Single molecule imaging to characterize protein interactions with the environment

In the past decade, single molecule imaging has advanced our understanding of processes at the molecular scale. Total internal reflection fluorescence (TIRF) microscopy is one implementation in particular that has been extensively applied in the study of protein adsorption to surfaces. The spatial and temporal resolution provided by TIRF has enabled dynamic measurements of individual proteins in solution, where previously only bulk measurements or static electron microscopy observations were possible. The ability to study individual proteins has revealed and sometimes clarified the complex interactions at their interfaces. Here, the utility of TIRF is expanded to introduce a new model of protein adsorption to the suface and to study the protein interface in contact with solution. Protein adsorption to surfaces has implications in surface biocompatibility, protein separation, and pharmaceutical nanoparticle development. For this reason, the phenomenon has been quantitatively by a variety of techniques, including single molecule imaging. The key data are the protein lifetimes on the surface, which have been shown to be broadly distributed and well-approximated by the sum of several exponential functions. The determined desorption rate constants are thought to reflect different interaction types between surface and protein, but the rates are not typically linked to a specific physical interaction. In the first part of this thesis, we establish appropriate imaging conditions and analysis methods for TIRF. A robust survival analysis technique is applied to capture the range of protein adsorption kinetics. In the second part, we utilize single molecule lifetime data from the adsorption of fibrinogen and bovine serum albumin (BSA) to glass surfaces and discover a heavy-tailed distribution: a very small fraction of proteins adsorbs effectively permanently, while the majority of proteins adsorb for a very short time. We then demonstrate that this characteristic power law behavior is well described by a model with a novel interpretation of the complex protein adsorption process. The second half of the thesis extends TIRF to study the solution-facing interface of the protein as opposed to the surface facing interface by establishing the parameters for a super-resolution imaging technique. Point accumulation for imaging nanoscale topography (PAINT) generates high-resolution images of the sample of interest through the positional tracking of many temporally-distinct instances of a fluorescent probe binding to the sample. Previously, this technique has been applied in the mapping of DNA nanostructures. Here, in the third part, we apply PAINT to the study of proteins. First, a workstream is established for a model system of Nile red and BSA. The kinetic parameters for the system are established to allow rational design of PAINT experiments with this system. The on-rate and off-rate for Nile red are determined. Additionally, the binding model between the two components is tested by studying how the presence of an inhibitor effects the parameters. In the final part, TIRF is used to study the protein-solution interface to examine the glycosylation of immunoglobulin A 1 (IgA1). Over 50% of eukaryotic proteins are glycosylated, and the glycan sequence is simultaneously difficult to study and crucial in the many functional roles proteins play. The glycosylation of IgA1, for example, plays a key role in the pathophysiology of IgA1 nephropathy. Lectins are proteins that bind to specifc glycan sequences and are often used to isolate glycosylated proteins. In this study, the appropriate surface conditions are established to allow specific binding between lectins and IgA1 glycans. The association and dissociation rate between lectins specific for the glycans on IgA1 are measured and affinity constants calculated. These efforts will help to rationally design experiments in the future to elucidate unknown glycan sequences on proteins

Promoting Faculty Scholarship Through the University Author Recognition Bibliography at Boise State University

One of the most important contributions by any university is its faculty members\u27 scholarship. Providing an interface to view the full scope of an institution\u27s academic accomplishments is vital for promoting both the scholarship and the university at large. Because of their unique information skills and services, librarians can facilitate the discovery of this scholarship on behalf of their institutions. This article explores how Albertsons Library at Boise State University utilizes an institutional repository to produce a faculty publication bibliography. Processes for collecting academic scholarship and organizing the citations within a repository structure are also discussed. Library staff found that this approach not only reduced redundancy and increased the usability of researcher publication data, it also increased the profile and value of the institutional repository

The Revolution of University-Based Information

Traditionally, information and scholarship produced by universities has been disseminated by for-profits publishers who charge for access to this scholarship. This approach to sharing the output of our nation\u27s academic community has significantly limited access to that scholarship. Institutional repositories are revolutionizing how university-based information is made accessible to society as a whole. This presentation will explore how libraries are supporting access to academic scholarship, issues involved in providing the scholarship such as types of information, intellectual property, and quality control, and ways users can access, evaluate, and utilize university-based information

An evaluation of the impact of a burn camp on children and young people’s concerns about social situations, satisfaction with appearance and behaviour

Introduction: This evaluation aimed to assess the impact of a burn camp on children and young people’s concerns about social situations, satisfaction with appearance and behaviour.Methods: Young people completed the Perceived Stigmatisation Questionnaire (PSQ), Social Comfort Questionnaire (SCQ) and Satisfaction with Appearance Scale (SWAP) one month before camp (n=23), on the last day of camp (n=21) and at a three-month follow-up (n=13). Parents completed the Strengths and Difficulties Questionnaire (SDQ) one month before camp (n = 22) and at follow-up (n=12). Parents and young people also completed open-ended questions before camp and at the follow-up.Results: Results in this evaluation were mixed. While parents’ reported scores on the SDQ were poorer after camp, young people’s reported outcomes on all three measures improved at the end of camp. PSQ and SWAP scores were maintained and improved, respectively, at the follow-up. Qualitative responses were generally consistent with these scores. Significant improvements were found between the scores before camp and at the three-month follow-up for both the SWAP and PSQ. These results indicate that the burncamp may help to improve young people’s satisfaction with their appearance and concerns about social situations. However, there was no comparison group and there was a significant loss of participants atfollow-up.Conclusion: Burn camps may therefore offer a range of psychosocial benefits to young people with burn injuries. This was the first evaluation to demonstrate a positive impact of a burn camp on satisfaction with appearance and concerns about social situations using outcome measures validated with the burns population

An informal learning program as a replicable model for student-led, industry-supported experiential learning

This research paper details the growth of an informal experiential learning program around hackathons and makeathons and presents the evolution of the program as a model of a successful co-curricular approach in engineering education. After six years of growing an informal learning program from a single hackathon event of 100 attendees to a complete experiential learning platform (OHI/O) consisting of over twelve events, sustained industry engagement, scholarships, and building a successful and stable team of student leaders, the authors will share and gather feedback on the development and evolution of the program.Publisher does not allow open access until after publicatio

Good Statistical Practice-development of tailored Good Clinical Practice training for statisticians

BACKGROUND: Statisticians are fundamental in ensuring clinical research, including clinical trials, are conducted with quality, transparency, reproducibility and integrity. Good Clinical Practice (GCP) is an international quality standard for the conduct of clinical trials research. Statisticians are required to undertake training on GCP but existing training is generic and, crucially, does not cover statistical activities. This results in statisticians undertaking training mostly unrelated to their role and variation in awareness and implementation of relevant regulatory requirements with regards to statistical conduct. The need for role-relevant training is recognised by the UK NHS Health Research Authority and the Medicines and Healthcare products Regulatory Agency (MHRA).METHODS: The Good Statistical Practice (GCP for Statisticians) project was instigated by the UK Clinical Research Collaboration (UKCRC) Registered Clinical Trials Unit (CTU) Statisticians Operational Group and funded by the National Institute for Health and Care Research (NIHR), to develop materials to enable role-specific GCP training tailored to statisticians. Review of current GCP training was undertaken by survey. Development of training materials were based on MHRA GCP. Critical review and piloting was conducted with UKCRC CTU and NIHR researchers with comment from MHRA. Final review was conducted through the UKCRC CTU Statistics group.RESULTS: The survey confirmed the need and desire for the development of dedicated GCP training for statisticians. An accessible, comprehensive, piloted training package was developed tailored to statisticians working in clinical research, particularly the clinical trials arena. The training materials cover legislation and guidance for best practice across all clinical trial processes with statistical involvement, including exercises and real-life scenarios to bridge the gap between theory and practice. Comprehensive feedback was incorporated. The training materials are freely available for national and international adoption.CONCLUSION: All research staff should have training in GCP yet the training undertaken by most academic statisticians does not cover activities related to their role. The Good Statistical Practice (GCP for Statisticians) project has developed and extensively piloted new, role-specific, comprehensive, accessible GCP training tailored to statisticians working in clinical research, particularly the clinical trials arena. This role-specific training will encourage best practice, leading to transparent and reproducible statistical activity, as required by regulatory authorities and funders.</p

Smartphone accessibility: Understanding the lived experience of users with cervical spinal cord injuries

Purpose: To explore accessibility challenges encountered by smartphone users with cervical spinal cord injuries (C1-C8).To investigate the suitability of current technology and make recommendations to help future technology meet user needs. Methods: The study uses a mixed-method approach combining an inductive thematic analysis of nine semi-structured interviews with a quantitative analysis of thirty-nine questionnaires. Results: The analysis generated four themes: ’the drive for independence and self-efficacy’; ’trying to make it work’; ’getting the right technology for me’; ’using the phone as and when I want to’. These themes highlighted how unresolved access issues and situational barriers limited independence and created unwanted privacy compromises for effective communication. There was a lack of information or support on available smartphone accessibility features and assistive technology (AT). Smartphone AT was regarded as overpriced, poorly designed and lacking the voices of people with disabilities. Conclusions: The smartphone’s potential to improve quality of life, participation, and well-being is limited by accessibility challenges hindering independent and private smartphone use. Future design work should focus on improving accessibility, investigating reasons for AT’s poor quality and high cost, and removing barriers to end-user inclusion. To enhance user awareness of available technology, stakeholders should build and maintain an open platform to act as an information source for peer and professional support on assistive technology

Fostering a Tech Culture through Campus Collaborations: A Case Study of a Hackathon and Library Partnership

Hackathons are time-bound, competitive coding contests that are often judged for prizes. Their name originates from joining hacking, playful exploration of hardware and software issues, with marathons, endurance competitions. The intent is to challenge participants to build working prototypes of hardware or software in a short time period, anywhere from one day to several weeks, though typically between 24-28 hours. While they are a mainstay in computer science fields, they are becoming increasingly popular in other domains, including libraries. Libraries have long championed life-long learning, a democratization of data, and access to information. These are similar mentalities of the maker movement, echoed in hackathons. Rapid iteration, problem solving, and cooperative learning are regularly present at events and within library systems. This paper details a case study of one institution’s growth from a hackathon event host to deeper library engagement and partnership with an informal learning program. The authors will highlight benefits that both partners observed and will end with a pitch for why other libraries should consider hosting similar events. Finally, several recommended resources for libraries who are contemplating hosting hackathon events will be presented.Publisher allows immediate open acces

Range and extinction dynamics of the steppe bison in Siberia : A pattern-oriented modelling approach

Aim To determine the ecological processes and drivers of range collapse, population decline and eventual extinction of the steppe bison in Eurasia. Location Siberia. Time period Pleistocene and Holocene. Major taxa studied Steppe bison (Bison priscus). Methods We configured 110,000 spatially explicit population models (SEPMs) of climate-human-steppe bison interactions in Siberia, which we ran at generational time steps from 50,000 years before present. We used pattern-oriented modelling (POM) and fossil-based inferences of distribution and demographic change of steppe bison to identify which SEPMs adequately simulated important interactions between ecological processes and biological threats. These "best models" were then used to disentangle the mechanisms that were integral in the population decline and later extinction of the steppe bison in its last stronghold in Eurasia. Results Our continuous reconstructions of the range and extinction dynamics of steppe bison were able to reconcile inferences of spatio-temporal occurrence and the timing and location of extinction in Siberia based on hundreds of radiocarbon-dated steppe bison fossils. We showed that simulating the ecological pathway to extinction for steppe bison in Siberia in the early Holocene required very specific ecological niche constraints, demographic processes and a constrained synergy of climate and human hunting dynamics during the Pleistocene-Holocene transition. Main conclusions Ecological processes and drivers that caused ancient population declines of species can be reconstructed at high spatio-temporal resolutions using SEPMs and POM. Using this approach, we found that climatic change and hunting by humans are likely to have interacted with key ecological processes to cause the extinction of the steppe bison in its last refuge in Eurasia.Peer reviewe