Analysis of a xyloglucan endotransglycosylase/hydrolase (XTH) from the lycopodiophyte Selaginella kraussiana suggests that XTH sequence characteristics and function are highly conserved during the evolution of vascular plants

A tissue print followed by a xyloglucan endotransglycosylase assay revealed that XET activity is present at sites of cell elongation in both roots and shoots of the lycopodiophyte Selaginella kraussiana. This paper provides the first report and analysis of a xyloglucan endotransglycosylase/hydrolase (XTH) cDNA sequence, isolated from a club moss. In silico analysis of the deduced amino acid sequence revealed a strong conservation of the XET-domain described in higher plants. The catalytic site (DEIDLEFLG) varies in only one amino acid compared with the consensus sequence and was shown to be functional after recombinant expression of Sk-XTH1 in Pichia pastoris. Sk-XTH1 displays xyloglucan endotransglycosylase activity over a broad pH (4.5-7.5) and temperature range (4-30 degrees C), but it shows no hydrolase activity. The catalytic site is followed by a consensus sequence for N-linked glycosylation. Four terminal cysteines were shown to stabilize a putative XET-C terminal extension region, which includes conserved amino acids, involved in the recognition and binding of the substrates. The N-linked sugar interactions as well as the disulphide bridges were shown to be necessary to perform XET activity. The presence of a highly conserved XTH sequence and function in a microphyllophyte suggests that XTHs were present before the divergence of lycopodiophytes and euphyllophytes. It also points to a possible key role for XTHs in the production of a cell wall that allowed the further evolution of land plants.     

Variable selection for logistic regression using a prediction-focused information criterion

In biostatistical practice, it is common to use information criteria as a guide for model selection. We propose new versions of the focused information criterion (FIC) for variable selection in logistic regression. The FIC gives, depending on the quantity to be estimated, possibly different sets of selected variables. The standard version of the FIC measures the mean squared error of the estimator of the quantity of interest in the selected model. In this article, we propose more general versions of the FIC, allowing other risk measures such as the one based on L(p) error. When prediction of an event is important, as is often the case in medical applications, we construct an FIC using the error rate as a natural risk measure. The advantages of using an information criterion which depends on both the quantity of interest and the selected risk measure are illustrated by means of a simulation study and application to a study on diabetic retinopathy.     

A novel family of lectins evolutionarily related to class V chitinases: an example of neofunctionalization in legumes

A lectin has been identified in black locust (Robinia pseudoacacia) bark that shares approximately 50% sequence identity with plant class V chitinases but is essentially devoid of chitinase activity. Specificity studies indicated that the black locust chitinase-related agglutinin (RobpsCRA) preferentially binds to high-mannose N-glycans comprising the proximal pentasaccharide core structure. Closely related orthologs of RobpsCRA could be identified in the legumes Glycine max, Medicago truncatula, and Lotus japonicus but in no other plant species, suggesting that this novel lectin family most probably evolved in an ancient legume species or possibly an earlier ancestor. This identification of RobpsCRA not only illustrates neofunctionalization in plants, but also provides firm evidence that plants are capable of developing a sugar-binding domain from an existing structural scaffold with a different activity and accordingly sheds new light on the molecular evolution of plant lectins.     

No direct linkage between proton pumping and photosynthate unloading from seed coats of Phaseolus vulgaris L.

The energization of the active sucrose release from bean seed-coat halves was investigated. For this purpose, seed coat tissues adjacent to the apoplastic space were exposed to a variety of treatments and proton and photosynthate release were measured. Fusicoccin (10^–5 moll^–1) stimulated proton pump activities. Orthovanadate (2×10^–4 moll^–1) and abscisic acid (10^–5 moll^–1) diminished the proton extrusion evoked by fusicoccin. Fusicoccin inhibited sucrose release, whereas orthovanadate and abscisic acid stimulated it. Addition of 100 mmoll^–1 K⁺ had a promotory effect on photosynthate unloading, fading away with time. This extra unloading was linearly related to an enhanced proton loss. It was concluded that the photosynthate unloading apparently is not a proton/sucrose antiport and that a pump-leak system for photosynthate release is unlikely. A tentative model for photosynthate/proton symport not directly linked to proton pumping is presented as the mechanism of unloading.Abbreviations ABA abscisic acid - CCCP carbonyl cyanide m-chlorophenyl hydrazone - DTE diethioerythritol - FC fusicoccin - MES 2-(N-morpholino) ethanesulfonic acid monohydrate - NEM n-ethylmaleimide - PCMBS p-chloromercuriphenylsulfonic acid - TRIS 2-amino-2-(hydroxymethyl) propane-1,3 diol - VAN sodium orthovanadate     

Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera

Background  

Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum.     

Wanda: a database of duplicated fish genes

Comparative genomics has shown that ray-finned fish (Actinopterygii) contain more copies of many genes than other vertebrates. A large number of these additional genes appear to have been produced during a genome duplication event that occurred early during the evolution of Actinopterygii (i.e. before the teleost radiation). In addition to this ancient genome duplication event, many lineages within Actinopterygii have experienced more recent genome duplications. Here we introduce a curated database named Wanda that lists groups of orthologous genes with one copy from man, mouse and chicken, one or two from tetraploid Xenopus and two or more ancient copies (i.e. paralogs) from ray-finned fish. The database also contains the sequence alignments and phylogenetic trees that were necessary for determining the correct orthologous and paralogous relationships among genes. Where available, map positions and functional data are also reported. The Wanda database should be of particular use to evolutionary and developmental biologists who are interested in the evolutionary and functional divergence of genes after duplication. Wanda is available at http://www.evolutionsbiologie.uni-konstanz.de/Wanda/.     

Spatial and temporal comparisons of salt marsh soil fungal communities following the deepwater horizon spill

Wetlands Ecology and Management - The unprecedented size of the deepwater horizon oil spill and scope of the subsequent response elicited intense and sustained interest in microbial responses to...     

Bionomics ofEotetranychus tiliarium and its phytoseiid predators

Under urban conditions,Eotetranychus tiliarium (Hermann) frequently develops into high population densities onTilia lining streets, in contrast to its development in natural habitats and on park trees. In mixed forest and on park trees, a regulating system precludes these outbreaks. In an earlier study it was shown that a change in the predacious mite species composition, leading to displacement of the most effective predator species by less effective ones, is the main reason for this phenomenon.The bionomics ofE. tiliarium on its host plantTilia spp. in various habitats were studied as well as the characteristics of the predacious mites which determine their potential for preventing spider-mite outbreaks.Predacious mites from the family Phytoseiidae were able to preventE. tiliarium outbreaks.Paraseiulus soleiger was the most effective predacious mite species, because it has a short development period, a long period of longevity, a long oviposition period, and has a clear preference forE. tiliarium and a high prey-consumption capacity. Eotetranychus tiliarium onTilia lining streets has a greater potential for increase than the spider mites from park trees and from forest trees. The nutritive value of leaves on trees in street habitats is increased by the increased salt content in the soil from snow control in winter. Also, the higher temperatures in urban conditions may stimulate population development.     

Effect of three pollination methods on embryo development and seedset in intra- and interspecific crosses between seven Lilium species

Summary Interspecific crosses were made between seven Lilium species, viz. L. candidum, L. concolor, L. dauricum, L. henryi, L. longiflorum, L. nepalense and L. rubellum. A complete diallel cross was carried out between these seven species, including self- and intraspecific pollinations using three pollination methods: normal pollination on the stigma, pollination on the ovary after cutting the style, and pollination on the stigma with the aid of mentor (non-functional, compatible) pollen. Embryo rescue, starting 35 days after pollination, was applied to all interspecific combinations. The percentage of successful crosses was about 2.8% after normal pollination, 5.4% after cut-style pollination and 3.8% with the mentor pollen technique. Crosses with L. nepalense were exceptional in that embryos died during the embryo culture phase. Seventeen cross combinations (including 4 reciprocals) yielded 62 embryo plantlets from 839 interspecific pollinations.     

X-chromosome polysomy in the male

Summary A review of 569 male patients with X-chromosome polysomies (544 Klinefelter and 25 patients with other types of X-chromosome polysomy) is presented here. These patients were detected among the 77000 persons karyotyped in the Leuven cytogenetic center between the years 1966 and 1987. In the group of 544 Klinefelter patients special attention was paid to (1) the age at diagnosis, (2) social and marital status of the postpubertal males, (3) physical and intellectual abilities of the prepubertal boys, (4) delineation of the concurrence of Klinefelter syndrome and fragile X syndrome, and (5) the frequency of malignancies. In 25 patients with other X-chromosome polysomies (2 n48 chromosomes) genotype/phenotype correlation is reviewed, especially for the patients with 48,XXYY and 49,XXXXY karyotypes. Finally, double aneuploidy and rare structural X-chromosome aberrations are briefly discussed.