Potential and challenges of a human cytome project

BACKGROUND: The elucidation of the molecular pathways from the 20-40.000 genes of the sequenced human genome via investigation of genetic networks and molecular pathways up to the cellular and organismal phenotypes is highly complex and time consuming. STRATEGY AND GOALS: The proposed upside-down research strategy of a human cytome project accesses the expressed molecular cell phenotypes by differential screening, for example of diseased versus healthy, or undifferentiated versus differentiated cells to obtain information on disease or differentiation related molecular hotspots at the single cell level. The genome serves as inventory of the biomolecular capacities of organisms while the mechanisms of genome realisation are initially entirely bypassed. Detected molecular hotspots are further investigated by backward directed systems biology, including molecular pathway modelling to elucidate disease related molecular pathways. New drug targets may be identified to specifically influence such pathways. Differential screening provides, in addition, individualized disease course predictions for everyday medicine, in form of "predictive medicine by cytomics." The early recognition of future disease complications enables an immediate application of preventive therapies. This is likely to lower disease related irreversible tissue destruction and adverse drug reactions and will allow to individually optimize patient therapy. OUTLOOK: Immediate medical use, facilitated access to the detection of new drug targets, increased research speed and the stimulation for advanced technological developments represent major driving forces for the efforts to establish a human cytome project.     

Current LCA database development in Japan -results of the LCA project

In 1998, the Japan’s Ministry of Economy, Trade, and Industry (METI) launched a five-year national project entitled ‘Development of Life Cycle Impact Assessment for Products’ (commonly known as ‘the LCA Project’). The purpose of the project is to develop common LCA methodology as well as a highly reliable database that can be shared in Japan. Activities over these five years have resulted in the supply of LCI data on some 250 products. Industrial associations voluntarily provided data. The results of these activities are currently being made available on the Internet on a trial basis in the form of an LCA database. In addition, a method entitled ‘Life-cycle Impact assessment Method based on Endpoint modeling (LIME)’ was developed. It is expected that these results will be widely used in Japan in the future. This paper presents an outline of the results of the research and development that has been conducted in the LCA Project in Japan.     

Unexpected findings in identifiable stored blood samples after analysis without consent: moral arguments for and against disclosure

Obtaining informed consent for using blood samples in research is mandatory. However, sometimes no consent is obtained for analysis of identifiable blood samples in a second study. As a result, a moral dilemma raises in case a possibly pathogenic mutation is found. Should the involved person be informed that such a mutation has been detected? We present a case in which this problem occurred and discuss arguments for and against information disclosure.     

HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project

HUGE is a database for human large proteins newly identified in the Kazusa cDNA project, the aim of which is to predict the primary structure of proteins from the sequences of human large cDNAs (>4 kb). In particular, cDNA clones capable of coding for large proteins (>50 kDa) are the current targets of the project. HUGE contains >1100 cDNA sequences and detailed information obtained through analysis of the sequences of cDNAs and the predicted proteins. Besides an increase in the number of cDNA entries, the amount of experimental data for expression profiling has been largely increased and data on chromosomal locations have been newly added. All of the protein-coding regions were examined by GeneMark analysis, and the results of a motif/domain search of each predicted protein sequence against the Pfam database have been newly added. HUGE is available through the WWW at http://www.kazusa.or.jp/huge     

HUGE: a database for human large proteins identified in the Kazusa cDNA sequencing project

We have been developing a HUGE database to summarize results from the sequence analysis of human novel large (>4 kb) cDNAs identified in the Kazusa cDNA sequencing project, systematically designated KIAA plus a four-digit number. HUGE currently contains nearly 2000 gene/protein characteristic tables harboring the results of the computer-assisted analysis of the cDNA and the predicted protein sequences together with those of expression profiling and chromosomal mapping. In the updated version of HUGE, we made it possible to compare each KIAA cDNA sequence with the corresponding entry in the human draft genome sequence that was published recently. Approximately 90% of KIAA cDNAs in HUGE can be localized along the human genome for at least half or more of the cDNA’s length. Any nucleotide differences between the cDNA and the corresponding genomic sequences are also presented in detail. This new version of HUGE greatly helps us evaluate the completeness of cDNA clones and the accuracy of cDNA/genomic sequences. More interestingly, in some cases, the ability to compare cDNA with genomic sequences allows us to identify candidate sites of RNA editing. HUGE is available on the World Wide Web at http://www.kazusa.or.jp/huge.     

Biotech round the world: Iceland

Facts and figures deCode genetics – An expert of the human genome Two important research supporters Biotech Companies     

Defining the supernatural in Iceland

This article does not have an abstract     

Refractions through culture: the new genomics in Iceland

This paper explores the processes whereby complex scientific developments are rendered into locally intelligible idioms as part of strategies to incorporate a ‘public’ in decisions which may have profound implications in the longer term. We focus in particular on the recent developments in genetic technologies and take as our example the deCode biogenetic project in Iceland. We trace how the images and metaphors drawn upon by all sides of the debate created powerful resonances with Icelandic history and culture. We analyse these representations and the broader themes of ethnicity and nationalism which they invoke.     

Expanding the moral circle: farmed fish as objects of moral concern

Until recently fish welfare attracted little attention, but international and national legislation and standards of fish welfare are now emerging and an overview of these developments is presented in this study. Whereas animal welfare legislation is based on public morality, animal ethics does not automatically accept public morality as normative and elaborates arguments regarding the way humans should treat animals (referred to as moral standards). In this study we present the most common animal ethics theories. For most of these, sentience is considered a demarcation line for moral concern: if an animal is sentient, then it should be included in the moral circle, i.e. receive moral consideration in its own right and some basic welfare should be ensured. As for fish, research has revealed that the sensory system of teleosts can detect noxious stimuli, and that some kind of phenomenal consciousness, allowing the fish to feel pain, seems to be present. This raises the ethical question as to how much evidence we need in order to act on such indications of fish sentience. A simple risk analysis shows that the probability that fishes can feel pain is not negligible and that if they do indeed experience pain the consequences in terms of the number of suffering individuals are great. We conclude that farmed fish should be given the benefit of the doubt and we should make efforts that their welfare needs are met as well as possible. Finally, the way forward is briefly discussed: efforts must be made to understand what fish welfare means in practical fish farming. This will involve the development of research and education, greater accountability and transparency, compliance with and control of policies, and quality assurance schemes.     

ICB database: the gyrB database for identification and classification of bacteria

The Identification and Classification of Bacteria (ICB) database (http:/www.mbio.co.jp/icb) contains currently available information about the DNA gyrase subunit B (gyrB) gene in bacteria. The database is designed to provide the scientific community with a reference point for using gyrB as an evolutionary and taxonomic marker. Nucleic and amino acid sequence data are currently available for over 850 strains, along with alignments at several different taxonomic levels and an exhaustive review of primer selection and background information.     

Meat made us moral: a hypothesis on the nature and evolution of moral judgment

In the first part of the article, an account of moral judgment in terms of emotional dispositions is given. This account provides an expressivist explanation of three important features of moral demands: inescapability, authority independence and meriting. In the second part of the article, some ideas initially put forward by Christopher Boehm are developed and modified in order to provide a hypothesis about the evolution of the ability to token moral judgments. This hypothesis makes evolutionary sense of inescapability, authority independence and meriting. It does so by referring to the selection pressures generated in the Late Pleistocene by large-game hunting. If the hypothesis is correct, we can say that, in a sense, meat made us moral.     

HUGE: a database for human large proteins identified by Kazusa cDNA sequencing project.

HUGE is a database for human large proteins newly identified by Kazusa cDNA project, which aims to predict protein primary structures from sequences of human large cDNAs (>4 kb). In particular, cDNA clones capable of coding for large proteins (>50 kDa) are current targets of the project. More than 700 sequences of human cDNAs (average size, 5.1 kb) have been determined to date and deposited in the public databases. Notable information implied from the cDNAs and the predicted protein sequences can be obtained through HUGE via the World Wide Web at URL http://www.kazusa.or.jp/huge