217 research outputs found
Structural and dynamic properties of translocase motor SecA:
No full textSecA is a large, 204 kDa, homodimeric, helicase-like protein that is a key component of the bacteria protein secretion machinery. SecA, being a motor protein, couples the translocation of polypeptide segments across or into biological membranes with the expenditure of metabolic energy extracted from ATP hydrolysis. SecA adopts a compact conformation in the cytoplasm but switches to a relaxed one when is engaged to translocation at the membrane. Specific interaction of SecA with SecYEG induces large conformational changes to both partners that result in the stimulation of SecA’s ATPase activity and trigger the opening of the channel.
We use a combination of NMR spectroscopy, Isothermal Titration Calorimetry (ITC) and biochemical techniques to characterize E. coli SecA along the protein secretion pathway. Recent advances in isotope labeling and NMR methodology (methyl-TROSY) enabled the NMR study of SecA.
We found that the nucleotide binding cleft of SecA exists in a metastable state that undergoes a disorder-order transition upon nucleotide binding. Our data show that SecA uses a novel mechanism wherein conserved regions lining the cleft undergo cycles of disorder-order transitions while switching among functional catalytic states. The structural relation of SecA to helicases suggests that these proteins may utilize similar mechanisms to convert the ATP binding/hydrolysis energy to mechanical work.
Our data reveal that C domain undergoes cycles of detachment and rebinding to the motor that are linked with the ATPase activation of SecA. When the contacts with the C domain are loosened, SecA becomes activated and this process is probably facilitated by the membrane. Moreover, allosteric communication between the preprotein binding and the motor domain of SecA is regulated by nucleotide and signal peptide binding. Finally, we found that the extreme C terminus of SecY (C6 loop) contacts both the motor and the C domain of SecA and we identified important residues from the loop C6 that mediate this interaction.
In summary, our studies revealed the intimate relation between flexibility and catalytic efficiency in SecA as well the allosteric communication among the domains.Ph.D.Includes bibliographical references (p. 131-144)by Dimitra Keramisano
Phylogeny, diversity and toxin production related to cyanobacterial symbioses
No full textPhylogeny and morphology were examined for the cyanobionts from the water fern Azolla and the cyanobacterial genus Nostoc originating from symbioses with different host plants (genera Gunnera, Cycas, Dioon, Encephalarthos, Macrozamia, and Anthoceros), the lichen genus Pannaria, and free-living Nostoc isolates from different habitats. Nostoc isolates of Pannaria formed a closely related group, but, in general, no monophyletic nature was attributed to the genus Nostoc, in contrast to the cyanobionts from Azolla which were contained in a unique monophyletic group. No correlation was detected between the diversity of the studied cyanobacteria and their geographical origin, while high host specificity was proved for the Azolla cyanobionts and the Nostoc isolates from the bipartite Pannaria lichen. Two patterns of evolution leading to symbiotically competent heterocystous cyanobacteria were distinguished, one comprising symbiotic Nostoc species and the other comprising cyanobacteria in association with the water fern Azolla. The production of the non-protein amino acid BMAA, a potential neurotoxin, was also examined. A rapid and sensitive method involving the lysis and extraction of amino acids from cyanobacteria combined with an HPLC assay for fluorescence detection of BMAA was developed. To determine whether the plant or the cyanobacterium was the origin of the BMAA in the cyanobacterium-Azolla symbiosis, the cyanobacterium-free Azolla pinnata var imbricata strain 511 was examined. HPLC analysis demonstrated a significant BMAA production in the absence of the cyanobacterium. However, PCR and cloning revealed the presence of bacteria of the genus Ochrobactrum in the plant
Geolinguistic spaces and the geopolitics of organization studies: movements across centers and peripheries: European group for organisational studies colloquium
No full textAcademic knowledge production and evaluation has been studied as a phenomenon situated across global and (semi)peripheral contexts (Lillis and Curry, 2010; Bennett, 2014). The metaphor of scales draws attention to the study of academic discourses as practices that develop across vertical, hierarchically organized layers (Blommaert, 2010). In this paper, we draw on 3 sub-corpora of organization studies journal articles, with each journal occupying a different position in the impact factor continuum. Building on the work of Lillis and Curry (2010), we study networked activities as social capital in the global academic economy. In our analysis we first examine the epistemological profile of organisation studies, as reflected in differentially ranked journals located in European contexts. We then explore the complex configuration of spaces/localities within and around which the production of knowledge takes place, by examining networks of author affiliations in relation to the identified sites in the empirical papers included in the corpus. Finally, we examine how constructions of the ‘local’ and the ‘global’ relate to the themes foregrounded in the aims and scope of each journal and we explore how discourses of the ‘local’ and the ‘global’ relate to key concepts in the field of organization studies, including institutions, alternatives and resistance, as well as power and gender
The right to childhoods : critical perspectives on rights, difference and knowledge in a transient world
No full textThis book offers an engaging study that analyses contemporary childhood by examining new lines of argument about diversity, disability and difference. The author critiques the key issues that affect both adults' and children's quality of life, including market-driven values, poverty and civic disengagement.In this fascinating study, Dimitra Hartas analyses contemporary childhood. She discusses the plurality inherent in childhood and the cultural, ideological, social and biological forces that shape children's experience of growing up in the 21st century. She engages with new lines of argument about diversity, disability and difference, and critiques the big issues that affect both adults' and children's quality of life such as market-driven values, poverty and civic disengagement.Hartas uncovers evidence of how the right to childhood is being violated in both the developed and developing world and how our consumerist culture is shaping children's lives in ways that are not always understood, and advocates the right to childhoods. She concludes by discussing the implications of her findings for both policy and practice in early childhood education, and examines pedagogies that are responsive to ethics, diversity and difference
Epigenetic chromatin modifiers in barley: IV. The study of barley Polycomb group (PcG) genes during seed development and in response to external ABA
No full textAbstract Background Epigenetic phenomena have been associated with the regulation of active and silent chromatin states achieved by modifications of chromatin structure through DNA methylation, and histone post-translational modifications. The latter is accomplished, in part, through the action of PcG (Polycomb group) protein complexes which methylate nucleosomal histone tails at specific sites, ultimately leading to chromatin compaction and gene silencing. Different PcG complex variants operating during different developmental stages have been described in plants. In particular, the so-called FIE/MEA/FIS2 complex governs the expression of genes important in embryo and endosperm development in Arabidopsis. In our effort to understand the epigenetic mechanisms regulating seed development in barley (Hordeum vulgare), an agronomically important monocot plant cultivated for its endosperm, we set out to characterize the genes encoding barley PcG proteins. Results Four barley PcG gene homologues, named HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b were identified and structurally and phylogenetically characterized. The corresponding genes HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b were mapped onto barley chromosomes 7H, 4H, 2H and 5H, respectively. Expression analysis of the PcG genes revealed significant differences in gene expression among tissues and seed developmental stages and between barley cultivars with varying seed size. Furthermore, HvFIE and HvE(Z) gene expression was responsive to the abiotic stress-related hormone abscisic acid (ABA) known to be involved in seed maturation, dormancy and germination. Conclusion This study reports the first characterization of the PcG homologues, HvFIE, HvE(Z), HvSu(z)12a and HvSu(z)12b in barley. All genes co-localized with known chromosomal regions responsible for malting quality related traits, suggesting that they might be used for developing molecular markers to be applied in marker assisted selection. The PcG differential expression pattern in different tissues and seed developmental stages as well as in two barley cultivars with different seed size is suggestive of a role for these genes in barley seed development. HvFIE and HvE(Z) were also found to be induced by the plant hormone ABA implying an association with ABA-mediated processes during seed development, germination and stress response.</p
SPECIAL ISSUE | Digital Role-Playing Games and Theatre: Retooling and Repurposing Entertainment, Art, Learning (Part 2)
No full textAuthors: Aikaterini Delikonstantinidou National and Kapodistrian University of Athens Dimitra Nikolaidou Aristotle University of Thessaloniki Download PDF version THEATRE AND/AS DIGITAL GAME As Lori M. Shyba has proposed, central among the benefits to be reaped by MMORPGs via the incorporation of theatre tools are enhanced gameplay experiences, games’ development as “a unique art form,” and their emergence as “an experiential way to rehearse social change” (2007, 779). The latter insof..
SPECIAL ISSUE | Digital Role-Playing Games and Theatre: Retooling and Repurposing Entertainment, Art, Learning (Part 1)
No full textAuthors: Aikaterini Delikonstantinidou National and Kapodistrian University of Athens Dimitra Nikolaidou Aristotle University of Thessaloniki Download PDF version INTRODUCTION What do Shakespeare’s The Tempest and modern gaming have in common? According to Gina Bloom’s Gaming the Stage (2018), the answer is a set of strategies of playing, such as withholding, divulging, speculating, and wagering on knowledge. These, on the one hand, allowed one to act upon their knowledge of gaming in ..
Split the cash from cache-friendly recommendations
No full textRecommender systems have been established as a key component of video streaming services, shaping up to 80% of content requests. Hence, recommendations are employed by the Content Providers (CPs) of these services to increase the viewing time and their revenues. Furthermore, it has been recently suggested that recommendations could be a means to reduce the operational costs of the Content Delivery Networks (CDNs) when they are related to already cached items, i.e., when they are cache-friendly. Clearly, these conflicting objectives, i.e., increasing revenue for the CP and reducing costs for the CDN, can create tensions between the two entities, and hence, prevent the full utilization of recommendations. In this work, we propose a model for capturing these tradeoffs, and an economic mechanism, based on the Nash bargaining solution, for reconciling the potentially conflicting objectives of the CP and the CDN. Our scheme enables the CP and CDN to jointly design the recommendations in a way that balances the revenue gains and cost savings, ensuring a fair and Pareto optimal split of the accrued benefits for both entities. Our numerical experiments in realistic scenarios show that the proposed scheme leads to important financial gains of up to 30%.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Embedded System
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