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  • Wiley-Blackwell  (43,084)
  • American Geophysical Union  (26,229)
  • American Association for the Advancement of Science (AAAS)
  • International Union of Crystallography
  • 2020-2022  (15,804)
  • 1980-1984  (74,481)
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  • 1
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    Millimeter wave spectroscopic measurements over the South Pole: 5. Morphology and evolution of HNO3vertical distribution, 1993 versus 1995 (2020)
    American Geophysical Union
    Details
    Publication Date: 2020-09-21
    Description: We compare differences and similarities in the annual stratospheric HNO3 cycle derived from ground‐based measurements at the South Pole during 1993 and 1995, after correcting an error in earlier published profile retrievals for 1993 which led to under estimation of mixing ratios. The data series presented here provide profiling over the range ∼16–48 km, and cover the fall‐winter‐spring cycle in the behavior of HNO3 in the extreme Antarctic with a large degree of temporal overlap. With the exception of one gap of 20 days, the combined data sets cover a full annual cycle. The record shows an increase in HNO3 above 30 km occurring about 20 days before sunset, which appears to be the result of higher altitude heterogeneous conversion of NOx as photolysis diminishes. Both years show a strong increase in HNO3 beginning about polar sunset, in a layer peaking at about 25 km, as additional NOx is heterogeneously converted to nitric acid. When temperatures drop to the polar stratospheric cloud (PSC) formation range near the end of May, gas phase HNO3 is rapidly reduced in the lower stratosphere, although at least 2–3 weeks of temperatures ≤192 K appear to be required to complete most of the gas‐phase removal at the upper end of the depletion range (22–25 km). Despite a significant difference in residual sulfate loading from the explosion of Mount Pinatubo, there appears to be little gross difference in the timing and effects of PSC formation in removing gas phase HNO3 in these 2 years, though removal may be more rapid in 1995. Incorporation of gas phase HNO3 into PSCs appears to be nearly complete up to ∼25 km by midwinter. We also see a repeat of the formation of gas phase HNO3 in the middle stratosphere in early midwinter of 1995 with about the same timing as in 1993, suggesting that this phenomenon is driven by a repetition of dynamical transport and appropriate temperatures and pressures in the polar night, and not (as has been suggested) by ion‐based heterogeneous chemistry that requires triggering by large relativistic electron fluxes. High‐altitude HNO3 production peaks during a period of ∼20 days, but appears to persist for up to ∼40 days in the 40–45 km range, ceasing well before sunrise. This HNO3 descends rapidly throughout the production period, at a rate in good agreement with theoretically determined midwinter subsidence rates. As noted in earlier studies, later warming of this region above PSC evaporation temperatures does not cause reappearance of large amounts of HNO3, indicating that most PSCs gravitationally sink out of the stratosphere before early spring. We present evidence that smaller PSCs do evaporate to ∼1 to 3.5 ppbv of HNO3 in the lower stratosphere, however, working downward from ∼25 km as temperatures rise during the late winter. There is a delay of ∼15 days after sunrise before photolysis causes significant depletion in the altitude range below ∼30 km, where subsidence has carried virtually all higher‐altitude HNO3 by polar sunrise. Some continued subsidence and photolysis combine to keep mixing ratios less than ∼5 ppbv below 30 km until the final breakdown of the vortex in November brings larger amounts of HNO3 with air from lower latitudes.
    Description: Published
    Description: 17739-17750
    Description: 5A. Ricerche polari e paleoclima
    Description: JCR Journal
    Keywords: ozone depletion ; HNO3 ; Antarctic stratosphere ; 01.01. Atmosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 2
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    Probabilistic Seismic Hazard Analysis at Regional and National Scales: State of the Art and Future Challenges (2020)
    American Geophysical Union
    Details
    Publication Date: 2020-09-01
    Description: Seismic hazard modeling is a multidisciplinary science that aims to forecast earthquake occurrence and its resultant ground shaking. Such models consist of a probabilistic framework that quantifies uncertainty across a complex system; typically, this includes at least two model components developed from Earth science: seismic source and ground motion models. Although there is no scientific prescription for the forecast length, the most common probabilistic seismic hazard analyses consider forecasting windows of 30 to 50 years, which are typically an engineering demand for building code purposes. These types of analyses are the topic of this review paper. Although the core methods and assumptions of seismic hazard modeling have largely remained unchanged for more than 50 years, we review the most recent initiatives, which face the difficult task of meeting both the increasingly sophisticated demands of society and keeping pace with advances in scientific understanding. A need for more accurate and spatially precise hazard forecasting must be balanced with increased quantification of uncertainty and new challenges such as moving from time‐independent hazard to forecasts that are time dependent and specific to the time period of interest. Meeting these challenges requires the development of science‐driven models, which integrate all information available, the adoption of proper mathematical frameworks to quantify the different types of uncertainties in the hazard model, and the development of a proper testing phase of the model to quantify its consistency and skill. We review the state of the art of the National Seismic Hazard Modeling and how the most innovative approaches try to address future challenges.
    Description: Published
    Description: e2019RG000653
    Description: 6T. Studi di pericolosità sismica e da maremoto
    Description: JCR Journal
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Assessment of earthquake locations in 3D deterministic velocity models: a case study from the Altotiberina Near Fault Observatory (Italy) (2020)
    American Geophysical Union
    Details
    Publication Date: 2021-07-14
    Description: An edited version of this paper was published by AGU. Copyright (2016) American Geophysical Union.
    Description: The accuracy of earthquake locations and their correspondence with subsurface geology depends strongly on the accuracy of the available seismic velocity model. Most modern methods to construct a velocity model for earthquake location are based on the inversion of passive source seismological data. Another approach is the integration of high-resolution geological and geophysical data to construct deterministic velocity models in which earthquake locations can be directly correlated to the geological structures. Such models have to be kinematically consistent with independent seismological data in order to provide precise hypocenter solutions. We present the Altotiberina (AT) seismic model, a three-dimensional velocity model for the Upper Tiber Valley region (Northern Apennines, Italy), constructed by combining 300 km of seismic reflection profiles, 6 deep boreholes (down to 5 km depth), detailed data from geological surveys and direct measurements of P- and S-wave velocities performed in situ and in laboratory. We assess the robustness of the AT seismic model by locating 11,713 earthquakes with a non-linear, global-search inversion method and comparing the probabilistic hypocenter solutions to those calculated in three previously published velocity models, constructed by inverting passive seismological data only. Our results demonstrate that the AT seismic model is able to provide higher-quality hypocenter locations than the previous velocity models. Earthquake locations are consistent with the subsurface geological structures and show a high degree of spatial correlation with specific lithostratigraphic units, suggesting a lithological control on the seismic activity evolution.
    Description: Published
    Description: 8113-8135
    Description: 4T. Sismicità dell'Italia
    Description: JCR Journal
    Keywords: deterministic velocity model ; earthquakes ; nonlinear hypocenter location ; lithological control on seismicity ; 04. Solid Earth::04.06. Seismology::04.06.99. General or miscellaneous
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 4
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    Intercomparison of stratospheric HNO3measurements over Antarctica: Ground-based millimeter-wave versus UARS/MLS Version 5 retrievals (2020)
    American Geophysical Union
    Details
    Publication Date: 2020-09-21
    Description: [1] We present the first intercomparison between the two most comprehensive records of gas‐phase HNO3 profiles in the Antarctic stratosphere, covering the greater part of 1993 and 1995. We compare measurements by the Stony Brook Ground‐Based Millimeter‐wave Spectrometer (GBMS) at the South Pole with Version 5 HNO3 data from the Microwave Limb Sounder (MLS) aboard the Upper Atmospheric Research Satellite. Trajectory tracing was used to select MLS measurements in the 70°–80°S latitude band that sampled air observed by the GBMS during passage over the Pole. When temperatures were near the HNO3 condensation range, additional screening was performed to select MLS measurements that sampled air parcels within 1.5 K of the temperature they experienced over the Pole. Quantitative comparisons are given at 7 different potential temperature levels spanning the range ∼19–30 km. Agreement between the data sets is quite good between 465 and 655 K (∼20–25 km) during a large fraction of the year. Agreement is best during winter and spring, when seasonally averaged differences are generally within 1 ppbv below ∼25 km. At higher altitudes, and during summer and fall, the agreement becomes worse, and GBMS measurements can exceed MLS values by more than 3 ppbv. We provide evidence that differences occurring in the lower stratosphere during fall are due to lack of colocation between the two data sets during a period of strong poleward gradients in HNO3. Remaining discrepancies between GBMS and MLS V5 HNO3 measurements are thought to be due to instrumental or retrieval biases.
    Description: Published
    Description: id 4809
    Description: 5A. Ricerche polari e paleoclima
    Description: JCR Journal
    Keywords: MLS ; Nitric acid ; polar stratosphere ; 01.01. Atmosphere
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
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    Tropical Rains Controlling Deposition of Saharan Dust Across the North Atlantic Ocean (2020)
    American Geophysical Union
    In:  EPIC3Geophysical Research Letters, American Geophysical Union, 47(5), ISSN: 0094-8276
    Details
    Publication Date: 2020-05-13
    Description: Mineral dust plays an important role in the atmospheric radiation budget as well as in the ocean carbon cycle through fertilization and by ballasting of settling organic matter. However, observational records of open‐ocean dust deposition are sparse. Here, we present the spatial and temporal evolution of Saharan dust deposition over 2 years from marine sediment traps across the North Atlantic, directly below the core of the Saharan dust plume, with highest dust fluxes observed in summer. We combined the observed deposition fluxes with model simulations and satellite observations and argue that dust deposition in the Atlantic is predominantly controlled by summer rains. The dominant depositional pathway changes from wet deposition in summer to dry deposition in winter. Wet deposition has previously been suggested to increase the release of dust‐derived nutrients and their bioavailability, which may be a key contributor to surface‐ocean productivity in remote and oligotrophic parts of the oceans.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 6
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    Arctic Continental Margin Sediments as Possible Fe and Mn Sources to Seawater as Sea Ice Retreats: Insights From the Eurasian Margin (2020)
    American Geophysical Union
    In:  EPIC3Global Biogeochemical Cycles, American Geophysical Union, 34(8), ISSN: 0886-6236
    Details
    Publication Date: 2020-09-02
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
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    Travel Time and Source Variation Explain the Molecular Transformation of Dissolved Organic Matter in an Alpine Stream Network (2020)
    Wiley-Blackwell
    In:  EPIC3JGR Biogeosciences, Wiley-Blackwell, ISSN: 2169-8961
    Details
    Publication Date: 2020-09-21
    Description: Streams and rivers are important components of the carbon cycle as they transport and transform dissolved organic matter (DOM). Using high‐resolution Fourier‐transform ion cyclotron resonance mass spectrometry, we studied the spatial distribution of DOM at the molecular level at more than 100 sites across a stream network during summer and winter baseflow. We developed a model approximating the time DOM spent in the fluvial network, a key constraint on the biogeochemical processing of DOM. Discharge‐weighted travel time explained the compositional changes of DOM, which differed markedly in summer and winter. We attribute these seasonal differences to variation in source material, putatively reflecting the dynamics of freshly produced DOM in summer and DOM with an imprint of leaf litter in winter. Hydrological mixing was an important driver of the spatial dynamics of DOM. From the convergence rate of DOM compound intensities to the network‐wide average, we inferred the spatial distribution of sources within the catchment. Finally, we estimated network‐wide apparent mass transfer coefficients (vf app) of individual DOM compounds, which describe the vertical velocity at which DOM compounds are removed by biotic and abiotic processes. We identified the oxidative state of carbon as an important factor explaining vf app, which we consequently attribute to biological uptake of thermodynamically favorable DOM compounds. This work contributes to our understanding of the spatial processes, temporal constraints, and chemical properties of DOM that regulate the transformation and diagenesis of DOM at the fluvial network scale.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
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    Ice flow and the conditions of the ice-bed interface at the onset of the Northeast Greenland Ice Stream (2020)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting 2020 - Online Everywhere, Online, 2020-12-01-2020-12-17American Geophysical Union
    Details
    Publication Date: 2020-12-15
    Description: The Northeast Greenland Ice Stream (NEGIS) is an important dynamic component contributing to the total mass balance of the Greenland ice sheet, as it reaches up to the central divide and drains 12% of the ice sheet. The ice stream geometry and surface velocities in the onset region of the NEGIS are not yet sufficiently well reproduced by ice sheet models. We present an assessment of the basal conditions of the onset region in a systematic analysis of airborne ultra-wideband radar data. Our data yield a new detailed model of ice-thickness distribution and basal topography in the upstream part of the ice stream. We observe a change from a smooth to a rougher bed where the ice stream widens from 10 to 60 km, and a distinct roughness anisotropy, indicating a preferred orientation of subglacial structures. The observation of off-nadir reflections that are symmetrical to the bed reflection in the radargrams suggests that these structures are elongated subglacial landforms, which in turn indicate potential streamlining of the bed. Together with basal water routing pathways, our observations hint to two different zones in this part of the NEGIS: an accelerating and smooth upstream region, which is collecting water, with reduced basal traction, and in the further downstream part, where the ice stream is slowing down and is widening, with a distribution of basal water towards the shear margins. Our findings support the hypothesis that the NEGIS is strongly interconnected to the subglacial water system in its onset region, but also to the subglacial substrate and morphology.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 9
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    Simulated Thermohaline Fingerprints in Response to Different Greenland‐Scotland Ridge and Fram Strait Subsidence Histories (2020)
    American Geophysical Union
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union, 35, ISSN: 2572-4525
    Details
    Publication Date: 2021-02-16
    Description: Changes in ocean gateway configuration can induce basin‐scale rearrangements in ocean current characteristics. However, there is large uncertainty in the relative timing of the Oligocene/Miocene subsidence histories of the Greenland‐Scotland Ridge (GSR) and the Fram Strait (FS). By using a climate model, we investigate the temperature and salinity changes in response to the subsidence of these two key ocean gateways during early to middle Miocene. For a singular subsidence of the GSR, we detect warming and a salinity increase in the Nordic Seas and the Arctic Ocean. As convection sites shift to the north of Iceland, North Atlantic Deep Water (NADW) is formed at cooler temperatures. The associated deep ocean cooling and upwelling of deep waters to the Southern Ocean surface can cause a cooling in the southern high latitudes. These characteristic responses to the GSR deepening are independent of the FS being shallow or deep. An isolated subsidence of the FS gateway for a deep GSR shows less pronounced warming and salinity increase in the Nordic Seas. Arctic temperatures remain unaltered, but a stronger salinity increase is detected, which further increases the density of NADW. The increase in salinity enhances the contribution of NADW to the abyssal ocean at the expense of the colder southern source water component. These relative changes largely counteract each other and cause a negligible warming in the upwelling regions of the Southern Ocean.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev , info:eu-repo/semantics/article
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  • 10
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    Planet Microbe: An Ontology-Enriched Cyberinfrastructure System for FAIR Marine ‘Omics Data (2020)
    American Geophysical Union
    In:  EPIC3Ocean Sciences Meeting 2020, 2020-02-16-2020-02-21American Geophysical Union
    Details
    Publication Date: 2020-02-12
    Repository Name: EPIC Alfred Wegener Institut
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  • 11
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    Antarctic Circumpolar Current Dynamics at the Pacific Entrance to the Drake Passage Over the Past 1.3 Million Years (2020)
    American Geophysical Union
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union, 35(7), pp. e2019PA003773, ISSN: 2572-4525
    Details
    Publication Date: 2021-02-01
    Description: The Antarctic Circumpolar Current (ACC) is the world's largest current system connecting all three major basins of the global ocean. Our knowledge of glacial‐interglacial changes in ACC dynamics in the southeast Pacific is not well constrained and presently only based on reconstructions covering the last glacial cycle. Here we use a combination of mean sortable silt grain size of the terrigenous sediment fraction (10–63 μm, "Sortable Silt") and X‐ray fluorescence scanner‐derived Zr/Rb ratios as flow strength proxies to examine ACC variations at the Pacific entrance to the Drake Passage (DP) in the vicinity of the Subantarctic Front. Our results indicate that at the DP entrance, ACC strength varied by ~6–16% on glacial‐interglacial time scales, yielding higher current speeds during interglacial times and reduced current speeds during glacials. We provide evidence that previous observations of a reduction in DP throughflow during the last glacial period are part of a consistent pattern extending for at least the last 1.3 Ma. The orbital‐scale cyclicity follows well‐known global climate changes from prevailing ca. 41‐kyr cycles in the early part of the record (1.3 Ma to 850 ka; marine isotope stage 21) across the mid‐Pleistocene transition into the middle and late Pleistocene 100‐kyr world. A comparison to a bottom water flow record from the deep western boundary current off New Zealand (Ocean Drilling Program Site 1123) reveals anti‐phased changes between the two sites. The enhanced supply of deep water along the DP and into the Atlantic Ocean during interglacials corresponds to a weakened flow of the SW Pacific deep western boundary current.
    Repository Name: EPIC Alfred Wegener Institut
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  • 12
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    Facilitated crystal handling using a simple device for evaporation reduction in microtiter plates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: In the past two decades, most of the steps in a macromolecular crystallography experiment have undergone tremendous development with respect to speed, feasibility and increase of throughput. The part of the experimental workflow that is still a bottleneck, despite significant efforts, involves the manipulation and harvesting of the crystals for the diffraction experiment. Here, a novel low‐cost device is presented that functions as a cover for 96‐well crystallization plates. This device enables access to the individual experiments one at a time by its movable parts, while minimizing evaporation of all other experiments of the plate. In initial tests, drops of many typically used crystallization cocktails could be successfully protected for up to 6 h. Therefore, the manipulation and harvesting of crystals is straightforward for the experimenter, enabling significantly higher throughput. This is useful for many macromolecular crystallography experiments, especially multi‐crystal screening campaigns.
    Description: A simple and low‐cost device has been developed to minimize evaporation in microtiter plates for easy crystal handling and harvesting. image
    Keywords: 548 ; evaporation reduction ; crystal handling ; crystal harvesting ; crystallographic fragment screening
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  • 13
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    Cation distribution in Cu2ZnSnSe4, Cu2FeSnS4 and Cu2ZnSiSe4 by multiple‐edge anomalous diffraction (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Semiconductors from this group of materials are promising candidates for photovoltaic applications. Their properties strongly depend on point defects, in particular related to cation order–disorder. However, Cu+, Zn2+ and Fe2+ have very similar scattering factors and are all but indistinguishable in usual X‐ray diffraction experiments. Anomalous diffraction utilizes the dependency of the atomic scattering factors f′ and f′′ of the energy of the radiation, especially close to the element‐specific absorption edges. In the MEAD technique, individual Bragg peaks are tracked over an absorption edge. The intensity changes depending on the structure factor can be highly characteristic for Miller indices selected for a specific structural problem, but require very exact measurements. Beamline KMC‐2 at synchrotron BESSY II, Berlin, has been recently upgraded for this technique. Anomalous X‐ray powder diffraction and XAFS compliment the data. Application of this technique confirmed established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS). In contrast to the literature, cation distribution in Cu2ZnSiSe4 (CZSiSe) is shown to adopt a highly ordered wurtz‐kesterite structure type.
    Description: Multiple‐Edge Anomalous Diffraction (MEAD) has been applied to various quaternary sulfosalts belonging to the adamantine compound family in order to validate the distribution of copper, zinc and iron cations in the structure. Application of this technique confirms established cation distribution in Cu2ZnSnSe4 (CZTSe) and Cu2FeSnS4 (CFTS), but in Cu2ZnSiSe4 (CZSiSe) the cation distribution is shown to adopt a highly ordered wurtz‐kesterite structure type in contrast to the literature. image
    Keywords: 548 ; synchrotron ; anomalous diffraction ; semiconductor ; MEAD
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  • 14
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    The copper(II)‐binding tripeptide GHK, a valuable crystallization and phasing tag for macromolecular crystallography (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: The growth of diffraction‐quality crystals and experimental phasing remain two of the main bottlenecks in protein crystallography. Here, the high‐affinity copper(II)‐binding tripeptide GHK was fused to the N‐terminus of a GFP variant and an MBP‐FG peptide fusion. The GHK tag promoted crystallization, with various residues (His, Asp, His/Pro) from symmetry molecules completing the copper(II) square‐pyramidal coordination sphere. Rapid structure determination by copper SAD phasing could be achieved, even at a very low Bijvoet ratio or after significant radiation damage. When collecting highly redundant data at a wavelength close to the copper absorption edge, residual S‐atom positions could also be located in log‐likelihood‐gradient maps and used to improve the phases. The GHK copper SAD method provides a convenient way of both crystallizing and phasing macromolecular structures, and will complement the current trend towards native sulfur SAD and MR‐SAD phasing.
    Description: A novel three‐residue tag containing the residues GHK that can be used to promote crystallization and in SAD phasing experiments using its tightly bound copper ion is described. image
    Keywords: 548 ; phasing ; crystallization ; GHK ; SAD
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  • 15
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    Determining paracrystallinity in mixed‐tacticity polyhydroxybutyrates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Recently, the authors reported on the development of crystallinity in mixed‐tacticity polyhydroxybutyrates. Comparable values reported in the literature vary depending on the manner of determination, the discrepancies being partially attributable to scattering from paracrystalline portions of the material. These portions can be qualified by peak profile fitting or quantified by allocation of scattered X‐ray intensities. However, the latter requires a good quality of the former, which in turn must additionally account for peak broadening inherent in the measurement setup, and due to limited crystallite sizes and the possible presence of microstrain. Since broadening due to microstrain and paracrystalline order both scale with scattering vector, they are easily confounded. In this work, a method to directionally discern these two influences on the peak shape in a Rietveld refinement is presented. Allocating intensities to amorphous, bulk and paracrystalline portions with changing tactic disturbance provided internal validations of the obtained directional numbers. In addition, the correlation between obtained thermal factors and Young's moduli, determined in earlier work, is discussed.
    Description: A method to robustly determine paracrystalline contents from Rietveld‐refined powder X‐ray data is presented and discussed for the example of mixed‐tacticity polyhydroxybutyrates. image
    Keywords: 548 ; polyhydroxybutyrates ; mixed tacticity ; paracrystallinity ; Rietveld refinement ; thermal factors
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  • 16
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    Concepts for nondestructive and depth‐resolved X‐ray residual stress analysis in the near‐surface region of nearly single crystalline materials with mosaic structure (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Two evaluation concepts for nondestructive depth‐resolved X‐ray residual stress analysis in the near‐surface region of materials with cubic symmetry and nearly single crystalline structure are introduced by simulated examples. Both concepts are based on the same data acquisition strategy, which consists in the determination of lattice‐spacing depth profiles along the ⟨hkl⟩ poles by stepwise sample rotation around the scattering vector. Segmentation of these profiles parallel to the sample surface provides the lattice strain state as a function of depth. The first evaluation concept extends the crystallite group method developed for materials with pronounced crystallographic texture by the feature of depth resolution and can be applied to samples with arbitrary orientation. The second evaluation concept, which adapts the linear regression approach of the sin2ψ method for the case of single crystalline materials, is restricted to samples with (001) orientation. The influence of the strain‐free lattice parameter a0 on residual stress analysis using both evaluation concepts is discussed on the basis of explicitly derived relations.
    Description: Two data evaluation concepts are proposed for nondestructive and depth‐resolved X‐ray residual stress analysis by means of energy‐dispersive diffraction on materials featuring cubic symmetry and a nearly single crystalline structure. image
    Keywords: 548 ; residual stress ; X‐ray diffraction ; depth‐resolved analysis ; mosaic crystals
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  • 17
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    X‐ray dichroism in polyimide caused by non‐resonant scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-30
    Description: Dichroism is one of the most important optical effects in both the visible and the X‐ray range. Besides absorption, scattering can also contribute to dichroism. This paper demonstrates that, based on the example of polyimide, materials can show tiny dichroism even far from electronic resonances due to scattering. Although the effect is small, it can lead to a measurable polarization change and might have influence on highly sensitive polarimetric experiments.
    Description: Aligned molecules, for example in polyimide foils, lead to small dichroism even far from resonances, which can be revealed by high‐precision X‐ray polarimetry. image
    Keywords: 548 ; polyimide ; polarization ; X‐ray polarimetry ; wide‐angle scattering ; X‐ray dichroism
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  • 18
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    Elastic stiffness coefficients of thiourea from thermal diffuse scattering (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-03-27
    Description: The complete elastic stiffness tensor of thiourea has been determined from thermal diffuse scattering (TDS) using high‐energy photons (100 keV). Comparison with earlier data confirms a very good agreement of the tensor coefficients. In contrast with established methods to obtain elastic stiffness coefficients (e.g. Brillouin spectroscopy, inelastic X‐ray or neutron scattering, ultrasound spectroscopy), their determination from TDS is faster, does not require large samples or intricate sample preparation, and is applicable to opaque crystals. Using high‐energy photons extends the applicability of the TDS‐based approach to organic compounds which would suffer from radiation damage at lower photon energies.
    Description: The elastic stiffness coefficients of thiourea are determined from thermal diffuse scattering. image
    Keywords: 548 ; thermal diffuse scattering ; elastic stiffness ; thiourea
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  • 19
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    Fast fitting of reflectivity data of growing thin films using neural networks (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-03
    Description: X‐ray reflectivity (XRR) is a powerful and popular scattering technique that can give valuable insight into the growth behavior of thin films. This study shows how a simple artificial neural network model can be used to determine the thickness, roughness and density of thin films of different organic semiconductors [diindenoperylene, copper(II) phthalocyanine and α‐sexithiophene] on silica from their XRR data with millisecond computation time and with minimal user input or a priori knowledge. For a large experimental data set of 372 XRR curves, it is shown that a simple fully connected model can provide good results with a mean absolute percentage error of 8–18% when compared with the results obtained by a genetic least mean squares fit using the classical Parratt formalism. Furthermore, current drawbacks and prospects for improvement are discussed.
    Description: Artificial neural networks trained with simulated data are shown to correctly and quickly determine film parameters from experimental X‐ray reflectivity curves.
    Keywords: 548 ; X‐ray reflectivity ; machine learning ; organic semi‐conductors ; neural networks
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    Numerically stable form factor of any polygon and polyhedron (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-05
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Apparent singularities, all removable, are discussed in detail. Cancellation near the singularities causes a loss of precision that can be avoided by using series expansions. An important application domain is small‐angle scattering by nanocrystals.
    Description: Coordinate‐free expressions for the form factors of arbitrary polygons and polyhedra are derived using the divergence theorem and Stokes's theorem. Series expansions are used to ensure numeric precision close to apparent singularities. image
    Keywords: 548 ; form factors ; polyhedra ; Fourier shape transform
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    ROBL‐II at ESRF: a synchrotron toolbox for actinide research (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-30
    Description: ROBL‐II provides four different experimental stations to investigate actinide and other alpha‐ and beta‐emitting radionuclides at the new EBS storage ring of ESRF within an energy range of 3 to 35 keV. The XAFS station consists of a highly automatized, high sample throughput installation in a glovebox, to measure EXAFS and conventional XANES of samples routinely at temperatures down to 10 K, and with a detection limit in the sub‐p.p.m. range. The XES station with its five bent‐crystal analyzer, Johann‐type setup with Rowland circles of 1.0 and 0.5 m radii provides high‐energy resolution fluorescence detection (HERFD) for XANES, XES, and RIXS measurements, covering both actinide L and M edges together with other elements accessible in the 3 to 20 keV energy range. The six‐circle heavy duty goniometer of XRD‐1 is equipped for both high‐resolution powder diffraction as well as surface‐sensitive CTR and RAXR techniques. Single crystal diffraction, powder diffraction with high temporal resolution, as well as X‐ray tomography experiments can be performed at a Pilatus 2M detector stage (XRD‐2). Elaborate radioprotection features enable a safe and easy exchange of samples between the four different stations to allow the combination of several methods for an unprecedented level of information on radioactive samples for both fundamental and applied actinide and environmental research.
    Description: ROBL‐II at ESRF provides four experimental stations to investigate actinides with X‐ray absorption and emission spectroscopy, and with surface, high‐resolution powder, and single‐crystal X‐ray diffractometry.
    Keywords: 549 ; actinides ; EXAFS ; XANES ; HERFD‐XANES ; XAS ; XES ; RIXS ; XRD ; CTR ; RAXR ; surface diffraction
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    ATSAS 3.0: expanded functionality and new tools for small‐angle scattering data analysis (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-30
    Description: The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small‐angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus‐based concentration‐independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi‐atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy – a PyMOL plugin to run a subset of ATSAS tools – to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl‐hamburg.de/biosaxs/software.html.
    Description: ATSAS is a comprehensive software suite for the processing, visualization, analysis and modelling of small‐angle scattering data. This article describes developments in the ATSAS 3.0 release, including new programs for data simulation and for the structural modelling of lipids, nucleic acids and polydisperse systems. image
    Keywords: 548 ; small‐angle scattering ; data analysis ; biological macromolecules ; structural modelling ; ATSAS
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    XGANDALF – extended gradient descent algorithm for lattice finding (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Serial crystallography records still diffraction patterns from single, randomly oriented crystals, then merges data from hundreds or thousands of them to form a complete data set. To process the data, the diffraction patterns must first be indexed, equivalent to determining the orientation of each crystal. A novel automatic indexing algorithm is presented, which in tests usually gives significantly higher indexing rates than alternative programs currently available for this task. The algorithm does not require prior knowledge of the lattice parameters but can make use of that information if provided, and also allows indexing of diffraction patterns generated by several crystals in the beam. Cases with a small number of Bragg spots per pattern appear to particularly benefit from the new approach. The algorithm has been implemented and optimized for fast execution, making it suitable for real‐time feedback during serial crystallography experiments. It is implemented in an open‐source C++ library and distributed under the LGPLv3 licence. An interface to it has been added to the CrystFEL software suite.
    Description: A description and evaluation are given of XGANDALF, extended gradient descent algorithm for lattice finding, an algorithm developed for fast and accurate indexing of snapshot diffraction patterns. image
    Keywords: 548 ; indexing ; XGANDALF ; CrystFEL ; multiple lattices ; serial crystallography
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    pinkIndexer – a universal indexer for pink‐beam X‐ray and electron diffraction snapshots (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink‐beam X‐ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit‐cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink‐beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi‐monochromatic X‐rays and with electrons the algorithm indexed more patterns than other programs tested.
    Description: pinkIndexer, an algorithm developed for indexing of snapshot diffraction patterns recorded with pink‐beam X‐rays, monochromatic X‐rays and electrons, is described and its use evaluated. image
    Keywords: 548 ; indexing ; pinkIndexer ; CrystFEL ; pink X‐ray beam ; serial electron diffraction
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    Crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-17
    Description: CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal‐binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2‐mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine‐dependent inhibitor compounds.
    Description: The covalent modification of human CRM1 by 2‐mercaptoethanol interferes with the characterization of cysteine‐dependent inhibitor compounds. image
    Keywords: 548 ; nuclear export ; cancer ; exportin 1 ; cysteine modification
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  • 26
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    Staircase array of inclined refractive multi‐lenses for large field of view pixel super‐resolution scanning transmission hard X‐ray microscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: Owing to the development of X‐ray focusing optics during the past decades, synchrotron‐based X‐ray microscopy techniques allow the study of specimens with unprecedented spatial resolution, down to 10 nm, using soft and medium X‐ray photon energies, though at the expense of the field of view (FOV). One of the approaches to increase the FOV to square millimetres is raster‐scanning of the specimen using a single nanoprobe; however, this results in a long data acquisition time. This work employs an array of inclined biconcave parabolic refractive multi‐lenses (RMLs), fabricated by deep X‐ray lithography and electroplating to generate a large number of long X‐ray foci. Since the FOV is limited by the pattern height if a single RML is used by impinging X‐rays parallel to the substrate, many RMLs at regular intervals in the orthogonal direction were fabricated by tilted exposure. By inclining the substrate correspondingly to the tilted exposure, 378000 X‐ray line foci were generated with a length in the centimetre range and constant intervals in the sub‐micrometre range. The capability of this new X‐ray focusing device was first confirmed using ray‐tracing simulations and then using synchrotron radiation at BL20B2 of SPring‐8, Japan. Taking account of the fact that the refractive lens is effective for focusing high‐energy X‐rays, the experiment was performed with 35 keV X‐rays. Next, by scanning a specimen through the line foci, this device was used to perform large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy (PSR‐STHXM) with a 780 ± 40 nm spatial resolution within an FOV of 1.64 cm × 1.64 cm (limited by the detector area) and a total scanning time of 4 min. Biomedical implant abutments fabricated via selective laser melting using Ti–6Al–4V medical alloy were measured by PSR‐STHXM, suggesting its unique potential for studying extended and thick specimens. Although the super‐resolution function was realized in one dimension in this study, it can be expanded to two dimensions by aligning a pair of presented devices orthogonally.
    Description: A new X‐ray focusing device generates hundreds of thousands of line foci, periodically spaced in the sub‐micrometre range, with centimetre length. It enables to achieve large FOV pixel super‐resolution scanning transmission hard X‐ray microscopy. image
    Keywords: 502.82 ; inclined refractive X‐ray multi‐lens array ; pixel super‐resolution ; scanning transmission hard X‐ray microscopy ; deep X‐ray lithography and electroplating
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    A new concept for temporal gating of synchrotron X‐ray pulses (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-02
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented. First experimental tests of the concept yield a diffraction efficiency of 0.18%; however, the calculations indicate a theoretical efficiency and contrast of 〉30% and 10−5, respectively. The full efficiency of the pulse picker has not been reached yet due to a long‐range thermal deformation of the sample after absorption of the excitation laser. This method can be implemented in a broad spectral range (100 eV to 20 keV) and is only minimally invasive to an existing setup.
    Description: A new concept for temporal gating of synchrotron X‐ray pulses based on laser‐induced thermal transient gratings is presented.
    Keywords: 548 ; synchrotron ; time‐resolved ; thermal deformation ; transient grating ; pulse picking
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    The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP at BESSY II (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-06
    Description: The time‐resolved hard X‐ray diffraction endstation KMC‐3 XPP for optical pump/X‐ray probe experiments at the electron storage ring BESSY II is dedicated to investigating the structural response of thin film samples and heterostructures after their excitation with ultrashort laser pulses and/or electric field pulses. It enables experiments with access to symmetric and asymmetric Bragg reflections via a four‐circle diffractometer and it is possible to keep the sample in high vacuum and vary the sample temperature between ∼15 K and 350 K. The femtosecond laser system permanently installed at the beamline allows for optical excitation of the sample at 1028 nm. A non‐linear optical setup enables the sample excitation also at 514 nm and 343 nm. A time‐resolution of 17 ps is achieved with the `low‐α' operation mode of the storage ring and an electronic variation of the delay between optical pump and hard X‐ray probe pulse conveniently accesses picosecond to microsecond timescales. Direct time‐resolved detection of the diffracted hard X‐ray synchrotron pulses use a gated area pixel detector or a fast point detector in single photon counting mode. The range of experiments that are reliably conducted at the endstation and that detect structural dynamics of samples excited by laser pulses or electric fields are presented.
    Description: The KMC‐3 XPP endstation of the synchrotron BESSY II is dedicated to time‐resolved studies of structural dynamics of matter upon optical and/or electrical excitation using hard X‐ray diffraction with an accessible time range from 17 ps to several microseconds. image
    Keywords: 548 ; beamline instrumentation ; time‐resolved X‐ray diffraction ; optical excitation ; thermal transport ; ferroelectric switching
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    Disordered sodium alkoxides from powder data: crystal structures of sodium ethoxide, propoxide, butoxide and pentoxide, and some of their solvates (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n‐propoxide (sodium n‐propanolate, NaOnPr), sodium n‐butoxide (sodium n‐butanolate, NaOnBu) and sodium n‐pentoxide (sodium n‐amylate, NaOnAm) were determined from powder X‐ray diffraction data. NaOEt crystallizes in space group P421m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space‐group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti‐PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n‐propoxide n‐propanol disolvate (NaOnPr·2nPrOH), sodium isopropoxide isopropanol pentasolvate (NaOiPr·5iPrOH) and sodium tert‐amylate tert‐amyl alcohol monosolvate (NaOtAm·tAmOH, tAm = 2‐methyl‐2‐butyl). Their crystal structures were determined by single‐crystal X‐ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen‐bond networks diverge widely among the solvate structures. The hydrogen‐bond topology of the iPrOH network in NaOiPr·5iPrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline iPrOH.
    Description: The crystal structures of NaOEt, NaOPr, NaOBu and NaOAm (Am = amyl = pentyl) were determined from powder data. These compounds crystallize in an anti‐PbO structure in the space groups P21m and P4/nmm. Additionally, solvates with the composition NaOEt·2EtOH, NaOPr·2PrOH, NaOiPr·5iPrOH and NaOtAm·tAmOH were synthesized, and their structures were determined from single crystals. They form interesting chain structures of different compositions and topologies. image
    Keywords: 548 ; sodium alkoxide ; powder data ; solvate ; isopropanol ; Bärnighausen tree ; PXRD
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    Small‐angle X‐ray scattering from GaN nanowires on Si(111): facet truncation rods, facet roughness and Porod's law (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: Small‐angle X‐ray scattering from GaN nanowires grown on Si(111) is measured in the grazing‐incidence geometry and modelled by means of a Monte Carlo simulation that takes into account the orientational distribution of the faceted nanowires and the roughness of their side facets. It is found that the scattering intensity at large wavevectors does not follow Porod's law I(q) ∝ q−4. The intensity depends on the orientation of the side facets with respect to the incident X‐ray beam. It is maximum when the scattering vector is directed along a facet normal, reminiscent of surface truncation rod scattering. At large wavevectors q, the scattering intensity is reduced by surface roughness. A root‐mean‐square roughness of 0.9 nm, which is the height of just 3–4 atomic steps per micrometre‐long facet, already gives rise to a strong intensity reduction.
    Description: The intensity of small‐angle X‐ray scattering from GaN nanowires on Si(111) depends on the orientation of the side facets with respect to the incident beam. This reminiscence of truncation rod scattering gives rise to a deviation from Porod's law. A roughness of just 3–4 atomic steps per micrometre‐long side facet notably changes the intensity curves. image
    Keywords: 548 ; nanowires ; Porod's law ; facet truncation rods ; small‐angle X‐ray scattering ; SAXS ; grazing‐incidence small‐angle X‐ray scattering ; GISAXS
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    The accuracy of protein models automatically built into cryo‐EM maps with ARP/wARP (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Recent developments in cryogenic electron microscopy (cryo‐EM) have enabled structural studies of large macromolecular complexes at resolutions previously only attainable using macromolecular crystallography. Although a number of methods can already assist in de novo building of models into high‐resolution cryo‐EM maps, automated and reliable map interpretation remains a challenge. Presented here is a systematic study of the accuracy of models built into cryo‐EM maps using ARP/wARP. It is demonstrated that the local resolution is a good indicator of map interpretability, and for the majority of the test cases ARP/wARP correctly builds 90% of main‐chain fragments in regions where the local resolution is 4.0 Å or better. It is also demonstrated that the coordinate accuracy for models built into cryo‐EM maps is comparable to that of X‐ray crystallographic models at similar local cryo‐EM and crystallographic resolutions. The model accuracy also correlates with the refined atomic displacement parameters.
    Keywords: 548 ; ARP/wARP ; model building ; cryo‐EM ; model accuracy ; sequence assignment
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    Synthesis, crystal structure and structure–property relations of strontium orthocarbonate, Sr2CO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-05
    Description: Carbonates containing CO4 groups as building blocks have recently been discovered. A new orthocarbonate, Sr2CO4 is synthesized at 92 GPa and at a temperature of 2500 K. Its crystal structure was determined by in situ synchrotron single‐crystal X‐ray diffraction, selecting a grain from a polycrystalline sample. Strontium orthocarbonate crystallizes in the orthorhombic crystal system (space group Pnma) with CO4, SrO9 and SrO11 polyhedra as the main building blocks. It is isostructural to Ca2CO4. DFT calculations reproduce the experimental findings very well and have, therefore, been used to predict the equation of state, Raman and IR spectra, and to assist in the discussion of bonding in this compound.
    Description: A new orthocarbonate, Sr2CO4, was synthesized under extreme pressure and temperature conditions of 92 GPa and 2500 K, respectively. The crystal structure of the compound s fully characterized in situ by synchrotron single‐crystal X‐ray diffraction and DFT calculations were employed to provide insight into its equation of state, Raman and IR spectra, and bonding. image
    Keywords: 548 ; orthocarbonates ; crystal structure ; single‐crystal X‐ray diffraction ; high pressure ; Sr2CO4
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    Anomalous SAXS at P12 beamline EMBL Hamburg: instrumentation and applications (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-28
    Description: Small‐angle X‐ray scattering (SAXS) is an established method for studying nanostructured systems and in particular biological macromolecules in solution. To obtain element‐specific information about the sample, anomalous SAXS (ASAXS) exploits changes of the scattering properties of selected atoms when the energy of the incident X‐rays is close to the binding energy of their electrons. While ASAXS is widely applied to condensed matter and inorganic systems, its use for biological macromolecules is challenging because of the weak anomalous effect. Biological objects are often only available in small quantities and are prone to radiation damage, which makes biological ASAXS measurements very challenging. The BioSAXS beamline P12 operated by the European Molecular Biology Laboratory (EMBL) at the PETRA III storage ring (DESY, Hamburg) is dedicated to studies of weakly scattering objects. Here, recent developments at P12 allowing for ASAXS measurements are presented. The beamline control, data acquisition and data reduction pipeline of the beamline were adapted to conduct ASAXS experiments. Modelling tools were developed to compute ASAXS patterns from atomic models, which can be used to analyze the data and to help designing appropriate data collection strategies. These developments are illustrated with ASAXS experiments on different model systems performed at the P12 beamline.
    Keywords: 548 ; ASAXS ; biological SAXS ; metalloproteins ; gold nanoparticles ; anomalous scattering ; beamline development
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    Symmetry relations in wurtzite nitrides and oxide nitrides and the curious case of Pmc21 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
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    Publication Date: 2021-06-27
    Description: Binary III–V nitrides such as AlN, GaN and InN in the wurtzite‐type structure have long been considered as potent semiconducting materials because of their optoelectronic properties, amongst others. With rising concerns over the utilization of scarce elements, a replacement of the trivalent cations by others in ternary and multinary nitrides has led to the development of different variants of nitrides and oxide nitrides crystallizing in lower‐symmetry variants of wurtzite. This work presents the symmetry relationships between these structural types specific to nitrides and oxide nitrides and updates some prior work on this matter. The non‐existence of compounds crystallizing in Pmc21, formally the highest subgroup of the wurtzite type fulfilling Pauling's rules for 1:1:2 stoichiometries, has been puzzling scientists for a while; a rationalization is given, from a crystallographic basis, of why this space group is unlikely to be adopted.
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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    Comparison and evaluation of pair distribution functions, using a similarity measure based on cross‐correlation functions (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-20
    Description: An approach for the comparison of pair distribution functions (PDFs) has been developed using a similarity measure based on cross‐correlation functions. The PDF is very sensitive to changes in the local structure, i.e. small deviations in the structure can cause large signal shifts and significant discrepancies between the PDFs. Therefore, a comparison based on pointwise differences (e.g. R values and difference curves) may lead to the assumption that the investigated PDFs as well as the corresponding structural models are not in agreement at all, whereas a careful visual inspection of the investigated structural models and corresponding PDFs may reveal a relatively good match. To quantify the agreement of different PDFs for those cases an alternative approach is introduced: the similarity measure based on cross‐correlation functions. In this paper, the power of this application of the similarity measure to the analysis of PDFs is highlighted. The similarity measure is compared with the classical Rwp values as representative of the comparison based on pointwise differences as well as with the Pearson product‐moment correlation coefficient, using polymorph IV of barbituric acid as an example.
    Description: A novel approach to the quantification of the agreement between pair distribution functions by a similarity measure based on cross‐correlation functions is introduced and evaluated. image
    Keywords: 548 ; pair distribution functions ; similarity measures ; total scattering techniques ; cross‐correlation functions ; R values
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    Novel experimental setup for megahertz X‐ray diffraction in a diamond anvil cell at the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser (EuXFEL) (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The high‐precision X‐ray diffraction setup for work with diamond anvil cells (DACs) in interaction chamber 2 (IC2) of the High Energy Density instrument of the European X‐ray Free‐Electron Laser is described. This includes beamline optics, sample positioning and detector systems located in the multipurpose vacuum chamber. Concepts for pump–probe X‐ray diffraction experiments in the DAC are described and their implementation demonstrated during the First User Community Assisted Commissioning experiment. X‐ray heating and diffraction of Bi under pressure, obtained using 20 fs X‐ray pulses at 17.8 keV and 2.2 MHz repetition, is illustrated through splitting of diffraction peaks, and interpreted employing finite element modeling of the sample chamber in the DAC.
    Description: The high‐precision X‐ray diffraction (XRD) setup for work with diamond anvil cells (DACs) in Interaction Chamber 2 of the High Energy Density (HED) instrument of the European X‐ray Free‐Electron Laser is described. image
    Keywords: 548 ; diamond anvil cells ; X‐ray free‐electron lasers ; high‐precision X‐ray diffraction ; finite element modeling
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    The anisotropy in the optical constants of quartz crystals for soft X‐rays (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from orientation‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. Owing to the anisotropy of the crystal structure in the (100) and (001) directions, a significant deviation of the measured reflectance at the Si L2,3 and O K absorption edges is observed. The anisotropy in the optical constants reconstructed from these data is also confirmed by ab initio Bethe–Salpeter equation calculations for the O K edge. This new experimental data set expands the existing literature data for quartz crystal optical constants significantly, particularly in the near‐edge regions.
    Description: The refractive index of a y‐cut SiO2 crystal surface is reconstructed from polarization‐dependent soft X‐ray reflectometry measurements in the energy range from 45 to 620 eV. The reconstructed anisotropy in the optical constants is also confirmed by ab initio Bethe–Salpeter equation calculations of the O K edge. image
    Keywords: 548 ; optical constants ; quartz ; anisotropy ; soft X‐ray reflectometry
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    Unravelling the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ mixed ionic electronic conductors (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-05
    Description: Mixed ionic electronic conducting ceramics Nd6−yWO12−δ (δ is the oxygen deficiency) provide excellent stability in harsh environments containing strongly reactive gases such as CO2, CO, H2, H2O or H2S. Due to this chemical stability, they are promising and cost‐efficient candidate materials for gas separation, catalytic membrane reactors and protonic ceramic fuel cell technologies. As in La6−yWO12−δ, the ionic/electronic transport mechanism in Nd6−yWO12−δ is expected to be largely controlled by the crystal structure, the conclusive determination of which is still lacking. This work presents a crystallographic study of Nd5.8WO12−δ and molybdenum‐substituted Nd5.7W0.75Mo0.25O12−δ prepared by the citrate complexation route. High‐resolution synchrotron and neutron powder diffraction data were used in combined Rietveld refinements to unravel the crystal structure of Nd5.8WO12−δ and Nd5.7W0.75Mo0.25O12−δ. Both investigated samples crystallize in a defect fluorite crystal structure with space group Fm3m and doubled unit‐cell parameter due to cation ordering. Mo replaces W at both Wyckoff sites 4a and 48h and is evenly distributed, in contrast with La6−yWO12−δ. X‐ray absorption spectroscopy as a function of partial pressure pO2 in the near‐edge regions excludes oxidation state changes of Nd (Nd3+) and W (W6+) in reducing conditions: the enhanced hydrogen permeation, i.e. ambipolar conduction, observed in Mo‐substituted Nd6−yWO12−δ is therefore explained by the higher Mo reducibility and the creation of additional – disordered – oxygen vacancies.
    Description: The crystal structures of non‐substituted and Mo‐substituted neodymium tungstates are described in detail through neutron diffraction and high‐resolution X‐ray diffraction. Combined X‐ray and neutron diffraction refinements and electron probe micro‐analysis were employed to locate Mo atoms in the crystal structure of Nd6−yW1−zMozO12−δ (z = 0, 0.25), while X‐ray absorption spectroscopy in the near‐edge regions confirmed no changes in the oxidation states of Nd and W.
    Keywords: 548 ; powder diffraction ; mixed conductors ; X‐ray absorption spectroscopy (XAS) ; Nd6−yWO12−δ
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    High‐temperature treatments of niobium under high vacuum, dilute air‐ and nitrogen‐atmospheres as investigated by in situ X‐ray absorption spectroscopy (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-30
    Description: Niobium metal foils were heat‐treated at 900°C under different conditions and in situ investigated with time‐resolved X‐ray absorption fine‐structure (EXAFS and XANES) measurements. The present study aims to mimic the conditions usually applied for heat treatments of Nb materials used for superconducting radiofrequency cavities, in order to better understand the evolving processes during vacuum annealing as well as for heat treatments in controlled dilute gases. Annealing in vacuum in a commercially available cell showed a substantial amount of oxidation, so that a designated new cell was designed and realized, allowing treatments under clean high‐vacuum conditions as well as under well controllable gas atmospheres. The experiments performed under vacuum demonstrated that the original structure of the Nb foils is preserved, while a detailed evaluation of the X‐ray absorption fine‐structure data acquired during treatments in dilute air atmospheres (10−5 mbar to 10−3 mbar) revealed a linear oxidation with the time of the treatment, and an oxidation rate proportional to the oxygen (air) pressure. The structure of the oxide appears to be very similar to that of polycrystalline NbO. The cell also permits controlled exposures to other reactive gases at elevated temperatures; here the Nb foils were exposed to dilute nitrogen atmospheres after a pre‐conditioning of the studied Nb material for one hour under high‐vacuum conditions, in order to imitate typical conditions used for nitrogen doping of cavity materials. Clear structural changes induced by the N2 exposure were found; however, no evidence for the formation of niobium nitride could be derived from the EXAFS and XANES experiments. The presented results establish the feasibility to study the structural changes of the Nb materials in situ during heat treatments in reactive gases with temporal resolution, which are important to better understand the underlaying mechanisms and the dynamics of phase formation during those heat treatments in more detail.
    Keywords: 548 ; in situ EXAFS ; high temperature ; time‐resolved EXAFS ; niobium
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    Pressure‐induced Pb–Pb bonding and phase transition in Pb2SnO4 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-03-27
    Description: High‐pressure single‐crystal to 20 GPa and powder diffraction measurements to 50 GPa, show that the structure of Pb2SnO4 strongly distorts on compression with an elongation of one axis. A structural phase transition occurs between 10 GPa and 12 GPa, with a change of space group from Pbam to Pnam. The resistivity decreases by more than six orders of magnitude when pressure is increased from ambient conditions to 50 GPa. This insulator‐to‐semiconductor transition is accompanied by a reversible appearance change from transparent to opaque. Density functional theory‐based calculations show that at ambient conditions the channels in the structure host the stereochemically‐active Pb 6s2 lone electron pairs. On compression the lone electron pairs form bonds between Pb2+ ions. Also provided is an assignment of irreducible representations to the experimentally observed Raman bands.
    Description: The structure of Pb2SnO4 is found to strongly distort on compression and a structural phase transition with a change of space group from Pbam to Pnam occurs at ∼11 GPa. Our complementary DFT‐based calculations show that at ambient conditions, the channels in the structure host the stereochemically active Pb 6s2 lone electron pairs which form bonds between the Pb2+ ions with increasing pressure. image
    Keywords: 548 ; lead stannate (Pb2SnO4) ; density functional theory ; high‐pressure X‐ray diffraction ; pressure‐induced phase transition ; insulator–semiconductor transition
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  • 41
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    A discussion on `Domain formation and phase transitions in the wurtzite‐based heterovalent ternaries: a Landau theory analysis' (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-05
    Description: Heterovalent ternary nitrides are considered one of the promising classes of materials for photovoltaics, combining attractive physical properties with low toxicity and element abundance. One of the front‐runner systems under consideration is ZnSnN2. Although it is nominally a ternary compound, no clear crystallographic evidence for cation ordering has been observed so far. An attempt to elucidate this discrepancy [Quayle (2020). Acta Cryst. A76, 410–420] was the trigger for an intensive discussion between the authors, and an agreement was reached to elaborate on some points in order to set things in perspective. Rather than using a conventional comment–answer scheme, this is published in the form of a joint discussion to celebrate constructive criticism and collegiality.
    Description: A scientific exchange on an earlier paper [Quayle (2020). Acta Cryst. A76, 410–420] has led to the clarification of some of the points. image
    Keywords: 548 ; group–subgroup relationships ; nitride materials ; wurtzite type
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  • 42
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    X‐SPEC: a 70 eV to 15 keV undulator beamline for X‐ray and electron spectroscopies (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: X‐SPEC is a high‐flux spectroscopy beamline at the KIT (Karlsruhe Institute of Technology) Synchrotron for electron and X‐ray spectroscopy featuring a wide photon energy range. The beamline is equipped with a permanent magnet undulator with two magnetic structures of different period lengths, a focusing variable‐line‐space plane‐grating monochromator, a double‐crystal monochromator and three Kirkpatrick–Baez mirror pairs. By selectively moving these elements in or out of the beam, X‐SPEC is capable of covering an energy range from 70 eV up to 15 keV. The flux of the beamline is maximized by optimizing the magnetic design of the undulator, minimizing the number of optical elements and optimizing their parameters. The beam can be focused into two experimental stations while maintaining the same spot position throughout the entire energy range. The first experimental station is optimized for measuring solid samples under ultra‐high‐vacuum conditions, while the second experimental station allows in situ and operando studies under ambient conditions. Measurement techniques include X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS).
    Description: X‐SPEC is a high‐flux undulator beamline for electron and X‐ray spectroscopy with an energy range from 70 eV to 15 keV. It offers X‐ray absorption spectroscopy (XAS), extended X‐ray absorption fine structure (EXAFS), photoelectron spectroscopy (PES) and hard X‐ray PES (HAXPES), as well as X‐ray emission spectroscopy (XES) and resonant inelastic X‐ray scattering (RIXS) for in vacuo, in situ and operando sample environments. image
    Keywords: 548 ; undulator beamline ; soft X‐ray ; tender X‐ray ; hard X‐ray ; in situ ; operando ; HAXPES ; RIXS ; XAS ; XES
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  • 43
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    Structure determination of organic compounds by a fit to the pair distribution function from scratch without prior indexing (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-06-26
    Description: A method for the ab initio crystal structure determination of organic compounds by a fit to the pair distribution function (PDF), without prior knowledge of lattice parameters and space group, has been developed. The method is called `PDF‐Global‐Fit' and is implemented by extension of the program FIDEL (fit with deviating lattice parameters). The structure solution is based on a global optimization approach starting from random structural models in selected space groups. No prior indexing of the powder data is needed. The new method requires only the molecular geometry and a carefully determined PDF. The generated random structures are compared with the experimental PDF and ranked by a similarity measure based on cross‐correlation functions. The most promising structure candidates are fitted to the experimental PDF data using a restricted simulated annealing structure solution approach within the program TOPAS, followed by a structure refinement against the PDF to identify the correct crystal structure. With the PDF‐Global‐Fit it is possible to determine the local structure of crystalline and disordered organic materials, as well as to determine the local structure of unindexable powder patterns, such as nanocrystalline samples, by a fit to the PDF. The success of the method is demonstrated using barbituric acid as an example. The crystal structure of barbituric acid form IV solved and refined by the PDF‐Global‐Fit is in excellent agreement with the published crystal structure data.
    Keywords: 548 ; pair distribution function analysis ; structure determination ; total scattering technique ; similarity measures ; PDF‐Global‐Fit
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  • 44
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    Structural basis of chitin utilization by a GH20 β‐N‐acetylglucosaminidase from Vibrio campbellii strain ATCC BAA‐1116 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-07-01
    Description: Vibrio species play a crucial role in maintaining the carbon and nitrogen balance between the oceans and the land through their ability to employ chitin as a sole source of energy. This study describes the structural basis for the action of the GH20 β‐N‐acetylglucosaminidase (VhGlcNAcase) in chitin metabolism by Vibrio campbellii (formerly V. harveyi) strain ATCC BAA‐1116. Crystal structures of wild‐type VhGlcNAcase in the absence and presence of the sugar ligand, and of the unliganded D437A mutant, were determined. VhGlcNAcase contains three distinct domains: an N‐terminal carbohydrate‐binding domain linked to a small α+β domain and a C‐terminal (β/α)8 catalytic domain. The active site of VhGlcNAcase has a narrow, shallow pocket that is suitable for accommodating a small chitooligosaccharide. VhGlcNAcase is a monomeric enzyme of 74 kDa, but its crystal structures show two molecules of enzyme per asymmetric unit, in which Gln16 at the dimeric interface of the first molecule partially blocks the entrance to the active site of the neighboring molecule. The GlcNAc unit observed in subsite −1 makes exclusive hydrogen bonds to the conserved residues Arg274, Tyr530, Asp532 and Glu584, while Trp487, Trp546, Trp582 and Trp505 form a hydrophobic wall around the −1 GlcNAc. The catalytic mutants D437A/N and E438A/Q exhibited a drastic loss of GlcNAcase activity, confirming the catalytic role of the acidic pair (Asp437–Glu438).
    Description: Crystal structures of a GH20 β‐N‐acetylglucosaminidase from V. campbellii reveal substrate specificity in chitin utilization.
    Keywords: 577.14 ; GH20 β‐N‐acetylglucosaminidase ; chitin recycling ; Vibrio spp ; marine bacteria
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  • 45
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    Estimating Bioturbation From Replicated Small‐Sample Radiocarbon Ages (2021)
    American Geophysical Union
    In:  EPIC3Paleoceanography and Paleoclimatology, American Geophysical Union, 36(7), ISSN: 2572-4517
    Details
    Publication Date: 2021-09-20
    Description: Marine sedimentary records are a key archive when reconstructing past climate; however, mixing at the seabed (bioturbation) can strongly influence climate records, especially when sedimentation rates are low. By commingling the climate signal from different time periods, bioturbation both smooths climate records, by damping fast climate variations, and creates noise when measurements are made on samples containing small numbers of individual proxy carriers, such as foraminifera. Bioturbation also influences radiocarbon-based age-depth models, as sample ages may not represent the true ages of the sediment layers from which they were picked. While these effects were first described several decades ago, the advent of ultra-small-sample $^{14}$C dating now allows samples containing very small numbers of foraminifera to be measured, thus enabling us to directly measure the age-heterogeneity of sediment for the first time. Here, we use radiocarbon dates measured on replicated samples of 3-30 foraminifera to estimate age-heterogeneity for five marine sediment cores with sedimentation rates ranging from 2-30 cm kyr$^{-1}$. From their age-heterogeneities and sedimentation rates we infer mixing depths of 10-20 cm for our core sites. Our results show that when accounting for age-heterogeneity, the true error of radiocarbon dating can be several times larger than the reported measurement. We present estimates of this uncertainty as a function of sedimentation rate and the number of individuals per radiocarbon date. A better understanding of this uncertainty will help us to optimise radiocarbon measurements, construct age models with appropriate uncertainties and better interpret marine paleo records.
    Repository Name: EPIC Alfred Wegener Institut
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    Resolution of a bent‐crystal spectrometer for X‐ray free‐electron laser pulses: diamond versus silicon (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: The resolution function of a spectrometer based on a strongly bent single crystal (bending radius of 10 cm or less) is evaluated. It is shown that the resolution is controlled by two parameters: (i) the ratio of the lattice spacing of the chosen reflection to the crystal thickness and (ii) a single parameter comprising crystal thickness, its bending radius, distance to a detector, and anisotropic elastic constants of the chosen crystal. The results allow the optimization of the parameters of bent‐crystal spectrometers for the hard X‐ray free‐electron laser sources.
    Description: The resolution function of a bent‐crystal spectrometer for pulses of an X‐ray free‐electron laser is evaluated. Under appropriate conditions, the energy resolution reaches the ratio of the lattice spacing to the crystal thickness. image
    Keywords: 548 ; X‐ray free‐electron lasers ; X‐ray spectroscopy ; bent crystals ; diamond crystal optics ; femtosecond X‐ray diffraction
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    Separation of the inelastic and elastic scattering in time‐of‐flight mode on the pinhole small‐angle neutron scattering diffractometer KWS‐2 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: To study and control the incoherent inelastic background in small‐angle neutron scattering, which makes a significant contribution to the detected scattering from hydrocarbon systems, the KWS‐2 small‐angle neutron scattering diffractometer operated by the Jülich Centre for Neutron Science (JCNS) at Heinz‐Maier Leibnitz Zentrum (MLZ), Garching, Germany, was equipped with a secondary single‐disc chopper that is placed in front of the sample stage. This makes it possible to record in time‐of‐flight mode the scattered neutrons in the high‐Q regime of the instrument (i.e. short incoming wavelengths and detection distances) and to discard the inelastic component from the measured data. Examples of measurements on different materials routinely used as standard samples, sample containers and solvents in the experiments at KWS‐2 are presented. When only the elastic region of the spectrum is used in the data‐reduction procedure, a decrease of up to two times in the incoherent background of the experimentally measured scattering cross section may be obtained. The proof of principle is demonstrated on a solution of bovine serum albumin in D2O.
    Description: A new chopper has been installed at the sample position in front of the sample stage at the KWS‐2 small‐angle neutron‐scattering diffractometer of the Jülich Centre for Neutron Science. The pulsed beam and the time‐of‐flight data acquisition enable the separation of elastic and inelastic scattering from hydrogenous samples.
    Keywords: 548 ; TOF‐SANS ; incoherent neutron scattering ; inelastic neutron scattering ; hydrocarbon systems
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    Czochralski growth of mixed cubic sesquioxide crystals in the ternary system Lu2O3–Sc2O3–Y2O3 (2021)
    International Union of Crystallography | 5 Abbey Square, Chester, Cheshire CH1 2HU, England
    Details
    Publication Date: 2021-09-29
    Description: Cubic rare‐earth sesquioxide crystals are strongly demanded host materials for high power lasers, but due to their high melting points investigations on their thermodynamics and the growth of large‐size crystals of high optical quality remain a challenge. Detailed thermal investigations of the ternary system Lu2O3–Sc2O3–Y2O3 revealing a large range of compositions with melting temperatures below 2200°C and a minimum of 2053°C for the composition (Sc0.45Y0.55)2O3 are presented. These reduced temperatures enable for the first time the growth of high optical quality mixed sesquioxide crystals with disordered structure by the conventional Czochralski method from iridium crucibles. An (Er0.07Sc0.50Y0.43)2O3 crystal is successfully grown and characterized with respect to its crystallographic properties as well as its composition, thermal conductivity and optical absorption in the 1 µm range.
    Description: The phase diagram of the ternary system Lu2O3–Sc2O3–Y2O3 is investigated and compositions with melting points below 2200°C are found. This allows for the first successful growth of the mixed cubic sesquioxide crystal (Er0.07Sc0.50Y0.43)2O3 by the Czochralski method from an iridium crucible. image
    Keywords: 548 ; crystal growth ; optical materials ; phase diagrams ; melting points ; rare earth sesquioxides
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    Methane Emissions from Northern Wetlands During the Holocene : A Synthesis Approach to Account for Wetland Expansion and Fen-Bog-Permafrost Transitions (Invited) (2021)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting, New Orleans, LA, USA, 2021-12-13-2021-12-17American Geophysical Union
    Details
    Publication Date: 2021-12-23
    Description: Methane emissions from northern high latitude wetlands constitute a major uncertainty in the atmospheric methane (CH4) budget during the Holocene. To reconstruct northern wetland methane emissions, we used an empirical model based on syntheses of observations of peat initiation from more than 3600 radiocarbon-dated basal peat ages, plant-macrofossil-derived peatland type from more than 250 peat cores from sites across the northern high latitudes, and observed CH4 emissions averaged from modern-day wetland types in order to explore the effects of wetland expansion and changes in wetland type. Peatland basal ages and plant macrofossil records showed the widespread formation of fens in major northern wetland complexes before 8000 BP. After 8000 BP, new fen formation continued, but widespread peatland succession (to bogs) and permafrost aggradation also occurred. Reconstructed CH4 emissions from peatlands increased rapidly between 10,600 BP and 6900 BP due to fen formation and expansion, then stabilized after 5000 BP at 42 ± 25 Tg CH4 y-1, as high methane-emitting fens transitioned to lower methane-emitting bogs and permafrost peatlands. Permafrost formation in northern peatlands after 1000 BP decreased CH4 emissions by 20% to 34 ± 21 Tg y-1 by the present day. Warming temperatures, changes in peatland hydrology, and permafrost thaw will likely change the magnitude of northern peatland emissions in the future.
    Repository Name: EPIC Alfred Wegener Institut
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    Monitoring the human footprint across the Arctic coastal region in the context of climate change impact assessment (2021)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting 2021, Online, 2021-12-13-2021-12-17American Geophysical Union
    Details
    Publication Date: 2021-12-26
    Description: Infrastructure and anthropogenic impacts are expanding across the Arctic. A consistent record of human impact is required in order to quantify the changes and to assess climate change impacts on the communities. We derived a first panarctic satellite-based record of expanding infrastructure and anthropogenic impacts along all permafrost affected coasts (100 km buffer) within the H2020 project Nunataryuk based on Sentinel-1/2 satellite imagery. C-band synthetic aperture radar and multi-spectral information is combined through a machine learning framework. Depending on region, we identified up to 50% more information (human presence) than in OpenStreetMap. The combination with satellite records on vegetation change (specifically NDVI from Landsat since 2000) allowed quantification of recent expansion of infrastructure. Most of the expanded human presence occurred in Russia related predominantly to oil/gas industry. The majority of areas with human presence will be subject to thaw by mid-21st century based on ground temperature trends derived from the ESA CCI+ Permafrost time series (1997-2019). Of specific concern in this context are also settlements located directly at permafrost affected coasts. An efficient erosion rate monitoring scheme needs to be developed and combined with settlement records in order to assess the risk for local communities and infrastructure. Relevant progress in the framework of the ESA EO4PAC project will be discussed.
    Repository Name: EPIC Alfred Wegener Institut
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    Evaluating a deep-learning approach for mapping retrogressive thaw slumps across the Arctic (2021)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting 2021, Online, 2021-12-13-2021-12-17American Geophysical Union
    Details
    Publication Date: 2021-12-26
    Description: Retrogressive thaw slumps (RTS) are typical landforms indicating processes of rapid thawing and degrading permafrost. Their abundance is increasing in many regions and quantifying their dynamics is of high importance for assessing geomorphic, hydrologic, and biogeochemical impacts of climate change in the Arctic. Here we present a deep-learning (DL) based semantic segmentation framework to detect RTS, using high-resolution multi-spectral PlanetScope, topographic (ArcticDEM elevation and slope), and medium-resolution multi-temporal Landsat Trend data. We created a highly automated processing pipeline, which is designed to allow reproducible results and to be flexible for multiple input data types. The processing workflow is based on the pytorch deep-learning framework and includes a variety of different segmentation architectures (UNet, UNet++, DeepLabV3), backbones and includes common data transformation techniques such as augmentation or normalization. We tested (training, validation) our DL based model in six different regions of 100 to 300 km² size across Canada, and Siberia. We performed a regional cross-validation (5 regions training, 1 region validation) to test the spatial robustness and transferability of the algorithm. Furthermore, we tested different architectures, backbones and loss-functions to identify the best performing and most robust parameter sets. For training the models we created a database of manually digitized and validated RTS polygons. The resulting model performance varied strongly between different regions with maximum Intersection over Union (IoU) scores between 0.15 and 0.58. The strong regional variation emphasizes the need for sufficiently large training data, which is representative of the diversity of RTS types. However, the creation of good training data proved to be challenging due to the fuzzy definition and delineation of RTS. We are further continuing to improve the usability and the functionality to add further datasets and classes. We will show first results from the upscaling beyond small test areas towards large spatial clusters of extensive RTS presence e.g. Peel Plateau in NW Canada.
    Repository Name: EPIC Alfred Wegener Institut
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    Evaluating the Effects of Tundra Fires on Soil Microtopography and Hydrologic Surface Networks in Polygonal Permafrost Landscapes (2021)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting 2021, Online, 2021-12-13-2021-12-17American Geophysical Union
    Details
    Publication Date: 2021-12-26
    Description: With the Earth’s climate rapidly warming, the Arctic represents one of the most vulnerable regions to environmental change. These northern high latitude regions experience intensified fire seasons and especially tundra fires are projected to become more frequent and severe. Fires in permafrost regions have extensive impacts, including the initiation of thermokarst (rapid thaw of ice-rich ground), as they combust the upper organic soil layers which provide insulation to the permafrost below. Rapid permafrost thaw is, thus, often observable in fire scars in the first years post-disturbance. In polygonal ice-wedge landscapes, this becomes most prevalent through melting ice wedges and degrading troughs. The further these ice wedges degrade, the more troughs will likely connect and build an extensive hydrological network with changing patterns and degrees of connectivity that influences hydrology and runoff. While subsiding troughs over melting ice wedges may host new ponds, an increasing connectivity may also subsequently lead to more drainage of ponds, which in turn can limit further thaw and help stabilize the landscape. To quantify the changes in such dynamic landscapes over large regions, highly automated methods are needed that allow extracting information on the geomorphic state and changes over time of ice-wedge trough networks from remote sensing data. We developed a computer vision algorithm to automatically derive ice-wedge polygonal networks and the current microtopography of the degrading troughs from very high resolution, airborne laserscanning-based digital terrain models. We represent the networks as graphs (a concept from the computer sciences to describe complex networks) and apply methods from graph theory to describe and quantify hydrological network characteristics of the changing landscape. In fire scars, we especially observe rapidly growing networks and fast micromorphological change in those degrading troughs. In our study, we provide a space-for-time substitution comparing fire scars throughout the Alaskan tundra of up to 70 years since the fire disturbance, to show how this type of disturbed landscape evolves over time.
    Repository Name: EPIC Alfred Wegener Institut
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    How to discover an unknown mega-landslide in the Siberian far-east (2021)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting 2021, Online, 2021-12-13-2021-12-17American Geophysical Union
    Details
    Publication Date: 2021-12-26
    Description: Using our custom visualization tool for multitemporal Landsat satellite imagery we discovered, to our knowledge, an undocumented mega-landslide in far-east Siberia, which occurred in summer 2017 (https://bit.ly/2WYRLM1; 61.55°N; 170.01°E). To create and visualize this unique dataset, we processed temporal trends of multispectral indices of 〉100,000 Landsat images for a period from 2000-2019 using the freely available Google Earth Engine cloud processing platform (https://ingmarnitze.users.earthengine.app/view/hotspottcvisapp). The megaslide has a size of 3.66 km² and using the ArcticDEM data we estimate a volume movement of ~20 Mm³. With this size and volume, the landslide is among the largest globally known in recent decades. The landslide is accompanied by a smaller one (0.31 km², 1 Mm³) about 600 m further east, which already occurred in summer 2015. The large landslide caused the formation of several small lakes by blocking two valleys with debris and within newly formed crevasses near the hilltop, which are still persisting as of August 2021. As this event occurred in a remote valley far from any settlement, no visible damage to infrastructure or human livelihoods was detected. The remoteness has likely led to being not detected, like many similar, albeit a lot smaller, erosion features in the Arctic permafrost region. In this presentation we will show the main properties of the landslide, potential trigger mechanisms in the traditional sense. As this region is located along the fringes of permafrost presence we will discuss its potential connection to the rapidly warming climate in the high latitudes. Further, we will discuss how such a large event remained undetected for several years. We discuss and highlight the value of our landscape change visualization tool based on Landsat trend analysis (see Nitze et al., AGU 2020), which helped us to identify this extreme event. With more and more available data sources, this tool in addition to automated image analysis (e.g. deep-learning) or seismic analysis will help to uncover the hidden processes and dynamics of the Earth’s surface.
    Repository Name: EPIC Alfred Wegener Institut
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    The future of community- and policy- relevant thermokarst research: Lessons learned and a call to action (2021)
    American Geophysical Union
    In:  EPIC3AGU Fall Meeting 2021, Online, 2021-12-13-2021-12-17American Geophysical Union
    Details
    Publication Date: 2021-12-26
    Description: Several decades of research have provided insight into patterns of and controls on thermokarst initiation and expansion, yet studies tend to focus on individual types of thermokarst (i.e., thaw lake formation and subsequent drainage) in particular regions. Today, we are left with uneven knowledge about abrupt permafrost thaw both conceptually and regionally. The goal of this presentation is to summarize recent advancements in monitoring thermokarst and its impact on soil, vegetation, and water while also framing a call to action for the next decade of research. Over the next decade, permafrost researchers must align their efforts on several fronts to not only increase our knowledge about changing permafrost but to align this knowledge with key community and policy needs. To support climate change planning and adaptation, northern communities need future thaw vulnerability mapped at scales relevant to their needs, which will require a suite of downscaled and new mapping and remote sensing products. Thermokarst predisposition maps based on circumpolar datasets greatly overestimate the area vulnerable to thermokarst, which can lead to poor planning and climate anxiety. In some situations, existing mapping products may be useful for downscaling with more detailed input data. In other situations, entirely new approaches may be required to support local action. A second key need for community relevant research is the ability to detect and monitor early warning indicators of thermokarst. Such information is needed to support scenario planning and to help mitigate the risks to social, cultural, and physical infrastructure created by permafrost change. We are evaluating the potential for using changes in vegetation, wetting/drying and topography as early warning indicators of thermokarst, all of which can be remotely sensed. Finally, integrating fine-scale disturbances such as thermokarst into large scale models remains a key challenge but critical for supporting sound climate policy. While a diversity of permafrost modeling approaches is necessary, we outline guiding principles that will help enhance model comparisons, assimilation of simulated data across spatiotemporal scales, and the ability for policy decisions to be rapidly informed by emerging science on permafrost change.
    Repository Name: EPIC Alfred Wegener Institut
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    Regulation of calcium distribution in bovine sperm cells: Cytochemical evidence for motility control mechanisms (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 225-242 
    Details
    ISSN: 0886-1544
    Keywords: spermatozoa ; calcium ion transport ; motility regulation ; cholinergic agonists ; ouabain ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Behavioral responses of mature spermatozoa treated with neurotropic factors suggest that calcium entry and intracellular transport may be regulated by a cholinergic mediated program. To test the validity of this proposed mechanism, the effect of several agents on Ca distribution in the sperm cell was examined cytochemically.Sites of Ca accumulation were visualized in thin sections of bull spermatozoa by the application of a modification of Gomori's histochemical procedure for phosphatases. Intact bull sperm cells incubated at room temperature in a buffered balanced salt solution containing 5 mM/liter of CaCl2 showed small, randomly scattered deposits of the reaction product. Similarly treated sperm cells, plasmolyzed in hypoosmotic KCl, revealed a greatly increased amount of deposit associated with the cell membranes (mitochondrial surfaces and plasmalemma), the axonemal complex components, and satellite fibers adjacent to the outer dense fibers. Preincubation of intact cells in nicotine or eserine considerably enhanced the entry of calcium into the cell and its association with the membranes and other intracellular organelles. Decamethonium, an irreversible depolarizer and blocker of cholinergic receptors, interfered with the uptake and intracellular distribution of the calcium. Ouabain, the digitalis glycoside that decreases progressive motility of bull sperm and inhibits Na-, K-ATPase, appears to block Ca efflux, causing an intense accumulation of electron-opaque particles in the plasma membrane while smaller numbers of particles are distributed sparsely throughout the cell interior.The cytochemical results showing enhanced calcium entry in the presence of cholinergic agents, depressed intracellular calcium in cells treated with cholinergic receptor blocker, and intense accumulation of calcium within the cell membrane in the presence of ouabain are consistent with spermatozoan behavioral responses to these agents. These observations support the concept that neurotropic factors may be involved in regulating transmembrane and intracellular transport of ions in control of sperm cell function.
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    URL: http://dx.doi.org/10.1002/cm.970020304
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    Persistence of the expression of β-tropomyosin in dystrophic avian pectoral muscle (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 309-315 
    Details
    ISSN: 0886-1544
    Keywords: tropomyosin ; avian muscular dystrophy ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The isotype pattern of tropomyosin was investigated in normal and dystrophic avian pectroal muscle using two-dimensional gel electrophoresis. Previous reports have shown that adult pectoral muscle of chickens contains only the α-subunit of tropomyosin and a breast-type troponin-T (TN-T), whereas pectoral fetal muscle contains both α- and β-tropomyosin and leg-type TN-T. The change from the fetal to the adult forms begins shortly after hatching. It has been previously reported that avian dystrophic pectoral muscle contains both the leg- and breast-type TN-T; we show that in avian dystrophic muscle there is also persistent expression of the β-subunit of tropomyosin.
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    URL: http://dx.doi.org/10.1002/cm.970020309
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    Masthead (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982) 
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    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970020401
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    A calcium- and pH-regulated actin binding protein from D. discoideum (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 287-308 
    Details
    ISSN: 0886-1544
    Keywords: actin-binding protein ; Dictyostelium ; cytoskeleton ; amoeboid movement ; calcium ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A protein from Dictyostelium discoideum with an apparent subunit molecular weight of 95,000 daltons (95K protein) was previously identified as an actin-binding protein ‘Hellewell and Taylor, 1979’. In this paper, we present a method for purifying the protein, and characterize some important aspects of its structure and function. Purification of the 95K protein is achieved by fractionation with ammonium sulfate followed by chromatography on DEAE-cellulose, gel filtration on 6% agarose, and final purification on hydroxyapatite. The 95K protein is a dimer, composed of apparently identical subunits. It is a rod-shaped molecule, 38 nm in length, with a Stokes radius of 74 Å. In these structural properties, the 95K protein is similar to muscle and nonmuscle α-actinins. The 95K protein and filamin are equally competent, when compared on a weight basis, to enhance the apparent viscosity of actin as determined by falling ball viscometry. The apparent viscosity of mixtures of the 95K protein and actin is dramatically reduced at pH greater than 7.0 or free ‘Ca2+’ greater than 10-7 M. We also examine the mechanism by which calcium regulates the interaction of the 95K protein and actin. A change in free ‘Ca2+’ induces no detectable change in the quaternary structure of the 95K protein. Our experiments indicate that the 95K protein does not dramatically alter the length distribution of actin filaments in the presence of micromolar free ‘Ca2+’. A large fraction of the 95K protein cosediments with actin in the presence of low free ‘Ca2+’ (ca. 3 × 10-8M), but not in the presence of high free ‘Ca2+’ (ca. 4 × 10-6M). We conclude that increased free ‘Ca2+’ inhibits gelation of actin by the 95K protein by reducing the affinity of the 95K protein for actin. We propose that 95K protein is an important component of the cytoskeletal/contractile system in D. discoideum amoebae.
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    URL: http://dx.doi.org/10.1002/cm.970020308
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    In situ demonstration of actin in normal and injured ocular tissues using 7-nitrobenz-2-oxa-1,3-diazole phallacidin (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 343-354 
    Details
    ISSN: 0886-1544
    Keywords: NBD-phallacidin ; actin ; ocular tissues ; wound repair ; stress fibers ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The fluorescent derivative of the actin-binding toxin phallacidin, 7-nitrobenz-2-oxa-1,3 diazole phallacidin, has been used to cytologically demonstrate the presence of actin in lens epithelium, corneal endothelium, and retinal pigment epithelium. In these noninjured tissues, no stress fibers are observed and fluorescence is confined mainly to an area at or near the cell membrane, although some diffuse cytoplasmic staining can also be seen. However, following injury to either the lens epithelium or corneal endothelium of rats and frogs, stress fibers are detected, but only in those cells that migrate into the wound area. Cells on the periphery of each tissue do not partake in would repair and thus maintain their normal appearance. After the tissue has regenerated, stress fibers disappear, and those cells involved in the injury response return to their normal morphology.When rabbit corneal endothelium is placed in tissue culture, stress fibers are observed as the cells migrate away from the initial explant. Upon reaching confluency, these cells spread out and each is surrounded by thick actin-containing bands. Furthermore, they exhibit some stress cables within their cytoplasm. This is in contrast to their appearance in vivo where stress fibers are absent and fluorescence is limited to a region near the cell membrane.
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    URL: http://dx.doi.org/10.1002/cm.970020404
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    Motility of the 6 + 0 flagellum of lecudina tuzetae (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 369-383 
    Details
    ISSN: 0886-1544
    Keywords: motility ; flagella ; cilia ; microtubules ; Gregarines ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The male gametes of the parasitic protozoan, Lecudina tuzetae, have a motile flagellum with a “6 + O” ultrastructure ‘Schrével and Besse, 1975’. These gametes were isolated from the cysts in which they develop and were observed and photographed under a variety of conditions. The flagella beat continuously, without stopping and starting, with a beat period of about 2 sec. They can beat in solutions whose viscosities are greater than 0.5 Nsm-2 (l Nsm-2 = 103 cP). The waveform can be approximated by a series of helical arcs and interconnecting straight regions that travel from the base to the tip. The helical regions have a radius of curvature of 3.2 μm and subtend a final angle of 1.7 radians. The straight portions are 2.0 μm in length. There are two sets of opposing bends, but they do not originate in the same plane. The resulting waveform is an approximately helical coil, with a pitch of 9.8 μm, a pitch angle of 0.6 radian and a peak-to-peak amplitude of 2.3 μm. The sense of the coil is left handed. The axoneme twists during beating. The main differences between the movement of this flagellum and that of typical 9 + 2 flagella are a low beat frequency and three-dimensional bends that produce relatively little forward movement of the cell. Twisting is discussed as a means of discriminating between some types of models of flagellar motility.
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    URL: http://dx.doi.org/10.1002/cm.970020406
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    Binding stoichiometry of 21S dynein to A and B subfiber microtubules (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 429-443 
    Details
    ISSN: 0886-1544
    Keywords: 21S dynein ; tubulin ; binding stoichiometry ; ATP sensitivity ; binding cooperativity ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The binding properties of Tetrahymena 21S dynein to doublet A and B subfiber microtubules were analyzed by both a turbidimetric assay (Δ A350 nm) and electron microscopy. KCl-extracted, sucrose-gradient, purified 21S dynein binds to each of the two kinds of axonemal microtubules in both ATP-insensitive and ATP-sensitive modes, even though only a single type of binding occurs to each of the subfibers in situ. Total dynein bound to axonemal microtubules is a composite of binding that is sensitive to dissociation by ATP and binding that is insensitive to ATP. Each exhibits a different binding profile. Total binding exhibits a sigmoid profile (h = 1.93) and saturates at 1.49 mg D/mg T. ATP-sensitive binding likewise exhibits a sigmoid profile (h = 2.66) but saturates at 1.06 mg D/mg T. Binding occurs with a similar affinity for both A and B subfibers. The Hill coefficient (h) for ATP-sensitive binding implies positive cooperativity between binding events. ATP-insensitive binding was studied independently in 20 μM ATP, 10 μM vanadate, which blocks ATP-sensitive binding. ATP-insensitive binding exhibits a hyperbolic profile (h = 1.0) and likewise occurs along each of the two kinds of axonemal tubules. Binding saturates at 0.87 mg D/mg T. The binding data suggest that the tubulin dimer has conserved both ATP-sensitive and ATP-insensitive binding sites for 21S dynein, even though the sites may not be expressed in vivo.
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    Videodisc Supplement. Announcement (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. i 
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    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970020602
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    Microtubule capping structures at the tips of tracheal cilia: Evidence for their firm attachment during ciliary bend formation and the restriction of microtubule sliding (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 549-572 
    Details
    ISSN: 0886-1544
    Keywords: flagella ; cilia ; trachea ; microtubules ; crowns ; microtubule assembly ; caps ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The distal tips of the central pair and A-microtubules are capped in mammalian and avian tracheal cilia. The capping structures are similar to those found in protozoan cilia and flagella [Dentler, 1981], and consist of a central microtubule cap that links the central microtubules to the membrane or to the ciliary crown and A-microtubule plugs that insert into the lumen of each of the A-microtubule plugs is bound to the central microtubule cap by distal filaments. The ends of the central and outer doublet microtubules are tightly bound to the cap in both intact and in demembranated and reactivated tracheal cilia. Analysis of the displacement of the microtubule tips in cilia fixed at various bend angles revealed that the displacements of A-microtubules are only partially in agreement with those predicted by the sliding filament model [Satir, 1968]. These results are discussed with respect to the regulation of microtubule sliding in capped cilia and the role of the microtubule capping structures in microtubule assembly.
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    Movement and coordination of tracheal cilia and the relation of these to mucus transport (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 19-24 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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    The identification and localization of actin and actin-like filaments in lactating guinea pig mammary gland alveolar cells (1981)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 1 (1981), S. 329-347 
    Details
    ISSN: 0886-1544
    Keywords: actin ; microfilaments ; heavy meromyosin ; mammary gland ; secretion ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Cytochalasin B, a microfilament-altering drug, inhibits lactose synthesis in lactating guinea pig mammary gland [Biochim. Biophys. Acta 392:20, 1975] but not primarily by inhibiting glucose transport [Eur. J. Cell Biol. 20:150, 1979]. In order to study the possible role of microfilaments in lactose synthesis and secretion, we isolated both the alveolar (milk-secreting) and myoepithelial (contractile) cells from lactating mammary gland. Light microscopy shows that the alveolar cell fraction (viability approximately 71%) is homogenous and that the cells retain strong polarity of secretory structures in the apical region. Two proteins were extracted from the alveolar cell fraction. One (mol wt 42,000) comigrates with skeletal muscle actin on SDS-PAGE gels. The other, a high-molecular-weight (180,000) protein (HMWP) may be analogous to actin-binding protein or clathrin. An extract from the myoepithelial cell fraction also contains a protein that comigrates with actin but no HMWP. Whole tissue extract contains the 42K protein, and a 185K HMWP. Examination of the alveolar cell extract by electron microscopic (EM) negative staining revealed meshworks of multistranded, interconnecting filaments, with attached globular structures (100-200 A) (possibly the HMWP) and single filaments (40-60 A diameter) branching off. To localize these filamentous structures in situ, whole tissue was glycerinated and incubated with rabbit skeletal muscle heavy meromyosin (HMM). Masses of filaments in myoepithelial cells served as convenient standards for HMM decoration. Decorated filaments have cross-arms or projections, unlike the narrow, smooth filaments of control tissue. Decorated filaments in alveolar cells are located beneath the plasma membrane, in close association with secretory vacuoles, and near the Golgi apparatus; filaments near the latter two are often oriented perpendicular to the plasma membrane. Microvesicles are embedded in meshworks under the plasmalemma and near the Golgi apparatus. Intermediate-sized (85-115 A diameter), non-decorated filaments diverge from the meshworks of decorated filaments. Microvesicles are associated with intermediate-sized filaments as well. The association of actin-like filaments with secretory vacuoles and microvesicles and their location in areas of the cell concerned with biosynthetic activities suggest a possible function in the intracellular transport of secretory products.
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    Motility of 9 + 0 mutants of Chlamydomonas rheinhardtii (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 165-168 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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    Role of calmodulin in the flagellar axoneme: Effect of phenothiazines on reactivated axonemes of Chlamydomonas (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 199-204 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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    Serum complement (C'3a and C'5)-induced inhibition of rabbit tracheal cilia (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 71-75 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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    Invited review: Bacterial flagellar sheaths: Structures in search of a function (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 93-103 
    Details
    ISSN: 0886-1544
    Keywords: bacterial motility ; flagella ; sheathed flagella ; complex flagella ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Although bacterial flagellar sheaths were observed over 30 years ago, they may still be characterized as structures in search of a function. In addition to true sheaths, bacterial flagella may possess other adornments that cause an increase in the organelle's cross-sectional diameter. These “complex flagella” are sharply differentiated from sheathed flagella. Immunological and chemical distinctions have been found between flagellar sheaths, flagellar cores, and LPS layers inferred to be the sheath sensu stricto. Although complex flagella may serve as specific receptors for flagellotropic phages or in allowing for more efficient swimming in viscous environments, similar functions have not yet been attributed to true sheaths. It is postulated that flagellar sheaths may allow for specific interaction between a bacterium and a surface. In addition, there is a problem as to the relationship between a rapidly rotating flagellum and the sheath.
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    Coelomocyte motility (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 113-121 
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    ISSN: 0886-1544
    Keywords: coelomocytes ; filopodia ; whole cell translocation ; video microscopy ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: We have utilized a video-enhanced contrast system coupled to a DIC-equipped microscope to examine the motility of both whole coelomocytes and individual filopodia. When the cells are left in diluted coelomic fluid, they exhibit a fibroblast-like mode of translocation across the substrate. These cells extend lamellipodia at their advancing margin and develop retraction fibers at the trailing edge. Filopodia are actively extended from the lamellipodia of the advancing margin. Cells that are washed free of the coelomic fluid and placed in an isotonic buffer lose their ability to translocate. Filopodia on these stationary cells are seen to undergo a series of waving and bending motions. These motions are rapid and result in a filopodium folding back upon itself only to reextend later. Both forms of motility are discussed in light of the existing structural and biochemical knowledge of this and other cell types.
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    Quantitative studies on polarization optical properties of living cells III: Cortical birefringence of the dividing sea urchin egg (1981)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 1 (1981), S. 387-397 
    Details
    ISSN: 0886-1544
    Keywords: birefringence ; polarizing microscope ; sea urchin egg ; cortex ; mitosis ; cleavage ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Birefringence (BR) at the cell surface of fertilized eggs of the sand-dollar, Clypeaster japonicus, during mitosis and cleavage was determined with a photoelectric BR detection apparatus [Hiramoto et al, 1981a]. The cortex of about 2 μm thickness is birefringent positive with respect to the normal to the cell surface. The hyaline layer is negatively birefringent. The halo-layer consisting of a row of microvilli surrounding the egg is positively birefringent in normal Ca-free sea water, while it is negatively birefringent in Ca-free sea water with high refractive index. The BR of the cortex gradually increases over the entire surface during mitosis until the onset of cleavage. The BR of the cortex at the polar region reaches a maximum shortly after the onset of cleavage and then decreases, while the BR of the cortex at the equatorial region begins to decrease shortly before the onset of cleavage, reaches a minimum shortly after the cleavage starts, and then increases again as the cleavage furrow advances. The coefficient of birefringence of the cortex is about 2.5 × 10-5 at the maximum. The BR change of the cortex during mitosis and cleavage is interpreted as a passive deformation caused by the constriction of the contractile ring as well as an active structural change of the cortex occurring in the dividing cell.
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    Microtubule-containing detergent-extracted cytoskeletons in sea urchin eggs from fertilization through cell division: Antitubulin immunofluorescence microscopy (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 213-226 
    Details
    ISSN: 0886-1544
    Keywords: microtubules ; fertilization ; cell division ; sea urchin ; cytoskeleton ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The microtubule-containing structures that appear in eggs during fertilization and cell division in the sea urchins Lytechinus variegatus and Arbacia punctulata were detected by antitubulin immunofluorescence microscopy of detergent extracted cytoskeletal preparations. The extraction buffer, which is composed of 0.55 mM MgCl2, 10 mM EGTA, 25 mM MES, 25% glycerol, 1% Nonidet P-40, and 25 μM PMSF, pH 6.7, allows for dramatically improved fluorescent images compared to those obtained using conventional staining procedures, with residual background staining being reduced to near zero.The immunofluorescent images obtained using this technique provide information on several motile events that occur during the first cell cycle. This technique demonstrates that all of the cytoplasmic microtubules are associated with the incorporated sperm's centrioles during female pronuclear migration. This changes during the centration of the male and female pronuclei at which time a monastral array of microtubules forms in the egg's cytoplasm. A large proportion of the monastral microtubules do not appear to be associated with the centrioles. At prophase and early metaphase, the centrioles are the dominant microtubule organizing centers (MTOCs) consistent with mitotic theories that the kinetochore catches, but does not initiate, microtubules. Observations of intercentriolar distances show that there are three stages of pole separation during the first cell cycle. The initial separation occurs during pronuclear centration, the second during the streak stage, and the final one during the late stages of mitosis. At telophase, polar microtubules appear to extend into the cortex supporting the cell surface at all regions except the presumptive cleavage site.
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    Masthead (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983) 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970030401
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    Characterization of the chlamydomonas flagellar collar (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 273-280 
    Details
    ISSN: 0886-1544
    Keywords: Chlamydomonas flagellar collars ; Chlamydomonas cell wall ; mating in Chlamydomonas ; cell wall proteins ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The flagella of Chlamydomonas reinhardtii protrude through the cell wall via short, tunnel-like openings that are lined with 11 nm × 500 nm fibers arranged in parallel array. These cylindrical collections of fibers presumably permit free movement of the flagella within the cell wall. In this report electron-microscopic evidence is presented showing that during the initial stages of the mating reaction intact collars slip off of the ends of the flagella when cell wall loss occurs. Electrophoretic analysis of isolated collars reveals one major protein and several minor species.
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    URL: http://dx.doi.org/10.1002/cm.970030307
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    Crawling caenorhabditis elegans spermatozoa contact the substrate only by their pseudopods and contain 2-nm filaments (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 333-347 
    Details
    ISSN: 0886-1544
    Keywords: Caenorhabditis elegans spermatozoa ; cell motility ; electron microscopy ; cell-substrate contact ; 2-nm filaments ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The locomotion of C. elegans spermatozoa resembles, in many respects, the crawling movements of other eukaryotic cells. However, these sperm contain surprising little actin, which plays no apparent role in this cell's motility. Electron microscopy has revealed that crawling spermatozoa retain a strict morphological polarity so that the organelle-filled cell body is separated from the pseudopod by an array of cytoplasmic laminar membranes. When sperm crawl only the pseudopod contacts the substrate; the cell body is either pulled behind or carried on top of the rear portion of the pseudopod. Fingerlike projections which extend forward from the leading edge of the pseudopod initiate contact with the substrate. The underside of the pseudopod exhibits areas of close (40 nm separation) membrane-substrate association with intervening areas of wide (up to 300 nm) membrane-substrate gaps. The pseudopod cytoplasm contains 2-nm filaments but no filamentous actin has been observed. These 2-nm filaments were detected in thin sections of crawling cells and in negative-stained remnants of spermatozoa disrupted by either hypotonic buffer on Triton X-100. The filaments are found both free in the cytoplasm and closely associated with the cytoplasmic face of the plasma membrane and are usually oriented along the long axis of the cell. Neither the identity nor the function of these filaments has been established although their location and orientation suggest that they may be involved in generating propulsion.
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    URL: http://dx.doi.org/10.1002/cm.970030405
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    Changes in cytoskeletal proteins of polymorphonuclear leukocytes induced by chemotactic peptides (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 349-361 
    Details
    ISSN: 0886-1544
    Keywords: myosin phosphorylation ; actin polymerization ; chemotactic factors ; leukocytes ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Changes in the state of polymerization of actin and phosphorylation of myosin have been observed in polymorphonuclear leukocytes (PMNs) soon after the addition of the chemotactic peptide N-formylnorleucylleucylphenylalanine. At a time when the cells are observed to extend many ruffles or lamellipodia from their surface, the fraction of the cellular actin present in a monomeric form is decreased by about 25% as assayed by the ability of the G-actin to inhibit DNAase. These changes are temporally correlated with an increase in the staining by nitrobenzooxadiazole (NBD)-phallacidin, a probe that binds F-actin selectively. The NBD-phallacidin staining is observed in the surface ruffles. When the peptide concentration is decreased by addition of a tenfold excess of buffer, cells withdraw their surface ruffles and form blebs. These changes correlate with an increase in the G-actin levels detected with the DNAase inhibition assay. An increase in phosphorylation of the 20,000-dalton light chain of myosin is also observed in leukocytes stimulated by addition of chemotactic peptide. These observations of changes in cytoskeletal proteins of PMNs provide a beginning for further studies on the regulation of cell motility by chemotactic factors.
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    Organization and function of structural elements in focal contacts of tissue culture cells (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 391-397 
    Details
    ISSN: 0886-1544
    Keywords: focal contacts ; microfilaments ; microinjection ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The role of structural elements in the organization and maintenance of focal contacts was studied by microinjecting into tissue culture cells specific probes which interfere with filamentous actin or with vinculin: actin interaction. Injection of actin capping proteins from Physarum and brain resulted in breakdown of microfilament bundles starting at their distal ends and in loss of focal contacts. This process was fully reversible. Injection of a high affinity antibody against chicken gizzard vinculin led to partial breakdown of microfilament bundles concomitant with disruption of focal contacts with vinculin remaining at the plasma membrane. This process was irreversible.
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    URL: http://dx.doi.org/10.1002/cm.970030507
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    Structural connections of the muscle-tendon junction (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 431-438 
    Details
    ISSN: 0886-1544
    Keywords: myotendinous junction ; laminin ; type IV collagen ; heparan sulfate proteoglycan ; alpha actinin ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The muscle-tendon junction of murine skeletal muscles has been analyzed by a variety of extraction techniques, by myosin subfragment-1 binding experiments, and by ultrastructural immunocytochemistry. The results indicate that the muscle-tendon junction is composed of four distinct domains: an intracellular domain, the internal lamina; a domain connecting the internal lamina with the lamina densa of the external lamina, the connecting domain; the lamina densa; and a domain which attaches the lamina densa to the collagen fibers, the matrix. Each of these domains is distinct with respect to position, three-dimensional organization, and molecular composition, and is therefore considered to have a unique role in the transmission of contractile force.
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    A covalently cross-linked matrix in skeletal muscle fibers (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 463-483 
    Details
    ISSN: 0886-1544
    Keywords: intracellular matrix ; extracellular matrix ; covalently cross-linked matrix ; ε-(γ-glutamic) lysine bonds ; skeletal muscle ; titin ; covalently cross-linked collagen ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: When skeletal, cardiac, and smooth muscle is exhaustively extracted with a protein-unfolding reagent such as 6 M guanidine HCl and a disulfide-reducing reagent such as 5% β-mercaptoethanol, a tissue ghost remains intact and retains the characteristic shape and dimensions of the tissue before extraction. In the case of chicken pectoral muscle, the tissue ghost contains 1% of the original muscle proteins. Guanidine HCl extraction followed by collagenase treatment of glycerol-extracted chicken pectoral muscle releases a clean preparation of elongated structures containing 0.2% of the original protein and representing the covalently cross-linked remnants of the muscle fibers. The material of these muscle fiber ghosts extends throughout the interior of the cell. Antibodies raised against the tissue ghosts of smooth muscle cross-react with glycerol extracted skeletal myofibrils, forming a banding pattern which coincides with the banding pattern observed when myofibrils are reacted with antibodies against titin. Titin, a large and soluble protein found in skeletal muscle, cross-reacts with our antigizzard antibody. However, amino acid analysis of the muscle fiber ghosts indicates that titin cannot be the only subunit of the insoluble polymer, but that one or more proteins with a very high glycine and alanine content and a very low basic and acidic amino acid content must also form part of the covalently cross-linked matrix. The possibility is presented that this matrix may be the basis of the superthin 2-3-nm filaments which have been observed in a variety of cell types.
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    URL: http://dx.doi.org/10.1002/cm.970030514
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    Actin-mediated surface motility during sea urchin fertilization (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 513-524 
    Details
    ISSN: 0886-1544
    Keywords: fertilization ; actin ; microfilaments ; sea urchin ; cell division ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The sea urchin egg at fertilization is an ideal model in which to study actin-mediated surface activity. Electron microscopy of unfertilized eggs demonstrates the presence of thousands of well-arrayed short microvilli, which appear supported by cytochalasin-sensitive actin oligomers as detected with rhodamine-labeled phalloidin staining of permeabilized eggs. At insemination, the previously short microvilli elongate and cluster around the successful sperm during incorporation. Phalloidin staining demonstrates a tremendous recruitement of polymerized actin into the site of sperm incorporation, resulting in the formation of the fertilization cone. Fertilization of cytochalasin-treated eggs results in the normal activation of the metabolic and bioeletric events, but sperm incorporation does not occur since the localized actin assembly required for fertilization cone formation is precluded. After sperm incorporation, the entire fertilized surface is restructured, as a result of a massive polymerization of actin to produce a burst in microvillar elongation. Addition of cytochalasin to eggs immediately following sperm incorporation demonstrates the recruitment of actin assembly for the proper progression through the first cell cycle. During normal cell divison, the egg surface retains the long microvilli. The furrow which forms at cytokinesis does not appear as a unique new structure, but rather as a reorganization of the cortical microfilaments. Quantitative fluorescence microscopy argues against an increase in microfilaments during early cytokinesis. At the latest stages of cytokinesis, a thickening of the cortical actin is noted, which could possibly be interpreted as a contractile ring. A minor basal level of actin assembly with numerous nucleation sites in unfertilized eggs and a tremendous but localized assembly of microfilaments surrounding the sperm during incorporation, followed by a massive global microfilament assembly event to elongate the fertilized egg microvilli resulting later in the reorganization of these microfilaments to produce the forces necessary for cytokinesis, highlight the utility of the study of sea urchin eggs at fertilization for understanding actin-membrane interactions.
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    URL: http://dx.doi.org/10.1002/cm.970030518
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    Cell surface and cytoskeletal interactions in a temperature-sensitive strain of SV40-transformed mouse fibroblasts (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 553-565 
    Details
    ISSN: 0886-1544
    Keywords: microfilaments ; cytoskeleton ; simian virus 40 ; cell adhesion ; cell surface ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In order to assess the role of cytoskeletal structure in modulating cell surface topography during cell transformation, cytoskeletal organization of 3T3 mouse cells transformed with a tsA mutant of simian virus 40 (SV40) was studied in detail by correlative light and electron microscopy. Detergent-extracted, criticalpoint dried whole cells observed in the electron microscope were seen to contain well-organized microfilament bundles (stress fibers) traversing the longitudinal axis of cells grown at the restrictive temperature (39°C). When grown at the permissive temperature (32°C), cells prepared in this manner were not observed to contain such structures. However, when semithin sections (0.5 μm) were viewed by transmission electron microscopy at 120 kV, short microfilament bundles were seen in 32°C-grown cells. There was an alteration in the morphology of these structures at sites of attachment to the substratum (focal contacts), and they were shorter in length than microfilament bundles of 39°C-grown cells. A difference was also observed between the two phenotypes in the layer of microfilaments associated with the dorsal cell surface. Since it is this layer that directly determines cell surface architecture, it is proposed that changes in microfilament bundle-generated surface tension are responsible for alterations of this layer, leading to an altered cell surface morphology. Tension may be modified by disturbances in focal contacts (or adjacent regions) or altered actin-associated protein(s).
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    Effects of abnormal cytoskeletal structure on erythrocyte membrane mechanical properties (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 609-622 
    Details
    ISSN: 0886-1544
    Keywords: erythrocyte membrane ; surface elastic shear modulus ; membrane viscosity ; hereditary disorders of blood ; membrane yield ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Measurements of the mechanical properties of the erythrocyte membrane provide a direct assessment of the proper function of its structural components. To assess the effects of alterations in molecular structure on membrane mechanical properties, measurements have been performed on cells from six individuals whose membranes contain inherited, biochemically characterized structural defects. Because the contribution of the memmbrane skeleton to the mechanical behavior of the membrane is most evident in shear deformation, mechanical experiments were performed to measure the material constants which characterize the response of the membrane to shear force resultants. The surface elastic shear modulus characterizes the elastic response of the membrane; the yield shear resultant is the maximum shear force resultant which the membrane can support elastically; and the plastic viscosity coefficient characterizes the rate of membrane deformation when the elastic limit has been exceeded.Generally, it was found that when the molecular defect is found to occur in a region of the skeleton which is stress-supporting, the maximum elastic strength of the membrane is reduced. However, the magnitude of the reduction can be quite different for membranes having similar or even identical defects. In some cases the differences can be attributed to the removal of the most fragile cells of the population by the spleen, but other results indicate that the biochemical description of the defects may be incomplete. These results emphasize the need for further refinements both in the biochemical characterization of membrane skeleton structure and in the description and measurement of membrane mechanical properties.
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    Effects of folic acid upon filopodia of Dictyostelium discoideum vegetative amoebae (1984)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 4 (1984), S. 129-135 
    Details
    ISSN: 0886-1544
    Keywords: amoeboid motion ; chemoattractants ; chemotaxis ; Dictyostelium ; filopodia ; folic acid ; pterins ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Living vegetative D. discoideum amoebae were studied to determine whether their filopodia respond to folic acid, a chemoattractant for these cells. Exponentially growing amoebae (ca. 10 μm diameter) exhibit 5-30 μm long filopodia; at stationary phase, aggregation competent amoebae have numerous multibranched filopodia up to 100 μm long. Folic acid was observed to stimulate production, elongation, and branching of filopodia with its effects progressively changing as the amoebae approach aggregation. Filopodial construction was also found to be dependent upon Mg2+ levels. The significance of these results is discussed with respect to progressive changes within the vegetative phase as well as to the mechanisms of amoeboid movement, pseudopodial activity, and chemotaxis.
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    Intracellular movement of fodrin (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 649-655 
    Details
    ISSN: 0886-1544
    Keywords: axonal transport ; lymphocyte capping ; spectrin ; fodrin ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Fodrin is an actin/calmodulin-binding protein with similarities to spectrin (erythrocytes) and TW 260/240 (brush border). It is concentrated beneath the plasma membranes of neurons and other cells. We have observed translocations of fodrin in both neurons and lymphocytes. Newly synthesized, radiolabeled fodrin moves down axons at a maximum velocity (about 50 mm/day) that is slower than the most rapidly axonally transported proteins (group I). A portion of fodrin appears to move more slowly at velocities (1-10 mm/day) resembling those of actin and myosin (group IV) and tubulin and neurofilament proteins (group V). In lymphocytes, when certain surface antigens are induced by cross-linking agents to migrate to one pole of the cell and form a cap, fodrin redistributes beneath the membrane and forms a subcap. The movements of fodrin in lympohocyte capping and in the axonal transport of group IV polypeptides have certain similarities. In both cases, the redistribution of fodrin is accompanied by concomitant redistributions of actin, myosin, and calmodulin, and both processes proceed at similar velocities. We consider the possibilities that these two processes are related, both being driven by a submembrane force-generating system comprising in part actin, myosin, and fodrin, and that fodrin serves to link various organelles or proteins to this system.
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    A quantitative comparison of cellular motile systems (1984)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 4 (1984), S. 1-5 
    Details
    ISSN: 0886-1544
    Keywords: motility ; power output ; muscle ; flagella ; cytokinetic furrow ; mitotic spindle ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Cellular motile systems as diverse as muscle and the mitotic spindle have been compared by their specific power output: the maximum power they develop per unit of engine volume. Striated muscles and flagella have high specific output; their performance is comparable to that of typical automobile engines. The cytokinetic furrow and the mitotic spindle have very much lower specific power output. The furrow's output is 7,000 times lower than muscle and the spindle's is 300,000 times lower. Different macromolecules have been used to generate power in systems with similar output (muscles and flagella) and, conversely, the same macromolecular motor has been used in systems with very different output (muscles and cytokinetic furrows). The common feature amid this diversity is adaptation to a particular biological role, which specific power output reflects very well. High values are found where a powerful, compact engine should be advantageous, while low values are found where precision, not power, matters most.
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    Announcement (1984)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 4 (1984), S. 76-76 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970040108
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    Coupling of photomovement and photosynthesis in desmids (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 73-82 
    Details
    ISSN: 0886-1544
    Keywords: desmids ; videomicrography ; photokinesis ; photophobic response ; photophosphorylation ; photosynthesis ; phototaxis ; uncouplers ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: The effects of the uncouplers CCCP and DNP on photokinesis, phototaxis, and the photophobic response in the desmid Cosmarium have been studied both in population systems and by videomicrographic, single-cell analysis. Light-dependent motility is specifically inhibited by both uncouplers, indicating that photokinesis is driven by photophosphorylation. In population experiments, phototaxis and accumulations in light traps due to photophobic responses are inhibited by drug concentrations comparable to those that inhibit photokinesis. Analysis of single-cell behavior demonstrated, however, that neither photophobic responses elicited by an increase in light intensity (step-up response) nor by a decrease (stepdown response) are inhibited, as long as the reduced motility allows the organisms to cross a light--dark border. Phototactic orientation is not impaired by DNP in the single cell analysis, but CCCP significantly reduced the degree of orientation. The results indicate that, although chlorophyll is the photoreceptor for all three photoresponses, at least the photophobic response is independent of both the photosynthetic electron transport chain and photophosphorylation.
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    Instructions for contributors (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 91-92 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
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    Masthead (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982) 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970020201
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    A motile system of singlet microtubules in spermatozoa (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 93-101 
    Details
    ISSN: 0886-1544
    Keywords: cell motility ; singlet microtubules ; dynein ; coccid insect ; aflagellate spermatozoa ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: In this report we demonstrate that in the coccid insects Pseudococcus, Phenacoccus, and Planococcus the whole spermatozoon is made up by a nuclear central core surrounded by two complete and one incomplete turns of concentric microtubule palisades. Microtubules of the outer row are linked by a system of short projections 6 nm long; those of the inner row are linked to each other by similar arms; a second system of 6 nm arms links the tubules of each inner row to those of the respective outer row. All these systems of arms are longitudinally spaced every ∼ 12 nm. The motility of this spermatozoon is due to waves progressing from the posterior extremity to the anterior one. By SDS polyacrylamide gel electrophoresis a group of high molecular weight polypeptides is detected, one of which migrates in coincidence with the A dynein band from sea urchin sperm. Our data suggest that occurrence in coccid spermatozoon of a motility due to singlet tubules-dynein interaction.
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    Effects of phalloidin microinjection and localization of fluorescein-labeled phalloidin in living sand dollar eggs (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 103-113 
    Details
    ISSN: 0886-1544
    Keywords: actin ; cleavage ; fluorescein-labeled phalloidin ; microinjection ; phalloidin ; sand dollar eggs ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Effects of microinjection of phalloidin on fertilization and cleavage of sand dollar (Clypeaster japonicus and Scaphechinus mirabilis) eggs were studied. The drug, previously injected into unfertilized eggs, showed no effect on the elevation of the fertilization membrane upon insemination up to an intracellular concentration of 50 μM. However, the movement of the egg pronucleus to the sperm pronucleus was inhibited and the fusion of pronuclei did not occur. The subsequent development no longer took place. When phalloidin was injected into fertilized eggs, the thickness of the cortical layer increased and the microvilli became conspicuous. Both nuclear division and cleavage were inhibited at the intracellular concentration of more than 20 μM, though the latter seemed to be more sensitive to phalloidin than the former.Fluorescein-labeled phalloidin (FL-phalloidin) was injected into eggs in order to investigate F-actin localization by fluorescence microscopy. In both unfertilized and fertilized eggs, FL-phalloidin was localized in the cortical layer within 1 min after injection. It was also localized in the cortical layer as radially oriented rodlike structures when injected into fertilized eggs before the disappearance of the nuclear membrane. No distinct fluorescence was detected in the mitotic apparatus or in the cleavage furrow. FL-phalloidin redistributed gradually into egg cytoplasm. In unfertilized eggs, fluorescent rods were found especially in the egg pronucleus 30 min after injection.
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    Tomato actin and myosin: Contractile proteins from a higher land plant (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 131-147 
    Details
    ISSN: 0886-1544
    Keywords: higher land plant contractile system ; actin activation of myosin ; S-1 decoration of actin ; polymerization of actin ; calcium sensitivity of actomyosin interaction ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: This paper describes the initial isolation of actin- and myosin-like proteins from the cytoplasm of the endocarp tissue cells of the fruit of the tomato, Lycopersicon esculentum. Low ionic strength buffers extracted the 42,000 molecular weight tomato actin in the depolymerized form. Tomato actin can be polymerized in 0.1 M KCl, 2 mM MgCl2 to form 6 nm diameter filaments resembling rabbit skeletal muscle F-actin in their ultrastructure and pattern of decoration with rabbit myosin subfragment-1 (S-1). Tomato F-actin activates the low ionic strength Mg2+ ATPase of rabbit S-1 up to ten-fold. High ionic strength extracts of tomato yield a myosinlike enzyme whose ATPase activity in 0.5 M KCl is maximal in the presence of K+-EDTA and is repressed in the presence of Mg2+. The column-purified enzyme forms a complex with rabbit F-actin, which can be dissociated by Mg2+ ATP. The low ionic strength Mg2+ ATPase of tomato myosin can be activated ten-fold by rabbit actin and up to nineteen-fold by tomato actin. No activation of the tomato myosin by rabbit F-actin occurs in the absence of free calcium ions.
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    URL: http://dx.doi.org/10.1002/cm.970020205
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    Cell locomotion in vitro by Xenopus laevis gastrula mesodermal cells (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 149-161 
    Details
    ISSN: 0886-1544
    Keywords: cell locomotion ; gastrulation ; contact paralysis ; collagen substratum ; serum factors ; morphogenetic movements ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Prospective mesodermal cells of Xenopus laevis gastrulae showed substantial locomotion in vitro, averaging 4.3 μM/min, when dissociated and cultured on a glass surface coated with collagen and fetal bovine serum. The cell translocate by making lamellipodia and filopodia whereas the main cell body remains rounded. When two mesodermal cells made contact with each other, they showed contact paralysis of lamellipodial activity. In contrast, when mesodermal cells contact ectodermal cells, contact paralysis does not occur. Rather, migrating mesodermal cells continue to translocate. The locomotion in vitro appears to mimic that in vivo during gastrulation, because of the similarities of the rate of movement and the cell shape in culture and in embryos. Neither prospective ectodermal cells from gastrulae nor prospective mesodermal cells from blastulae showed locomotion under the same culture conditions.
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    URL: http://dx.doi.org/10.1002/cm.970020206
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    Abstracts (1982)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 2 (1982), S. 191-194 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970020736
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    Ciliary but not saltatory movements are inhibited by vanadate microinjected into living cultured cells (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 167-184 
    Details
    ISSN: 0886-1544
    Keywords: saltatory organelle movements ; ciliary movement ; dynein ; vanadate ; microinjection ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: To test the idea that saltatory organelle movements of nonmuscle cells might be driven by microtubule-dynein interactions, we microinjected vanadate into several different types of cultured cell. Solutions of sodium metavanadate made up in a simple buffered salt solution were pressure microinjected into fully spread cells in an open-topped culture chamber placed on the stage of an inverted microscope. The cells were observed by oil-immersion phase-contrast optics and results were recorded on movie film. Vanadate, at 10-5-10-2 M, microinjected into cultured chick embryo fibroblasts, failed to inhibit organelle movements. To test the effectiveness of vanadate's inhibitory action under living cell conditions, ciliated epithelial cells were micro-injected. In these cells even the smallest microinjection of 5 × 10-5 M vanadate caused an immediate cessation of ciliary beating. Moreover, in cells that were well spread it was found that whereas vanadate, at 5 × 10-5 × 10-3M, inhibited ciliary motion, it failed to inhibit organelle saltations in the same cell. To determine whether vanadate would inhibit a living actin-myosin system, myocardial cells were also microinjected. Following microinjection of 5 × 10-5 and 5 × 10-4M vanadate a temporary tonic contraction (which also occurred following microinjection of buffer alone) was followed by regular beating. Taken together these results demonstrate that in living cell systems microtubule-dynein interactions are as sensitive to vanadate inhibition as they are in demembranated model systems, and that a working actin-myosin system in a living muscle cell does not share this great sensitivity. In light of the pronounced differential inhibitory effects of vanadate on the movements of cilia and organelles, our results suggest that saltatory organelle movements in chick embryo fibroblasts and rabbit oviduct epithelial cells are unlikely to be brought about by microtubule-dynein interactions.
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    URL: http://dx.doi.org/10.1002/cm.970030206
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    Masthead (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983) 
    Details
    ISSN: 0886-1544
    Keywords: Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/cm.970030301
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    Quantitative analysis of axonemal bends and twists in the quiescent state of ciona sperm flagella (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 247-259 
    Details
    ISSN: 0886-1544
    Keywords: spermatozoa ; Ciona ; axoneme ; quiescence ; twist ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A simple planar model of sliding can predict the amount of sliding required to form a certain degree of bend. The accuracy of this prediction relies on the assumptions that no twists occur in the axoneme and that no sliding occurs at the base. However, previous studies indicated that twists may occur.This paper explores a new method for quantitating and analyzing twists. Preliminary results using this method showed that there were twists. In order to control for possible artifacts due to fixation and other preparative procedures, the characteristic S-shaped quiescent state of Ciona spermatozoa was studied.Analyses of platinum replicas of those flagella in which this waveform is well preserved suggest that most, if not all, of the twists observed are due to the artifact of a curved shape settling onto a surface. Detailed analyses indicate that if twists do occur in quiescent sperm, they are probably less than 0.4 radian. Since axonemes are evidently easily twisted in rigor, and even after fixation, caution should be exercised in interpretation of axonemal twists.
    Additional Material: 9 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970030305
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    Chromosome movement during meiotic prophase in crane-fly spermatocytes. II. Analysis of polarization of chromosomes and their association with the nuclear envelope (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 261-271 
    Details
    ISSN: 0886-1544
    Keywords: chromosome movement ; meiosis ; spermatocytes ; prophase ; nuclear envelope ; aster ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Association of bivalent chromosomes with the astral centers and nuclear envelope was analyzed in crane-fly spermatocytes during the final hours of diakinesis. In contrast to other systems in which movement of chromosomes during diakinesis correlates with the clustering of bivalents near the astral centers, such clustering is not prevalent in crane-fly spermatocytes. Polarization indices of bivalents calculated 5 to 10 minutes before the end of diakinesis provided evidence for polarization of only a fraction of all bivalents. Similar results were obtained in a large number of fixed cells in which asters and chromosomes were preferentially stained. Ultrastructural analysis of cells in late diakinesis revealed significant contact between bivalents and the nuclear envelope in all 46 cells that were analyzed. The extent of contact in some cells was greater than in others. Sites of contact included the telomeric ends of bivalents, and in some cases the distribution of contact sites suggested the possible involvement of centromeres in chromosome-nuclear envelope association. The results are consistent with the hypothesis that a dynamic interaction between chromosomes and nuclear envelope may exist during late prophase, when the movement of chromosomes is known to occur.
    Additional Material: 6 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970030306
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    The effects of taxol on cytoskeletal components in cultured fibroblasts and epithelial cells (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 283-305 
    Details
    ISSN: 0886-1544
    Keywords: taxol ; microtubules ; intermediate filaments ; fibroblasts ; epithelial cells ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: Taxol promotes microtubule (MT) assembly in vitro and induces the reorganization of the cytoskeleton into unusual MT arrays in cultured cells. The possibility that taxol also has an indirect effect on intermediate filaments (IF) was investigated. In baby hamster kidney (BHK-21) and human skin (ENSON) fibroblasts treated with 1-10 μM taxol for 1-24 h, the drug induces changes which are similar to those produced by colchicine. These include a loss of major cellular extensions, a redistribution of organelles to a perinuclear location, and an inhibition of locomotion. Saltatory particle movements are not inhibited, however. Ruffling and filopod formation continue, indicating that cells are viable up to 24 h.Polarized light microscopy of living fibroblasts treated with taxol reveals the presence of perinuclear birefringent material which has been examined by immunofluorescence. In control cells, IF and MT radiate from a juxtanuclear region and extend to the cell periphery. In taxol-treated cells, MT and IF are excluded from cell margins, forming large central bundles.In the epithelial cell lines PtK2 and PAM, the keratin system of IF does not become redistributed; in PtK2, however, a second fibroblastlike system of IF does become redistributed to a perinuclear position during taxol treatment.Ultrastructural analyses show that taxol-treated fibroblasts contain parallel arrays of cross-bridged MT-IF as well as bundles of MT exclusive of IF. Epithelial cells contain a predominance of IF-free MT bundles which are organized into hexagonally packed arrays. In these bundles MT frequently exhibit hooks or other incomplete MT profiles and are linked by filamentous material.
    Additional Material: 14 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970030402
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    Complexes containing actin and spectrin from erythrocyte and brain (1983)
    New York, NY : Wiley-Blackwell
    Cell Motility and the Cytoskeleton 3 (1983), S. 375-382 
    Details
    ISSN: 0886-1544
    Keywords: actin ; spectrin ; band 4.1 ; cytochalasins ; erythrocyte ; brain ; actin-membrane attachment ; Life and Medical Sciences ; Cell & Developmental Biology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Medicine
    Notes: A complex of proteins with properties similar to those of erythrocyte spectrinband 4.1-actin complex has been idientified in a preparation derived from bovine brain. The complex has an apparent sedimentation coefficient of about 26S, and contains brain spectrin (also called fodrin) and actin as major components. The actin in the complex is in the oligomeric form, which nucleates assembly of actin filaments that grow from the “barbed” end. The complex cross-links actin filaments, resulting in an increase in low-shear viscosity. Whether the complex contains a protein analogous to erythrocyte band 4.1 is not known. However, it can be demonstrated that brain spectrin has the capability to interact with band 4.1 in a way which increases its ability to cross-link actin filaments.
    Additional Material: 3 Ill.
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    URL: http://dx.doi.org/10.1002/cm.970030505
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