Three-Dimensional Anisotropic Noise Reduction with Automated Parameter Tuning: Application to Electron Cryotomography

2007 ◽  
pp. 60-69 ◽  
Author(s):  
J. J. Fernández ◽  
S. Li ◽  
V. Lucic
Keyword(s):  
Noise Reduction ◽  
Three Dimensional ◽  
Parameter Tuning ◽  
Electron Cryotomography

scholarly journals Electron Cryotomography of Tula Hantavirus Suggests a Unique Assembly Paradigm for Enveloped Viruses

2010 ◽  
Vol 84 (10) ◽  
pp. 4889-4897 ◽  
Author(s):  
Juha T. Huiskonen ◽  
Jussi Hepojoki ◽  
Pasi Laurinmäki ◽  
Antti Vaheri ◽  
Hilkka Lankinen ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Hemorrhagic Fever ◽  
Membrane Curvature ◽  
Emerging Viruses ◽  
Enveloped Viruses ◽  
Viral Membrane ◽  
Density Maps ◽  
Virion Structure ◽  
Electron Cryotomography ◽  
Assembly Principles

ABSTRACT Hantaviruses (family Bunyaviridae) are rodent-borne emerging viruses that cause a serious, worldwide threat to human health. Hantavirus diseases include hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome. Virions are enveloped and contain a tripartite single-stranded negative-sense RNA genome. Two types of glycoproteins, GN and GC, are embedded in the viral membrane and form protrusions, or “spikes.” The membrane encloses a ribonucleoprotein core, which consists of the RNA segments, the nucleocapsid protein, and the RNA-dependent RNA polymerase. Detailed information on hantavirus virion structure and glycoprotein spike composition is scarce. Here, we have studied the structures of Tula hantavirus virions using electron cryomicroscopy and tomography. Three-dimensional density maps show how the hantavirus surface glycoproteins, membrane, and ribonucleoprotein are organized. The structure of the GN-GC spike complex was solved to 3.6-nm resolution by averaging tomographic subvolumes. Each spike complex is a square-shaped assembly with 4-fold symmetry. Spike complexes formed ordered patches on the viral membrane by means of specific lateral interactions. These interactions may be sufficient for creating membrane curvature during virus budding. In conclusion, the structure and assembly principles of Tula hantavirus exemplify a unique assembly paradigm for enveloped viruses.

scholarly journals Nanogold as a Specific Marker for Electron Cryotomography

2009 ◽  
Vol 15 (3) ◽  
pp. 183-188 ◽  
Author(s):  
Yongning He ◽  
Grant J. Jensen ◽  
Pamela J. Bjorkman
Keyword(s):  
Lipid Bilayers ◽  
Outer Surface ◽  
Three Dimensional ◽  
Fc Receptor ◽  
Specific Marker ◽  
Neonatal Fc Receptor ◽  
Membrane Bound ◽  
Nanogold Particles ◽  
Intracellular Vesicles ◽  
Electron Cryotomography

AbstractWhile electron cryotomography (ECT) provides “molecular” resolution, three-dimensional images of unique biological specimens, sample crowdedness, and/or resolution limitations can make it difficult to identify specific macromolecular components. Here we used a 1.4 nm Nanogold® cluster specifically attached to the Fc fragment of IgG to monitor its interaction with the neonatal Fc receptor (FcRn), a membrane-bound receptor that transports IgG across cells in acidic intracellular vesicles. ECT was used to image complexes formed by Nanogold-labeled Fc bound to FcRn attached to the outer surface of synthetic liposomes. In the resulting three-dimensional reconstructions, 1.4 nm Nanogold particles were distributed predominantly along the interfaces where 2:1 FcRn-Fc complexes bridged adjacent lipid bilayers. These results demonstrate that the 1.4 nm Nanogold cluster is visible in tomograms of typically thick samples (∼250 nm) recorded with defocuses appropriate for large macromolecules and is thus an effective marker.

scholarly journals Novel Three-Dimensional Surface Treatments for Trailing-Edge Noise Reduction

AIAA Journal ◽  
2019 ◽  
Vol 57 (10) ◽  
pp. 4527-4535 ◽  
Author(s):  
Abbas Afshari ◽  
Ali A. Dehghan ◽  
Mahdi Azarpeyvand
Keyword(s):  
Noise Reduction ◽  
Three Dimensional ◽  
Surface Treatments ◽  
Trailing Edge ◽  
Trailing Edge Noise ◽  
Dimensional Surface

scholarly journals Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo

2016 ◽  
Vol 27 (21) ◽  
pp. 3357-3368 ◽  
Author(s):  
Chen Chen ◽  
Hong Hwa Lim ◽  
Jian Shi ◽  
Sachiko Tamura ◽  
Kazuhiro Maeshima ◽  
...  
Keyword(s):  
Budding Yeast ◽  
Three Dimensional ◽  
Chromatin Organization ◽  
Three Dimensions ◽  
Yeast Saccharomyces Cerevisiae ◽  
Nuclear Structures ◽  
Three Dimensional Models ◽  
Electron Cryotomography ◽  
Fundamental Units

Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin—nucleosomes—are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae. Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an “open” configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome–nucleosome associations.

scholarly journals Optimized PID Controller Based on Beetle Antennae Search Algorithm for Electro-Hydraulic Position Servo Control System

Sensors ◽  
2019 ◽  
Vol 19 (12) ◽  
pp. 2727 ◽  
Author(s):  
Yuqi Fan ◽  
Junpeng Shao ◽  
Guitao Sun
Keyword(s):  
Control System ◽  
Pid Controller ◽  
Search Algorithm ◽  
Three Dimensional ◽  
Parameter Tuning ◽  
Servo Control ◽  
Dimensional Parameter ◽  
Servo Control System ◽  
Position Servo Control ◽  
Position Servo

To improve the controllability of an electro-hydraulic position servo control system while simultaneously enhancing the anti-jamming ability of a PID controller, a compound PID controller that combines the beetle antennae search algorithm with PID strategy was proposed, and used to drive the position servo control system of the electro-hydraulic servo system. A BAS-PID controller was designed, and the beetle antennae search algorithm was used to tune PID parameters so that the disturbance signal of the system was effectively restrained. Initially, the basic mathematical model of the electro-hydraulic position servo control system was established through theoretical analysis. The transfer function model was obtained by identifying system parameters. Then, the PID parameter-tuning problem was converted into a class of three-dimensional parameter optimization problem, and gains of PID controllers were adjusted using the beetle antennae search algorithm. Finally, by comparing the effectiveness of different algorithms, simulation and experimental results revealed that the BAS-PID controller can greatly enhance the performance of the electro-hydraulic position servo control system and inhibit external disturbances when different interference signals are used to test the system’s robustness.

scholarly journals Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins

2018 ◽  
Vol 29 (11) ◽  
pp. 1318-1331 ◽  
Author(s):  
Lam T. Nguyen ◽  
Matthew T. Swulius ◽  
Samya Aich ◽  
Mithilesh Mishra ◽  
Grant J. Jensen
Keyword(s):  
Cell Wall ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Eukaryotic Cells ◽  
Ring Assembly ◽  
Assembly Result ◽  
Microscope Images ◽  
Coarse Grained Simulations ◽  
Electron Cryotomography

Cytokinesis in many eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by the existing literature and new three-dimensional (3D) molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin cross-linkers, and membranes and simulate their interactions. Assuming that local force on the membrane results in inward growth of the cell wall, we explored a matrix of possible actomyosin configurations and found that node-based architectures like those presently described for ring assembly result in membrane puckers not seen in electron microscope images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.

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