Objective: Digital symptom-checkers (SCs) have potential to improve rheumatology triage and reduce diagnostic delays. In addition to being accurate, SCs should be user friendly and meet patient's... Show moreObjective: Digital symptom-checkers (SCs) have potential to improve rheumatology triage and reduce diagnostic delays. In addition to being accurate, SCs should be user friendly and meet patient's needs. Here, we examined usability and acceptance of Rheumatic?-a new and freely available online SC (currently with >44 000 users)-in a real-world setting. Methods: Study participants were recruited from an ongoing prospective study, and included people >= 18 years with musculoskeletal complaints completing Rheumatic? online. The user experience survey comprised five usability and acceptability questions (11-point rating scale), and an open-ended question regarding improvement of Rheumatic? Data were analysed in R using t-test or Wilcoxon rank test (group comparisons), or linear regression (continuous variables). Results: A total of 12 712 people completed the user experience survey. The study population had a normal age distribution, with a peak at 50-59 years, and 78% women. A majority found Rheumatic? useful (78%), thought the questionnaire gave them an opportunity to describe their complaints well (76%), and would recommend Rheumatic? to friends and other patients (74%). Main shortcoming was that 36% thought there were too many questions. Still, 39% suggested more detailed questions, and only 2% suggested a reduction of questions.Conclusion: Based on real-world data from the largest user evaluation study of a digital SC in rheumatology, we conclude that Rheumatic? is well accepted by women and men with rheumatic complaints, in all investigated age groups. Wide-scale adoption of Rheumatic?, therefore, seems feasible, with promising scientific and clinical implications on the horizon. Show less
Objective Digital symptom-checkers (SCs) have potential to improve rheumatology triage and reduce diagnostic delays. In addition to being accurate, SCs should be user friendly and meet patient’s... Show moreObjective Digital symptom-checkers (SCs) have potential to improve rheumatology triage and reduce diagnostic delays. In addition to being accurate, SCs should be user friendly and meet patient’s needs. Here, we examined usability and acceptance of Rheumatic?—a new and freely available online SC (currently with >44 000 users)—in a real-world setting.Methods Study participants were recruited from an ongoing prospective study, and included people ≥18 years with musculoskeletal complaints completing Rheumatic? online. The user experience survey comprised five usability and acceptability questions (11-point rating scale), and an open-ended question regarding improvement of Rheumatic? Data were analysed in R using t-test or Wilcoxon rank test (group comparisons), or linear regression (continuous variables).Results A total of 12 712 people completed the user experience survey. The study population had a normal age distribution, with a peak at 50–59 years, and 78% women. A majority found Rheumatic? useful (78%), thought the questionnaire gave them an opportunity to describe their complaints well (76%), and would recommend Rheumatic? to friends and other patients (74%). Main shortcoming was that 36% thought there were too many questions. Still, 39% suggested more detailed questions, and only 2% suggested a reduction of questions.Conclusion Based on real-world data from the largest user evaluation study of a digital SC in rheumatology, we conclude that Rheumatic? is well accepted by women and men with rheumatic complaints, in all investigated age groups. Wide-scale adoption of Rheumatic?, therefore, seems feasible, with promising scientific and clinical implications on the horizon. Show less
Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT... Show moreNucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family. Show less
Bacteria often experience external challenges, such as changes in environmental conditions or attacks by bacteriophages. To cope with these challenges, bacteria need to be able to adapt quickly to... Show moreBacteria often experience external challenges, such as changes in environmental conditions or attacks by bacteriophages. To cope with these challenges, bacteria need to be able to adapt quickly to the challenges. Key to the survival of bacteria is to be able to adapt to environmental stresses, to acquire new genetic characteristics through horizontal gene transfer to remain competitive and to silence these foreign genes as long as they do not provide any benefits. The Histone-like nucleoid structuring (H-NS) protein is a key regulator of the dynamic bacterial genome. The protein is conserved among enterobacteria and plays a determinant role in the architecture of their nucleoid acting as a global genome organizer and gene regulator. We used a homolog of H-NS, MvaT from P. aeruginosa, in which we scrutinized its structural/function relationship in response to changes in the surrounding ionic strength. We have combined integrative structural biology methods and biochemical assays to decipher the structural changes in MvaT that drive the switch between its DNA stiffening and bridging activities under different salt conditions. These structural changes appear to be conserved within the H-NS family of proteins: analysis of primary sequences of H-NS family members revealed conserved positions of charged residues. Show less
H-NS proteins act as osmotic sensors translating changes in osmolarity into altered DNA binding properties, thus, regulating enterobacterial genome organization and genes transcription. The... Show moreH-NS proteins act as osmotic sensors translating changes in osmolarity into altered DNA binding properties, thus, regulating enterobacterial genome organization and genes transcription. The molecular mechanism underlying the switching process and its conservation among H-NS family members remains elusive. Here, we focus on the H-NS family protein MvaT from Pseudomonas aeruginosa and demonstrate experimentally that its protomer exists in two different conformations, corresponding to two different functional states. In the half-opened state (dominant at low salt) the protein forms filaments along DNA, in the fully opened state (dominant at high salt) the protein bridges DNA. This switching is a direct effect of ionic strength on electrostatic interactions between the oppositely charged DNA binding and N-terminal domains of MvaT. The asymmetric charge distribution and intramolecular interactions are conserved among the H-NS family of proteins. Therefore, our study establishes a general paradigm for the molecular mechanistic basis of the osmosensitivity of H-NS proteins. Show less
Qin, L.; Erkelens, A.M.; Ben Bdira, F.; Dame, R.T. 2019
Every organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial... Show moreEvery organism across the tree of life compacts and organizes its genome with architectural chromatin proteins. While eukaryotes and archaea express histone proteins, the organization of bacterial chromosomes is dependent on nucleoid-associated proteins. In Escherichia coli and other proteobacteria, the histone-like nucleoid structuring protein (H-NS) acts as a global genome organizer and gene regulator. Functional analogues of H-NS have been found in other bacterial species: MvaT in Pseudomonas species, Lsr2 in actinomycetes and Rok in Bacillus species. These proteins complement hns− phenotypes and have similar DNA-binding properties, despite their lack of sequence homology. In this review, we focus on the structural and functional characteristics of these four architectural proteins. They are able to bridge DNA duplexes, which is key to genome compaction, gene regulation and their response to changing conditions in the environment. Structurally the domain organization and charge distribution of these proteins are conserved, which we suggest is at the basis of their conserved environment responsive behaviour. These observations could be used to find and validate new members of this protein family and to predict their response to environmental changes. Show less
The maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA and... Show moreThe maintenance and organization of the chromosome plays an important role in the development and survival of bacteria. Bacterial chromatin proteins are architectural proteins that bind DNA and modulate its conformation, and by doing so affect a variety of cellular processes. No bacterial chromatin proteins of Clostridium difficile have been characterized to date. Here, we investigate aspects of the C. difficile HupA protein, a homologue of the histone-like HU proteins of Escherichia coli. HupA is a 10-kDa protein that is present as a homodimer in vitro and self-interacts in vivo. HupA co-localizes with the nucleoid of C. difficile. It binds to the DNA without a preference for the DNA G + C content. Upon DNA binding, HupA induces a conformational change in the substrate DNA in vitro and leads to compaction of the chromosome in vivo. The present study is the first to characterize a bacterial chromatin protein in C. difficile and opens the way to study the role of chromosomal organization in DNA metabolism and on other cellular processes in this organism. Show less
Acoustic Force Spectroscopy (AFS) is a single-molecule micromanipulation technique that uses sound waves to exert force on surface-tethered DNA molecules in a microfluidic chamber. As large numbers... Show moreAcoustic Force Spectroscopy (AFS) is a single-molecule micromanipulation technique that uses sound waves to exert force on surface-tethered DNA molecules in a microfluidic chamber. As large numbers of individual protein-DNA complexes are tracked in parallel, AFS provides insight into the individual properties of such complexes as well as their population averages. In this chapter, we describe in detail how to perform AFS experiments specifically on bare DNA, protein-DNA complexes, and how to extract their (effective) persistence length and contour length from force-extension relations. Show less
DNA looping is important for genome organization in all domains of life. The basis of DNA loop formation is the bridging of two separate DNA double helices. Detecting DNA bridge formation generally... Show moreDNA looping is important for genome organization in all domains of life. The basis of DNA loop formation is the bridging of two separate DNA double helices. Detecting DNA bridge formation generally involves the use of complex single-molecule techniques (atomic force microscopy, magnetic, or optical tweezers). Although DNA bridging can be qualitatively described, quantification of DNA bridging and bridging dynamics using these techniques is challenging. Here, we describe a novel biochemical assay capable of not only detecting DNA bridge formation, but also allowing for quantification of DNA bridging efficiency and the effects of physico-chemical conditions on DNA bridge formation. Show less
Boudreau, B.A.; Hron, D.R.; Qin, L.; Valk, R.A. van der; Kotlajich, M.V.; Dame, R.T.; Landick, R. 2018
Structure of CC chemokine receptor 2 with orthosteric and allosteric antagonistsYi Zheng, Ling Qin, Natalia V. Ortiz Zacarías, Henk de Vries, Gye Won Han, Martin Gustavsson, Marta Dabros, Chunxia...Show moreStructure of CC chemokine receptor 2 with orthosteric and allosteric antagonistsYi Zheng, Ling Qin, Natalia V. Ortiz Zacarías, Henk de Vries, Gye Won Han, Martin Gustavsson, Marta Dabros, Chunxia Zhao, Robert J. Cherney, Percy Carter, Dean Stamos, Ruben Abagyan, Vadim Cherezov, Raymond C. Stevens, Adriaan P. IJzerman, Laura H. Heitman, Andrew Tebben, Irina Kufareva & Tracy M. HandelCC chemokine receptor 2 (CCR2) is one of 19 members of the chemokine receptor subfamily of human class A G-protein-coupled receptors. CCR2 is expressed on monocytes, immature dendritic cells, and T-cell subpopulations, and mediates their migration towards endogenous CC chemokine ligands such as CCL2 (ref. 1). CCR2 and its ligands are implicated in numerous inflammatory and neurodegenerative diseases2 including atherosclerosis, multiple sclerosis, asthma, neuropathic pain, and diabetic nephropathy, as well as cancer3. These disease associations have motivated numerous preclinical studies and clinical trials4 (see http://www.clinicaltrials.gov) in search of therapies that target the CCR2–chemokine axis. To aid drug discovery efforts5, here we solve a structure of CCR2 in a ternary complex with an orthosteric (BMS-681 (ref. 6)) and allosteric (CCR2-RA-[R]7) antagonist. BMS-681 inhibits chemokine binding by occupying the orthosteric pocket of the receptor in a previously unseen binding mode. CCR2-RA-[R] binds in a novel, highly druggable pocket that is the most intracellular allosteric site observed in class A G-protein-coupled receptors so far; this site spatially overlaps the G-protein-binding site in homologous receptors. CCR2-RA-[R] inhibits CCR2 non-competitively by blocking activation-associated conformational changes and formation of the G-protein-binding interface. The conformational signature of the conserved microswitch residues observed in double-antagonist-bound CCR2 resembles the most inactive G-protein-coupled receptor structures solved so far. Like other protein–protein interactions, receptor–chemokine complexes are considered challenging therapeutic targets for small molecules, and the present structure suggests diverse pocket epitopes that can be exploited to overcome obstacles in drug design. Show less
Methylation of the 5'-cap structure of viral RNAs plays important roles in genome replication and evasion of innate recognition of viral RNAs by cellular sensors. It is known that coronavirus nsp14... Show moreMethylation of the 5'-cap structure of viral RNAs plays important roles in genome replication and evasion of innate recognition of viral RNAs by cellular sensors. It is known that coronavirus nsp14 acts as an N7-(guanine)-methyltransferase (MTase) and nsp16 as a 2'-O-MTase, which are involved in the modification of RNA cap structure. However, these enzymatic activities have not been shown for any other nidoviruses beyond coronaviruses in the order Nidovirales. In this study, we identified a 2'-O-methyltransferase encoded by ronivirus that shows common and unique features in comparison with that of coronaviruses. Ronivirus 2'-O-MTase does not need a protein cofactor for MTase activity, whereas coronavirus nsp16 needs the stimulating factor nsp10 for its full activity. The conserved K-D-K-E catalytic tetrad is identified in ronivirus 2'-O-MTase. These results extend our understanding of nidovirus RNA capping and methylation beyond coronaviruses and also strengthen the evolutionary and functional links between roniviruses and coronaviruses. Show less
