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Genome Biology 2005, 6(5):323
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Recommended
F1000 Factor 3.0


Functional evolution of a cis-regulatory module.
Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, Kreitman M
PLoS Biol 2005 Apr 3(4):e93 [
abstract on PubMed][FREE full text]
Selected by | John True
Evaluated 20 Apr 2005

Faculty Comments
Faculty Member Comments
John True
State University of New York at Stony Brook, United States of America
DEVELOPMENTAL BIOLOGY


Confirmation
These authors confirm that cis-regulatory elements evolve according to different rules than coding regions. Ludwig and colleagues conduct functional tests of the even-skipped stripe 2 enhancer, whose spatial pattern of expression is conserved among Drosophila species, to determine whether elements from distantly related species can rescue eve expression and viability in flies bearing an engineered deletion of this element. The biggest surprises are that functional evolution of the enhancer does not follow clocklike dynamics and that phylogenetic relatedness is not a good predictor of the degree of functional conservation.

Evaluated 20 Apr 2005

Recommended
F1000 Factor 3.0


A systems analysis of importin-{alpha}-{beta} mediated nuclear protein import.
Riddick G, Macara IG
J Cell Biol 2005 Mar 28 168(7):1027-38 [
abstract on PubMed] [request from library]
Selected by | Tom Misteli
Evaluated 13 Apr 2005

Faculty Comments
Faculty Member Comments
Tom Misteli
National Cancer Institute, NIH, USA, United States of America
CELL BIOLOGY


Hypothesis
New Finding
Tech Advance
This study represents the most comprehensive computational analysis of nuclear protein import to date. The computational analysis is based on a multitude of experimentally determined rate constants and several unexpected predictions generated by the model regarding mechanistic details of nuclear import were experimentally confirmed.

Evaluated 13 Apr 2005

Recommended
F1000 Factor 3.0


Drosophila genome-scale screen for PAN GU kinase substrates identifies Mat89Bb as a cell cycle regulator.
Lee LA, Lee E, Anderson MA, Vardy L, Tahinci E, Ali SM, Kashevsky H, Benasutti M, Kirschner MW, Orr-Weaver TL
Dev Cell 2005 Mar 8(3):435-42 [
abstract on PubMed] [request from library]
Selected by | Prasad Jallepalli
Evaluated 7 Apr 2005

Faculty Comments
Faculty Member Comments
Prasad Jallepalli
Memorial Sloan-Kettering Cancer Center, United States of America
CELL BIOLOGY


New Finding
This paper takes advantage of the Drosophila Gene Collection to identify substrates for the Pan Gu kinase, which plays a key role in ensuring S-M phase alternation during the embyronic cell cycles. Using the IVEC (in vitro expression cloning) technique to in vitro translate a normalized and annotation collection of full-length Drosophila cDNAs, Lee et al. identify one protein, Mat89Bb, which is modified by Pan Gu-dependent phosphorylation. Gene depletion studies in Drosophila, Xenopus, and HeLa cells implicate Mat89Bb in suppression of polyploidy. While more will need to be done to understand Mat89Bb's mechanism of action, this study shows the power of coupled genomic/proteomic techniques in identifying kinase substrates.

Evaluated 7 Apr 2005

Recommended
F1000 Factor 3.0


The stability of the Arabidopsis transcriptome in transgenic plants expressing the marker genes nptII and uidA.
El Ouakfaoui S, Miki B
Plant J 2005 Mar 41(6):791-800 [
abstract on PubMed] [request from library]
Selected by | Seth J Davis
Evaluated 13 Apr 2005

Faculty Comments
Faculty Member Comments
Seth J Davis
Max Planck Institute for Plant Breeding Research, Germany
PLANT BIOLOGY


Tech Advance
This is an important technical paper as it reveals that introduction of the most common foreign proteins into Arabidopsis does not have a dramatic effect on global transcription patterns. This paper provides a "sigh of relief" for the plant transgenic community.

Evaluated 13 Apr 2005

Recommended
F1000 Factor 3.0


Dynamic chromatin modifications characterise the first cell cycle in mouse embryos.
Santos F, Peters AH, Otte AP, Reik W, Dean W
Dev Biol 2005 Apr 1 280(1):225-36 [
abstract on PubMed] [request from library]
Selected by | Richard J Chaillet
Evaluated 14 Apr 2005

Faculty Comments
Faculty Member Comments
Richard J Chaillet
Children's Hospital of Pittsburgh, United States of America
GENOMICS & GENETICS


Hypothesis
New Finding
This article details important epigenetic changes in maternal and paternal chromatin during the critical first embryonic cell cycle in the mouse. The result is an intriguing model of rapid and coordinated histone and DNA modifications leading to an active, remodelled and reprogrammed embryonic genome.

Evaluated 14 Apr 2005













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