My research mainly focused on the functional redundancy and expression divergence of gene duplicates to address currently unsolved problems. Herein, we employed a method based on GO terms to measure functional overlap between paralogs. We established that functional similarity between duplicate genes is the key determinant of their backup capacity. Later, we also investigated expression divergence. Recent studies suggest that only a small proportion of expression variation can be explained by transcriptional variation between paralogs. Here, the contribution from diverged TF-regulations was re-examined and differential promoter chromatin status was also found as an important contributor to expression divergence. To better understand the role of gene duplication in great detail, a case study was performed on the yeast chaperone system, which includes many gene duplicates. Taken together, this study sheds light on the roles of redundancy and divergence in long-term retention of gene duplicates.

My research mainly focused on the functional redundancy and expression divergence of gene duplicates to address currently unsolved problems. Herein, we employed a method based on GO terms to measure functional overlap between paralogs. We established that functional similarity between duplicate genes is the key determinant of their backup capacity. Later, we also investigated expression divergence. Recent studies suggest that only a small proportion of expression variation can be explained by transcriptional variation between paralogs. Here, the contribution from diverged TF-regulations was re-examined and differential promoter chromatin status was also found as an important contributor to expression divergence. To better understand the role of gene duplication in great detail, a case study was performed on the yeast chaperone system, which includes many gene duplicates. Taken together, this study sheds light on the roles of redundancy and divergence in long-term retention of gene duplicates.

The paper describes a problem particular to universal knowledge classifications with a disciplinary structure. These types of classification present concepts subsumed to the disciplines in which they are studied and thus have to resolve the problem of concepts being repeated in different fields of knowledge. The author looks into how the impact the repetition of concepts in the UDC disciplinary structure may have on information retrieval. He considers advantages and disadvantages of different approaches in presenting re-used concepts in the scheme.

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No description available.

The shikimate pathway connects primary metabolism with the biosynthesis of the three aromatic amino acids (phenylalanine, tyrosine and tryptophan), which are essential protein building blocks. This pathway also provides precursors for a wide array of plant secondary metabolites with adaptive functions in plant adaptation and defense. The third and fourth steps of the shikimate pathway (the conversion of shikimate from 3-dehydroquinate via 3-dehydroshikimate) are catalyzed by a bi-functional enzyme called 3-dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH). DQD/SDHs have been biochemically characterized in a few plant species including Arabidopsis thaliana, Solanum lycopersicum and Nicotiana tabacum. The embryo-lethal phenotype of Arabidopsis null mutants lacking DQD/SDH highlights a critical role of shikimate in primary metabolism. Quinate shares high structural similarity with shikimate and is an important secondary metabolite present in many plant species. Quinate and its derivatives (e.g. chlorogenic acid) serve important functions in plant defense due to their astringent (i.e. bitterness) and antimicrobial properties. Quinate can be derived from 3-dehydroquinate, and this reaction is catalyzed by quinate dehydrogense (QDH), the reaction mechanism of which resembles that of SDH. With a functional genomics approach, I demonstrated that two of the five poplar putative DQD/SDHs (Poptr1 and Poptr5, poplar DQD/SDH1 and 2) have exclusive specificity for shikimate, while the other three (Poptr2 to Poptr4, poplar QDH1 to 3) are involved in quinate biosynthesis. Phylogenetic reconstruction of the DQD/SDH/QDH superfamily has identified two distinct clades in seed plants that may act preferentially on either shikimate or quinate, whereas lineages that have diverged prior to the angiosperm/gymnosperm split, only have a single copy DQD/SDH. An evolutionary analysis was carried out, and the sequence of the immediate pre-duplication ancestral DQD/SDH (>300MYA) was estimated and reconstructed. Protein structure modelling and in vitro biochemical characterization of the ancestral recombinant protein was performed along with some extant members of this family (pre-duplication representatives: Rhodopirellula baltica (Rhoba), Chlamydomonas reinhardtii (Chlre), Physcomitrella patens (Phypa) and Selaginella moellendorffii (Selmo); post-duplication species: Pinus taeda (Pinta1 & Pinta2) and Populus trichocarpa (Poptr1 & Poptr3). Together, the results indicate that quinate biosynthetic activity was gained prior to duplication and remained low until it became beneficial and favored by selection. The optimization of quinate biosynthetic activity was at the expense of losing some primary shikimate biosynthetic function creating a pleiotropic conflict. This was then resolved by gene duplication and further specialization leading to genes encoding specialized enzymes (either SDH or QDH). Diversification of the DQD/SDH/QDH superfamily likely occurred through sub-functionalization via a mechanism described as “Escape from Adaptive Conflict.” / Graduate / 0307 / guojia@uvic.ca

No description available.

La plupart des plantes à fleurs ont connu au moins un évènement de duplication de génome entier (WGD) au cours de leur histoire évolutive et en particulier les membres des Brassicaceae. Ainsi, l’ancêtre commun de la tribu des Brassiceae aurait subi deux évènements successifs de WGD, générant une triplication de génome (WGT). Les évènements de WGD sont généralement suivis d’une diploïdisation impliquant des modifications génétiques, épi-génétiques et transcriptionnelles aboutissant à la formation d’un génome diploïde. Par ailleurs, après un événement de WGD, la dynamique des éléments transposables est perturbée, ce qui peut conduire à une augmentation des évènements de translocation. Dans une lignée de Brassiceae, une réduction de la divergence moléculaire entre allèles ainsi qu’une translocation génomique ont été observées au locus d'auto-incompatibilité (locus S). On suspecte ces patrons d’être associés aux évènements de WGD. A partir d’approches phylogénomiques et d’analyse de la diversité du locus S dans la tribu des Brassiceae, nous souhaitons déterminer si le goulot d’étranglement observé au locus S chez les Brassiceae est contemporain à l’événement de WGT et s’il est associé à une translocation du locus S. Mes analyses suggèrent que toutes les espèces de Brassiceae partagent un même événement de WGT mais aussi que la perte de diversité phylogénétique au locus S semble précéder la diversification des Brassiceae. Néanmoins, mes données ne me permettent pas de conclure fermement quant au lien entre translocation génomique du locus S et événement de WGT, bien qu’elles indiquent que la translocation observée chez Brassica est partagée par plusieurs clades de Brassiceae. / Whole genome duplication events are common in flowering plants and especially within the Brassicaceae family. For example, the common ancestor of the Brassiceae tribe has experienced two successive WGD events, generating a whole genome triplication (WGT). WGD events are generally followed by a diploidization process involving genetic, epigenetic and structural changes leading to a diploid genome. Furthermore, after such an event, the dynamic of transposable elements is disturbed, which can lead to an increase in translocation events. In one lineage of the Brassiceae tribe, a decrease of molecular divergence among alleles and a genomic translocation have been observed at the self-incompatibility locus (S locus). We suspect that these patterns are associated with the allopolyploidy events. Using phylogenomic approaches combined with S-locus diversity analyses, we aim at determining whether the bottleneck observed at the S-locus in the Brassiceae tribe is contemporaneous with the inferred whole genome triplication and whether these events are also associated with the translocation of the S-locus. My analyses suggest that all Brassiceae species share the same whole genome triplication event as well as a loss of phylogenetic diversity at the S-locus predating the divergence of Brassiceae lineages. Nevertheless, my data do not allow me to conclude about the association between the genomic translocation of the S locus and the whole genome triplication event, although they indicate that the translocation found in Brassica is shared by several Brassiceae clades.

Thesis (Ph. D.)--University of Washington, 2005. / Vita. Includes bibliographical references (p. 119-126).

Meiosis is a specialized cell division that produces haploid gametes from a diploid progenitor cell. It consists of one round of DNA replication followed by two consecutive rounds of chromosome segregation. Homologous chromosomes segregate in meiosis I and sister chromatids segregate in meiosis II. Failure to correctly regulate meiosis can result in aneuploidy, where daughter cells inherit an incorrect number of chromosomes. Aneuploidy is usually poorly tolerated in eukaryotes, and is associated with infertility, miscarriages and birth defects. At the meiosis I to meiosis II transition, DNA replication does not occur between chromosome segregation steps despite the need for Spindle Pole Bodies (SPBs) to be re-licensed in order to build meiosis II spindles. The mechanisms that make this distinction are not yet known. In budding yeast, the protein phosphatase Cdc14 is essential for the progression of cells into meiosis II. Cdc14 is sequestered for the majority of the cell cycle in the nucleolus by the inhibitor Cfi1/Net, and is only released in anaphase. We have observed Cdc14 localizing to and interacting with SPB components when nucleolar sequestration is inhibited. Through fluorescence microscopy and EM analysis, we have determined that Cdc14 is required for the re-duplication of SPBs after meiosis I. Our data implies a role for Cdc14 in the phospho-regulation of SPB half-bridge component Sfi1. Cdc14 is therefore essential for the relicensing of SPB duplication, a crucial step necessary to ensure accurate chromosome segregation in meiosis.