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PubMed2004

The Tübingen approach: identification, selection, and validation of tumor-associated HLA peptides for cancer therapy.

There is substantial need for molecularly defined tumor antigens to prime cytotoxic T cells in vivo for cancer immunotherapy, especially in the case of tumor entities for which only a few tumor antigens have been defined so far. In this review, we present the "Tübingen approach" to identify, select, and validate large numbers of MHC/HLA class I-associated peptides derived from tumor-associated antigens. Step 1 is the identification of naturally presented HLA-associated peptides directly from primary tumor cells. Step 2 is selection of tumor-associated peptides from step 1 by differential gene expression analysis and data mining. Step 3 is validation of selected candidates by monitoring in vivo T-cell responses in the context of patient-individualized immunizations. Our approach combines methods from genomics, proteomics, bioinformatics, and T-cell immunology. The aim is to develop effective immunotherapeutics consisting of multiple tumor-associated epitopes in order to induce a broad and specific immune response against cancer cells.

Antigens, Neoplasm↗
PubMed2006

Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model.

MOTIVATION: Comparative genomic hybridization array experiments that investigate gene copy number changes present new challenges for statistical analysis and call for methods that incorporate spatial dependence between sequences along the chromosome. For this purpose, we propose a novel method called CGHmix. It is based on a spatially structured mixture model with three states corresponding to genomic sequences that are either unmodified, deleted or amplified. Inference is performed in a Bayesian framework. From the output, posterior probabilities of belonging to each of the three states are estimated for each genomic sequence and used to classify them. RESULTS: Using simulated data, CGHmix is validated and compared with both a conventional unstructured mixture model and with a recently proposed data mining method. We demonstrate the good performance of CGHmix for classifying copy number changes. In addition, the method provides a good estimate of the false discovery rate. We also present the analysis of a cancer related dataset. SUPPLEMENTARY INFORMATION: http://www.bgx.org.uk/papers.html

Algorithms↗
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↗
PubMed2004

An ensemble method for gene discovery based on DNA microarray data.

The advent of DNA microarray technology has offered the promise of casting new insights onto deciphering secrets of life by monitoring activities of thousands of genes simultaneously. Current analyses of microarray data focus on precise classification of biological types, for example, tumor versus normal tissues. A further scientific challenging task is to extract disease-relevant genes from the bewildering amounts of raw data, which is one of the most critical themes in the post-genomic era, but it is generally ignored due to lack of an efficient approach. In this paper, we present a novel ensemble method for gene extraction that can be tailored to fulfill multiple biological tasks including (i) precise classification of biological types; (ii) disease gene mining; and (iii) target-driven gene networking. We also give a numerical application for (i) and (ii) using a public microarrary data set and set aside a separate paper to address (iii).

Algorithms↗
PubMed2006

ProtRepeatsDB: a database of amino acid repeats in genomes.

BACKGROUND: Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB http://bioinfo.icgeb.res.in/repeats/ is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. DESCRIPTION: ProtRepeatsDB (v1.2) consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO) annotation IDs and regular expressions (REGEXP) describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. CONCLUSION: ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific repeat markers, interspecies variations and polymorphism.

Amino Acid Sequence↗
PubMed2005

Mining yeast in silico unearths a golden nugget for mitochondrial biology.

NADH:ubiquinone oxidoreductase (complex I) of the electron transport chain is a multimeric mitochondrial enzyme of approximately 1000 kDa consisting of 46 different proteins encoded by both the mitochondrial and nuclear genomes. Little is known about the cellular mechanisms and protein chaperones that guide its assembly. In this issue of the JCI, Ogilvie et al. use genomic sequence data to compare the proteins produced by yeasts with and without complex I in order to generate a list of proteins whose human orthologs might serve as complex I assembly proteins. The gene encoding one of these candidate proteins, B17.2L, was found to harbor a nonsense mutation in one of 28 patients with a deficiency of complex I. B17.2L associated with subcomplexes that are seen when complex I assembly is incomplete. The research described here combines clever model organism genomics and bioinformatics with sophisticated human molecular and biochemical genetics to identify the first mammalian protein required for the normal assembly of complex I.

Animals↗
PubMed2000

Human genetics in health care.

UNLABELLED: The Human Genome Project, the mapping of our 100,000 genes and the sequencing of all of our DNA, will have major impact on biomedical research and the whole of therapeutic and preventive health care. The tracing of genetic diseases to their molecular causes is rapidly expanding diagnostic and preventive options, while the increased insights into molecular pathways open tremendous perspectives for pharmacological and genetic therapies. The design of animal model systems for the functional study of disease and development and the use of bioinformatics and biostatistics to improve our pattern recognition abilities are greatly accelerating progress. However, the optimal value from the current explosion of 'data mining' possibilities will only be gained when the basic data are made and kept publicly accessible, while at the same time safeguarding the protection of intellectual property arising from downstream inventions. This is one of the goals of the international Human Genome Organisation, established 10 years ago to assist coordinating data acquisition and exchange and societal implementation of the genome project. Additional points of major attention in this historic endeavour are the safeguarding of a worldwide balance in the contribution and benefits to countries and populations, the prevention of stigmatisation and discrimination of individuals and groups and the maintenance of respect for the diversity of our world's cultures and traditions. CONCLUSION: The acquisition and use of genomic information for health care benefit should be seen in the light of a worldwide improvement without prejudice.

Ethics, Medical↗
PubMed2006

Purdue ionomics information management system. An integrated functional genomics platform.

The advent of high-throughput phenotyping technologies has created a deluge of information that is difficult to deal with without the appropriate data management tools. These data management tools should integrate defined workflow controls for genomic-scale data acquisition and validation, data storage and retrieval, and data analysis, indexed around the genomic information of the organism of interest. To maximize the impact of these large datasets, it is critical that they are rapidly disseminated to the broader research community, allowing open access for data mining and discovery. We describe here a system that incorporates such functionalities developed around the Purdue University high-throughput ionomics phenotyping platform. The Purdue Ionomics Information Management System (PiiMS) provides integrated workflow control, data storage, and analysis to facilitate high-throughput data acquisition, along with integrated tools for data search, retrieval, and visualization for hypothesis development. PiiMS is deployed as a World Wide Web-enabled system, allowing for integration of distributed workflow processes and open access to raw data for analysis by numerous laboratories. PiiMS currently contains data on shoot concentrations of P, Ca, K, Mg, Cu, Fe, Zn, Mn, Co, Ni, B, Se, Mo, Na, As, and Cd in over 60,000 shoot tissue samples of Arabidopsis (Arabidopsis thaliana), including ethyl methanesulfonate, fast-neutron and defined T-DNA mutants, and natural accession and populations of recombinant inbred lines from over 800 separate experiments, representing over 1,000,000 fully quantitative elemental concentrations. PiiMS is accessible at www.purdue.edu/dp/ionomics.

Arabidopsis↗
PubMed2004

HGVbase: a curated resource describing human DNA variation and phenotype relationships.

The Human Genome Variation Database (HGVbase; http://hgvbase.cgb.ki.se) has provided a curated summary of human DNA variation for more than 5 years, thus facilitating research into DNA sequence variation and human phenotypes. The database has undergone many changes and improvements to accommodate increasing volumes and new types of data. The focus of HGVbase has recently shifted towards information on haplotypes and phenotypes, relationships between phenotypes and DNA variation, and collaborative efforts to provide a global resource for genome-phenome data. Open sharing and precise phenotype definitions are necessary to advance the current understanding of common diseases that are typified by complex aetiologies, small genetic effect sizes and multiple confounding factors that obscure positive study results. Association data will increasingly be collected as part of this new project thrust. This report describes the evolving features of HGVbase, and covers in detail the technological choices we have made to enable efficient storage and data mining of increasingly large and complex data sets.

Computational Biology↗
PubMed2003

Screening of genes that respond to cryopreservation stress using yeast DNA microarray.

We studied the response of yeast cells after cryopreservation treatment using DNA microarray technology. Genes that contribute to "Cell rescue, defense and virulence," "energy," and "metabolism," were significantly induced. These genes were classified as encoding heat shock proteins, oxidative stress scavenger, and enzymes involved in glucose metabolism. The expression profile of mRNA after cryopreservation treatment was calculated to be closer to that following treatment with detergent or plant oils rather than by other stress factors such as heavy metals and agricultural chemicals. These results suggest that the cryopreservation treatment caused damage to the structure of the cell wall and cellular organelles. This was supported by the localization of the products of the induced genes at the cell wall and within cellular organelles.

Cell Wall↗
PubMedDate not supplied

Microarray expression profiling identifies early signaling transcripts associated with 6-OHDA-induced dopaminergic cell death.

The parkinsonian mimetic 6-hydroxydopamine (6-OHDA) has been shown to cause transcriptional changes associated with cellular stress and the unfolded protein response. As these cellular sequelae depend on upstream signaling events, the present study used functional genomics and proteomic approaches to aid in deciphering toxin-mediated regulatory pathways. Microarray analysis of RNA collected from multiple time points following 6-OHDA treatment was combined with data mining and clustering techniques to identify distinct functional subgroups of genes. Notably, stress-induced transcription factors such as ATF3, ATF4, CHOP, and C/EBP beta were robustly up-regulated, yet exhibited unique kinetic patterns. Genes involved in the synthesis and modification of proteins (various tRNA synthetases), protein degradation (e.g., ubiquitin, Herpud1, Sqstm1), and oxidative stress (Hmox1, Por) could be subgrouped into distinct kinetic profiles as well. Realtime PCR and/or two-dimensional electrophoresis combined with western blotting validated data derived from microarray analyses. Taken together, these data support the notion that oxidative stress and protein dysfunction play a role in Parkinson's disease, as well as provide a time course for many of the molecular events associated with 6-OHDA neurotoxicity.

Animals↗
PubMed2005

In silico analysis of 2085 clones from a normalized rat vestibular periphery 3' cDNA library.

The inserts from 2400 cDNA clones isolated from a normalized Rattus norvegicus vestibular periphery cDNA library were sequenced and characterized. The Wackym-Soares vestibular 3' cDNA library was constructed from the saccular and utricular maculae, the ampullae of all three semicircular canals and Scarpa's ganglia containing the somata of the primary afferent neurons, microdissected from 104 male and female rats. The inserts from 2400 randomly selected clones were sequenced from the 5' end. Each sequence was analyzed using the BLAST algorithm compared to the Genbank nonredundant, rat genome, mouse genome and human genome databases to search for high homology alignments. Of the initial 2400 clones, 315 (13%) were found to be of poor quality and did not yield useful information, and therefore were eliminated from the analysis. Of the remaining 2085 sequences, 918 (44%) were found to represent 758 unique genes having useful annotations that were identified in databases within the public domain or in the published literature; these sequences were designated as known characterized sequences. 1141 sequences (55%) aligned with 1011 unique sequences had no useful annotations and were designated as known but uncharacterized sequences. Of the remaining 26 sequences (1%), 24 aligned with rat genomic sequences, but none matched previously described rat expressed sequence tags or mRNAs. No significant alignment to the rat or human genomic sequences could be found for the remaining 2 sequences. Of the 2085 sequences analyzed, 86% were singletons. The known, characterized sequences were analyzed with the FatiGO online data-mining tool (http://fatigo.bioinfo.cnio.es/) to identify level 5 biological process gene ontology (GO) terms for each alignment and to group alignments with similar or identical GO terms. Numerous genes were identified that have not been previously shown to be expressed in the vestibular system. Further characterization of the novel cDNA sequences may lead to the identification of genes with vestibular-specific functions. Continued analysis of the rat vestibular periphery transcriptome should provide new insights into vestibular function and generate new hypotheses. Physiological studies are necessary to further elucidate the roles of the identified genes and novel sequences in vestibular function.

Afferent Pathways↗
PubMed2006

Database mining and transcriptional analysis of genes encoding inulin-modifying enzymes of Aspergillus niger.

As a soil fungus, Aspergillus niger can metabolize a wide variety of carbon sources, employing sets of enzymes able to degrade plant-derived polysaccharides. In this study the genome sequence of A. niger strain CBS 513.88 was surveyed, to analyse the gene/enzyme network involved in utilization of the plant storage polymer inulin, and of sucrose, the substrate for inulin synthesis in plants. In addition to three known activities, encoded by the genes suc1 (invertase activity; designated sucA), inuE (exo-inulinase activity) and inuA/inuB (endo-inulinase activity), two new putative invertase-like proteins were identified. These two putative proteins lack N-terminal signal sequences and therefore are expected to be intracellular enzymes. One of these two genes, designated sucB, is expressed at a low level, and its expression is up-regulated when A. niger is grown on sucrose- or inulin-containing media. Transcriptional analysis of the genes encoding the sucrose- (sucA) and inulin-hydrolysing enzymes (inuA and inuE) indicated that they are similarly regulated and all strongly induced on sucrose and inulin. Analysis of a DeltacreA mutant strain of A. niger revealed that expression of the extracellular inulinolytic enzymes is under control of the catabolite repressor CreA. Expression of the inulinolytic enzymes was not induced by fructose, not even in the DeltacreA background, indicating that fructose did not act as an inducer. Evidence is provided that sucrose, or a sucrose-derived intermediate, but not fructose, acts as an inducer for the expression of inulinolytic genes in A. niger.

Aspergillus niger↗
PubMed2002

The Human Genome Project and the future of diagnostics, treatment and prevention.

The Human Genome Project, the mapping of our 30,000-50,000 genes and the sequencing of all of our DNA, will have major impact on biomedical research and the whole of therapeutic and preventive health care. The tracing of genetic diseases to their molecular causes is rapidly expanding diagnostic and preventive options. The increased insights into molecular pathways, gained from high-throughput 'functional genomics', using DNA-chip and protein-chip approaches and specially designed animal model systems, will open great prospects for pharmacological and genetic therapies. Powerful bioinformatics and biostatistics will further improve our pattern recognition and accelerate progress. A rapidly expanding area of high expectations is that of 'pharmacogenomics': the design of more effective drugs with lower toxicity through tailoring of drug treatment to individual, genetically determined differences in drug metabolism. Not only will this decrease the cost of health care through reduction of adverse drug reactions, but a better stratification of populations will also provide more statistical power farther upstream in drug trials. However, the optimal benefits from the current explosion of 'data mining' will only be realized when the basic data are made and kept publicly accessible, while at the same time safeguarding the protection of intellectual property arising from downstream inventions. This is one of the goals of HUGO, the international Human Genome Organization, established 13 years ago to assist coordination of data acquisition and exchange and societal implementation of the genome project. Additional points of attention in this historic endeavour are the prevention of stigmatization and discrimination and the safeguarding of a worldwide balance in the contribution by--and benefits to--different populations, while respecting the diversity in cultures and traditions.

Ethics, Medical↗
PubMed2005

Ancient origin of elicitin gene clusters in Phytophthora genomes.

The genus Phytophthora belongs to the oomycetes in the eukaryotic stramenopile lineage and is comprised of over 65 species that are all destructive plant pathogens on a wide range of dicotyledons. Phytophthora produces elicitins (ELIs), a group of extracellular elicitor proteins that cause a hypersensitive response in tobacco. Database mining revealed several new classes of elicitin-like (ELL) sequences with diverse elicitin domains in Phytophthora infestans, Phytophthora sojae, Phytophthora brassicae, and Phytophthora ramorum. ELIs and ELLs were shown to be unique to Phytophthora and Pythium species. They are ubiquitous among Phytophthora species and belong to one of the most highly conserved and complex protein families in the Phytophthora genus. Phylogeny construction with elicitin domains derived from 156 ELIs and ELLs showed that most of the diversified family members existed prior to divergence of Phytophthora species from a common ancestor. Analysis to discriminate diversifying and purifying selection showed that all 17 ELI and ELL clades are under purifying selection. Within highly similar ELI groups there was no evidence for positively selected amino acids suggesting that purifying selection contributes to the continued existence of this diverse protein family. Characteristic cysteine spacing patterns were found for each phylogenetic clade. Except for the canonical clade ELI-1, ELIs and ELLs possess C-terminal domains of variable length, many of which have a high threonine, serine, or proline content suggesting an association with the cell wall. In addition, some ELIs and ELLs have a predicted glycosylphosphatidylinositol site suggesting anchoring of the C-terminal domain to the cell membrane. The eli and ell genes belonging to different clades are clustered in the genomes. Overall, eli and ell genes are expressed at different levels and in different life cycle stages but those sharing the same phylogenetic clade appear to have similar expression patterns.

Algal Proteins↗
PubMed1998

The Human Genome Project and the role of genetics in health care.

The Human Genome Project, the mapping of our 100,000 genes and the sequencing of all of our DNA, will have major impact on biomedical research and the therapeutic and preventive health care. The tracing of genetic diseases to their molecular causes is rapidly expanding diagnostic and preventive options, while the increased insights into molecular pathways open tremendous perspectives for pharmacological and genetic therapies. The design of animal model systems for the functional study of disease and development of bioinformatics and biostatistics to improve our pattern recognition abilities are greatly accelerating progress. However, the optimal value from the current explosion of 'data mining' possibilities will only be gained when the basic data are made and kept publicly accessible, at the same time preventing the jeopardisation of the protection of intellectual property, arising from downstream inventions. This is one of the goals of HUGO, the international Human Genome Organisation, established 9 years ago to assist coordinating data acquisition and exchange and societal implementation of the genome project. Additional points of major importance in this historic endeavour are the safeguarding of a worldwide balance in the contribution and benefits to countries and population, the prevention of stigmatisation and discrimination of individuals and groups and the maintenance of respect for the priceless diversity of our world's cultures and traditions.

Delivery of Health Care↗
PubMed2005

Haplotype-based linkage disequilibrium mapping via direct data mining.

MOTIVATION: With the availability of large-scale, high-density single-nucleotide polymorphism markers and information on haplotype structures and frequencies, a great challenge is how to take advantage of haplotype information in the association mapping of complex diseases in case-control studies. RESULTS: We present a novel approach for association mapping based on directly mining haplotypes (i.e. phased genotype pairs) produced from case-control data or case-parent data via a density-based clustering algorithm, which can be applied to whole-genome screens as well as candidate-gene studies in small genomic regions. The method directly explores the sharing of haplotype segments in affected individuals that are rarely present in normal individuals. The measure of sharing between two haplotypes is defined by a new similarity metric that combines the length of the shared segments and the number of common alleles around any marker position of the haplotypes, which is robust against recent mutations/genotype errors and recombination events. The effectiveness of the approach is demonstrated by using both simulated datasets and real datasets. The results show that the algorithm is accurate for different population models and for different disease models, even for genes with small effects, and it outperforms some recently developed methods.

Algorithms↗