Sequence analysis of a genomic clone encoding a Zc2 protein from Zea mays W64A

A genomic clone (p268c) coding for the 28 kD storage protein Zc2 from maize endosperm has been isolated and sequenced.

Sequence analysis of a genomic clone encoding a Zc2 protein from Zea mays W64A

A genomic clone (p268c) coding for the 28 kD storage protein Zc2 from maize endosperm has been isolated and sequenced.

Antibiotic prescription in the treatment of odontogenic infection by health professionals: a factor to consensus

Objective: To observe the attitude of dentists and family doctors in prescribing antibiotics for the treatment of dental infections. Study Design: A poll was performed to determine the differences in the prescription of antibiotics for the treatment of odontogenic infection by dentists and family doctors of the primary care department of the Catalan Health Care Service. Results: A hundred polls were distributed among family doctors, and another 100 ones among primary care dentists assigned to the Catalan Health Care Service of the Generalitat de Catalunya. Of the total of questionnaires distributed, 63 were retuned and answered from dentists and 71 from family doctors. Eighty-one percent of dentists included in the opinion poll considered amoxicillin as the first antibiotic choice for the treatment of odontogenic infections, while 73.2% of family doctors preferred the combination of amoxicillin and clavulanic acid. With regard to antibiotics of choice in patients allergic to penicillin, 67.7% of family doctors preferred macrolides (25.4% opted for clarithromycin, 25.4% for erythromycin and 16.9% for spiramycin). However, clindamycin was the antibiotic most frequently prescribed by dentists (66.7%), followed by erythromycin (28.6%). Conclusions: The results of this study show a large discrepancy in the criteria for the treatment of odontogenic infections on the part of leading professionals involved in the management of this condition. Although the most common prescription involved beta-lactam antibiotics in both groups, several significant differences have been detected with regard to the second antibiotic choice

Antibiotic prescription in the treatment of odontogenic infection by health professionals: a factor to consensus

Objective: To observe the attitude of dentists and family doctors in prescribing antibiotics for the treatment of dental infections. Study Design: A poll was performed to determine the differences in the prescription of antibiotics for the treatment of odontogenic infection by dentists and family doctors of the primary care department of the Catalan Health Care Service. Results: A hundred polls were distributed among family doctors, and another 100 ones among primary care dentists assigned to the Catalan Health Care Service of the Generalitat de Catalunya. Of the total of questionnaires distributed, 63 were retuned and answered from dentists and 71 from family doctors. Eighty-one percent of dentists included in the opinion poll considered amoxicillin as the first antibiotic choice for the treatment of odontogenic infections, while 73.2% of family doctors preferred the combination of amoxicillin and clavulanic acid. With regard to antibiotics of choice in patients allergic to penicillin, 67.7% of family doctors preferred macrolides (25.4% opted for clarithromycin, 25.4% for erythromycin and 16.9% for spiramycin). However, clindamycin was the antibiotic most frequently prescribed by dentists (66.7%), followed by erythromycin (28.6%). Conclusions: The results of this study show a large discrepancy in the criteria for the treatment of odontogenic infections on the part of leading professionals involved in the management of this condition. Although the most common prescription involved beta-lactam antibiotics in both groups, several significant differences have been detected with regard to the second antibiotic choice

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Background: It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements.Results: Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA. Conclusion: We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.

Complete DNA sequence of Kuraishia capsulata illustrates novel genomic features among budding yeasts (Saccharomycotina)

The numerous yeast genome sequences presently available provide a rich source of information for functional as well as evolutionary genomics but unequally cover the large phylogenetic diversity of extant yeasts. We present here the complete sequence of the nuclear genome of the haploid-type strain of Kuraishia capsulata (CBS1993(T)), a nitrate-assimilating Saccharomycetales of uncertain taxonomy, isolated from tunnels of insect larvae underneath coniferous barks and characterized by its copious production of extracellular polysaccharides. The sequence is composed of seven scaffolds, one per chromosome, totaling 11.4 Mb and containing 6,029 protein-coding genes, ~13.5% of which being interrupted by introns. This GC-rich yeast genome (45.7%) appears phylogenetically related with the few other nitrate-assimilating yeasts sequenced so far, Ogataea polymorpha, O. parapolymorpha, and Dekkera bruxellensis, with which it shares a very reduced number of tRNA genes, a novel tRNA sparing strategy, and a common nitrate assimilation cluster, three specific features to this group of yeasts. Centromeres were recognized in GC-poor troughs of each scaffold. The strain bears MAT alpha genes at a single MAT locus and presents a significant degree of conservation with Saccharomyces cerevisiae genes, suggesting that it can perform sexual cycles in nature, although genes involved in meiosis were not all recognized. The complete absence of conservation of synteny between K. capsulata and any other yeast genome described so far, including the three other nitrate-assimilating species, validates the interest of this species for long-range evolutionary genomic studies among Saccharomycotina yeasts.

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10 000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.

DnaSP Version 5. DNA Sequence Polymorphism

DnaSP, DNA Sequence Polymorphism, is a software package for the analysis of nucleotide polymorphism from aligned DNA sequence data. DnaSP can estimate several measures of DNA sequence variation within and between populations (in noncoding, synonymous or nonsynonymous sites, or in various sorts of codon positions), as well as linkage disequilibrium, recombination, gene flow and gene conversion parameters. DnaSP can also carry out several tests of neutrality: Hudson, Kreitman and Aguadé (1987), Tajima (1989), McDonald and Kreitman (1991), Fu and Li (1993), and Fu (1997) tests. Additionally, DnaSP can estimate the confidence intervals of some test-statistics by the coalescent. The results of the analyses are displayed on tabular and graphic form.

Allelic diversity and population structure in Vibrio cholerae O139 Bengal based on nucleotide sequence analysis

Comparative analysis of gene fragments of six housekeeping loci, distributed around the two chromosomes of Vibrio cholerae, has been carried out for a collection of 29 V. cholerae O139 Bengal strains isolated from India during the first epidemic period (1992 to 1993). A toxigenic O1 ElTor strain from the seventh pandemic and an environmental non-O1/non-O139 strain were also included in this study. All loci studied were polymorphic, with a small number of polymorphic sites in the sequenced fragments. The genetic diversity determined for our O139 population is concordant with a previous multilocus enzyme electrophoresis study in which we analyzed the same V. cholerae O139 strains. In both studies we have found a higher genetic diversity than reported previously in other molecular studies. The results of the present work showed that O139 strains clustered in several lineages of the dendrogram generated from the matrix of allelic mismatches between the different genotypes, a finding which does not support the hypothesis previously reported that the O139 serogroup is a unique clone. The statistical analysis performed in the V. cholerae O139 isolates suggested a clonal population structure. Moreover, the application of the Sawyer's test and split decomposition to detect intragenic recombination in the sequenced gene fragments did not indicate the existence of recombination in our O139 population.

Draft genome sequence of Aeromonas molluscorum strain 848TT, isolated from bivalve molluscs

We report here the draft genome sequence of Aeromonas molluscorum 848T, the type strain of this Aeromonas species, which was isolated from wedge shells (Donax trunculus) obtained from a retail market in Barcelona, Spain, in 1997.

Genome sequence of Plesiomonas shigelloides strain 302-73 (serotype O1)

Plesiomonas shigelloides, the only species of the genus, is an emergent pathogenic bacterium associated with human diarrheal and extraintestinal disease. We present the whole-genome sequence analysis of the representative strain for the O1 serotype (strain 302-73), providing a tool for studying bacterial outbreaks, virulence factors, and accurate diagnostic methods.

Establishing the Stages and Processes of Change for Weight Loss by Consensus of Experts

The present study aimed to establish, by a consensus of experts, the stages and processes of change for weight management in overweight and obese people. The first step involved developing two questionnaires aimed at assessing stages and processes of change for weight loss in overweight and obese people. The processes-ofchange questionnaire consisted of 12 subscales, and contained 107 items. A three-round Delphi study was carried out through a website, where participants were asked to give their opinion about the representativeness and clarity of the scale items. The stages-of-change questionnaire consisted of five items and was presented in the final round of the study. A team of 66 experts in the obesity field from 29 countries participated in the study. They were selected either because they belonged to the organizing committee of international associations related to obesity, or because of their research career. The required changes in the questionnaire were made according to the opinions of the participants. Some of these were the result of the group statistical response, whereas others were due to the suggestions made by the participants. A final version of the questionnaire consisting of 63 items was eventually obtained. The present study produced two questionnaires to assess stages and processes of change for weight management. The strength of the study lies in the consensus reached by the panel of experts in order to establish the required content of the questionnaires. The two measures provide useful tools for practitioners who wish to tailor weight-management interventions according to transtheoretical model constructs.

Complete genome sequence of the type strain of Bacillus toyonensis BCT-7112T, the active ingredient of the feed additive preparation Toyocerin

Strain BCT-7112, previously identified as Bacillus cereus var. toyoi, is the type strain of the species Bacillus toyonensis, a novel species of the B. cereus group. The complete genome of this strain, which is the active ingredient of the feed additive preparation Toyocerin, has been sequenced and annotated to reveal the genetic properties of this probiotic organism with a long history of safe use in animal nutrition.

High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes

Turbot (Scophthalmus maximus L.) is an important aquacultural resource both in Europe and Asia. However, there is little information on gene sequences available in public databases. Currently, one of the main problems affecting the culture of this flatfish is mortality due to several pathogens, especially viral diseases which are not treatable. In order to identify new genes involved in immune defense, we conducted 454-pyrosequencing of the turbot transcriptome after different immune stimulations.

Draft genome sequence of the Aeromonas diversa type strain

We present here the first genome sequence of the Aeromonas diversa type strain (CECT 4254T). This strain was isolated from the leg wound of a patient in New Orleans (Louisiana, USA) and was originally described as Enteric Group 501 and distinguished from A. schubertii by DNADNA hybridization and phenotypical characterization.