Animal Inhalation Models to Investigate Modulation of Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBDs) comprise primarily two disease manifestations, ulcerative colitis (UC) and Crohn’s disease (CD), each with distinctive clinical and pathological features. Environmental and clinical factors strongly affect the development and clinical outcomes of IBDs. Among environmental factors, cigarette smoke (CS) is considered the most important risk factor for CD, while it attenuates the disease course of UC. Various animal models have been used to assess the impact of CS on intestinal pathophysiology. This chapter examines the suitability of animal inhalation/smoke exposure models for assessing the contrary effects of CS on UC and CD. It presents an updated literature review of IBD mouse models and a description of possible mechanisms relevant to relationships between IBD and smoking. In addition, it summarises various technical inhalation approaches, in the context of mouse disease models of IBD

Spin disorder in maghemite nanoparticles investigated using polarized neutrons and nuclear resonant scattering

The manuscript reports the investigation of spin disorder in maghemite nanoparticles of different shape by a combination of polarized small-angle neutron scattering (SANSPOL) and nuclear forward scattering (NFS) techniques. Both methods are sensitive to magnetization on the nanoscale. SANSPOL allows for investigation of the particle morphology and spatial magnetization distribution and NFS extends this nanoscale information to the atomic scale, namely the orientation of the hyperfine field experienced by the iron nuclei. The studied nanospheres and nanocubes with diameters of 7.4 nm and 10.6 nm, respectively, exhibit a significant spin disorder. This effect leads to a reduction of the magnetization to 44% and 58% of the theoretical maghemite bulk value, observed consistently by both techniques

Intensity interferometry of single x-ray pulses from a synchrotron storage ring

We report on measurements of second-order intensity correlations at the high brilliance storage ring PETRA III using a prototype of the newly developed Adaptive Gain Integrating Pixel Detector (AGIPD). The detector recorded individual synchrotron radiation pulses with an x-ray photon energy of 14.4 keV and repetition rate of about 5 MHz. The second-order intensity correlation function was measured simultaneously at different spatial separations that allowed to determine the transverse coherence length at these x-ray energies. The measured values are in a good agreement with theoretical simulations based on the Gaussian Schell-model.Comment: 16 pages, 6 figures, 42 reference

Enhancement of COPD Biological Networks Using a Web-Based Collaboration Interface

The construction and application of biological network models is an approach that offers a holistic way to understand biological processes involved in disease. Chronic obstructive pulmonary disease (COPD) is a progressive inflammatory disease of the airways for which therapeutic options currently are limited after diagnosis, even in its earliest stage. COPD network models are important tools to better understand the biological components and processes underlying initial disease development. With the increasing amounts of literature that are now available, crowdsourcing approaches offer new forms of collaboration for researchers to review biological findings, which can be applied to the construction and verification of complex biological networks. We report the construction of 50 biological network models relevant to lung biology and early COPD using an integrative systems biology and collaborative crowd-verification approach. By combining traditional literature curation with a data-driven approach that predicts molecular activities from transcriptomics data, we constructed an initial COPD network model set based on a previously published non-diseased lung-relevant model set. The crowd was given the opportunity to enhance and refine the networks on a website (https://bionet.sbvimprover.com/) and to add mechanistic detail, as well as critically review existing evidence and evidence added by other users, so as to enhance the accuracy of the biological representation of the processes captured in the networks. Finally, scientists and experts in the field discussed and refined the networks during an in-person jamboree meeting. Here, we describe examples of the changes made to three of these networks: Neutrophil Signaling, Macrophage Signaling, and Th1-Th2 Signaling. We describe an innovative approach to biological network construction that combines literature and data mining and a crowdsourcing approach to generate a comprehensive set of COPD-relevant models that can be used to help understand the mechanisms related to lung pathobiology. Registered users of the website can freely browse and download the networks

Coherent control of collective nuclear quantum states via transient magnons

Ultrafast and precise control of quantum systems at x-ray energies involves photons with oscillation periods below 1 as. Coherent dynamic control of quantum systems at these energies is one of the major challenges in hard x-ray quantum optics. Here, we demonstrate that the phase of a quantum system embedded in a solid can be coherently controlled via a quasi-particle with subattosecond accuracy. In particular, we tune the quantum phase of a collectively excited nuclear state via transient magnons with a precision of 1 zs and a timing stability below 50 ys. These small temporal shifts are monitored interferometrically via quantum beats between different hyperfine-split levels. The experiment demonstrates zeptosecond interferometry and shows that transient quasi-particles enable accurate control of quantum systems embedded in condensed matter environments

X-ray resonant photoexcitation: line widths and energies of K{\alpha} transitions in highly charged Fe ions

Photoabsorption by and fluorescence of the K{\alpha} transitions in highly charged iron ions are essential mechanisms for X-ray radiation transfer in astrophysical environments. We study photoabsorption due to the main K{\alpha} transitions in highly charged iron ions from heliumlike to fluorinelike (Fe 24+...17+) using monochromatic X-rays around 6.6 keV at the PETRA III synchrotron photon source. Natural linewidths were determined with hitherto unattained accuracy. The observed transitions are of particular interest for the understanding of photoexcited plasmas found in X-ray binaries and active galactic nuclei.Comment: Revised versio

Quantum Imaging with Incoherently Scattered Light from a Free-Electron Laser

The advent of accelerator-driven free-electron lasers (FEL) has opened new avenues for high-resolution structure determination via diffraction methods that go far beyond conventional x-ray crystallography methods. These techniques rely on coherent scattering processes that require the maintenance of first-order coherence of the radiation field throughout the imaging procedure. Here we show that higher-order degrees of coherence, displayed in the intensity correlations of incoherently scattered x-rays from an FEL, can be used to image two-dimensional objects with a spatial resolution close to or even below the Abbe limit. This constitutes a new approach towards structure determination based on incoherent processes, including Compton scattering, fluorescence emission or wavefront distortions, generally considered detrimental for imaging applications. Our method is an extension of the landmark intensity correlation measurements of Hanbury Brown and Twiss to higher than second-order paving the way towards determination of structure and dynamics of matter in regimes where coherent imaging methods have intrinsic limitations

In situ

Growth of magnetron sputtered Fe films on clean single crystalline MgO (001) substrate has been studied using in situ grazing incidence small angle x-ray scattering (GISAXS) and grazing incidence nuclear resonant scattering (GINRS) measurements. While GISAXS provides information about morphological changes, GINRS provides information about structural and magnetic properties, thus making it possible to correlate the evolution of magnetic properties with that of morphology and structure of the film. The film exhibits a Volmer-Weber type growth, with percolation transition occurring around 2 nm film thickness. Presence of a finite quadrupole splitting, as seen in GINRS measurements, suggests a significant distortion from cubic symmetry up to a film thickness of 3.5 nm, which can be attributed to hybridization between Fe 3d and O 2p orbitals at the interface as well as in-plane tensile strain induced as a result of coalescence of islands. Initially Fe islands exhibit superparamagnetic relaxation, while finite magnetic moment appears upon formation of macroscopic percolation islands. The film exhibits a weak perpendicular magnetic anisotropy (PMA), which vanishes concurrently with disappearance of structural distortion, suggesting that the observed PMA at least partly originates from inherent strain in the film. No presence of any known oxide of Fe was detected at the interface. More precise information about topological and magnetic structure of the interfaces between Fe and MgO layers is obtained using combined x-ray reflectivity and nuclear resonance reflectivity measurements on a $^{57}$Fe/MgO multilayer. Measurements show that about two monolayers of Fe at the interface have a reduced hyperfine field, providing evidence for hybridization with O atoms, as predicted by theory

Construction of a computable cell proliferation network focused on non-diseased lung cells

<p>Abstract</p> <p>Background</p> <p>Critical to advancing the systems-level evaluation of complex biological processes is the development of comprehensive networks and computational methods to apply to the analysis of systems biology data (transcriptomics, proteomics/phosphoproteomics, metabolomics, etc.). Ideally, these networks will be specifically designed to capture the normal, non-diseased biology of the tissue or cell types under investigation, and can be used with experimentally generated systems biology data to assess the biological impact of perturbations like xenobiotics and other cellular stresses. Lung cell proliferation is a key biological process to capture in such a network model, given the pivotal role that proliferation plays in lung diseases including cancer, chronic obstructive pulmonary disease (COPD), and fibrosis. Unfortunately, no such network has been available prior to this work.</p> <p>Results</p> <p>To further a systems-level assessment of the biological impact of perturbations on non-diseased mammalian lung cells, we constructed a lung-focused network for cell proliferation. The network encompasses diverse biological areas that lead to the regulation of normal lung cell proliferation (Cell Cycle, Growth Factors, Cell Interaction, Intra- and Extracellular Signaling, and Epigenetics), and contains a total of 848 nodes (biological entities) and 1597 edges (relationships between biological entities). The network was verified using four published gene expression profiling data sets associated with measured cell proliferation endpoints in lung and lung-related cell types. Predicted changes in the activity of core machinery involved in cell cycle regulation (RB1, CDKN1A, and MYC/MYCN) are statistically supported across multiple data sets, underscoring the general applicability of this approach for a network-wide biological impact assessment using systems biology data.</p> <p>Conclusions</p> <p>To the best of our knowledge, this lung-focused Cell Proliferation Network provides the most comprehensive connectivity map in existence of the molecular mechanisms regulating cell proliferation in the lung. The network is based on fully referenced causal relationships obtained from extensive evaluation of the literature. The computable structure of the network enables its application to the qualitative and quantitative evaluation of cell proliferation using systems biology data sets. The network is available for public use.</p