Molecular aspects of biomolecule structure and function

All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity

The SHU Social Media CoLab: developing a social media strategy through open dialogue and collaborative guidance

This paper shares the strategy we have developed at Sheffield Hallam University (SHU) to educate and guide staff and students in their use of social media. Students need to understand their responsibilities to themselves and the institution, to develop sustainable strategies for using social media to enhance their learning and to develop their employability skills as future graduates. They need to place value in the development of a professional online presence, appreciate the difference between their personal and professional uses of social media tools, and understand the impact that one can have on the other. Staff want to feel confident in the application of authentic social media learning activities. They need to see the value of social media competence in graduates within their disciplines, and easily access shared practice and guidance. To facilitate such learning activities they also need to understand and consider aspects such as online safety, professional impact and configuration. We discuss how we developed and are now implementing our strategy; how this features a strong emphasis on collaborative relationships across different areas of the institution; and our recognition that social media guidance is not the sole domain of any one team. It also considers the importance of digital literacy skills, and that care is needed in the management of sometimes conflicting priorities. We will show how our work is informed by the needs and priorities of our staff and students in order to be fit for purpose. Our initial findings showed that we must address the constantly evolving nature of social media, and not consider guidance that we develop to be finite - there will always be more to do. In addition, we must acknowledge the significant overlap between personal and professional use of tools, since one might easily have implications for the other (positively or negatively), and people often draw on experiences for different contexts, or allow their future practice to be dictated by them. We will include how we have engaged staff and students to revisit their digital literacy skill set and develop new ways to connect, communicate, collaborate, create and curate. The enablers to achieve these outcomes include a rich collection of resources using different media, the development of a 'Social Media CoLab' and communities of practice exploring, using and evaluating their use of social media; and the support of the university to embed the use of these and other technologies to enhance the learning experience

Experiences of social media in higher education: barriers, enablers and next steps.

There are many examples of social media being used in higher education to enhance learning and teaching. While some academics are confident in exploring multiple strands of social media and blend them instinctively for a multi-dimensional learning experience; others are more tentative, preferring to understand the nature of the tool or process thoroughly, often by learning from others before embarking on a social media based activity (Beckingham, Purvis and Rodger 2014). However there are a broad range of factors, experiences and perceptions that may influence an individual and their resulting use of, and expectations of, social media as a learning construct. The aim of the study was to examine current institutional practice in the use of social media in this context, to inform strategic direction and consider implications for future academic development in order to achieve a positive impact on the learning experience for students. Fifty individuals responded to an online survey. While the majority of these (n=35) were already using social media in some way in their teaching practice, and mostly had positive attitudes towards it, the remainder had not. Some were open to the idea, though naturally cautious, while others were clear that it had no place in their teaching practice. This rich picture revealed a variety of barriers and enablers: where confidence was high and support available; uptake of social media as a tool for learning was more prevalent and more successful. There was a strong connection between support (formal and informal) and individual confidence, and a subsequent willingness to try new things to enhance learning. Recent research advocates the development of digital capabilities including the confident use of social media for communication and collaboration (Beetham 2015); and that where embedded, its use provides essential skills for future graduates. It is therefore timely to review the skill sets and development needs of staff in order to support the learning of students

Protein fiber linear dichroism for structure determination and kinetics in a low-volume, low-wavelength couette flow cell

High-resolution structure determination of soluble globular proteins relies heavily on x-ray crystallography techniques. Such an approach is often ineffective for investigations into the structure of fibrous proteins as these proteins generally do not crystallize. Thus investigations into fibrous protein structure have relied on less direct methods such as x-ray fiber diffraction and circular dichroism. Ultraviolet linear dichroism has the potential to provide additional information on the structure of such biomolecular systems. However, existing systems are not optimized for the requirements of fibrous proteins. We have designed and built a low-volume (200 μL), low-wavelength (down to 180 nm), low-pathlength (100 μm), high-alignment flow-alignment system (couette) to perform ultraviolet linear dichroism studies on the fibers formed by a range of biomolecules. The apparatus has been tested using a number of proteins for which longer wavelength linear dichroism spectra had already been measured. The new couette cell has also been used to obtain data on two medically important protein fibers, the all-β-sheet amyloid fibers of the Alzheimer's derived protein Aβ and the long-chain assemblies of α1-antitrypsin polymers

Protein secondary structure prediction from circular dichroism spectra using a self-organizing map with concentration correction

Collecting circular dichroism (CD) spectra for protein solutions is a simple experiment, yet reliable extraction of secondary structure content is dependent on knowledge of the concentration of the protein—which is not always available with accuracy. We previously developed a self-organizing map (SOM), called Secondary Structure Neural Network (SSNN), to cluster a database of CD spectra and use that map to assign the secondary structure content of new proteins from CD spectra. The performance of SSNN is at least as good as other available protein CD structure-fitting algorithms. In this work we apply SSNN to a collection of spectra of experimental samples where there was suspicion that the nominal protein concentration was incorrect. We show that by plotting the normalized root mean square deviation of the SSNN predicted spectrum from the experimental one versus a concentration scaling-factor it is possible to improve the estimate of the protein concentration while providing an estimate of the secondary structure. For our implementation (51 data points 240–190 nm in nm increments) good fits and structure estimates were obtained if the NRMSD (normalized root mean square displacement, RMSE/data range) is <0.03; reasonable for NRMSD <0.05; and variable above this. We also augmented the reference database with 100% helical spectra and truly random coil spectra

SSNN, a method for neural network protein secondary structure fitting using circular dichroism data

Circular dichroism (CD) spectroscopy is a quick method for measuring data that can be used to determine the average secondary structures of proteins, probe their interactions with their environment, and aid in drug discovery. This paper describes the operation and testing of a self-organising map (SOM) structure-fitting methodology named Secondary Structure Neural Network (SSNN), which is a methodology for estimating protein secondary structure from CD spectra of unknown proteins using CD spectra of proteins with known X-ray structures. SSNN comes in two standalone MATLAB applications for estimating unknown proteins' structures, one that uses a pre-trained map and one that begins by training the SOM with a reference set of the user's choice. These are available at http://www2.warwick.ac.uk/fac/sci/chemistry/research/arodger/arodgergroup/research_intro/instrumentation/ssnn/ as SSNNGUI and SSNN1_2 respectively. They are available for both Macintosh and Windows formats with two reference sets: one obtained from the CDPro website, referred to as CDDATA.48 which has 48 protein spectra and structures, and one with 53 proteins (CDDATA.48 with 5 additional spectra). Here we compare SSNN with CDSSTR, a widely-used secondary structure methodology, and describe how to use the standalone SSNN applications. Current input format is Δε per amino acid residue from 240 nm to 190 nm in 1 nm steps for the known and unknown proteins and a vector summarising the secondary structure elements of the known proteins. The format is readily modified to include input data with e.g. extended wavelength ranges or different assignment of secondary structures

Synthetic metallomolecules as agents for the control of DNA structure

This tutorial review summarises B-DNA structure and metallomolecule binding modes and illustrates some DNA structures induced by molecules containing metallic cations. The effects of aquated metal ions, cobalt amines, ruthenium octahedral metal complexes, metallohelicates and platinum complexes such as cis-platin are discussed alongside the techniques of NMR, X-ray crystallography, gel electrophoresis, circular dichroism, linear dichroism and molecular dynamics. The review will be of interest to people interested in both DNA structure and roles of metallomolecules in biological systems

The long term outcomes of community acquired hepatitis C infection in a cohort with sera stored from 1971-1975

Aim: To examine the long term outcomes of hepatitis C virus (HCV) infection in a cohort of patients admitted with acute viral hepatitis between 1971 and 1975. The availability of stored sera enabled testing to identify anti-HCV positive subjects. Methods: A retrospective cohort study design was chosen. The exposure of interest was the presence of anti-HCV in stored sera. Systematic approaches were used to locate the cohort and outcomes assessed with the SF-36 questionnaire, a study specific questionnaire and by clinical, serological, virological and biochemical assessment. Results: Sixteen percent (n=238) of the cohort tested anti-HCV positive and formed the exposed group. The unexposed group (n=476) was randomly selected from those who were anti-HCV negative. Complete follow up was achieved on 98 anti- HCV positive individuals and 202 negatives. At 25 years follow-up, 54% of the anti-HCV positive group had evidence of chionic HCV infection (both anti-HCV and HCV RNA positive). Of those chronically infected 69% had elevated serum ALT levels, but only 8% had progressed to overt chronically and no cases of HCC were identified. Anti-HCV positive subjects were 4 times more likely to have died from suicide or drug overdose than from HCV related disease. Quality of life measures were significantly reduced in the exposed group and significantly worse for anti-HCV positive individuals aware of their serostatus, compared to those unaware. Discussion: The reduced quality of life in those aware of their HCV diagnosis may be partially an effect of 'labelling'. Anti-HCV positive study subjects were at increased risk of liver related pathology after 25 years follow up, but few had progressed to overt cirrhotic liver disease- Excess mortality in the anti-HCV positive group was not due to liver disease. This suggests that the natural history of community acquired HCV may be more benign than previously thought