Characterization of DnmA, the Dnmt2 homolog in Dictyostelium discoideum

Eukaryotic DNA m5C methyltransferases (MTases) play a major role in many epigenetic regulatory processes like genomic imprinting, X-chromosome inactivation, silencing of transposons and gene expression. Members of the two DNA m5C MTase families, Dnmt1 and Dnmt3, are relatively well studied and many details of their biological functions, biochemical properties as well as interaction partners are known. In contrast, the biological functions of the highly conserved Dnmt2 family, which appear to have non-canonical dual substrate specificity, remain enigmatic despite the efforts of many researchers. The genome of the social amoeba Dictyostelium encodes Dnmt2-homolog, the DnmA, as the only DNA m5C MTase which allowed us to study Dnmt2 function in this organism without interference by the other enzymes. The dnmA gene can be easily disrupted but the knock-out clones did not show obvious phenotypes under normal lab conditions, suggesting that the function of DnmA is not vital for the organism. It appears that the dnmA gene has a low expression profile during vegetative growth and is only 5-fold upregulated during development. Fluorescence microscopy indicated that DnmA-GFP fusions were distributed between both the nucleus and cytoplasm with some enrichment in nuclei. Interestingly, the experiments showed specific dynamics of DnmA-GFP distribution during the cell cycle. The proteins colocalized with DNA in the interphase and were mainly removed from nuclei during mitosis. DnmA functions as an active DNA m5C MTase in vivo and is responsible for weak but detectable DNA methylation of several regions in the Dictyostelium genome. Nevertheless, gel retardation assays showed only slightly higher affinity of the enzyme to dsDNA compared to ssDNA and no specificity towards various sequence contexts, although weak but detectable specificity towards AT-rich sequences was observed. This could be due to intrinsic curvature of such sequences. Furthermore, DnmA did not show denaturant-resistant covalent complexes with dsDNA in vitro, although it could form covalent adducts with ssDNA. Low binding and methyltransfer activity in vitro suggest the necessity of additional factor in DnmA function. Nevertheless, no candidates could be identified in affinity purification experiments with different tagged DnmA fusions. In this respect, it should be noted that tagged DnmA fusion preparations from Dictyostelium showed somewhat higher activity in both covalent adduct formation and methylation assays than DnmA expressed in E.coli. Thus, the presence of co-purified factors cannot be excluded. The low efficiency of complex formation by the recombinant enzyme and the failure to define interacting proteins that could be required for DNA methylation in vivo, brought up the assumption that post-translational modifications could influence target recognition and enzymatic activity. Indeed, sites of phosphorylation, methylation and acetylation were identified within the target recognition domain (TRD) of DnmA by mass spectrometry. For phosphorylation, the combination of MS data and bioinformatic analysis revealed that some of the sites could well be targets for specific kinases in vivo. Preliminary 3D modeling of DnmA protein based on homology with hDNMT2 allowed us to show that several identified phosphorylation sites located on the surface of the molecule, where they would be available for kinases. The presence of modifications almost solely within the TRD domain of DnmA could potentially modulate the mode of its interaction with the target nucleic acids. DnmA was able to form denaturant-resistant covalent intermediates with several Dictyostelium tRNAs, using as a target C38 in the anticodon loop. The formation of complexes not always correlated with the data from methylation assays, and seemed to be dependent on both sequence and structure of the tRNA substrate. The pattern, previously suggested by the Helm group for optimal methyltransferase activity of hDNMT2, appeared to contribute significantly in the formation of covalent adducts but was not the only feature of the substrate required for DnmA and hDNMT2 functions. Both enzymes required Mg2+ to form covalent complexes, which indicated that the specific structure of the target tRNA was indispensable. The dynamics of covalent adduct accumulation was different for DnmA and different tRNAs. Interestingly, the profiles of covalent adduct accumulation for different tRNAs were somewhat similar for DnmA and hDNMT2 enzymes. According to the proposed catalytic mechanism for DNA m5C MTases, the observed denaturant-resistant complexes corresponded to covalent enamine intermediates. The apparent discrepancies in the data from covalent complex formation and methylation assays may be interpreted by the possibility of alternative pathways of the catalytic mechanism, leading not to methylation but to exchange or demethylation reactions. The reversibility of enamine intermediate formation should also be considered. Curiously, native gel retardation assays showed no or little difference in binding affinities of DnmA to different RNA substrates and thus the absence of specificity in the initial enzyme binding. The meaning of the tRNA methylation as well as identification of novel RNA substrates in vivo should be the aim of further experiments.

Cultivating the City: Infrastructures of abundance in urban Brazil

Urban agriculture, if it is to become integrated into the city, needs landscape architectural thinking in order to be woven into the larger urban fabric. Thinking at the scale of ecosystems running through a city creates a framework for spatial change; thinking in assemblages of stakeholders and actors creates a framework for social investment and development. These overlapping frameworks are informed and perhaps even defined by the emergent field of landscape democracy. Cultivating the City is a prospective design project seeking to embody landscape democratic principles. The intention is to reclaim the meaning of landscape as the relationship between people and place, both shaping each other. The design in question is a proposed network of urban agriculture typologies in Porto Alegre, Brazil. These hypothetical designs, emphasizing agroforestry with native species, serve as a basis for dialogue between potential stakeholders and as catalysts for future projects. This landscape architecture project sets out to be a mediator in processes of spatial evolution in order to envision just and sustainable urban landscapes.

Role of the cultural values as a key part in the implementing of healthy practices : exploratory research

El concepto de organización saludable cada vez toma más fuerza en el ámbito empresarial y académico, a razón de su enfoque integral y al impacto generado en distintos grupos de interés. Debido a su reciente consolidación como concepto, existe un limitado cuerpo de investigación en torno al tema. Para contribuir a la generación de conocimiento en este sentido, se desarrolló un estudio exploratorio el cual tenía como objetivo identificar la relación existente entre la implementación de prácticas saludables en las organizaciones y los valores culturales. En el estudio participaron 66 sujetos a quienes se les administró un cuestionario compuesto por nueve variables, cinco provenientes del modelo de Hofstede (1980) y cuatro más que evaluaban la implementación de prácticas organizacionales saludables. Los resultados obtenidos muestran que los valores culturales predicen la implementación de prácticas saludables.

Miniature Carvings in the Canadian Dorset Culture: the Paleo-Eskimo Belief System

En este estudio, intento resumir los debates relacionados con la última cultura paleoesquimal de Canadá Ártica y la de Groenlandia, y llamar la atención sobre las analogías culturales desde Asia, además de crear un cuadro complejo sobre el chamanismo y el culto al oso de los Dorset. Los temas como el origen del arte de los Dorset, la transición Pre-Dorset-Dorset, y los contactos entre los Dorset y los Thule son relevantes para reconstruir el sistema de creencias de los Dorset. Sin embargo, la totalidad del sistema de creencias de los paleoesquimales no se puede comprender sobre la base de los hallazgos arqueológicosy las analogías etnográficas remotas.

Small-area variation in health care affecting the choice of cesarean delivery: the case of a Colombian health insurer

In the midst of health care reform, Colombia has succeeded in increasing health insurance coverage and the quality of health care. In spite of this, efficiency continues to be a matter of concern, and small-area variations in health care are one of the plausible causes of such inefficiencies. In order to understand this issue, we use individual data of all births from a Contributory-Regimen insurer in Colombia. We perform two different specifications of a multilevel logistic regression model. Our results reveal that hospitals account for 20% of variation on the probability of performing cesarean sections. Geographic area only explains 1/3 of the variance attributable to the hospital. Furthermore, some variables from both demand and supply sides are found to be also relevant on the probability of undergoing cesarean sections. This paper contributes to previous research by using a hierarchical model and by defining hospitals as cluster. Moreover, we also include clinical and supply induced demand variables.

The sight of silence : the conceptualisation of silence in the visual cultures of sign language communities

Deaf people are perceived by hearing people as living in a silent world. Yet, silence cannot exist without sound, so if sound is not heard, can there be silence? From a linguistic point of view silence is the absence of, or intermission in, communication. Silence can be communicative or noncommunicative. Thus, silence must exist in sign languages as well. Sign languages are based on visual perception and production through movement and sight. Silence must, therefore, be visually perceptible; and, if there is such a thing as visual silence, how does it look? The paper will analyse the topic of silence from a Deaf perspective. The main aspects to be explored are the perception and evaluation of acoustic noise and silence by Deaf people; the conceptualisation of silence in visual languages, such as sign languages; the qualities of visual silence; the meaning of silence as absence of communication (particularly between hearing and Deaf people); social rules for silence; and silencing strategies.

O Cuidador de Enfermagem e o Cuidar em Uma Unidade de Terapia Intensiva; The Nursing Caregiver and the Caring in Intensive Care Units

There are several aggressive factors in Intensive Care Units (ICU), which reach not only patients, but the nursing caregivers, since they participate in complex procedures and death of patients. Nursing caregivers may have difficulties on their daily work routine that can influence the way of care. The goal of this study was to identify the aspects of nursing caregivers working in adult ICU. It is a describe-exploratory study with qualitative approach, developed among 21 ICU adult nursing caregivers of a school hospital in Paraná. The data were collected in May and July, 2009 by recorded and transcribed semi-structured interviews. Four categories for analysis were identified: the aspects of ICU assistance, the meaning of healthcare for the nursing caregivers, the understanding of healthcare positive aspects and disclosing the difficulties of caring. The results revealed that caring is related to some factors such as mixed feelings, the mental and physical damage caused by stress; the understanding of total caring, scientific-technique procedures, family engagement in the assistance and humanization. The positive aspects are related to the welfare due to satisfaction in the work done and recognition of work. The difficulties involved death situations, psychological and biological damages, establishing links with patients and the uncaring toward the nursing caregivers.

The School of Museology Celje: regular, continuous, topical, quality form of education

At the School of Museology, a project with ten years of tradition, we carry out module-based programmes to educate and qualify different target audiences working in the filed of cultural heritage. Our development and realization of educational programmes and training courses directed at practical applicability, including life-long learning of adults, topic complementarity with related professional and scientific fields, connection with universities offering undergraduate and postgraduate studies of heritages, promotion of theoretical museological discourses raising awareness of the meaning of cultural heritage, firm placement in an international network of related institutions and promotion of international relations with special emphasis on neighbouring countries. We encourage project partnership and cooperate with different domestic and foreign associates in forming and carrying out programmes.

Significance of cross correlations in the stress relaxation of polymer melts

According to linear response theory, all relaxation functions in the linear regime can be obtained using time correlation functions calculated under equilibrium. In this paper, we demonstrate that the cross correlations make a significant contribution to the partial stress relaxation functions in polymer melts. We present two illustrations in the context of polymer rheology using (1) Brownian dynamics simulations of a single chain model for entangled polymers, the slip-spring model, and (2) molecular dynamics simulations of a multichain model. Using the single chain model, we analyze the contribution of the confining potential to the stress relaxation and the plateau modulus. Although the idea is illustrated with a particular model, it applies to any single chain model that uses a potential to confine the motion of the chains. This leads us to question some of the assumptions behind the tube theory, especially the meaning of the entanglement molecular weight obtained from the plateau modulus. To shed some light on this issue, we study the contribution of the nonbonded excluded-volume interactions to the stress relaxation using the multichain model. The proportionality of the bonded/nonbonded contributions to the total stress relaxation (after a density dependent "colloidal" relaxation time) provides some insight into the success of the tube theory in spite of using questionable assumptions. The proportionality indicates that the shape of the relaxation spectrum can indeed be reproduced using the tube theory and the problem is reduced to that of finding the correct prefactor. (c) 2007 American Institute of Physics

Creating a greater partnership: analysing partnership in the Catholic Church development chain

This paper presents results from a project designed to explore the meaning and function of partnership within the Catholic Church development chain. The geography literature has had little to say about such aid chains, especially those founded on faith-based groups. The relationships between three Catholic Church-based donors - referred to as A, B and C - with development personnel of the diocese of the Abuja Ecclesiastical Province (AEP) as well as other Catholic Church structures in Nigeria were analysed. The aim was to explore the forces behind the relationships and how 'patchy' these relationships were in AEP. Respondents were asked to give each of the donors a score in relation to four questions covering their relationship with the donors. Results suggest that the modus operandi of donor 'A' allows it to be perceived as the 'best' partner, while 'B' was scored less favourably because of a perception that it attempts to act independently of existing structures in Nigeria rather than work through them. There was significant variation between diocese in this regard, as well as between the diocese and other structures of the Church (Provinces, Inter-Provinces and National Secretariat). Thus 'partnership' in the Catholic Church aid chain is a highly complex, contested and 'visioned' term and the development of an analytical framework has to take account of these fundamentals.

The role of drama in the teaching of speaking and listening as the basis for social capital

This paper explores how the concept of 'social capital' relates to the teaching of speaking and listening. The argument draws on Bourdieu's notion that a common language is an illusion but posits that an understanding of the grammar of speech can be productive in the development of both an understanding of what constitutes effective speech and the development of competence in speaking. It is argued that applying structuralist notions of written grammar is an inadequate approach to understanding speech acts or enhancing the creative use of speech. An analysis is made of how typical features of speech relate to dramatic dialogue and how the meaning of what is said is contingent upon aural and visual signifiers. On this basis a competent speaker is seen as being one who produces expressions appropriate for a range of situations by intentionally employing such signifiers. The paper draws on research into the way drama teachers make explicit reference to and use of semiotics and dramatic effectiveness in order to improve students' performance and by so doing empower them to increase their social capital. Ultimately, it is concluded that helping students identify, analyse and employ the aural, visual and verbal grammar of spoken English is not an adjunct to the subject of drama, but an intrinsic part of understanding the art form. What is called for is a re-appraisal by drama teachers of their own understanding of concepts relating to speech acts in order to enhance this area of their work.

Borg's rating of perceived exertion scales: do the verbal anchors mean the same for different clinical groups?

Objective: To examine the interpretation of the verbal anchors used in the Borg rating of perceived exertion (RPE) scales in different clinical groups and a healthy control group. Design: Prospective experimental study. Setting: Rehabilitation center. Participants: Nineteen subjects with brain injury, 16 with chronic low back pain (CLBP), and 20 healthy controls. Interventions: Not applicable. Main Outcome Measures: Subjects used a visual analog scale (VAS) to rate their interpretation of the verbal anchors from the Borg RPE 6-20 and the newer 10-point category ratio scale. Results: All groups placed the verbal anchors in the order that they occur on the scales. There were significant within-group differences (P > .05) between VAS scores for 4 verbal anchors in the control group, 8 in the CLBP group, and 2 in the brain injury group. There was no significant difference in rating of each verbal anchor between the groups (P > .05). Conclusions: All subjects rated the verbal anchors in the order they occur on the scales, but there was less agreement in rating of each verbal anchor among subjects in the brain injury group. Clinicians should consider the possibility of small discrepancies in the meaning of the verbal anchors to subjects, particularly those recovering from brain injury, when they evaluate exercise perceptions.

The price of risk in construction projects: contingency approximation model (CAM)

Little attention has been focussed on a precise definition and evaluation mechanism for project management risk specifically related to contractors. When bidding, contractors traditionally price risks using unsystematic approaches. The high business failure rate our industry records may indicate that the current unsystematic mechanisms contractors use for building up contingencies may be inadequate. The reluctance of some contractors to include a price for risk in their tenders when bidding for work competitively may also not be a useful approach. Here, instead, we first define the meaning of contractor contingency, and then we develop a facile quantitative technique that contractors can use to estimate a price for project risk. This model will help contractors analyse their exposure to project risks; and help them express the risk in monetary terms for management action. When bidding for work, they can decide how to allocate contingencies strategically in a way that balances risk and reward.

Pricing the options inherent in leased commercial property: a UK case study

This paper sets out the findings of a group of research and development projects carried out at the Department of Real Estate & Planning at the University of Reading and at Oxford Property Systems over the period 1999 – 2003. The projects have several aims: these are to identify the fundamental drivers of the pricing of different lease terms in the UK property sector; to identify current and best market practice and uncover the main variations in lease terms; to identify key issues in pricing lease terms; and to develop a model for the pricing of rent under a variety of lease variations. From the landlord’s perspective, the main factors driving the required ‘compensation’ for a lease term amendment include expected rental volatility, expected probability of tenant vacation, and the expected costs of tenant vacation. These data are used in conjunction with simulation technology to reflect the options inherent in certain lease types to explore the required rent adjustment. The resulting cash flows have interesting qualities which illustrate the potential importance of option pricing in a non-complex and practical way.

A functional coefficient model view of the Feldstein–Horioka puzzle

What does the saving–investment (SI) relation really measure and how should the SI relation be measured? These are two of the most discussed issues triggered by the so-called Feldstein–Horioka puzzle. Based on panel data we introduce a new variant of functional coefficient models that allows to separate long and short to medium run parameter dependence. The new modeling framework is applied to uncover the determinants of the SI relation. Macroeconomic state variables such as openness, the age dependency ratio, government current and consumption expenditures are found to affect the SI relation significantly in the long run.