Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map

<p>Abstract</p> <p>Background</p> <p>Determining the position and order of contigs and scaffolds from a genome assembly within an organism's genome remains a technical challenge in a majority of sequencing projects. In order to exploit contemporary technologies for DNA sequencing, we developed a strategy for whole genome single nucleotide polymorphism sequencing allowing the positioning of sequence contigs onto a linkage map using the bin mapping method.</p> <p>Results</p> <p>The strategy was tested on a draft genome of the fungal pathogen <it>Venturia inaequalis</it>, the causal agent of apple scab, and further validated using sequence contigs derived from the diploid plant genome <it>Fragaria vesca</it>. Using our novel method we were able to anchor 70% and 92% of sequences assemblies for <it>V. inaequalis </it>and <it>F. vesca</it>, respectively, to genetic linkage maps.</p> <p>Conclusions</p> <p>We demonstrated the utility of this approach by accurately determining the bin map positions of the majority of the large sequence contigs from each genome sequence and validated our method by mapping single sequence repeat markers derived from sequence contigs on a full mapping population.</p

Wear and corrosion interactions on titanium in oral environment : literature review

The oral cavity is a complex environment where corrosive substances from dietary, human saliva, and oral biofilms may accumulate in retentive areas of dental implant systems and prostheses promoting corrosion at their surfaces. Additionally, during mastication, micromovements may occur between prosthetic joints causing a relative motion between contacting surfaces, leading to wear. Both processes (wear and corrosion) result in a bio-tribocorrosion system once that occurs in contact with biological tissues and fluids. This review paper is focused on the aspects related to the corrosion and wear behavior of titanium-based structures in the oral environment. Furthermore, the clinical relevance of the oral environment is focused on the harmful effect that acidic substances and biofilms, formed in human saliva, may have on titanium surfaces. In fact, a progressive degradation of titanium by wear and corrosion (tribocorrosion) mechanisms can take place affecting the performance of titanium-based implant and prostheses. Also, the formation of wear debris and metallic ions due to the tribocorrosion phenomena can become toxic for human tissues. This review gathers knowledge from areas like materials sciences, microbiology, and dentistry contributing to a better understanding of bio-tribocorrosion processes in the oral environment.(undefined

Contextualização no ensino de estatística: uma proposta para os anos finais do ensino fundamental

Acompanha: Sequência de ensino contemplando a estatística nos anos finais do ensino fundamental segundo pressupostos da contextualizaçãoThe present study aimed to examine the contributions that a sequence of teaching based on assumptions of contextualization can bring to the teaching of statistics in the final years of basic school. The literature review concerning the teaching of statistics relies on Cazorla (2002), Lopes (2003, 2008, 2010a, 2010b), Silva (2007), Andrade (2008), Cazorla, Kataoka and Silva (2010), Jacobini et al. (2010), Campos, Wodewotzki and Jacobini (2011), among others. As for context, the literature review supported by Brazil (1998b, 1999), Tufano (2001), Pais (2002, 2010), Ramos (2004), (2005), Sadovsky (2007), Luccas (2011), among others. With the intention of achieving the proposed goal, was developed in the year 2011 a applied research, interpretive analysis and qualitative, descriptive in a batch of students of 7° year of basic school to a State public College of the city of Ponta Grossa, Paraná. The review of literature pertaining to the search features based on Gil (1991, 2006), Chizzotti (2003, 2008), Silva and Menezes (2005), Moreira and Caleffe (2008), Alves-Mazzotti (2011), Sarmento (2011), Teixeira (2011), among others. First was conducted an analysis of previous performance of the students on the basic content of statistics, based on a diagnostic instrument called pre-test. Then it was applied a sequence of teaching directed to basic statistical content, through the use of data collected in their own class, i.e. through contextualization. It emerged during the implementation of education, a greater interest and motivation of students to classes, as well as greater involvement of learners with the contents. The results of the analysis of the performance of the students after teaching sequence showed that this contributed to a significant gain on the acquisition of basic statistical content by students of the final years basic school. It is considered that the activities undertaken with learners, contributed to the development of the skills of reasoning, thinking, and statistical literacy of those forming the necessary basis for that in the future these students can reach the level of statistical literacy that contemporary society requires. As the final product of this work was to elaborate a courseware to support teacher education sequence containing a contextualized on basic statistical content aimed at the basic school, which is attached to this dissertation.O presente trabalho teve como objetivo analisar as contribuições que uma sequência de ensino pautada nos pressupostos da contextualização poderá trazer para o ensino e aprendizagem de Estatística nos anos finais do Ensino Fundamental. A revisão de literatura referente ao ensino de Estatística apoia-se em Cazorla (2002), Lopes (2003, 2008, 2010a, 2010b), Silva (2007), Andrade (2008), Cazorla, Kataoka e Silva (2010), Jacobini et al. (2010), Campos, Wodewotzki e Jacobini (2011), dentre outros. Quanto a contextualização, a revisão de literatura apoia-se em Brasil (1998b, 1999), Tufano (2001), Pais (2002, 2010), Ramos (2004), Mello (2005), Sadovsky (2007), Luccas (2011), além de outros. Com a intenção de alcançar o objetivo proposto, foi desenvolvida no ano de 2011 uma pesquisa aplicada, qualitativa com análise interpretativa e, descritiva em uma turma de alunos do 7° ano do Ensino Fundamental de um colégio público estadual do município de Ponta Grossa, Paraná. A revisão de literatura referente às características da pesquisa fundamenta-se em Gil (1991, 2006), Chizzotti (2003, 2008), Silva e Menezes (2005), Moreira e Caleffe (2008), Alves-Mazzotti (2011), Sarmento (2011), Teixeira (2011), dentre outros. Primeiramente foi realizada uma análise do desempenho prévio dos alunos em relação a conteúdos básicos de Estatística, tendo como base um instrumento diagnóstico chamado pré – teste. Depois foi aplicada uma sequência de ensino direcionada a conteúdos básicos de Estatística, por meio da utilização de dados coletados na própria turma, ou seja, por meio da contextualização. Verificou-se durante a aplicação da sequência de ensino, um maior interesse e motivação dos alunos para as aulas, além de um maior envolvimento dos educandos com os conteúdos estudados. Os resultados da análise do desempenho dos alunos após a aplicação da sequência de ensino mostraram que essa contribuiu para que houvesse um ganho significativo quanto à aquisição de conteúdos básicos de Estatística por parte de educandos dos anos finais do Ensino Fundamental. Considera-se que as atividades realizadas com os educandos, contribuíram para o desenvolvimento das competências de raciocínio, pensamento e, letramento estatísticos desses, formando a base necessária para que futuramente esses alunos possam atingir o nível de letramento estatístico que a sociedade contemporânea exige. Como produto final deste trabalho foi elaborado um material didático de apoio ao professor contendo uma sequência de ensino contextualizada sobre conteúdos básicos de Estatística voltada ao Ensino Fundamental, o qual se encontra anexado a esta dissertação

A candidate gene of Malus x robusta 5 for breeding towards fire blight resistance

Fire blight (FB) is the most important bacterial disease in apple and pear orchards. The disease is caused by Erwinia amylovora and difficult to control because the application of antibiotics is either banned or undesired in many apple production areas. Current breeding programs introgress strong resistance from wild sources such as Malus × robusta 5 (MR5). Previous work attributed the resistance derived from this accession to a QTL located on top of linkage group 3. We enriched this region with molecular markers and isolated the region by means of a genomic library. The genomic sequence encompassed by two flanking markers was analysed in silico and led to the identification of a gene with structural homology to known bacterial resistance genes in model plants. It is differentially expressed in fire blight resistant and susceptible plants, respectively. We therefore indicate it as candidate fire blight resistance gene MR5

Fine mapping of fire blight resistance locus in Malus x Robusta 5 on linkage group 3

Fire blight is one of the most damaging diseases in the majority of apple (Malus x domestica) producing countries worldwide. The region of the quantitative trait for resistance to Erwinia amylovora and the same data mapped as single gene in the wild apple Malus x robusta 5 was enriched with additional molecular markers. Generated phenotypic data of individuals that carry a crossing over in the region of interest allowed to position the locus coding for resistance into a short section at the top of linkage group 3 flanked by molecular markers

QTL mapping for resistance to fire blight using several Erwinia amylovora strains resulting in different host-pathogen interactions

QTL mapping of fire blight resistance in apple is an effective tool to determine associations between regions in the genome of apple and resistance to the bacterial disease. Several wild Malus accessions of different apple species have been identified as resistant to fire blight making them valuable as donors for the introgression of resistance to the cultivated apple Malus × domestica Borkh. Resistant accessions of the wild species M. baccata, M. fusca and M. × robusta 5 (Mr5) were inoculated with the wild type strain Ea1189 and the AvrRpt2EA deletion mutant (pZYRKD3-1). While M. baccata and M. fusca showed no symptoms to pZYRKD3-1, the resistance of M. × robusta 5 was overcome by pZYRKD3-1 with an average necrosis length of 52% respectively. Inoculation of the mapping population ‘Idared’ × Mr5 with the strain Ea 1189 results in the confirmation of the QTL on LG 3 in Mr5; this QTL completely broke down after inoculation with pZYRKD3-1, but two minor QTLs on LG 7 and LG 11 were detected

Fusion hindrance for the positive Q-value system 12C+30Si

The fusion excitation function for the positive-Q-value system 12C+30Si (Qfus = +14.1 MeV) has been measured in inverse kinematics down to the μb level and compared with standard coupled-channel calculations. The appearance of the fusion hindrance phenomenon and the evidence of a S-factor maximum have been observed. This result can be significant to extrapolate the behavior of lighter astrophysical relevant systems at deep sub-barrier energies, where existing experimental data are still contradicting and affected by large errors