A scoping review protocol to map the evidence on interventions to prevent overweight and obesity in children

Introduction. Obesity has become one of the biggest public health problems of the 21st century. Prevalence of obesity in children and adolescents has increased dramatically worldwide over the last 20 years, and this trend is expected to continue. Obesity in childhood is concerning as it predicts obesity in adulthood, a common risk factors for a wide array of chronic diseases and poor health outcomes. Obesity is preventable and a vast but fragmented body of evidence on preventative interventions is now available. This article outlines the protocol for a scoping review of published literature reviews on interventions to prevent obesity in children. The scoping review addresses the broad research question: What is the evidence on interventions to prevent childhood obesity? It aims to give an overview of the various interventions available, to understand those which are effective and to identify barriers and facilitators to their effectiveness. Methods and analysis. The six-staged Arksey and O'Malley methodology framework is used to guide the scoping review process. Following the definition of the research questions (stage 1), the eligibility criteria and search strategy are defined (stage 2). The study selection process based on the eligibility criteria identified will follow (stage 3). A framework developed for this review will then inform the extraction and charting of data from the included reviews (stage 4) and results will be aggregated and summarized with criteria relevant for health professionals and policy makers (stage 5). The optional consultation (stage 6) exercise is not planned. Ethics and dissemination. Since the scoping review methodology aims at synthetizing information from available publications, this study does not require ethical approval. An article reporting the results of the scoping review will be submitted for publication to a scientific journal, presented at relevant conferences and disseminated as part of future workshops with professionals involved in obesity prevention

Einfluss gekrümmter Sequenzen auf Fernwechselwirkungen in superhelikaler DNA

Gekrümmte Sequenzbereiche nehmen bevorzugt eine Endschleifenposition in scDNA ein. Daraus sollte eine festgelegte dreidimensionale scDNA-Konformation resultieren, die die Wechselwirkungswahrscheinlichkeit von entfernt liegenden Orten in der DNA beeinflusst. Der Einfluss von Krümmung auf Fernwechselwirkungen in scDNA wurde durch kinetische Messungen der intramolekularen Vernetzung zweier sequenzspezifisch biotinylierter Stellen in der DNA über Streptavidin charakterisiert. Die Markierung der DNA erfolgte über triplexbildende Oligonukleotide (TFOs), die mit Biotin modifiziert waren. Die Biotinylierungsstellen lagen flankierend zu einer Insertion, die eine sequenzinduzierte Krümmung aufweist. Es wurde die lokale Konzentration JM einer Biotinylierungsposition in der Umgebung der zweiten und intramolekulare Reaktionskonstanten bestimmt. Die jM-Werte wurden mit Computersimulationen der untersuchten DNAs verglichen. Für scDNA ohne Krümmung stimmten experimentelle und simulierte Befunde nahezu genau überein. Weiterhin sank jM in quantitativer Übereinstimmung mit den Simulationen für zunehmend asymmetrische Positionen der Marker in Relation zur Krümmung. Allerdings widersprach eine geringe Erhöhung von jM in scDNA mit Krümmung gegenüber einer Kontrolle ohne Krümmung den Simulationen, die einen stärkeren Einfluss erwarten ließen. Dies ist wahrscheinlich auf eine sterische Behinderung des an einer biotinylierten Stelle gebundenen Strept-POD in der Superhelix zurückzuführen. Der Effekt trat in scDNA mit Krümmung, dessen Bewegungsfreiheitsgrade wegen der Endschleifenposition der Krümmung reduziert sind, deutlich hervor. Die Befunde deuten darauf hin, dass eine lokale Krümmung in scDNA Interaktionen zwischen Orten über große Entfernungen beeinflussen kan

Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR

The Escherichia coli low-copy-number plasmid R1 contains a segregation machinery composed of parC, ParR and parM. The R1 centromere-like site parC contains two separate sets of repeats. By atomic force microscopy (AFM) we show here that ParR molecules bind to each of the 5-fold repeated iterons separately with the intervening sequence unbound by ParR. The two ParR protein complexes on parC do not complex with each other. ParR binds with a stoichiometry of about one ParR dimer per each single iteron. The measured DNA fragment lengths agreed with B-form DNA and each of the two parC 5-fold interon DNA stretches adopts a linear path in its complex with ParR. However, the overall parC/ParR complex with both iteron repeats bound by ParR forms an overall U-shaped structure: the DNA folds back on itself nearly completely, including an angle of ∼150°. Analysing linear DNA fragments, we never observed dimerized ParR complexes on one parC DNA molecule (intramolecular) nor a dimerization between ParR complexes bound to two different parC DNA molecules (intermolecular). This bacterial segrosome is compared to other bacterial segregation complexes. We speculate that partition complexes might have a similar overall structural organization and, at least in part, common functional properties

Segrosome assembly at the pliable parH centromere

The segrosome of multiresistance plasmid TP228 comprises ParF, which is a member of the ParA ATPase superfamily, and the ParG ribbon–helix–helix factor that assemble jointly on the parH centromere. Here we demonstrate that the distinctive parH site (∼100-bp) consists of an array of degenerate tetramer boxes interspersed by AT-rich spacers. Although numerous consecutive AT-steps are suggestive of inherent curvature, parH lacks an intrinsic bend. Sequential deletion of parH tetramers progressively reduced centromere function. Nevertheless, the variant subsites could be rearranged in different geometries that accommodated centromere activity effectively revealing that the site is highly elastic in vivo. ParG cooperatively coated parH: proper centromere binding necessitated the protein's N-terminal flexible tails which modulate the centromere binding affinity of ParG. Interaction of the ParG ribbon–helix–helix domain with major groove bases in the tetramer boxes likely provides direct readout of the centromere. In contrast, the AT-rich spacers may be implicated in indirect readout that mediates cooperativity between ParG dimers assembled on adjacent boxes. ParF alone does not bind parH but instead loads into the segrosome interactively with ParG, thereby subtly altering centromere conformation. Assembly of ParF into the complex requires the N-terminal flexible tails in ParG that are contacted by ParF

Protein/DNA interactions in complex DNA topologies: expect the unexpected

DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology

Organisation of nucleosomal arrays reconstituted with repetitive African green monkey α-satellite DNA as analysed by atomic force microscopy

Alpha-satellite DNA (AS) is part of centromeric DNA and could be relevant for centromeric chromatin structure: its repetitive character may generate a specifically ordered nucleosomal arrangement and thereby facilitate kinetochore protein binding and chromatin condensation. Although nucleosomal positioning on some satellite sequences had been shown, including AS from African green monkey (AGM), the sequence-dependent nucleosomal organisation of repetitive AS of this species has so far not been analysed. We therefore studied the positioning of reconstituted nucleosomes on AGM AS tandemly repeated DNA. Enzymatic analysis of nucleosome arrays formed on an AS heptamer as well as the localisation of mononucleosomes on an AS dimer by atomic force microscopy (AFM) showed one major positioning frame, in agreement with earlier results. The occupancy of this site was in the range of 45–50%, in quite good agreement with published in vivo observations. AFM measurements of internucleosomal distances formed on the heptamer indicated that the nucleosomal arrangement is governed by sequence-specific DNA-histone interactions yielding defined internucleosomal distances, which, nevertheless, are not compatible with a uniform phasing of the nucleosomes with the AGM AS repeats

Filamentous Biopolymers on Surfaces: Atomic Force Microscopy Images Compared with Brownian Dynamics Simulation of Filament Deposition

Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarly on the interaction strength between the filament and the support: i) For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii) For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a ‘trapping’ mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these ‘ideal’ adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica (‘ideal’ trapping) and on glass (‘ideal’ equilibrated) with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions

Efficient preparation of internally modified single-molecule constructs using nicking enzymes

Investigations of enzymes involved in DNA metabolism have strongly benefited from the establishment of single molecule techniques. These experiments frequently require elaborate DNA substrates, which carry chemical labels or nucleic acid tertiary structures. Preparing such constructs often represents a technical challenge: long modified DNA molecules are usually produced via multi-step processes, involving low efficiency intermolecular ligations of several fragments. Here, we show how long stretches of DNA (>50 bp) can be modified using nicking enzymes to produce complex DNA constructs. Multiple different chemical and structural modifications can be placed internally along DNA, in a specific and precise manner. Furthermore, the nicks created can be resealed efficiently yielding intact molecules, whose mechanical properties are preserved. Additionally, the same strategy is applied to obtain long single-strand overhangs subsequently used for efficient ligation of ss- to dsDNA molecules. This technique offers promise for a wide range of applications, in particular single-molecule experiments, where frequently multiple internal DNA modifications are required

The most frequent short sequences in non-coding DNA

The purpose of this work is to determine the most frequent short sequences in non-coding DNA. They may play a role in maintaining the structure and function of eukaryotic chromosomes. We present a simple method for the detection and analysis of such sequences in several genomes, including Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster and Homo sapiens. We also study two chromosomes of man and mouse with a length similar to the whole genomes of the other species. We provide a list of the most common sequences of 9–14 bases in each genome. As expected, they are present in human Alu sequences. Our programs may also give a graph and a list of their position in the genome. Detection of clusters is also possible. In most cases, these sequences contain few alternating regions. Their intrinsic structure and their influence on nucleosome formation are not known. In particular, we have found new features of short sequences in C. elegans, which are distributed in heterogeneous clusters. They appear as punctuation marks in the chromosomes. Such clusters are not found in either A. thaliana or D. melanogaster. We discuss the possibility that they play a role in centromere function and homolog recognition in meiosis

Enzymatic Digestion of Single DNA Molecules Anchored on Nanogold-Modified Surfaces

To study enzyme–DNA interactions at single molecular level, both the attachment points and the immediate surroundings of surfaces must be carefully considered such that they do not compromise the structural information and biological properties of the sample under investigation. The present work demonstrates the feasibility of enzymatic digestion of single DNA molecules attached to nanoparticle-modified surfaces. With Nanogold linking DNA to the mica surface by electrostatic interactions, advantageous conditions with fewer effects on the length and topography of DNA are obtained, and an appropriate environment for the activities of DNA is created. We demonstrate that by using Dip-Pen Nanolithography, individual DNA molecules attached to modified mica surfaces can be efficiently digested by DNase I