Z-DNA forming regions in the human genome

Z-DNA is the left-handed helical structure of the usually right-handed B-DNA double helix structure. Z-DNA conformations have been found to cause mutagenesis and genetic instability [1]. In this study, human genome sequences potentially forming Z-DNA regions (ZDRs) were extracted and analysed for functional implications

Teaching in the eyes of others: a review of teaching square group

The project's main objective is to learn through peer observation. The Teaching Squares program provides faculty an opportunity to gain new insight into their teaching through a non-evaluative process of reciprocal classroom observation and self-reflection. The four faculty in each "teaching square" agree to visit each other's classes over the course of a semester and then meet to discuss what they learned from their observations

Teaching in the eyes of others: a review of teaching square group

The project's main objective is to learn through peer observation. The Teaching Squares program provides faculty an opportunity to gain new insight into their teaching through a non-evaluative process of reciprocal classroom observation and self-reflection. The four faculty in each "teaching square" agree to visit each other's classes over the course of a semester and then meet to discuss what they learned from their observations

Cytokine-related genes identified from the RIKEN full-length mouse cDNA data set

To identify novel cytokine-related genes, we searched the set of 60,770 annotated RIKEN mouse cDNA clones (FANTOM2 clones), using keywords such as cytokine itself or cytokine names (such as interferon, interleukin, epidermal growth factor, fibroblast growth factor, and transforming growth factor). This search produced 108 known cytokines and cytokine-related products such as cytokine receptors, cytokine-associated genes, or their products (enhancers, accessory proteins, cytokine-induced genes). We found 15 clusters of FANTOM2 clones that are candidates for novel cytokine-related genes. These encoded products with strong sequence similarity to guanylate-binding protein (GBP-5), interleukin-1 receptor-associated kinase 2 (IRAK-2), interleukin 20 receptor alpha isoform 3, a member of the interferon-inducible proteins of the Ifi 200 cluster, four members of the membrane-associated family 1-8 of interferon-inducible proteins, one p27-like protein, and a hypothetical protein containing a Toll/Interleukin receptor domain. All four clones representing novel candidates of gene products from the family contain a novel highly conserved cross-species domain. Clones similar to growth factor-related products included transforming growth factor beta-inducible early growth response protein 2 (TIEG-2), TGFbeta-induced factor 2, integrin beta-like 1, latent TGF-binding protein 4S, and FGF receptor 4B. We performed a detailed sequence analysis of the candidate novel genes to elucidate their likely functional properties

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis

<p>Abstract</p> <p>Background</p> <p>The identification of mutations that confer unique properties to a pathogen, such as host range, is of fundamental importance in the fight against disease. This paper describes a novel method for identifying amino acid sites that distinguish specific sets of protein sequences, by comparative analysis of matched alignments. The use of mutual information to identify distinctive residues responsible for functional variants makes this approach highly suitable for analyzing large sets of sequences. To support mutual information analysis, we developed the AVANA software, which utilizes sequence annotations to select sets for comparison, according to user-specified criteria. The method presented was applied to an analysis of influenza A PB2 protein sequences, with the objective of identifying the components of adaptation to human-to-human transmission, and reconstructing the mutation history of these components.</p> <p>Results</p> <p>We compared over 3,000 PB2 protein sequences of human-transmissible and avian isolates, to produce a catalogue of sites involved in adaptation to human-to-human transmission. This analysis identified 17 characteristic sites, five of which have been present in human-transmissible strains since the 1918 Spanish flu pandemic. Sixteen of these sites are located in functional domains, suggesting they may play functional roles in host-range specificity. The catalogue of characteristic sites was used to derive sequence signatures from historical isolates. These signatures, arranged in chronological order, reveal an evolutionary timeline for the adaptation of the PB2 protein to human hosts.</p> <p>Conclusion</p> <p>By providing the most complete elucidation to date of the functional components participating in PB2 protein adaptation to humans, this study demonstrates that mutual information is a powerful tool for comparative characterization of sequence sets. In addition to confirming previously reported findings, several novel characteristic sites within PB2 are reported. Sequence signatures generated using the characteristic sites catalogue characterize concisely the adaptation characteristics of individual isolates. Evolutionary timelines derived from signatures of early human influenza isolates suggest that characteristic variants emerged rapidly, and remained remarkably stable through subsequent pandemics. In addition, the signatures of human-infecting H5N1 isolates suggest that this avian subtype has low pandemic potential at present, although it presents more human adaptation components than most avian subtypes.</p

The fire safety of TV set enclosure materials, a survey of European statistics

The composition of enclosure materials used in many TV sets sold on the European market has changed significantly since the early 1990s. To determine the potential impact of this change on TV fire safety, a review of European and US TV set fire statistics has been carried out. TV set fires can have internal electrical causes due to faults not apparent at the time of manufacture, simple wear and tear, or a variety of external causes. Recent detailed statistics suggest that about one third of all TV fires are due to external ignition. Available data show that the significant drop in the rate of TV set fires experienced in Europe during the 1980s is not continuing today. In fact, the rate appears to be increasing in some countries, such as the UK and Sweden. The number of TV set fires in Europe is estimated as 100 fires per million TV sets per year due to internal ignition sources, at least an order of magnitude higher than in the USA where the fire safety classifications for TV set enclosure materials has been historically high. TV set fires have a dramatic impact on life and property. To avoid an increase in TV set fires, fire safety requirements should be increased, and public awareness of the importance of fire safety in TVs heightened. Copyright (C) 2000 John Wiley & Sons, Ltd