Alanine-scanning mutagenesis of Aspergillus γ-tubulin yields diverse and novel phenotypes

This is the publisher's version, also available electronically from "www.molbiolcell.org".We have created 41 clustered charged-to-alanine scanning mutations of the mipA, γ-tubulin, gene of Aspergillus nidulans and have created strains carrying these mutations by two-step gene replacement and by a new procedure, heterokaryon gene replacement. Most mutant alleles confer a wild-type phenotype, but others are lethal or conditionally lethal. The conditionally lethal alleles exhibit a variety of phenotypes under restrictive conditions. Most have robust but highly abnormal mitotic spindles and some have abnormal cytoplasmic microtubule arrays. Two alleles appear to have reduced amounts of γ-tubulin at the spindle pole bodies and nucleation of spindle microtubule assembly may be partially inhibited. One allele inhibits germ tube formation. The cold sensitivity of two alleles is strongly suppressed by the antimicrotubule agents benomyl and nocodazole and a third allele is essentially dependent on these compounds for growth. Together our data indicate that γ-tubulin probably carries out functions essential to mitosis and organization of cytoplasmic microtubules in addition to its well-documented role in microtubule nucleation. We have also placed our mutations on a model of the structure of γ-tubulin and these data give a good initial indication of the functionally important regions of the molecule

Visualizing energy landscapes with metric disconnectivity graphs

The visualization of multidimensional energy landscapes is important, providing insight into the kinetics and thermodynamics of a system, as well the range of structures a system can adopt. It is, however, highly nontrivial, with the number of dimensions required for a faithful reproduction of the landscape far higher than can be represented in two or three dimensions. Metric disconnectivity graphs provide a possible solution, incorporating the landscape connectivity information present in disconnectivity graphs with structural information in the form of a metric. In this study, we present a new software package, PyConnect, which is capable of producing both disconnectivity graphs and metric disconnectivity graphs in two or three dimensions. We present as a test case the analysis of the 69-bead BLN coarse-grained model protein and show that, by choosing appropriate order parameters, metric disconnectivity graphs can resolve correlations between structural features on the energy landscape with the landscapes energetic and kinetic properties

Antigen depot is not required for alum adjuvanticity

Alum adjuvants have been in continuous clinical use for more than 80 yr. While the prevailing theory has been that depot formation and the associated slow release of antigen and/or inflammation are responsible for alum enhancement of antigen presentation and subsequent T- and B-cell responses, this has never been formally proven. To examine antigen persistence, we used the chimeric fluorescent protein EαGFP, which allows assessment of antigen presentation in situ, using the Y-Ae antibody. We demonstrate that alum and/or CpG adjuvants induced similar uptake of antigen, and in all cases, GFP signal did not persist beyond 24 h in draining lymph node antigen-presenting cells. Antigen presentation was first detectable on B cells within 6–12 h of antigen administration, followed by conventional dendritic cells (DCs) at 12–24 h, then finally plasmacytoid DCs at 48 h or later. Again, alum and/or CpG adjuvants did not have an effect on the magnitude or sequence of this response; furthermore, they induced similar antigen-specific T-cell activation in vivo. Notably, removal of the injection site and associated alum depot, as early as 2 h after administration, had no appreciable effect on antigen-specific T- and B-cell responses. This study clearly rules out a role for depot formation in alum adjuvant activity

Interventions to reduce the risk of surgically transmitted Creutzfeldt–Jakob disease: a cost-effective modelling review

Background Creutzfeldt–Jakob disease is a fatal neurological disease caused by abnormal infectious proteins called prions. Prions that are present on surgical instruments cannot be completely deactivated; therefore, patients who are subsequently operated on using these instruments may become infected. This can result in surgically transmitted Creutzfeldt–Jakob disease. Objective To update literature reviews, consultation with experts and economic modelling published in 2006, and to provide the cost-effectiveness of strategies to reduce the risk of surgically transmitted Creutzfeldt–Jakob disease. Methods Eight systematic reviews were undertaken for clinical parameters. One review of cost-effectiveness was undertaken. Electronic databases including MEDLINE and EMBASE were searched from 2005 to 2017. Expert elicitation sessions were undertaken. An advisory committee, convened by the National Institute for Health and Care Excellence to produce guidance, provided an additional source of information. A mathematical model was updated focusing on brain and posterior eye surgery and neuroendoscopy. The model simulated both patients and instrument sets. Assuming that there were potentially 15 cases of surgically transmitted Creutzfeldt–Jakob disease between 2005 and 2018, approximate Bayesian computation was used to obtain samples from the posterior distribution of the model parameters to generate results. Heuristics were used to improve computational efficiency. The modelling conformed to the National Institute for Health and Care Excellence reference case. The strategies evaluated included neither keeping instruments moist nor prohibiting set migration; ensuring that instruments were kept moist; prohibiting instrument migration between sets; and employing single-use instruments. Threshold analyses were undertaken to establish prices at which single-use sets or completely effective decontamination solutions would be cost-effective. Results A total of 169 papers were identified for the clinical review. The evidence from published literature was not deemed sufficiently strong to take precedence over the distributions obtained from expert elicitation. Forty-eight papers were identified in the review of cost-effectiveness. The previous modelling structure was revised to add the possibility of misclassifying surgically transmitted Creutzfeldt–Jakob disease as another neurodegenerative disease, and assuming that all patients were susceptible to infection. Keeping instruments moist was estimated to reduce the risk of surgically transmitted Creutzfeldt–Jakob disease cases and associated costs. Based on probabilistic sensitivity analyses, keeping instruments moist was estimated to on average result in 2.36 (range 0–47) surgically transmitted Creutzfeldt–Jakob disease cases (across England) caused by infection occurring between 2019 and 2023. Prohibiting set migration or employing single-use instruments reduced the estimated risk of surgically transmitted Creutzfeldt–Jakob disease cases further, but at considerable cost. The estimated costs per quality-adjusted life-year gained of these strategies in addition to keeping instruments moist were in excess of £1M. It was estimated that single-use instrument sets (currently £350–500) or completely effective cleaning solutions would need to cost approximately £12 per patient to be cost-effective using a £30,000 per quality-adjusted life-year gained value. Limitations As no direct published evidence to implicate surgery as a cause of Creutzfeldt–Jakob disease has been found since 2005, the estimations of potential cases from elicitation are still speculative. A particular source of uncertainty was in the number of potential surgically transmitted Creutzfeldt–Jakob disease cases that may have occurred between 2005 and 2018. Conclusions Keeping instruments moist is estimated to reduce the risk of surgically transmitted Creutzfeldt–Jakob disease cases and associated costs. Further surgical management strategies can reduce the risks of surgically transmitted Creutzfeldt–Jakob disease but have considerable associated costs. Study registration This study is registered as PROSPERO CRD42017071807. Funding This project was funded by the National Institute for Health Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 24, No. 11. See the NIHR Journals Library website for further project information

Revisiting Qualitative Data Reuse

Secondary analysis of qualitative data entails reusing data created from previous research projects for new purposes. Reuse provides an opportunity to study the raw materials of past research projects to gain methodological and substantive insights. In the past decade, use of the approach has grown rapidly in the United Kingdom to become sufficiently accepted that it must now be regarded as mainstream. Several factors explain this growth: the open data movement, research funders’ and publishers’ policies supporting data sharing, and researchers seeing benefits from sharing resources, including data. Another factor enabling qualitative data reuse has been improved services and infrastructure that facilitate access to thousands of data collections. The UK Data Service is an example of a well-established facility; more recent has been the proliferation of repositories being established within universities. This article will provide evidence of the growth of data reuse in the United Kingdom and in Finland by presenting both data and case studies of reuse that illustrate the breadth and diversity of this maturing research method. We use two distinct data sources that quantify the scale, types, and trends of reuse of qualitative data: (a) downloads of archived data collections held at data repositories and (b) publication citations. Although the focus of this article is on the United Kingdom, some discussion of the international environment is provided, together with data and examples of reuse at the Finnish Social Science Data Archive. The conclusion summarizes the major findings, including some conjectures regarding what makes qualitative data attractive for reuse and sharing. </jats:p

Hyperinnervation Produces Inhibitory Interactions between Two Taste Nerves a

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74872/1/j.1749-6632.1987.tb43629.x.pd

Hunting for answers: Linking lectures with the real world using a mobile treasure hunt app

Plants underpin our society providing food, fuel, medicines, clean air and water, positive mental health, and are central to biodiversity conservation. Despite this importance and an increasing need for people with plant-identification skills, many societies are becoming increasingly ignorant to the species with which they interact. To benefit both our undergraduates and the society they will enter, we applied mobile technology to improve plant identification and appreciation , while providing opportunities to practice transferable team work and verbal communication skills. Encouraging 'plant vision' will improve conservation efforts while increasing personal connections with green spaces, leading to mental health improvements for society. Summary • Despite the importance of plants to human civilization, many societies are becoming increasingly ignorant to the plants that inhabit their surrounding environment. A phenomenon known as 'plant blindness'. To address plant blindness in undergraduate students we designed an outdoor activity using a mobile phone app. Our aims were to identify the level of 'plant blindness' in our students; investigate engagement with the app and activity ; determine if we can raise awareness of links between lecture content and real world scenarios; and assess the student experience as a result of the activity in large classes. • The app chosen was ActionBound. Students were asked to find and photograph local examples of four plant families, along with identifying physiological benefits of features covered in lectures. Two different first year classes were exposed to this activity-Plant Science and Life on Earth. • The Plant Science students (60% success rate for three families; 55 students) were less plant blind than Life on Earth students (less than 44% success rate in any of the four families; 200 students). Students engaged well with the activity with all groups submitting sensible attempts at the responses. Most students reported that the activity increased links to lecture material and all but one student reported positive experiences. • Our students found the treasure hunt learning environment is a fun way to engage with the plant topics covered in lectures. In future iterations, we will more explicitly explain the links to potential careers and will address some of the logistical challenges faced in this first cohort. K E Y W O R D S collaborative learning, fun learning, inclusivity, large classes, mobile learning, plant blindness, situational learning, treasure hun

Ethical issues in the use of in-depth interviews: literature review and discussion

This paper reports a literature review on the topic of ethical issues in in-depth interviews. The review returned three types of article: general discussion, issues in particular studies, and studies of interview-based research ethics. Whilst many of the issues discussed in these articles are generic to research ethics, such as confidentiality, they often had particular manifestations in this type of research. For example, privacy was a significant problem as interviews sometimes probe unexpected areas. For similar reasons, it is difficult to give full information of the nature of a particular interview at the outset, hence informed consent is problematic. Where a pair is interviewed (such as carer and cared-for) there are major difficulties in maintaining confidentiality and protecting privacy. The potential for interviews to harm participants emotionally is noted in some papers, although this is often set against potential therapeutic benefit. As well as these generic issues, there are some ethical issues fairly specific to in-depth interviews. The problem of dual role is noted in many papers. It can take many forms: an interviewer might be nurse and researcher, scientist and counsellor, or reporter and evangelist. There are other specific issues such as taking sides in an interview, and protecting vulnerable groups. Little specific study of the ethics of in-depth interviews has taken place. However, that which has shows some important findings. For example, one study shows participants are not averse to discussing painful issues provided they feel the study is worthwhile. Some papers make recommendations for researchers. One such is that they should consider using a model of continuous (or process) consent rather than viewing consent as occurring once, at signature, prior to the interview. However, there is a need for further study of this area, both philosophical and empirical

The Autism Spectrum Disorder Evaluative Education Model: a school-based method of assessing and selecting interventions for classroom use

Evaluating educational programs and interventions is generally considered a normal part of curriculum development and improvement, and published findings are readily accessible through peer-reviewed journals. Recently, however, researchers and practicing educators have identified a lack of evaluative research regarding Autism Spectrum Disorder (ASD) educational practices in the peer-reviewed literature. Autism Spectrum Australia (Aspect) has an established evidence-informed ASD curriculum that is constantly reviewed and updated to meet the needs of the students in Aspect schools and classes. Through a methodical evaluative process, all educational interventions and support processes and devices undergo a series of Evidence-Based Research Trials and evaluations before they are implemented in classes. This article demonstrates how a workflow model can deliver a systematic method for identifying, evaluating, implementing, and disseminating the research findings of a program or support intervention. The Autism Spectrum Disorder Evaluative Education (ASDEE) model is discussed