Analysis of Hepatitis C Virus Intrahost Diversity across the Coding Region by Ultradeep Pyrosequencing

Hepatitis C virus (HCV) is the leading cause of liver disease worldwide. In this study, we analyzed four treatment-naive patients infected with subtype 1a and performed Roche/454 pyrosequencing across the coding region. We report the presence of low-level drug resistance mutations that would most likely have been missed using conventional sequencing methods. The approach described here is broadly applicable to studies of viral diversity and could help to improve the efficacy of direct-acting antiviral agents (DAA) in the treatment of HCV-infected patients.

Functional characterisation of the non-essential protein kinases and phosphatases regulating Aspergillus nidulans hydrolytic enzyme production

Abstract Background Despite recent advances in the understanding of lignocellulolytic enzyme regulation, less is known about how different carbon sources are sensed and the signaling cascades that result in the adaptation of cellular metabolism and hydrolase secretion. Therefore, the role played by non-essential protein kinases (NPK) and phosphatases (NPP) in the sensing of carbon and/or energetic status was investigated in the model filamentous fungus Aspergillus nidulans. Results Eleven NPKs and seven NPPs were identified as being involved in cellulase, and in some cases also hemicellulase, production in A. nidulans. The regulation of CreA-mediated carbon catabolite repression (CCR) in the parental strain was determined by fluorescence microscopy, utilising a CreA: GFP fusion protein. The sensing of phosphorylated glucose, via the RAS signalling pathway induced CreA repression, while carbon starvation resulted in derepression. Growth on cellulose represented carbon starvation and derepressing conditions. The involvement of the identified NPKs in the regulation of cellulose-induced responses and CreA derepression was assessed by genome-wide transcriptomics (GEO accession 47810). CreA:GFP localisation and the restoration of endocellulase activity via the introduction of the ∆creA mutation, was assessed in the NPK-deficient backgrounds. The absence of either the schA or snfA kinase dramatically reduced cellulose-induced transcriptional responses, including the expression of hydrolytic enzymes and transporters. The mechanism by which these two NPKs controlled gene transcription was identified, as the NPK-deficient mutants were not able to unlock CreA-mediated carbon catabolite repression under derepressing conditions, such as carbon starvation or growth on cellulose. Conclusions Collectively, this study identified multiple kinases and phosphatases involved in the sensing of carbon and/or energetic status, while demonstrating the overlapping, synergistic roles of schA and snfA in the regulation of CreA derepression and hydrolytic enzyme production in A. nidulans. The importance of a carbon starvation-induced signal for CreA derepression, permitting transcriptional activator binding, appeared paramount for hydrolase secretion.

Science publication workshops as a strategy to improve the visibility of scholarly production: the experience of the University of Sao Paulo (USP) - Brazil

The objective of this work is to present the experience of workshops that have been developed at the University of Sao Paulo by the Integrated Library System in partnership with Research Commission. The poster presents the main results of workshops that were made in 2011, in two knowledge areas: life science and engineering, about science publication processes, and directed to graduates, pos-doctorates, researchers, professors and library staff. The realization of workshops made possible identifies gaps in different aspects of scholarly communication such as research planning, search information strategy, information organization, submission process, identification of journals with high impact, and so on, areas where professors and librarians can help. Besides, workshops reveal that the majority of participants believe in its importance. Despite the ubiquity of digital technology that transversely impacts all academic activities, it is imperative to promote efforts to find a convergence between information and media literacy in higher education and university research activities. This is particularly important when we talk about how science is produced, communicated and preserved for future use. In this scenario, libraries and librarians assume a new, more active and committed role.

Accessibility and visibility of academic and scientific production of the University of São Paulo (USP), Brazil

ACADEMIC CONTENTS: Digital Library of Theses and Dissertations, eAULAS, Open Educational Resources. SCIENTIFIC CONTENTS: Digital Library of USP Intellectual Production, Scientific Journals Portal. OTHER CONTENTS: Rare books, Maps, Images.

University of São Paulo, Brazil: open access movement

USP scientific production. USP journals. USP Open Access Movement.

Investigating strategies and indicators for sustainable campus: Comparison and synergies between University of Bologna and Delft University of Technology

Sustainable development is one of the biggest challenges of the twenty fist-century. Various university has begun the debate about the content of this concept and the ways in which to integrate it into their policy, organization and activities. Universities have a special responsibility to take over a leading position by demonstrating best practices that sustain and educate a sustainable society. For that reason universities have the opportunity to create the culture of sustainability for today’s student, and to set their expectations for how the world should be. This thesis aim at analyzing how Delft University of Technology and University of Bologna face the challenge of becoming a sustainable campus. In this context, both universities have been studied and analyzed following the International Sustainable Campus Network (ISCN) methodology that provides a common framework to formalize commitments and goals at campus level. In particular this work has been aimed to highlight which key performance indicators are essential to reach sustainability as a consequence the following aspects has been taken into consideration: energy use, water use, solid waste and recycling, carbon emission. Subsequently, in order to provide a better understanding of the current state of sustainability on University of Bologna and Delft University of Technology, and potential strategies to achieve the stated objective, a SWOT Analysis has been undertaken. Strengths, weaknesses, opportunities and threats have been shown to understand how the two universities can implement a synergy to improve each other. In the direction of framing a “Sustainable SWOT” has been considered the model proposed by People and Planet, so it has been necessary to evaluate important matters as for instance policy, investment, management, education and engagement. Regarding this, it has been fundamental to involve the main sustainability coordinators of the two universities, this has been achieved through a brainstorming session. Partnerships are key to the achievement of sustainability. The creation of a bridge between two universities aims to join forces and to create a new generation of talent. As a result, people can become able to support universities in the exchange of information, ideas, and best practices for achieving sustainable campus operations and integrating sustainability in research and teaching. For this purpose the project "SUCCESS" has been presented, the project aims to create an interactive European campus network that can be considered a strategic key player for sustainable campus innovation in Europe. Specifically, the main key performance indicators have been analyzed and the importance they have for the two universities and their strategic impact have been highlighted. For this reason, a survey was conducted with people who play crucial roles for sustainability within the two universities and they were asked to evaluate the KPIs of the project. This assessment has been relevant because has represented the foundation to develop a strategy to create a true collaboration.

Channels and transporters. Mini-symposium of the Division of Medicinal Chemistry (DMC) of the Swiss Chemical Society (SCS) at the Department of Chemistry, University of Basel, May 27, 2010

During a half-day symposium, the topic 'Channels and Transporters' was covered with five lectures, including a presentation on 'Introduction and Basics of Channels and Transporters' by Beat Ernst, lectures on structure, function and physiology of channels and transporters ('The Structural Basis for Ion Conduction and Gating in Pentameric Ligand-Gated Ion Channels' by Raimund Dutzler and 'Uptake and Efflux Transporters for Endogenous Substances and for Drugs' by Dietrich Keppler), and a case study lecture on 'Avosentan' by Werner Neidhart. The program was completed by Matthias Hediger who introduced to the audience the National Center of Competence in Research (NCCR)-TransCure in his lecture entitled 'From Transport Physiology to Identification of Therapeutic Targets'.