Analysis of the nucleotide sequence of the coat protein and 3'-untranslated region of two Brazilian Potato virus Y isolates

Two Brazilian Potato virus Y (PVY) isolates were biologically characterized as necrotic (PVY-NBR) and common (PVY-OBR) based upon symptoms on test plants. Additional characterization was performed by sequencing a cDNA corresponding to the 3' terminal region of the viral genome. The sequence consisted of 195 nucleotides (nt) coding part of the nuclear inclusion body b (NIb) gene, 804 nt of the coat protein (CP) gene, and 328 nt (PVY-OBR) or 326 nt (PVY-NBR) of the 3'-untranslated region (UTR). Translation of the sequence resulted in one single open reading frame with part of the NIb and a CP of 267 amino acids. The two isolates shared 95.1% similarity in the CP amino acid sequence. The CP and the 3'-UTR sequence of the Brazilian isolates were compared to those of other PVY isolates previously reported and unrooted phylogenetic trees were constructed. The trees revealed a separation of two distinct clusters, one comprising most of the common strains and the other comprising the necrotic strains. PVY-OBR was clustered in the common group and PVY-NBR in the necrotic one.

Virulence and rep-PCR analysis of Pyricularia grisea isolates from two Brazilian upland rice cultivars

The phenotypic and genetic diversity of 77 isolates of Pyricularia grisea collected from two upland rice cultivars, Maravilha and Primavera, was studied. Isolates exhibiting compatible reaction to cv.Primavera were incompatible to cv.Maravilha and vice versa, with the exception of six isolates that were compatible to both cultivars. The virulence of isolates from cv. Maravilha on 32 test genotypes of rice was significantly higher (t = 9.09, p < 0.0001) than the isolates from cv.Primavera. A phenogram constructed from virulence data showed two main groups, one constituted mainly of isolates from cv.Primavera (97.6%) and the other of isolates from cv.Maravilha (91.17%). Rep-PCR analysis of isolates using two primers designed from sequences of Pot2 showed that isolates could be clustered broadly into two groups. The average similarity within a cluster of isolates from cv.Primavera was significantly greater than the average similarity among the isolates of cv.Maravilha (t = 5.37, p < 0.0001). There was close correspondence between clusters based on PCR and virulence data (r = 0.48, p < 0.011). The results showed that isolates of P. grisea were cultivar specific and had low phenotypic and genetic diversity.

Genetic and antigenic analysis of Babesia bigemina isolates from five geographical regions of Brazil

A molecular epidemiological study was performed with Babesia bigemina isolates from five geographical regions of Brazil. The genetic analysis was done with random amplification of polymorphic DNA (RAPD), repetitive extragenic palindromic elements-polymerase chain reaction (REP-PCR) and enterobacterial repetitive intergenic consensus sequences-polymerase chain reaction (ERIC-PCR) that showed genetic polymorphism between these isolates and generated fingerprinting. In RAPD, ILO872 and ILO876 primers were able to detect at least one fingerprinting for each B. bigemina isolate. The amplification of B. bigemina DNA fragments by REP-PCR and ERIC-PCR gave evidence for the presence in this haemoprotozoan of the sequences described previously in microorganisms of the bacterial kingdom. For the first time it was demonstrated that both techniques can be used for genetic analysis of a protozoan parasite, although the ERIC-PCR was more discriminatory than REP-PCR. The dendogram with similarity coefficient among isolates showed two clusters and one subcluster. The Northeastern and Mid-Western isolates showed the greatest genetic diversity, while the Southeastern and Southern isolates were the closest. The antigenic analysis was done through indirect fluorescent antibody technique and Western blotting using a panel of monoclonal antibodies directed against epitopes on the merozoite membrane surface, rhoptries and membrane of infected erythrocytes. As expected, the merozoite variable surface antigens, major surface antigen (MSA)-1 and MSA-2 showed antigenic diversity. However, B cell epitopes on rhoptries and infected erythrocytes were conserved among all isolates studied. In this study it was possible to identify variable and conserved antigens, which had already been described as potential immunogens. Considering that an attenuated Babesia clone used as immunogen selected populations capable of evading the immunity induced by this vaccine, it is necessary to evaluate more deeply the cross-protection conferred by genetically more distant Brazilian B. bigemina isolates and make an evaluation of the polymorphism degree of variable antigens such as MSA-1 and MSA-2.

Clonal study of avian Escherichia coli strains by fliC conserved-DNA-sequence regions analysis

The clonal relationship among avian Escherichia coli strains and their genetic proximity with human pathogenic E. coli, Salmonela enterica, Yersinia enterocolitica and Proteus mirabilis, was determined by the DNA sequencing of the conserved 5' and 3'regions fliC gene (flagellin encoded gene). Among 30 commensal avian E. coli strains and 49 pathogenic avian E. coli strains (APEC), 24 commensal and 39 APEC strains harbored fliC gene with fragments size varying from 670bp to 1,900bp. The comparative analysis of these regions allowed the construction of a dendrogram of similarity possessing two main clusters: one compounded mainly by APEC strains and by H-antigens from human E. coli, and another one compounded by commensal avian E. coli strains, S. enterica, and by other H-antigens from human E. coli. Overall, this work demonstrated that fliC conserved regions may be associated with pathogenic clones of APEC strains, and also shows a great similarity among APEC and H-antigens of E. coli strains isolated from humans. These data, can add evidence that APEC strains can exhibit a zoonotic risk.

Identification of research trends in the field of separation processes. Application of epidemiological model, citation analysis, text mining, and technical analysis of the financial markets

Choice of industrial development options and the relevant allocation of the research funds become more and more difficult because of the increasing R&D costs and pressure for shorter development period. Forecast of the research progress is based on the analysis of the publications activity in the field of interest as well as on the dynamics of its change. Moreover, allocation of funds is hindered by exponential growth in the number of publications and patents. Thematic clusters become more and more difficult to identify, and their evolution hard to follow. The existing approaches of research field structuring and identification of its development are very limited. They do not identify the thematic clusters with adequate precision while the identified trends are often ambiguous. Therefore, there is a clear need to develop methods and tools, which are able to identify developing fields of research. The main objective of this Thesis is to develop tools and methods helping in the identification of the promising research topics in the field of separation processes. Two structuring methods as well as three approaches for identification of the development trends have been proposed. The proposed methods have been applied to the analysis of the research on distillation and filtration. The results show that the developed methods are universal and could be used to study of the various fields of research. The identified thematic clusters and the forecasted trends of their development have been confirmed in almost all tested cases. It proves the universality of the proposed methods. The results allow for identification of the fast-growing scientific fields as well as the topics characterized by stagnant or diminishing research activity.

Genetic analysis of the porcine group B rotavirus NSP2 gene from wild-type Brazilian strains

Group B rotaviruses (RV-B) were first identified in piglet feces, being later associated with diarrhea in humans, cattle, lambs, and rats. In human beings, the virus was only described in China, India, and Bangladesh, especially infecting adults. Only a few studies concerning molecular analysis of the RV-B NSP2 gene have been conducted, and porcine RV-B has not been characterized. In the present study, three porcine wild-type RV-B strains from piglet stool samples collected from Brazilian pig herds were used for analysis. PAGE results were inconclusive for those samples, but specific amplicons of the RV-B NSP2 gene (segment 8) were obtained in a semi-nested PCR assay. The three porcine RV-B strains showed the highest nucleotide identity with the human WH1 strain and the alignments with other published sequences resulted in three groups of strains divided according to host species. The group of human strains showed 92.4 to 99.7% nucleotide identity while the porcine strains of the Brazilian RV-B group showed 90.4 to 91.8% identity to each other. The identity of the Brazilian porcine RV-B strains with outer sequences consisting of group A and C rotaviruses was only 35.3 to 38.8%. A dendrogram was also constructed to group the strains into clusters according to host species: human, rat, and a distinct third cluster consisting exclusively of the Brazilian porcine RV-B strains. This is the first study of the porcine RV-B NSP2 gene that contributes to the partial characterization of this virus and demonstrates the relationship among RV-B strains from different host species.

Application of exploratory factor analysis to assess fish consumption in a university community

The objective of this research was to use the technique of Exploratory Factor Analysis (EFA) for the adequacy of a tool for the assessment of fish consumption and the characteristics involved in this process. Data were collected during a campaign to encourage fish consumption in Brazil with the voluntarily participation of members of a university community. An assessment instrument consisting of multiple-choice questions and a five-point Likert scale was designed and used to measure the importance of certain attributes that influence the choice and consumption of fish. This study sample was composed of of 224 individuals, the majority were women (65.6%). With regard to the frequency of fish consumption, 37.67% of the volunteers interviewed said they consume the product two or three times a month, and 29.6% once a week. The Exploratory Factor Analysis (EFA) was used to group the variables; the extraction was made using the principal components and the rotation using the Quartimax method. The results show clusters in two main constructs, quality and consumption with Cronbach Alpha coefficients of 0.75 and 0.69, respectively, indicating good internal consistency.

Characterization and classification of pequi trees (Caryocar brasiliense Camb.) based on the profile of volatile constituents using headspace solid-phase microextraction - gas chromatography - mass spectrometry and multivariate analysis

In order to determine the variability of pequi tree (Caryocar brasiliense Camb.) populations, volatile compounds from fruits of eighteen trees representing five populations were extracted by headspace solid-phase microextraction and analyzed by gas chromatography-mass spectrometry. Seventy-seven compounds were identified, including esters, hydrocarbons, terpenoids, ketones, lactones, and alcohols. Several compounds had not been previously reported in the pequi fruit. The amount of total volatile compounds and the individual compound contents varied between plants. The volatile profile enabled the differentiation of all of the eighteen plants, indicating that there is a characteristic profile in terms of their origin. The use of Principal Component Analysis and Cluster Analysis enabled the establishment of markers (dendrolasin, ethyl octanoate, ethyl 2-octenoate and β-cis-ocimene) that discriminated among the pequi trees. According to the Cluster Analysis, the plants were classified into three main clusters, and four other plants showed a tendency to isolation. The results from multivariate analysis did not always group plants from the same population together, indicating that there is greater variability within the populations than between pequi tree populations.

In Search of Convergence: A Co-citation Analysis of Three Sport Management Journals

Responding to a series of articles in sport management literature calling for more diversity in terms of areas of interest or methods, this study warns against the danger of excessively fragmenting this field of research. The works of Kuhn (1962) and Pfeffer (1993) are taken as the basis of an argument that connects convergence with scientific strength. However, being aware of the large number of counterarguments directed at this line of reasoning, a new model of convergence, which focuses on clusters of research contributions with similar areas of interest, methods, and concepts, is proposed. The existence of these clusters is determined with the help of a bibliometric analysis of publications in three sport management journals. This examination determines that there are justified reasons to be concerned about the level of convergence in the field, pointing out to a reduced ability to create large clusters of contributions in similar areas of interest.

HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Investigation of clusters of giardiasis using GIS and a spatial scan statistic

Affiliation: Pascal Michel : Département de pathologie et microbiologie, Faculté de médecine vétérinaire

Detection of microcalcifications in mammograms using local maxima andadaptive wavelet transform analysis

A method for computer- aided diagnosis of micro calcification clusters in mammograms images presented . Micro calcification clus.eni which are an early sign of bread cancer appear as isolated bright spots in mammograms. Therefore they correspond to local maxima of the image. The local maxima of the image is lint detected and they are ranked according to it higher-order statistical test performed over the sub band domain data

Time Resolved Analysis of C2 Emission from Laser Induced Graphite Plasma in Helium Atmosphere

We report time resolved study of C2 emission from laser produced carbon plasma in presence of ambient helium gas. The 1.06µm: radiation from a Nd:YAG laser was focused onto a graphite target where it·produced a transient plasma. We observed double peak structure in the time profile of C2 species. The twin peaks were observed only after a threshold laser fluence. It is proposed that the faster velocity component in the temporal profiles originates mainly due to recombination processes. The laser fluence and ambient gas dependence of the double peak intensity distribution is also reported.

Two-dimensional clusters of liquid 4He

The binding energies of two-dimensional clusters (puddles) of¿4He are calculated in the framework of the diffusion Monte Carlo method. The results are well fitted by a mass formula in powers of x=N-1/2, where N is the number of particles. The analysis of the mass formula allows for the extraction of the line tension, which turns out to be 0.121 K/Å. Sizes and density profiles of the puddles are also reported.

Spectral clustering independent component analysis for tissue classification from brain MRI

A spectral angle based feature extraction method, Spectral Clustering Independent Component Analysis (SC-ICA), is proposed in this work to improve the brain tissue classification from Magnetic Resonance Images (MRI). SC-ICA provides equal priority to global and local features; thereby it tries to resolve the inefficiency of conventional approaches in abnormal tissue extraction. First, input multispectral MRI is divided into different clusters by a spectral distance based clustering. Then, Independent Component Analysis (ICA) is applied on the clustered data, in conjunction with Support Vector Machines (SVM) for brain tissue analysis. Normal and abnormal datasets, consisting of real and synthetic T1-weighted, T2-weighted and proton density/fluid-attenuated inversion recovery images, were used to evaluate the performance of the new method. Comparative analysis with ICA based SVM and other conventional classifiers established the stability and efficiency of SC-ICA based classification, especially in reproduction of small abnormalities. Clinical abnormal case analysis demonstrated it through the highest Tanimoto Index/accuracy values, 0.75/98.8%, observed against ICA based SVM results, 0.17/96.1%, for reproduced lesions. Experimental results recommend the proposed method as a promising approach in clinical and pathological studies of brain diseases