Type II aromatic polyketide biosynthetic tailoring enzymes: diversity and adaptation in Streptomyces secondary metabolism.

Members of the bacterial genus Streptomyces are well known for their ability to produce an exceptionally wide selection of diverse secondary metabolites. These include natural bioactive chemical compounds which have potential applications in medicine, agriculture and other fields of commerce. The outstanding biosynthetic capacity derives from the characteristic genetic flexibility of Streptomyces secondary metabolism pathways: i) Clustering of the biosynthetic genes in chromosome regions redundant for vital primary functions, and ii) the presence of numerous genetic elements within these regions which facilitate DNA rearrangement and transfer between non-progeny species. Decades of intensive genetic research on the organization and function of the biosynthetic routes has led to a variety of molecular biology applications, which can be used to expand the diversity of compounds synthesized. These include techniques which, for example, allow modification and artificial construction of novel pathways, and enable gene-level detection of silent secondary metabolite clusters. Over the years the research has expanded to cover molecular-level analysis of the enzymes responsible for the individual catalytic reactions. In vitro studies of the enzymes provide a detailed insight into their catalytic functions, mechanisms, substrate specificities, interactions and stereochemical determinants. These are factors that are essential for the thorough understanding and rational design of novel biosynthetic routes. The current study is a part of a more extensive research project (Antibiotic Biosynthetic Enzymes; www.sci.utu.fi/projects/biokemia/abe), which focuses on the post-PKS tailoring enzymes involved in various type II aromatic polyketide biosynthetic pathways in Streptomyces bacteria. The initiative here was to investigate specific catalytic steps in anthracycline and angucycline biosynthesis through in vitro biochemical enzyme characterization and structural enzymology. The objectives were to elucidate detailed mechanisms and enzyme-level interactions which cannot be resolved by in vivo genetic studies alone. The first part of the experimental work concerns the homologous polyketide cyclases SnoaL and AknH. These catalyze the closure of the last carbon ring of the tetracyclic carbon frame common to all anthracycline-type compounds. The second part of the study primarily deals with tailoring enzymes PgaE (and its homolog CabE) and PgaM, which are responsible for a cascade of sequential modification reactions in angucycline biosynthesis. The results complemented earlier in vivo findings and confirmed the enzyme functions in vitro. Importantly, we were able to identify the amino acid -level determinants that influence AknH and SnoaL stereoselectivity and to determine the complex biosynthetic steps of the angucycline oxygenation cascade of PgaE and PgaM. In addition, the findings revealed interesting cases of enzyme-level adaptation, as some of the catalytic mechanisms did not coincide with those described for characterised homologs or enzymes of known function. Specifically, SnoaL and AknH were shown to employ a novel acid-base mechanism for aldol condenzation, whereas the hydroxylation reaction catalysed by PgaM involved unexpected oxygen chemistry. Owing to a gene-level fusion of two ancestral reading frames, PgaM was also shown to adopt an unusual quaternary sturucture, a non-covalent fusion complex of two alternative forms of the protein. Furthermore, the work highlighted some common themes encountered in polyketide biosynthetic pathways such as enzyme substrate specificity and intermediate reactivity. These are discussed in the final chapters of the work.

'L’escriptura del jo', una proposta d’educació intercultural i tractament de la diversitat per a l’ensenyament secundari obligatori = The writing of I, an intercultural educational proposal and treatment of diversity for Compulsory Secondary Education

The writing of I is a project that starts an itinerary through past, present and future experiences of each of our students based on following research activities. Reading, creation and recreation of text and other items that turn essentially around autobiographical writing and culminate with the elaboration of a free autobiography

On affirmation and becoming : a Deleuzian reading of Nietzsche's critique of nihilism

The main thrust of this thesis is the re-exploration of Friedrich Nietzsche's "critique of nihilism" through the lenses of Gilles Deleuze. A Deleuzian reading of Nietzsche is motivated by a post-deconstrnctive style of interpretation, inasmuch as Deleuze goes beyond, or in between, henneneutics and deconstrnction. Deleuze's post-deconstrnctive reading of Nietzsche is, however, only secondary to the main aim of this thesis. The primary thrust of this study is the critique of a way of thinking characterized by Nietzsche as nihilistic. Therefore, it should be noted that this study is not about Deleuze's reading per se; rather, it is an appraisal of Nietzsche's "critique of nihilism" using Deleuze's experimental reading. We will accrue Nietzsche's critique and Deleuze's post-deconstrnctive reading in order to appraise Nietzsche's critique itself. Insofar as we have underscored Deleuze's purported experimentation of Nietzschean themes, this study is also an experiment in itself. Through this experimentation, we will find out whether it is possible to partly gloss Nietzsche's critique of nihilism through Deleuzian phraseology. Far from presenting a mere exposition of Nietzsche's text, we are, rather, re-reading, that is, re-evaluating Nietzsche's critique of nihilism through Deleuze's experimentation. This is our way of thinking with Nietzsche. Nihilism is the central problem upon which Nietzsche's philosophical musings are directed; he deems nihilism as a cultural experience and, as such, a phenomenon to be reckoned with. In our reconstruction of Nietzsche's critique of nihilism, we locate two related elements which constitute the structure of the prescription of a cure, Le., the ethics of affirmation and the ontology of becoming. Appraising Nietzsche's ethics and ontology amounts to clarifying what Deleuze thinks as the movement from the "dogmatic image of thought" to the "new image of thought." Through this new image of thought, Deleuze makes sense of a Nietzschean counterculture which is a perspective that resists traditional or representational metaphysics. Deleuze takes the reversal of Platonism or the transmutation of values to be the point of departure. We have to, according to Deleuze, abandon our old image of the world in order to free ourselves from the obscurantism of foundationalist or essentialist thinking. It is only through the transmutation of values that we can make sense of Nietzsche's ethics of affirmation and ontology of becoming. We have to think of Nietzsche's ethics as an "ethics" and not a moral philosophy, and we have to think of his ontology as 1/ ontology" and not as metaphysics. Through Deleuze, we are able to avoid reading Nietzsche as a moral philosopher and metaphysician. Rather, we are able to read Nietzsche as one espousing an ethical imperative through the thought of the eternal return and one advocating a theory of existence based on an immanent, as opposed to transcendent, image of the world.

A comparison of two computer-assisted remedial reading programs for adolescent unskilled readers : component reading skills and repeated reading

This study compared the relative effectiveness of two computerized remedial reading programs in improving the reading word recognition, rate, and comprehension of adolescent readers demonstrating significant and longstanding reading difficulties. One of the programs involved was Autoskill Component Reading Subskills Program, which provides instruction in isolated letters, syllables, and words, to a point of rapid automatic responding. This program also incorporates reading disability subtypes in its approach. The second program, Read It Again. Sam, delivers a repeated reading strategy. The study also examined the feasibility of using peer tutors in association with these two programs. Grade 9 students at a secondary vocational school who satisfied specific criteria with respect to cognitive and reading ability participated. Eighteen students were randomly assigned to three matched groups, based on prior screening on a battery of reading achievement tests. Two I I groups received training with one of the computer programs; the third group acted as a control and received the remedial reading program offered within the regular classroom. The groups met daily with a trained tutor for approximately 35 minutes, and were required to accumulate twenty hours of instruction. At the conclusion of the program, the pretest battery was repeated. No significant differences were found in the treatment effects of the two computer groups. Each of the two treatment groups was able to effect significantly improved reading word recognition and rate, relative to the control group. Comprehension gains were modest. The treatment groups demonstrated a significant gain, relative to the control group, on one of the three comprehension measures; only trends toward a gain were noted on the remaining two measures. The tutoring partnership appeared to be a viable alternative for the teacher seeking to provide individualized computerized remedial programs for adolescent unskilled readers. Both programs took advantage of computer technology in providing individualized drill and practice, instant feedback, and ongoing recordkeeping. With limited cautions, each of these programs was considered effective and practical for use with adolescent unskilled readers.

Using HeadSprout Early Reading with a child with Autism Spectrum Disorder: An examination of phonological awareness, participant engagement, and participant enjoyment

This study examined the effectiveness of a 9-week reading program in improving the phonological awareness (PA) skills of a seven year old boy with Autism Spectrum Disorder (ASD), Attention Deficit Hyperactivity Disorder (ADHD), and Oppositional Defiant Disorder (ODD). The study’s secondary goal was to describe how the participant engaged with and enjoyed the HeadSprout computer program. The participant attended a one hour reading program incorporating 30 minutes of HeadSprout Early Reading three days a week for 9 weeks. Results demonstrated that the participant’s PA scores increased from the 16th percentile at pre-test to the 35th percentile post program. Four of five measures of PA increased, segmenting nonwords decreased to the 2nd percentile post program. Momentary time sampling procedures revealed the participant was engaged with the computer program 94.5% of the time. Perceived ratings of enjoyment indicated the participant enjoyed using the program. Specific components of the program which may have influenced participant enjoyment and engagement are discussed. Study limitations and implications of these findings are discussed in reference to future research.

Teaching reading Shakespeare.

Plantea los problemas que presenta la lectura de Shakespeare, en la actualidad, a los jóvenes lectores y ayuda a los profesores de secundaria a hacer frente a las dificultades lingüísticas de estas obras como el uso de palabras antiguas, la gramática, la retórica y la metáfora. La enseñanza de los textos de Shakespeare se realiza en el marco contextual, interpretativo y lingüístico exigido para el título del General Certificate Secondary Education (GCSE) y del A-level.

Practice tests for IGCSE English as a second language : reading and writing book 1.

El libro contiene 4 test prácticos completos con formato de examen para los ejercicios 1 y 2 de la prueba Cambridge IGCSE (International General Certificate of Secondary Education) de inglés como segundo idioma. Los test permiten desarrollar las técnicas de examen de los alumnos familiarizándose con el formato de los ejercicios de lectura y redacción, y con el tipo de temas y textos que pueden encontrar en el examen oficial. El nivel de la prueba es intermedio e intermedio-alto.

Practice tests for IGCSE English as a second language : reading and writing book 1 with key.

El libro contiene 4 test prácticos completos con formato de examen para los ejercicios 1 y 2 de la prueba Cambridge IGCSE (International General Certificate of Secondary Education) de inglés como segundo idioma. Los test permiten desarrollar las técnicas de examen de los alumnos familiarizándose con el formato de los ejercicios de lectura y redacción, y con el tipo de temas y textos que pueden encontrar en el examen oficial. El nivel de la prueba es intermedio e intermedio-alto. Incluye respuestas y redacciones de ejemplo.

Practice tests for IGCSE English as a second language : reading and writing book 2.

El libro contiene cuatro tests prácticos completos con formato de examen para el ejercicio 2 de la prueba Cambridge IGCSE (International General Certificate of Secondary Education) de inglés como segundo idioma. Los tests permiten desarrollar las técnicas de examen de los alumnos familiarizándose con el formato de los ejercicios de lectura, compresión y escritura, y con el tipo de temas que pueden encontrar en el examen oficial. El nivel de la prueba es intermedio e intermedio-alto.

Practice tests for IGCSE English as a second language : reading and writing book 2 with key.

El libro contiene cuatro tests prácticos completos con formato de examen para el ejercicio 2 de la prueba Cambridge IGCSE (International General Certificate of Secondary Education) de inglés como segundo idioma. Los tests permiten desarrollar las técnicas de examen de los alumnos familiarizándose con el formato de los ejercicios de lectura, compresión y redacción, y con el tipo de temas y textos que pueden encontrar en el examen oficial. El nivel de la prueba es intermedio e intermedio-alto. Incluye las respuestas de los tests y redacciones de ejemplo.

Preparation of consistent soil data sets for modelling purposes: Secondary SOTER data for four case study areas

The common GIS-based approach to regional analyses of soil organic carbon (SOC) stocks and changes is to define geographic layers for which unique sets of driving variables are derived, which include land use, climate, and soils. These GIS layers, with their associated attribute data, can then be fed into a range of empirical and dynamic models. Common methodologies for collating and formatting regional data sets on land use, climate, and soils were adopted for the project Assessment of Soil Organic Carbon Stocks and Changes at National Scale (GEFSOC). This permitted the development of a uniform protocol for handling the various input for the dynamic GEFSOC Modelling System. Consistent soil data sets for Amazon-Brazil, the Indo-Gangetic Plains (IGP) of India, Jordan and Kenya, the case study areas considered in the GEFSOC project, were prepared using methodologies developed for the World Soils and Terrain Database (SOTER). The approach involved three main stages: (1) compiling new soil geographic and attribute data in SOTER format; (2) using expert estimates and common sense to fill selected gaps in the measured or primary data; (3) using a scheme of taxonomy-based pedotransfer rules and expert-rules to derive soil parameter estimates for similar soil units with missing soil analytical data. The most appropriate approach varied from country to country, depending largely on the overall accessibility and quality of the primary soil data available in the case study areas. The secondary SOTER data sets discussed here are appropriate for a wide range of environmental applications at national scale. These include agro-ecological zoning, land evaluation, modelling of soil C stocks and changes, and studies of soil vulnerability to pollution. Estimates of national-scale stocks of SOC, calculated using SOTER methods, are presented as a first example of database application. Independent estimates of SOC stocks are needed to evaluate the outcome of the GEFSOC Modelling System for current conditions of land use and climate. (C) 2007 Elsevier B.V. All rights reserved.

Exploring other childhoods through quantitative secondary analyses of large scale surveys: opportunities and challenges for children's geographers

This paper considers the potential contribution of secondary quantitative analyses of large scale surveys to the investigation of 'other' childhoods. Exploring other childhoods involves investigating the experience of young people who are unequally positioned in relation to multiple, embodied, identity locations, such as (dis)ability, 'class', gender, sexuality, ethnicity and race. Despite some possible advantages of utilising extensive databases, the paper outlines a number of methodological problems with existing surveys which tend to reinforce adultist and broader hierarchical social relations. It is contended that scholars of children's geographies could overcome some of these problematic aspects of secondary data sources by endeavouring to transform the research relations of large scale surveys. Such endeavours would present new theoretical, ethical and methodological complexities, which are briefly considered.

Temporal patterns of nutrient availability around nests of leaf-cutting ants (Atta colombica) in secondary moist tropical forest

Leaf-cutting ants consume up to 10% of canopy leaves in the foraging area of their colony and therefore represent a key perturbation in the nutrient cycle of tropical forests. We used a chronosequence of nest sites on Barro, Colorado Island, Panama, to assess the influence of leaf-cutting ants (Atta colombica) on nutrient availability in a neotropical rainforest. Twelve nest sites were sampled, including active nests, recently abandoned nests (<1 year) and long-abandoned nests (>1 year). Waste material discarded by the ants down-slope from the nests contained large concentrations of nitrogen and phosphorus in both total and soluble forms, but decomposed within one year after the nests were abandoned. Despite this, soil under the waste material contained high concentrations of nitrate and ammonium that persisted after the disappearance of the waste, although soluble phosphate returned to background concentrations within one year of nest abandonment. Fine roots were more abundant in soil under waste than control soils up to one year after nest abandonment, but were not significantly different for older sites. In contrast to the waste dumps, soil above the underground nest chambers consistently contained lower nutrient concentrations than control soils, although this was not statistically significant. We conclude that the 'islands of fertility' created by leaf-cutting ants provide a nutritional benefit to nearby plants for less than one year after nest abandonment in the moist tropical environment of Barro Colorado Island. Published by Elsevier Ltd.