DNA Spools under Tension

DNA-spools, structures in which DNA is wrapped and helically coiled onto itself or onto a protein core are ubiquitous in nature. We develop a general theory describing the non-equilibrium behavior of DNA-spools under linear tension. Two puzzling and seemingly unrelated recent experimental findings, the sudden quantized unwrapping of nucleosomes and that of DNA toroidal condensates under tension are theoretically explained and shown to be of the same origin. The study provides new insights into nucleosome and chromatin fiber stability and dynamics

Gamifying self-management of chronic illnesses: amixed-methods study

Background: Self-management of chronic illnesses is an ongoing issue in health care research. Gamification is a concept that arose in the field of computer science and has been borrowed by many other disciplines. It is perceived by many that gamification can improve the self-management experience of people with chronic illnesses. This paper discusses the validation of a framework (called The Wheel of Sukr) that was introduced to achieve this goal.Objective: This research aims to (1) discuss a gamification framework targeting the self-management of chronic illnesses and (2) validate the framework by diabetic patients, medical professionals, and game experts.Methods: A mixed-method approach was used to validate the framework. Expert interviews (N=8) were conducted in order to validate the themes of the framework. Additionally, diabetic participants completed a questionnaire (N=42) in order to measure their attitudes toward the themes of the framework.Results: The results provide a validation of the framework. This indicates that gamification might improve the self-management of chronic illnesses, such as diabetes. Namely, the eight themes in the Wheel of Sukr (fun, esteem, socializing, self-management, self-representation, motivation, growth, sustainability) were perceived positively by 71% (30/42) of the participants with P value <.001.Conclusions: In this research, both the interviews and the questionnaire yielded positive results that validate the framework (The Wheel of Sukr). Generally, this study indicates an overall acceptance of the notion of gamification in the self-management of diabete

A Phase 1B, randomized, double blind, placebo controlled, multiple-dose escalation study of NSI-189 phosphate, a neurogenic compound, in depressed patients

We wanted to examine tolerability and efficacy of NSI-189, a benzylpiperizine-aminiopyridine neurogenic compound for treating major depressive disorder (MDD). This was a Phase 1B, double blind, randomized, placebo controlled, multiple-dose study with three cohorts. The first cohort received 40 mg q.d. (n=6) or placebo (n=2), the second cohort 40 mg b.i.d. (n=6) or placebo (n=2), and the third cohort 40 mg t.i.d. (n=6) or placebo (n=2). Twenty-four patients with MDD were recruited, with the diagnosis and severity confirmed through remote interviews. Eligible patients received NSI-189 or placebo for 28 days in an inpatient setting with assessments for safety, pharmacokinetics (PK) and efficacy. Outpatient follow-up visits were conducted until day 84 (±3). NSI-189 was relatively well tolerated at all doses, with no serious adverse effects. NSI-189 area under the curve increased in a dose-related and nearly proportional manner across the three cohorts, with a half-life of 17.4–20.5 h. The exploratory efficacy measurements, including Symptoms Of Depression Questionnaire (SDQ), Montgomery-Asberg Depression Scale (MADRS), Clinical Global Impressions—Improvement (CGI-I), and The Massachusetts General Hospital (MGH) Cognitive and Physical Functioning Questionnaire (CPFQ) showed a promising reduction in depressive and cognitive symptoms across all measures for NSI-189, with significant improvement in the SDQ and CPFQ, and a medium to large effect size for all measures. These improvements persisted during the follow-up phase. In summary, NSI-189 shows potential as a treatment for MDD in an early phase study. The main limitation of this preliminary study was the small sample size of each cohort

Single-molecule experiments in biological physics: methods and applications

I review single-molecule experiments (SME) in biological physics. Recent technological developments have provided the tools to design and build scientific instruments of high enough sensitivity and precision to manipulate and visualize individual molecules and measure microscopic forces. Using SME it is possible to: manipulate molecules one at a time and measure distributions describing molecular properties; characterize the kinetics of biomolecular reactions and; detect molecular intermediates. SME provide the additional information about thermodynamics and kinetics of biomolecular processes. This complements information obtained in traditional bulk assays. In SME it is also possible to measure small energies and detect large Brownian deviations in biomolecular reactions, thereby offering new methods and systems to scrutinize the basic foundations of statistical mechanics. This review is written at a very introductory level emphasizing the importance of SME to scientists interested in knowing the common playground of ideas and the interdisciplinary topics accessible by these techniques. The review discusses SME from an experimental perspective, first exposing the most common experimental methodologies and later presenting various molecular systems where such techniques have been applied. I briefly discuss experimental techniques such as atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers (MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I then present several applications of SME to the study of nucleic acids (DNA, RNA and DNA condensation), proteins (protein-protein interactions, protein folding and molecular motors). Finally, I discuss applications of SME to the study of the nonequilibrium thermodynamics of small systems and the experimental verification of fluctuation theorems. I conclude with a discussion of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond. Matt

Glucagon-Like Peptide-1 Protects Human Islets against Cytokine-Mediated β-Cell Dysfunction and Death: A Proteomic Study of the Pathways Involved

Glucagon-like peptide-1 (GLP-1) has been shown to protect pancreatic β-cells against cytokine-induced dysfunction and destruction. The mechanisms through which GLP-1 exerts its effects are complex and still poorly understood. The aim of this study was to analyze the protein expression profiles of human islets of Langerhans treated with cytokines (IL-1β and IFN-γ) in the presence or absence of GLP-1 by 2D difference gel electrophoresis and subsequent protein interaction network analysis to understand the molecular pathways involved in GLP-1-mediated β-cell protection. Co-incubation of cytokine-treated human islets with GLP-1 resulted in a marked protection of β-cells against cytokine-induced apoptosis and significantly attenuated cytokine-mediated inhibition of glucose-stimulated insulin secretion. The cytoprotective effects of GLP-1 coincided with substantial alterations in the protein expression profile of cytokine-treated human islets, illustrating a counteracting effect on proteins from different functional classes such as actin cytoskeleton, chaperones, metabolic proteins, and islet regenerating proteins. In summary, GLP-1 alters in an integrated manner protein networks in cytokine-exposed human islets while protecting them against cytokine-mediated cell death and dysfunction. These data illustrate the beneficial effects of GLP-1 on human islets under immune attack, leading to a better understanding of the underlying mechanisms involved, a prerequisite for improving therapies for diabetic patients.status: publishe

Deletion and Down-Regulation of HRH4 Gene in Gastric Carcinomas: A Potential Correlation with Tumor Progression

Background: Histamine is an established growth factor for gastrointestinal malignancies. The effect of histamine is largely determined locally by the histamine receptor expression pattern. Histamine receptor H4 (HRH4), the newest member of the histamine receptor family, is positively expressed on the epithelium of the gastrointestinal tract, and its function remains to be elucidated. Previously, we reported the decreased expression of HRH4 in colorectal cancers and revealed its correlation with tumor proliferation. In the current study, we aimed to investigate the abnormalities of HRH4 gene in gastric carcinomas (GCs). Methodology/Principal Findings: We analyzed H4R expression in collected GC samples by quantitative PCR, Western blot analysis, and immunostaining. Our results showed that the protein and mRNA levels of HRH4 were reduced in some GC samples, especially in advanced GC samples. Copy number decrease of HRH4 gene was observed (17.6%, 23 out of 131), which was closely correlated with the attenuated expression of H4R. In vitro studies, using gastric cancer cell lines, showed that the alteration of HRH4 expression on gastric cancer cells influences tumor growth upon exposure to histamine. Conclusions/Significance: We show for the first time that deletion of HRH4 gene is present in GC cases and is closely correlated with attenuated gene expression. Down-regulation of HRH4 in gastric carcinomas plays a role in histaminemediate

DOGS: Reaction-Driven de novo Design of Bioactive Compounds

We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds. The quality of the designed compounds is assessed by a graph kernel method measuring their similarity to known bioactive reference ligands in terms of structural and pharmacophoric features. We implemented a deterministic compound construction procedure that explicitly considers compound synthesizability, based on a compilation of 25'144 readily available synthetic building blocks and 58 established reaction principles. This enables the software to suggest a synthesis route for each designed compound. Two prospective case studies are presented together with details on the algorithm and its implementation. De novo designed ligand candidates for the human histamine H4 receptor and γ-secretase were synthesized as suggested by the software. The computational approach proved to be suitable for scaffold-hopping from known ligands to novel chemotypes, and for generating bioactive molecules with drug-like properties

Perceptions of quality across the maternal care continuum in the context of a health financing intervention: Evidence from a mixed methods study in rural Malawi

Background: In 2013, Malawi with its development partners introduced a Results-Based Financing for Maternal and Newborn Health (RBF4MNH) intervention to improve the quality of maternal and newborn health-care services. Financial incentives are awarded to health facilities conditional on their performance and to women for delivering in the health facility. We assessed the effect of the RBF4MNH on quality of care from women’s perspectives. Methods: We used a mixed-method prospective sequential controlled pre- and post-test design. We conducted 3060 structured client exit interviews, 36 in-depth interviews and 29 focus group discussions (FGDs) with women and 24 in-depth interviews with health service providers between 2013 and 2015. We used difference-in-differences regression models to measure the effect of the RBF4MNH on experiences and perceived quality of care. We used qualitative data to explore the matter more in depth. Results: We did not observe a statistically significant effect of the intervention on women’s perceptions of technical care, quality of amenities and interpersonal relations. However, in the qualitative interviews, most women reported improved health service provision as a result of the intervention. RBF4MNH increased the proportion of women reporting to have received medications/treatment during childbirth. Participants in interviews expressed that drugs, equipment and supplies were readily available due to the RBF4MNH. However, women also reported instances of neglect, disrespect and verbal abuse during the process of care. Providers attributed these negative instances to an increased workload resulting from an increased number of women seeking services at RBF4MNH facilities. Conclusion: Our qualitative findings suggest improvements in the availability of drugs and supplies due to RBF4MNH. Despite the intervention, challenges in the provision of quality care persisted, especially with regard to interpersonal relations. RBF interventions may need to consider including indicators that specifically target the provision of respectful maternity care as a means to foster providers’ positive attitudes towards women in labour. In parallel, governments should consider enhancing staff and infrastructural capacity before implementing RBF