Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

A Comparative Policy Analysis of Seat Belt Laws, RB37-013, 2014

This analysis examined data from a variety of sources to estimate the benefit of enhancing Iowa’s current law to require all passengers to use seat belts. In addition to assessing Iowans’ opinions about changing the law, a literature review, a legislative policy review, and analysis of Iowa crash data were completed. Currently 28 states enforce seat belt laws for all passengers. Belted passengers riding with an unbelted passenger are 2 to 5 times more likely to suffer fatal injuries in a crash relative to when all occupants are using seat belts. Iowans are highly compliant (90%-94%) with the current seat belt law for front seat occupants. Of more than 1000 Iowans surveyed, 85% said they always use a seat belt when riding in the front seat, but only 36% always do so when they ride in the back seat. The most common reasons given for not using seat belts in the back seat are forgetting to buckle up and because it is not the law. Iowans widely support strengthening Iowa’s seat belt law — 62% said Iowa law should require all rear seat passengers to use seat belts. Four out of five respondents said they would use seat belts more often when sitting in the rear seat if it was the law. It is estimated rear seat fatalities would decrease about 48%, from 13 to 7 fatalities annually, if an all-passenger law was implemented in Iowa.

Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds.

Pseudomonas knackmussii B13 was the first strain to be isolated in 1974 that could degrade chlorinated aromatic hydrocarbons. This discovery was the prologue for subsequent characterization of numerous bacterial metabolic pathways, for genetic and biochemical studies, and which spurred ideas for pollutant bioremediation. In this study, we determined the complete genome sequence of B13 using next generation sequencing technologies and optical mapping. Genome annotation indicated that B13 has a variety of metabolic pathways for degrading monoaromatic hydrocarbons including chlorobenzoate, aminophenol, anthranilate and hydroxyquinol, but not polyaromatic compounds. Comparative genome analysis revealed that B13 is closest to Pseudomonas denitrificans and Pseudomonas aeruginosa. The B13 genome contains at least eight genomic islands [prophages and integrative conjugative elements (ICEs)], which were absent in closely related pseudomonads. We confirm that two ICEs are identical copies of the 103 kb self-transmissible element ICEclc that carries the genes for chlorocatechol metabolism. Comparison of ICEclc showed that it is composed of a variable and a 'core' region, which is very conserved among proteobacterial genomes, suggesting a widely distributed family of so far uncharacterized ICE. Resequencing of two spontaneous B13 mutants revealed a number of single nucleotide substitutions, as well as excision of a large 220 kb region and a prophage that drastically change the host metabolic capacity and survivability.

Comparative sequence analysis of the P-, M- and L-coding region of the measles virus CAM-70 live attenuated vaccine strain

Measles virus is a highly contagious agent which causes a major health problem in developing countries. The viral genomic RNA is single-stranded, nonsegmented and of negative polarity. Many live attenuated vaccines for measles virus have been developed using either the prototype Edmonston strain or other locally isolated measles strains. Despite the diverse geographic origins of the vaccine viruses and the different attenuation methods used, there was remarkable sequence similarity of H, F and N genes among all vaccine strains. CAM-70 is a Japanese measles attenuated vaccine strain widely used in Brazilian children and produced by Bio-Manguinhos since 1982. Previous studies have characterized this vaccine biologically and genomically. Nevertheless, only the F, H and N genes have been sequenced. In the present study we have sequenced the remaining P, M and L genes (approximately 1.6, 1.4 and 6.5 kb, respectively) to complete the genomic characterization of CAM-70 and to assess the extent of genetic relationship between CAM-70 and other current vaccines. These genes were amplified using long-range or standard RT-PCR techniques, and the cDNA was cloned and automatically sequenced using the dideoxy chain-termination method. The sequence analysis comparing previously sequenced genotype A strains with the CAM-70 Bio-Manguinhos strain showed a low divergence among them. However, the CAM-70 strains (CAM-70 Bio-Manguinhos and a recently sequenced CAM-70 submaster seed strain) were assigned to a specific group by phylogenetic analysis using the neighbor-joining method. Information about our product at the genomic level is important for monitoring vaccination campaigns and for future studies of measles virus attenuation.

Comparative proteomics analysis of chronic atrophic gastritis: changes of protein expression in chronic atrophic gastritis without Helicobacter pylori infection

Chronic atrophic gastritis (CAG) is a very common gastritis and one of the major precursor lesions of gastric cancer, one of the most common cancers worldwide. The molecular mechanism underlying CAG is unclear, but its elucidation is essential for the prevention and early detection of gastric cancer and appropriate intervention. A combination of two-dimensional gel electrophoresis and mass spectrometry was used in the present study to analyze the differentially expressed proteins. Samples from 21 patients (9 females and 12 males; mean age: 61.8 years) were used. We identified 18 differentially expressed proteins in CAG compared with matched normal mucosa. Eight proteins were up-regulated and 10 down-regulated in CAG when compared with the same amounts of proteins in individually matched normal gastric mucosa. Two novel proteins, proteasome activator subunit 1 (PSME1), which was down-regulated in CAG, and ribosomal protein S12 (RPS12), which was up-regulated in CAG, were further investigated. Their expression was validated by Western blot and RT-PCR in 15 CAG samples matched with normal mucosa. The expression level of RPS12 was significantly higher in CAG than in matched normal gastric mucosa (P < 0.05). In contrast, the expression level of PSME1 in CAG was significantly lower than in matched normal gastric mucosa (P < 0.05). This study clearly demonstrated that there are some changes in protein expression between CAG and normal mucosa. In these changes, down-regulation of PSME1 and up-regulation of RPS12 could be involved in the development of CAG. Thus, the differentially expressed proteins might play important roles in CAG as functional molecules.

The role of ‘Shared Memories’ in shaping nationalist movements : a comparative historical analysis of the Flemish and Québécois nationalist movements

Les mouvements nationalistes flamands et québécois divergent en concernant leur structure; par exemple le nationalisme flamand s'est développé comme un mouvement chrétien-démocrate, alors que le nationalisme québécois contemporain s’est galvanisé autour d'une idéologie laïque de gauche. Par ailleurs, il existe un contraste entre les poids sociodémographique, politique et économique portés par la région de Flandres en Belgique, et ceux portés dans la province du Québec au Canada. Cependant, malgré les influences divergentes structurelles et systémiques, les mouvements nationalistes flamand et québécois ont développé et maintenu des profils très similaires. Par exemple, les deux mouvements nationalistes se définissent par une distinction ethnolinguistique, les deux ont un discours nationaliste parallèle axé sur la nécessité de préserver et de protéger la langue et la culture de la communauté nationale, et les deux se concentrent sur l'obtention d'une redistribution des pouvoirs culturels et politiques. Dans ce mémoire, nous proposons que le profil nationaliste ressemblant du mouvement nationaliste flamand et québécois puisse être expliqué par le développement d'un « nationalisme ethnolinguistique de contestation », qui était initialement mis en place par les nationalistes flamands et québécois cherchant à corriger les effets d'une « division culturelle du travail ». Ce sentiment d’un nationalisme de contestation ethnolinguistique est instrumentalisé et perpétué par les nationalistes flamands et québécois en évoquant certains « souvenirs partagés », qui sont trouvés dans le récit historique de la communauté nationale. Ces souvenirs partagés, ainsi que leurs représentations symboliques, reflètent les sentiments de protestation, injustice et victimisation, qui sont vitaux pour les nationalistes flamands et québécois dans le maintien de leur expression parallèlement à un nationalisme de contestation ethnolinguistique en Flandres et au Québec.

Comparative expression analysis of transcription factor genes in the endostyle of invertebrate chordates

The endostyle of invertebrate chordates is a pharyngeal organ that is thought to be homologous with the follicular thyroid of vertebrates. Although thyroid-like features such as iodine-concentrating and peroxidase activities are located in the dorsolateral part of both ascidian and amphioxus endostyles, the structural organization and numbers of functional units are different. To estimate phylogenetic relationships of each functional zone with special reference to the evolution of the thyroid, we have investigated, in ascidian and amphioxus, the expression patterns of thyroid-related transcription factors such as TTF-2/MoxE4 and Pax2/5/8, as well as the forkhead transcription factors FoxQ1 and FoxA. Comparative gene expression analyses depicted an overall similarity between ascidians and amphioxus endostyles, while differences in expression patterns of these genes might be specifically related to the addition or elimination of a pair of glandular zones. Expressions of Ci-FoxE and BbFoxE4 suggest that the ancestral FoxE class might have been recruited for the formation of thyroid-like region in a possible common ancestor of chordates. Furthermore, coexpression of FoxE4, Pax2/5/8, and TPO in the dorsolateral part of both ascidian and amphioxus endostyles suggests that genetic basis of the thyroid function was already in place before the vertebrate lineage. (c) 2005 Wiley-Liss, Inc.

Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum.

A recently emerging bleeding canker disease, caused by Pseudomonas syringae pathovar aesculi (Pae), is threatening European horse chestnut in northwest Europe. Very little is known about the origin and biology of this new disease. We used the nucleotide sequences of seven commonly used marker genes to investigate the phylogeny of three strains isolated recently from bleeding stem cankers on European horse chestnut in Britain (E-Pae). On the basis of these sequences alone, the E-Pae strains were identical to the Pae type-strain (I-Pae), isolated from leaf spots on Indian horse chestnut in India in 1969. The phylogenetic analyses also showed that Pae belongs to a distinct clade of P. syringae pathovars adapted to woody hosts. We generated genome-wide Illumina sequence data from the three E-Pae strains and one strain of I-Pae. Comparative genomic analyses revealed pathovar-specific genomic regions in Pae potentially implicated in virulence on a tree host, including genes for the catabolism of plant-derived aromatic compounds and enterobactin synthesis. Several gene clusters displayed intra-pathovar variation, including those encoding type IV secretion, a novel fatty acid biosynthesis pathway and a sucrose uptake pathway. Rates of single nucleotide polymorphisms in the four Pae genomes indicate that the three E-Pae strains diverged from each other much more recently than they diverged from I-Pae. The very low genetic diversity among the three geographically distinct E-Pae strains suggests that they originate from a single, recent introduction into Britain, thus highlighting the serious environmental risks posed by the spread of an exotic plant pathogenic bacterium to a new geographic location. The genomic regions in Pae that are absent from other P. syringae pathovars that infect herbaceous hosts may represent candidate genetic adaptations to infection of the woody parts of the tree.

Exchange rate pass-through to prices in macrodata: a comparative sensitivity analysis

This paper compares exchange rate pass-through to aggregate prices in the US, Germany and Japan across a number of dimensions. Building on the empirical approaches in the recent literature, our contribution is to perform a thorough sensitivity analysis of pass-through estimates. We find that the econometric method, data frequency and variable proxy employed matter for the precision of details, yet they often agree on some general trends. Thus, pass-through to import prices has declined in the 1990s relative to the 1980s, pass-through to export prices remains country-specific and pass-through to consumer prices is nowadays negligible in all three economies we considered.

A comparative performance analysis of TRMM 3B42 (TMPA) versions 6 and 7 for hydrological applications over Andean-Amazon river basins

The Tropical Rainfall Measuring Mission 3B42 precipitation estimates are widely used in tropical regions for hydrometeorological research. Recently, version 7 of the product was released. Major revisions to the algorithm involve the radar refl ectivity - rainfall rates relationship, surface clutter detection over high terrain, a new reference database for the passive microwave algorithm, and a higher quality gauge analysis product for monthly bias correction. To assess the impacts of the improved algorithm, we compare the version 7 and the older version 6 product with data from 263 rain gauges in and around the northern Peruvian Andes. The region covers humid tropical rainforest, tropical mountains, and arid to humid coastal plains. We and that the version 7 product has a significantly lower bias and an improved representation of the rainfall distribution. We further evaluated the performance of versions 6 and 7 products as forcing data for hydrological modelling, by comparing the simulated and observed daily streamfl ow in 9 nested Amazon river basins. We find that the improvement in the precipitation estimation algorithm translates to an increase in the model Nash-Sutcliffe effciency, and a reduction in the percent bias between the observed and simulated flows by 30 to 95%.

A Comparative Cytogenetic Analysis of 2 Bothriuridae Species and Overview of the Chromosome Data of Scorpiones

The order Scorpiones is one of the most cytogenetically interesting groups within Arachnida by virtue of the combination of chromosome singularities found in the 59 species analyzed so far. In this work, mitotic and meiotic chromosomes of 2 species of the family Bothriuridae were detailed. This family occupies a basal position within the superfamily Scorpionoidea. Furthermore, review of the cytogenetic data of all previously studied scorpions is presented. Light microscopy chromosome analysis showed that Bothriurus araguayae and Bothriurus rochensis possess low diploid numbers compared with those of species belonging to closely related families. Gonadal cells examined under light and in transmission electron microscopy revealed, for the first time, that the Bothriuridae species possess typical monocentric chromosomes, and male meiosis presented chromosomes with synaptic and achiasmatic behavior. Moreover, in the sample of B. araguayae studied, heterozygous translocations were verified. The use of techniques to highlight specific chromosomal regions also revealed additional differences between the 2 Bothriurus species. The results herein recorded and the overview elaborated using the available cytogenetic information of Scorpiones elucidated current understanding regarding the processes of chromosome evolution that have occurred in Bothriuridae and in Scorpiones as a whole.

Comparative Histopathological Analysis of Human Pulps after Class I Cavity Preparation with a High-Speed Air-Turbine Handpiece or Er:YAG Laser

The purpose of this study was to comparatively evaluate the response of human pulps after cavity preparation with different devices. Deep class I cavities were prepared in sound mandibular premolars using either a high-speed air-turbine handpiece (Group 1) or an Er: YAG laser (Group 2). Following total acid etching and the application of an adhesive system, all cavities were restored with composite resin. Fifteen days after the clinical procedure, the teeth were extracted and processed for analysis under optical microscopy. In Group 1 in which the average for the remaining dentin thickness (RDT) between the cavity floor and the coronal pulp was 909.5 mu m, a discrete inflammatory response occurred in only one specimen with an RDT of 214 mu m. However, tissue disorganization occurred in most specimens. In Group 2 (average RDT = 935.2 mu m), the discrete inflammatory pulp response was observed in only one specimen (average RDT = 413 mu m). It may be concluded that the high-speed air-turbine handpiece caused greater structural alterations in the pulp, although without inducing inflammatory processes.

Comparative transcriptome analysis of Paracoccidioides brasiliensis during in vitro adhesion to type I collagen and fibronectin: identification of potential adhesins

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Comparative Histopathological Analysis of Human Pulps after Class I Cavity Preparation with a High-Speed Air-Turbine Handpiece or Er:YAG Laser

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)