| 1. |
- Hillier, Ladeana W, et al.
(author)
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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
- 2004
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In: Nature. - 0028-0836 .- 1476-4687. ; 432:7018, s. 695-716
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Journal article (peer-reviewed)abstract
- We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
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| 2. |
- Giele, Walter, et al.
(author)
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The QCD / SM working group: Summary report
- 2002
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In: Physics at TeV colliders. Proceedings, Euro Summer School, Les Houches, France, May 21-June 1, 2001. ; , s. 275-426, s. 275-426
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Conference paper (other academic/artistic)
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| 3. |
- Augustin, Ingo, et al.
(author)
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HEP Applications Evaluation of the EDG Testbed and Middleware
- 2003
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Conference paper (peer-reviewed)abstract
- Workpackage 8 of the European Datagrid project was formed in January 2001 with representatives from the four LHC experiments, and with experiment independent people from five of the six main EDG partners. In September 2002 WP8 was strengthened by the addition of effort from BaBar and D0. The original mandate of WP8 was, following the definition of short- and long-term requirements, to port experiment software to the EDG middleware and testbed environment. A major additional activity has been testing the basic functionality and performance of this environment. This paper reviews experiences and evaluations in the areas of job submission, data management, mass storage handling, information systems and monitoring. It also comments on the problems of remote debugging, the portability of code, and scaling problems with increasing numbers of jobs, sites and nodes. Reference is made to the pioneeering work of Atlas and CMS in integrating the use of the EDG Testbed into their data challenges. A forward look is made to essential software developments within EDG and to the necessary cooperation between EDG and LCG for the LCG prototype due in mid 2003.
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| 4. |
- Moss, B, et al.
(author)
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The determination of ecological status in shallow lakes - a tested system (ECOFRAME) for implementation of the European Water Framework Directive
- 2003
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In: Aquatic Conservation: Marine and Freshwater Ecosystems. - : Wiley. - 1052-7613. ; 13:6, s. 507-549
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Journal article (peer-reviewed)abstract
- 1. The European Water Framework Directive requires the determination of ecological status in European fresh and saline waters. This is to be through the establishment of a typology of surface water bodies, the determination of reference (high status) conditions in each element (ecotype) of the typology and of lower grades of status (good, moderate, poor and bad) for each ecotype. It then requires classification of the status of the water bodies and their restoration to at least 'good status' in a specified period. 2. Though there are many methods for assessing water quality, none has the scope of that defined in the Directive. The provisions of the Directive require a wide range of variables to be measured and give only general guidance as to how systems of classification should be established. This raises issues of comparability across States and of the costs of making the determinations. 3. Using expert workshops and subsequent field testing, a practicable pan-European typology and classification system has been developed for shallow lakes, which can easily be extended to all lakes. It is parsimonious in its choice of determinands, but based on current limnological understanding and therefore as cost-effective as possible. 4. A core typology is described, which can be expanded easily in particular States to meet local conditions. The core includes 48 ecotypes across the entire European climate gradient and incorporates climate, lake area, geology of the catchment and conductivity. 5. The classification system is founded on a liberal interpretation of Annexes in the Directive and uses variables that are inexpensive to measure and ecologically relevant. The need for taxonomic expertise is minimized. 6. The scheme has been through eight iterations, two of which were tested in the field on tranches of 66 lakes. The final version, Version 8, is offered for operational testing and further refinement by statutory authorities.
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| 5. |
- Reiser, Philip G.K., et al.
(author)
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Developing a Logical Model of Yeast Metabolism
- 2001
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Reports (other academic/artistic)abstract
- With the completion of the sequencing of genomes of an increasing number of organisms, the focus of biology is moving to determining the role of these genes (functional genomics). To this end it is useful to view the cell as a biochemical machine: it consumes simple molecules to manufacture more complex ones by chaining together biochemical reactions into long sequences referred to as metabolic pathways. Such metabolic pathways are not linear but often intersect to form a complex network. Genes play a fundamental role in this network by synthesising the enzymes that catalyse biochemical reactions. Although developing a complete model of metabolism is of fundamental importance to biology and medicine, the size and complexity of the network has proven beyond the capacity of human reasoning. This paper presents intermediate results in the Robot Scientist research programme that aims to discover the function of genes in the metabolism of the yeast Saccharomyces cerevisiae. Results include: (1) the first logical model of metabolism; (2) a method to predict phenotype by deductive inference; and (3) a method to infer reactions and gene function by abductive inference. We describe the in vivo experimental set-up which will allow these in silico inferences to be automatically tested by a laboratory robot.
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| 6. |
- Stephen, D, et al.
(author)
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Continental-scale patterns of nutrient and fish effects on shallow lakes: introduction to a pan-European mesocosm experiment
- 2004
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In: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 49:12, s. 1517-1524
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Journal article (peer-reviewed)abstract
- 1. Shallow lake ecosystems are normally dominated by submerged and emergent plants. Biological stabilising mechanisms help preserve this dominance. The systems may switch to dominance by phytoplankton, however, with loss of submerged plants. This process usually takes place against a background of increasing nutrient loadings but also requires additional switch mechanisms, which damage the plants or interfere with their stabilising mechanisms. 2. The extent to which the details or even major features of this general model may change with geographical location are not clear. Manipulation of the fish community (biomanipulation) has often been used to clear the water of algae and restore the aquatic plants in northerly locations, but it is again not clear whether this is equally appropriate at lower latitudes. 3. Eleven parallel experiments (collectively the International Mesocosm Experiment, IME) were carried out in six lakes in Finland, Sweden, England, the Netherlands and Spain in 1998 and 1999 to investigate the between-year and large-scale spatial variation in relationships between nutrient loading and zooplanktivorous fish on submerged plant and plankton communities in shallow lakes. 4. Comparability of experiments in different locations was achieved to a high degree. Cross-laboratory comparisons of chemical analyses revealed some systematic differences between laboratories. These are unlikely to lead to major misinterpretations. 5. Nutrient addition, overall, had its greatest effect on water chemistry then substantial effects on phytoplankton and zooplankton. Fish addition had its major effect on zooplankton and did not systematically change the water chemistry. There was no trend in the relative importance of fish effects with latitude, but nutrient addition affected more variables with decreasing latitude. 6. The relative importance of top-down and bottom-up influences on the plankton differed in different locations and between years at the same location. The outcome of the experiments in different years was more predictable with decreasing latitude and this was attributed to more variable weather at higher latitudes that created more variable starting conditions for the experiments.
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| 7. |
- Vakkilainen, K, et al.
(author)
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Response of zooplankton to nutrient enrichment and fish in shallow lakes: a pan-European mesocosm experiment
- 2004
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In: Freshwater Biology. - : Wiley. - 0046-5070 .- 1365-2427. ; 49:12, s. 1619-1632
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Journal article (peer-reviewed)abstract
- 1. Responses of zooplankton to nutrient enrichment and fish predation were studied in 1998 and 1999 by carrying out parallel mesocosm experiments in six lakes across Europe. 2. Zooplankton community structure, biomass and responses to nutrient and fish manipulation showed geographical and year-to-year differences. Fish had a greater influence than nutrients in regulating zooplankton biomass and especially the relative abundances of different functional groups of zooplankton. When fish reduced the biomass of large crustaceans, there was a complementary increase in the biomasses of smaller crustacean species and rotifers. 3. High abundance of submerged macrophytes provided refuge for zooplankton against fish predation but this refuge effect differed notably in magnitude among sites. 4. Large crustacean grazers (Daphnia, Diaphanosoma, Sida and Simocephalus) were crucial in controlling algal biomass, while smaller crustacean grazers and rotifers were of minor importance. Large grazers were able to control phytoplankton biomass even under hypereutrophic conditions (up to 1600 mug TP L-1) when grazer biomass was high (>80-90 mug dry mass L-1) or accounted for >30% of the grazer community. 5. The littoral zooplankton community was less resistant to change following nutrient enrichment in southern Spain, at high temperatures (close to 30degreesC), than at lower temperatures (17-23degreesC) characterising the other sites. This lower resistance was because of a greater importance of nutrients than zooplankton in controlling algal biomass. 6. Apart from the reduced role of large crustacean grazers at the lowest latitude, no consistent geographical patterns were observed in the responses of zooplankton communities to nutrient and fish manipulation.
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| 8. |
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| 9. |
- Avakian, Maureen D., et al.
(author)
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The origin, fate, and health effects of combustion by-products : A research framework
- 2002
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In: Journal of Environmental Health Perspectives. - : National Institute of Environmental Health Sciences. - 0091-6765 .- 1552-9924. ; 110:11, s. 1155-1162
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Journal article (peer-reviewed)abstract
- Incomplete combustion processes can emit organic pollutants, metals, and fine particles. Combustion by-products represent global human and environmental health challenges that are relevant not only in heavily industrialized nations, but also in developing nations where up to 90% of rural households rely on unprocessed biomass fuels for cooking, warmth, and light. These issues were addressed at the Seventh International Congress on Combustion BY-Products, which convened 4-6 June 2001 in Research Triangle Park, North Carolina. This congress included a diverse group of multidisciplinary researchers and practitioners who discussed recent developments and future goals in the control of combustion by-products and their effects of exposure on human and ecologic health. Participants recommended that interdisciplinary, coordinated research efforts should be focused to capitalize on the important potential synergisms between efforts to reduce the adverse human health effects linked to exposures to combustion by-products and broader efforts to reduce greenhouse gas emissions and save energy through efficiency. In this article we summarize the principal findings and recommendations for research focus and direction.
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| 10. |
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