Phylogenetic diversity of indigenous cowpea bradyrhizobia from soils in Japan based on sequence analysis of the 16S-23S rRNA internal transcribed spacer (ITS) region

Cowpea [Vigna unguiculata (L.) Walp.] is an important legume crop and yet its rhizobia have not been well characterized in many areas. In the present study, sequence analysis of the bacterial 16S-23S rRNA internal transcribed spacer (ITS) region was performed to characterize genetically 76 indigenous cowpea rhizobia from five different geographic regions (Okinawa, Miyazaki, Kyoto, Fukushima and Hokkaido) of Japan. The sequence analysis clustered all isolates in the genus Bradyrhizobium. They were conspecific with B. japonicum, B. yuanmingense, B. elkanii and Bradyrhizobium sp., although none of them grouped with B. liaoningense, B. canariense, B. betae or B. iriomotense. B. yuanmingense was only isolated from the southern region (Okinawa) where it achieved the highest frequency of 69%. B. japonicum was predominant at Miyazaki, Fukushima and Hokkaido with more than 60% of the isolates. B. elkanii was mainly recorded in the southern (Okinawa: 31%, Miyazaki: 33%) and middle (Kyoto: 33%) regions. This species was present at a very low frequency in Fukushima and absent in Hokkaido in the northern area. Bradyrhizobium sp. like-strains were absent in the southern part (Okinawa, Miyazaki) but were concentrated either in the middle regions with 67% of Kyoto isolates and 28% of Fukushima isolates, and in the northern region with 40% of the Hokkaido isolates. This study revealed a geographical distribution of cowpea bradyrhizobia which seemed to be related to the differences in the environmental characteristics (soil type and soil pH, temperature, climate, moisture) of the different regions in Japan.     

Genetic polymorphism of glutamine synthetase and delta-9 desaturase in families of Pacific oyster Crassostrea gigas and susceptibility to summer mortality

Large-scale mortality events have been observed in Pacific oyster Crassostrea gigas on the west coast of France since the early 1980s, particularly during summer. In order to understand the causes of this mortality, two generations of oysters from single-pair matings were studied in three sites on the French Atlantic coast (Baie-des-Veys, Auray and Ronce-les-Bains). The present paper examines the role of two candidate genes in the susceptibility of oysters to summer mortality, and the selective pressure exerted by such mortality on their polymorphism. Glutamine synthetase (amino-acid metabolism) and delta-9 desaturase (lipid metabolism) genes were studied in the successive generations, using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP). Observed and expected genotypic frequencies were compared. Three different alleles were detected for the glutamine synthetase gene and two for delta-9 desaturase. Allele C of glutamine synthetase seemed to be counter-selected in some second generation families. Allele B of delta-9 desaturase gene was potentially counter-selected at Auray in the families showing higher mortality, and strong selection against BB homozygotes was observed. These observations led us to conclude that any selective effect of summer mortality on allele C of glutamine synthetase gene or allele B of delta-9 desaturase gene could be mediated either directly or via linkage to other loci involved in physiological pathways affecting susceptibility.     

Fine structure of bovine lens epithelial cells in vitro in relation to modifications induced by a retinal extract (EDGF)

Cultured bovine lens epithelial cells are polygonal in shape. In confluent and multilayer cultures they exhibit elaborate arrays of 6 nm filaments, bundles of intermediate-sized filaments, and a fibrous meshwork of subcellular and intercellular material. Cells grown in the presence of a retinal extract (RE) have a higher growth rate, and are smaller and more regular in shape. In them the 6 nm filaments are mostly aligned in sheets, the intermediate-sized filaments form a fine network, and the cells are closely apposed to the plastic substratum. Some homogeneous material is formed intercellularly in older cultures. Cellular elongation, induced in the former cultures by the addition of RE, is accompanied by an alignment of cytoskeletal elements, including microtubules, parallel to the long axis. Other structural features are similar in all cell types. The response to RE is discussed in terms of shape modulations associated with the restricted expression of structural characteristics acquired in vitro.     

The representation of heart development in the gene ontology

An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling.In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development. This work also aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject.The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area.     

Regulation of adenylate cyclase in cultured cardiocytes from neonatal rats by adenosine and other agonists

The presence of adenosine receptors coupled to adenylate cyclase in cultured cardiocytes from atria and ventricles from neonatal rats is demonstrated in these studies. N-Ethylcarboxamideadenosine (NECA), l-N⁶-phenylisopropyladenosine (PIA), and 2-chloroadenosine (2-cl-Ado) stimulated adenylate cyclase in a concentration-dependent manner in both cultured atrial and ventricular cells. The order of potency of stimulation was NECA > PIA > 2-cl-Ado. The stimulation of adenylate cyclase by NECA was enhanced by guanine nucleotides and was blocked by 3-isobutyl-1-methylxanthine in both these cells. Other agonists such as epinephrine, norepinephrine, dopamine, F^?, and forskolin were also able to stimulate adenylate cyclase, although the extent of stimulation by these agents was higher in ventricular than in atrial cells. The stimulation of adenylate cyclase by epinephrine and norepinephrine was inhibited by propranolol but not by phentolamine. On the other hand, phentolamine, propranolol, and haloperidol inhibited dopamine-stimulated adenylate cyclase activity to the same extent. Forskolin, at its maximal concentration, potentiated the stimulatory effect of epinephrine, norepinephrine, and dopamine on adenylate cyclase in both atrial and ventricular cardiocytes, but the interaction of NECA with epinephrine, norepinephrine, or dopamine was different in atrial and ventricular cells. The stimulation by an optimal concentration of NECA was additive with maximal stimulation by the catecholamines in atrial cells but not in ventricular cells. The data suggest the existence of adenosine “Ra” and catecholamine receptors in cultured atrial and ventricular cardiocytes. It can be postulated that adenosine in addition to its role as a potent vasodilator might regulate cardiac performance through its interaction with “Ra” receptors associated with adenylate cyclase. The difference in the mode of interaction of adenosine with catecholamines in atrial and ventricular cells suggests that the mechanism by which these agents activate adenylate cyclase may be different in these cells.     

Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer

Divergence in function of homologous proteins is based on both sequence and structural changes. Overall enzyme function has been reported to diverge earlier (50% sequence identity) than overall structure (35%). We herein study the functional conservation of enzymes and non-enzyme sequences using the protein domain families in CATH-Gene3D. Despite the rapid increase in sequence data since the last comprehensive study by Tian and Skolnick, our findings suggest that generic thresholds of 40% and 60% aligned sequence identity are still sufficient to safely inherit third-level and full Enzyme Commission numbers, respectively. This increases to 50% and 70% on the domain level, unless the multi-domain architecture matches. Assignments from the Kyoto Encyclopedia of Genes and Genomes and the Munich Information Center for Protein Sequences Functional Catalogue seem to be less conserved with sequence, probably due to a more pathway-centric view: 80% domain sequence identity is required for safe function transfer. Comparing domains (more pairwise relationships) and the use of family-specific thresholds (varying evolutionary speeds) yields the highest coverage rates when transferring functions to model proteomes. An average twofold increase in enzyme annotations is seen for 523 proteomes in Gene3D. As simple ‘rules of thumb’, sequence identity thresholds do not require a bioinformatics background. We will provide and update this information with future releases of CATH-Gene3D.     

Methionine Sulfoxide Reductase B Displays a High Level of Flexibility

Methionine sulfoxide reductases (Msrs) are enzymes that catalyze the reduction of methionine sulfoxide back to methionine. In vivo, Msrs are essential in the protection of cells against oxidative damage to proteins and in the virulence of some bacteria. Two structurally unrelated classes of Msrs, named MsrA and MsrB, exist. MsrB are stereospecific to R epimer on the sulfur of sulfoxide. All MsrB share a common reductase step with the formation of a sulfenic acid intermediate. For the subclass of MsrB whose recycling process passes through the formation of an intradisulfide bond, the recycling reducer is thioredoxin. In the present study, X-ray structures of Neisseria meningitidis MsrB have been determined. The structures have a fold based on two β-sheets, similar to the fold already described for other MsrB, with the recycling Cys63 located in a position favorable for disulfide bond formation with the catalytic Cys117. X-ray structures of Xanthomonas campestris MsrB have also been determined. In the C117S MsrB structure with a bound substrate, the recycling Cys31 is far from Ser117, with Trp65 being essential in the reductase step located in between. This positioning prevents the formation of the Cys31-Cys117 disulfide bond. In the oxidized structure, a drastic conformational reorganization of the two β-sheets due to withdrawal of the Trp65 region from the active site, which remains compatible with an efficient thioredoxin-recycling process, is observed. The results highlight the remarkable structural malleability of the MsrB fold.     

Altered levels of focal adhesion and extracellular matrix-receptor interacting proteins were identified in Hailey-Hailey disease by quantitative iTRAQ proteome analysis

Benign chronic familial pemphigus or Hailey-Hailey disease (HHD, OMIM 169600) is a rare, autosomal dominant blistering skin disorder characterized by suprabasal cell separation (acantholysis) of the epidermis. To date, the proteomic changes in skin lesions from HHD patients has not been reported yet. In this study, a sample of skin lesions from HHD patients was collected for isobaric tags for relative and absolute quantitation to analyze proteome changes compared with unaffected individuals. The 134 differentially expressed proteins were assigned to at least one Gene Ontology term, and 123 annotated proteins with significant matches were assigned to 187 known metabolic or signaling pathways listed in the Kyoto Encyclopedia of Genes and Genomes. Most of the altered proteins in skin lesions of HHD patients were enriched in pathways involved in the PI3K-Akt signaling, focal adhesion, extracellular matrix (ECM)-receptor interaction, and protein digestion and absorption, such as collagen family members, microfibril-associated glycoprotein 4 and plakophilin. The changes of proteins related to cell adhesion, ECM-receptor interaction, and protein folding and glycosylation suggested that strategy targeted to alter cell junction and extracellular microenvironment might provide a potential treatment for HHD.     

Tracing Ancestors and Relatives of Escherichia coli B, and the Derivation of B Strains REL606 and BL21(DE3)

Antecedents of Escherichia coli B have been traced through publications, inferences, and personal communication to a strain from the Institut Pasteur in Paris used by d'Herelle in his studies of bacteriophages as early as 1918 (a strain not in the current collection). This strain appears to have passed from d'Herelle to Bordet in 1920, and from Bordet to at least three other laboratories by 1925. The strain that Gratia received from Bordet was apparently passed to Bronfenbrenner by 1924 and from him to Luria around 1941. Delbrück and Luria published the first paper calling this strain B in 1942. Its choice as the common host for phages T1-T7 by the phage group that developed around Delbrück, Luria, and Hershey in the 1940s led to widespread use of B along with E. coli K-12, chosen about the same time for biochemical and genetic studies by Tatum and Lederberg. Not all currently available strains related to B are descended from the B of Delbrück and Luria; at least three strains with somewhat different characteristics were derived independently by Hershey directly from the Bronfenbrenner strain, and a strain that appears to have passed from Bordet to Wollman is in the current Collection of the Institut Pasteur. The succession of manipulations and strains that led from the B of Delbrück and Luria to REL606 and BL21(DE3) is given, established in part through evidence from their recently determined complete genome sequences.     

Composition des faunes de mammifères quaternaires en Chine selon un gradient Nord-Sud

During Pleistocene Epoch, quite a number of meridionale mammals inhabited north China, such as Stegodon, Macaca, Hystrix, Dicerorhinus, Bubalus and several kinds of other probscideans. On the contrary, some boreal mammals once appeared in south China, such as Megaloceros and Ursus arctos etc. The frequent appearance of warm-adapted mammals in North China can be explained by two alternative assumptions: one is that those mammals were of palearctic origin; the other is the climate-driven northward dispersal. According to the fossil evidences, it seems that the northward dispersal events were much more frequent than the southward ones during Pleistocene in China. It maybe means that during Pleistocene, the temperature fluctuated very frequently and the boundary between the Paleartic and Oriental Regions were always keeping on shifting. But it's still not clear how many episodes or phases of such dispersal events had occurred. The Qinling Mountains weren't responsible for the faunal differentiation between the North and the South, neither was the Yangtze River; because the former is not big enough, and the latter cannot be regarded as an efficient barrier for those animals, which are capable of flying and swimming. Maybe the climate zonation is the root cause of zoogeographical changes.     

L’origine des Imerites Rouchadze, 1933 : résultat d’une innovation chez les Gassendiceratinae Bert,Delanoy et Bersac, 2006 (Ammonoidea,Ancyloceratina)

The recent discoveries of remarkably preserved specimens of Imerites dichotomum (Ammonoidea, Ancyloceratina) bring new palaeontological precisions on this genus. The study of the ontogenic development demonstrates that Imerites directly derives from genus Pseudoshasticrioceras. So, their origin is within the Gassendiceratinae and not in the Heteroceratidae like it was usually admitted. On the other hand, the coexistence of macroconch and microconch specimens in the species of the genus Imerites confirms the hypothesis of a dimorphism. The new palaeontological data prove that “Crioceras” cristatus is a nomen dubium and must be abandoned.     

Anglesites gen. nov. (Ammonoidea, Ancyloceratina), un nouveau genre d’ammonites hétéromorphes du Barrémien supérieur du Sud-Est de la France

The revision of the Crioceras puzosianum d’Orbigny, 1842 made during the revision of the Paléontologie Française of d’Orbigny, shows that this taxon belongs to a new genus: Anglesites gen. nov. This new genus, from upper Barremian age, is monospecific for the moment and is homeomorphic to the Leptoceratoides from the Lower Barremian. It is temporarily included in the subfamily of the Leptoceratoidinae. A neotype for the “Crioceras” puzosianum d’Orbigny, 1842 is herein designated.     

Role of magnesium cations in the yeast orotate phosphoribosyltransferase catalyzed reaction. Mechanism of the inhibition by Cu++ and Ni++ ions

The magnesium chelate of the N(3)H tautomer of orotate, L₃Mg, is the true substrate in the biosynthesis of orotidine 5′-monophosphate (OMP) catalyzed by yeast orotate phosphoribosyltransferase (OPRTase, E.C. 2.4.210) with a Michaelis constant K_m^L₃Mg equal to 12(2) μM. It is postulated that Mg⁺⁺ cations activate the transport of orotate to the active site by neutralizing the orotate charges; the ligand N(3)H is then exchanged between the incoming cation and the cation bound to the enzyme, thus ensuring the stabilization of the appropriate isomeric structure of orotate. This scheme, together with kinetic and thermodynamic data on orotate complexation by Mg⁺⁺ and Ca⁺⁺, accounts for the role of Ca⁺⁺ cations that neither activate nor inhibit OMP synthesis.Cu⁺⁺ and Ni⁺⁺ inhibiting properties arise from the formation of inert complexes of orotate. Ni⁺⁺ complexes have a poor affinity for the protein, whereas Cu⁺⁺ complexes have a Michaelis constant similar to that of the L₃Mg active species. The inertness of these complexes is tentatively understood in terms of low phosphoribosyl transfer rates as postulated from the kinetic study of the protonation of the complexes in water.     

Gene function prediction based on Gene Ontology Hierarchy Preserving Hashing

Gene Ontology (GO) uses structured vocabularies (or terms) to describe the molecular functions, biological roles, and cellular locations of gene products in a hierarchical ontology. GO annotations associate genes with GO terms and indicate the given gene products carrying out the biological functions described by the relevant terms. However, predicting correct GO annotations for genes from a massive set of GO terms as defined by GO is a difficult challenge. To combat with this challenge, we introduce a Gene Ontology Hierarchy Preserving Hashing (HPHash) based semantic method for gene function prediction. HPHash firstly measures the taxonomic similarity between GO terms. It then uses a hierarchy preserving hashing technique to keep the hierarchical order between GO terms, and to optimize a series of hashing functions to encode massive GO terms via compact binary codes. After that, HPHash utilizes these hashing functions to project the gene-term association matrix into a low-dimensional one and performs semantic similarity based gene function prediction in the low-dimensional space. Experimental results on three model species (Homo sapiens, Mus musculus and Rattus norvegicus) for interspecies gene function prediction show that HPHash performs better than other related approaches and it is robust to the number of hash functions. In addition, we also take HPHash as a plugin for BLAST based gene function prediction. From the experimental results, HPHash again significantly improves the prediction performance. The codes of HPHash are available at: http://mlda.swu.edu.cn/codes.php?name=HPHash.