The intersectional hybrid between Weigela hortensis and W. maximowiczii (Caprifoliaceae)

Morphologically intermediate plants between Weigela hortensis (Siebold & Zucc.) K.Koch and W. maximowiczii (S.Moore) Rehder have been found in Miyagi and Yamagata Pref., northern Japan. Quantitative character analyses of flowers, pollen stainability and molecular analyses indicated that the intermediate plants were hybrids of those two species. This is the first record of an intersectional hybrid with W. maximowiczii (sect. Weigelastrum ) as one of the parent species. The morphological differences among hybrid individuals imply the possibility of backcrosses or formation of second or later generations of hybrids, although those may be quite rare because of a low frequency of viable pollen grains. Causes of hybridization between two distantly-related species in Weigela are discussed. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 138 , 369–380.     

Structural variability of C3larvin toxin. Intrinsic dynamics of the α/β fold of the C3-like group of mono-ADP-ribosyltransferase toxins

C3larvin toxin is a new member of the C3 class of the mono-ADP-ribosyltransferase toxin family. The C3 toxins are known to covalently modify small G-proteins, e.g. RhoA, impairing their function, and serving as virulence factors for an offending pathogen. A full-length X-ray structure of C3larvin (2.3 Å) revealed that the characteristic mixed α/β fold consists of a central β-core flanked by two helical regions. Topologically, the protein can be separated into N and C lobes, each formed by a β-sheet and an α-motif, and connected by exposed loops involved in the recognition, binding, and catalysis of the toxin/enzyme, i.e. the ADP-ribosylation turn–turn and phosphate–nicotinamide PN loops. Herein, we provide two new C3larvin X-ray structures and present a systematic study of the toxin dynamics by first analyzing the experimental variability of the X-ray data-set followed by contrasting those results with theoretical predictions based on Elastic Network Models (GNM and ANM). We identify residues that participate in the stability of the N-lobe, putative hinges at loop residues, and energy-favored deformation vectors compatible with conformational changes of the key loops and 3D-subdomains (N/C-lobes), among the X-ray structures. We analyze a larger ensemble of known C3bot1 conformations and conclude that the characteristic ‘crab-claw’ movement may be driven by the main intrinsic modes of motion. Finally, via computational simulations, we identify harmonic and anharmonic fluctuations that might define the C3larvin ‘native state.’ Implications for docking protocols are derived.     

Comparing multiple correspondence and principal component analyses with biomechanical signals. Example with turning the steering wheel

The purpose of this article is to compare Principal Component Analysis (PCA) and a much less used method, i.e. MCA (Multiple Correspondence Analysis) with data being first changed into membership values to fuzzy space windows. For such a comparison, data from an experimental study about turning the steering wheel is used. In a didactic perspective, this article only considers one multidimensional signal with 5 components: 3 linked to the steering wheel angle and hand positions and 2 to hand effort variables. A discussion weighs out the pros and the cons of both methods with criteria such as the possibility to show complex relational phenomena, the analysis/computing time or the information loss inherent to the averaging stage (in the perspective to analyze several hundreds of large multidimensional signals).     

In-depth Profiling and Quantification of the Lysine Acetylome in Hepatocellular Carcinoma with a Trapped Ion Mobility Mass Spectrometer

Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related death worldwide with limited therapeutic options. Comprehensive investigation of protein posttranslational modifications in HCC is still limited. Lysine acetylation is one of the most common types of posttranslational modification involved in many cellular processes and plays crucial roles in the regulation of cancer. In this study, we analyzed the proteome and K-acetylome in eight pairs of HCC tumors and normal adjacent tissues using a timsTOF Pro instrument. As a result, we identified 9219 K-acetylation sites in 2625 proteins, of which 1003 sites exhibited differential acetylation levels between tumors and normal adjacent tissues. Interestingly, many novel tumor-specific K-acetylation sites were characterized, for example, filamin A (K865), filamin B (K697), and cofilin (K19), suggesting altered activities of these cytoskeleton-modulating molecules, which may contribute to tumor metastasis. In addition, we observed an overall suppression of protein K-acetylation in HCC tumors, especially for enzymes from various metabolic pathways, for example, glycolysis, tricarboxylic acid cycle, and fatty acid metabolism. Moreover, the expression of deacetylase sirtuin 2 (SIRT2) was upregulated in HCC tumors, and its role of deacetylation in HCC cells was further explored by examining the impact of SIRT2 overexpression on the proteome and K-acetylome in Huh7 HCC cells. SIRT2 overexpression reduced K-acetylation of proteins involved in a wide range of cellular processes, including energy metabolism. Furthermore, cellular assays showed that overexpression of SIRT2 in HCC cells inhibited both glycolysis and oxidative phosphorylation. Taken together, our findings provide valuable information to better understand the roles of K-acetylation in HCC and to treat this disease by correcting the aberrant acetylation patterns.     

Instrumental test to estimate a model of forecast yield: a non-parametric application to the pollen index in South Italy

A statistical test is described to verify the characteristics of the biological information contained in the dynamics of the flowering process. The test focuses on interactions between the pollen index and climatic variables to investigate if the biological indicator can synthesise the information of the pre-flowering phases. The multiple-regression model is built upon two pre-flowering climate macro-indicators extracted by Principal Component Analysis (PCA) and the optimised pollen index is obtained by non-parametric estimation. The empirical analysis is applied to 15 stations located in southern Italy in regions that have a longstanding tradition of olive production. Using the variance explained, we find that an optimised pollen index is fairly well predicted by the pre-flowering climatic data. We conclude that the optimised pollen index makes more parsimonious the modelling for predicting olive production.     

A gene (Bmn) controllingβ-mannosidase activity in the mouse is located in the distal part of chromosome 3

A gene (Bmn) with a major effect on -mannosidase activity in kidney and liver of the house mouse was revealed by assay with the synthetic substratep-nitrophenyl--d-mannoside. Activity is low in DBA/2J and CSB mice and high in C57BL/6J mice. By the use of the BXD series of recombinant inbred strains and by crosses between C57BL and CSB, it was possible to map the gene to the distal part of chromosome 3 by demonstration of linkage to a gene for cadmium resistance,cdm, as well as to theAdh-3 locus.This work was supported by Swedish Natural Science Research Council Project B-BU 2992-108.     

Morphometric comparison of populations of Orchis sitnia Lam. (Orchidaceae) from Oxfordshire and Kent

BATEMAN, R. M. & FARRINGTON, O. S., 1989. Morphometric comparison of populations of Orchis sitnia Lam. (Orchidaceae) from Oxfordshire and Kent. Univariate and multivariate morphometric analyses of Orchis simia Lam. from its two remaining naturally-founded populations in Britain (Goring, Oxfordshire and Faversham, Kent) reveal only minor morphological differences between the populations and suprisingly low levels of intra-population variation. This probably reflects recent founding from Continental seed at Faversham and penecontemporaneous, human-induced, catastrophic contraction of the gene pool at Goring. The apparently restricted gene pools of these populations may adversely effect their long-term survival.     

Quantitative comparison of Fusarium oxysporum competitiveness in relation to carbon utilization

Abstract The competitive saprophytic interaction between pathogenic and non-pathogenic strains of Fusarium oxysporum was investigated by studying their ability to competitively colonize sterilized soil. It was demonstrated that carbon was the first limiting substrate of Fusarium oxysporum growth in sterilized soil. Moreover, the efficiency with which glucose was utilized in the formation of propagules varied from one strain to another. Results of competitiion experiments showed that a linear relationship existed between the ratio of inoculum densities at the plateau (carrying capacity) and the ratio of inoculum densities incorporated into non-amended sterilized soil. The slope of the regression line indicated the competitiveness index, i.e. the competitiveness of a non-pathogenic strain in relation to that of a pathogenic strain. This parameter could be related to the yield coefficient of the strains in glucose-amended soil.     

Plasmid content in Yersinia pestis strains of different origin

Plasmid content in 242 Yersinia pestis strains from various natural plague foci of the U.S.S.R. and other countries was studied. Of these strains, 172 (71%) were shown to carry three plasmids described previously of about 6, 45-50 and 60 MDa, respectively. Twenty strains (8%) from different foci harboured additional cryptic plasmids, most often of about 20 mDa in size. Plasmid pPst displayed considerable constancy of its molecular mass. On the contrary, size variations of pCad (45-49 MDa) and, especially, pFra (60-190 MDa) were found. Molecular mass of these plasmids correlated with the host strain origin.