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For a comprehensive review of the most interesting recent articles published in the biological sciences, visit Faculty of 1000 Biology, an online literature awareness tool published by BioMed Central. Faculty of 1000 Biology systematically highlights exciting recent publications on the basis of recommendations of a faculty of well over 1,000 of the world's leading researchers. |
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Jurg Bahler
The Wellcome Trust Sanger Institute, United Kingdom States
CELL BIOLOGY
 Confirmation
 New Finding
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This is the first genome-wide survey of TATA-box protein (TBP) binding, revealing a universal importance of TBP in determining transcript levels. This careful study shows that RNA polymerase III promoters are most prevalent as binding targets for TBP, and there is a clear correlation between transcript levels and recruitment of TBP to promoters. Surprisingly, consensus TATA elements do not appear to be critical for TBP binding or high gene expression levels.
Evaluated 29 Nov 2004 |
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Richard Leegood
University of Sheffield, United Kingdom
PLANT BIOLOGY
 Tech Advance
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This paper provides the first comprehensive set of data on the relationship between transcripts and enzyme activity in plants. It shows clearly that diurnal changes in transcript abundance are not immediately linked to changes in enzyme activity. The findings have important implications for reseachers using changes in gene expression to infer physiological changes in plants.
Evaluated 15 Dec 2004 |
Wolf B. Frommer
Carnegie Institution of Washington, United States of America
PLANT BIOLOGY
Tech Advance
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A sensitive high throughput platform was developed for parallel measurement of enzyme activities using cycling assays. Proof of concept is provided to compare diurnal cycles for enzyme activities and corresponding transcriptome data. The results are highly relevant for interpretations derived from transcript profiling.
Evaluated 7 Dec 2004 |
Nico Von Wiren
University of Hohenheim, Germany
PLANT BIOLOGY
Tech Advance
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This study describes the first development of an automated platform for the high-throughput determination of enzyme activities in plant extracts. A comparison between enzyme activities and transcript profiles showed that transcripts of many central enzymes of C and N metabolism followed a diurnal cycle while most enzyme activities did not correlate to that. It has been concluded that enzyme activities provide a more reliable integration of different regulatory levels and have a higher potential for the diagnosis of the physiological state of a plant.
Evaluated 6 Dec 2004 |
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Matthew Sachs
Oregon Health and Science University, United States
CELL BIOLOGY
New Finding
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This is the first description of analyses of a large group of ascomycete fungi that combines genome-scale analyses of cis-acting regulatory motifs with direct experimental analyses. It reveals important similarities and differences in the distribution of regulatory motifs that are known to be functional, and identifies additional potential regulatory sequences that appear conserved, in different fungal genomes.
Evaluated 3 Dec 2004 |
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Paula Sundstrom
Dartmouth Medical school, United States
MICROBIOLOGY
 Hypothesis
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This article was interesting because it sheds light on the relatedness of Candida albicans to C. dubliniensis as well as on the differences that may be the cause of the variation in pathogenicity of the two strains. Sequence divergence was identified in several genes with putative virulence functions, including the gene encoding the hypha-specific human transglutaminase substrate Hwp1p as well as other cell wall proteins and secreted aspartyl proteinases. The study prompts an interest in further comparisons of the genomes to determine if C. dubliniensis contains novel genes not present in C. albicans.
Evaluated 3 Dec 2004 |
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F1000 Factor 3.0 |
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From ORFeome to biology: a functional genomics pipeline.
Wiemann S, Arlt D, Huber W, Wellenreuther R, Schleeger S, Mehrle A, Bechtel S, Sauermann M, Korf U, Pepperkok R, Sültmann H, Poustka A
Genome Res 2004 Oct 14(10B):2136-44 [abstract on PubMed] [request from library] 
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Selected by | Deyou Zheng
Evaluated 3 Dec 2004
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Deyou Zheng
Yale University, United States
STRUCTURAL BIOLOGY
Hypothesis
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This paper presents a pipeline for identifying protein functions using a systematic approach. The pipeline integrates information from subcellular localizations, biochemical activities, interactions and differential expressions. Two points in this study deserve special attention. First, the authors found that in 1/3 of the cases the fusion of GFP could alter the cellular localization of a target protein (Fig 3). This suggests that it is important to be cautious when interpreting the results of using GFP fusion to study protein localizations. Second, the authors emphasized that statistics should be applied in both experiment designs and analyses in order to draw real biological conclusions. The assignment of a protein activity should not be made from just one or a few measurements. Instead, statistically significant observations are required to account for the biological and experimental noise from an assay (Fig 8).
Evaluated 3 Dec 2004 |
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