Ana Maria Ramalho Correia

Reforming scholarly publishing and knowledge communication: From the advent of the scholarly journal to the challenges of open access

Purpose – The purpose of this paper is to provide an overview of the continuous evolution of scholarly publishing and knowledge communication as a result of the internet revolution.Design/methodology/approach – Information was obtained from a literature review of the main contributions on “self‐archiving” – the broad term often applied to electronic publishing of author‐supplied documents on the web without commercial publisher mediation. The paper analyses the impact of the open access movement, which came to fruition after the OAI Metadata Harvesting Protocol was established, as it creates the potential for interoperability between e‐print repositories. It concludes by outlining the challenges for information managers in developing the full potential of open access.Findings – With regard to the future of self‐archiving, particularly in relation to peer‐reviewed journals, information managers have a very important role to perform within their organization.Originality/value – The paper highlights the bene...

Dynamics, stability and iron‐binding activity of frataxin clinical mutants

Friedreich’s ataxia results from a deficiency in the mitochondrial protein frataxin, which carries single point mutations in some patients. In the present study, we analysed the consequences of different disease‐related mutations in vitro on the stability and dynamics of human frataxin. Two of the mutations, G130V and D122Y, were investigated for the first time. Analysis by CD spectroscopy demonstrated a substantial decrease in the thermodynamic stability of the variants during chemical and thermal unfolding (wild‐type > W155R > I154F > D122Y > G130V), which was reversible in all cases. Protein dynamics was studied in detail and revealed that the mutants have distinct propensities towards aggregation. It was observed that the mutants have increased correlation times and different relative ratios between soluble and insoluble/aggregated protein. NMR showed that the clinical mutants retained a compact and relatively rigid globular core despite their decreased stabilities. Limited proteolysis assays coupled with LC‐MS allowed the identification of particularly flexible regions in the mutants; interestingly, these regions included those involved in iron‐binding. In agreement, the iron metallochaperone activity of the Friedreich’s ataxia mutants was affected: some mutants precipitate upon iron binding (I154F and W155R) and others have a lower binding stoichiometry (G130V and D122Y). Our results suggest that, in heterozygous patients, the development of Friedreich’s ataxia may result from a combination of reduced efficiency of protein folding and accelerated degradation in vivo, leading to lower than normal concentrations of frataxin. This hypothesis also suggests that, although quite different from other neurodegenerative diseases involving toxic aggregation, Friedreich’s ataxia could also be linked to a process of protein misfolding due to specific destabilization of frataxin.

Conformational stability of human frataxin and effect of Friedreich's ataxia-related mutations on protein folding

The neurodegenerative disorder FRDA (Friedreichs ataxia) results from a deficiency in frataxin, a putative iron chaperone, and is due to the presence of a high number of GAA repeats in the coding regions of both alleles of the frataxin gene, which impair protein expression. However, some FRDA patients are heterozygous for this triplet expansion and contain a deleterious point mutation on the other allele. In the present study, we investigated whether two particular FRDA-associated frataxin mutants, I154F and W155R, result in unfolded protein as a consequence of a severe structural modification. A detailed comparison of the conformational properties of the wild-type and mutant proteins combining biophysical and biochemical methodologies was undertaken. We show that the FRDA mutants retain the native fold under physiological conditions, but are differentially destabilized as reflected both by their reduced thermodynamic stability and a higher tendency towards proteolytic digestion. The I154F mutant has the strongest effect on fold stability as expected from the fact that the mutated residue contributes to the hydrophobic core formation. Functionally, the iron-binding properties of the mutant frataxins are found to be partly impaired. The apparently paradoxical situation of having clinically aggressive frataxin variants which are folded and are only significantly less stable than the wild-type form in a given adverse physiological stress condition is discussed and contextualized in terms of a mechanism determining the pathology of FRDA heterozygous.

Iron-binding activity in yeast frataxin entails a trade off with stability in the alpha1/beta1 acidic ridge region.

Frataxin is a highly conserved mitochondrial protein whose deficiency in humans results in Friedreichs ataxia (FRDA), an autosomal recessive disorder characterized by progressive ataxia and cardiomyopathy. Although its cellular function is still not fully clear, the fact that frataxin plays a crucial role in Fe-S assembly on the scaffold protein Isu is well accepted. In the present paper, we report the characterization of eight frataxin variants having alterations on two putative functional regions: the alpha1/beta1 acidic ridge and the conserved beta-sheet surface. We report that frataxin iron-binding capacity is quite robust: even when five of the most conserved residues from the putative iron-binding region are altered, at least two iron atoms per monomer can be bound, although with decreased affinity. Furthermore, we conclude that the acidic ridge is designed to favour function over stability. The negative charges have a functional role, but at the same time significantly impair frataxins stability. Removing five of those charges results in a thermal stabilization of approximately 24 degrees C and reduces the inherent conformational plasticity. Alterations on the conserved beta-sheet residues have only a modest impact on the protein stability, highlighting the functional importance of residues 122-124.

The zebrafish homologue of Parkinson's disease ATP13A2 is essential for embryonic survival.

ATP13A2 is a lysosome-specific transmembrane ATPase protein of unknown function. This protein was initially linked to Kufor-Rakeb syndrome where it is absent or mutated. More recently, point mutations in ATP13A2 were linked to familial cases of Parkinsons disease. Zebrafish is commonly used as a vertebrate model for the study of different neurodegenerative diseases and has homologues of several Parkinsons disease associated proteins. Here, we describe for the first time the zebrafish homologue of human ATP13A2, demonstrating the homology between the protein sequences, which supports a conserved biological role. Furthermore, the spatial pattern of protein expression was studied and the lethality of the knockdown of ATP13A2 suggests it plays a crucial role during embryonic development. Our findings bring new insight into the biology of ATP13A2 and open novel opportunities for its study using zebrafish as a model organism.

The conserved Trp155 in human frataxin as a hotspot for oxidative stress related chemical modifications.

Frataxin is a mitochondrial protein that is defective in Friedreichs ataxia resulting in iron accumulation and an environment prone to Fenton reactions. We report that frataxin is susceptible to carbonylation and nitration modifications in residues from the beta-sheet surface (Tyr143, Tyr174, Tyr205 and Trp155). Frataxin functions are not significantly affected: frataxin-mediated protection against ROS is still observed, as well as iron-binding (5 Fe(3+)mol(-1), K(d) from 13-36 microM) necessary for the metallochaperone activity. However, the protein is up to 1.0 kcal mol(-1) destabilized, with conformational opening. Interestingly, the strictly conserved Trp155, which is mutated in patients, may be a functional hotspot in frataxin.

Reforming scholarly publishing and knowledge communication: From the advent of the scholarly journal to the challenges of Open Access

This paper provides an overview of the continuing evolution of scholarly publishing, leveraged in the last decades by the tremendous potential of Internet technology. It introduces “self-archiving”, the broad term often applied to the electronic publishing of author-supplied documents on the World Wide Web without commercial publisher mediation, and examines its impact on scholarly communication along with the Open Access Movement. The intensity of self-archiving and its pivotal role in scholarly communication is put into perspective through reference to some self-archiving initiatives set in motion in several countries. Finally, the paper concludes by outlining the challenges for information managers in developing the full potential of Open Access.

Overexpression, purification, crystallization and preliminary X-ray characterization of the fourth scaffoldin A cohesin from Acetivibrio cellulolyticus in complex with a dockerin from a family 5 glycoside hydrolase.

Cellulosomes are cell-bound multienzyme complexes secreted by anaerobic bacteria that play a crucial role in carbon turnover by degrading plant cell walls to simple sugars. Integration of cellulosomal components occurs via highly ordered protein-protein interactions between cohesin modules located in a molecular scaffold and dockerin modules found in cellulosomal enzymes. Acetivibrio cellulolyticus possesses a complex cellulosome arrangement which is organized by a primary enzyme-binding scaffoldin (ScaA), two anchoring scaffoldins (ScaC and ScaD) and an unusual adaptor scaffoldin (ScaB). A dockerin from a family 5 glycoside hydrolase (GH5), which was engineered to inactivate one of the two putative cohesin-binding interfaces, complexed with one of the ScaA cohesins from A. cellulolyticus has been purified and crystallized, and data were processed to a resolution of 1.57 Å in the orthorhombic space group P212121.

Probing the Kinetic Stabilities of Friedreich’s Ataxia Clinical Variants Using a Solid Phase GroEL Chaperonin Capture Platform

Numerous human diseases are caused by protein folding defects where the protein may become more susceptible to degradation or aggregation. Aberrant protein folding can affect the kinetic stability of the proteins even if these proteins appear to be soluble in vivo. Experimental discrimination between functional properly folded and misfolded nonfunctional conformers is not always straightforward at near physiological conditions. The differences in the kinetic behavior of two initially folded frataxin clinical variants were examined using a high affinity chaperonin kinetic trap approach at 25 °C. The kinetically stable wild type frataxin (FXN) shows no visible partitioning onto the chaperonin. In contrast, the clinical variants FXN-p.Asp122Tyr and FXN-p.Ile154Phe kinetically populate partial folded forms that tightly bind the GroEL chaperonin platform. The initially soluble FXN-p.Ile154Phe variant partitions onto GroEL more rapidly and is more kinetically liable. These differences in kinetic stability were confirmed using differential scanning fluorimetry. The kinetic and aggregation stability differences of these variants may lead to the distinct functional impairments described in Friedreich’s ataxia, the neurodegenerative disease associated to frataxin functional deficiency. This chaperonin platform approach may be useful for identifying small molecule stabilizers since stabilizing ligands to frataxin variants should lead to a concomitant decrease in chaperonin binding.

Learning in higher education: strategies to overcome challenges faced by adult students – lessons drawn from two case studies in Portugal

The development of a knowledge-based society needs a technological infrastructure and a workforce with the necessary knowledge and competences, supported by a well-structured initial education and a continuous learning program, available to all citizens, including those who did not have the opportunity to attend Higher Education (HE) when they were younger. We recognize that these students may be rich in experience but they also have some difficulties in adapting to the pedagogical approaches of learning and teaching. Furthermore, their attitudes and problems are not necessarily the same as those of traditional students but they are still expected to fit into educational institutions designed for younger students. The project LIHE – Learning in Higher Education aimed to improve the learning experience and environment of adults, particularly non-traditional adults as well as to promote lifelong learning in HE, within a European dimen-sion. In this paper we will present this project together with some of the results.