Quantification of the elevated rate of domain rearrangements in metazoa

Most eukaryotic proteins consist of multiple domains created through gene fusions or internal duplications. The most frequent change of a domain architecture (DA) is insertion or deletion of a domain at the N or C terminus. Still, the mechanisms underlying the evolution of multidomain proteins are not very well studied.Here, we have studied the evolution of multidomain architectures (MDA), guided by evolutionary information in the form of a phylogenetic tree. Our results show that Pfam domain families and MDAs have been created with comparable rates (0.1-1 per million years (My)). The major changes in DA evolution have occurred in the process of multicellularization and within the metazoan lineage. In contrast, creation of domains seems to have been frequent already in the early evolution. Furthermore, most of the architectures have been created from older domains or architectures, whereas novel domains are mainly found in single-domain proteins. However, a particular group of exon-bordering domains may have contributed to the rapid evolution of novel multidomain proteins in metazoan organisms. Finally, MDAs have evolved predominantly through insertions of domains, whereas domain deletions are less common.In conclusion, the rate of creation of multidomain proteins has accelerated in the metazoan lineage, which may partly be explained by the frequent insertion of exon-bordering domains into new architectures. However, our results indicate that other factors have contributed as well.     

Glutamate in plants: metabolism, regulation, and signalling

Glutamate occupies a central position in amino acid metabolism in plants. The acidic amino acid is formed by the action of glutamate synthase, utilizing glutamine and 2-oxoglutarate. However, glutamate is also the substrate for the synthesis of glutamine from ammonia, catalysed by glutamine synthetase. The alpha-amino group of glutamate may be transferred to other amino acids by the action of a wide range of multispecific aminotransferases. In addition, both the carbon skeleton and alpha-amino group of glutamate form the basis for the synthesis of gamma-aminobutyric acid, arginine, and proline. Finally, glutamate may be deaminated by glutamate dehydrogenase to form ammonia and 2-oxoglutarate. The possibility that the cellular concentrations of glutamate within the plant are homeostatically regulated by the combined action of these pathways is examined. Evidence that the well-known signalling properties of glutamate in animals may also extend to the plant kingdom is reviewed. The existence in plants of glutamate-activated ion channels and their possible relationship to the GLR gene family that is homologous to ionotropic glutamate receptors (iGluRs) in animals are discussed. Glutamate signalling is examined from an evolutionary perspective, and the roles it might play in plants, both in endogenous signalling pathways and in determining the capacity of the root to respond to sources of organic N in the soil, are considered.     

Activity of Nidus Vespae extract and chemical fractions against Streptococcus mutans biofilms

AIMS: To evaluate the effect of Nidus Vespae extract and chemical fractions on the viability and architecture of Streptococcus mutans biofilms. METHODS AND RESULTS: The raw material was first extracted using 95% ethanol/water. Subsequent fractions were prepared from this extract using cyclohexane/ethyl acetate, petroleum ether/ethyl acetate and chloroform/methanol. The biomass dry weight and total protein of samples treated with Nidus Vespae extract and chemical fractions were significantly less than those treated with the vehicle control (P < 0.05). Biofilms treated with Nidus Vespae also resulted in lower percentage of polysaccharide composition. The pH decrease in the biofilm matrix was retarded by Nidus Vespae compared with the vehicle control. Architecture of biofilms treated with Nidus Vespae was different than in the vehicle control and 0.05% chlorhexidine. CONCLUSIONS: Chloroform/methanol fraction was the most effective treatment. SIGNIFICANCE AND IMPACT OF THE STUDY: The significant antibiofilm activity demonstrated by Nidus Vespae shows it to be a promising source of novel anticariogenic agents.     

Floral initiation and inflorescence architecture: a comparative view

BACKGROUND: A huge variety of plant forms can be found in nature. This is particularly noticeable for inflorescences, the region of the plant that contains the flowers. The architecture of the inflorescence depends on its branching pattern and on the relative position where flowers are formed. In model species such as Arabidopsis thaliana or Antirrhinum majus the key genes that regulate the initiation of flowers have been studied in detail and much is known about how they work. Studies being carried out in other species of higher plants indicate that the homologues of these genes are also key regulators of the development of their reproductive structures. Further, changes in these gene expression patterns and/or function play a crucial role in the generation of different plant architectures. SCOPE: In this review we aim to present a summarized view on what is known about floral initiation genes in different plants, particularly dicotyledonous species, and aim to emphasize their contribution to plant architecture.     

Architecture of the pruned tree: impact of contrasted pruning procedures over 2 years on shoot demography and spatial distribution of leaf area in apple (Malus domestica)

BACKGROUND AND AIMS: Demography and spatial distribution of shoots are rarely studied on pruned trees. The present 2-year study deals with the effect of pruning strategies on shoot demography and development, and consequences on the spatial distribution of leaf area in three architecturally contrasted - from type II to IV - apple cultivars: 'Scarletspur Delicious', 'Golden Delicious' and 'Granny Smith'. METHODS: All trees were initially subjected during 5 years to Central Leader training with winter heading on all long shoots. For 2 years, half of the trees were further trained with Centrifugal training, where removal of flowering shoots - called extinction pruning - was carried out along the trunk and at the bottom of branches at flowering time. During these 2 years, shoot type (vegetative, inflorescence) and length, and the three-dimensional spatial distribution of all shoots were assessed with an electromagnetic digitizer. KEY RESULTS: Shoot demography, frequency of transitions toward an inflorescence from either an inflorescence (bourse-over-bourse) or a vegetative shoot (trend toward flowering), and the number of bourse-shoots per bourse were strongly affected by cultivar, with little influence of tree manipulation. In contrast, the proportion of vegetative long shoots developing from previous year latent buds was significantly lower in Centrifugal-trained trees for the three cultivars. Canopy volume showed large variations between cultivars, but only that of 'Granny Smith' was affected by tree manipulation in the 2 years. Spatial distribution of shoots varied significantly according to cultivar and manipulation. In 'Scarletspur Delicious' and, to a lesser extent 'Golden Delicious', the distribution of vegetative and flowering shoots in the outer and the inner parts, respectively, was not affected by tree manipulation. In contrast, in 'Granny Smith', vegetative shoots were stimulated in the periphery of Central Leader trees, whereas flowering shoots were stimulated in the periphery of Centrifugal-trained trees. CONCLUSIONS: In apple, the variability of responses to contrasted pruning strategies partly depends on the genetically determined growth and flowering habit of the cultivar.     

Architectural evolution and its implications for domestication in grasses

BACKGROUND: The cereal crops domesticated from grasses provide a large percentage of the calories consumed by humans. Domestication and breeding in individual cereals has historically occurred in isolation, although this is rapidly changing with comparative genomics of the sequenced or soon-to-be sequenced genomes of rice, sorghum, maize and Brachypodium. Genetic information transferred through genomic comparisons is helping our understanding of genetically less tractable crops such as the hexaploid wheats and polyploid sugarcane, as well as the approx. 10 000 species of wild grasses. In turn, phylogenetic analysis helps put our knowledge of the morphology of cereal crops into an evolutionary context. GRASS ARCHITECTURE: Domestication often involves a change in the pattern and timing of branching, which affects both vegetative and inflorescence architecture, and ultimately yield. Cereal grasses exhibit two main forms of vegetative architecture: the pooid and erhartoid cereals such as wheat and rice have multiple basal tillers, while panicoid cereals such as maize, sorghum and the millets have few tillers or even only a single main stem. These differences are reflected in the differences between the wild species of pooid and some erhartoid grasses, which emphasize basal branching over axillary branching, and the panicoid grasses, where axillary branching is more frequently found. A combination of phylogenetic and genomic analysis is beginning to reveal the similarities and differences between different cereal crops, and relate these to the diversity of wild grasses to which they are related. Recent work on genes controlling branching emphasizes that developmental genetics needs to be viewed in both an evolutionary and ecological framework, if it is to be useful in understanding how morphology evolves. Increasingly, exploring the phylogenetic context of the crop grasses will suggest new ways to identify and create combinations of morphological traits that will best suit our future needs.     

狗牙根花序发育过程的形态学观察

对狗牙根(Cynodon dactylon‘C299’)花序发育过程中的形态学变化进行了观察。结果表明,‘C299’花序的整个发育过程可分为8个阶段,即营养生长期、穗轴发生期、苞叶原基分化期、小穗原基分化期、小穗分化期、小花分化期、颖片和内外稃发育期及花药和柱头形成期。其中,穗轴发生期(直立茎上有6~9片叶)是抑制花序形成和决定种子产量的关键时期。     

Gene delivery to airway epithelial cells in vivo: a direct comparison of apical and basolateral transduction strategies using pseudotyped lentivirus vectors

Lentivirus vectors are being investigated as gene delivery vehicles for cystic fibrosis airway gene therapy. Vesicular stomatitis virus G glycoprotein (VSV-G)-pseudotyped vectors transduce airway epithelia via receptors that are located predominantly on the basolateral surface of the airway epithelium. Effective transduction with VSV-G-pseudotyped vectors requires the use of a pre-treatment that disrupts epithelial tight junctions, allowing access to these basolateral receptors. In contrast, it has been reported that apically targeted lentiviral vectors allow efficient gene transfer in the absence of any pre-treatment. In a direct comparison of transduction by a VSV-G-pseudotyped vector, in combination with a pre-treatment with lysophosphatidylcholine (LPC), and the same vector pseudotyped with the apically targeted baculovirus GP64 envelope (without any pre-treatment), the GP64 vector was found to be significantly less efficient. However, when a pre-treatment with LPC was used the level of transduction with the GP64-pseudotyped lentiviral vector was not significantly different to that resulting from the VSV-G-pseudotyped vector. The cell types transduced with each vector were essentially the same, with the majority of cells transduced being respiratory (ciliated cells). However, unlike the VSV-G-pseudotyped vector, which results in persisting gene expression, transduction with the GP64-pseudotyped vector resulted in gene expression that declined to undetectable levels over six months, whether or not an LPC pre-treatment was used.     

An Overview of Structural DNA Nanotechnology

Structural DNA Nanotechnology uses unusual DNA motifs to build target shapes and arrangements. These unusual motifs are generated by reciprocal exchange of DNA backbones, leading to branched systems with many strands and multiple helical domains. The motifs may be combined by sticky ended cohesion, involving hydrogen bonding or covalent interactions. Other forms of cohesion involve edge-sharing or paranemic interactions of double helices. A large number of individual species have been developed by this approach, including polyhedral catenanes, a variety of single-stranded knots, and Borromean rings. In addition to these static species, DNA-based nanomechanical devices have been produced that are ultimately targeted to lead to nanorobotics. Many of the key goals of structural DNA nanotechnology entail the use of periodic arrays. A variety of 2D DNA arrays have been produced with tunable features, such as patterns and cavities. DNA molecules have be used successfully in DNA-based computation as molecular representations of Wang tiles, whose self-assembly can be programmed to perform a calculation. About 4 years ago, on the fiftieth anniversary of the double helix, the area appeared to be at the cusp of a truly exciting explosion of applications; this was a correct assessment, and much progress has been made in the intervening period.     

Nuclear DNA content of ploidy chimeras of Hosta Tratt. (Hostaceae) demonstrate three apical layers in all organs, but not in the adventitious root

A unique combination of chloroplast and ploidy chimeras is found in some Hosta Tratt. (Hostaceae) cultivars. The absence of endopolyploidy in the above–ground parts made it possible to study the fate of the apical or germ layers in all organs. Moreover, we would like to address the question of the number of apical cell layers in Hosta also to explain breeding results. Nuclear DNA content in twelve different organs of Hosta was determined by flow cytometric analysis of four chimeric cultivars with a 4-2-2 or 2-2-4 composition. The margin of the leaf, derived from the L1, can be determined separately and has a 4C amount of DNA in 4-2-2 ploidy chimeras but a 2C amount of DNA in 2-2-4 chimeras. The presence of three layers in Hosta was deduced from comparisons of the percentage of 4C nuclei in (2)-2-4 and (4)-2-2 chimeras. If Hosta organs derive only from two layers the percentage of 4C cells in the different ploidy chimeras should add up to 100%, but they do not. The absence of nuclei with a 2C amount of DNA in the roots of 2-2-4 plants shows that only the L3 participates in adventitious root formation. Gametes and consequently seedlings are mainly derived from the L2. The often found correlation between the color of the centre of the leaf and the color of the seedlings is the consequence of the way these cultivars originate. The presence of three apical layers is visualized in the tricolored leaves of Hosta cultivars like `Striptease'. The nuclear DNA amounts show unequivocally, that in all the above ground parts of Hosta the three apical layers L1, L2 and L3 are present. However, only the L3 participates in adventitious root formation.