Atomic mutagenesis of the ribosomal Sarcin-Ricin-Loop to study EF-G GTPase activation

Translocation factor EF-G, possesses a low basal GTPase activity, which is stimulated by the ribosome. One potential region of the ribosome that triggers GTPase activity of EF-G is the Sarcin-Ricin-Loop (SRL) (helix 95) in domain VI of the 23S rRNA. Structural data showed that the tip of the SRL closely approaches GTP in the active center of EF-G, structural probing data confirmed that EF-G interacts with nucleotides G2655, A2660, G2661 and A2662.1-3 The exocyclic group of adenine at A2660 is required for stimulation of EF-G GTPase activity by the ribosome as demonstrated using atomic mutagenesis.4 Recent crystal structures of EF-G on the ribosome, gave more insights into the molecular mechanism of EF-G GTPase activity.5 Based on the structure of EF-Tu on the ribosome1, the following mechanism of GTPase activation was proposed: upon binding of EF-G to the ribosome, the conserved His92 (E.coli) changes its position, pointing to the γ-phosphate of GTP. In this activated state, the phosphate of residue A2662 of the SRL positions the catalytic His in its active conformation. It was further proposed that the phosphate oxygen of A2662 is involved in a charge-relay system, enabling GTP hydrolysis. In order to test this mechanism, we use the atomic mutagenesis approach, which allows introducing non-natural modifications in the SRL, in the context of the complete 70S ribosome. Therefore, we replaced one of the non-bridging oxygens of A2662 by a methyl group. A methylphosphonat is not able to position or activate a histidine, as it has no free electrons and therefore no proton acceptor function. These modified ribosomes were then tested for stimulation of EF-G GTPase activity. First experiments show that one of the two stereoisomers incorporated into ribosomes does not stimulate GTPase activity of EF-G, whereas the other is active. From this we conclude that indeed the non-bridging phosphate oxygen of A2662 is involved in EF-G GTPase activation by the ribosome. Ongoing experiments aim at revealing the contribution of this non-bridging oxygen at A2662 to the mechanism of EF-G GTPase activation at the atomic level.

Atomic mutagenesis of the ribosomal Sarcin-Ricin-Loop to study EF-G GTPase activation

Translocation factor EF-G, possesses a low basal GTPase activity, which is stimulated by the ribosome. One potential region of the ribosome that triggers GTPase activity of EF-G is the Sarcin-Ricin-Loop (SRL) (helix 95) in domain VI of the 23S rRNA. Structural data showed that the tip of the SRL closely approaches GTP in the active center of EF-G, structural probing data confirmed that EF-G interacts with nucleotides G2655, A2660, G2661 and A2662.1-3 The exocyclic group of adenine at A2660 is required for stimulation of EF-G GTPase activity by the ribosome as demonstrated using atomic mutagenesis.4 Recent crystal structures of EF-G on the ribosome, gave more insights into the molecular mechanism of EF-G GTPase activity.5 Based on the structure of EF-Tu on the ribosome1, the following mechanism of GTPase activation was proposed: upon binding of EF-G to the ribosome, the conserved His92 (E.coli) changes its position, pointing to the γ-phosphate of GTP. In this activated state, the phosphate of residue A2662 of the SRL positions the catalytic His in its active conformation. It was further proposed that the phosphate oxygen of A2662 is involved in a charge-relay system, enabling GTP hydrolysis. In order to test this mechanism, we use the atomic mutagenesis approach, which allows introducing non-natural modifications in the SRL, in the context of the complete 70S ribosome. Therefore, we replaced one of the non-bridging oxygens of A2662 by a methyl group. A methylphosphonat is not able to position or activate a histidine, as it has no free electrons and therefore no proton acceptor function. These modified ribosomes were then tested for stimulation of EF-G GTPase activity. First experiments show that one of the two stereoisomers incorporated into ribosomes does not stimulate GTPase activity of EF-G, whereas the other is active. From this we conclude that indeed the non-bridging phosphate oxygen of A2662 is involved in EF-G GTPase activation by the ribosome. Ongoing experiments aim at revealing the contribution of this non-bridging oxygen at A2662 to the mechanism of EF-G GTPase activation at the atomic level.

Replication Data Management,needs and solutions: an initial evaluation of conceptual approaches for integrating heterogeneous replication study data

Replication Data Management (RDM) aims at enabling the use of data collections from several iterations of an experiment. However, there are several major challenges to RDM from integrating data models and data from empirical study infrastructures that were not designed to cooperate, e.g., data model variation of local data sources. [Objective] In this paper we analyze RDM needs and evaluate conceptual RDM approaches to support replication researchers. [Method] We adapted the ATAM evaluation process to (a) analyze RDM use cases and needs of empirical replication study research groups and (b) compare three conceptual approaches to address these RDM needs: central data repositories with a fixed data model, heterogeneous local repositories, and an empirical ecosystem. [Results] While the central and local approaches have major issues that are hard to resolve in practice, the empirical ecosystem allows bridging current gaps in RDM from heterogeneous data sources. [Conclusions] The empirical ecosystem approach should be explored in diverse empirical environments.

MOOCs, Open educational resources and social networking: bridging the gap between informal and formal learning

MOOCs and open educational resources (OER) provide a wealth of learning opportunities for people around the globe, many of whom have no access to formal higher education. OER are often difficult to locate and are accessed on their own without support from or dialogue with subject experts and peers. This paper looks at whether it is possible to develop effective learning communities around OER and whether these communities can emerge spontaneously and in a self-organised way without moderation. It examines the complex interplay between formal and informal learning, and examines whether MOOCs are the answer to providing effective interaction and dialogue for those wishing to study at university level for free on the Internet.

Chiral, Three-Dimensional Supramolecular Compounds: Homo- and Bimetallic Oxalate- and 1,2-Dithiooxalate-Bridged Networks. A Structural and Photophysical Study.

In analogy to the [M(II)(bpy)(3)](2+) cations, where M(II) is a divalent transition-metal and bpy is 2,2'-bipyridine, the tris-chelated [M(III)(bpy)(3)](3+) cations, where M(III) is Cr(III) or Co(III), induce the crystallization of chiral, anionic three-dimensional (3D) coordination polymers of oxalate-bridged (&mgr;-ox) metal complexes with stoichiometries [M(II)(2)(ox)(3)](n)()(2)(n)()(-) or [M(I)M(III)(ox)(3)](n)()(2)(n)()(-). The tripositive charge is partially compensated by inclusion of additional complex anions like ClO(4)(-), BF(4)(-), or PF(6)(-) which are encapsulated in cubic shaped cavities formed by the bipyridine ligands of the cations. Thus, an elaborate structure of cationic and anionic species within a polymeric anionic network is realized. The compounds isolated and structurally characterized include [Cr(III)(bpy)(3)][ClO(4)] [NaCr(III)(ox)(3)] (1), [Cr(III)(bpy)(3)][ClO(4)][Mn(II)(2)(ox)(3)] (2), [Cr(III)(bpy)(3)][BF(4)] [Mn(II)(2)(ox)(3)] (3), [Co(III)(bpy)(3)][PF(6)][NaCr(III)(ox)(3)] (4). Crystal data: 1, cubic, P2(1)3, a = 15.523(4) Å, Z = 4; 2, cubic, P4(1)32, a = 15.564(3) Å, Z = 4; 3, cubic, P4(1)32, a = 15.553(3) Å, Z = 4; 4, cubic, P2(1)3, a = 15.515(3) Å, Z = 4. Furthermore, it seemed likely that 1,2-dithiooxalate (dto) could act as an alternative to the oxalate bridging ligand, and as a result the compound [Ni(II)(phen)(3)][NaCo(III)(dto)(3)].C(3)H(6)O (5) has successfully been isolated and structurally characterized. Crystal data: 5, orthorhombic, P2(1)2(1)2(1), a = 16.238(4) Å, b = 16.225(4) Å, c = 18.371(5) Å, Z = 4. In addition, the photophysical properties of compound 1 have been investigated in detail. In single crystal absorption spectra of [Cr(III)(bpy)(3)][ClO(4)][NaCr(III)(ox)(3)] (1), the spin-flip transitions of both the [Cr(bpy)(3)](3+) and the [Cr(ox)(3)](3)(-) chromophores are observed and can be clearly distinguished. Irradiating into the spin-allowed (4)A(2) --> (4)T(2) absorption band of [Cr(ox)(3)](3)(-) results in intense luminescence from the (2)E state of [Cr(bpy)(3)](3+) as a result of rapid energy transfer processes.

The role of Community Health Workers. Historical perspective of facilitators and barriers. Case study in Vaupés, Colombia

Thesis (Master's)--University of Washington, 2016-06

Physical activity promotion in primary care: Bridging the gap between research and practice

Background: Aflifle a growing literature supports the effectiveness of physical activity interventions delivered in the primary care setting, few studies have evaluated efforts to increase physician counseling on physical activity during routine practice (i.e., outside the context of controlled research). This paper reports the results of a dissemination trial of a primary care-based physical activity counseling intervention conducted within the context of a larger, multi-strategy, Australian community-based, physical activity intervention, the 10,000 Steps Rockhampton Project. Methods: All 23 general practices and 66 general practitioners (GPs, the Australian equivalent of family physicians) were invited to participate. Practice visits were made to consenting practices during which instruction in brief physical activity counseling was offered, along with physical activity promotion resources (print materials and pedometers). The evaluation, guided by the RE-AIM framework, included collection of process data, as well as pre-and post-inteivention data from a mailed GP survey, and data from the larger project's random-digit-dialed, community-based, cross-sectional telephone survey that was conducted in Rockhampton and a comparison community, Results: Ninety-one percent of practices were visited by 10,000 Steps staff and agreed to participate, with 58% of GPs present during the visits. General practitioner survey response rates were 67% (n =44/66 at baseline) and 71% (n =37/52, at 14-month follow-up). At follow-up, 62% had displayed the poster, 81% were using the brochures, and 70% had loaned pedometers to patients, although the number loaned was relatively small. No change was seen in GP self-report of the percentage of patients counseled on physical activity. However, data from the telephone surveys showed a 31% increase in the likelihood of recalling GP advice on physical activity in Rockhampton (95% confidence interval [CI]=1.11-1.54) compared to a 16% decrease (95% CI=0.68-1.04) in the comparison community. Conclusions: This dissemination study achieved high rates of GP uptake, reasonable levels of implementation, and a significant increase in the number of community residents counseled on physical activity. These results suggest that evidence-based primary care physical activity counseling protocols can be translated into routine practice, although the initial and ongoing investment of time to develop partnerships with relevant healthcare organizations, and the interest generated by the overall 10,000 Steps program should not be underestimated. ((C) 2004 American journal of Preventive Medicine.

Synthetic, spectroscopic and X-ray crystallographic structural study of the monomeric [Cu(pysme)(sac)(MeOH)] and dimeric [Cu(6mptsc)(sac)](2) complexes [pysme = anion of the pyridine-2-carboxaldehyde Schiff base of S-methyldithiocarbazate, 6mptsc=the anio

New mixed-ligand copper(II) complexes of empirical formulas [Cu(pysme)(sac) (CH3OH)] and [Cu(6mptsc)(sac)](2) have been synthesized and characterized by conductance, magnetic, IR and electronic spectroscopic techniques. X-ray crystallographic structure analyses of these complexes indicate that in both complexes the copper(II) ions adopt a five-coordinate distorted square-pyramidal geometry with an N3SO donor environment. The Schiff bases are coordinated to the copper(II) ions as tridentate NNS chelates via the pyridine nitrogen atom, the azomethine nitrogen atom and the thiolate sulfur atom. In the monomeric [Cu(pysme)(sac)(MeOH)] complex, the saccharinate anion acts as a monodentate ligand coordinating the copper(II) ion via the imino nitrogen atom whereas in the dimeric [Cu(6mptsc)(sac)](2) complex, the sac anion behaves as a bridging bidentate ligand providing the imino nitrogen donor atom to one of the copper(II) ions and the carbonyl oxygen as a weakly coordinated axial ligand atom to the other Cu(II) ion. In both complexes, the copper(II) ions have distorted square-pyramidal environments. The distortion from an ideal square-pyramidal geometry is attributed to the restricted bite angles of the planar tridentate ligand. (C) 2004 Elsevier Ltd. All rights reserved.

Mechanistic aspects of proton chain transfer: A computational study for the green fluorescent protein chromophore

We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging “water” that already has substantial negative charge.

User involvement in UK cancer services:bridging the policy gap

Recent UK government initiatives aim to increase user involvement in the National Health Service (NHS) in two ways: by encouraging service users to take an active role in making decisions about their own care; and by establishing opportunities for wider public participation in service development. The purpose of this study was to examine how UK cancer service users understand and relate to the concept of user involvement. The data were collected through in-depth interviews, which were analysed for content according to the principles of grounded theory. The results highlight the role of information and communication in effective user involvement. Perhaps more importantly, this study suggests that the concept of user involvement is unclear to many cancer service users. This paper argues the need for increased awareness and understanding of what user involvement is and how it can work.

Self-efficacy in depression: Bridging the gap between competence and real-world functioning

Background: Depression is the largest contributing factor to years lost to disability, and symptom remission does not always result in functional improvement. Comprehensive analysis of functioning requires investigation both of the competence to perform behaviours, as well as actual performance in the real world. Further, two independent domains of functioning have been proposed: adaptive (behaviours conducive to daily living skills and independent functioning) and interpersonal (behaviours conducive to the successful initiation and maintenance of social relationships). To date, very little is known about the relationship between these constructs in depression, and the factors that may play a key role in the disparity between competence and real-world performance in adaptive and interpersonal functioning. Purpose: This study used a multidimensional (adaptive and interpersonal functioning), multi-level (competence and performance) approach to explore the potential discrepancy between competence and real-world performance in depression, specifically investigating whether self-efficacy (one’s beliefs of their capability to perform particular actions) predicts depressed individuals’ underperformance in the real world relative to their ability. A comparison sample of healthy participants was included to investigate the level of depressed individuals’ impairment, across variables, relative to healthy individuals. Method: Forty-two participants with depression and twenty healthy participants without history of, or current, psychiatric illness were recruited in the Kingston, Ontario community. Competence, self-efficacy, and real-world functioning all in both adaptive and interpersonal domains, and symptoms were assessed during a single-visit assessment. Results: Relative to healthy individuals, depressed individuals showed significantly poorer adaptive and interpersonal competence, adaptive and interpersonal functioning, and significantly lower self-efficacy for adaptive and interpersonal behaviours. Self-efficacy significantly predicted functional disability both in the domain of adaptive and interpersonal functioning. Interpersonal self-efficacy accounted for significant variance in the discrepancy between interpersonal competence and functioning. Conclusions: The current study provides the first data regarding relationships among competence, functioning, and self-efficacy in depression. Self-efficacy may play an important role in the deployment of functional skills in everyday life. This has implications for therapeutic interventions aimed at enhancing depressed individuals’ engagement in functional activities. There may be additional intrinsic or extrinsic factors that influence the relationships among competence and functioning in depression.

Bridging the link between trauma, brain development and depression: epigenetic mechanisms

Despite its large impact on the individual and society, we currently have only a rudimentary understanding of the biological basis of Major Depressive Disorder, even less so in adolescent populations. This thesis focuses on two research questions. First, how do adolescents with depression differ from adolescents who have never been depressed on (1a) brain morphology and (1b) DNA methylation? We studied differences in the fronto-limbic system (a collection of areas responsible for emotion regulation) and methylation at the serotonin transporter (SLC6A4) and FK506 binding protein gene (FKBP5) genes (two genes strongly linked to stress regulation and depression). Second, how does childhood trauma, which is known to increase risk for depression, affect (2a) brain development and (2b) SLC6A4 and FKBP5 methylation? Further, (2c) how might DNA methylation explain how trauma affects brain development in depression? We studied these questions in 24 adolescent depressed patients and 21 controls. We found that (1a) depressed adolescents had decreased left precuneus volume and greater volume of the left precentral gyrus compared to controls; however, no differences in fronto-limbic morphology were identified. Moreover, (1b) individuals with depression had lower levels of FKBP5 methylation than controls. In line with our second hypothesis (2a) greater levels of trauma were associated with decreased volume of a number of fronto-limbic regions. Further, we found that (2b) greater trauma was associated with decreased SLC6A4, but not FKBP5, methylation. Finally, (2c) greater FKBP5, but not SLC6A4, methylation was associated with decreased volume of a number of fronto-limbic regions. The results of this study suggest an association among trauma, DNA methylation and brain development in youth, but the direction of these relationships appears to be inconsistent. Future studies using a longitudinal design will be necessary to clarify these results and help us understand how the brain and epigenome change over time in depressed youth.

Bridging Perspectives

People’s ability to change their social and economic circumstances may be constrained by various forms of social, cultural and political domination. Thus to consider a social actor’s particular lifeworld in which the research is embedded assists in the understanding of how and why different trajectories of change occur or are hindered and how those changes fundamentally affect livelihood opportunities and constraints. In seeking to fulfill this condition this thesis adopted an actor-oriented approach to the study of rural livelihoods. A comprehensive livelihoods study requires grasping how social reality is being historically constituted. That means to understand how the interaction of modes of production and symbolical reproduction produces the socio-space. Research is here integrated to action through the facilitation of farmer groups. The overall aim of the groups was to prompt agency, as essential conditions to build more resilient livelihoods. The smallholder farmers in the Mabalane District of Mozambique are located in a remote semi-arid area. Their livelihoods customarily depend at least as much on livestock as on (mostly) rain-fed food crops. Increased climate variability exerts pressure on the already vulnerable production system. An extensive 10-month duration of participant observation divided into 3 periods of fieldwork structured the situated multi-method approach that drew on a set of interview categories. The actor-oriented appraisal of livelihoods worked in building a mutually shared definition of the situation. This reflection process was taken up by the facilitation of the farmer groups, one in Mabomo and one in Mungazi, which used an inquiry iteratively combining individual interviews and facilitated group meetings. Integration of action and reflection was fundamental for group constitution as spaces for communicative action. They needed to be self-organized and to achieve understanding intersubjectively, as well as to base action on cooperation and coordination. Results from this approach focus on how learning as collaboratively generated was enabled, or at times hindered, in (a) selecting meaningful options to test; (b) in developing mechanisms for group functioning; and (c) in learning from steering the testing of options. The study of livelihoods looked at how the different assets composing livelihoods are intertwined and how the increased severity of dry spells is contributing to escalated food insecurity. The reorganization of the social space, as households moved from scattered homesteads to form settlements, further exerts pressure on the already scarce natural resource-based livelihoods. Moreover, this process disrupted a normative base substantiating the way that the use of resources is governed. Hence, actual livelihood strategies and response mechanisms turn to diversification through income-generating activities that further increase pressure on the resource-base in a rather unsustainable way. These response mechanisms are, for example, the increase in small-livestock keeping, which has easier conversion to cash, and charcoal production. The latter results in ever more precarious living and working conditions. In the majority of the cases such responses are short-term and reduce future opportunities in a downward spiral of continuously decreasing assets. Thus, by indicating the failure of institutions in the mediation of smallholders’ adaptive capabilities, the livelihood assessment in Mabomo and Mungazi sheds light on the complex underlying structure of present day social vulnerability, linking the macro-context to the actual situation. To assist in breaking this state of “subordination”, shaped by historical processes, weak institutions and food insecurity, the chosen approach to facilitation of farmer groups puts farmer knowledge at the center of an evolving process of intersubjective co-construction of knowledge towards emancipation.

Bridging discourses in a writing classroom

The aim of this study is to describe and analyse the writing discourse in one classroom and how students learn through studying a topic, i.e. the teaching and learning of written argument. The study takes its stance from a sociocultural perspective and is influenced by discourse analyses, new literacy studies and critical literacy (Fairclough1989; Barton 2007; Janks 2010; Ivanič 2004). Data from year 6 in Sweden consists of observations, informal conversations, teachers’ planning and students’ written texts, i.e. letters to a newspaper editor. The results are presented in terms of four themes that became apparent during the reading of the data, viz. (1) teaching for learning - deconstruction; (2) dialogue and scaffolding for learning – enabling access; (3) reconstruction, feedback and students’ reflections for learning; and (4) writing to learn. The data is analysed and discussed on the basis of four concepts for developing critical literacy, viz. access, deconstruction, reconstruction and domination (cf. Janks 2010:21 – 32). The study indicates that explicit teaching of a written argument gives students access to the dominating structure of the genre if they are given the time and tools to reflect and be given feedback from the teacher.

Stuck in the middle with you: The role of bridging organisations in urban regeneration

The literature on the governance of social-ecological systems increasingly recognizes a key role of bridging organisations (BOs) in transition processes towards sustainability. BOs can be defined as facilitators who allow for interorganisational collaboration. Our paper provides a more nuanced understanding of specific BO activities and their contributions towards urban sustainability. Our analysis is based on applying three complementary methodological angles (drawing on geolocalised data, interviews and action research) to 20 years of urban renovation investments in the city-region of Brussels. We distinguish between multi-scale, multi-actor and multi-dimensional tensions in urban renovation programmes and link these tensions to bridging challenges for BOs. Results suggest that the corresponding three types of bridging roles form a trilemma rather than a trilogy: the BOs in study have mediated one tension by de facto exacerbating another. Lessons from action research suggest that a wider use of temporality and shared language to communicate about urban renovation projects could attenuate the bridging trilemma.