Chromosomal Evolution and Patterns of Introgression in Helianthus

Knowledge of the nature and extent of karyotypic differences between species provides insight into the evolutionary history of the genomes in question and, in the case of closely related species, the potential for genetic exchange between taxa. We constructed high-density genetic maps of the silverleaf sunflower (Helianthus argophyllus) and Algodones Dune sunflower (H. niveus ssp. tephrodes) genomes and compared them to a consensus map of cultivated sunflower (H. annuus) to identify chromosomal rearrangements between species. The genetic maps of H. argophyllus and H. niveus ssp. tephrodes included 17 linkage groups each and spanned 1337 and 1478 cM, respectively. Comparative analyses revealed greater divergence between H. annuus and H. niveus ssp. tephrodes (13 inverted segments, 18 translocated segments) than between H. annuus and H. argophyllus (10 inverted segments, 8 translocated segments), consistent with their known phylogenetic relationships. Marker order was conserved across much of the genome, with 83 and 64% of the H. argophyllus and H. niveus ssp. tephrodes genomes, respectively, being syntenic with H. annuus. Population genomic analyses between H. annuus and H. argophyllus, which are sympatric across a portion of the natural range of H. annuus, revealed significantly elevated genetic structure in rearranged portions of the genome, indicating that such rearrangements are associated with restricted gene flow between these two species.     

Stereoselective ring contraction of 2,5-diketopiperazines: An innovative approach to the synthesis of promising bioactive 5-membered scaffolds

Ring contraction of 2,5-diketopiperazines by TRAL-alkylation led us to the stereoselective synthesis of original pyrrolidine-2,4-diones, a novel series of promising molecules with moderate anti-proliferative activity on breast cancer cells.     

Synthesis and enantioselective rearrangement of (Z)-4-triphenylmethoxy-2,3-epoxybutan-1-ol enantiomers

Efficient enzyme catalyzed kinetic resolutions of a synthetically useful chiral building block, (Z)-4-triphenylmethoxy-2,3-epoxybutan-1-ol, are reported. The highest selectivities were achieved by Lipozyme TL IM and Amano Lipase PS enzymes in the presence of vinyl acetate. Enantiomeric enrichment of the optically active acetate isomer was accomplished by selective crystallization of the racemic part of the enantiomeric mixture. Enzyme catalyzed hydrolysis of the acetate also provided an optically pure epoxybutanol derivative. O-Benzylation of (+)-(Z)-1-hydroxy-4-triphenylmethoxy-2,3-epoxybutane followed by super base promoted diastereo- and enantio-selective rearrangement resulted in (+)-(2R,3R,1'R)-3-[1-hydroxy-2-(triphenylmethoxy)ethyl]-2-phenyloxetane in >98% ee and de. Configurations of the new optically active products were determined by chemical correlation.     

Population genomics and speciation in yeasts

The advent of efficient whole genome sequencing and the large molecular and genetic toolbox available for studies in Saccharomyces cerevisiae and related species have allowed unprecedented analysis of big issues such as: what causes reproductive isolation and eventual speciation? The species complex encompassing S. cerevisiae and relatives consists of six species and several naturally occurring hybrids, which have nearly collinear genomes. They fit the biological species definition of within species fertility and between species sterility. There are examples of chromosome rearrangements and of genetic incompatibilities between species of the complex, which contribute to reproductive isolation but these are not universally present. In addition, simple sequence divergence has been shown to cause reproductive isolation via the action of the mismatch repair system. Although all three of these mechanisms contribute to extant reproductive isolation, which if any, drive the speciation process is still an open question. Population genomic surveys of whole genome sequences reveal introgressions and horizontal gene transfers between species, indicating that the species barriers are not complete. This gene flow between species, although infrequent, brings into question the nature of yeast species.     

Novel Repetitive Structures, Deviant Protein-Encoding Sequences andUnidentified ORFs in the Mitochondrial Genome of the BrachiopodLingula anatina

Complete sequence determination of the brachiopod Lingula anatina mtDNA (28,818 bp) revealed an organization that is remarkably atypical for an animal mt-genome. In addition to the usual set of 37 animal mitochondrial genes, which make up only 57% (16,555 bp) of the entire sequence, the genome contains lengthy unassigned sequences. All the genes are encoded in the same DNA strand, generally in a compact way, whereas the overall gene order is highly divergent in comparison with known animal mtDNA. Individual genes are generally longer and deviate considerably in sequence from their homologues in other animals. The genome contains two major repeat regions, in which 11 units of unassigned sequences and six genes (atp8, trnM, trnQ, trnV, and part of cox2 and nad2) are found in repetition, in the form of nested direct repeats of unparalleled complexity. One of the repeat regions contains unassigned repeat units dispersed among several unique sequences, novel repetitive structure for animal mtDNAs. Each of those unique sequences contains an open reading frame for a polypeptide between 80 and 357 amino acids long, potentially encoding a functional molecule, but none of them has been identified with known proteins. In both repeat regions, tRNA genes or tRNA gene-like sequences flank major repeated units, supporting the view that those structures play a role in the mitochondrial gene rearrangements. Although the intricate repeated organization of this genome can be explained by recurrent tandem duplications and subsequent deletions mediated by replication errors, other mechanisms, such as nonhomologous recombinations, appear to explain certain structures more easily.     

Enantioselective synthesis of 2- and 3-substituted 2,3-dihydro[1,4]dioxino[2,3-b]pyridine derivatives and enantiomeric purity control by capillary electrophoresis

A rapid and simple procedure for enantioselective preparation of 2- and 3-substituted 2,3-dihydro[1,4]dioxino[2,3-b]pyridine derivatives (A and B, respectively) is described. The enantiomeric purity of each isomer was determined by capillary electrophoresis using a dual-cyclodextrin system (S-beta-CD/beta-CD) dissolved in formic acid-ammonia buffer (pH 4, ionic strength 50 mM).     

Rearrangements of large-insert T-DNAs in transgenic rice

Introduction of large-DNA fragments into cereals by Agrobacterium-mediated transformation is a useful technique for map-based cloning and molecular breeding. However, little is known about the organization and stability of large fragments of foreign DNA introduced into plant genomes. In this study, we produced transgenic rice plants by Agrobacterium-mediated transformation with a large-insert T-DNA containing a 92-kb region of the wheat genome. The structures of the T-DNA in four independent transgenic lines were visualized by fluorescence in situ hybridization on extended DNA fibers (fiber FISH). By using this cytogenetic technique, we showed that rearrangements of the large-insert T-DNA, involving duplication, deletion and insertion, had occurred in all four lines. Deletion of long stretches of the large-insert DNA was also observed in Agrobacterium.     

Differential effect of IL-4 and IL-13 on the expression of recombination-activating genes in mature B cells from human peripheral blood

We examined the expression of recombination-activating genes (RAG-1 and RAG-2) and activation-induced cytidine deaminase (AID) by mature human blood B cells stimulated with anti-CD40 in the presence of IL-4 or IL-13. IL-4 was an effective cofactor for RAG-1 and RAG-2 expression, whereas IL-13 was not. In addition, IL-4-dependent RAG expression combined with AID and IgE expression allowed predominant expression of newly rearranged lambda light chains on IgE+ cells generated from kappa+ cells. Although the magnitudes of IL-4- and IL-13-dependent AID and IgE expression were related to expression levels of binding subunits of the IL-4 and IL-13 receptors, IL-13 was ineffective for light chain replacement in the induced IgE+ cells due to the failure in RAG expression. Our studies using mature blood B cells indicate that IL-4-responsive cells, unlike IL-13-responsive cells, undergo lambda gene rearrangement leading to replacement in parallel with RAG expression and suggest that this replacement may contribute to the regulation of affinity maturation of IgE antibodies.