Controlling protein molecular dynamics:how to accelerate folding while preserving the native state

The dynamics of peptides and proteins generated by classical molecular dynamics (MD) is described by using a Markov model. The model is built by clustering the trajectory into conformational states and estimating transition probabilities between the states. Assuming that it is possible to influence the dynamics of the system by varying simulation parameters, we show how to use the Markov model to determine the parameter values that preserve the folded state of the protein and at the same time, reduce the folding time in the simulation. We investigate this by applying the method to two systems. The first system is an imaginary peptide described by given transition probabilities with a total folding time of 1 micros. We find that only small changes in the transition probabilities are needed to accelerate (or decelerate) the folding. This implies that folding times for slowly folding peptides and proteins calculated using MD cannot be meaningfully compared to experimental results. The second system is a four residue peptide valine-proline-alanine-leucine in water. We control the dynamics of the transitions by varying the temperature and the atom masses. The simulation results show that it is possible to find the combinations of parameter values that accelerate the dynamics and at the same time preserve the native state of the peptide. A method for accelerating larger systems without performing simulations for the whole folding process is outlined.

The impact of visual-verbal relationships on native-nonnative english speakers' reading processes and comprehension

The aim of this study was to comparatively investigate the impact of visual-verbal relationships that exist in expository texts on the reading process and comprehension of readers from different language background: native speakers of English (LI) and speakers of English as a foreign language (EFL). The study focussed, in this respect, on the visual elements (VEs) mainly graphs and tables that accompanied the selected texts. Two major experiments were undertaken. The first, was for the reading process using the post-reading questionnaire technique. Participants were 163 adult readers representing three groups: 77 (LI), 56 (EFL postgraduates); and 30 (EFL undergraduates). The second experiment was for the reading comprehension using cloze procedure. Participants were 123 representing the same above gorups: 50, 33 and 40 respectively. It was hypothesised that the LI readers would make use of VEs in the reading process in ways different from both EFL groups and that use would enhance each group's comprehension in different aspects and to different levels. In the analysis of the data of both experiments two statistical measurements were used. The chi-square was used to measure the differences between frequencies and the t-test was used to measure the differences between means. The results indicated a significant relationship between readers' language background and the impact of visual-verbal relationships on their reading processes and comprehension of such type of texts. The results also revealed considerable similarities between the two EFL groups in the reading process of texts accompanied by VEs. In the reading comprehension, however, the EFL undergraduates seemed to benefit from the visual-verbal relationships in their comprehension more than the postgraduates, suggesting a weak relationship of this impact for older EFL readers. Furthermore, the results showed considerable similarities between the reading process of texts accompanied by VEs and of whole prose texts. Finally an evaluation of this study was undertaken as well as practical implications for EFL readers and suggestions for future research.

Coherence and understanding in informal conversations between native and non-native speakers of English

This study investigates informal conversations between native English speakers and international students living and studying in the UK. 10 NNS participants recorded themselves during conversations with native speakers. The audio-recordings were transcribed and a fine-grained, qualitative analysis was employed to examine how the participants jointly achieved both coherence and understanding in the conversations, and more specifically how the NNSs contributed to this achievement. The key areas of investigation focused on features of topic management, such as topic initiations, changes and transitions, and on the impact which any communicative difficulties may have on the topical continuity of the conversations. The data suggested that these conversations flowed freely and coherently, and were marked by a relative scarcity of the communicative difficulties often associated with NS-NNS interactions. Moreover, language difficulties were found to have minimal impact on the topic development of the conversations. Unlike most previous research in the field, the data further indicated that the NNSs were able to make active contributions to the initiation and change of topics, and to employ a range of strategies to manage these effectively and coherently. The study considers the implications which the findings may have for teaching and learning, for second language acquisition research, and for non-native speakers everywhere.

Surfactant-free purification of membrane proteins with intact native membrane environment

In order to study the structure and function of a protein, it is generally required that the protein in question is purified away from all others. For soluble proteins, this process is greatly aided by the lack of any restriction on the free and independent diffusion of individual protein particles in three dimensions. This is not the case for membrane proteins, as the membrane itself forms a continuum that joins the proteins within the membrane with one another. It is therefore essential that the membrane is disrupted in order to allow separation and hence purification of membrane proteins. In the present review, we examine recent advances in the methods employed to separate membrane proteins before purification. These approaches move away from solubilization methods based on the use of small surfactants, which have been shown to suffer from significant practical problems. Instead, the present review focuses on methods that stem from the field of nanotechnology and use a range of reagents that fragment the membrane into nanometre-scale particles containing the protein complete with the local membrane environment. In particular, we examine a method employing the amphipathic polymer poly(styrene-co-maleic acid), which is able to reversibly encapsulate the membrane protein in a 10 nm disc-like structure ideally suited to purification and further biochemical study.

Topic continuity in informal conversations between native and non-native speakers of English

Topic management by non-native speakers (NNSs) during informal conversations has received comparatively little attention from researchers, and receives surprisingly little attention in second language learning and teaching. This article reports on one of the topic management strategies employed by international students during informal, social interactions with native-speaker peers, exploring the process of maintaining topic continuity following temporary suspensions of topics. The concept of side sequences is employed to illustrate the nature of different types of topic suspension, as well as the process of jointly negotiating a return to the topic. Extracts from the conversations show that such sequences were not exclusively occasioned by language difficulties, and that the non-native speaker participants were able to effect successful returns to the main topic of the conversations.

A description of the french passive for non-native speakers

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Degradation, receptor binding, insulin secreting and antihyperglycaemic actions of palmitate-derivatised native and Ala8-substituted GLP-1 analogues

The hormone glucagon-like peptide-1(7-36)amide (GLP-1) is released in response to ingested nutrients and acts to promote glucose-dependent insulin secretion ensuring efficient postprandial glucose homeostasis. Unfortunately, the beneficial actions of GLP-1 which give this hormone many of the desirable properties of an antidiabetic drug are short lived due to degradation by dipeptidylpeptidase IV (DPP IV) and rapid clearance by renal filtration. In this study we have attempted to extend GLP-1 action through the attachment of palmitoyl moieties to the E-amino group in the side chain of the LyS26 residue and to combine this modification with substitutions of the Ala 8 residue, namely Val or amino-butyric acid (Abu). In contrast to native GLP-1, which was rapidly degraded, [Lys(pal) 26]GLP-1, [Abu8,Lys(pal)26]GLP-1 and [Val8,Lys-(pal)26]GLP-1 all exhibited profound stability during 12 h incubations with DPP IV and human plasma. Receptor binding affinity and the ability to increase cyclic AMP in the clonal β-cell line BRIN-BD11 were decreased by 86- to 167-fold and 15- to 62-fold, respectively compared with native GLP-1. However, insulin secretory potency tested using BRIN-BD11 cells was similar, or in the case of [Val8,Lys(pal)26]GLP-1 enhanced. Furthermore, when administered in vivo together with glucose to diabetic (ob/ob) mice, [Lys(pal)26]GLP-1, [Abu8,Lys(pal) 26]GLP-1 and [Val8,Lys(pal) 26]GLP-1 did not demonstrate acute glucose-lowering or insulinotropic activity as observed with native GLP-1. These studies support the potential usefulness of fatty acid linked analogues of GLP-1 but indicate the importance of chain length for peptide kinetics and bioavailability. Copyright © by Walter de Gruyter.

From Spanish paintings to murder:topic transitions in casual conversations between native and non-native speakers of English

This article explores some of the strategies used by international students of English to manage topic shifts in casual conversations with English-speaking peers. It therefore covers aspects of discourse which have been comparatively under-researched, and where research has also tended to focus on the problems rather than the communicative achievements of non-native speakers. A detailed analysis of the conversations under discussion, which were recorded by the participants themselves, showed that they all flowed smoothly, and this was in large measure due to the ways in which topic shifts were managed. The paper will focus on a very distinct type of topic shift, namely that of topic transitions, which enable a smooth flow from one topic to another, but which do not explicitly signal that a shift is taking place. It will examine how the non-native speakers achieved coherence in the topic transitions which they initiated, which strategies or procedures they employed, and show how their initiations were effective in enabling the proposed topic to be understood, taken up and developed. It therefore adds to our understanding of the interactional achievements of international speakers in informal, social contexts. © 2013 Elsevier B.V.

A proteo-liposome system for the analysis of the intracellular interactome of membrane proteins using amyloid precursor protein as a model

Transmembrane proteins play crucial roles in many important physiological processes. The intracellular domain of membrane proteins is key for their function by interacting with a wide variety of cytosolic proteins. It is therefore important to examine this interaction. A recently developed method to study these interactions, based on the use of liposomes as a model membrane, involves the covalent coupling of the cytoplasmic domains of membrane proteins to the liposome membrane. This allows for the analysis of interaction partners requiring both protein and membrane lipid binding. This thesis further establishes the liposome recruitment system and utilises it to examine the intracellular interactome of the amyloid precursor protein (APP), most well-known for its proteolytic cleavage that results in the production and accumulation of amyloid beta fragments, the main constituent of amyloid plaques in Alzheimer’s disease pathology. Despite this, the physiological function of APP remains largely unclear. Through the use of the proteo-liposome recruitment system two novel interactions of APP’s intracellular domain (AICD) are examined with a view to gaining a greater insight into APP’s physiological function. One of these novel interactions is between AICD and the mTOR complex, a serine/threonine protein kinase that integrates signals from nutrients and growth factors. The kinase domain of mTOR directly binds to AICD and the N-terminal amino acids of AICD are crucial for this interaction. The second novel interaction is between AICD and the endosomal PIKfyve complex, a lipid kinase involved in the production of phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) from phosphatidylinositol-3-phosphate, which has a role in controlling ensdosome dynamics. The scaffold protein Vac14 of the PIKfyve complex binds directly to AICD and the C-terminus of AICD is important for its interaction with the PIKfyve complex. Using a recently developed intracellular PI(3,5)P2 probe it is shown that APP controls the formation of PI(3,5)P2 positive vesicular structures and that the PIKfyve complex is involved in the trafficking and degradation of APP. Both of these novel APP interactors have important implications of both APP function and Alzheimer’s disease. The proteo-liposome recruitment method is further validated through its use to examine the recruitment and assembly of the AP-2/clathrin coat from purified components to two membrane proteins containing different sorting motifs. Taken together this thesis highlights the proteo-liposome recruitment system as a valuable tool for the study of membrane proteins intracellular interactome. It allows for the mimicking of the protein in its native configuration therefore identifying weaker interactions that are not detected by more conventional methods and also detecting interactions that are mediated by membrane phospholipids.

Native language identification (NLID) for forensic authorship analysis of weblogs

This chapter introduces Native Language Identification (NLID) and considers the casework applications with regard to authorship analysis of online material. It presents findings from research identifying which linguistic features were the best indicators of native (L1) Persian speakers blogging in English, and analyses how these features cope at distinguishing between native influences from languages that are linguistically and culturally related. The first chapter section outlines the area of Native Language Identification, and demonstrates its potential for application through a discussion of relevant case history. The next section discusses a development of methodology for identifying influence from L1 Persian in an anonymous blog author, and presents findings. The third part discusses the application of these features to casework situations as well as how the features identified can form an easily applicable model and demonstrates the application of this to casework. The research presented in this chapter can be considered a case study for the wider potential application of NLID.

Negotiating topic changes:native and non-native speakers of English in conversation

There is a tendency to view conversations involving non-native speakers (NNSs) as inevitably fraught with problems, including an inability to handle topic management. This article, in contrast, will focus on effective topic changes made by non-native speakers during informal conversations with native speakers of English. A micro-analysis of ten conversations revealed several ways of shifting conversational topics; however, the article concentrates on those strategies which the participants used to effect a particular type of topic move, namely 'marked topic changes', where there is no connection at all with previous talk. The findings show how these topic changes were jointly negotiated, and that the non-native speakers' contributions to initiating new topics were competently managed.

Participatory design with older adults for healthcare apps

The global population of people aged 60 years and older is growing rapidly [1]. Ongoing advances in mobile technologies have the potential to improve independence and quality of life of older adults by supporting the delivery of personalised and ubiquitous healthcare solutions. Suggested healthcare reforms reflect the need for a future model of healthcare delivery wherein older adults take more responsibility for their own healthcare in their own homes in an attempt to moderate healthcare costs without impairing healthcare quality. For such a paradigm shift to be realised, the supporting technology must address the needs of older patients efficiently and effectively to ensure technology acceptance and use. We argue this is not possible without employing participatory approaches for the informed and effective design and development of such technologies and outline recommendations for engaging in participatory design with older adults with impairments based on practical experience.

Action Plan to Conserve the Native Plants of Florida

In this document, a strategy aimed at conserving the native flora of Florida is presented. The strategy is developed in a four-step sequence. Following the Introduction (Part I), The Florida Native Plant Resource (Part II) describes the resource and the threats to it. That section includes a brief description of the vegetation of Florida prior to the demographic explosion of the last century, a report on the current status of plants in the state, and discussion of some factors responsible for the evident and continuing decline in the quality and quantity of the vegetation resource. In Part III (The Florida Plant Conservation Process), an explicit goal for plant conservation in Florida is expressed, a model describing the plant conservation process is presented, and activities included with each component of the model are examined and evaluated for the state as a whole. Finally, in Part IV (Recommendations To Improve The Process), changes are presented that we believe would help create a more effective plant conservation environment in Florida.

Wayside Trees of Tropical Florida : a guide to the native and exotic trees and palms of Miami and tropical south Florida

Wayside Trees is an beautifully illustrated guide to Florida trees growing south of Lake Okeechobee. It covers both native and exotic species in the areas of Miami to Palm Beach on the east coast, and Naples to Fort Meyers on the west. The introduction describes environmental, cultural and economic importance of trees, while a non-technical key provides a means for even non-specialists to identify the 167 most common species. The bulk of the book consists of illustrated descriptions of the trees, arranged by plant family, and includes ecological and cultural information on each species. Lavishly illustrated with over 1200 color photographs and diagrams, the book is designed to serve homeowners, gardeners, teachers and students, as well as environmental professionals. It is also a useful guide to urban tropical trees growing outside south Florida. The authors, a botanist and a graphic artist, have 70 collective years of experience living, working, and loving the trees of south Florida.