Asymmetric Genome Organization in an RNA Virus Revealed via Graph-Theoretical Analysis of Tomographic Data

Cryo-electron microscopy permits 3-D structures of viral pathogens to be determined in remarkable detail. In particular, the protein containers encapsulating viral genomes have been determined to high resolution using symmetry averaging techniques that exploit the icosahedral architecture seen in many viruses. By contrast, structure determination of asymmetric components remains a challenge, and novel analysis methods are required to reveal such features and characterize their functional roles during infection. Motivated by the important, cooperative roles of viral genomes in the assembly of single-stranded RNA viruses, we have developed a new analysis method that reveals the asymmetric structural organization of viral genomes in proximity to the capsid in such viruses. The method uses geometric constraints on genome organization, formulated based on knowledge of icosahedrally-averaged reconstructions and the roles of the RNA-capsid protein contacts, to analyse cryo-electron tomographic data. We apply this method to the low-resolution tomographic data of a model virus and infer the unique asymmetric organization of its genome in contact with the protein shell of the capsid. This opens unprecedented opportunities to analyse viral genomes, revealing conserved structural features and mechanisms that can be targeted in antiviral drug desig

Tracking the evolution of hospice palliative care in Canada: A comparative case study analysis of seven provinces

<p>Abstract</p> <p>Background</p> <p>An aging population, rise in chronic illnesses, increase in life expectancy and shift towards care being provided at the community level are trends that are collectively creating an urgency to advance hospice palliative care (HPC) planning and provision in Canada. The purpose of this study was to analyze the evolution of HPC in seven provinces in Canada so as to inform such planning and provision elsewhere. We have endeavoured to undertake this research out of awareness that good future planning for health and social care, such as HPC, typically requires us to first look backwards before moving forward.</p> <p>Methods</p> <p>To identify key policy and practice events in HPC in Canada, as well as describe facilitators of and barriers to progress, a qualitative comparative case study design was used. Specifically, the evolution and development of HCP in 7 strategically selected provinces is compared. After choosing the case study provinces, the grey literature was searched to create a preliminary timeline for each that described the evolution of HPC beginning in 1970. Key informants (<it>n </it>= 42) were then interviewed to verify the content of each provincial timeline and to discuss barriers and facilitators to the development of HPC. Upon completion of the primary data collection, a face-to-face meeting of the research team was then held so as to conduct a comparative study analysis that focused on provincial commonalities and differences.</p> <p>Results</p> <p>Findings point to the fact that HPC continues to remain at the margins of the health care system. The development of HPC has encountered structural inheritances that have both sped up progress as well as slowed it down. These structural inheritances are: (1) foundational health policies (e.g., the Canada Health Act); (2) service structures and planning (e.g., the dominance of urban-focused initiatives); and (3) health system decisions (e.g., regionalization). As a response to these inheritances, circumventions of the established system of care were taken, often out of necessity. Three kinds of circumventions were identified from the data: (1) interventions to shift the system (e.g., the role of advocacy); (2) service innovations (e.g., educational initiatives); and (3) new alternative structures (e.g., the establishment of independent hospice organizations). Overall, the evolution of HPC across the case study provinces has been markedly slow, but steady and continuous.</p> <p>Conclusions</p> <p>HPC in Canada remains at the margins of the health care system. Its integration into the primary health care system may ensure dedicated and ongoing funding, enhanced access, quality and service responsiveness. Though demographics are expected to influence HPC demand in Canada, our study confirms that concerned citizens, advocacy organizations and local champions will continue to be the agents of change that make the necessary and lasting impacts on HPC in Canada.</p

Materials characterisation and software tools as key enablers in Industry 5.0 and wider acceptance of new methods and products

Recently, the NMBP-35 Horizon 2020 projects -NanoMECommons, CHARISMA, and Easi-stress -organised a collaborative workshop to increase awareness of their contributions to the industry "commons" in terms of characterisation and digital transformation. They have established interoperability standards for knowledge management in characterisation and introduced new solutions for materials testing, aided by the standardisation of faster and more accurate assessment methods. The lessons learned from these projects and the discussions during the joint workshop emphasised the impact of recent developments and emerging needs in the field of characterisation. Specifically, the focus was on enhancing data quality through harmonisation and stand-ardisation, as well as making advanced technologies and instruments accessible to a broader community with the goal of fostering increased trust in new products and a more skilled society. Experts also highlighted how characterisation and the corresponding experimental data can drive future innovation agendas towards tech-nological breakthroughs. The focus of the discussion revolved around the characterisation and standardisation processes, along with the collection of modelling and characterisation tools, as well as protocols for data ex-change. The broader context of materials characterisation and modelling within the materials community was explored, drawing insights from the Materials 2030 Roadmap and the experiences gained from NMBP-35 pro-jects. This whitepaper has the objective of addressing common challenges encountered by the materials com-munity, illuminating emerging trends and evolving techniques, and presenting the industry's perspective on emerging requirements and past success stories. It accomplishes this by providing specific examples and high-lighting how these experiences can create fresh opportunities and strategies for newcomers entering the market. These advancements are anticipated to facilitate a more efficient transition from Industry 4.0 to 5.0 during the industrial revolution

Antibacterial activity testing methods for hydrophobic patterned surfaces

One strategy to decrease the incidence of hospital-acquired infections is to avoid the survival of pathogens in the environment by the development of surfaces with antimicrobial activity. To study the antibacterial behaviour of active surfaces, different approaches have been developed of which ISO 22916 is the standard. To assess the performance of different testing methodologies to analyse the antibacterial activity of hydrophobic surface patterned plastics as part of a Horizon 2020 European research project. Four different testing methods were used to study the antibacterial activity of a patterned film, including the ISO 22916 standard, the immersion method, the touch-transfer inoculation method, and the swab inoculation method, this latter developed specifically for this project. The non-realistic test conditions of the ISO 22916 standard showed this method to be non-appropriate in the study of hydrophobic patterned surfaces. The immersion method also showed no differences between patterned films and smooth controls due to the lack of attachment of testing bacteria on both surfaces. The antibacterial activity of films could be demonstrated by the touch-transfer and the swab inoculation methods, that more precisely mimicked the way of high-touch surfaces contamination, and showed to be the best methodologies to test the antibacterial activity of patterned hydrophobic surfaces. A new ISO standard would be desirable as the reference method to study the antibacterial behaviour of patterned surfaces.The present study was carried out as part of a European project called “Antimicrobial FLEXible POLymers for its use in hospital environments” (FLEXPOL Grant agreement No. 721062) funded by Horizon 2020 Framework Programme for Research and Innovation (2014-2020)

Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures

Long RNA molecules are at the core of gene regulation across all kingdoms of life, whilst also serving as genomes in RNA viruses. Few studies have addressed the basic physical properties of long single-stranded RNAs. Long RNAs with non-repeating sequences usually adopt highly ramified secondary structures and are better described as branched polymers. In order to test whether a branched polymer model can estimate the overall sizes of large RNAs we employed fluorescence correlation spectroscopy to examine the hydrodynamic radii of a broad spectrum of biologically important RNAs, ranging from viral genomes to long non-coding regulatory RNAs. The relative sizes of long RNAs measured at low ionic strength correspond well to those predicted by two theoretical approaches that treat the effective branching associated with secondary structure formation – one employing the Kramers theorem for calculating radii of gyration, and the other featuring the metric of “maximum ladder distance”. Upon addition of multivalent cations, most RNAs are found to be compacted as compared with their original, low-ionic-strength sizes. These results suggest that sizes of long RNAmolecules are determined by the branching pattern of their secondary structures. They also experimentally validate the proposed computational approaches for estimating hydrodynamic radii of single-stranded RNAs, which use generic RNA structure prediction tools and thus can be universally applied to a wide range of long RNAs

Identification of novel RNA secondary structures within the hepatitis C virus genome reveals a cooperative involvement in genome packaging

The specific packaging of the hepatitis C virus (HCV) genome is hypothesised to be driven by Core- RNA interactions. To identify the regions of the viral genome involved in this process, we used SELEX (systematic evolution of ligands by exponential enrichment) to identify RNA aptamers which bind specifically to Core in vitro. Comparison of these aptamers to multiple HCV genomes revealed the presence of a conserved terminal loop motif within short RNA stem-loop structures. We postulated that interactions of these motifs, as well as sub-motifs which were present in HCV genomes at statistically significant levels, with the Core protein may drive virion assembly. We mutated 8 of these predicted motifs within the HCV infectious molecular clone JFH-1, thereby producing a range of mutant viruses predicted to possess altered RNA secondary structures. RNA replication and viral titre were unaltered in viruses possessing only one mutated structure. However, infectivity titres were decreased in viruses possessing a higher number of mutated regions. This work thus identified multiple novel RNA motifs which appear to contribute to genome packaging. We suggest that these structures act as cooperative packaging signals to drive specific RNA encapsidation during HCV assembly

Mechanical and Assembly Units of Viral Capsids Identified via Quasi-Rigid Domain Decomposition

Key steps in a viral life-cycle, such as self-assembly of a protective protein container or in some cases also subsequent maturation events, are governed by the interplay of physico-chemical mechanisms involving various spatial and temporal scales. These salient aspects of a viral life cycle are hence well described and rationalised from a mesoscopic perspective. Accordingly, various experimental and computational efforts have been directed towards identifying the fundamental building blocks that are instrumental for the mechanical response, or constitute the assembly units, of a few specific viral shells. Motivated by these earlier studies we introduce and apply a general and efficient computational scheme for identifying the stable domains of a given viral capsid. The method is based on elastic network models and quasi-rigid domain decomposition. It is first applied to a heterogeneous set of well-characterized viruses (CCMV, MS2, STNV, STMV) for which the known mechanical or assembly domains are correctly identified. The validated method is next applied to other viral particles such as L-A, Pariacoto and polyoma viruses, whose fundamental functional domains are still unknown or debated and for which we formulate verifiable predictions. The numerical code implementing the domain decomposition strategy is made freely available

Exploiting protein flexibility to predict the location of allosteric sites

Background: Allostery is one of the most powerful and common ways of regulation of protein activity. However, for most allosteric proteins identified to date the mechanistic details of allosteric modulation are not yet well understood. Uncovering common mechanistic patterns underlying allostery would allow not only a better academic understanding of the phenomena, but it would also streamline the design of novel therapeutic solutions. This relatively unexplored therapeutic potential and the putative advantages of allosteric drugs over classical active-site inhibitors fuel the attention allosteric-drug research is receiving at present. A first step to harness the regulatory potential and versatility of allosteric sites, in the context of drug-discovery and design, would be to detect or predict their presence and location. In this article, we describe a simple computational approach, based on the effect allosteric ligands exert on protein flexibility upon binding, to predict the existence and position of allosteric sites on a given protein structure. Results: By querying the literature and a recently available database of allosteric sites, we gathered 213 allosteric proteins with structural information that we further filtered into a non-redundant set of 91 proteins. We performed normal-mode analysis and observed significant changes in protein flexibility upon allosteric-ligand binding in 70% of the cases. These results agree with the current view that allosteric mechanisms are in many cases governed by changes in protein dynamics caused by ligand binding. Furthermore, we implemented an approach that achieves 65% positive predictive value in identifying allosteric sites within the set of predicted cavities of a protein (stricter parameters set, 0.22 sensitivity), by combining the current analysis on dynamics with previous results on structural conservation of allosteric sites. We also analyzed four biological examples in detail, revealing that this simple coarse-grained methodology is able to capture the effects triggered by allosteric ligands already described in the literature. Conclusions: We introduce a simple computational approach to predict the presence and position of allosteric sites in a protein based on the analysis of changes in protein normal modes upon the binding of a coarse-grained ligand at predicted cavities. Its performance has been demonstrated using a newly curated non-redundant set of 91 proteins with reported allosteric properties. The software developed in this work is available upon request from the authors

Materials characterisation and software tools as key enablers in Industry 5.0 and wider acceptance of new methods and products

Recently, the NMBP-35 Horizon 2020 projects - NanoMECommons, CHARISMA, and Easi-stress - organised a collaborative workshop to increase awareness of their contributions to the industry “commons” in terms of characterisation and digital transformation. They have established interoperability standards for knowledge management in characterisation and introduced new solutions for materials testing, aided by the standardisation of faster and more accurate assessment methods. The lessons learned from these projects and the discussions during the joint workshop emphasised the impact of recent developments and emerging needs in the field of characterisation. Specifically, the focus was on enhancing data quality through harmonisation and standardisation, as well as making advanced technologies and instruments accessible to a broader community with the goal of fostering increased trust in new products and a more skilled society. Experts also highlighted how characterisation and the corresponding experimental data can drive future innovation agendas towards technological breakthroughs. The focus of the discussion revolved around the characterisation and standardisation processes, along with the collection of modelling and characterisation tools, as well as protocols for data exchange. The broader context of materials characterisation and modelling within the materials community was explored, drawing insights from the Materials 2030 Roadmap and the experiences gained from NMBP-35 projects. This whitepaper has the objective of addressing common challenges encountered by the materials community, illuminating emerging trends and evolving techniques, and presenting the industry's perspective on emerging requirements and past success stories. It accomplishes this by providing specific examples and highlighting how these experiences can create fresh opportunities and strategies for newcomers entering the market. These advancements are anticipated to facilitate a more efficient transition from Industry 4.0 to 5.0 during the industrial revolution. © 2023The Workshop was supported by EU H2020 project NanoMECommons, GA 952869, CHARISMA, GA 952921, EASI-STRESS, GA 953219, and EsSENce COST ACTION CA19118. This article/publication is based upon work from COST Action EsSENce COST ACTION CA19118, supported by COST (European Cooperation in Science and Technology). Miguel A. Bañares, Raquel Portela, Nina Jeliazkova, Enrique Lozano, Bastian Barton and Iván Moya have received financial support from the EU H2020 project CHARISMA, GA n. 952921, Bojan Boskovic, Ennio Capria, Costas Charitidis, Donna Dykeman, Spyros Diplas, Gerhard Goldbeck, Marco Sebastiani, Elias Koumoulos, Silvia Giovanna Avataneo, Miguel A. Bañares, Raquel Portela, Anastasia Alexandratou, Athanasios Katsavrias, Fotis Mystakopoulos have received financial support from the EU H2020 project NanoMECommons, GA n. 952869, Nikolaj Zangernberg and Ennio Capria have received financial support from the EU H2020 project EASI-STRESS, GA n. 953219, Natalia Konchakova has received financial support from the EU H2020 project VIPCOAT, GA n. 952903, Costas Charitidis, Elias Koumoulos, and Spyros Diplas have received financial support from the EsSENce COST ACTION CA19118. All authors would like to specially acknowledge Anastasia Alexandratou, Athanasios Katsavrias and Fotis Mystakopoulos for their support in NMBP-35 joint Workshop organisation and documentation, and Steffen Neumann for his insights during the NMBP-35 joint Workshop discussions.Peer reviewe

The development of the Teachers’ Attitudes toward Career Learning Index (TACLI).

Teachers play an important role supporting young people to form their career identities and to make successful transitions into further learning and work. In England there has been limited research that has looked specifically at the role of teachers and none which has tried to establish a measure of teacher attitude toward careers work. This article details the development of the Teachers Attitude toward Career Learning Index (TACLI) which was created to measure attitudes and engagement in career learning on teachers in England. The instrument went through a survey design process which included content validity and construct validity components. The process identified a five underlying factors in teachers attitude and engagement in careers work: (1) career learning and support practices, (2) school career strategy attitudes, (3) subject career learning attitudes, (4) career support attitudes, and (5) school career strategy practices. This process helped refined initial theoretical constructs regarding teachers’ roles in careers learning.Teach Firs