Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.Comment: ReVTeX, 15 pages, 18 figure

European guideline (EuroGuiDerm) on atopic eczema - part II: non-systemic treatments and treatment recommendations for special AE patient populations.

The evidence- and consensus-based guideline on atopic eczema was developed in accordance with the EuroGuiDerm Guideline and Consensus Statement Development Manual. Four consensus conferences were held between December 2020 and July 2021. Twenty-nine experts (including clinicians and patient representatives) from 12 European countries participated. This second part of the guideline includes recommendations and detailed information on basic therapy with emollients and moisturizers, topical anti-inflammatory treatment, antimicrobial and antipruritic treatment and UV phototherapy. Furthermore, this part of the guideline covers techniques for avoiding provocation factors, as well as dietary interventions, immunotherapy, complementary medicine and educational interventions for patients with atopic eczema and deals with occupational and psychodermatological aspects of the disease. It also contains guidance on treatment for paediatric and adolescent patients and pregnant or breastfeeding women, as well as considerations for patients who want to have a child. A chapter on the patient perspective is also provided. The first part of the guideline, published separately, contains recommendations and guidance on systemic treatment with conventional immunosuppressive drugs, biologics and janus kinase (JAK) inhibitors, as well as information on the scope and purpose of the guideline, and a section on guideline methodology

First update of the living European guideline (EuroGuiDerm) on atopic eczema

First update of the living European guideline (EuroGuiDerm) on atopic eczem

High Diversity of vacA and cagA Helicobacter pylori Genotypes in Patients with and without Gastric Cancer

BACKGROUND: Helicobacter pylori is associated with chronic gastritis, peptic ulcers, and gastric cancer. The aim of this study was to assess the topographical distribution of H. pylori in the stomach as well as the vacA and cagA genotypes in patients with and without gastric cancer. METHODOLOGY/PRINCIPAL FINDINGS: Three gastric biopsies, from predetermined regions, were evaluated in 16 patients with gastric cancer and 14 patients with dyspeptic symptoms. From cancer patients, additional biopsy specimens were obtained from tumor centers and margins; among these samples, the presence of H. pylori vacA and cagA genotypes was evaluated. Positive H. pylori was 38% and 26% in biopsies obtained from the gastric cancer and non-cancer groups, respectively (p = 0.008), and 36% in tumor sites. In cancer patients, we found a preferential distribution of H. pylori in the fundus and corpus, whereas, in the non-cancer group, the distribution was uniform (p = 0.003). A majority of the biopsies were simultaneously cagA gene-positive and -negative. The fundus and corpus demonstrated a higher positivity rate for the cagA gene in the non-cancer group (p = 0.036). A mixture of cagA gene sizes was also significantly more frequent in this group (p = 0.003). Ninety-two percent of all the subjects showed more than one vacA gene genotype; s1b and m1 vacA genotypes were predominantly found in the gastric cancer group. The highest vacA-genotype signal-sequence diversity was found in the corpus and 5 cm from tumor margins. CONCLUSION/SIGNIFICANCE: High H. pylori colonization diversity, along with the cagA gene, was found predominantly in the fundus and corpus of patients with gastric cancer. The genotype diversity observed across systematic whole-organ and tumor sampling was remarkable. We find that there is insufficient evidence to support the association of one isolate with a specific disease, due to the multistrain nature of H. pylori infection shown in this work

A Participatory Return-to-Work Program for Temporary Agency Workers and Unemployed Workers Sick-Listed Due to Musculoskeletal Disorders: a Process Evaluation Alongside a Randomized Controlled Trial

Introduction Beside (cost-)effectiveness, the feasibility of an intervention is important for successful implementation in daily practice. This study concerns the process evaluation of a newly developed participatory return-to-work (RTW) program for workers without an employment contract, sick-listed due to musculoskeletal disorders. The program consisted of a stepwise process, guided by an independent RTW coordinator, aimed at making a consensus-based RTW plan with the possibility of a temporary (therapeutic) workplace. The aims of this study were to describe the reach and extent of implementation of the new program, the satisfaction and experiences of all stakeholders, and the perceived barriers and facilitators for implementation of the program in daily practice. Methods Temporary agency workers and unemployed workers, sick-listed for 2–8 weeks due to musculoskeletal disorders were eligible for this study. Data were collected from the workers; their insurance physicians and labour experts at the Dutch Social Security Agency; RTW coordinators; and case managers from participating vocational rehabilitation agencies. Data collection took place using professionals’ reports, standardized matrices, questionnaires at baseline and at 3-month follow-up, and group interviews with the professionals. Results Of the 79 workers who were allocated to the participatory RTW program group, 72 workers actually started with the intervention. Overall, implementation of the program was performed according to protocol. However, offering of suitable temporary workplaces was delayed with 44.5 days. Results showed satisfaction with the RTW coordinator among the workers and three quarters of the labour experts experienced a minor or major contribution of the presence of the RTW coordinator. Several barriers for implementation were identified, such as the administrative time-investment, unclear information about the program, no timely offering of temporary (therapeutic) workplaces, and the need for additional support in case of complex health problems. Conclusions This study indicates overall feasibility for implementation of the participatory RTW program in daily practice. However, to overcome important barriers, more attention should be paid to improve timely offering of suitable temporary workplaces, to describe more clearly the program goals and the professional’s roles, and to offer additional support for workers suffering from complex multi-causal health problems. Trial registration NTR1047

European guideline (EuroGuiDerm) on atopic eczema – part II: non-systemic treatments and treatment recommendations for special AE patient populations

The evidence- and consensus-based guideline on atopic eczema was developed in accordance with the EuroGuiDerm Guideline and Consensus Statement Development Manual. Four consensus conferences were held between December 2020 and July 2021. Twenty-nine experts (including clinicians and patient representatives) from 12 European countries participated. This second part of the guideline includes recommendations and detailed information on basic therapy with emollients and moisturizers, topical anti-inflammatory treatment, antimicrobial and antipruritic treatment and UV photo- therapy. Furthermore, this part of the guideline covers techniques for avoiding provocation factors, as well as dietaryinterventions, immunotherapy, complementary medicine and educational interventions for patients with atopic eczema and deals with occupational and psychodermatological aspects of the disease. It also contains guidance on treatment for paediatric and adolescent patients and pregnant or breastfeeding women, as well as considerations for patients who want to have a child. A chapter on the patient perspective is also provided. The first part of the guideline, published sepa- rately, contains recommendations and guidance on systemic treatment with conventional immunosuppressive drugs, biologics and janus kinase (JAK) inhibitors, as well as information on the scope and purpose of the guideline, and a sec- tion on guideline methodology. Received: 17 February 2022; Accepted: 3 June 202

Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae

<p>Abstract</p> <p>Background</p> <p>Recent advances in the field of high-throughput genomics have rendered possible the performance of genome-scale studies to define the nucleosomal landscapes of eukaryote genomes. Such analyses are aimed towards providing a better understanding of the process of nucleosome positioning, for which several models have been suggested. Nevertheless, questions regarding the sequence constraints of nucleosomal DNA and how they may have been shaped through evolution remain open. In this paper, we analyze in detail different experimental nucleosome datasets with the aim of providing a hypothesis for the emergence of nucleosome-forming sequences.</p> <p>Results</p> <p>We compared the complete sets of nucleosome positions for the budding yeast (<it>Saccharomyces cerevisiae</it>) as defined in the output of two independent experiments with the use of two different experimental techniques. We found that < 10% of the experimentally defined nucleosome positions were consistently positioned in both datasets. This subset of well-positioned nucleosomes, when compared with the bulk, was shown to have particular properties at both sequence and structural levels. Consistently positioned nucleosomes were also shown to occur preferentially in pairs of dinucleosomes, and to be surprisingly less conserved compared with their adjacent nucleosome-free linkers.</p> <p>Conclusion</p> <p>Our findings may be combined into a hypothesis for the emergence of a weak nucleosome-positioning code. According to this hypothesis, consistent nucleosomes may be partly guided by nearby nucleosome-free regions through statistical positioning. Once established, a set of well-positioned consistent nucleosomes may impose secondary constraints that further shape the structure of the underlying DNA. We were able to capture these constraints through the application of a recently introduced structural property that is related to the symmetry of DNA curvature. Furthermore, we found that both consistently positioned nucleosomes and their adjacent nucleosome-free regions show an increased tendency towards conservation of this structural feature.</p

Intervention mapping for development of a participatory return-to-work intervention for temporary agency workers and unemployed workers sick-listed due to musculoskeletal disorders

BACKGROUND: In the past decade in activities aiming at return-to-work (RTW), there has been a growing awareness to change the focus from sickness and work disability to recovery and work ability. To date, this process in occupational health care (OHC) has mainly been directed towards employees. However, within the working population there are two vulnerable groups: temporary agency workers and unemployed workers, since they have no workplace/employer to return to, when sick-listed. For this group there is a need for tailored RTW strategies and interventions. Therefore, this paper aims to describe the structured and stepwise process of development, implementation and evaluation of a theory- and practise-based participatory RTW program for temporary agency workers and unemployed workers, sick-listed due to musculoskeletal disorders (MSD). This program is based on the already developed and cost-effective RTW program for employees, sick-listed due to low back pain. METHODS: The Intervention Mapping (IM) protocol was used to develop a tailor-made RTW program for temporary agency workers and unemployed workers, sick-listed due to MSD. The Attitude-Social influence-self-Efficacy (ASE) model was used as a theoretical framework for determinants of behaviour regarding RTW of the sick-listed worker and development of the intervention. To ensure participation and facilitate successful adoption and implementation, important stakeholders were involved in all steps of program development and implementation. Results of semi-structured interviews and 'fine-tuning' meetings were used to design the final participatory RTW program. RESULTS: A structured stepwise RTW program was developed, aimed at making a consensus-based RTW implementation plan. The new program starts with identifying obstacles for RTW, followed by a brainstorm session in which the sick-listed worker and the labour expert of the Social Security Agency (SSA) formulate solutions/possibilities for suitable (therapeutic) work. This process is guided by an independent RTW coordinator to achieve consensus. Based on the resulting RTW implementation plan, to create an actual RTW perspective, a vocational rehabilitation agency is assigned to find a matching (therapeutic) workplace. The cost-effectiveness of this participatory RTW program will be evaluated in a randomised controlled trial. CONCLUSION: IM is a promising tool for the development of tailor-made OHC interventions for the vulnerable working populatio

Dengue Virus Capsid Protein Binds Core Histones and Inhibits Nucleosome Formation in Human Liver Cells

Dengue virus (DENV) is a member of the Flaviviridae and a globally (re)emerging pathogen that causes serious human disease. There is no specific antiviral or vaccine for dengue virus infection. Flavivirus capsid (C) is a structural protein responsible for gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. Flaviviral replication is known to occur in the cytoplasm yet a large portion of capsid protein localizes to the nucleus during infection. The reasons for the nuclear presences of capsid are not completely understood. Here, we expressed mature DENV C in a tandem affinity purification assay to identify potential binding partners in human liver cells. DENV C targeted the four core histones, H2A, H2B, H3 and H4. DENV C bound recombinant histones in solution and colocalized with histones in the nucleus and cytoplasm of liver cells during DENV infection. We show that DENV C acts as a histone mimic, forming heterodimers with core histones, binding DNA and disrupting nucleosome formation. We also demonstrate that DENV infection increases the amounts of core histones in livers cells, which may be a cellular response to C binding away the histone proteins. Infection with DENV additionally alters levels of H2A phosphorylation in a time-dependent manner. The interactions of C and histones add an interesting new role for the presence of C in the nucleus during DENV infection