Non-coding RNAs: the architects of eukaryotic complexity

Around 98% of all transcriptional output in humans is noncoding RNA. RNA-mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference, co-suppression, transgene silencing, imprinting, methylation, and possibly position-effect variegation and transvection, all involve intersecting pathways based on or connected to RNA signaling. I suggest that the central dogma is incomplete, and that intronic and other non-coding RNAs have evolved to comprise a second tier of gene expression in eukaryotes, which enables the integration and networking of complex suites of gene activity. Although proteins are the fundamental effectors of cellular function, the basis of eukaryotic complexity and phenotypic variation may lie primarily in a control architecture composed of a highly parallel system of trans-acting RNAs that relay state information required for the coordination and modulation of gene expression, via chromatin remodeling, RNA-DNA, RNA-RNA and RNA-protein interactions. This system has interesting and perhaps informative analogies with small world networks and dataflow computing.

Phenotypic characterization of five dendritic cell subsets in human tonsils

Heterogeneous expression of several antigens on the three currently defined tonsil dendritic cell (DC) subsets encouraged us to re-examine tonsil DCs using a new method that minimized DC differentiation and activation during their preparation. Three-color flow cytometry and dual-color immunohistology was used in conjunction with an extensive panel of antibodies to relevant DC-related antigens to analyze lin(-) HLA-DR+ tonsil DCs. Here we identify, quantify, and locate five tonsil DC subsets based on their relative expression of the HLA-DR, CD11c, CD13, and CD123 antigens. In situ localization identified four of these DC subsets as distinct interdigitating DC populations. These included three new interdigitating DC subsets defined as HLA-DRhi CD11c(+) DCs, HLA-DRmod CD11c+ CD13(+) DCs, and HLA-DRmod CD11c(-) CD123(-) DCs, as well as the plasmacytoid DCs (HLA-DRmod CD11c- CD123(+)). These subsets differed in their expression of DC-associated differentiation/activation antigens and co-stimulator molecules including CD83, CMRF-44, CMRF-56, 2-7, CD86, and 4-1BB ligand. The fifth HLA-DRmod CD11c(+) DC subset was identified as germinal center DCs, but contrary to previous reports they are redefined as lacking the CD13 antigen. The definition and extensive phenotypic analysis of these five DC subsets In human tonsil extends our understanding of the complexity of DC biology.

Young children's performance on the balance scale: The influence of relational complexity

Three experiments investigated the effect of complexity on children's understanding of a beam balance. In nonconflict problems, weights or distances varied, while the other was held constant. In conflict items, both weight and distance varied, and items were of three kinds: weight dominant, distance dominant, or balance (in which neither was dominant). In Experiment 1, 2-year-old children succeeded on nonconflict-weight and nonconflict-distance problems. This result was replicated in Experiment 2, but performance on conflict items did not exceed chance. In Experiment 3, 3- and 4-year-olds succeeded on all except conflict balance problems, while 5- and 6-year-olds succeeded on all problem types. The results were interpreted in terms of relational complexity theory. Children aged 2 to 4 years succeeded on problems that entailed binary relations, but 5- and 6-year-olds also succeeded on problems that entailed ternary relations. Ternary relations tasks from other domains-transitivity and class inclusion-accounted for 93% of the age-related variance in balance scale scores. (C) 2002 Elsevier Science (USA).

Becoming a teacher: student teachers´ experiences and perceptions about teaching practice

In an attempt to build a more comprehensive and holistic understanding of the complexity, dynamics and idiosyncrasies involved in becoming a teacher, this study focussed on the experiences of 295 student teachers. Their feelings, cognitions and perceptions regarding teaching practice were analysed using the short version of the Inventory of Experiences and Perceptions of the Teaching Practice. Results emphasise some of the difficulties experienced during this period (e.g., stress, sense of weariness and ‘vulnerability’), as well the positive perceptions of these student teachers regarding their growing knowledge and skilfulness, as well as their sense of efficacy, flexibility and spontaneity in their performance and interactions. Their perception of their accomplishments in achieving reasonable levels of acceptance and recognition within the school community and their positive evaluation of the guidance and support provided by their supervisors are also emphasised. Differences were found – in terms of gender and graduate course background – in the way these student teachers experienced some aspects of teaching practice.

Functional studies on BolA and related genes: increasing the understanding of a protein with pleiotropic effects

Dissertation presented to obtain a Doctoral degree in Biology by Instituto de Tecnologia Química e Biológica

Systems biology approaches for the design of novel Saccharomyces cerevisiae winemaking strains for enhanced flavour compounds synthesis

Tese de Doutoramento em Biologia Ambiental e Molecular

Evolutionary patterns of MHC class II B in owls and their implications for the understanding of avian MHC evolution

Owing to its special mode of evolution and central role in the adaptive immune system, the major histocompatibility complex (MHC) has become the focus of diverse disciplines such as immunology, evolutionary ecology, and molecular evolution. MHC evolution has been studied extensively in diverse vertebrate lineages over the last few decades, and it has been suggested that birds differ from the established mammalian norm. Mammalian MHC genes evolve independently, and duplication history (i.e., orthology) can usually be traced back within lineages. In birds, this has been observed in only 3 pairs of closely related species. Here we report strong evidence for the persistence of orthology of MHC genes throughout an entire avian order. Phylogenetic reconstructions of MHC class II B genes in 14 species of owls trace back orthology over tens of thousands of years in exon 3. Moreover, exon 2 sequences from several species show closer relationships than sequences within species, resembling transspecies evolution typically observed in mammals. Thus, although previous studies suggested that long-term evolutionary dynamics of the avian MHC was characterized by high rates of concerted evolution, resulting in rapid masking of orthology, our results question the generality of this conclusion. The owl MHC thus opens new perspectives for a more comprehensive understanding of avian MHC evolution.

Modelling hydrodynamics in the Rio Parana, Argentina : an evaluation and inter-comparison of reduced-complexity and physics based models applied to a large sand-bed river

Depth-averaged velocities and unit discharges within a 30 km reach of one of the world's largest rivers, the Rio Parana, Argentina, were simulated using three hydrodynamic models with different process representations: a reduced complexity (RC) model that neglects most of the physics governing fluid flow, a two-dimensional model based on the shallow water equations, and a three-dimensional model based on the Reynolds-averaged Navier-Stokes equations. Row characteristics simulated using all three models were compared with data obtained by acoustic Doppler current profiler surveys at four cross sections within the study reach. This analysis demonstrates that, surprisingly, the performance of the RC model is generally equal to, and in some instances better than, that of the physics based models in terms of the statistical agreement between simulated and measured flow properties. In addition, in contrast to previous applications of RC models, the present study demonstrates that the RC model can successfully predict measured flow velocities. The strong performance of the RC model reflects, in part, the simplicity of the depth-averaged mean flow patterns within the study reach and the dominant role of channel-scale topographic features in controlling the flow dynamics. Moreover, the very low water surface slopes that typify large sand-bed rivers enable flow depths to be estimated reliably in the RC model using a simple fixed-lid planar water surface approximation. This approach overcomes a major problem encountered in the application of RC models in environments characterised by shallow flows and steep bed gradients. The RC model is four orders of magnitude faster than the physics based models when performing steady-state hydrodynamic calculations. However, the iterative nature of the RC model calculations implies a reduction in computational efficiency relative to some other RC models. A further implication of this is that, if used to simulate channel morphodynamics, the present RC model may offer only a marginal advantage in terms of computational efficiency over approaches based on the shallow water equations. These observations illustrate the trade off between model realism and efficiency that is a key consideration in RC modelling. Moreover, this outcome highlights a need to rethink the use of RC morphodynamic models in fluvial geomorphology and to move away from existing grid-based approaches, such as the popular cellular automata (CA) models, that remain essentially reductionist in nature. In the case of the world's largest sand-bed rivers, this might be achieved by implementing the RC model outlined here as one element within a hierarchical modelling framework that would enable computationally efficient simulation of the morphodynamics of large rivers over millennial time scales. (C) 2012 Elsevier B.V. All rights reserved.

Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Thinking Outside the Box: Enhancing Science Teaching by Combining (Instead of Contrasting) Laboratory and Simulation Activities

The focus of the present work was on 10- to 12-year-old elementary school students’ conceptual learning outcomes in science in two specific inquiry-learning environments, laboratory and simulation. The main aim was to examine if it would be more beneficial to combine than contrast simulation and laboratory activities in science teaching. It was argued that the status quo where laboratories and simulations are seen as alternative or competing methods in science teaching is hardly an optimal solution to promote students’ learning and understanding in various science domains. It was hypothesized that it would make more sense and be more productive to combine laboratories and simulations. Several explanations and examples were provided to back up the hypothesis. In order to test whether learning with the combination of laboratory and simulation activities can result in better conceptual understanding in science than learning with laboratory or simulation activities alone, two experiments were conducted in the domain of electricity. In these experiments students constructed and studied electrical circuits in three different learning environments: laboratory (real circuits), simulation (virtual circuits), and simulation-laboratory combination (real and virtual circuits were used simultaneously). In order to measure and compare how these environments affected students’ conceptual understanding of circuits, a subject knowledge assessment questionnaire was administered before and after the experimentation. The results of the experiments were presented in four empirical studies. Three of the studies focused on learning outcomes between the conditions and one on learning processes. Study I analyzed learning outcomes from experiment I. The aim of the study was to investigate if it would be more beneficial to combine simulation and laboratory activities than to use them separately in teaching the concepts of simple electricity. Matched-trios were created based on the pre-test results of 66 elementary school students and divided randomly into a laboratory (real circuits), simulation (virtual circuits) and simulation-laboratory combination (real and virtual circuits simultaneously) conditions. In each condition students had 90 minutes to construct and study various circuits. The results showed that studying electrical circuits in the simulation–laboratory combination environment improved students’ conceptual understanding more than studying circuits in simulation and laboratory environments alone. Although there were no statistical differences between simulation and laboratory environments, the learning effect was more pronounced in the simulation condition where the students made clear progress during the intervention, whereas in the laboratory condition students’ conceptual understanding remained at an elementary level after the intervention. Study II analyzed learning outcomes from experiment II. The aim of the study was to investigate if and how learning outcomes in simulation and simulation-laboratory combination environments are mediated by implicit (only procedural guidance) and explicit (more structure and guidance for the discovery process) instruction in the context of simple DC circuits. Matched-quartets were created based on the pre-test results of 50 elementary school students and divided randomly into a simulation implicit (SI), simulation explicit (SE), combination implicit (CI) and combination explicit (CE) conditions. The results showed that when the students were working with the simulation alone, they were able to gain significantly greater amount of subject knowledge when they received metacognitive support (explicit instruction; SE) for the discovery process than when they received only procedural guidance (implicit instruction: SI). However, this additional scaffolding was not enough to reach the level of the students in the combination environment (CI and CE). A surprising finding in Study II was that instructional support had a different effect in the combination environment than in the simulation environment. In the combination environment explicit instruction (CE) did not seem to elicit much additional gain for students’ understanding of electric circuits compared to implicit instruction (CI). Instead, explicit instruction slowed down the inquiry process substantially in the combination environment. Study III analyzed from video data learning processes of those 50 students that participated in experiment II (cf. Study II above). The focus was on three specific learning processes: cognitive conflicts, self-explanations, and analogical encodings. The aim of the study was to find out possible explanations for the success of the combination condition in Experiments I and II. The video data provided clear evidence about the benefits of studying with the real and virtual circuits simultaneously (the combination conditions). Mostly the representations complemented each other, that is, one representation helped students to interpret and understand the outcomes they received from the other representation. However, there were also instances in which analogical encoding took place, that is, situations in which the slightly discrepant results between the representations ‘forced’ students to focus on those features that could be generalised across the two representations. No statistical differences were found in the amount of experienced cognitive conflicts and self-explanations between simulation and combination conditions, though in self-explanations there was a nascent trend in favour of the combination. There was also a clear tendency suggesting that explicit guidance increased the amount of self-explanations. Overall, the amount of cognitive conflicts and self-explanations was very low. The aim of the Study IV was twofold: the main aim was to provide an aggregated overview of the learning outcomes of experiments I and II; the secondary aim was to explore the relationship between the learning environments and students’ prior domain knowledge (low and high) in the experiments. Aggregated results of experiments I & II showed that on average, 91% of the students in the combination environment scored above the average of the laboratory environment, and 76% of them scored also above the average of the simulation environment. Seventy percent of the students in the simulation environment scored above the average of the laboratory environment. The results further showed that overall students seemed to benefit from combining simulations and laboratories regardless of their level of prior knowledge, that is, students with either low or high prior knowledge who studied circuits in the combination environment outperformed their counterparts who studied in the laboratory or simulation environment alone. The effect seemed to be slightly bigger among the students with low prior knowledge. However, more detailed inspection of the results showed that there were considerable differences between the experiments regarding how students with low and high prior knowledge benefitted from the combination: in Experiment I, especially students with low prior knowledge benefitted from the combination as compared to those students that used only the simulation, whereas in Experiment II, only students with high prior knowledge seemed to benefit from the combination relative to the simulation group. Regarding the differences between simulation and laboratory groups, the benefits of using a simulation seemed to be slightly higher among students with high prior knowledge. The results of the four empirical studies support the hypothesis concerning the benefits of using simulation along with laboratory activities to promote students’ conceptual understanding of electricity. It can be concluded that when teaching students about electricity, the students can gain better understanding when they have an opportunity to use the simulation and the real circuits in parallel than if they have only the real circuits or only a computer simulation available, even when the use of the simulation is supported with the explicit instruction. The outcomes of the empirical studies can be considered as the first unambiguous evidence on the (additional) benefits of combining laboratory and simulation activities in science education as compared to learning with laboratories and simulations alone.

Towards a contextual understanding of B2B salespeople's selling competencies – An exploratory study among purchasing decision-makers of internationally-oriented technology firms

ABSTRACT Towards a contextual understanding of B2B salespeople’s selling competencies − an exploratory study among purchasing decision-makers of internationally-oriented technology firms The characteristics of modern selling can be classified as follows: customer retention and loyalty targets, database and knowledge management, customer relationship management, marketing activities, problem solving and system selling, and satisfying needs and creating value. For salespeople to be successful in this environment, they need a wide range of competencies. Salespeople’s selling skills are well documented in seller side literature through quantitative methods, but the knowledge, skills and competencies from the buyer’s perspective are under-researched. The existing research on selling competencies should be broadened and updated through a qualitative research perspective due to the dynamic nature and the contextual dependence of selling competencies. The purpose of the study is to increase understanding of the professional salesperson’s selling competencies from the industrial purchasing decision- makers’ viewpoint within the relationship selling context. In this study, competencies are defined as sales-related knowledge and skills. The scope of the study includes goods, materials and services managed by a company’s purchasing function and used by an organization on a daily basis. The abductive approach and ‘systematic combining’ have been applied as a research strategy. In this research, data were generated through semi- structured, person-to-person interviews and open-ended questions. The study was conducted among purchasing decision-makers in the technology industry in Finland. The branches consisted of the electronics and electro-technical industries and the mechanical engineering and metals industries. A total of 30 companies and one purchasing decision-maker from each company were purposively chosen for the sampling. The sample covers different company sizes based on their revenues, their differing structures – varying from public to family companies –that represent domestic and international ownerships. Before analyzing the data, they were organized by the purchasing orientations of the buyers: the buying, procurement or supply management orientation. Thematic analysis was chosen as the analysis method. After analyzing the data, the results were contrasted with the theory. There was a continuous interaction between the empirical data and the theory. Based on the findings, a total of 19 major knowledge and skills were identified from the buyers’ perspective. The specific knowledge and skills from the viewpoint of customers’ prevalent purchasing orientations were divided into two categories, generic and contextual. The generic knowledge and skills apply to all purchasing orientations, and the contextual knowledge and skills depend on customers’ prevalent purchasing orientations. Generic knowledge and skills relate to price setting, negotiation, communication and interaction skills, while contextual ones relate to knowledge brokering, ability to present solutions and relationship skills. Buying-oriented buyers value salespeople who are ‘action oriented experts, however at a bit of an arm’s length’, procurement buyers value salespeople who are ‘experts deeply dedicated to the customer and fostering the relationship’ and supply management buyers value salespeople who are ‘corporate-oriented experts’. In addition, the buyer’s perceptions on knowledge and selling skills differ from the seller’s ones. The buyer side emphasizes managing the subject matter, consisting of the expertise, understanding the customers’ business and needs, creating a customized solution and creating value, reliability and an ability to build long-term relationships, while the seller side emphasizes communica- tion, interaction and salesmanship skills. The study integrates the selling skills of the current three-component model− technical knowledge, salesmanship skills, interpersonal skills− and relationship skills and purchasing orientations, into a selling competency model. The findings deepen and update the content of these knowledges and skills in the B2B setting and create new insights into them from the buyer’s perspective, and thus the study increases contextual understanding of selling competencies. It generates new knowledge of the salesperson’s competencies for the relationship selling and personal selling and sales management literature. It also adds knowledge of the buying orientations to the buying behavior literature. The findings challenge sales management to perceive salespeople’s selling skills both from a contingency and competence perspective. The study has several managerial implications: it increases understanding of what the critical selling knowledge and skills from the buyer’s point of view are, understanding of how salespeople effectively implement the relationship marketing concept, sales management’s knowledge of how to manage the sales process more effectively and efficiently, and the knowledge of how sales management should develop a salesperson’s selling competencies when managing and developing the sales force. Keywords: selling competencies, knowledge, selling skills, relationship skills, purchasing orientations, B2B selling, abductive approach, technology firms

Gaining a better understanding of how Outward Bound Western Canada course outcomes are achieved : a research study /

This study examined how Outward Bound Western Canada (OBWC) course outcomes are achieved by exploring the relationships among course components, students' characteristics, and course outcomes. OBWC is a wilderness-based adventure education organization that helps students achieve outcomes such as increased self-awareness, self-confidence, motivation, interpersonal skills, concern for others, and concern for the environment. This study explored the ways in which the various components of courses and the characteristics of students contribute to determining the outcomes students experience as a result of their courses. The purpose of the study was to gain a better understanding of how OBWC course outcomes are achieved in order to strengthen adventure education theory, enhance practice at OBWC and other adventure education organizations, and provide a foundation for further research on this topic. As an interpretive case study, this study sought to describe how OBWC course outcomes are achieved and to provide interpretations of the research findings. Data was gathered from OBWC students and instructors using the quantitative and qualitative data collection techniques of questionnaire, interview, and observation. Data collected from 98 participants ensured a considerable breadth to the study, while interviews with a number of participants also enabled the collection of in-depth data. Analysis and triangulation of the data from the various sources allowed discernment of the research findings. A comprehensive and detailed picture of how course outcomes are achieved emerged from the findings. Twenty-nine course components were found to influence course outcomes, including various aspects of course activities, the physical environment, instructors, and the group. The findings indicated that certain course components were most influential in determining increases to students' self-awareness, self-confidence, self-reliance, self-esteem, self-concept, motivation, self-responsibility, interpersonal skills, concern for others, and concern for the environment. A number of course components were found to indirectly contribute to positive course outcomes by helping maximize the effectiveness of other components, by increasing students' motivation while on course, or by facilitating the processing and transference of new information. The findings also suggested that several course components either directly or indirectly affected course outcomes in negative ways. In addition, the gender, age, population, and expectations of students were found to play a role in determining the course outcomes they experienced and in determining which course components caused those outcomes. Interpretation of the findings resulted in the generation of research-based theory. The main theoretical argument derived from the results of the study was that course outcomes are influenced by a combination of course components and characteristics of students. More specifically, the theory generated by the study indicated that five groupings of factors contribute to course outcomes, including course activities, the physical environment, instructors, the group, and students' characteristics. The study was considered in relation to existing adventure education literature and larger theoretical issues. The generated theory and research findings were then used to develop suggestions for improving practice at OBWC and other adventure education organizations, as well as for enhancing future research studies.