Targeting Limb Muscle Dysfunction in COPD

Chronic obstructive pulmonary disease (COPD), is today one of the world’s most common chronic diseases, estimated by the World Health Organization to be the third leading cause of death worldwide by the year 2030. An often neglected aspect of COPD is that the course of the disease is linked to extrapulmonary manifestations that are currently not dealt with optimally, but that has a direct and substantial impact on the condition. Limb muscle dysfunction, at the functional level defined as the reduction of either strength or endurance (or both) properties of the muscle, is highly prevalent in COPD, closely linked to critical clinical and prognostic outcomes including functional status, quality of life, and even mortality. If the goal is to improve limb muscle function among people with COPD is exercise training recommended before other treatment modalities, highly prioritized in international guidelines. In this chapter, why and how to assess and manage limb muscle dysfunction among people with COPD will be targeted, highlighting the vital role of physical therapy and the physiotherapist

Exploring DNA-protein interactions on the single DNA molecule level using nanofluidic tools

DNA-protein interactions are at the core of the cellular machinery and single molecule methods have revolutionized the possibilities to study, and our understanding of these interactions on the molecular level. Nanofluidic channels have been extensively used for studying single DNA molecules during the last twelve years and in this review, we discuss how this experimental platform has been extended to studies of DNA-protein interactions. We first present how the design of the device can be tailored for the specific DNA-protein system studied and how the channels can be passivated to avoid non-specific binding of proteins. We then focus on describing the different kinds of DNA-interacting proteins that have been studied in nanofluidic devices, including proteins that compact DNA and proteins that form filaments on DNA. Our main objective is to highlight the diverse functionalitiesof DNA-protein systems that have been characterized using nanofluidic structures and hence demonstrate the versatility of these experimental tools. We finally discuss potential future directions studies of DNA-protein complexes in nanochannels might take, including specific DNA-protein systems that are difficult to analyze with traditional techniques, devices with increased complexity, and fully integrated lab-on-a-chip devices for analysis of material extracted from (single) cells

Raising awareness for water polution based on game activities using internet of things

Awareness among young people regarding the environment and its resources and comprehension of the various factors that interplay, is key to changing human behaviour towards achieving a sustainable planet. In this paper IoT equipment, utilizing sensors for measuring various parameters of water quality, is used in an educational context targeting at a deeper understanding of the use of natural resources towards the adoption of environmentally friendly behaviours. We here note that the use of water sensors in STEM gameful learning is an area which has not received a lot of attention in the previous years. The IoT water sensing and related scenaria and practices, addressing children via discovery, gamification, and educational activities, are discussed in detail

Aspects of DNA Strand Exchange: Recombination Proteins and Model System Studies

<p>DNA recombination is of fundamental importance to all living cells; it is part of the DNA repair machinery and a means to generate genetic diversity. DNA strand exchange, the exchange of strands between homologous DNA molecules, is the central reaction of the recombination process. The work presented in this Thesis has the aim of gaining insight into the mechanism of this reaction by investigating different aspects of DNA strand exchange. Structural studies of recombinase nucleoprotein filaments, which constitute the scaffold for the reaction in vivo, are reported together with investigations of artificial strand exchange in two different model systems.</p> <p>The structures of active RecA and Rad51 nucleoprotein filaments have been studied by Site-Specific Linear Dichroism (SSLD), a spectroscopic approach based on linear dichroism in combination with molecular replacement of individual amino acids. In this Thesis it is shown how LD data of systematically engineered proteins can provide angular orientations for specific residues and how these coordinates can be used to build a structural model of the protein. From SSLD data of RecA it is concluded that the protein adopts similar structures in the initial and final states of strand exchange, indicating a static role for RecA during the reaction. The study of the human Rad51 protein illustrates how experimental data from SSLD can be successfully combined with theoretical molecular modelling. The outcome is a model structure of the protein in its active complex with DNA, the first detailed structure reported so far for the complete human Rad51 protein.</p> <p>This Thesis reports on artificial strand exchange catalysis aided by cationic lipid vesicles and it is shown that DNA opens up in a zipper-like fashion, which facilitates strand exchange. It is further concluded that the exchange mechanism on the liposome surface is fundamentally different from that in bulk solution. Non-ionic catalysis has been investigated by the use of PEG to induce molecular crowding and provide possibilities for hydrophobic interactions. PEG accelerates strand exchange dramatically and the results emphasize the importance of hydrophobic interactions between DNA and its environment for the dynamic behaviour of DNA strands.</p

Hairpins in the conformations of a confined polymer

If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.Comment: Revised version. 22 pages, 7 figures, 2 tables, supplementary materia

DNA in Nanochannels - Theory and Applications

Nanofluidic structures have over the last two decades emerged as a powerful platform for detailed analysis of DNA on the kilobase pair length scale. When DNA is confined to a nanochannel, the combination of excluded volume and DNA stiffness leads to the DNA being stretched to near its full contour length. Importantly, this stretching takes place at equilibrium, without any chemical modifications to the DNA. As a result, any DNA can be analyzed, such as DNA extracted from cells or circular DNA, and it is relatively easy to study reactions on the ends of linear DNA. In this comprehensive review, we first give a thorough description of the current understanding of the polymer physics of DNA and how that leads to stretching in nanochannels. We then describe how the versatility of nanofabrication can be used to design devices specifically tailored for the problem at hand, either by controlling the degree of confinement or enabling facile exchange of reagents to measure DNA-protein reaction kinetics. The remainder of the review focuses on two important applications of confining DNA in nanochannels. The first is optical DNA mapping, which provides kilobase pair resolution of the genomic sequence of intact DNA molecules in excess of 100 kilobase pairs in size through labeling strategies that are suitable for fluorescence microscopy. In this section, we highlight solutions to the technical aspects of genomic mapping, rather than recent applications in human genetics, including the use of enzyme-based labeling and affinity-based labeling to produce the genomic maps. The second is DNA-protein interactions, and several recent examples of such studies on DNA compaction, filamentous protein complexes, and reactions with the chain ends are presented. Taken together, these two applications demonstrate the power of DNA confinement and nanofluidics in genomics, molecular biology and biophysics

Ca2+ improves organization of single-stranded DNA bases in human Rad51 filament, explaining stimulatory effect on gene recombination

Human RAD51 protein (HsRad51) catalyses the DNA strand exchange reaction for homologous recombination. To clarify the molecular mechanism of the reaction in vitro being more effective in the presence of Ca2+ than of Mg2+, we have investigated the effect of these ions on the structure of HsRad51 filament complexes with single- and double-stranded DNA, the reaction intermediates. Flow linear dichroism spectroscopy shows that the two ionic conditions induce significantly different structures in the HsRad51/single-stranded DNA complex, while the HsRad51/double-stranded DNA complex does not demonstrate this ionic dependence. In the HsRad51/single-stranded DNA filament, the primary intermediate of the strand exchange reaction, ATP/Ca2+ induces an ordered conformation of DNA, with preferentially perpendicular orientation of nucleobases relative to the filament axis, while the presence of ATP/Mg2+, ADP/Mg2+ or ADP/Ca2+ does not. A high strand exchange activity is observed for the filament formed with ATP/Ca2+, whereas the other filaments exhibit lower activity. Molecular modelling suggests that the structural variation is caused by the divalent cation interfering with the L2 loop close to the DNA-binding site. It is proposed that the larger Ca2+ stabilizes the loop conformation and thereby the protein–DNA interaction. A tight binding of DNA, with bases perpendicularly oriented, could facilitate strand exchange