The dynamic ups and downs of genome size evolution in Brassicaceae

Crucifers (Brassicaceae, Cruciferae) are a large family comprisingsome 338 genera and c. 3,700 species. The family includes importantcrops as well as several model species in various fields ofplant research. This paper reports new genome size (GS) datafor more than 100 cruciferous species in addition to previouslypublished C-values (the DNA amount in the unreplicated gameticnuclei) to give a data set comprising 185 Brassicaceae taxa,including all but 1 of the 25 tribes currently recognized. Evolutionof GS was analyzed within a phylogenetic framework based ongene trees built from five data sets (matK, chs, adh, trnLF,and ITS). Despite the 16.2-fold variation across the family,most Brassicaceae species are characterized by very small genomeswith a mean 1C-value of 0.63 pg. The ancestral genome size (ancGS)for Brassicaceae was reconstructed as ^anc1C = 0.50 pg. Approximately50% of crucifer taxa analyzed showed a decrease in GS comparedwith the ancGS. The remaining species showed an increase inGS although this was generally moderate, with significant increasesin C-value found only in the tribes Anchonieae and Physarieae.Using statistical approaches to analyze GS, evolutionary gainsor losses in GS were seen to have accumulated disproportionatelyfaster within longer branches. However, we also found that GShas not changed substantially through time and most likely evolvespassively (i.e., a tempo that cannot be distinguished betweenneutral evolution and weak forms of selection). The data revealan apparent paradox between the narrow range of small GSs overlong evolutionary time periods despite evidence of dynamic genomicprocesses that have the potential to lead to genome obesity(e.g., transposable element amplification and polyploidy). Toresolve this, it is suggested that mechanisms to suppress amplificationand to eliminate amplified DNA must be active in Brassicaceaealthough their control and mode of operation are still poorlyunderstood.     

Novel factor Xa inhibitors based on a benzoic acid scaffold and incorporating a neutral P1 ligand

A series of novel, highly potent, achiral factor Xa inhibitors based on a benzoic acid scaffold and containing a chlorophenethyl moiety directed towards the protease S1 pocket is described. A number of structural features, such as the requirements of the P1, P4 and ester-binding pocket ligands were explored with respect to inhibition of factor Xa. Compound 46 was found to be the most potent compound in a series of antithrombotic secondary assays.     

PatentMatrix: an automated tool to survey patents related to large sets of genes or proteins

Background  

The enormity of the information contained in large data sets makes it difficult to develop intuitive understanding. It would be useful to have software that allows visualization of possible correlations between properties that can be associated with a core data set. In the case of bacterial genomes, existing visualization tools focus on either global properties such as variations in composition or detailed local displays of the features that comprise the annotation. It is not easy to visualize other information in the context of this core information.     

Functional analysis of D-alanylation of lipoteichoic acid in the probiotic strain Lactobacillus rhamnosus GG

Lipoteichoic acid (LTA) is a macroamphiphile molecule which performs several functions in gram-positive bacteria, such as maintenance of cell wall homeostasis. D-alanylation of LTA requires the proteins encoded by the dlt operon, and this process is directly related to the charge properties of this polymer strongly contributing to its function. The insertional inactivation of dltD of the probiotic strain Lactobacillus rhamnosus GG (ATCC 53103) resulted in the complete absence of D-alanyl esters in the LTA as confirmed by nuclear magnetic resonance analysis. This was reflected in modifications of the bacterial cell surface properties. The dltD strain showed 2.4-fold-increased cell length, a low survival capacity in response to gastric juice challenge, an increased sensitivity to human beta-defensin-2, an increased rate of autolysis, an increased capacity to initiate growth in the presence of an anionic detergent, and a decreased capacity to initiate growth in the presence of cationic peptides compared to wild-type results. However, in vitro experiments revealed no major differences for adhesion to human intestinal epithelial cells, biofilm formation, and immunomodulation. These properties are considered to be important for probiotics. The role of the dlt operon in lactobacilli is discussed in view of these results.     

Rudist decline in the Maastrichtian Cardenas Formation (East-central Mexico)

Five sections of the Cardenas and Tabaco formations in east-central Mexico have been analyzed by means of bio-, Sr-isotope, and sequence stratigraphy, in order to evaluate their age as well as the timing of rudist decline.Ammonites [Pachydiscus (Pachydiscus) neubergicus (Hauer), Sphenodiscus pleurisepta (Conrad), Coahuilites sheltoni Böse] indicate an early Maastrichtian age for the topmost lower member of the Cardenas Formation and planktic foraminifera [e.g., Globotruncanita stuarti (de Lapparent), Archaeoglobigerina cretacea (d’Orbigny), Globotruncanella petaloidea (Gandolfi), Gansserina gansseri (Bolli), Globotruncana linneiana (d’Orbigny)] a late early Maastrichtian age for the middle member corresponding to the foraminiferal zones CF5 and CF6. Sr-isotope stratigraphic data yield an early late Maastrichtian age (66.93 Ma < 67.98 Ma < 68.96 Ma) for the last rudist assemblage in the topmost upper member of the Cardenas Formation, coinciding with the foraminiferal zone CF4.17 small-scale and 3 large-scale depositional cycles have been identified, which correspond to para- and depositional sequences. The progradational pattern of the large-scale cycles indicates an overall regression trend, which terminated in subaerial exposure of the area, indicated by paleosoils in the red beds of the Tabaco Formation. The correlation of the large-scale cycles with the global sea level charts indicate that eustatic sea level fall caused the regression and led to the exposure during the middle late Maastrichtian. This subaerial exposure resulted in the loss of habitat and thus the disappearance of rudists in east-central Mexico.     

Activation of the heterodimeric central complex SoxYZ of chemotrophic sulfur oxidation is linked to a conformational change and SoxY-Y interprotein disulfide formation

The central protein of the four component sulfur oxidizing (Sox) enzyme system of Paracoccus pantotrophus, SoxYZ, carries at the SoxY subunit the covalently bound sulfur substrate which the other three proteins bind, oxidize, and release as sulfate. SoxYZ of different preparations resulted in different specific thiosulfate-oxidizing activities of the reconstituted Sox enzyme system. From these preparations SoxYZ was activated up to 24-fold by different reductants with disodium sulfide being the most effective and yielded a uniform specific activity of the Sox system. The activation comprised the activities with hydrogen sulfide, thiosulfate, and sulfite. Sulfide-activation decreased the predominant beta-sheet character of SoxYZ by 4%, which caused a change in its conformation as determined by infrared spectroscopy. Activation of SoxYZ by sulfide exposed the thiol of the C-terminal Cys-138 of SoxY as evident from alkylation by 4-acetamido-4'-maleimidylstilbene-2,2'-disulfonic acid. Also, SoxYZ activation enhanced the formation of the Sox(YZ)2 heterotetramer as evident from density gradient gel electrophoresis. The tetramer was formed due to an interprotein disulfide between SoxY to yield a SoxY-Y dimer as determined by combined high pressure liquid chromatography and mass spectrometry. The significance of the conformational change of SoxYZ and the interprotein disulfide between SoxY-Y is discussed.     

<Emphasis Type="Italic">Decapentaplegic</Emphasis> (<Emphasis Type="Italic">dpp</Emphasis>) regulates the growth of a morphological novelty,beetle horns

Studies focusing on the development of morphological novelties suggest that patterning genes underlying traditional appendage development (i.e. mouthparts, legs, and wings) also play important roles in patterning novel morphological structures. In this study, we examine whether the expression and function of a member of the TGF-β signaling pathway, decapentaplegic (dpp), promotes development of a morphologically novel structure: beetle horns. Beetle horns are complex secondary sexual structures that develop in the head and/or prothorax, lack obvious homology to other insect outgrowths, and vary remarkably between species and sexes. We studied dpp expression through in situ hybridization, performed functional analyses with RNA interference, and gathered allometric measurements to determine the role of dpp during both pronotal and head horn development in both sexes of two morphologically dissimilar species in the Onthophagus genus, Onthophagus binodis and Onthophagus sagittarius. Our findings show that in addition to affecting growth and patterning of traditional appendages, dpp regulates beetle horn growth and remodeling.