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  • Al/Si orderingvacancy orderingceramicssuperspaceincommensurate structures
  • Microscopy
  • X-ray lasersXFELsbiologystructuredynamics
  • protein crystalscrystal lattices
  • International Union of Crystallography (IUCr)  (5)
  • Frontiers Media SA  (3)
  • Cell Press  (2)
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  • 1
    Publication Date: 2023-12-21
    Description: NETosis, a form of cell death that manifests by the release of decondensed chromatin to the extracellular space, provides valuable insights into mechanisms and consequences of cellular demise. Because extracellular chromatin can immobilize microbes, the extended nucleohistone network was called a neutrophil extracellular trap (NET), and the process of chromatin release was proposed to serve an innate immune defense function. Extracellular chromatin NETs were initially observed in studies of neutrophils and are most prominent in these types of granulocytes. Subsequent studies showed that other granulocytes and, in a limited way, other cells of the innate immune response may also release nuclear chromatin following certain kinds of stimulation. Variations of NETosis were noted with cells that remain temporarily motile after the release of chromatin. Numerous stimuli for NETosis were discovered, including bacterial breakdown products, inflammatory stimuli, particulate matter, certain crystals, immune complexes and activated thrombocytes. Fundamental explorations into the mechanisms of NETosis observed that neutrophil enzyme activity (PAD4, neutrophil elastase, proteinase 3 and myeloperoxidase) and signal transduction pathways contribute to the regulation of NETosis. Histones in NET chromatin become modified by peptidylarginine deiminase 4 (PAD4) and cleaved at specific sites by proteases, leading to extensive chromatin externalization. In addition, NETs serve for attachment of bactericidal enzymes including myeloperoxidase, leukocyte proteases, and the cathelicidin LL-37. NETs are decorated with proteases and may thus contribute to tissue destruction. However, the attachment of these enzymes to NET-associated supramolecular structures restricts systemic spread of the proteolytic activity. While the benefit of NETs in an infection appears obvious, NETs also participate as key protagonists in various pathologic states. Therefore, it is essential for NETs to be efficiently cleared; otherwise digestive enzymes may gain access to tissues where inflammation takes place. Persistent NET exposure at sites of inflammation may lead to a further complication: NET antigens may provoke acquired immune responses and, over time, could initiate autoimmune reactions, serve as antigen for nuclear autoantibodies and foster DNA immune complex-related inflammation. Neutrophil products and deiminated proteins comprise an important group of autoantigens in musculoskeletal disorders. Aberrant NET synthesis and/or clearance are often associated with inflammatory and autoimmune conditions. Recent evidence also implicates aberrant NET formation in the development of endothelial damage, atherosclerosis and thrombosis. Intravital microscopy provides evidence for conditions that induce NETosis in vivo. Furthermore, NETs can easily be detected in synovial fluid and tissue sections of patients with arthritis and gout. NETosis is thus of interest to researchers who investigate innate immune responses, host-pathogen interactions, chronic inflammatory disorders, cell and vascular biology, biochemistry, and autoimmunity. As we enter the second decade of research on NETosis, it is useful and timely to review the mechanisms and pathways of NET formation, their role in bacterial and fungal defense and their importance as inducers of autoimmune responses.
    Keywords: R5-920 ; RC581-607 ; Infection ; Autoimmunity ; Microscopy ; Immune Cell Interactions ; Neutrophil Extracellular Traps ; Inflammation ; Mechanisms of Cell Death ; Chronic Disease ; bic Book Industry Communication::M Medicine
    Language: English
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  • 2
    Publication Date: 2023-12-21
    Description: Early studies recognized the unique phenotype and attributes of T cells found in mucosal tissues, such as the intestines, skin, lung and female reproductive tract. This special topic issue will cover many aspects of mucosal-resident T cell biology during infection and disease and is dedicated to Leo Lefrancois, a pioneer in this field who recently passed away. A major proportion of these mucosal T cells are memory T cells, now recognized as a major constituent of memory T cells referred to as tissue-resident memory T cells. Unlike central and effector memory T cell subsets, tissue-resident memory T cells exhibit tissue specificity with minimal systemic migration. Nonetheless, tissue-resident memory T cells share a similar origin and display some overlapping phenotypes with their other memory T cell counterparts. Articles in this issue will describe the different types of memory T cells residing in mucosal tissues, their origins and functions as well as how they vary among discrete mucosal sites. Manuscripts will consider the unique physiological environments and cellular constituents which facilitate tissue residency while preserving tissue function. Additionally, there will be descriptions of the various mechanisms responsible for the migration and segregation of tissue resident memory CD8 T cells from the peripheral T cell pool. Although the mechanisms facilitating the sequestration of tissue-resident memory T cells within a respective tissue has not well characterized, various theories will also be discussed. Lastly, how these T cells contribute to immunity to pathogens, cancer, and autoimmunity and could be modified through vaccination or therapeutic intervention will be described. As mucosal tissues are the major portals of pathogen entry and frequent transformation, the activities and persistence of tissue resident memory T cells is crucial for mediating protection at these sites.
    Keywords: R5-920 ; RC581-607 ; pathogens ; Microscopy ; Migration ; Mucosa ; T cell differentiation ; Vaccination ; Inflammation ; Epithelium ; CD103 ; bic Book Industry Communication::M Medicine
    Language: English
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  • 3
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    Frontiers Media SA
    Publication Date: 2024-04-04
    Description: This eBook is a collection of articles from a Frontiers Research Topic. Frontiers Research Topics are very popular trademarks of the Frontiers Journals Series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area! Find out more on how to host your own Frontiers Research Topic or contribute to one as an author by contacting the Frontiers Editorial Office: frontiersin.org/about/contact
    Keywords: optogenetics ; Neurophonics ; Microscopy ; Neuroscience ; imaging ; thema EDItEUR::P Mathematics and Science::PD Science: general issues ; thema EDItEUR::P Mathematics and Science::PS Biology, life sciences::PSA Life sciences: general issues::PSAN Neurosciences
    Language: English
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  • 4
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-07-01
    Keywords: X-ray lasersXFELsbiologystructuredynamics
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 5
    Publication Date: 2018-05-12
    Keywords: protein crystalscrystal lattices
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 6
    Publication Date: 2018-05-12
    Keywords: protein crystalscrystal lattices
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 7
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2018-06-26
    Description: Synchrotron single-crystal X-ray diffraction has revealed diffuse scattering alongside sharp satellite reflections for different samples of mullite (Al4+2xSi2−2xO10−x). Structural models have been developed in (3+1)-dimensional superspace that account for vacancy ordering and Al/Si ordering based on harmonic modulation functions. A constraint scheme is presented which explains the crystal-chemical relationships between the split sites of the average structure. The modulation amplitudes of the refinements differ significantly by a factor of ∼3, which is explained in terms of different degrees of ordering, i.e. vacancies follow the same ordering principle in all samples but to different extents. A new approach is applied for the first time to determine Al/Si ordering by combining density functional theory with the modulated volumes of the tetrahedra. The presence of Si–Si diclusters indicates that the mineral classification of mullite needs to be reviewed. A description of the crystal structure of mullite must consider both the chemical composition and the degree of ordering. This is of particular importance for applications such as advanced ceramics, because the physical properties depend on the intrinsic structure of mullite.
    Keywords: Al/Si orderingvacancy orderingceramicssuperspaceincommensurate structures
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 8
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    International Union of Crystallography (IUCr)
    In: IUCrJ
    Publication Date: 2017-05-11
    Description: The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump–probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallography to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.
    Keywords: X-ray lasersXFELsbiologystructuredynamics
    Electronic ISSN: 2052-2525
    Topics: Geosciences , Physics
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  • 9
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Hirst, W. G., Kiefer, C., Abdosamadi, M. K., Schäffer, E., & Reber, S. In Vitro reconstitution and imaging of microtubule dynamics by fluorescence and label-free microscopy. STAR Protocols, 1(3), (2020): 100177, doi:10.1016/j.xpro.2020.100177.
    Description: Dynamic microtubules are essential for many processes in the lives of eukaryotic cells. To study and understand the mechanisms of microtubule dynamics and regulation, in vitro reconstitution with purified components has proven a vital approach. Imaging microtubule dynamics can be instructive for a given species, isoform composition, or biochemical modification. Here, we describe two methods that visualize microtubule dynamics at high speed and high contrast: (1) total internal reflection fluorescence microscopy and (2) label-free interference reflection microscopy.
    Description: We thank the AMBIO imaging facility (Charité, Berlin) and Nikon at MBL for imaging support. We thank all former and current members of the Reber lab for discussion and helpful advice, in particular Christoph Hentschel and Soma Zsoter for technical assistance. S.R. acknowledges funding by the IRI Life Sciences (Humboldt-Universität zu Berlin, Excellence Initiative/DFG). W.H. was supported by the Alliance Berlin Canberra co-funded by a grant from the Deutsche Forschungsgemeinschaft (DFG) for the International Research Training Group (IRTG) 2290 and the Australian National University. C.K. thanks the Deutsche Forschungsgesellschaft (DFG, JA 2589/1-1). C.K. and M.A. thank Steve Simmert and Tobias Jachowski former and current members of the Schäffer lab.
    Keywords: Biophysics ; Cell Biology ; Microscopy
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 10
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geisterfer, Z. M., Oakey, J., & Gatlin, J. C. . Microfluidic encapsulation of Xenopus laevis cell-free extracts using hydrogel photolithography. STAR Protocols, 1(3), (2020): 100221, doi:10.1016/j.xpro.2020.100221.
    Description: Cell-free extract derived from the eggs of the African clawed frog Xenopus laevis is a well-established model system that has been used historically in bulk aliquots. Here, we describe a microfluidic approach for isolating discrete, biologically relevant volumes of cell-free extract, with more expansive and precise control of extract shape compared with extract-oil emulsions. This approach is useful for investigating the mechanics of intracellular processes affected by cell geometry or cytoplasmic volume, including organelle scaling and positioning mechanisms. For complete details on the use and execution of this protocol, please refer to Geisterfer et al. (2020).
    Description: This work was made possible by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant no. 2P20GM103432. It was also supported by additional funding provided by the NIGMS under grant no. R01GM113028, the NSF Faculty CAREER Program under award no. BBBE 1254608, Whitman Center fellowships at the Marine Biological Laboratory, and the Biomedical Scholars program of the Pew Charitable Trusts. We thank Drs. Aaron Groen and Tim Mitchison for their intellectual contributions and involvement in some of the pioneering experiments that set the foundation for this approach.
    Keywords: Biophysics ; Cell Biology ; Cell isolation ; Microscopy ; Model Organisms
    Repository Name: Woods Hole Open Access Server
    Type: Article
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