Search

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

CASP assessments primarily rely on comparing predicted coordinates with experimental reference structures. However, experimental structures by their nature are only models themselves-their construction involves a certain degree of subjectivity in interpreting density maps and translating them to atomic coordinates. Here, we directly utilized density maps to evaluate the predictions by employing a method for ranking the quality of protein chain predictions based on their fit into the experimental density. The fit-based ranking was found to correlate well with the CASP assessment scores. Overall, the evaluation against the density map indicated that the models are of high accuracy, and occasionally even better than the reference structure in some regions of the model. Local assessment of predicted side chains in a 1.52 Å resolution map showed that side-chains are sometimes poorly positioned. Additionally, the top 118 predictions associated with 9 protein target reference structures were selected for automated refinement, in addition to the top 40 predictions for 11 RNA targets. For both proteins and RNA, the refinement of CASP15 predictions resulted in structures that are close to the reference target structure. This refinement was successful despite large conformational changes often being required, showing that predictions from CASP-assessed methods could serve as a good starting point for building atomic models in cryo-EM maps for both proteins and RNA. Loop modeling continued to pose a challenge for predictors, and together with the lack of consensus amongst models in these regions suggests that modeling, in combination with model-fit to the density, holds the potential for identifying more flexible regions within the structure.

Computing protein structure from amino acid sequence information has been a long-standing grand challenge. Critical assessment of structure prediction (CASP) conducts community experiments aimed at advancing solutions to this and related problems. Experiments are conducted every 2 years. The 2020 experiment (CASP14) saw major progress, with the second generation of deep learning methods delivering accuracy comparable with experiment for many single proteins. There is an expectation that these methods will have much wider application in computational structural biology. Here we summarize results from the most recent experiment, CASP15, in 2022, with an emphasis on new deep learning-driven progress. Other papers in this special issue of proteins provide more detailed analysis. For single protein structures, the AlphaFold2 deep learning method is still superior to other approaches, but there are two points of note. First, although AlphaFold2 was the core of all the most successful methods, there was a wide variety of implementation and combination with other methods. Second, using the standard AlphaFold2 protocol and default parameters only produces the highest quality result for about two thirds of the targets, and more extensive sampling is required for the others. The major advance in this CASP is the enormous increase in the accuracy of computed protein complexes, achieved by the use of deep learning methods, although overall these do not fully match the performance for single proteins. Here too, AlphaFold2 based method perform best, and again more extensive sampling than the defaults is often required. Also of note are the encouraging early results on the use of deep learning to compute ensembles of macromolecular structures. Critically for the usability of computed structures, for both single proteins and protein complexes, deep learning derived estimates of both local and global accuracy are of high quality, however the estimates in interface regions are slightly less reliable. CASP15 also included computation of RNA structures for the first time. Here, the classical approaches produced better agreement with experiment than the new deep learning ones, and accuracy is limited. Also, for the first time, CASP included the computation of protein-ligand complexes, an area of special interest for drug design. Here too, classical methods were still superior to deep learning ones. Many new approaches were discussed at the CASP conference, and it is clear methods will continue to advance.

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

Prediction categories in the Critical Assessment of Structure Prediction (CASP) experiments change with the need to address specific problems in structure modeling. In CASP15, four new prediction categories were introduced: RNA structure, ligand-protein complexes, accuracy of oligomeric structures and their interfaces, and ensembles of alternative conformations. This paper lists technical specifications for these categories and describes their integration in the CASP data management system.

Abstract We report the results of a comprehensive copy number variant (CNV) reanalysis of 9171 exome sequencing datasets from 5757 families affected by a rare disease (RD). The data reanalysed was extremely heterogeneous, having been generated using 28 different enrichment kits by 42 different research groups across Europe partnering in the Solve-RD project. Each research group had previously undertaken their own analysis of the data but failed to identify disease-causing variants. We applied three CNV calling algorithms to maximise sensitivity, and rare CNVs overlapping genes of interest, provided by four partner European Reference Networks, were taken forward for interpretation by clinical experts. This reanalysis has resulted in a molecular diagnosis being provided to 51 families in this sample, with ClinCNV performing the best of the three algorithms. We also identified partially explanatory pathogenic CNVs in a further 34 individuals. This work illustrates the value of reanalysing ES cold cases for CNVs.

Introduction: Wilson’s disease is a rare autosomal recessive disorder that disrupts copper metabolism. It presents with distinctive ocular manifestations. Oculodermal melanosis, commonly referred to as nevus of Ota, is a painless condition characterized by hyperpigmentation in and around the eye. In this case report, we describe the unique occurrence of both conditions in this pediatric patient. Case Presentation: A 10-year-old girl exhibited classic ocular signs associated with Wilson’s disease, including Kayser-Fleischer rings and sunflower-type cataracts. Additionally, she displayed unilateral confluent gray-blue hyperpigmentation consistent with a nevus of Ota. As of now, the patient remains asymptomatic, with preserved visual acuity. Conclusions: To the best of our knowledge, this case represents the first report of nevus of Ota in a child diagnosed with Wilson’s disease.

In the previous article, we defined the scholarship of teaching and learning (SoTL) and the scholarship of practice (SoP) and identified characteristics and qualities related to these topics. In this article, we provide examples of scholars who have conducted a SoTL project related to student affairs. Each of these entries describes the project and gives us insights into why scholars choose to engage in this work and the impact of their work on teaching and learning.

The concepts of scholarship of teaching and learning and the scholarship of practice are relatively new; therefore, their value within student affairs and institutions of higher education may be questioned. Unfamiliarity with these activities may also impede student affairs graduate faculty and scholar-practitioners from engaging in this work. In this article, we outline why these activities should be viewed as scholarship and demonstrate how student affairs faculty and practitioners may already possess the skills needed to engage in this work.

Since its conception as a distinctive form of scholarship, the Scholarship of Teaching and Learning (SoTL) has evolved into a legitimized field. Despite its rapid evolution, there still exists confusion surrounding its definition and distinctions from scholarly teaching. Additionally, although it is widely recognized across many disciplines, there have been few conversations about the role of SoTL within the field of student affairs and student affairs graduate preparation programs. This article sets the foundation for this discussion. It provides an overview of the definitions and characteristics of SoTL and offers suggestions for the potential role of SoTL in student affairs.

This article introduces the concept of a scholarship of practice and its potential for improving student affairs research and practice. Student affairs graduate preparation faculty members and student affairs scholar-practitioners can engage in a scholarship of practice by using research to inform their practice and using the findings of their research to guide their own work. We focus on the notion of the scholarship of practice as a two-way loop between practitioners to researchers and researchers back to practitioners. We apply these concepts to student affairs.

The Scholarship of Teaching and Learning (SoTL) aligns with many institutionally espoused values regarding the value of teaching and learning excellence. SoTL has increased in prestige and value in the past decade, but less information about the proliferation of SoTL within one institution is known. Through an examination of 10 years of curriculum vitae submitted for successful promotion and tenure, our study investigated faculty members' engagement in SoTL over time and differences in engagement by rank, race, gender, discipline, and type of SoTL artifact. Over the 10-year period, the percentage of faculty engaged in SoTL did not differ significantly. We did uncover differences by disciplinary type and race. Faculty were most likely to engage in grants and presentations related to SoTL and least likely to have a peer-reviewed journal artifact. Our findings suggest that although SoTL efforts continue to gain acceptance within the higher education milieu, institutional and disciplinary realities may be powerful determiners of SoTL participation.

Renal physiology is considered one of the most challenging medical disciplines to understand and to teach. Eight academic nephrologists have come together to produce a podcast devoted to helping learners at any level improve their understanding of this difficult topic. Using Dr Burton D. Rose’s classic textbook: Clinical Physiology of Acid-Base and Electrolyte Disorders, the podcast faculty systematically attack each chapter of the book in a didactic yet fun-flowing interactive discussion. This education model is unique and helps demystify complex topics.

Abstract The use of head‐mounted augmented reality (AR) for surgeries has grown rapidly in recent years. AR aids in intraoperative surgical navigation through overlaying three‐dimensional (3D) holographic reconstructions of medical data. However, performing AR surgeries on complex areas such as the head and neck region poses challenges in terms of accuracy and speed. This study explores the feasibility of an AR guidance system for resections of positive tumour margins in a cadaveric specimen. The authors present an intraoperative solution that enables surgeons to upload and visualize holographic reconstructions of resected cadaver tissues. The solution involves using a 3D scanner to capture detailed scans of the resected tissue, which are subsequently uploaded into our software. The software converts the scans of resected tissues into specimen holograms that are viewable through a head‐mounted AR display. By re‐aligning these holograms with cadavers with gestures or voice commands, surgeons can navigate the head and neck tumour site. This workflow can run concurrently with frozen section analysis. On average, the authors achieve an uploading time of 2.98 min, visualization time of 1.05 min, and re‐alignment time of 4.39 min, compared to the 20 to 30 min typical for frozen section analysis. The authors achieve a mean re‐alignment error of 3.1 mm. The authors’ software provides a foundation for new research and product development for using AR to navigate complex 3D anatomy in surgery.

In January 2020, a workshop was held at EMBL-EBI (Hinxton, UK) to discuss data requirements for the deposition and validation of cryoEM structures, with a focus on single-particle analysis. The meeting was attended by 47 experts in data processing, model building and refinement, validation, and archiving of such structures. This report describes the workshop's motivation and history, the topics discussed, and the resulting consensus recommendations. Some challenges for future methods-development efforts in this area are also highlighted, as is the implementation to date of some of the recommendations.

Background: Positive margins are frequently observed in total laryngectomy (TL) specimens. Effective communication of margin sampling sites and final margin status between surgeons and pathologists is crucial. In this study, we evaluate the utility of multimedia visual pathology reports to facilitate interdisciplinary discussion of margin status in laryngeal cancer surgery. Methods: Ex vivo laryngeal cancer surgical specimens were three-dimensional (3D) scanned before standard of care pathological analysis. Using computer-aided design software, the 3D model was annotated to reflect inking, sectioning, and margin sampling sites, generating a visual pathology report. These reports were distributed to head and neck surgeons and pathologists postoperatively. Results: Fifteen laryngeal cancer surgical specimens were 3D scanned and virtually annotated from January 2022 to December 2023. Most specimens (73.3%) were squamous cell carcinomas (SCCs). Among the cases, 26.7% had final positive surgical margins, whereas 13.3% had close margins, defined as

We communicate a versatile and user-friendly Cu-based catalytic method that allows for the selective hydrogenation of enoates and alkynes. The introduced protocol is free from any ex ante modifications of the used Cu(I) precursors by air-sensitive phosphines or elaborate N-heterocyclic carbene ligands. The conjugate hydrogenation of enoates and the (selective) reduction of C≡C bonds is achieved through a [Cu(CH3CN)4]+/tert-butoxide pair whereby we describe a delicate influence of the base cation on the chemoselectivity of the respective transformation. In case of the ester-to-alcohol reduction, a combination of simple CuI and NaOtBu proved to be successful. Deuteration experiments are included to address certain mechanistic aspects of the introduced catalytic system. All requisite chemicals are readily obtainable through commercial channels and the catalyst assembly is set up on the bench without the need for special lab-technical precautions.

An individuals immune and metabolic status is coupled to their microbiome. Probiotics offer a promising, safe route to influence host health, possibly via the microbiome. Here, we report an 18-week, randomized prospective study that explores the effects of a probiotic vs. placebo supplement on 39 adults with elevated parameters of metabolic syndrome. We performed longitudinal sampling of stool and blood to profile the human microbiome and immune system. While we did not see changes in metabolic syndrome markers in response to the probiotic across the entire cohort, there were significant improvements in triglycerides and diastolic blood pressure in a subset of probiotic arm participants. Conversely, the non-responders had increased blood glucose and insulin levels over time. The responders had a distinct microbiome profile at the end of the intervention relative to the non-responders and placebo arm. Importantly, diet was a key differentiating factor between responders and non-responders. Our results show participant-specific effects of a probiotic supplement on improving parameters of metabolic syndrome and suggest that dietary factors may enhance stability and efficacy of the supplement.

Cytoplasmic and nuclear iron-sulfur (Fe-S) enzymes that are essential for genome maintenance and replication depend on the cytoplasmic Fe-S assembly (CIA) machinery for cluster acquisition. The core of the CIA machinery consists of a complex of CIAO1, MMS19 and FAM96B. The physiological consequences of loss of function in the components of the CIA pathway have thus far remained uncharacterized. Our study revealed that patients with biallelic loss of function in CIAO1 developed proximal and axial muscle weakness, fluctuating creatine kinase elevation, and respiratory insufficiency. In addition, they presented with CNS symptoms including learning difficulties and neurobehavioral comorbidities, along with iron deposition in deep brain nuclei, mild normocytic to macrocytic anemia, and gastrointestinal symptoms. Mutational analysis revealed reduced stability of the variants compared with WT CIAO1. Functional assays demonstrated failure of the variants identified in patients to recruit Fe-S recipient proteins, resulting in compromised activities of DNA helicases, polymerases, and repair enzymes that rely on the CIA complex to acquire their Fe-S cofactors. Lentivirus-mediated restoration of CIAO1 expression reversed all patient-derived cellular abnormalities. Our study identifies CIAO1 as a human disease gene and provides insights into the broader implications of the cytosolic Fe-S assembly pathway in human health and disease., Introduction Iron-sulfur (Fe-S) clusters are ancient and evolutionarily conserved prosthetic groups with unique chemical properties that enable the proteins that contain them (Fe-S proteins) to function in several essential cellular [...]

Abstract Due to the anatomic complexity of the head and neck and variable proximity between laboratory and operating room (OR), effective communication during frozen section analysis (FSA) between surgeons and pathologists is challenging. This proof‐of‐concept study investigates an augmented reality (AR) protocol that allows pathologists to virtually join the OR from the laboratory. Head and neck cancer specimens were scanned ex vivo using a 3‐dimensional scanner and uploaded into an AR platform. Eight head and neck specimens were discussed by surgeons and pathologists in an AR environment. AR‐guided intraoperative consultation was used for specimen orientation and discussion of FSA margin sampling sites. One patient had positive initial margins on FSA and was re‐resected to negative final margins. AR‐guided FSA is possible and allows pathologists to join the operating from any location for intraoperative discussion.

ABSTRACT The Gardnerella genus, comprising at least 13 species, is associated with the polymicrobial disorder bacterial vaginosis (BV). However, the details of BV pathogenesis are poorly defined, and the contributions made by individual species, including Gardnerella spp., are largely unknown. We report here that colony phenotypes characterized by size (large and small) and opacity (opaque and translucent) are phase variable and are conserved among all tested Gardnerella strains, representing at least 10 different species. With the hypothesis that these different variants could be an important missing piece to the enigma of how BV develops in vivo, we characterized their phenotypic, proteomic, and genomic differences. Beyond increased colony size, large colony variants showed reduced vaginolysin secretion and faster growth rate relative to small colony variants. The ability to inhibit the growth of Neisseria gonorrhoeae and commensal Lactobacillus species varied by strain and, in some instances, differed between variants. Proteomics analyses indicated that 127–173 proteins were differentially expressed between variants. Proteins with increased expression in large variants of both strains were associated with amino acid and protein synthesis and protein folding, whereas those increased in small variants were related to nucleotide synthesis, phosphate transport, ABC transport, and glycogen breakdown. Furthermore, whole genome sequencing analyses revealed an abundance of genes associated with variable homopolymer tracts, implicating slipped strand mispairing in Gardnerella phase variation and illuminating the potential for previously unrecognized heterogeneity within clonal populations. Collectively, these results suggest that phase variants may be primed to serve different roles in BV pathogenesis.IMPORTANCEBacterial vaginosis is the most common gynecological disorder in women of childbearing age. Gardnerella species are crucial to the development of this dysbiosis, but the mechanisms involved in the infection are not understood. We discovered that Gardnerella species vary between two different forms, reflected in bacterial colony size. A slow-growing form makes large amounts of the toxin vaginolysin and is better able to survive in human cervix tissue. A fast-growing form is likely the one that proliferates to high numbers just prior to symptom onset and forms the biofilm that serves as a scaffold for multiple BV-associated anaerobic bacteria. Identification of the proteins that vary between different forms of the bacteria as well as those that vary randomly provides insight into the factors important for Gardnerella infection and immune avoidance.

BackgroundThe provision of audio recordings of their own medical encounters to patients, termed consultation recordings, has demonstrated promising benefits, particularly in addressing information needs of cancer patients. While this intervention has been explored globally, there is limited research specific to Germany. This study investigates the attitudes and experiences of cancer patients in Germany toward consultation recordings.MethodsWe conducted a nationwide cross-sectional quantitative online survey, informed by semi-structured interviews with cancer patients. The survey assessed participants’ attitudes, experiences and desire for consultation recordings in the future. The data was analyzed using descriptive statistics and subgroup analyses.ResultsA total of 287 adult cancer patients participated. An overwhelming majority (92%) expressed a (very) positive attitude. Overall, participants strongly endorsed the anticipated benefits of the intervention, such as improved recall and enhanced understanding. Some participants expressed concerns that physicians might feel pressured and could become more reserved in their interactions with the use of such recordings. While a small proportion (5%) had prior experience with audio recording medical encounters, the majority (92%) expressed interest in having consultation recordings in the future.DiscussionWe observed positive attitudes of cancer patients in Germany toward consultation recordings, paralleling international research findings. Despite limited experiences, participants acknowledged the potential benefits of the intervention, particularly related to recalling and comprehending information from medical encounters. Our findings suggest that the potential of the intervention is currently underutilized in German cancer care. While acknowledging the possibility of a positive bias in our results, we conclude that this study represents an initial exploration of the intervention’s potential within the German cancer care context, laying the groundwork for its further evaluation.

This study examines the lived experiences of seven internationally diverse scholars from Canada, the United States, New Zealand, and Australia to answer the question: how do we make meaning of our collective boundary crossing experiences across disciplines and positions within SoTL? Our positions range from graduate student, faculty, and academic developers, to department chair and centre director. We conducted a phenomenological study, based on narratives of experience, and drew on Wenger-Trayner and Wenger-Trayner's (2015) theoretical framework that explores the features of a landscape of practice. Guided by this framework, we analyze our boundary crossings and brokering across the "diverse, political and flat" features of the SoTL landscape. Our collective findings highlight the critical role brokers play in facilitating boundary crossings. Brokering is precarious, bringing people together, building trusting relationships, and developing legitimacy while negotiating deadlocks, bureaucracy, authorities, and a multitude of challenges. Brokers, we found, require strength and resilience to mobilise, influence, and drive change in the landscape to transform existing practices or create new ones. We suggest that our analytical process can be used as a tool of analysis for future research about how brokers influence the SoTL landscape of practice and how brokering enhances SoTL development, support, and leadership.

Abstract Exploring the molecular basis of disease severity in rare disease scenarios is a challenging task provided the limitations on data availability. Causative genes have been described for Congenital Myasthenic Syndromes (CMS), a group of diverse minority neuromuscular junction (NMJ) disorders; yet a molecular explanation for the phenotypic severity differences remains unclear. Here, we present a workflow to explore the functional relationships between CMS causal genes and altered genes from each patient, based on multilayer network community detection analysis of complementary biomedical information provided by relevant data sources, namely protein-protein interactions, pathways and metabolomics. Our results show that CMS severity can be ascribed to the personalized impairment of extracellular matrix components and postsynaptic modulators of acetylcholine receptor (AChR) clustering. This work showcases how coupling multilayer network analysis with personalized -omics information provides molecular explanations to the varying severity of rare diseases; paving the way for sorting out similar cases in other rare diseases.

Abstract Cryo-EM experiments produce images of macromolecular assemblies that are combined to produce three-dimensional density maps. Typically, atomic models of the constituent molecules are fitted into these maps, followed by a density-guided refinement. We introduce TEMPy-ReFF, a method for atomic structure refinement in cryo-EM density maps. Our method represents atomic positions as components of a Gaussian mixture model, utilising their variances as B-factors, which are used to derive an ensemble description. Extensively tested on a substantial dataset of 229 cryo-EM maps from EMDB ranging in resolution from 2.1-4.9 Å with corresponding PDB and CERES atomic models, our results demonstrate that TEMPy-ReFF ensembles provide a superior representation of cryo-EM maps. On a single-model basis, it performs similarly to the CERES re-refinement protocol, although there are cases where it provides a better fit to the map. Furthermore, our method enables the creation of composite maps free of boundary artefacts. TEMPy-ReFF is useful for better interpretation of flexible structures, such as those involving RNA, DNA or ligands.

BACKGROUND: Valosin-containing protein (VCP) disease, caused by mutations in the VCP gene, results in myopathy, Pagets disease of bone (PBD) and frontotemporal dementia (FTD). Natural history and genotype-phenotype correlation data are limited. This study characterises patients with mutations in VCP gene and investigates genotype-phenotype correlations. METHODS: Descriptive retrospective international study collecting clinical and genetic data of patients with mutations in the VCP gene. RESULTS: Two hundred and fifty-five patients (70.0% males) were included in the study. Mean age was 56.8±9.6 years and mean age of onset 45.6±9.3 years. Mean diagnostic delay was 7.7±6 years. Symmetric lower limb weakness was reported in 50% at onset progressing to generalised muscle weakness. Other common symptoms were ventilatory insufficiency 40.3%, PDB 28.2%, dysautonomia 21.4% and FTD 14.3%. Fifty-seven genetic variants were identified, 18 of these no previously reported. c.464G>A (p.Arg155His) was the most frequent variant, identified in the 28%. Full time wheelchair users accounted for 19.1% with a median time from disease onset to been wheelchair user of 8.5 years. Variant c.463C>T (p.Arg155Cys) showed an earlier onset (37.8±7.6 year) and a higher frequency of axial and upper limb weakness, scapular winging and cognitive impairment. Forced vital capacity (FVC) below 50% was as risk factor for being full-time wheelchair user, while FVC