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- Dujon, B, et al.
(författare)
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The nucleotide sequence of Saccharomyces cerevisiae chromosome XV
- 1997
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 387:6632, s. 98-102
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Tidskriftsartikel (refereegranskat)abstract
- Chromosome XV was one of the last two chromosomes of Saccharomyces cerevisiae to be discovered(1). It is the third-largest yeast chromosome after chromosomes XII and IV, and is very similar in size to chromosome VII. It alone represents 9% of the yeast genome (8% if ribosomal DNA is included). When systematic sequencing of chromosome XV was started, 93 genes or markers were identified, and most of them were mapped(2). However, very little else was known about chromosome XV which, in contrast to shorter chromosomes, had not been the object of comprehensive genetic or molecular analysis. It was therefore decided to start sequencing chromosome XV only in the third phase of the European Yeast Genome Sequencing Programme, after experience was gained on chromosomes III, XI and II (refs 3-5). The sequence of chromosome XV has been determined from a set of partly overlapping cosmid clones derived from a unique yeast strain, and physically mapped at 3.3-kilobase resolution before sequencing. As well as numerous new open reading frames (ORFs) and genes encoding tRNA or small RNA molecules, the sequence of 1,091,283 base pairs confirms the high proportion of orphan genes and reveals a number of ancestral and successive duplications with other yeast chromosomes.
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| 3. |
- Moss, B, et al.
(författare)
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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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Ingår i: Aquatic Conservation: Marine and Freshwater Ecosystems. - : Wiley. - 1052-7613. ; 13:6, s. 507-549
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Tidskriftsartikel (refereegranskat)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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- Jacobsen, Marc, et al.
(författare)
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Deconfounding microarray analysis : independent measurements of cell type proportions used in a regression model to resolve tissue heterogeneity bias
- 2006
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Ingår i: Methods of Information in Medicine. - Stuttgart, Germany : Schattauer Gmbh. - 0026-1270 .- 2511-705X. ; 45:5, s. 557-63
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Microarray analysis requires standardized specimens and evaluation procedures to achieve acceptable results. A major limitation of this method is caused by heterogeneity in the cellular composition of tissue specimens, which frequently confounds data analysis. We introduce a linear model to deconfound gene expression data from tissue heterogeneity for genes exclusively expressed by a single cell type.Methods: Gene expression data are deconfounded from tissue heterogeneity effects by analyzing them using an appropriate linear regression model. In our illustrating data set tissue heterogeneity is being measured using flow cytometry. Gene expression data are determined in parallel by real time quantitative polymerase chain reaction (qPCR) and microarray analyses. Verification of deconfounding is enabled using protein quantification for the respective marker genes.Results: For our illustrating dataset, quantification of cell type proportions for peripheral blood mononuclear cells (PBMC) from tuberculosis patients and controls revealed differences in B cell and monocyte proportions between both study groups, and thus heterogeneity for the tissue under investigation. Gene expression analyses reflected these differences in celltype distribution. Fitting an appropriate linear model allowed us to deconfound measured transcriptome levels from tissue heterogeneity effects. In the case of monocytes, additional differential expression on the single cell level could be proposed. Protein quantification verified these deconfounded results.Conclusions: Deconfounding of transcriptome analyses for cellular heterogeneity greatly improves interpretability, and hence the validity of transcriptome profiling results.
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| 5. |
- Mobasher, B., et al.
(författare)
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Photometric redshifts of galaxies in COSMOS
- 2007
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Ingår i: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 172:1, s. 117-131
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Tidskriftsartikel (refereegranskat)abstract
- We present photometric redshifts for the COSMOS survey derived from a new code, optimized to yield accurate and reliable redshifts and spectral types of galaxies down to faint magnitudes and redshifts out to z similar to 1.2. The technique uses chi (2) template fitting, combined with luminosity function priors and with the option to estimate the internal extinction [ or E( B-V)]. The median most probable redshift, best-fit spectral type and reddening, absolute magnitude, and stellarmass are derived in addition to the full redshift probability distributions. Using simulations with sampling and noise similar to those in COSMOS, the accuracy and reliability is estimated for the photometric redshifts as a function of the magnitude limits of the sample, S/N ratios, and the number of bands used. We find from the simulations that the ratio of derived 95% confidence interval in the chi (2) probability distribution to the estimated photometric redshift (D-95) can be used to identify and exclude the catastrophic failures in the photometric redshift estimates. To evaluate the reliability of the photometric redshifts, we compare the derived redshifts with high-reliability spectroscopic redshifts for a sample of 868 normal galaxies with z < 1: 2 from zCOSMOS. Considering different scenarios, depending on using prior, no prior, and/or extinction, we compare the photometric and spectroscopic redshifts for this sample. The rms scatter between the estimated photometric redshifts and known spectroscopic redshifts is sigma(Delta( z))= 0. 031, where Delta(z) ( z(phot) - z(spec))/( 1+ z(spec)) with a small fraction of outliers (< 2.5%) [ outliers are defined as objects with Delta( z) > 3 sigma(Delta( z)), where sigma(Delta(z)) is the rms scatter in Delta( z)]. We also find good agreement [sigma(Delta(z))= 0.10] between photometric and spectroscopic redshifts for type II AGNs. We compare results fromour photometric redshift procedure with three other independent codes and find them in excellent agreement. We show preliminary results, based on photometric redshifts for the entire COSMOS sample ( to i < 25 mag).
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