Identifying Ciliary Proteins in Mammalian Retinas using a Gentle Extraction Method.

Mutations in retinal primary cilia are responsible for human blindness but the mechanisms are not fully understood (Wheway et al., 2014). Characterizing the proteome of an organelle such as cilia, is a fruitful way to understand its function but methods often require considerable sample quantities. Here we develop a method to isolate the primary cilia of photoreceptor cells from bovine retinas. Through LC/MS/MS proteomics analysis we identify proteins enriched for cilia function including ciliopathy disease. This study shows our method can be used to isolate retinal primary cilia to obtain sufficient quantities of native protein samples.

Transferability of the NHS low-calorie diet programme: A qualitative exploration of factors influencing the programme's transfer ahead of wide-scale adoption.

INTRODUCTION: Although behavioural interventions have been found to help control type 2 diabetes (T2D), it is important to understand how the delivery context can influence implementation and outcomes. The NHS committed to testing a low-calorie diet (LCD) programme designed to support people living with excess weight and T2D to lose weight and improve diabetes outcomes. Understanding what influenced implementation during the programme pilot is important in optimising rollout. This study explored the transferability of the NHS LCD Programme prior to wider adoption. METHODS: Twenty-five interviews were undertaken with stakeholders involved in implementing the LCD programme in pilot sites (health service leads, referring health professionals and programme deliverers). Interviews with programme participants (people living with T2D) were undertaken within a larger programme of work, exploring what worked, for whom and why, which is reported separately. The conceptual Population-Intervention-Environment-Transfer Model of Transferability (PIET-T) guided study design and data collection. Constructs of the model were also used as a deductive coding frame during data analysis. Key themes were identified which informed recommendations to optimise programme transfer. RESULTS: Population: Referral strategies in some areas lacked consideration of population characteristics. Many believed that offering a choice of delivery model would promote acceptability and accessibility of the eligible population. INTERVENTION: Overall, stakeholders had confidence in the LCD programme due to the robust evidence base along with anecdotal evidence, but some felt the complex referral process hindered engagement from GP practices. ENVIRONMENT: Stakeholders described barriers to accessing the programme, including language and learning difficulties. Transferability: Multidisciplinary working and effective communication supported successful implementation. CONCLUSION: Referral strategies to reach underrepresented groups should be considered during programme transfer, along with timely data from service providers on access and programme benefits. A choice of delivery models may optimise uptake. Knowledge sharing between sites on good working practices is encouraged, including increasing engagement with key stakeholders.

Ancient eukaryotic protein interactions illuminate modern genetic traits and disorders.

All eukaryotes share a common ancestor from roughly 1.5 - 1.8 billion years ago, a single-celled, swimming microbe known as LECA, the Last Eukaryotic Common Ancestor. Nearly half of the genes in modern eukaryotes were present in LECA, and many current genetic diseases and traits stem from these ancient molecular systems. To better understand these systems, we compared genes across modern organisms and identified a core set of 10,092 shared protein-coding gene families likely present in LECA, a quarter of which are uncharacterized. We then integrated >26,000 mass spectrometry proteomics analyses from 31 species to infer how these proteins interact in higher-order complexes. The resulting interactome describes the biochemical organization of LECA, revealing both known and new assemblies. We analyzed these ancient protein interactions to find new human gene-disease relationships for bone density and congenital birth defects, demonstrating the value of ancestral protein interactions for guiding functional genetics today.

A Qualitative evaluation in community settings in England exploring the experiences of coaches delivering the NHS Low Calorie Diet programme pilot to ethnically diverse participants.

BACKGROUND: The management of type 2 diabetes (T2D) within diverse ethnic populations requires a culturally tailored approach. However, little is known about the experiences of coaches delivering interventions for T2D, such as the National Health Service (NHS) Low Calorie Diet (LCD) programme, to people from diverse ethnic backgrounds. OBJECTIVE: To explore the experiences of coaches delivering an NHS programme using total diet replacement approaches to individuals from diverse ethnic backgrounds, to inform the effective tailoring and equitable delivery of future interventions. DESIGN: Qualitative study. SETTING: Individuals delivering the NHS LCD programme. PARTICIPANTS: One-to-one semistructured interviews were conducted with seven health coaches delivering the NHS LCD programme. Inclusion criteria included participants delivering the NHS LCD programme either from a minoritised ethnic background or delivering the programme to those from ethnic minority and white British backgrounds. MAIN OUTCOME MEASURES: Qualitative semistructured interviews conducted through different stages of the programme. Reflexive thematic analysis was used to analyse the transcripts. RESULTS: Key themes highlighted the following experiences of delivering the LCD programme: (1) training and support needs; (2) needing to understand culture and ethnicity; (3) the impact of language; (4) the use of resources in providing dietary advice and (5) experiences of cultural tailoring. The themes highlight the need to prioritise person-centred care, to integrate culturally tailored approaches and for provision of education and training to those delivering health programmes. CONCLUSION: These findings describe the experiences of health coaches in tailoring delivery and emphasise the role of cultural competence in ensuring equitable and effective healthcare interventions for diverse populations. This learning can inform future programmes and policies aimed at promoting inclusive healthcare practices.

Is the NHS low-calorie diet programme delivered as planned? An observational study examining adherence of intervention delivery to service specification.

Obesity and Type 2 Diabetes Mellitus (T2DM) are chronic conditions with significant personal, societal, and economic impacts. Expanding on existing trial evidence, the NHS piloted a 52-week low-calorie diet programme for T2DM, delivered by private providers using total diet replacement products and behaviour change support. This study aimed to determine the extent to which providers and coaches adhered to the service specification outlined by NHS England. An observational qualitative study was conducted to examine the delivery of both one-to-one and group-based delivery of programme sessions. Observations of 122 sessions across eight programme delivery samples and two service providers were completed. Adherence to the service specification was stronger for those outcomes that were easily measurable, such as weight and blood glucose, while less tangible elements of the specification, such as empowering service users, and person-centred delivery were less consistently observed. One-to-one sessions were more successful in their person-centred delivery, and the skills of the coaches delivering the sessions had a strong impact on adherence to the specification. Overall, the results show that there was variability by provider and delivery mode in the extent to which sessions of the NHS Low-Calorie Diet Programme reflected the intended service specification. In subsequent programmes it is recommended that one-to-one sessions are used, with accompanying peer support, and that providers improve standardised training and quality assurance to ensure specification adherence.

Views, perceptions, and experiences of type 2 diabetes or weight management programs among minoritized ethnic groups living in high-income countries: A systematic review of qualitative evidence.

BACKGROUND: Prevalence of both obesity and type 2 diabetes can be higher in patients from certain ethnic groups, yet uptake and adherence to current support within these groups is lower, leading to widening health inequalities in high-income countries. OBJECTIVES: The main objective of this study is to understand the views, perceptions, and experiences of and barriers and facilitators in relation to the uptake and adherence to weight management and type 2 diabetes programs in minoritized ethnic groups in high-income countries. METHODS: CINAHL, MEDLINE, PsycINFO, Scopus, Academic Search Complete, and PubMed were searched for English language studies undertaken in community-dwelling adults residing in high-income countries, who are from a minoritized ethnic group within the country of study. RESULTS: Seventeen studies were synthesized using the JBI System for the Unified Management of the Assessment and Review of Information. From these studies, 115 findings were retrieved, and seven key themes were identified: (1) family health status and program education, (2) social support, (3) challenges, (4) cultural beliefs, (5) increased awareness and dietary changes, (6) impact of psychological evaluations, and (7) considerations for future. CONCLUSIONS: Nutritional considerations for type 2 diabetes mellitus and weight management programs in high-income countries should include social, habitual, economic, and conceptual components, which should include consideration of local ethnic and cultural norms and building community relationships while creating culturally tailored programs.

Normalisation and equity of referral to the NHS Low Calorie Diet programme pilot; a qualitative evaluation of the experiences of health care staff.

BACKGROUND: Health and wellbeing can be profoundly impacted by both obesity and type 2 diabetes, while the normalisation and equity of care for people living with these non-communicable diseases remain as challenges for local health systems. The National Health Service Low Calorie Diet programme in England, aims to support people to achieve type 2 diabetes remission, while also reducing health inequalities. We have explored the experiences of health care staff who have made a referral to the LCD programme, while identifying effective and equitable delivery of programme referrals, and their normalisation into routine care. METHODS: Nineteen individual semi-structured interviews were completed health care staff in the first year of the Low Calorie Diet programme. Interviewees were purposively sampled from the ten localities who undertook the Low Calorie Diet programme pilot. Each interview explored a number of topics of interest including communication and training, referrals, equity, and demands on primary care, before being subjected to a thematic analysis. RESULTS: From the data, five core themes were identified: Covid-19 and the demands on primary care, the expertise and knowledge of referrers, patient identification and the referral process, barriers to referrals and who gets referred to the NHS LCD programme. Our findings demonstrate the variation in the real world settings of a national diabetes programme. It highlights the challenge of COVID-19 for health care staff, whereby the increased workload of referrals occurred at a time when capacity was curtailed. We have also identified several barriers to referral and have shown that referrals had not yet been normalised into routine care at the point of data collection. We also raise issues of equity in the referral process, as not all eligible people are informed about the programme. CONCLUSIONS: Referral generation had not yet been consistently normalised into routine care, yet our findings suggest that the LCD programme runs the risk of normalising an inequitable referral process. Inequalities remain a significant challenge, and the adoption of an equitable referral process, normalised at a service delivery level, has the capacity to contribute to the improvement of health inequalities.

Can the delivery of behavioural support be improved in the NHS England Low-Calorie Diet Programme? An observational study of behaviour change techniques.

BACKGROUND: Previous research has illustrated a drift in the fidelity of behaviour change techniques (BCTs) during the design of the pilot NHS England Low-Calorie Diet (NHS-LCD) Programme. This study evaluated a subsequent domain of fidelity, intervention delivery. Two research questions were addressed: (1) To what extent were BCTs delivered with fidelity to providers programme plans? (2) What were the observed barriers and facilitators to delivery? METHODS: A mixed-methods sequential explanatory design was employed. Remote delivery of one-to-one and group-based programmes were observed. A BCT checklist was developed using the BCT Taxonomy v1; BCTs were coded as present, partially delivered, or absent during live sessions. Relational content analysis of field notes identified observed barriers and facilitators to fidelity. RESULTS: Observations of 122 sessions across eight samples and two service providers were completed. Delivery of the complete NHS-LCD was observed for five samples. Fidelity ranged from 33% to 70% across samples and was higher for group-based delivery models (64%) compared with one-to-one models (46%). Barriers and facilitators included alignment with the programme's target behaviours and outcomes, session content, time availability and management, group-based remote delivery, and deviation from the session plan. CONCLUSIONS: Overall, BCTs were delivered with low-to-moderate fidelity. Findings indicate a dilution in fidelity during the delivery of the NHS-LCD and variation in the fidelity of programmes delivered across England. Staff training could provide opportunities to practice the delivery of BCTs. Programme-level changes such as structured activities supported by participant materials and with sufficient allocated time, might improve the delivery of BCTs targeting self-regulation.

Scaffold Matcher: A CMA-ES based algorithm for identifying hotspot aligned peptidomimetic scaffolds.

The design of protein interaction inhibitors is a promising approach to address aberrant protein interactions that cause disease. One strategy in designing inhibitors is to use peptidomimetic scaffolds that mimic the natural interaction interface. A central challenge in using peptidomimetics as protein interaction inhibitors, however, is determining how best the molecular scaffold aligns to the residues of the interface it is attempting to mimic. Here we present the Scaffold Matcher algorithm that aligns a given molecular scaffold onto hotspot residues from a protein interaction interface. To optimize the degrees of freedom of the molecular scaffold we implement the covariance matrix adaptation evolution strategy (CMA-ES), a state-of-the-art derivative-free optimization algorithm in Rosetta. To evaluate the performance of the CMA-ES, we used 26 peptides from the FlexPepDock Benchmark and compared with three other algorithms in Rosetta, specifically, Rosetta's default minimizer, a Monte Carlo protocol of small backbone perturbations, and a Genetic algorithm. We test the algorithms' performance on their ability to align a molecular scaffold to a series of hotspot residues (i.e., constraints) along native peptides. Of the 4 methods, CMA-ES was able to find the lowest energy conformation for all 26 benchmark peptides. Additionally, as a proof of concept, we apply the Scaffold Match algorithm with CMA-ES to align a peptidomimetic oligooxopiperazine scaffold to the hotspot residues of the substrate of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our implementation of CMA-ES into Rosetta allows for an alternative optimization method to be used on macromolecular modeling problems with rough energy landscapes. Finally, our Scaffold Matcher algorithm allows for the identification of initial conformations of interaction inhibitors that can be further designed and optimized as high-affinity reagents.

South Asian individuals' experiences on the NHS low-calorie diet programme: a qualitative study in community settings in England.

BACKGROUND: Existing literature examines barriers to the provision of ethnically diverse dietary advice, however, is not specific to total diet replacement (TDR). There is a lack of literature from the UK, limiting the potential applicability of existing findings and themes to the UK context. This study addresses this gap in research by interviewing participants of South Asian ethnicity who have undertaken the National Health Service (NHS) low-calorie diet programme (LCD) for people with type 2 diabetes living with overweight or obesity. This study explores factors that may affect the uptake and acceptability of its TDR, food reintroduction and weight maintenance stages. This aims to provide rich data that can inform effective tailoring of future programmes with South Asian participants. OBJECTIVE: To explore the perspectives of individuals of South Asian ethnicity on an NHS programme using TDR approaches for the management of type 2 diabetes (T2D). DESIGN: Qualitative study. SETTING: Individuals in the community undertaking the NHS LCD programme. PARTICIPANTS: Twelve one-to-one interviews were conducted with individuals from a South Asian ethnicity participating in the NHS LCD. MAIN OUTCOME MEASURES: Qualitative semistructured interviews conducted through different stages of the programme. Reflexive thematic analysis was used to analyse the transcripts. RESULTS: Key themes highlighted positive and negative experiences of the programme: (1) more work is needed in the programme for person centeredness; (2) it is not the same taste; (3) needing motivation to make changes and feel better; (4) a mixed relationship with the coach; (5) social experiences; (6) culture-related experiences. CONCLUSION: This study provides important experience-based evidence of the need for culturally tailored T2D programmes. Action to address these findings and improve the tailoring of the NHS LCD may improve experience, retention and outcomes on the programme for people of South Asian ethnicity and thereby reduce inequalities.

Come for the atmosphere, stay for the interactions: Deciphering small molecule partitioning into biomolecular condensates.

Optimizing pharmacokinetic properties remains challenging but is generally guided by a set of structural rules. However, no such rule set exists for intracellular distribution. Kilgore et al.1 have examined small molecule partitioning within biomolecular condensates, yielding findings that could open a new window in the drug design and discovery process.

The protein organization of a red blood cell.

Red blood cells (RBCs) (erythrocytes) are the simplest primary human cells, lacking nuclei and major organelles and instead employing about a thousand proteins to dynamically control cellular function and morphology in response to physiological cues. In this study, we define a canonical RBC proteome and interactome using quantitative mass spectrometry and machine learning. Our data reveal an RBC interactome dominated by protein homeostasis, redox biology, cytoskeletal dynamics, and carbon metabolism. We validate protein complexes through electron microscopy and chemical crosslinking and, with these data, build 3D structural models of the ankyrin/Band 3/Band 4.2 complex that bridges the spectrin cytoskeleton to the RBC membrane. The model suggests spring-like compression of ankyrin may contribute to the characteristic RBC cell shape and flexibility. Taken together, our study provides an in-depth view of the global protein organization of human RBCs and serves as a comprehensive resource for future research.

hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies.

A general principle of biology is the self-assembly of proteins into functional complexes. Characterizing their composition is, therefore, required for our understanding of cellular functions. Unfortunately, we lack knowledge of the comprehensive set of identities of protein complexes in human cells. To address this gap, we developed a machine learning framework to identify protein complexes in over 15,000 mass spectrometry experiments which resulted in the identification of nearly 7,000 physical assemblies. We show our resource, hu.MAP 2.0, is more accurate and comprehensive than previous state of the art high-throughput protein complex resources and gives rise to many new hypotheses, including for 274 completely uncharacterized proteins. Further, we identify 253 promiscuous proteins that participate in multiple complexes pointing to possible moonlighting roles. We have made hu.MAP 2.0 easily searchable in a web interface (http://humap2.proteincomplexes.org/), which will be a valuable resource for researchers across a broad range of interests including systems biology, structural biology, and molecular explanations of disease.

Co-fractionation/mass spectrometry to identify protein complexes.

Co-fractionation/mass spectrometry (CF/MS) is a flexible and powerful method to detect physical associations of proteins. CF/MS can be applied to any tissue or organism without the need for protein-specific antibodies or epitope tags. Here, we outline two alternate protocols for MS preparation of samples (containing low or high salt) and a computational pipeline (cfmsflow) that together allow the successful application of this approach. These protocols are based on CF/MS of over 16 diverse organisms including plants and animals. For complete details on the use and execution of this protocol, please refer to McWhite et al. (2020).

Systematic Identification of Protein Phosphorylation-Mediated Interactions.

Protein phosphorylation is a key regulatory mechanism involved in nearly every eukaryotic cellular process. Increasingly sensitive mass spectrometry approaches have identified hundreds of thousands of phosphorylation sites, but the functions of a vast majority of these sites remain unknown, with fewer than 5% of sites currently assigned a function. To increase our understanding of functional protein phosphorylation we developed an approach (phospho-DIFFRAC) for identifying the phosphorylation-dependence of protein assemblies in a systematic manner. A combination of nonspecific protein phosphatase treatment, size-exclusion chromatography, and mass spectrometry allowed us to identify changes in protein interactions after the removal of phosphate modifications. With this approach we were able to identify 316 proteins involved in phosphorylation-sensitive interactions. We recovered known phosphorylation-dependent interactors such as the FACT complex and spliceosome, as well as identified novel interactions such as the tripeptidyl peptidase TPP2 and the supraspliceosome component ZRANB2. More generally, we find phosphorylation-dependent interactors to be strongly enriched for RNA-binding proteins, providing new insight into the role of phosphorylation in RNA binding. By searching directly for phosphorylated amino acid residues in mass spectrometry data, we identified the likely regulatory phosphosites on ZRANB2 and FACT complex subunit SSRP1. This study provides both a method and resource for obtaining a better understanding of the role of phosphorylation in native macromolecular assemblies. All mass spectrometry data are available through PRIDE (accession #PXD021422).

Functional partitioning of a liquid-like organelle during assembly of axonemal dyneins.

Ciliary motility is driven by axonemal dyneins that are assembled in the cytoplasm before deployment to cilia. Motile ciliopathy can result from defects in the dyneins themselves or from defects in factors required for their cytoplasmic pre-assembly. Recent work demonstrates that axonemal dyneins, their specific assembly factors, and broadly-acting chaperones are concentrated in liquid-like organelles in the cytoplasm called DynAPs (Dynein Axonemal Particles). Here, we use in vivo imaging in Xenopus to show that inner dynein arm (IDA) and outer dynein arm (ODA) subunits are partitioned into non-overlapping sub-regions within DynAPs. Using affinity- purification mass-spectrometry of in vivo interaction partners, we also identify novel partners for inner and outer dynein arms. Among these, we identify C16orf71/Daap1 as a novel axonemal dynein regulator. Daap1 interacts with ODA subunits, localizes specifically to the cytoplasm, is enriched in DynAPs, and is required for the deployment of ODAs to axonemes. Our work reveals a new complexity in the structure and function of a cell-type specific liquid-like organelle that is directly relevant to human genetic disease.

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery.

Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application of DIF-FRAC to cultured tissue explants of Xenopus mucociliary epithelium identified dozens of known RNA-associated proteins as expected, but also several novel RNA-associated proteins, including proteins related to assembly of the mitotic spindle and regulation of ciliary beating. In particular, we show that the inner dynein arm tether Cfap44 is an RNA-associated protein that localizes not only to axonemes, but also to liquid-like organelles in the cytoplasm called DynAPs. This result led us to discover that DynAPs are generally enriched for RNA. Together, these data provide a useful resource for a deeper understanding of mucociliary epithelia and demonstrate that DIF-FRAC will be broadly applicable for systematic identification of RNA-associated proteins from embryonic tissues.

A Pan-plant Protein Complex Map Reveals Deep Conservation and Novel Assemblies.

Plants are foundational for global ecological and economic systems, but most plant proteins remain uncharacterized. Protein interaction networks often suggest protein functions and open new avenues to characterize genes and proteins. We therefore systematically determined protein complexes from 13 plant species of scientific and agricultural importance, greatly expanding the known repertoire of stable protein complexes in plants. By using co-fractionation mass spectrometry, we recovered known complexes, confirmed complexes predicted to occur in plants, and identified previously unknown interactions conserved over 1.1 billion years of green plant evolution. Several novel complexes are involved in vernalization and pathogen defense, traits critical for agriculture. We also observed plant analogs of animal complexes with distinct molecular assemblies, including a megadalton-scale tRNA multi-synthetase complex. The resulting map offers a cross-species view of conserved, stable protein assemblies shared across plant cells and provides a mechanistic, biochemical framework for interpreting plant genetics and mutant phenotypes.

Professional football clubs' involvement in health promotion in Spain: an audit of current practices.

The implementation of effective community-based health interventions within Spanish football clubs has the potential to positively influence the public health agenda and enable the healthcare system in Spain to be more successful and sustainable. This paper aims to explore the involvement of Spanish football clubs in health promotion activities, their potential for future involvement and what that would require. A mixed methods explanatory sequential design, with a purposive sample of La Liga clubs. Data collection included online questionnaires and phone interviews. Quantitative methods enabled us to describe the number and types of programmes the clubs are currently involved in. Qualitative data was useful to further unpick the processes followed by the clubs in planning and developing health promotion programmes, while identifying any determinants to change. Seventeen clubs completed questionnaires and 11 participated in interviews. Clubs generally support inclusive programmes that target disadvantaged groups. Health-related programmes focus on healthy eating, physical activity and blood donation. Thematic analysis of interviews with 11 representatives of La Liga clubs resulted in three-key themes. These related to: (i) Diversity of programmes; (ii) (Lack of) evidence-based approaches to intervention design and evaluation and (iii) Contrasting views about a club's role in health promotion interventions. Spanish football clubs have potential to reach into communities that are currently underserved. However, there is limited infrastructure and understanding within the clubs to do this. Nevertheless, there is huge opportunity for organizations with public health responsibility in Spain to implement translational approaches within football-based settings.