- beg-evodevo@psb.ugent.be - maillist.psb.ugent.be

[Beg-evodevo] MicroRNAs and the advent of vertebrate morphologic...[Proc Natl Acad Sci U S A. 2008] - PubMed Result
by Yves Van de Peer 24 Feb '08

24 Feb '08

http://www.ncbi.nlm.nih.gov/pubmed/18287013?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] FYI: Duplicate gene evolution and expression in the wake of vertebrate allopolyploidization
by Steven Maere 18 Feb '08

18 Feb '08

-- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] FYI: Functional protein divergence in the evolution of Homo sapiens, Teichmann groep
by Steven Maere 15 Feb '08

15 Feb '08

-- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] Book review :: The Origins of Genome Architecture, , by Michael Lynch
by Klaas Vandepoele 13 Feb '08

13 Feb '08

http://www.nature.com/nature/journal/v451/n7180/full/451771b.html

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[Beg-evodevo] Protein under-wrapping causes dosage sensitivity and decreases gene duplicability
by Stefanie De Bodt 11 Feb '08

11 Feb '08

http://genetics.plosjournals.org/archive/1553-7404/4/1/pdf/10.1371_journal.… -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Bioinformatics and Evolutionary Genomics Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://bioinformatics.psb.ugent.be ==================================================================

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[Beg-evodevo] Coevolution of gene families in prokaryotes
by Klaas Vandepoele 30 Jan '08

30 Jan '08

Coevolution of gene families in prokaryotes * Otto X. Cordero^1 , Berend Snel, and Paulien Hogeweg * / Theoretical Biology and Bioinformatics, University of Utrecht, 3584 CH Utrecht, The Netherlands / We study gene family coevolution on a tree of life based on^ a large-scale ancestral gene content reconstruction, which includes^ gene duplication and deletion events. The insights obtained^ from this study are threefold: (1) Global properties, such as^ the distribution of coevolution partners and the formation of^ disconnected clusters of coevolving families, can be an inevitable^ consequence of evolution along a tree. (2) Concerted family^ expansion (gene duplication) and contraction (gene deletion)^ reflect functional constraints and therefore lead to better^ function prediction. (3) "Long-range" coevolutionary relationships,^ caused mostly by large family expansions or contractions, reveal^ high-level evolutionary organization of cellular processes in^ prokaryotes. -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] PubMed :: Duplicated P5CS genes of Arabidopsis play distinct roles in stress regulation and developmental control of proline biosynthesis
by Klaas Vandepoele 21 Dec '07

21 Dec '07

*Duplicated P5CS genes of Arabidopsis play distinct roles in stress regulation and developmental control of proline biosynthesis* ?-1-pyrroline-5-carboxylate synthetase enzymes, which catalyse the rate-limiting step of proline biosynthesis, are encoded _by two closely related P5CS genes in Arabidopsis_. Transcription of the P5CS genes is differentially regulated by drought, salinity and abscisic acid, suggesting that these genes play specific roles in the control of proline biosynthesis. Here we describe the genetic characterization of p5cs insertion mutants, which indicates that P5CS1 is required for proline accumulation under osmotic stress. Knockout mutations of P5CS1 result in the reduction of stress-induced proline synthesis, hypersensitivity to salt stress, and accumulation of reactive oxygen species. By contrast, p5cs2 mutations cause embryo abortion during late stages of seed development. The desiccation sensitivity of p5cs2 embryos does not reflect differential control of transcription, as both P5CS mRNAs are detectable throughout embryonic development. Cellular localization studies with P5CS--GFP gene fusions indicate that P5CS1 is sequestered into subcellular bodies in embryonic cells, where P5CS2 is dominantly cytoplasmic. Although proline feeding rescues the viability of mutant embryos, p5cs2 seedlings undergo aberrant development and fail to produce fertile plants even when grown on proline. In seedlings, specific expression of P5CS2--GFP is seen in leaf primordia where P5CS1--GFP levels are very low, and P5CS2--GFP also shows a distinct cell-type-specific and subcellular localization pattern compared to P5CS1--GFP in root tips, leaves and flower organs. _These data demonstrate that the Arabidopsis P5CS enzymes perform non-redundant functions, and that P5CS1 is insufficient for compensation of developmental defects caused by inactivation of P5CS2_. http://www.blackwell-synergy.com/doi/full/10.1111/j.1365-313X.2007.03318.x -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] Reconstruction of ancestral protein interaction networks for the bZIP transcription factors
by Klaas Vandepoele 21 Dec '07

21 Dec '07

Greg in action! Klaas -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-evodevo] [Fwd: (no subject)]
by Yves Van de Peer 09 Dec '07

09 Dec '07

-- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-evodevo] Extensive concerted evolution of rice paralogs and the road to regaining independence [Genetics. 2007] - PubMed Result
by Klaas Vandepoele 03 Dec '07

03 Dec '07

Extensive concerted evolution of rice paralogs and the road to regaining independence. Wang X, Tang H, Bowers JE, Feltus FA, Paterson AH. Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602. Many genes duplicated by whole-genome duplications (WGDs) are more similar to one another than expected. We investigated whether concerted evolution through conversion and crossing over, well-known to affect tandem gene clusters, also affects dispersed paralogs. Genome sequences for two Oryza subspecies reveal appreciable gene conversion in the approximately 0.4 MY since their divergence, with a gradual progression toward independent evolution of older paralogs. Since divergence from subspecies indica, approximately 8% of japonica paralogs produced 5-7 MYA on chromosomes 11 and 12 have been affected by gene conversion and several reciprocal exchanges of chromosomal segments, while approximately 70-MY-old "paleologs" resulting from a genome duplication (GD) show much less conversion. Sequence similarity analysis in proximal gene clusters also suggests more conversion between younger paralogs. About 8% of paleologs may have been converted since rice-sorghum divergence approximately 41 MYA. Domain-encoding sequences are more frequently converted than nondomain sequences, suggesting a sort of circularity-that sequences conserved by selection may be further conserved by relatively frequent conversion. The higher level of concerted evolution in the 5-7 MY-old segmental duplication may reflect the behavior of many genomes within the first few million years after duplication or polyploidization. http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&dopt=AbstractPlus&db=… -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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