Design of experiment approach to identify the dominant geometrical feature of left coronary artery influencing atherosclerosis.

Background and Objective. Coronary artery geometry heavily influences local hemodynamics, potentially leading to atherosclerosis. Consequently, the unique geometrical configuration of an individual by birth can be associated with future risk of atherosclerosis. Although current researches focus on exploring the relationship between local hemodynamics and coronary artery geometry, this study aims to identify the order of influence of the geometrical features through systematic experiments, which can reveal the dominant geometrical feature for future risk assessment.Methods. According to Taguchi's method of design of experiment (DoE), the left main stem (LMS) length (lLMS), curvature (kLMS), diameter (dLMS) and the bifurcation angle between left anterior descending (LAD) and left circumflex (LCx) artery (αLAD-LCx) of two reconstructed patient-specific left coronary arteries (LCA) were varied in three levels to create L9 orthogonal array. Computational fluid dynamic (CFD) simulations with physiological boundary conditions were performed on the resulting eighteen LCA models. Average helicity intensity (h2) and relative atheroprone area (RAA) of near-wall hemodynamic descriptors were analyzed.Results. The proximal LAD (LADproximal) was identified to be the most atheroprone region of the left coronary artery due to higherh2,large RAA of time averaged wall shear stress (TAWSS < 0.4 Pa), oscillatory shear index (OSI ∼ 0.5) and relative residence time (RRT > 4.17 Pa-1). In both patient-specific cases, based onh2and TAWSS,dlmsis the dominant geometric parameter while based on OSI and RRT,αLAD-LCxis the dominant one influencing hemodynamic condition in proximal LAD (p< 0.05). Based on RRT, the rank of the geometrical factors is:αLAD-LCx>dLMS>lLMS>kLMS, indicating thatαLAD-LCxis the most dominant geometrical factor affecting hemodynamics at proximal LAD which may influence atherosclerosis.Conclusion. The proposed identification of the rank of geometrical features of LCA and the dominant feature may assist clinicians in predicting the possibility of atherosclerosis, of an individual, long before it will occur. This study can further be translated to be used to rank the influence of several arterial geometrical features at different arterial locations to explore detailed relationships between the arterial geometrical features and local hemodynamics.

Co-transcriptional assembly mechanisms of protein-RNA complexes.

This graphical review provides a mechanistic overview of different molecular processes that are tightly coupled and cooperate to achieve efficient and spatial-temporally regulated co-transcriptional protein-RNA complex assembly, including co-transcriptional RNA folding, processing, modification and the assembly in context of biomolecular condensates.

1H, 13C and 15N chemical shift assignment of the stem-loops 5b + c from the 5'-UTR of SARS-CoV-2.

The ongoing pandemic of the respiratory disease COVID-19 is caused by the SARS-CoV-2 (SCoV2) virus. SCoV2 is a member of the Betacoronavirus genus. The 30 kb positive sense, single stranded RNA genome of SCoV2 features 5'- and 3'-genomic ends that are highly conserved among Betacoronaviruses. These genomic ends contain structured cis-acting RNA elements, which are involved in the regulation of viral replication and translation. Structural information about these potential antiviral drug targets supports the development of novel classes of therapeutics against COVID-19. The highly conserved branched stem-loop 5 (SL5) found within the 5'-untranslated region (5'-UTR) consists of a basal stem and three stem-loops, namely SL5a, SL5b and SL5c. Both, SL5a and SL5b feature a 5'-UUUCGU-3' hexaloop that is also found among Alphacoronaviruses. Here, we report the extensive 1H, 13C and 15N resonance assignment of the 37 nucleotides (nts) long sequence spanning SL5b and SL5c (SL5b + c), as basis for further in-depth structural studies by solution NMR spectroscopy.

Metabolomics and Inflammatory Mediator Profiling for the Differentiation of Life-Threatening and Non-Severe Appendicitis in the Pediatric Population.

While children with appendicitis often have excellent clinical outcomes, some develop life-threatening complications including sepsis and organ dysfunction requiring pediatric intensive care unit (PICU) support. Our study applied a metabolomics and inflammatory protein mediator (IPM) profiling approach to determine the bio-profiles of children who developed severe appendicitis compared with those that did not. We performed a prospective case-control study of children aged 0-17 years with a diagnosis of appendicitis. Cases had severe disease resulting in PICU admission. Primary controls had moderate appendicitis (perforation without PICU); secondary controls had mild appendicitis (non-perforated). Serum samples were analyzed using Proton Nuclear Magnetic Resonance (1H NMR) Spectroscopy and Gas Chromatography-Mass Spectrometry (GC-MS); IPM analysis was performed using plasma bead-based multiplex profiling. Comparisons were made using multivariate data statistical analysis. Fifty-three children were included (15 severe, 38 non-severe). Separation between severe and moderate appendicitis demonstrated excellent sensitivity and specificity (100%, 88%; 14 compounds), separation between severe and mild appendicitis also showed excellent sensitivity and specificity (91%, 90%; 16 compounds). Biomarker patterns derived from metabolomics and IPM profiling are capable of distinguishing children with severe appendicitis from those with less severe disease. These findings provide an important first step towards developing non-invasive diagnostic tools for clinicians in early identification of children who are at a high risk of developing severe appendicitis.

Switching at the ribosome: riboswitches need rProteins as modulators to regulate translation.

Translational riboswitches are cis-acting RNA regulators that modulate the expression of genes during translation initiation. Their mechanism is considered as an RNA-only gene-regulatory system inducing a ligand-dependent shift of the population of functional ON- and OFF-states. The interaction of riboswitches with the translation machinery remained unexplored. For the adenine-sensing riboswitch from Vibrio vulnificus we show that ligand binding alone is not sufficient for switching to a translational ON-state but the interaction of the riboswitch with the 30S ribosome is indispensable. Only the synergy of binding of adenine and of 30S ribosome, in particular protein rS1, induces complete opening of the translation initiation region. Our investigation thus unravels the intricate dynamic network involving RNA regulator, ligand inducer and ribosome protein modulator during translation initiation.

1H, 13C and 15N assignment of stem-loop SL1 from the 5'-UTR of SARS-CoV-2.

The stem-loop (SL1) is the 5'-terminal structural element within the single-stranded SARS-CoV-2 RNA genome. It is formed by nucleotides 7-33 and consists of two short helical segments interrupted by an asymmetric internal loop. This architecture is conserved among Betacoronaviruses. SL1 is present in genomic SARS-CoV-2 RNA as well as in all subgenomic mRNA species produced by the virus during replication, thus representing a ubiquitous cis-regulatory RNA with potential functions at all stages of the viral life cycle. We present here the 1H, 13C and 15N chemical shift assignment of the 29 nucleotides-RNA construct 5_SL1, which denotes the native 27mer SL1 stabilized by an additional terminal G-C base-pair.

Exploring the Druggability of Conserved RNA Regulatory Elements in the SARS-CoV-2 Genome.

SARS-CoV-2 contains a positive single-stranded RNA genome of approximately 30 000 nucleotides. Within this genome, 15 RNA elements were identified as conserved between SARS-CoV and SARS-CoV-2. By nuclear magnetic resonance (NMR) spectroscopy, we previously determined that these elements fold independently, in line with data from in vivo and ex-vivo structural probing experiments. These elements contain non-base-paired regions that potentially harbor ligand-binding pockets. Here, we performed an NMR-based screening of a poised fragment library of 768 compounds for binding to these RNAs, employing three different 1 H-based 1D NMR binding assays. The screening identified common as well as RNA-element specific hits. The results allow selection of the most promising of the 15 RNA elements as putative drug targets. Based on the identified hits, we derive key functional units and groups in ligands for effective targeting of the RNA of SARS-CoV-2.

1H, 13C, 15N and 31P chemical shift assignment for stem-loop 4 from the 5'-UTR of SARS-CoV-2.

The SARS-CoV-2 virus is the cause of the respiratory disease COVID-19. As of today, therapeutic interventions in severe COVID-19 cases are still not available as no effective therapeutics have been developed so far. Despite the ongoing development of a number of effective vaccines, therapeutics to fight the disease once it has been contracted will still be required. Promising targets for the development of antiviral agents against SARS-CoV-2 can be found in the viral RNA genome. The 5'- and 3'-genomic ends of the 30 kb SCoV-2 genome are highly conserved among Betacoronaviruses and contain structured RNA elements involved in the translation and replication of the viral genome. The 40 nucleotides (nt) long highly conserved stem-loop 4 (5_SL4) is located within the 5'-untranslated region (5'-UTR) important for viral replication. 5_SL4 features an extended stem structure disrupted by several pyrimidine mismatches and is capped by a pentaloop. Here, we report extensive 1H, 13C, 15N and 31P resonance assignments of 5_SL4 as the basis for in-depth structural and ligand screening studies by solution NMR spectroscopy.

Assessment of Pericyte Phenotype by Flow Cytometry.

Pericytes are mural cells closely associated with endothelial cells in capillaries and microvessels. They are precursors of mesenchymal stem/stromal cells that have historically been retrospectively characterized in culture. We established a protocol, described in this chapter, to characterize and isolate pericytes from multiple human organs by flow cytometry and fluorescence-activated cell sorting. This prospective purification of pericytes brings us a step forward in the development of strategies for their use in the clinic.

Characterization of Human Pericyte Phenotype by Immunohistochemistry.

Pericytes are found in all vascularized organs and are defined anatomically as perivascular cells that closely surround endothelial cells in capillaries and microvessels and are embedded within the same basement membrane. They have been shown to have diverse physiological and pathological functions including regulation of blood pressure, and tissue regeneration and scarring. Fundamental to understanding the role these cells play in these diverse processes is the ability to accurately identify and localize them in vivo. To do this, we have developed multicolor immunohistochemistry protocols described in this chapter.

Role of Pericytes in the Development of the Renin/Angiotensin System: Induction of Functional Renin in Cultures of Pericytes.

Renal pericytes have a critical importance for angiogenesis and vascular remodeling, medullary blood flow regulation, and development of fibrosis. An emerging role for kidney pericytes is their ability to induce renin expression and synthesis. Here, we present methods for purification of human renal pericytes, their primary culture, and differentiation into renin-producing cells. Possible applications of these protocols include investigations into (1) renin cell recruitment mechanisms, (2) modulation of renin expression/secretion by small molecules, and (3) renin expression/secretion in nonrenal pericytes. A potential therapeutic application of this work is the identification of new players regulating the renin-angiotensin system.

1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5'-UTR of SARS-CoV-2.

The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5'- and 3'-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5'-untranslated region (5'-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5'-UUUCGU-3' hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive 1H, 13C and 15N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.

Assessing Unperceived Learning Needs in Continuing Medical Education for Primary Care Physicians: A Scoping Review.

INTRODUCTION: Assessing needs before developing continuing medical education/continuing professional development (CME/CPD) programs is a crucial step in the education process. A previous systematic literature review described a lack of objective evaluation for learning needs assessments in primary care physicians. This scoping review updates the literature on uses of objective evaluations to assess physicians' unperceived learning needs in CME/CPD. Identifying and understanding these approaches can inform the development of educational programs that are relevant to clinical practice and patient care. The study objectives were to (1) scope the literature since the last systematic review published in 1999; (2) conduct a comprehensive search for studies and reports that explore innovative tools and approaches to identify physicians' unperceived learning needs; (3) summarize, compare, and classify the identified approaches; and (4) map any gaps in the literature to identify future areas of research. METHODS: A scoping review was used to "map" the literature on current knowledge regarding approaches to unperceived needs assessment using conceptual frameworks for planning and assessing CME/CPD activities. RESULTS: Two prominent gaps were identified: (1) performance-based assessment strategies are highly recommended in nonresearch articles yet have low levels of implementation in published studies and (2) analysis of secondary data through patient input or environmental scanning is emphasized in grey literature implementation strategies more so than in peer-reviewed theoretical and research articles. DISCUSSION: Future evaluations should continue to incorporate multiple strategies and focus on making unperceived needs assessments actionable by describing strategies for resource management.

Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy.

The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5' end, the ribosomal frameshift segment and the 3'-untranslated region (3'-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.

1H, 13C, and 15N backbone chemical shift assignments of the nucleic acid-binding domain of SARS-CoV-2 non-structural protein 3e.

The ongoing pandemic caused by the Betacoronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) demonstrates the urgent need of coordinated and rapid research towards inhibitors of the COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome encodes for approximately 30 proteins, among them are the 16 so-called non-structural proteins (Nsps) of the replication/transcription complex. The 217-kDa large Nsp3 spans one polypeptide chain, but comprises multiple independent, yet functionally related domains including the viral papain-like protease. The Nsp3e sub-moiety contains a putative nucleic acid-binding domain (NAB) with so far unknown function and consensus target sequences, which are conceived to be both viral and host RNAs and DNAs, as well as protein-protein interactions. Its NMR-suitable size renders it an attractive object to study, both for understanding the SARS-CoV-2 architecture and drugability besides the classical virus' proteases. We here report the near-complete NMR backbone chemical shifts of the putative Nsp3e NAB that reveal the secondary structure and compactness of the domain, and provide a basis for NMR-based investigations towards understanding and interfering with RNA- and small-molecule-binding by Nsp3e.

Tasks, Techniques, and Tools for Genomic Data Visualization.

Genomic data visualization is essential for interpretation and hypothesis generation as well as a valuable aid in communicating discoveries. Visual tools bridge the gap between algorithmic approaches and the cognitive skills of investigators. Addressing this need has become crucial in genomics, as biomedical research is increasingly data-driven and many studies lack well-defined hypotheses. A key challenge in data-driven research is to discover unexpected patterns and to formulate hypotheses in an unbiased manner in vast amounts of genomic and other associated data. Over the past two decades, this has driven the development of numerous data visualization techniques and tools for visualizing genomic data. Based on a comprehensive literature survey, we propose taxonomies for data, visualization, and tasks involved in genomic data visualization. Furthermore, we provide a comprehensive review of published genomic visualization tools in the context of the proposed taxonomies.

Nutrition Center of Excellence (COE) in Inflammatory Bowel Disease-A Model and Rationale for Development.

GOALS: The goal of this study was to develop a multi-disciplinary consensus of nutrition care priorities for implementation in an IBD nutrition center of excellence (COE). BACKGROUND: The role for nutrition care in inflammatory bowel disease is broad and encompasses multiple domains. Gaps exist in the published literature around best nutrition care practices in inflammatory bowel disease and highlight the need for an evidence based approach acceptable to patients, and generalizable to a wide inflammatory bowel disease population. STUDY: Twelve health leaders in inflammatory bowel disease care attended a 1-day retreat. Two focus groups were completed using traditional focus group methodology for the first half of the retreat and a World Café method for the second half. Data analysis included review of analytic memos and conceptual analysis completed at the time of discussion, theme identification and team consensus for conceptual development. RESULTS: Three primary themes were identified as the main pillars of a COE in an IBD nutrition center of excellence. These include: a) excellence in clinical care, b) novel discovery and research, and c) knowledge translation to patients and practitioners. The key initial steps identified in this study included standardizing malnutrition screening and support while creating an environment where nutrition therapy is included as a standard of care, developing and examining the effectiveness of novel diet therapies, and translating knowledge to build capacity among care providers and patients. CONCLUSIONS: Using a 1-day retreat to identify a future direction for a center focused on nutrition excellence and align our coalition towards common goals was a successful strategy to develop consensus and identify nutrition care priorities for action.

Metabolomic and inflammatory mediator based biomarker profiling as a potential novel method to aid pediatric appendicitis identification.

Various limitations hinder the timely and accurate diagnosis of appendicitis in pediatric patients. The present study aims to investigate the potential of metabolomics and cytokine profiling for improving the diagnosis of pediatric appendicitis. Serum and plasma samples were collected from pediatric patients for metabolic and inflammatory mediator analyses respectively. Targeted metabolic profiling was performed using Proton Nuclear Magnetic Resonance Spectroscopy and Flow Injection Analysis Mass Spectrometry/Mass Spectrometry and targeted cytokine/chemokine profiling was completed using a multiplex platform to compare children with and without appendicitis. Twenty-three children with appendicitis and 35 control children without appendicitis from the Alberta Sepsis Network pediatric cohorts were included. Metabolomic profiling revealed clear separation between the two groups with very good sensitivity (80%), specificity (97%), and AUROC (0.93 ± 0.05) values. Inflammatory mediator analysis also distinguished the two groups with high sensitivity (82%), specificity (100%), and AUROC (0.97 ± 0.02) values. A biopattern comprised of 9 metabolites and 7 inflammatory compounds was detected to be significant for the separation between appendicitis and control groups. Integration of these 16 significant compounds resulted in a combined metabolic and cytokine profile that also demonstrated strong separation between the two groups with 81% sensitivity, 100% specificity and AUROC value of 0.96 ± 0.03. The study demonstrated that metabolomics and cytokine mediator profiling is capable of distinguishing children with appendicitis from those without. These results suggest a potential new approach for improving the identification of appendicitis in children.