Phenotypic evolution studied by layered stochastic differential equations

Time series of cell size evolution in unicellular marine algae (division Haptophyta; Coccolithus lineage), covering 57 million years, are studied by a system of linear stochastic differential equations of hierarchical structure. The data consists of size measurements of fossilized calcite platelets (coccoliths) that cover the living cell, found in deep-sea sediment cores from six sites in the world oceans and dated to irregular points in time. To accommodate biological theory of populations tracking their fitness optima, and to allow potentially interpretable correlations in time and space, the model framework allows for an upper layer of partially observed site-specific population means, a layer of site-specific theoretical fitness optima and a bottom layer representing environmental and ecological processes. While the modeled process has many components, it is Gaussian and analytically tractable. A total of 710 model specifications within this framework are compared and inference is drawn with respect to model structure, evolutionary speed and the effect of global temperature.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS559 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

The oxygen-independent metabolism of cyclic monoterpenes in Castellaniella defragrans 65Phen

BACKGROUND: The facultatively anaerobic betaproteobacterium Castellaniella defragrans 65Phen utilizes acyclic, monocyclic and bicyclic monoterpenes as sole carbon source under oxic as well as anoxic conditions. A biotransformation pathway of the acyclic β-myrcene required linalool dehydratase-isomerase as initial enzyme acting on the hydrocarbon. An in-frame deletion mutant did not use myrcene, but was able to grow on monocyclic monoterpenes. The genome sequence and a comparative proteome analysis together with a random transposon mutagenesis were conducted to identify genes involved in the monocyclic monoterpene metabolism. Metabolites accumulating in cultures of transposon and in-frame deletion mutants disclosed the degradation pathway. RESULTS: Castellaniella defragrans 65Phen oxidizes the monocyclic monoterpene limonene at the primary methyl group forming perillyl alcohol. The genome of 3.95 Mb contained a 70 kb genome island coding for over 50 proteins involved in the monoterpene metabolism. This island showed higher homology to genes of another monoterpene-mineralizing betaproteobacterium, Thauera terpenica 58Eu(T), than to genomes of the family Alcaligenaceae, which harbors the genus Castellaniella. A collection of 72 transposon mutants unable to grow on limonene contained 17 inactivated genes, with 46 mutants located in the two genes ctmAB (cyclic terpene metabolism). CtmA and ctmB were annotated as FAD-dependent oxidoreductases and clustered together with ctmE, a 2Fe-2S ferredoxin gene, and ctmF, coding for a NADH:ferredoxin oxidoreductase. Transposon mutants of ctmA, B or E did not grow aerobically or anaerobically on limonene, but on perillyl alcohol. The next steps in the pathway are catalyzed by the geraniol dehydrogenase GeoA and the geranial dehydrogenase GeoB, yielding perillic acid. Two transposon mutants had inactivated genes of the monoterpene ring cleavage (mrc) pathway. 2-Methylcitrate synthase and 2-methylcitrate dehydratase were also essential for the monoterpene metabolism but not for growth on acetate. CONCLUSIONS: The genome of Castellaniella defragrans 65Phen is related to other genomes of Alcaligenaceae, but contains a genomic island with genes of the monoterpene metabolism. Castellaniella defragrans 65Phen degrades limonene via a limonene dehydrogenase and the oxidation of perillyl alcohol. The initial oxidation at the primary methyl group is independent of molecular oxygen

Functional analysis of the magnetosome island in Magnetospirillum gryphiswaldense: the mamAB operon is sufficient for magnetite biomineralization

Bacterial magnetosomes are membrane-enveloped, nanometer-sized crystals of magnetite, which serve for magnetotactic navigation. All genes implicated in the synthesis of these organelles are located in a conserved genomic magnetosome island (MAI). We performed a comprehensive bioinformatic, proteomic and genetic analysis of the MAI in Magnetospirillum gryphiswaldense. By the construction of large deletion mutants we demonstrate that the entire region is dispensable for growth, and the majority of MAI genes have no detectable function in magnetosome formation and could be eliminated without any effect. Only <25% of the region comprising four major operons could be associated with magnetite biomineralization, which correlated with high expression of these genes and their conservation among magnetotactic bacteria. Whereas only deletion of the mamAB operon resulted in the complete loss of magnetic particles, deletion of the conserved mms6, mamGFDC, and mamXY operons led to severe defects in morphology, size and organization of magnetite crystals. However, strains in which these operons were eliminated together retained the ability to synthesize small irregular crystallites, and weakly aligned in magnetic fields. This demonstrates that whereas the mamGFDC, mms6 and mamXY operons have crucial and partially overlapping functions for the formation of functional magnetosomes, the mamAB operon is the only region of the MAI, which is necessary and sufficient for magnetite biomineralization. Our data further reduce the known minimal gene set required for magnetosome formation and will be useful for future genome engineering approaches

Bacillus subtilis as heterologous host for the secretory production of the non-ribosomal cyclodepsipeptide enniatin

The heterologous expression of genes or gene clusters in microbial hosts, followed by metabolic engineering of biosynthetic pathways, is key to access industrially and pharmaceutically relevant compounds in an economically affordable and sustainable manner. Therefore, platforms need to be developed, which provide tools for the controlled synthesis of bioactive compounds. The Gram-positive bacterium Bacillus subtilis is a promising candidate for such applications, as it is generally regarded as a safe production host, its physiology is well investigated and a variety of tools is available for its genetic manipulation. Furthermore, this industrially relevant bacterium provides a high secretory potential not only for enzymes but also for primary and secondary metabolites. In this study, we present the first heterologous expression of an eukaryotic non-ribosomal peptide synthetase gene (esyn) coding for the biosynthesis of the small molecule enniatin in B. subtilis. Enniatin is a pharmaceutically used cyclodepsipeptide for treatment of topical bacterial and fungal infections. We generated various enniatin-producing B. subtilis strains, allowing for either single chromosomal or plasmid-based multi-copy expression of the esyn cluster under the control of an acetoin-inducible promoter system. Optimization of cultivation conditions, combined with modifications of the genetic background and multi-copy plasmid-based esyn expression, resulted in a secretory production of enniatin B. This work presents B. subtilis as a suitable host for the expression of heterologous eukaryotic non-ribosomal peptide synthetases (NRPS) clusters

Uso de simuladores em atividades de laboratório de física moderna: análise de sua contribuição para o ensino e aprendizagem na modalidade de educação à distância

Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Ciências da Educação, Programa de Pós-Graduação em Educação Científica e Tecnológica, Florianópolis, 2015.Neste trabalho nos preocupamos com o Ensino de Física Moderna (FM), pois percebemos o problema da não inserção da FM no Ensino Médio. Entendemos que existem dificuldades em relação ao entendimento de conceitos e também empecilhos na realização de experimentos de FM. A proposta desta dissertação é investigar o uso de simuladores, que vêm como uma alternativa para auxiliar na visualização e representação dos fenômenos físicos. No entanto, também é fundamental olhar para a sequência didática de uma disciplina que tenha como proposta o uso de simuladores e que seja parte integrante da formação em FM. Apontamos também a importância das perguntas para o entendimento conceitual. Dessa forma, foi escolhido um episódio de aula sobre  espectros atômicos da disciplina de Laboratório de Física Moderna na modalidade de Educação a Distância da UFSC. A coleta de informações é feita através de uma descrição da sequência didática e gravação de áudio das falas de alunos e professores da disciplina. Para análise, criamos um instrumento para categorizar os tipos de perguntas que os licenciandos fizeram durante os momentos de aula presencial, de onde emergiram as categorias. A turma analisada compreendia um total de 20 licenciandos da nona fase do curso de Licenciatura em Física EaD da UFSC, esta, dividida em Turma A e B. A Turma A que começava com a atividade experimental e depois seguia para a atividade com simuladores, e Turma B, invertia a ordem. Como resultado de nossa análise, percebemos: que a maior parte das perguntas feitas pelos alunos foram de caráter de confirmação, sendo mais evidente nos momentos experimentais; que falta compreensão conceitual por parte dos alunos para relacionar os conceitos vistos nas disciplinas teóricas com a prática experimental; que pela mudança na sequência didática promovida na atividade com o simulador, o professor propicia um espaço para discussão com a Turma B e, como consequência disso, os licenciandos fazem mais perguntas de apropriação conceitual. Concluímos que a ordem das atividades com o uso de simuladores integrados às atividades experimentais pode auxiliar na compreensão de fenômenos, desde que sejam pensados os recursos TIC com a apropriação no ensino. Assim, para que se tenha melhor aproveitamento do uso de simuladores, devese repensar as atividades dentro de uma proposta de educação que promova momentos de discussões conceituais e que propicie a feitura de perguntas mais reflexivas, para que contribua para o aprendizado de FM.Abstract : In this paper we care about Modern Physics (MP) Education as we perceive the problem of non inclusion of MP in high school. There are difficulties regarding the understanding of concepts and also obstacles in performing MF experiments. The purpose of this dissertation is to investigate the use of simulators, which come as an alternative to help in the visualization and in representation of physical phenomena. However, it is also critical to look at the teaching process, the didactic sequence, during a course that has the use of simulators as proposal and nonetheless it is an integral part of training in MP. We highlighted the importance of question making for conceptual understanding. Thus, it was chosen an episode of classes about "atomic spectra" content during the subject Modern Physics Laboratory in a Distance Education course at UFSC. The information was obtained through a description of the didactic sequence and audio recordings of speeches proffered by students and teachers in the class. For analyzing, we created an analytical tool to categorize the types of questions that undergraduates did during class time, giving birth to the categories. The group analyzed included a total of 20 licensees of the ninth phase of the Distance Education graduation in Physics at UFSC, divided into Group A, starting the class with the experimentation followed by the use of simulations, and Group B, which inverted the process. As a result of our analysis, we realized that: most of the questions asked by the students was confirmation-type, being more evident in experimental moments; it lacks conceptual understanding by the students to relate the concepts seen in theoretical subjects with experimental practice; by changing the didactic sequence in the use of the simulator, the teacher provides a space for discussion with the Class B and, as a result, the licensees ask more questions of conceptual appropriation. We concluded that the use of the experimental activities integrated with simulators can help in understanding phenomena. Thus, in order to achieve better results in the use of simulators, one should rethink the activities within an educational proposal that promotes moments of conceptual discussions and leads to the making of more reflexive questions, contributing to the MP learning

Die Baltischen Wirbeltiere nach ihren Merkmalen: und mit ihren lateinischen, deutschen, russischen. und lettischen Benennungen

http://www.ester.ee/record=b4010830*es

Untersuchungen zum extrazellulären und intrazellulären Sauerstofftransfer

[no abstract

Validation and Reliability of the German Version of the School Burnout Inventory

This study investigates the validity and reliability of the German version of the School Burnout Inventory (SBI-G) in 1,570 secondary-school students (Mage = 14.11, SD = 0.78; 51.7 % girls). Results indicate that school burnout consists of two correlated but separate dimensions including (1) exhaustion at school, (2) cynicism toward the meaning of school and sense of inadequacy. The study revealed that school burnout can be measured as a two-factor model, which provided good reliability and validity indices. Further, we verified concurrent validity, finding that students suffering from general stress also reported overall school burnout as well as exhaustion, cynicism, and inadequacy. Students who exhibited cynicism and inadequacy also reported lower levels of behavioral, emotional, and cognitive school engagement, while exhausted students reported lower emotional school engagement but higher cognitive school engagement.Peer reviewe