Role taking and knowledge building in a blended university course

Role taking is an established approach for promoting social cognition. Playing a specific role within a group could lead students to exercise collective cognitive responsibility for collaborative knowledge building. Two studies explored the relationship of role taking to participation in a blended university course. Students participated in the same knowledge-building activity over three consecutive, five-week modules and enacted four roles designed in alignment with knowledge building pedagogy (Scardamalia and Bereiter 2010). In Study 1, 59 students were distributed into groups with two conditions: students who took a role in Module 2 and students who did not take a role, using Module 1 and 3 as pre and post tests. Results showed no differences in participation in Module 1, higher levels of writing and reading for role takers in Module 2, and this pattern was sustained in Module 3. Students with the Synthesizer role were the most active in terms of writing and the second most active for reading; students with the Social Tutor role were the most active for reading. In Study 2, 143 students were divided into groups with two conditions: students who took a role in Module 1 and students who did not take a role. Content analysis revealed that role takers tended to vary their contributions more than non-role takers by proposing more problems, synthesizing the discourse, reflecting on the process and organization of activity. They also assumed appropriate responsibilities for their role: the Skeptic prioritizes questioning of content, the Synthesizer emphasizes synthesizing of content, and the Social Tutor privileges maintaining of relationships. Implications of designing role taking to foster knowledge building in university blended courses are discussed

Influence of participation, facilitator styles, and metacognitive reflection on knowledge building in online university courses

Understanding how to foster knowledge building in online and blended learning environments is a key for computer-supported collaborative learning research. Knowledge building is a deeply constructivist pedagogy and kind of inquiry learning focused on theory building. A strong indicator of engagement in knowledge building activity is the socio-cognitive dynamic of epistemic agency, in which students exercise a higher level of agency for setting forth their ideas and negotiating fit with those of others rather than relying on their teacher. The purpose of this paper is to investigate the influence of (a) levels of participation, (b) facilitator styles and (c) metacognitive reflection on knowledge building in two blended, post-secondary education contexts. A study of a total of 67 undergraduate students suggest that high levels of participation, a supportive facilitator style, and ample opportunities for metacognitive reflection on the students’ own participation strategies are most conducive for fostering epistemic agency for knowledge building. Implications of these results for research and instructional design of online courses are discussed

Developing knowledge work skills in a university course

In this paper, we present a blended university course whose design is inspired by the Trialogical Learning Approach and its six Design Principles. The structure, activities, and content of the course are described in detail. The course description is followed by an explorative case-study conducted on data collected during the 2017-2018 edition of the course. The general aim was to understand the impact of the course on students’ perceptions of their acquisition of knowledge work skills and on their overall appreciation of the course. One hundred and nine psychology students (27 male, 82 female, aged 20-23 years) voluntarily participated in a course titled ‘Experimental Pedagogy’ held at Sapienza, University of Rome (IT). The data collection was informed by the trialogical design principles that inspired the course and defined the knowledge work skills to be observed, i.e. collaboration, continuous improvement, and digital skills. Two self-report anonymous questionnaires were administered; one was completed at the end of the course and one at the end of each of the three modules composing the course. Data was analysed using a mixed-methods (qualitative and quantitative) approach. Results indicated that the course was perceived to effectively promote the majority of the intended skills. Moreover, students appreciated the possibility to concretely work on a project-based learning activity that allowed them to create a shared and meaningful object and reflect their actual learning as intended by the theoretical approach

MINT, the molecular interaction database: 2012 update

The Molecular INTeraction Database (MINT, http://mint.bio.uniroma2.it/mint/) is a public repository for protein-protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235,000 binary interactions captured from over 4750 publications. The web interface allows the users to search, visualize and download interactions data. MINT is one of the members of the International Molecular Exchange consortium (IMEx) and adopts the Molecular Interaction Ontology of the Proteomics Standard Initiative (PSI-MI) standards for curation and data exchange. MINT data are freely accessible and downloadable at http://mint.bio.uniroma2.it/mint/download.do. We report here the growth of the database, the major changes in curation policy and a new algorithm to assign a confidence to each interaction

Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes

The Network of Cancer Genes (NCG) collects and integrates data on 736 human genes that are mutated in various types of cancer. For each gene, NCG provides information on duplicability, orthology, evolutionary appearance and topological properties of the encoded protein in a comprehensive version of the human protein-protein interaction network. NCG also stores information on all primary interactors of cancer proteins, thus providing a complete overview of 5357 proteins that constitute direct and indirect determinants of human cancer. With the constant delivery of results from the mutational screenings of cancer genomes, NCG represents a versatile resource for retrieving detailed information on particular cancer genes, as well as for identifying common properties of precompiled lists of cancer genes. NCG is freely available at: http://bio.ifom-ieo-campus.it/ncg

The IntAct database:Efficient access to fine-grained molecular interaction data

The IntAct molecular interaction database (https://www.ebi.ac.uk/intact) is a curated resource of molecular interactions, derived from the scientific literature and from direct data depositions. As of August 2021, IntAct provides more than one million binary interactions, curated by twelve global partners of the International Molecular Exchange consortium, for which the IntAct database provides a shared curation and dissemination platform. The IMEx curation policy has always emphasised a fine-grained data and curation model, aiming to capture the relevant experimental detail essential for the interpretation of the provided molecular interaction data. Here, we present recent curation focus and progress, as well as a completely redeveloped website which presents IntAct data in a much more user-friendly and detailed way

HIV-1 Vpu Protein Mediates the Transport of Potassium in Saccharomyces cerevisiae

Human immunodeficiency virus type 1 (HIV-1) Vpu is an integral membrane protein that belongs to the viroporin family. Viroporins interact with cell membranes, triggering membrane permeabilization and promoting release of viral particles. In vitro electrophysiological methods have revealed changes in membrane ion currents when Vpu is present; however, in vivo the molecular mechanism of Vpu at the plasma membrane is still uncertain. We used the yeast Saccharomyces cerevisiae as a genetic model system to analyze how Vpu ion channel impacts cellular homeostasis. Inducible expression of Vpu impaired cell growth, suggesting that this viral protein is toxic to yeast cultures. This toxicity decreased with extracellular acidic pH. Also, Vpu toxicity diminished as the extracellular K(+) concentration was increased. However, expression of the Vpu protein suppresses the growth defect of K(+) uptake-deficient yeast (Δtrk1,2). The phenotype rescue of these highly hyperpolarized cells was almost total when they were grown in medium supplemented with high concentrations of KCl (100 mM) at pH 7.0 but was significantly reduced when the extracellular K(+) concentration or pH was decreased. These results indicate that Vpu has the ability to modify K(+) transport in both yeast strains. Here, we show also that Vpu confers tolerance to the aminoglycoside antibiotic hygromycin B in Δtrk1,2 yeast. Our results suggest that Vpu interferes with cell growth of wild-type yeast but improves proliferation of the hyperpolarized trk1,2 mutant by inducing plasma membrane depolarization. Furthermore, evaluation of the ion channel activity of the Vpu protein in Δtrk1,2 yeast could aid in the development of a high-throughput screening assay for molecules that target the retroviral protein.This study was supported by Grants PI PI05/00013 and PI08/0912 from Fondo de Investigación Sanitaria. L.H. and N.M. were holders of Predoctoral Fellowships from Instituto de Salud Carlos III.S

Encompassing new use cases - level 3.0 of the HUPO-PSI format for molecular interactions.

BACKGROUND: Systems biologists study interaction data to understand the behaviour of whole cell systems, and their environment, at a molecular level. In order to effectively achieve this goal, it is critical that researchers have high quality interaction datasets available to them, in a standard data format, and also a suite of tools with which to analyse such data and form experimentally testable hypotheses from them. The PSI-MI XML standard interchange format was initially published in 2004, and expanded in 2007 to enable the download and interchange of molecular interaction data. PSI-XML2.5 was designed to describe experimental data and to date has fulfilled this basic requirement. However, new use cases have arisen that the format cannot properly accommodate. These include data abstracted from more than one publication such as allosteric/cooperative interactions and protein complexes, dynamic interactions and the need to link kinetic and affinity data to specific mutational changes. RESULTS: The Molecular Interaction workgroup of the HUPO-PSI has extended the existing, well-used XML interchange format for molecular interaction data to meet new use cases and enable the capture of new data types, following extensive community consultation. PSI-MI XML3.0 expands the capabilities of the format beyond simple experimental data, with a concomitant update of the tool suite which serves this format. The format has been implemented by key data producers such as the International Molecular Exchange (IMEx) Consortium of protein interaction databases and the Complex Portal. CONCLUSIONS: PSI-MI XML3.0 has been developed by the data producers, data users, tool developers and database providers who constitute the PSI-MI workgroup. This group now actively supports PSI-MI XML2.5 as the main interchange format for experimental data, PSI-MI XML3.0 which additionally handles more complex data types, and the simpler, tab-delimited MITAB2.5, 2.6 and 2.7 for rapid parsing and download

Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule's interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release