals featuring the completion of human genome draft sequences by the Human Genome Project Consortium and the company Celera. I have compared changes in rethoric employed by molecular biologists in 2001 and in April 2003, when the final sequence was announced. The comparison suggests that researchers are concerned about the sustainability of society's investment in this field, though not explicitly.

Bibliometrics↗

PubMed2004

Architecture of a grid-enabled research platform with location-transparency for bioinformatics.

The recent advance in information technologies has bought about the borderlessness in every field of both science and business. The borderlessness has increasingly made activities in interdisciplinary field more important. This current situation produces a strong demand that people want to establish a virtual group, organization and society for their business and scientific purposes irrespective of the actual structure formed by organizations. Remarkably, bio sciences require a research platform that satisfies such demand for further development. In this paper, we present a research platform for bioinformatics in detail. The prominent feature of the research platform is the use of Grid and its location transparency, which means that bio scientists and researchers are able to utilize a large amount of computational power for their analysis and to access data of their interest without being aware of where data and computational resources are located. The usefulness and feasibility of the architecture of the research platform is shown as well as future issues to achieve toward the final goal of our research in this paper.

Biomedical Research↗

PubMed2004

Genetics and bioinformatics of primary open angle glaucoma: an Indian perspective.

Glaucoma is the second largest blinding disorder, after cataract, affecting about 67 million people worldwide. In India about 1.5 million people are blind due to glaucoma. Primary open angle glaucoma is the major sub-type of glaucoma affecting all ages and is genetically complex. Myocilin and optineurin are two different genes that have been implicated for primary open angle glaucoma. This review is focused on the studies being conducted in India on primary open angle glaucoma to identify the molecular defects and new directions undertaken using bioinformatic approaches towards a better understanding of the disease.

Blindness↗

PubMed2005

ProGenGrid: a grid-enabled platform for bioinformatics.

In this paper we describe the ProGenGrid (Proteomics and Genomics Grid) system, developed at the CACT/ISUFI of the University of Lecce which aims at providing a virtual laboratory where e-scientists can simulate biological experiments, composing existing analysis and visualization tools, monitoring their execution, storing the intermediate and final output and finally, if needed, saving the model of the experiment for updating or reproducing it. The tools that we are considering are software components wrapped as Web Services and composed through a workflow. Since bioinformatics applications need to use high performance machines or a high number of workstations to reduce the computational time, we are exploiting a Grid infrastructure for interconnecting wide-spread tools and hardware resources. As an example, we are considering some algorithms and tools needed for drug design, providing them as services, through easy to use interfaces such as the Web and Web service interfaces built using the open source gSOAP Toolkit, whereas as Grid middleware we are using the Globus Toolkit 3.2, exploiting some protocols such as GSI and GridFTP.

Computational Biology↗

PubMed2004

[Sequencing and bioinformatic analysis of NRDRiso cDNA].

This study describes the cDNA sequencing and the bioinformatic analysis of a novel NADP(H)-dependent retinol dehydrogenase/reductases isoform (NRDRiso). Based upon the concensus sequences of human and mouse NRDR coding region, we have identified a short 377 bp RT-PCR product from human liver tissue. The cDNA sequence of a NRDR isoform was then isolated using RACE approach and its sequence was analysed. The full-length cDNA is 1,003bp in length and was submitted to GenBank as NADP-dependent retinol dehydrogenase/reductase short isoform (NRDRiso). The open reading frames of NRDRiso cDNA is 525 bp.

Alcohol Oxidoreductases↗

PubMed2005

Bioinformatics visualization and integration with open standards: the Bluejay genomic browser.

We have created a new Java-based integrated computational environment for the exploration of genomic data, called Bluejay. The system is capable of using almost any XML file related to genomic data. Non-XML data sources can be accessed via a proxy server. Bluejay has several features, which are new to Bioinformatics, including an unlimited semantic zoom capability, coupled with Scalable Vector Graphics (SVG) outputs; an implementation of the XLink standard, which features access to MAGPIE Genecards as well as any BioMOBY service accessible over the Internet; and the integration of gene chip analysis tools with the functional assignments. The system can be used as a signed web applet, Web Start, and a local stand-alone application, with or without connection to the Internet. It is available free of charge and as open source via http://bluejay.ucalgary.ca.

Computational Biology↗

PubMed2004

[Sequence of Escherichia coli O138 O-antigen gene cluster and gne identification by bioinformatics].

E. coli O138 is one of the enterotoxigenic Escherichia coli, causing the postweaning diarrhea and edema disease of weaned pigs. The O-antigen gene cluster of E. coli O138 was sequenced and found to contain the genes rmlB-DAC and gne, gna for the biosynthesis of nucleotide sugars dTDP-rhamnose and UDP-GalNAcA, respectively, genes encoding for O unit flippase(wzx), O-antigen polymerase(wzy) and 3 potential transferase genes. The possible biosynthesis pathway for rare UDP-GalNAcA was proposed. Two genes specific to E. coli O138 were identified. This work provides the basis for a sensitive test by PCR for the rapid detection of E. coli O138. Phylogenetic tree for Gne and GalE proteins was generated and comparisons were made among different strains, and results revealed that these proteins are similar in the second structure, and Gne of E. coli O138 was identified by bioinformatics.

Computational Biology↗

PubMed2005

An ontology for carcinoma classification for clinical bioinformatics.

There are a plenty of existing classifications and staging schemes for carcinomas, one of the most frequently used being the TNM classification. Such classifications involve entities which exist at various anatomical levels of granularity and in order to apply such classifications to the Electronic Health Care Records, one needs to build ontologies which are not only based on the formal principles but also take into consideration the diversity of the domains which are involved in clinical bioinformatics. Here we outline a formal theory for addressing these issues in a way that inferences drawn upon the ontologies would be helpful in interpreting and inferring on the entities which exist at different anatomical levels of granularity. Our case study is on the colon carcinoma, one of the commonest carcinomas prevalent within the European population.

Computational Biology↗

PubMed2005

A framework based on Web service orchestration for bioinformatics workflow management.

Bioinformatics activities are growing all over the world, with proliferation of data and tools. This brings new challenges: how to understand and organize these resources and how to provide interoperability among tools to achieve a given goal. We defined and implemented a framework to help meet some of these challenges. Four issues were considered: the use of Web services as a basic unit, the notion of a Semantic Web to improve interoperability at the syntactic and semantic levels, and the use of scientific workflows to coordinate services to be executed, including their interdependencies and service orchestration.

Algorithms↗

PubMed2005

An I/O device driver for bioinformatics tools: the case for BLAST.

There are many bioinformatics tools that deal with input/output (I/O) issues by using filing systems from the most common operating systems, such as Linux or MS Windows. However, as data volumes increase, there is a need for more efficient disk access, ad hoc memory management and specific page-replacement policies. We propose a device driver that can be used by multiple applications. It keeps the application code unchanged, providing a non-intrusive and flexible strategy for I/O calls that may be adopted in a straightforward manner. With our approach, database developers can define their own I/O management strategies. We used our device driver to manage Basic Local Alignment Search Tool (BLAST) I/O calls. Based on preliminary experimental results with National Center for Biotechnology Information (NCBI) BLAST, this approach can provide database management systems-like data management features, which may be used for BLAST and many other computational biology applications.

Algorithms↗

PubMedDate not supplied

Bioinformatic analysis of changes in expression level of tyrosyl-tRNA synthetase during sporulation process in Saccharomyces cerevisiae.

Study of tyrosyl-tRNA synthetases (TyrRS) gene expression during sporulation cycle in Saccharomyces cerevisiae by bioinformatic analysis of microarray data showed high correlation of TyrRS expression to genes that participate in cell wall assembly. Furthermore, the cell wall biogenesis protein KNR4 which physically interacts with TyrRS and cooperates in beta-1,3 glucan biosynthesis falls into a single gene cluster with TyrRS. One third of genes (13 from 42) in TyrRS gene cluster are responsible for the functions directly related to cell wall assembly and maintenance during sporulation. Putative transcription factor binding site on TyrRS upstream sequences was localized with expectation maximization algorithm. The site could be involved in the control of TyrRS expression during sporulation. Absence of correlation in gene expression between KNR4 and TyrRS in S. cerevisiae and their homologues in Schizosaccharomyces pombe--genes SPBC30D10.17 and TYR1 as well as the lack of correlation in the expression level of TyrRS with other sporulation cycle genes indicates that participation of TyrRS in cell wall assembly in S. cerevisiae appeared later in evolution after divergence of S. pombe and S. cerevisiae.

Base Sequence↗

PubMed2005

Identification and characterization of Bombyx mori eIF5A gene through bioinformatics approaches.

As the genome of B. mori is available in GenBank and the EST database of B. mori is expanding, identification of novel genes of B. mori was conceivable by data-mining techniques and bioinformatics tools. In this study, we used the in silico cloning method to identify eukaryotic initiation factor 5A (eIF5A) gene in B. mori. With the hypusine formation, eIF5A is involved in the regulation of cell proliferation and apoptosis. Using the computer program MEGA3, we conducted a search for homologs of eIF5A among many eukaryotic species and confirmed that the eIF5A was conserved in all organisms investigated. This gene has been registered in GenBank under the accession number DQ104412.

Amino Acid Sequence↗

PubMed2006

[Immunological screening for multiple myeloma-associated antigens and their bioinformatics analysis].

This study was aimed to screen the cell cDNA expression library of multiple myeloma HMy2 (MM HMy2) by using "serological analysis of cDNA expression library (SEREX)" technique. The obtained 30 positive clones were all sequenced, and analyzed by BLAST (basic local alignment search tool). The results indicated that 6 known genes and 12 new MM-associated genes were obtained, part of which sequences were spliced by EST (expressed sequence tag) splicing. 6 known genes such as for ring finger protein 167, KLF10, TPT1 protein, p02 protein, cDNA FLJ46859 fis, DNMT1 methyltrasferase etc. have been demonstrated a certain relationship with other tumor's formation, progress and prognosis. The structures and functions of the new genes preliminarily analyzed and predicted by means of bioinformatics showed that MMSA-3, MMSA-8 and MMSA-11 encoding 215, 160 and 122 amino acid residues respectively had the full open reading frames (ORF). All the new genes might be located at euchromosomes but MMSA-1 at sex chromosome. MMSA-4 was highly similar to the protein controlling the transcription of tumor antigen, MMSA-5 might take part in cell phagocytosis, MMSA-7 might inactivated NF-kappaB, and MMSA-12 might be a lymphocytic cytoplasmic protein. The specificity of new genes such as MMSA-3 and MMSA-7 were higher, by a preliminary analysis using CrELISA. It is concluded that tumor antigens screened by this study can be used for early immunological diagnosis, surveillance of minor residual foci, assessment of prognosis, and preparation of tumor vaccine and so on.

Antigens, Neoplasm↗

PubMed2006

Functional annotation and analysis of Korean patented biological sequences using bioinformatics.

A recent report of the Korean Intellectual Property Office (KIPO) showed that the number of biological sequence-based patents is rapidly increasing in Korea. We present biological features of Korean patented sequences though bioinformatic analysis. The analysis is divided into two steps. The first is an annotation step in which the patented sequences were annotated with the Reference Sequence (RefSeq) database. The second is an association step in which the patented sequences were linked to genes, diseases, pathway, and biological functions. We used Entrez Gene, Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Through the association analysis, we found that nearly 2.6% of human genes were associated with Korean patenting, compared to 20% of human genes in the U.S. patent. The association between the biological functions and the patented sequences indicated that genes whose products act as hormones on defense responses in the extra-cellular environments were the most highly targeted for patenting. The analysis data are available at http://www.patome.net.

Base Sequence↗

PubMed2006

GPS@ bioinformatics portal: from network to EGEE grid.

Bioinformatics analysis of data produced by complete genome sequencing projects is one of the major challenges of the current years. Integrating up-to-date databanks and relevant algorithms is a clear requirement of such analysis. Grid computing would be a viable solution to distribute data, algorithms, computing and storage resources for Genomics. Providing bioinformaticians with a good interface to grid infrastructure, such as the one provided by the EGEE European project, is also a challenge to take up. The GPS@ web portal, "Grid Protein Sequence Analysis", aims to provide such a user-friendly interface for these grid genomic resources on the EGEE grid.

Computational Biology↗

PubMed2006

Constructing a semantically enriched biomedical service space: a paradigm with bioinformatics resources.

Biomedical applications are becoming increasingly reliant on resource integration and information exchange within global solution frameworks that offer seamless connectivity and data sharing in distributed environments. Resource autonomy and data heterogeneity are the most important impediments towards this potential. Aiming to overcome these limitations, we propose an implementation of the service-oriented model towards the construction of an open, semantically enriched biomedical service space that enables advanced service registration, selection and access capabilities, as well as service interoperability. The proposed system is realised by defining service annotation ontologies and applying software agent technology as the means for service registration, matchmaking and interfacing in a Grid environment. The applicability of the envisioned biomedical service space is illustrated on a set of bioinformatics resources, addressing computational identification of protein-coding genes.

Computational Biology↗