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At least 91 records · Page 5Linked to original sources

Genomics in sudden cardiac death.

Sudden cardiac death (SCD) remains a public health problem of major magnitude. Contrary to earlier expectations, and despite decreased overall cardiac mortality, SCD rates appear to be rising in concert with escalating global prevalence of coronary disease and heart failure, the two major conditions predisposing to SCD. With the exception of the implantable defibrillator, there are few effective approaches to SCD prevention and even fewer clues concerning patient phenotypes predisposed to life-threatening arrhythmias. Clinical variables such as ejection fraction predict mortality but are not sensitive enough to identify many high SCD risk patients. The predictive power of autonomic dysregulation and markers such as lipid levels, hypertension, diabetes, and smoking is quite low in subclinical heart disease, the population in which the majority of SCDs occur. This review addresses advances in genomic science applicable to the SCD public health problem in both rare and common forms of heart disease. These include novel bioinformatic approaches to both identify candidate genes/pathways and identify previously unknown functional genetic elements, as well as methods to comprehensively screen these elements. We also discuss the possibility of applying high-density genome-wide SNP analyses to examine genetic contributions to arrhythmia susceptibility in community-based, case-control studies of common forms of SCD. The development of novel strategies to identify contributors to susceptibility in common cardiac phenotypes is most likely to lead to new and relevant therapeutic targets for SCD.

Arrhythmias, Cardiac↗

The European dimension for the mouse genome mutagenesis program.

The European Mouse Mutagenesis Consortium is the European initiative contributing to the international effort on functional annotation of the mouse genome. Its objectives are to establish and integrate mutagenesis platforms, gene expression resources, phenotyping units, storage and distribution centers and bioinformatics resources. The combined efforts will accelerate our understanding of gene function and of human health and disease.

Animals↗

Genomics. University company to exploit heart data.

This month, Boston University, which directs the Framingham Heart Study, a massive government effort begun in 1948 to monitor the cardiovascular health of more than 10,000 residents of this suburb of Boston, announced plans to form a bioinformatics company that will mine the data. The university will own 20% of Framingham Genomic Medicine Inc., which hopes to raise $21 million to begin modernizing the immense database and packaging it in a format that will be valuable to the pharmaceutical industry. The plan raises a host of difficult ethical issues, including patient privacy, academic conflicts of interest, and reciprocal value to the Framingham residents whose medical data will form the basis for the new enterprise.

Bioethics↗

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↗

Stochastic optimal therapy for enhanced immune response.

Therapeutic enhancement of humoral immune response to microbial attack is addressed as the stochastic optimal control of a dynamic system. Without therapy, the modeled immune response depends upon the initial concentration of pathogens in a simulated attack. Immune response can be augmented by agents that kill the pathogen directly, that stimulate the production of plasma cells or antibodies, or that enhance organ health. Using a generic mathematical model of immune response to the infection (i.e., of the dynamic state of the system), previous papers demonstrated optimal (open-loop) and neighboring-optimal (closed-loop) control solutions that defeat the pathogen and preserve organ health, given initial conditions that otherwise would be lethal [Optimal Contr. Appl. Methods 23 (2002) 91, Bioinformatics 18 (2002) 1227]. Therapies based on separate and combined application of the agents were derived by minimizing a quadratic cost function that weighted both system response and drug usage, providing implicit control over harmful side effects. Here, we focus on the effects that corrupted or incomplete measurements of the dynamic state may have on neighboring-optimal feedback control. Imperfect measurements degrade the precision of feedback adjustments to therapy; however, optimal state estimation allows the feedback strategy to be implemented with incomplete measurements and minimizes the expected effects of measurement error. Complete observability of the perturbed state for this four state example is provided by measurement of four of the six possible pairs of two variables, either set of three variables, or all four variables. The inclusion of state estimation extends the applicability of optimal control theory for developing new therapeutic protocols to enhance immune response.

Anti-Infective Agents↗

Preparing for the third millennium: the views of life informatics.

The chief aspects of this paper are the condition of the birth of life informatics and its tasks, basic concepts, principles, and structure. There are three phases of combining informatics with medicine: product, technological, and theoretic application of which the goals are respectively the informatization of numerical and word processing, data of medical treatment, and the knowledge of medicine. While reached the third phase we have dealt with two types of biological information, physical and nonphysical, i.e., body information (i.e., the information about body's components and structure), and life information (i.e., the information about life codes and life programs). Life informatics is a main branch of bioinformatics. It is a new member of the medical informatics family, and as such is younger than health informatics, nursing informatics, and dental informatics. It's task is to assist biologists and medical doctors to recognize and interfere the human life information procedure just as they are doing well with human body's matter and energy system. Its basic concepts are life information, life information medicine, and life information therapy. Its most important principles are information materialism, general informatics, and information determinism. Its main branches are biomolecule, cellular, organic, individual, and social informatics. In the third millennium, the life informatics will be a leading discipline in biology, medicine and informatics, which will gradually influence modern philosophy and other humanities.

Biology↗

The genome projects: implications for dental practice and education.

Information from the Human Genome Project (HGP) and the integration of information from related areas of study and technology will dramatically change health care for the craniofacial complex. Approaches to risk assessment and diagnosis, prevention, early intervention, and management of craniofacial conditions are and will continue to evolve through the application of this new knowledge. While this information will advance our health care abilities, it is clear that the dental profession will face challenges regarding the acquisition, application, transfer, and effective and efficient use of this knowledge with regards to dental research, dental education, and clinical practice. Unraveling the human genomic sequence now allows accurate diagnosis of numerous craniofacial conditions. However, the greatest oral disease burden results from dental caries and periodontal disease that are complex disorders having both hereditary and environmental factors determining disease risk, progression, and course. Disease risk assessment, prevention, and therapy, based on knowledge from the HGP, will likely vary markedly for the different complex conditions affecting the head and neck. Integration of Information from the human genome, comparative and microbial genomics, proteomics, bioinformatics, and related technologies will provide the basis for proactive prevention and intervention and novel and more efficient treatment approaches. Oral health care practitioners will increasingly require knowledge of human genetics and the application of new molecular-based diagnostic and therapeutic technologies.

Bacteria↗

Applications of bioinformatics and computational biology to influenza surveillance and vaccine strain selection.

In recent years, collaborations often between mathematical and computational biologists and scientists in the World Health Organization (WHO) global influenza surveillance network, have resulted in a number of mathematical and computational advances including: increasing the resolution at which antigenic surveillance data can be analyzed, providing methods for genetic analysis and prediction, and an increased understanding of the determinants of repeated influenza vaccination. These advances increase the information extracted from influenza surveillance and increase the quantitative data available for the vaccine strain selection process. This mathematical and computational work is possible because of the wealth of information collected over many years by the WHO global influenza surveillance network, and further advances will be greatly facilitated by implementation of the proposed strengthening of virological and epidemiological surveillance in the WHO global agenda on influenza surveillance and control.

Computational Biology↗

Programmatic access to ICTV virus taxonomy through a public ontology API.

BACKGROUND: The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. FINDINGS: To address this, we developed a public and sustainable solution leveraging ontology-based APIs. All available ICTV Master Species List (MSL) releases, from MSL1 to MSL41, were transformed into a unified, semantically structured ontology comprising more than 195,000 current and historical entities and deployed through the Ontology Lookup Service (OLS). The ontology is automatically rebuilt and republished whenever a new MSL release becomes available. Complementary ICTV-NCBI mappings and helper libraries support integration into downstream systems. CONCLUSIONS: Together, these resources enable, for the first time, public programmatic retrieval of current and historical ICTV taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints, including resolution of former taxonomic terms to their current accepted taxon or taxa and retrieval of taxon histories across releases. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗

Programmatic access to ICTV virus taxonomy through a public ontology API.

The International Committee on Taxonomy of Viruses (ICTV) is responsible for developing and maintaining a universal virus taxonomy. As the reference framework for organising the viral world, it is essential for virology and related fields. Despite its widespread use in research and public health, programmatic access to ICTV taxonomy has remained limited, posing challenges for integration, versioning, and interoperability across databases and bioinformatics resources requiring up-to-date virus taxonomy. To address this, we developed a public and sustainable solution leveraging ontology-based APIs. Successive ICTV Master Species List (MSL) releases were transformed into a structured ontology and deployed as a unified representation through the Ontology Lookup Service (OLS). The framework also provides ICTV-NCBI mappings and helper libraries for integration into downstream systems. This enables, for the first time, public programmatic retrieval of current and historical virological taxon names, taxonomic relationships, metadata, and persistent identifiers through stable endpoints. More broadly, this work illustrates a general strategy for transforming structured biological datasets into semantically enriched graph resources exposed through scalable public APIs. These developments enhance interoperability, reduce manual curation, and support FAIR-aligned taxonomic data management in virology and pandemic preparedness.

API↗

Expressed sequence tag analysis of human RPE/choroid for the NEIBank Project: over 6000 non-redundant transcripts, novel genes and splice variants.

PURPOSE: The retinal pigment epithelium (RPE) and choroid comprise a functional unit of the eye that is essential to normal retinal health and function. Here we describe expressed sequence tag (EST) analysis of human RPE/choroid as part of a project for ocular bioinformatics. METHODS: A cDNA library (cs) was made from human RPE/choroid and sequenced. Data were analyzed and assembled using the program GRIST (GRouping and Identification of Sequence Tags). Complete sequencing, Northern and Western blots, RH mapping, peptide antibody synthesis and immunofluorescence (IF) have been used to examine expression patterns and genome location for selected transcripts and proteins. RESULTS: Ten thousand individual sequence reads yield over 6300 unique gene clusters of which almost half have no matches with named genes. One of the most abundant transcripts is from a gene (named "alpha") that maps to the BBS1 region of chromosome 11. A number of tissue preferred transcripts are common to both RPE/choroid and iris. These include oculoglycan/opticin, for which an alternative splice form is detected in RPE/choroid, and "oculospanin" (Ocsp), a novel tetraspanin that maps to chromosome 17q. Antiserum to Ocsp detects expression in RPE, iris, ciliary body, and retinal ganglion cells by IF. A newly identified gene for a zinc-finger protein (TIRC) maps to 19q13.4. Variant transcripts of several genes were also detected. Most notably, the predominant form of Bestrophin represented in cs contains a longer open reading frame as a result of splice junction skipping. CONCLUSIONS: The unamplified cs library gives a view of the transcriptional repertoire of the adult RPE/choroid. A large number of potentially novel genes and splice forms and candidates for genetic diseases are revealed. Clones from this collection are being included in a large, nonredundant set for cDNA microarray construction.

Aged↗

Chipping into the human genome: novel insights for transplantation.

High throughput, high density platforms for transcriptional, proteomic, and metabonomic analyses are opening new doors for improving our understanding of the complexity and redundancy of the immune system in the interplay of the innate and allo-immune responses in organ transplantation. New insights are being obtained into the possible discrepancies between the gold standard of tissue pathological diagnosis and clinical graft outcomes, as new transcriptional categories of transplant rejection evolve. The bystander effects of chronic immunosuppression underlying the complexities of graft dysfunction are beginning to be understood. Non-invasive mechanisms to monitor transplants, by following 'footprints' of biomarker sets that reflect the disease phenotype, are being pursued for their clinical application for direct patient care. Utilization of these same biomarker sets may also offer a unique means to titrate immunosuppression and predict specific graft dysfunction events prior to clinical decline, thus bringing in the potential to reduce patient morbidity from infection and malignancy, preserve graft integrity, and limit the progression of chronic graft injury. Bioinformatics support is integral to the unraveling of the mysteries of the human genome, proteome, and metabolome in disease and in health.

Genome, Human↗

The severe acute respiratory syndrome (SARS).

The world was shocked in early 2003 when a pandemic of severe acute respiratory syndrome (SARS) was imminent. The outbreak of this novel disease, caused by a novel coronavirus (the SARS-coronavirus), hit hardest in the Asian Pacific region, though eventually it spread to five continents. The speed of the spread of the SARS epidemic was unprecedented due to the highly efficient intercontinental transportation. An international collaborative effort through the World Health Organization (WHO) has helped to identify the aetiological agent about 1 month after the onset of the epidemic. The power of molecular biology and bioinformatics has enabled the complete decoding of the viral genome within weeks. Over 1000 publications on the phylogeny, epidemiology, genomics, laboratory diagnostics, antiviral, immunization, pathogenesis, clinical disease, and management accumulated within just 1 year. Although the exact animal reservoir of virus and how it evolved into a human pathogen are still obscure, accurate diagnosis and epidemiological control of the disease are now possible. This article reviews what is currently known about the virus and the disease.

Animals↗

Biomarkers, yesterday, today and tomorrow: the basis for health claims.

The development of useful and accurate biomarkers for predicting outcomes of food based interventions is becoming more and more important, given the emphasis being placed on ingredients in foods contributing to disease risk reduction and optimal health promotion. With the human genome now laid bare, opportunities abound to barcode individuals with their risk profiles. The massive increase in DNA sequence information together with the development of new technologies such as genomics, proteomics and bioinformatics, has resulted in a much greater capacity to determine individual risk profiles. Screening for biomarkers at the gene or protein expression level using microarray technology has the potential to identify new biomarkers for disease diagnosis. Whether these techniques will enable a better understanding of food-gene interactions to permit health claims rather than better therapeutic treatment (at high economic cost) remains to be demonstrated.

Biomarkers↗