Molecular dynamics simulations:bring biomolecular structures alive on a computer

The molecular dynamics (MD) simulations play a very important role in science today. They have been used successfully in binding free-energy calculations and rational design of drugs and vaccines. MD simulations can help visualize and understand structures and dynamics at an atomistic level when combined with molecular graphics programs. The molecular and atomistic properties can be displayed on a computer in a time-dependent way, which opens a road toward a better understanding of the relationship of structure, dynamics, and function. In this chapter, the basics of MD are explained, together with a step-by-step description of setup and running an MD simulation.

Metallocene ethylene-1-octene copolymers:influence of comonomer content on thermo-mechanical, rheological, and thermo-oxidative behaviours before and after melt processing in an internal mixer

The influence of the comonomer content in a series of metallocene-based ethylene-1-octene copolymers (m-LLDPE) on thermo-mechanical, rheological, and thermo-oxidative behaviours during melt processing were examined using a range of characterisation techniques. The amount of branching was calculated from 13C NMR and studies using differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA) were employed to determine the effect of short chain branching (SCB, comonomer content) on thermal and mechanical characteristics of the polymer. The effect of melt processing at different temperatures on the thermo-oxidative behaviour of the polymers was investigated by examining the changes in rheological properties, using both melt flow and capillary rheometry, and the evolution of oxidation products during processing using infrared spectroscopy. The results show that the comonomer content and catalyst type greatly affect thermal, mechanical and oxidative behaviour of the polymers. For the metallocene polymer series, it was shown from both DSC and DMA that (i) crystallinity and melting temperatures decreased linearly with comonomer content, (ii) the intensity of the ß-transition increased, and (iii) the position of the tan δmax peak corresponding to the a-transition shifted to lower temperatures, with higher comonomer content. In contrast, a corresponding Ziegler polymer containing the same level of SCB as in one of the m-LLDPE polymers, showed different characteristics due to its more heterogeneous nature: higher elongational viscosity, and a double melting peak with broader intensity that occurred at higher temperature (from DSC endotherm) indicating a much broader short chain branch distribution. The thermo-oxidative behaviour of the polymers after melt processing was similarly influenced by the comonomer content. Rheological characteristics and changes in concentrations of carbonyl and the different unsaturated groups, particularly vinyl, vinylidene and trans-vinylene, during processing of m-LLDPE polymers, showed that polymers with lower levels of SCB gave rise to predominantly crosslinking reactions at all processing temperatures. By contrast, chain scission reactions at higher processing temperatures became more favoured in the higher comonomer-containing polymers. Compared to its metallocene analogue, the Ziegler polymer showed a much higher degree of crosslinking at all temperatures because of the high levels of vinyl unsaturation initially present.

Late development of metric part-relational processing in object recognition

Four experiments with unfamiliar objects examined the remarkably late consolidation of part-relational relative to part-based object recognition (Jüttner, Wakui, Petters, Kaur, & Davidoff, 2013). Our results indicate a particularly protracted developmental trajectory for the processing of metric part relations. Schoolchildren aged 7 to 14 years and adults were tested in 3-Alternative-Forced-Choice tasks to judge the correct appearance of upright and inverted newly learned multipart objects that had been manipulated in terms of individual parts or part relations. Experiment 1 showed that even the youngest tested children were close to adult levels of performance for recognizing categorical changes of individual parts and relative part position. By contrast, Experiment 2 demonstrated that performance for detecting metric changes of relative part position was distinctly reduced in young children compared with recognizing metric changes of individual parts, and did not approach the latter until 11 to 12 years. A similar developmental dissociation was observed in Experiment 3, which contrasted the detection of metric relative-size changes and metric part changes. Experiment 4 showed that manipulations of metric size that were perceived as part (rather than part-relational) changes eliminated this dissociation. Implications for theories of object recognition and similarities to the development of face perception are discussed. © 2014 American Psychological Association.

Ultra-endurance exercise:unanswered questions in redox biology and immunology

Ultra-endurance races are extreme exercise events that can take place over large parts of a day, several consecutive days or over weeks and months interspersed by periods of rest and recovery. Since the first ultraendurance races in the late 1970s, around 1000 races are now held worldwide each year, and more than 100000 people take part. Although these athletes appear to be fit and healthy, there have been occasional reports of severe complications following ultra-endurance exercise. Thus there is concern that repeated extreme exercise events could have deleterious effects on health, which might be brought about by the high levels of ROS (reactive oxygen species) produced during exercise. Studies that have examined biomarkers of oxidative damage following ultra-endurance exercise have found measurements to be elevated for several days, which has usually been interpreted to reflect increased ROS production. Levels of the antioxidant molecule GSH (reduced glutathione) are depleted for 1 month or longer following ultra-endurance exercise, suggesting an impaired capacity to copewith ROS. The present paper summarizes studies that have examined the oxidative footprint of ultra-endurance exercise in light of current thinking in redox biology and the possible health implications of such extreme exercise. © The Authors Journal compilation © 2014 Biochemical Society.

Immunoinformatics:predicting immunogenicity in silico

This volume both engages the reader and provides a sound foundation for the use of immunoinformatics techniques in immunology and vaccinology. It addresses databases, HLA supertypes, MCH binding, and other properties of immune systems. The book contains chapters written by leaders in the field and provides a firm background for anyone working in immunoinformatics in one easy-to-use, insightful volume.

The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review)

Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.

Optimising yeast as a host for recombinant protein production (review)

Having access to suitably stable, functional recombinant protein samples underpins diverse academic and industrial research efforts to understand the workings of the cell in health and disease. Synthesising a protein in recombinant host cells typically allows the isolation of the pure protein in quantities much higher than those found in the protein's native source. Yeast is a popular host as it is a eukaryote with similar synthetic machinery to the native human source cells of many proteins of interest, while also being quick, easy, and cheap to grow and process. Even in these cells the production of some proteins can be plagued by low functional yields. We have identified molecular mechanisms and culture parameters underpinning high yields and have consolidated our findings to engineer improved yeast cell factories. In this chapter, we provide an overview of the opportunities available to improve yeast as a host system for recombinant protein production.

New business histories! Plurality in business history research methods

We agree with de Jong et al.'s argument that business historians should make their methods more explicit and welcome a more general debate about the most appropriate methods for business historical research. But rather than advocating one ‘new business history’, we argue that contemporary debates about methodology in business history need greater appreciation for the diversity of approaches that have developed in the last decade. And while the hypothesis-testing framework prevalent in the mainstream social sciences favoured by de Jong et al. should have its place among these methodologies, we identify a number of additional streams of research that can legitimately claim to have contributed novel methodological insights by broadening the range of interpretative and qualitative approaches to business history. Thus, we reject privileging a single method, whatever it may be, and argue instead in favour of recognising the plurality of methods being developed and used by business historians – both within their own field and as a basis for interactions with others.

The roles of family history of dyslexia, language, speech production and phonological processing in predicting literacy progress

It is well established that speech, language and phonological skills are closely associated with literacy, and that children with a family risk of dyslexia (FRD) tend to show deficits in each of these areas in the preschool years. This paper examines what the relationships are between FRD and these skills, and whether deficits in speech, language and phonological processing fully account for the increased risk of dyslexia in children with FRD. One hundred and fifty-three 4-6-year-old children, 44 of whom had FRD, completed a battery of speech, language, phonology and literacy tasks. Word reading and spelling were retested 6 months later, and text reading accuracy and reading comprehension were tested 3 years later. The children with FRD were at increased risk of developing difficulties in reading accuracy, but not reading comprehension. Four groups were compared: good and poor readers with and without FRD. In most cases good readers outperformed poor readers regardless of family history, but there was an effect of family history on naming and nonword repetition regardless of literacy outcome, suggesting a role for speech production skills as an endophenotype of dyslexia. Phonological processing predicted spelling, while language predicted text reading accuracy and comprehension. FRD was a significant additional predictor of reading and spelling after controlling for speech production, language and phonological processing, suggesting that children with FRD show additional difficulties in literacy that cannot be fully explained in terms of their language and phonological skills. It is well established that speech, language and phonological skills are closely associated with literacy, and that children with a family risk of dyslexia (FRD) tend to show deficits in each of these areas in the preschool years. This paper examines what the relationships are between FRD and these skills, and whether deficits in speech, language and phonological processing fully account for the increased risk of dyslexia in children with FRD. One hundred and fifty-three 4-6-year-old children, 44 of whom had FRD, completed a battery of speech, language, phonology and literacy tasks. © 2014 John Wiley & Sons Ltd.

Event trigger identification for biomedical events extraction using domain knowledge

Motivation: In molecular biology, molecular events describe observable alterations of biomolecules, such as binding of proteins or RNA production. These events might be responsible for drug reactions or development of certain diseases. As such, biomedical event extraction, the process of automatically detecting description of molecular interactions in research articles, attracted substantial research interest recently. Event trigger identification, detecting the words describing the event types, is a crucial and prerequisite step in the pipeline process of biomedical event extraction. Taking the event types as classes, event trigger identification can be viewed as a classification task. For each word in a sentence, a trained classifier predicts whether the word corresponds to an event type and which event type based on the context features. Therefore, a well-designed feature set with a good level of discrimination and generalization is crucial for the performance of event trigger identification. Results: In this article, we propose a novel framework for event trigger identification. In particular, we learn biomedical domain knowledge from a large text corpus built from Medline and embed it into word features using neural language modeling. The embedded features are then combined with the syntactic and semantic context features using the multiple kernel learning method. The combined feature set is used for training the event trigger classifier. Experimental results on the golden standard corpus show that >2.5% improvement on F-score is achieved by the proposed framework when compared with the state-of-the-art approach, demonstrating the effectiveness of the proposed framework. © 2014 The Author 2014. The source code for the proposed framework is freely available and can be downloaded at http://cse.seu.edu.cn/people/zhoudeyu/ETI_Sourcecode.zip.

Premonitory urges and sensorimotor processing in Tourette syndrome

Most patients with Tourette syndrome report characteristic sensory experiences (premonitory urges) associated with the expression of tic symptoms. Despite the central role of these experiences to the clinical phenomenology of Tourette syndrome, little is known about their underlying brain processes. In the present article we present the results of a systematic literature review of the published studies addressing the pathophysiological mechanisms of premonitory urges. We identified some preliminary evidence for specific alterations in sensorimotor processing at both cortical and subcortical levels. A better insight into the brain correlates of premonitory urges could lead to the identification of new targets to treat the sensory initiators of tics in patients with Tourette syndrome. © 2013 - IOS Press and the authors. All rights reserved.

Short cycle times for cost-efficient processing in lyophilized formulations

Pharmaceutical scientists who bulk freeze dry need to foremost identify what quality factors are of a priority during cycle development since the economics of freeze-drying do not allow for both the cost-efficient production and the ability to obtain the highest quality score across all quality factors. Consider; morphology, activity, dissolution, long-term storage, packaging and cost.

The relationship between spoken language and speech and nonspeech processing in children with autism:a magnetic event-related field study

It has been proposed that language impairments in children with Autism Spectrum Disorders (ASD) stem from atypical neural processing of speech and/or nonspeech sounds. However, the strength of this proposal is compromised by the unreliable outcomes of previous studies of speech and nonspeech processing in ASD. The aim of this study was to determine whether there was an association between poor spoken language and atypical event-related field (ERF) responses to speech and nonspeech sounds in children with ASD (n = 14) and controls (n = 18). Data from this developmental population (ages 6-14) were analysed using a novel combination of methods to maximize the reliability of our findings while taking into consideration the heterogeneity of the ASD population. The results showed that poor spoken language scores were associated with atypical left hemisphere brain responses (200 to 400 ms) to both speech and nonspeech in the ASD group. These data support the idea that some children with ASD may have an immature auditory cortex that affects their ability to process both speech and nonspeech sounds. Their poor speech processing may impair their ability to process the speech of other people, and hence reduce their ability to learn the phonology, syntax, and semantics of their native language.

Membrane protein production in the Yeast, S. cerevisiae

The first crystal structures of recombinant mammalian membrane proteins were solved in 2005 using protein that had been produced in yeast cells. One of these, the rabbit Ca2+-ATPase SERCA1a, was synthesized in Saccharomyces cerevisiae. All host systems have their specific advantages and disadvantages, but yeast has remained a consistently popular choice in the eukaryotic membrane protein field because it is quick, easy and cheap to culture, whilst being able to post-translationally process eukaryotic membrane proteins. Very recent structures of recombinant membrane proteins produced in S. cerevisiae include those of the Arabidopsis thaliana NRT1.1 nitrate transporter and the fungal plant pathogen lipid scramblase, TMEM16. This chapter provides an overview of the methodological approaches underpinning these successes.