Sample records for cryo magnetic separation

  1. A Magnetic Resonance (MR) Microscopy System using a Microfluidically Cryo-Cooled Planar Coil

    PubMed Central

    Koo, Chiwan; Godley, Richard F.; Park, Jaewon; McDougall, Mary P.; Wright, Steven M.; Han, Arum

    2011-01-01

    We present the development of a microfluidically cryo-cooled planar coil for magnetic resonance (MR) microscopy. Cryogenically cooling radiofrequency (RF) coils for magnetic resonance imaging (MRI) can improve the signal to noise ratio (SNR) of the experiment. Conventional cryostats typically use a vacuum gap to keep samples to be imaged, especially biological samples, at or near room temperature during cryo-cooling. This limits how close a cryo-cooled coil can be placed to the sample. At the same time, a small coil-to-sample distance significantly improves the MR imaging capability due to the limited imaging depth of planar MR microcoils. These two conflicting requirements pose challenges to the use of cryo-cooling in MR microcoils. The use of a microfluidic based cryostat for localized cryo-cooling of MR microcoils is a step towards eliminating these constraints. The system presented here consists of planar receive-only coils with integrated cryo-cooling microfluidic channels underneath, and an imaging surface on top of the planar coils separated by a thin nitrogen gas gap. Polymer microfluidic channel structures fabricated through soft lithography processes were used to flow liquid nitrogen under the coils in order to cryo-cool the planar coils to liquid nitrogen temperature (−196°C). Two unique features of the cryo-cooling system minimize the distance between the coil and the sample: 1) The small dimension of the polymer microfluidic channel enables localized cooling of the planar coils, while minimizing thermal effects on the nearby imaging surface. 2) The imaging surface is separated from the cryo-cooled planar coil by a thin gap through which nitrogen gas flows to thermally insulate the imaging surface, keeping it above 0°C and preventing potential damage to biological samples. The localized cooling effect was validated by simulations, bench testing, and MR imaging experiments. Using this cryo-cooled planar coil system inside a 4.7 Tesla MR system

  2. A magnetic resonance (MR) microscopy system using a microfluidically cryo-cooled planar coil.

    PubMed

    Koo, Chiwan; Godley, Richard F; Park, Jaewon; McDougall, Mary P; Wright, Steven M; Han, Arum

    2011-07-07

    We present the development of a microfluidically cryo-cooled planar coil for magnetic resonance (MR) microscopy. Cryogenically cooling radiofrequency (RF) coils for magnetic resonance imaging (MRI) can improve the signal to noise ratio (SNR) of the experiment. Conventional cryostats typically use a vacuum gap to keep samples to be imaged, especially biological samples, at or near room temperature during cryo-cooling. This limits how close a cryo-cooled coil can be placed to the sample. At the same time, a small coil-to-sample distance significantly improves the MR imaging capability due to the limited imaging depth of planar MR microcoils. These two conflicting requirements pose challenges to the use of cryo-cooling in MR microcoils. The use of a microfluidic based cryostat for localized cryo-cooling of MR microcoils is a step towards eliminating these constraints. The system presented here consists of planar receive-only coils with integrated cryo-cooling microfluidic channels underneath, and an imaging surface on top of the planar coils separated by a thin nitrogen gas gap. Polymer microfluidic channel structures fabricated through soft lithography processes were used to flow liquid nitrogen under the coils in order to cryo-cool the planar coils to liquid nitrogen temperature (-196 °C). Two unique features of the cryo-cooling system minimize the distance between the coil and the sample: (1) the small dimension of the polymer microfluidic channel enables localized cooling of the planar coils, while minimizing thermal effects on the nearby imaging surface. (2) The imaging surface is separated from the cryo-cooled planar coil by a thin gap through which nitrogen gas flows to thermally insulate the imaging surface, keeping it above 0 °C and preventing potential damage to biological samples. The localized cooling effect was validated by simulations, bench testing, and MR imaging experiments. Using this cryo-cooled planar coil system inside a 4.7 Tesla MR system

  3. Structural, microstructural and magnetic evolution in cryo milled carbon doped MnAl.

    PubMed

    Fang, Hailiang; Cedervall, Johan; Hedlund, Daniel; Shafeie, Samrand; Deledda, Stefano; Olsson, Fredrik; von Fieandt, Linus; Bednarcik, Jozef; Svedlindh, Peter; Gunnarsson, Klas; Sahlberg, Martin

    2018-02-06

    The low cost, rare earth free τ-phase of MnAl has high potential to partially replace bonded Nd 2 Fe 14 B rare earth permanent magnets. However, the τ-phase is metastable and it is experimentally difficult to obtain powders suitable for the permanent magnet alignment process, which requires the fine powders to have an appropriate microstructure and high τ-phase purity. In this work, a new method to make high purity τ-phase fine powders is presented. A high purity τ-phase Mn 0.55 Al 0.45 C 0.02 alloy was synthesized by the drop synthesis method. The drop synthesized material was subjected to cryo milling and  followed by a flash heating process. The crystal structure and microstructure of the drop synthesized, cryo milled and flash heated samples were studied by X-ray in situ powder diffraction, scanning electron microscopy, X-ray energy dispersive spectroscopy and electron backscatter diffraction. Magnetic properties and magnetic structure of the drop synthesized, cryo milled, flash heated  samples were characterized by magnetometry and neutron powder diffraction, respectively. The results reveal that the 2 and 4 hours cryo milled and flash heated samples both exhibit high τ-phase purity and micron-sized round particle shapes. Moreover, the flash heated samples display high saturation magnetization as well as increased coercivity.

  4. Correlative cryo-fluorescence light microscopy and cryo-electron tomography of Streptomyces.

    PubMed

    Koning, Roman I; Celler, Katherine; Willemse, Joost; Bos, Erik; van Wezel, Gilles P; Koster, Abraham J

    2014-01-01

    Light microscopy and electron microscopy are complementary techniques that in a correlative approach enable identification and targeting of fluorescently labeled structures in situ for three-dimensional imaging at nanometer resolution. Correlative imaging allows electron microscopic images to be positioned in a broader temporal and spatial context. We employed cryo-correlative light and electron microscopy (cryo-CLEM), combining cryo-fluorescence light microscopy and cryo-electron tomography, on vitrified Streptomyces bacteria to study cell division. Streptomycetes are mycelial bacteria that grow as long hyphae and reproduce via sporulation. On solid media, Streptomyces subsequently form distinct aerial mycelia where cell division leads to the formation of unigenomic spores which separate and disperse to form new colonies. In liquid media, only vegetative hyphae are present divided by noncell separating crosswalls. Their multicellular life style makes them exciting model systems for the study of bacterial development and cell division. Complex intracellular structures have been visualized with transmission electron microscopy. Here, we describe the methods for cryo-CLEM that we applied for studying Streptomyces. These methods include cell growth, fluorescent labeling, cryo-fixation by vitrification, cryo-light microscopy using a Linkam cryo-stage, image overlay and relocation, cryo-electron tomography using a Titan Krios, and tomographic reconstruction. Additionally, methods for segmentation, volume rendering, and visualization of the correlative data are described. © 2014 Elsevier Inc. All rights reserved.

  5. Process optimization of helium cryo plant operation for SST-1 superconducting magnet system

    NASA Astrophysics Data System (ADS)

    Panchal, P.; Panchal, R.; Patel, R.; Mahesuriya, G.; Sonara, D.; Srikanth G, L. N.; Garg, A.; Christian, D.; Bairagi, N.; Sharma, R.; Patel, K.; Shah, P.; Nimavat, H.; Purwar, G.; Patel, J.; Tanna, V.; Pradhan, S.

    2017-02-01

    Several plasma discharge campaigns have been carried out in steady state superconducting tokamak (SST-1). SST-1 has toroidal field (TF) and poloidal field (PF) superconducting magnet system (SCMS). The TF coils system is cooled to 4.5 - 4.8 K at 1.5 - 1.7 bar(a) under two phase flow condition using 1.3 kW helium cryo plant. Experience revealed that the PF coils demand higher pressure heads even at lower temperatures in comparison to TF coils because of its longer hydraulic path lengths. Thermal run away are observed within PF coils because of single common control valve for all PF coils in distribution system having non-uniform lengths. Thus it is routine practice to stop the cooling of PF path and continue only TF cooling at SCMS inlet temperature of ˜ 14 K. In order to achieve uniform cool down, different control logic is adopted to make cryo stable system. In adopted control logic, the SCMS are cooled down to 80 K at constant inlet pressure of 9 bar(a). After authorization of turbine A/B, the SCMS inlet pressure is gradually controlled by refrigeration J-T valve to achieve stable operation window for cryo system. This paper presents process optimization for cryo plant operation for SST-1 SCMS.

  6. Whole mouse cryo-imaging

    NASA Astrophysics Data System (ADS)

    Wilson, David; Roy, Debashish; Steyer, Grant; Gargesha, Madhusudhana; Stone, Meredith; McKinley, Eliot

    2008-03-01

    The Case cryo-imaging system is a section and image system which allows one to acquire micron-scale, information rich, whole mouse color bright field and molecular fluorescence images of an entire mouse. Cryo-imaging is used in a variety of applications, including mouse and embryo anatomical phenotyping, drug delivery, imaging agents, metastastic cancer, stem cells, and very high resolution vascular imaging, among many. Cryo-imaging fills the gap between whole animal in vivo imaging and histology, allowing one to image a mouse along the continuum from the mouse -> organ -> tissue structure -> cell -> sub-cellular domains. In this overview, we describe the technology and a variety of exciting applications. Enhancements to the system now enable tiled acquisition of high resolution images to cover an entire mouse. High resolution fluorescence imaging, aided by a novel subtraction processing algorithm to remove sub-surface fluorescence, makes it possible to detect fluorescently-labeled single cells. Multi-modality experiments in Magnetic Resonance Imaging and Cryo-imaging of a whole mouse demonstrate superior resolution of cryo-images and efficiency of registration techniques. The 3D results demonstrate the novel true-color volume visualization tools we have developed and the inherent advantage of cryo-imaging in providing unlimited depth of field and spatial resolution. The recent results continue to demonstrate the value cryo-imaging provides in the field of small animal imaging research.

  7. Magnetic separation anxiety

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Canning, C.

    1992-01-01

    This paper reports that only a few years ago superconducting magnetic separation was viewed as the next major market for superconducting magnets. The first commercial units had been installed, worked flawlessly, and demonstrated real economic viability. The potential market was seen as quite large, and many people believed that superconducting magnetic separation would soon show the same rapid growth that MRI had demonstrated after its initial success. These hopes even prompted IGC, one of the top MRI magnet builders, to form a separate division devoted to magnetic separation. Despite the existence of Magstream, IGC has not been overly active inmore » the market. As a technology that has applications from the clay on the Earth to the soil on the moon, superconducting magnetic separation has yet to become widely used.« less

  8. Cryo-planing of frozen-hydrated samples using cryo triple ion gun milling (CryoTIGM™).

    PubMed

    Chang, Irene Y T; Joester, Derk

    2015-12-01

    Cryo-SEM is a high throughput technique for imaging biological ultrastructure in its most pristine state, i.e. without chemical fixation, embedding, or drying. Freeze fracture is routinely used to prepare internal surfaces for cryo-SEM imaging. However, the propagation of the fracture plane is highly dependent on sample properties, and the resulting surface frequently shows substantial topography, which can complicate image analysis and interpretation. We have developed a broad ion beam milling technique, called cryogenic triple ion gun milling (CryoTIGM™ ['krī-ə-,tīm]), for cryo-planing frozen-hydrated biological specimens. Comparing sample preparation by CryoTIGM™ and freeze fracture in three model systems, Baker's yeast, mouse liver tissue, and whole sea urchin embryos, we find that CryoTIGM™ yields very large (∼700,000 μm(2)) and smooth sections that present ultrastructural details at similar or better quality than freeze-fractured samples. A particular strength of CryoTIGM™ is the ability to section samples with hard-soft contrast such as brittle calcite (CaCO3) spicules in the sea urchin embryo. Copyright © 2015 Elsevier Inc. All rights reserved.

  9. Cryo-electron microscopy and cryo-electron tomography of nanoparticles.

    PubMed

    Stewart, Phoebe L

    2017-03-01

    Cryo-transmission electron microscopy (cryo-TEM or cryo-EM) and cryo-electron tomography (cryo-ET) offer robust and powerful ways to visualize nanoparticles. These techniques involve imaging of the sample in a frozen-hydrated state, allowing visualization of nanoparticles essentially as they exist in solution. Cryo-TEM grid preparation can be performed with the sample in aqueous solvents or in various organic and ionic solvents. Two-dimensional (2D) cryo-TEM provides a direct way to visualize the polydispersity within a nanoparticle preparation. Fourier transforms of cryo-TEM images can confirm the structural periodicity within a sample. While measurement of specimen parameters can be performed with 2D TEM images, determination of a three-dimensional (3D) structure often facilitates more spatially accurate quantization. 3D structures can be determined in one of two ways. If the nanoparticle has a homogeneous structure, then 2D projection images of different particles can be averaged using a computational process referred to as single particle reconstruction. Alternatively, if the nanoparticle has a heterogeneous structure, then a structure can be generated by cryo-ET. This involves collecting a tilt-series of 2D projection images for a defined region of the grid, which can be used to generate a 3D tomogram. Occasionally it is advantageous to calculate both a single particle reconstruction, to reveal the regular portions of a nanoparticle structure, and a cryo-electron tomogram, to reveal the irregular features. A sampling of 2D cryo-TEM images and 3D structures are presented for protein based, DNA based, lipid based, and polymer based nanoparticles. WIREs Nanomed Nanobiotechnol 2017, 9:e1417. doi: 10.1002/wnan.1417 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

  10. CryoTran user's manual, version 1.0

    NASA Technical Reports Server (NTRS)

    Cowgill, Glenn R.; Chato, David J.; Saad, Ehab

    1989-01-01

    The development of cryogenic fluid management systems for space operation is a major portion of the efforts of the Cryogenic Fluids Technology Office (CFTO) at the NASA Lewis Research Center. Analytical models are a necessary part of experimental programs which are used to verify the results of experiments and are also used as a predictor for parametric studies. The CryoTran computer program is a bridge to obtain analytical results. The object of CryoTran is to coordinate these separate analyses into an integrated framework with a user-friendly interface and a common cryogenic property database. CryoTran is an integrated software system designed to help solve a diverse set of problems involving cryogenic fluid storage and transfer in both ground and low-g environments.

  11. Cryo-FIB specimen preparation for use in a cartridge-type cryo-TEM.

    PubMed

    He, Jie; Hsieh, Chyongere; Wu, Yongping; Schmelzer, Thomas; Wang, Pan; Lin, Ying; Marko, Michael; Sui, Haixin

    2017-08-01

    Cryo-electron tomography (cryo-ET) is a well-established technique for studying 3D structural details of subcellular macromolecular complexes and organelles in their nearly native context in the cell. A primary limitation of the application of cryo-ET is the accessible specimen thickness, which is less than the diameters of almost all eukaryotic cells. It has been shown that focused ion beam (FIB) milling can be used to prepare thin, distortion-free lamellae of frozen biological material for high-resolution cryo-ET. Commercial cryosystems are available for cryo-FIB specimen preparation, however re-engineering and additional fixtures are often essential for reliable results with a particular cryo-FIB and cryo-transmission electron microscope (cryo-TEM). Here, we describe our optimized protocol and modified instrumentation for cryo-FIB milling to produce thin lamellae and subsequent damage-free cryotransfer of the lamellae into our cartridge-type cryo-TEM. Published by Elsevier Inc.

  12. Magnetic separation of antibiotics by electrochemical magnetic seeding

    NASA Astrophysics Data System (ADS)

    Ihara, I.; Toyoda, K.; Beneragama, N.; Umetsu, K.

    2009-03-01

    Magnetic separation of several classes of antibiotics was investigated using electrochemical magnetic seeding. Electrocoagulation with a sacrificial anode followed by addition of magnetite particles was applied for the magnetic seeding of antibiotics. With electrochemical magnetic seeding using an iron anode, tetracycline antibiotics (oxytetracycline, chlortetracycline, doxycycline and tetracycline) and cephalosporin antibiotic (cefdinir) were rapidly removed from synthetic wastewater by magnetic separation using a neodymium magnet. Iron and aluminium anodes were suitable for magnetic seeding of the antibiotics. The results indicated that the ability of antibiotics to form strong complex with iron and aluminium allowed the higher removal by magnetic separation. This method would be appropriate for rapid treatment of antibiotics in wastewater.

  13. Continuous magnetic separator and process

    DOEpatents

    Oder, Robin R.; Jamison, Russell E.

    2008-04-22

    A continuous magnetic separator and process for separating a slurry comprising magnetic particles into a clarified stream and a thickened stream. The separator has a container with a slurry inlet, an overflow outlet for the discharge of the clarified slurry stream, and an underflow outlet for the discharge of a thickened slurry stream. Magnetic particles in the slurry are attracted to, and slide down, magnetic rods within the container. The slurry is thus separated into magnetic concentrate and clarified slurry. Flow control means can be used to control the ratio of the rate of magnetic concentrate to the rate of clarified slurry. Feed control means can be used to control the rate of slurry feed to the slurry inlet.

  14. Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm.

    PubMed

    Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

    2016-01-01

    In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis.

  15. Imaging endosomes and autophagosomes in whole mammalian cells using correlative cryo-fluorescence and cryo-soft X-ray microscopy (cryo-CLXM)☆

    PubMed Central

    Duke, Elizabeth M.H.; Razi, Minoo; Weston, Anne; Guttmann, Peter; Werner, Stephan; Henzler, Katja; Schneider, Gerd; Tooze, Sharon A.; Collinson, Lucy M.

    2014-01-01

    Cryo-soft X-ray tomography (cryo-SXT) is a powerful imaging technique that can extract ultrastructural information from whole, unstained mammalian cells as close to the living state as possible. Subcellular organelles including the nucleus, the Golgi apparatus and mitochondria have been identified by morphology alone, due to the similarity in contrast to transmission electron micrographs. In this study, we used cryo-SXT to image endosomes and autophagosomes, organelles that are particularly susceptible to chemical fixation artefacts during sample preparation for electron microscopy. We used two approaches to identify these compartments. For early and recycling endosomes, which are accessible to externally-loaded markers, we used an anti-transferrin receptor antibody conjugated to 10 nm gold particles. For autophagosomes, which are not accessible to externally-applied markers, we developed a correlative cryo-fluorescence and cryo-SXT workflow (cryo-CLXM) to localise GFP-LC3 and RFP-Atg9. We used a stand-alone cryo-fluorescence stage in the home laboratory to localise the cloned fluorophores, followed by cryo-soft X-ray tomography at the synchrotron to analyse cellular ultrastructure. We mapped the 3D ultrastructure of the endocytic and autophagic structures, and discovered clusters of omegasomes arising from ‘hotspots’ on the ER. Thus, immunogold markers and cryo-CLXM can be used to analyse cellular processes that are inaccessible using other imaging modalities. PMID:24238600

  16. Magnetic separations in biotechnology.

    PubMed

    Borlido, L; Azevedo, A M; Roque, A C A; Aires-Barros, M R

    2013-12-01

    Magnetic separations are probably one of the most versatile separation processes in biotechnology as they are able to purify cells, viruses, proteins and nucleic acids directly from crude samples. The fast and gentle process in combination with its easy scale-up and automation provide unique advantages over other separation techniques. In the midst of this process are the magnetic adsorbents tailored for the envisioned target and whose complex synthesis spans over multiple fields of science. In this context, this article reviews both the synthesis and tailoring of magnetic adsorbents for bioseparations as well as their ultimate application. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. Magnetic Separation Using HTS Bulk Magnet for Cs-Bearing Fe precipitates

    NASA Astrophysics Data System (ADS)

    Oka, T.; Ichiju, K.; Sasaki, S.; Ogawa, J.; Fukui, S.; Sato, T.; Ooizumi, M.; Yokoyama, K.; Aoki, S.; Ohnishi, N.

    2017-09-01

    A peculiar magnetic separation technique has been examined in order to remove the Cs-bearing Fe precipitates formed of the waste ash from the withdrawn incinerator furnaces in Fukushima. The separation system was constructed in combination with high temperature superconducting bulk magnets which generates the intensive magnetic field over 2 T, which was activated by the pulsed field magnetization process. The separation experiment has been operated with use of the newly-built alternating channel type magnetic separating device, which followed the high-gradient magnetic separation technique. The magnetic stainless steel filters installed in the water channels are magnetized by the applied magnetic fields, and are capable of attracting the precipitates bearing the Fe compound and thin Cs contamination. The experimental results clearly exhibited the positive feasibility of HTS bulk magnets.

  18. Unsupervised Cryo-EM Data Clustering through Adaptively Constrained K-Means Algorithm

    PubMed Central

    Xu, Yaofang; Wu, Jiayi; Yin, Chang-Cheng; Mao, Youdong

    2016-01-01

    In single-particle cryo-electron microscopy (cryo-EM), K-means clustering algorithm is widely used in unsupervised 2D classification of projection images of biological macromolecules. 3D ab initio reconstruction requires accurate unsupervised classification in order to separate molecular projections of distinct orientations. Due to background noise in single-particle images and uncertainty of molecular orientations, traditional K-means clustering algorithm may classify images into wrong classes and produce classes with a large variation in membership. Overcoming these limitations requires further development on clustering algorithms for cryo-EM data analysis. We propose a novel unsupervised data clustering method building upon the traditional K-means algorithm. By introducing an adaptive constraint term in the objective function, our algorithm not only avoids a large variation in class sizes but also produces more accurate data clustering. Applications of this approach to both simulated and experimental cryo-EM data demonstrate that our algorithm is a significantly improved alterative to the traditional K-means algorithm in single-particle cryo-EM analysis. PMID:27959895

  19. First operational experience with the HIE-Isolde helium cryogenic system including several RF cryo-modules

    NASA Astrophysics Data System (ADS)

    Guillotin, N.; Dupont, T.; Gayet, Ph; Pirotte, O.

    2017-12-01

    The High Intensity and Energy ISOLDE (HIE-ISOLDE) upgrade project at CERN includes the deployment of new superconducting accelerating structures operated at 4.5 K (ultimately of six cryo-modules) installed in series, and the refurbishing of the helium cryo-plant previously used to cool the ALEPH magnet during the operation of the LEP accelerator from 1989 to 2000. The helium refrigerator is connected to a new cryogenic distribution line, supplying a 2000-liter storage dewar and six interconnecting valve boxes (i.e jumper boxes), one for each cryo-module. After a first operation period with one cryo-module during six months in 2015, a second cryo-module has been installed and operated during 2016. The operation of the cryo-plant with these two cryo-modules has required significant technical enhancements and tunings for the compressor station, the cold-box and the cryogenic distribution system in order to reach nominal and stable operational conditions. The present paper describes the commissioning results and the lessons learnt during the operation campaign of 2016 together with the preliminary experience acquired during the 2017 operation phase with a third cryo-module.

  20. Magnetic separation of algae

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nath, Pulak; Twary, Scott N.

    Described herein are methods and systems for harvesting, collecting, separating and/or dewatering algae using iron based salts combined with a magnetic field gradient to separate algae from an aqueous solution.

  1. Method of magnetic separation and apparatus therefore

    NASA Technical Reports Server (NTRS)

    Oder, Robin R. (Inventor)

    1991-01-01

    An apparatus for magnetically separating and collecting particulate matter fractions of a raw sample according to relative magnetic susceptibilities of each fraction so collected is disclosed. The separation apparatus includes a splitter which is used in conjunction with a magnetic separator for achieving the desired fractionation.

  2. Magnetically Enhanced Solid-Liquid Separation

    NASA Astrophysics Data System (ADS)

    Rey, C. M.; Keller, K.; Fuchs, B.

    2005-07-01

    DuPont is developing an entirely new method of solid-liquid filtration involving the use of magnetic fields and magnetic field gradients. The new hybrid process, entitled Magnetically Enhanced Solid-Liquid Separation (MESLS), is designed to improve the de-watering kinetics and reduce the residual moisture content of solid particulates mechanically separated from liquid slurries. Gravitation, pressure, temperature, centrifugation, and fluid dynamics have dictated traditional solid-liquid separation for the past 50 years. The introduction of an external field (i.e. the magnetic field) offers the promise to manipulate particle behavior in an entirely new manner, which leads to increased process efficiency. Traditional solid-liquid separation typically consists of two primary steps. The first is a mechanical step in which the solid particulate is separated from the liquid using e.g. gas pressure through a filter membrane, centrifugation, etc. The second step is a thermal drying process, which is required due to imperfect mechanical separation. The thermal drying process is over 100-200 times less energy efficient than the mechanical step. Since enormous volumes of materials are processed each year, more efficient mechanical solid-liquid separations can be leveraged into dramatic reductions in overall energy consumption by reducing downstream drying requirements have a tremendous impact on energy consumption. Using DuPont's MESLS process, initial test results showed four very important effects of the magnetic field on the solid-liquid filtration process: 1) reduction of the time to reach gas breakthrough, 2) less loss of solid into the filtrate, 3) reduction of the (solids) residual moisture content, and 4) acceleration of the de-watering kinetics. These test results and their potential impact on future commercial solid-liquid filtration is discussed. New applications can be found in mining, chemical and bioprocesses.

  3. Quantitative Magnetic Separation of Particles and Cells using Gradient Magnetic Ratcheting

    PubMed Central

    Murray, Coleman; Pao, Edward; Tseng, Peter; Aftab, Shayan; Kulkarni, Rajan; Rettig, Matthew; Di Carlo, Dino

    2016-01-01

    Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting (MACS), are robust but perform coarse, qualitative separations based on surface antigen expression. We report a quantitative magnetic separation technology using high-force magnetic ratcheting over arrays of magnetically soft micro-pillars with gradient spacing, and use the system to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micro-pillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic-field. Particles with higher IOC separate and equilibrate along the miro-pillar array at larger pitches. We develop a semi-analytical model that predicts behavior for particles and cells. Using the system, LNCaP cells were separated based on the bound quantity of 1μm anti-EpCAM particles as a metric for expression. The ratcheting cytometry system was able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof of concept, EpCAM-labeled cells from patient blood were isolated with 74% purity, demonstrating potential towards a quantitative magnetic separation instrument. PMID:26890496

  4. Quantitative Magnetic Separation of Particles and Cells Using Gradient Magnetic Ratcheting.

    PubMed

    Murray, Coleman; Pao, Edward; Tseng, Peter; Aftab, Shayan; Kulkarni, Rajan; Rettig, Matthew; Di Carlo, Dino

    2016-04-13

    Extraction of rare target cells from biosamples is enabling for life science research. Traditional rare cell separation techniques, such as magnetic activated cell sorting, are robust but perform coarse, qualitative separations based on surface antigen expression. A quantitative magnetic separation technology is reported using high-force magnetic ratcheting over arrays of magnetically soft micropillars with gradient spacing, and the system is used to separate and concentrate magnetic beads based on iron oxide content (IOC) and cells based on surface expression. The system consists of a microchip of permalloy micropillar arrays with increasing lateral pitch and a mechatronic device to generate a cycling magnetic field. Particles with higher IOC separate and equilibrate along the miropillar array at larger pitches. A semi-analytical model is developed that predicts behavior for particles and cells. Using the system, LNCaP cells are separated based on the bound quantity of 1 μm anti-epithelial cell adhesion molecule (EpCAM) particles as a metric for expression. The ratcheting cytometry system is able to resolve a ±13 bound particle differential, successfully distinguishing LNCaP from PC3 populations based on EpCAM expression, correlating with flow cytometry analysis. As a proof-of-concept, EpCAM-labeled cells from patient blood are isolated with 74% purity, demonstrating potential toward a quantitative magnetic separation instrument. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Magnetic precipitate separation for Ni plating waste liquid using HTS bulk magnets

    NASA Astrophysics Data System (ADS)

    Oka, T.; Kimura, T.; Mimura, D.; Fukazawa, H.; Fukui, S.; Ogawa, J.; Sato, T.; Ooizumi, M.; Yokoyama, K.; Tsujimura, M.; Terasawa, T.

    2013-01-01

    The magnetic separation experiment for recycling the nickel-bearing precipitates in the waste liquid from the electroless plating processes has been practically conducted under the high gradient magnetic separation technique with use of the face-to-face HTS bulk magnet system. A couple of facing magnetic poles containing Sm123 bulk superconductors were activated through the pulsed field magnetization process to 1.86 T at 38 K and 2.00 T at 37 K, respectively. The weakly magnetized metallic precipitates of Ni crystals and Ni-P compounds deposited from the waste solution after heating it and pH controlling. The high gradient magnetic separation technique was employed with the separation channels filled with the stainless steel balls with dimension of 1 and 3 mm in diameter, which periodically moved between and out of the facing magnetic poles. The Ni-bearing precipitates were effectively attracted to the magnetized ferromagnetic balls. We have succeeded in obtaining the separation ratios over 90% under the flow rates less than 1.35 L/min.

  6. Phase-separation induced extraordinary toughening of magnetic hydrogels

    NASA Astrophysics Data System (ADS)

    Tang, Jingda; Li, Chenghai; Li, Haomin; Lv, Zengyao; Sheng, Hao; Lu, Tongqing; Wang, T. J.

    2018-05-01

    Phase separation markedly influences the physical properties of hydrogels. Here, we find that poly (N, N-dimethylacrylamide) (PDMA) hydrogels suffer from phase separation in aqueous sodium hydroxide solutions when the concentration is higher than 2 M. The polymer volume fraction and mechanical properties show an abrupt change around the transition point. We utilize this phase separation mechanism to synthesize tough magnetic PDMA hydrogels with the in-situ precipitation method. For comparison, we also prepared magnetic poly (2-acrylamido-2-methyl-propane sulfonic acid sodium) (PNaAMPS) magnetic hydrogels, where no phase separation occurs. The phase-separated magnetic PDMA hydrogels exhibit an extraordinarily high toughness of ˜1000 J m-2; while non-phase-separated magnetic PNaAMPS hydrogels only show a toughness of ˜1 J m-2, three orders of magnitude lower than that of PDMA hydrogels. This phase separation mechanism may become a new approach to prepare tough magnetic hydrogels and inspire more applications.

  7. Thinning of Large Biological Cells for Cryo-TEM Characterization by Cryo-FIB Milling

    PubMed Central

    Strunk, Korrinn M.; Ke, Danxia; Gray, Jennifer L.; Zhang, Peijun

    2013-01-01

    SUMMARY Focused ion beam milling at cryogenic temperatures (cryo-FIB) is a valuable tool that can be used to thin vitreous biological specimens for subsequent imaging and analysis in a cryo-transmission electron microscope (cryo-TEM) in their frozen-hydrated state. This technique offers the potential benefit of eliminating the mechanical artifacts that are typically found with cryo-ultramicrotomy. However, due to the additional complexity in transferring samples in and out of the FIB, contamination and devitrification of the amorphous ice is commonly encountered. In order to address these problems, we have designed a new sample cryo-shuttle that specifically accepts Polara TEM cartridges directly in order to simplify the transfer process between the FIB and TEM. We used the quality of the ice in the sample as an indicator to test various parameters used the process, and demonstrated with successful milling of large mammalian cells. By comparing the results from larger HeLa cells to those from E. coli cells, we discuss some of the artifacts and challenges we have encountered using this technique. PMID:22906009

  8. New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography.

    PubMed

    Schorb, Martin; Gaechter, Leander; Avinoam, Ori; Sieckmann, Frank; Clarke, Mairi; Bebeacua, Cecilia; Bykov, Yury S; Sonnen, Andreas F-P; Lihl, Reinhard; Briggs, John A G

    2017-02-01

    Correlative light and electron microscopy allows features of interest defined by fluorescence signals to be located in an electron micrograph of the same sample. Rare dynamic events or specific objects can be identified, targeted and imaged by electron microscopy or tomography. To combine it with structural studies using cryo-electron microscopy or tomography, fluorescence microscopy must be performed while maintaining the specimen vitrified at liquid-nitrogen temperatures and in a dry environment during imaging and transfer. Here we present instrumentation, software and an experimental workflow that improves the ease of use, throughput and performance of correlated cryo-fluorescence and cryo-electron microscopy. The new cryo-stage incorporates a specially modified high-numerical aperture objective lens and provides a stable and clean imaging environment. It is combined with a transfer shuttle for contamination-free loading of the specimen. Optimized microscope control software allows automated acquisition of the entire specimen area by cryo-fluorescence microscopy. The software also facilitates direct transfer of the fluorescence image and associated coordinates to the cryo-electron microscope for subsequent fluorescence-guided automated imaging. Here we describe these technological developments and present a detailed workflow, which we applied for automated cryo-electron microscopy and tomography of various specimens. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  9. A Versatile High-Vacuum Cryo-transfer System for Cryo-microscopy and Analytics

    PubMed Central

    Tacke, Sebastian; Krzyzanek, Vladislav; Nüsse, Harald; Wepf, Roger Albert; Klingauf, Jürgen; Reichelt, Rudolf

    2016-01-01

    Cryogenic microscopy methods have gained increasing popularity, as they offer an unaltered view on the architecture of biological specimens. As a prerequisite, samples must be handled under cryogenic conditions below their recrystallization temperature, and contamination during sample transfer and handling must be prevented. We present a high-vacuum cryo-transfer system that streamlines the entire handling of frozen-hydrated samples from the vitrification process to low temperature imaging for scanning transmission electron microscopy and transmission electron microscopy. A template for cryo-electron microscopy and multimodal cryo-imaging approaches with numerous sample transfer steps is presented. PMID:26910419

  10. Plasma separation from magnetic field lines in a magnetic nozzle

    NASA Technical Reports Server (NTRS)

    Kaufman, D. A.; Goodwin, D. G.; Sercel, J. C.

    1993-01-01

    This paper discusses conditions for separation of a plasma from the magnetic field of a magnetic nozzle. The analysis assumes a collisionless, quasineutral plasma, and therefore the results represent a lower bound on the amount of detachment possible for a given set of plasma conditions. We show that collisionless separation can occur because finite electron mass inhibits the flow of azimuthal currents in the nozzle. Separation conditions are governed by a parameter G which depends on plasma and nozzle conditions. Several methods of improving plasma detachment are presented, including moving the plasma generation zone downstream from the region of strongest magnetic field and using dual magnets to focus the plasma beam. Plasma detachment can be enhanced by manipulation of the nozzle configuration.

  11. A comparative analysis of the cryo-compression and cryo-adsorption hydrogen storage methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Petitpas, G; Benard, P; Klebanoff, L E

    2014-07-01

    While conventional low-pressure LH₂ dewars have existed for decades, advanced methods of cryogenic hydrogen storage have recently been developed. These advanced methods are cryo-compression and cryo-adsorption hydrogen storage, which operate best in the temperature range 30–100 K. We present a comparative analysis of both approaches for cryogenic hydrogen storage, examining how pressure and/or sorbent materials are used to effectively increase onboard H₂ density and dormancy. We start by reviewing some basic aspects of LH₂ properties and conventional means of storing it. From there we describe the cryo-compression and cryo-adsorption hydrogen storage methods, and then explore the relationship between them, clarifyingmore » the materials science and physics of the two approaches in trying to solve the same hydrogen storage task (~5–8 kg H₂, typical of light duty vehicles). Assuming that the balance of plant and the available volume for the storage system in the vehicle are identical for both approaches, the comparison focuses on how the respective storage capacities, vessel weight and dormancy vary as a function of temperature, pressure and type of cryo-adsorption material (especially, powder MOF-5 and MIL-101). By performing a comparative analysis, we clarify the science of each approach individually, identify the regimes where the attributes of each can be maximized, elucidate the properties of these systems during refueling, and probe the possible benefits of a combined “hybrid” system with both cryo-adsorption and cryo-compression phenomena operating at the same time. In addition the relationships found between onboard H₂ capacity, pressure vessel and/or sorbent mass and dormancy as a function of rated pressure, type of sorbent material and fueling conditions are useful as general designing guidelines in future engineering efforts using these two hydrogen storage approaches.« less

  12. Apparatus and method for continuous separation of magnetic particles from non-magnetic fluids

    DOEpatents

    Oder, Robin R.; Jamison, Russell E.

    2010-02-09

    A magnetic separator vessel (1) for separating magnetic particles from non-magnetic fluid includes a separation chamber having an interior and exterior wall, a top and bottom portion; a magnet (3) having first and second poles (2) positioned adjacent to the exterior wall, wherein the first pole is substantially diametrically opposed to the second pole; a inlet port (5) is directed into the top portion of the separation chamber, wherein the inlet port (5) is positioned adjacent to one of the first and second poles (2), wherein the inlet port (5) is adapted to transfer a mixture into the separation chamber; an underflow port (6) in communication with the bottom portion, wherein the underflow port (6) is adapted to receive the magnetic particles; and an overflow port (9) in communication with the separation chamber, wherein the overflow port (9) is adapted to receive the non-magnetic fluid.

  13. 3D Structure Determination of Native Mammalian Cells using Cryo-FIB and Cryo-electron Tomography

    PubMed Central

    Wang, Ke; Strunk, Korrinn; Zhao, Gongpu; Gray, Jennifer L.; Zhang, Peijun

    2012-01-01

    Cryo-electron tomography (cryo-ET) has enabled high resolution three-dimensional (3D) structural analysis of virus and host cell interactions and many cell signaling events; these studies, however, have largely been limited to very thin, peripheral regions of eukaryotic cells or to small prokaryotic cells. Recent efforts to make thin, vitreous sections using cryo-ultramicrotomy have been successful, however, this method is technically very challenging and with many artifacts. Here, we report a simple and robust method for creating in situ, frozen-hydrated cell lamellas using a focused ion beam at cryogenic temperature (cryo-FIB), allowing access to any interior cellular regions of interest. We demonstrate the utility of cryo-FIB with high resolution 3D cellular structures from both bacterial cells and large mammalian cells. The method will not only facilitate high-throughput 3D structural analysis of biological specimens, but is also broadly applicable to sample preparation of thin films and surface materials without the need for FIB “lift-out”. PMID:22796867

  14. Measuring Thermal Conductivity and Moisture Absorption of Cryo-Insulation Materials

    NASA Technical Reports Server (NTRS)

    Lambert, Michael A.

    1998-01-01

    separate TPS and cryo-insulation materials, which are connected by means of adhesives or stand-offs (spacers). Three concepts are being considered: (1) the TPS is bonded directly to the cryo-insulation which, in turn, is bonded to the exterior of the tank, (2) stand-offs are used to make a gap between the TPS and the cryo-insulation, which is bonded externally to the tank, (3) TPS is applied directly or with stand-offs to the exterior so the tank, and cryo-insulation is applied directly to the interior of the tank. Many potential problems are inherent in these approaches. For example, mismatch between coefficients of thermal expansion of the TPS and cryo-insulation, as well as aerodynamic loads, could lead to failure of the bond. Internal cryo-insulation must be prevent from entering the sump of the fuel turbo-pump. The mechanical integrity of the stand-off structure (if used) must withstand multiple missions. During ground hold (i.e., prior to launch) moisture condensation must be minimized in the gap between the cryo-insulation and the TPS. The longer term solution requires the development of a single material to act as cryo- insulation during ground hold and as TPS during re-entry. Such a material minimizes complexity and weight while improving reliability and reducing cost.

  15. MSWI boiler fly ashes: magnetic separation for material recovery.

    PubMed

    De Boom, Aurore; Degrez, Marc; Hubaux, Paul; Lucion, Christian

    2011-07-01

    Nowadays, ferrous materials are usually recovered from Municipal Solid Waste Incineration (MSWI) bottom ash by magnetic separation. To our knowledge, such a physical technique has not been applied so far to other MSWI residues. This study focuses thus on the applicability of magnetic separation on boiler fly ashes (BFA). Different types of magnet are used to extract the magnetic particles. We investigate the magnetic particle composition, as well as their leaching behaviour (EN 12457-1 leaching test). The magnetic particles present higher Cr, Fe, Mn and Ni concentration than the non-magnetic (NM) fraction. Magnetic separation does not improve the leachability of the NM fraction. To approximate industrial conditions, magnetic separation is also applied to BFA mixed with water by using a pilot. BFA magnetic separation is economically evaluated. This study globally shows that it is possible to extract some magnetic particles from MSWI boiler fly ashes. However, the magnetic particles only represent from 23 to 120 g/kg of the BFA and, though they are enriched in Fe, are composed of similar elements to the raw ashes. The industrial application of magnetic separation would only be profitable if large amounts of ashes were treated (more than 15 kt/y), and the process should be ideally completed by other recovery methods or advanced treatments. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Magnetic separation of general solid particles realised by a permanent magnet

    PubMed Central

    Hisayoshi, K.; Uyeda, C.; Terada, K.

    2016-01-01

    Most existing solids are categorised as diamagnetic or weak paramagnetic materials. The possibility of magnetic motion has not been intensively considered for these materials. Here, we demonstrate for the first time that ensembles of heterogeneous particles (diamagnetic bismuth, diamond and graphite particles, as well as two paramagnetic olivines) can be dynamically separated into five fractions by the low field produced by neodymium (NdFeB) magnets during short-duration microgravity (μg). This result is in contrast to the generally accepted notion that ordinary solid materials are magnetically inert. The materials of the separated particles are identified by their magnetic susceptibility (χ), which is determined from the translating velocity. The potential of this approach as an analytical technique is comparable to that of chromatography separation because the extraction of new solid phases from a heterogeneous grain ensemble will lead to important discoveries about inorganic materials. The method is applicable for the separation of the precious samples such as lunar soils and/or the Hayabusa particles recovered from the asteroids, because even micron-order grains can be thoroughly separated without sample-loss. PMID:27929081

  17. Magnetic separation of general solid particles realised by a permanent magnet

    NASA Astrophysics Data System (ADS)

    Hisayoshi, K.; Uyeda, C.; Terada, K.

    2016-12-01

    Most existing solids are categorised as diamagnetic or weak paramagnetic materials. The possibility of magnetic motion has not been intensively considered for these materials. Here, we demonstrate for the first time that ensembles of heterogeneous particles (diamagnetic bismuth, diamond and graphite particles, as well as two paramagnetic olivines) can be dynamically separated into five fractions by the low field produced by neodymium (NdFeB) magnets during short-duration microgravity (μg). This result is in contrast to the generally accepted notion that ordinary solid materials are magnetically inert. The materials of the separated particles are identified by their magnetic susceptibility (χ), which is determined from the translating velocity. The potential of this approach as an analytical technique is comparable to that of chromatography separation because the extraction of new solid phases from a heterogeneous grain ensemble will lead to important discoveries about inorganic materials. The method is applicable for the separation of the precious samples such as lunar soils and/or the Hayabusa particles recovered from the asteroids, because even micron-order grains can be thoroughly separated without sample-loss.

  18. Magnetic separation of general solid particles realised by a permanent magnet.

    PubMed

    Hisayoshi, K; Uyeda, C; Terada, K

    2016-12-08

    Most existing solids are categorised as diamagnetic or weak paramagnetic materials. The possibility of magnetic motion has not been intensively considered for these materials. Here, we demonstrate for the first time that ensembles of heterogeneous particles (diamagnetic bismuth, diamond and graphite particles, as well as two paramagnetic olivines) can be dynamically separated into five fractions by the low field produced by neodymium (NdFeB) magnets during short-duration microgravity (μg). This result is in contrast to the generally accepted notion that ordinary solid materials are magnetically inert. The materials of the separated particles are identified by their magnetic susceptibility (χ), which is determined from the translating velocity. The potential of this approach as an analytical technique is comparable to that of chromatography separation because the extraction of new solid phases from a heterogeneous grain ensemble will lead to important discoveries about inorganic materials. The method is applicable for the separation of the precious samples such as lunar soils and/or the Hayabusa particles recovered from the asteroids, because even micron-order grains can be thoroughly separated without sample-loss.

  19. National Cryo-Electron Microscopy Facility

    Cancer.gov

    Information about the National Cryo-EM Facility at NCI, created to provide researchers access to the latest cryo-EM technology for high resolution imaging. Includes timeline for installation and how to access the facility.

  20. Experimental investigation of magnetically actuated separation using tangential microfluidic channels and magnetic nanoparticles.

    PubMed

    Munir, Ahsan; Zhu, Zanzan; Wang, Jianlong; Zhou, Hong Susan

    2014-06-01

    A novel continuous switching/separation scheme of magnetic nanoparticles (MNPs) in a sub-microlitre fluid volume surrounded by neodymium permanent magnet is studied in this work using tangential microfluidic channels. Polydimethylsiloxane tangential microchannels are fabricated using a novel micromoulding technique that can be done without a clean room and at much lower cost and time. Negligible switching of MNPs is seen in the absence of magnetic field, whereas 90% of switching is observed in the presence of magnetic field. The flow rate of MNPs solution had dramatic impact on separation performance. An optimum value of the flow rate is found that resulted in providing effective MNP separation at much faster rate. Separation performance is also investigated for a mixture containing non-magnetic polystyrene particles and MNPs. It is found that MNPs preferentially moved from lower microchannel to upper microchannel resulting in efficient separation. The proof-of-concept experiments performed in this work demonstrates that microfluidic bioseparation can be efficiently achieved using functionalised MNPs, together with tangential microchannels, appropriate magnetic field strength and optimum flow rates. This work verifies that a simple low-cost magnetic switching scheme can be potentially of great utility for the separation and detection of biomolecules in microfluidic lab-on-a-chip systems.

  1. Particle acceleration at a reconnecting magnetic separator

    NASA Astrophysics Data System (ADS)

    Threlfall, J.; Neukirch, T.; Parnell, C. E.; Eradat Oskoui, S.

    2015-02-01

    Context. While the exact acceleration mechanism of energetic particles during solar flares is (as yet) unknown, magnetic reconnection plays a key role both in the release of stored magnetic energy of the solar corona and the magnetic restructuring during a flare. Recent work has shown that special field lines, called separators, are common sites of reconnection in 3D numerical experiments. To date, 3D separator reconnection sites have received little attention as particle accelerators. Aims: We investigate the effectiveness of separator reconnection as a particle acceleration mechanism for electrons and protons. Methods: We study the particle acceleration using a relativistic guiding-centre particle code in a time-dependent kinematic model of magnetic reconnection at a separator. Results: The effect upon particle behaviour of initial position, pitch angle, and initial kinetic energy are examined in detail, both for specific (single) particle examples and for large distributions of initial conditions. The separator reconnection model contains several free parameters, and we study the effect of changing these parameters upon particle acceleration, in particular in view of the final particle energy ranges that agree with observed energy spectra.

  2. How good can cryo-EM become?

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Glaeser, Robert M.

    The suddenness with which single-particle cryo-electron microscopy (cryo-EM) has emerged as a method for determining high-resolution structures of biological macromolecules invites the questions, how much better can this technology get, and how fast is that likely to happen? While we can rightly celebrate the maturation of cryo-EM as a high-resolution structure-determination tool, I believe there still are many developments to look forward to.

  3. Magnetic reconnection in 3D magnetosphere models: magnetic separators and open flux production

    NASA Astrophysics Data System (ADS)

    Glocer, A.; Dorelli, J.; Toth, G.; Komar, C. M.; Cassak, P.

    2014-12-01

    There are multiple competing definitions of magnetic reconnection in 3D (e.g., Hesse and Schindler [1988], Lau and Finn [1990], and Boozer [2002]). In this work we focus on separator reconnection. A magnetic separator can be understood as the 3D analogue of a 2D x line with a guide field, and is defined by the line corresponding to the intersection of the separatrix surfaces associated with the magnetic nulls. A separator in the magnetosphere represents the intersection of four distinct magnetic topologies: solar wind, closed, open connected to the northern hemisphere, and open connected to the southern hemisphere. The integral of the parallel electric field along the separator defines the rate of open flux production, and is one measure of the reconnection rate. We present three methods for locating magnetic separators and apply them to 3D resistive MHD simulations of the Earth's magnetosphere using the BATS-R-US code. The techniques for finding separators and determining the reconnection rate are insensitive to IMF clock angle and can in principle be applied to any magnetospheric model. The present work examines cases of high and low resistivity, for two clock angles. We also examine the separator during Flux Transfer Events (FTEs) and Kelvin-Helmholtz instability.

  4. Tessellated permanent magnet circuits for flow-through, open gradient separations of weakly magnetic materials.

    PubMed

    Moore, Lee R; Williams, P Stephen; Chalmers, Jeffrey J; Zborowski, Maciej

    2017-04-01

    Emerging microfluidic-based cell assays favor label-free red blood cell (RBC) depletion. Magnetic separation of RBC is possible because of the paramagnetism of deoxygenated hemoglobin but the process is slow for open-gradient field configurations. In order to increase the throughput, periodic arrangements of the unit magnets were considered, consisting of commercially available Nd-Fe-B permanent magnets and soft steel flux return pieces. The magnet design is uniquely suitable for multiplexing by magnet tessellation, here meaning the tiling of the magnet assembly cross-sectional plane by periodic repetition of the magnet and the flow channel shapes. The periodic pattern of magnet magnetizations allows a reduction of the magnetic material per channel with minimal distortion of the field cylindrical symmetry inside the magnet apertures. A number of such magnet patterns are investigated for separator performance, size and economy with the goal of designing an open-gradient magnetic separator capable of reducing the RBC number concentration a hundred-fold in 1 mL whole blood per hour.

  5. Fundamental study of phosphor separation by controlling magnetic force

    NASA Astrophysics Data System (ADS)

    Wada, Kohei; Mishima, Fumihito; Akiyama, Yoko; Nishijima, Shigehiro

    2013-11-01

    The phosphor wastes consist of phosphors with different emission colors, green (LAP), red (YOX), blue (BAM) and white (HP). It is required to recover and reuse the rare earth phosphors with high market value. In this study, we tried to separate the phosphor using the magnetic separation by HTS bulk magnet utilizing the differences of magnetic susceptibility by the type of phosphors. We succeeded in the successive separation of HP with low market value from YOX and BAM including the rare earth using the magnetic Archimedes method. In this method, vertical and radial components of the magnetic force were used.

  6. Physical and Structural Studies on the Cryo-cooling of Insulin Crystals

    NASA Technical Reports Server (NTRS)

    Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

    2003-01-01

    Reflection profiles were analyzed from microgravity-(mg) and earth-grown insulin crystals to measure mosaicity (h) and to reveal mosaic domain structure and composition. The effects of cryocooling on single and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were larger, more homogeneous, and more perfect than earth crystals. Several mg crystals contained primarily a single mosaic domain with havg of 0.005deg. The earth crystals varied in quality and all contained multiple domains with havg of 0.031deg. Cryocooling caused a 43-fold increase in h for mg crystals (havg=0.217deg) and an %fold increase for earth crystals (havg=0.246deg). These results indicate that very well-ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryo-cooling. Cryo-cooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryo-cooled single domain crystals relative to cryo-cooled multi-domain crystals. This improved signal, along with the increase in crystal size, facilitated the measurement of the weaker high- resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit cell dimensions which may be linked to cryo-cooling-associated structural changes and disorder.

  7. Theoretical validation for changing magnetic fields of systems of permanent magnets of drum separators

    NASA Astrophysics Data System (ADS)

    Lozovaya, S. Y.; Lozovoy, N. M.; Okunev, A. N.

    2018-03-01

    This article is devoted to the theoretical validation of the change in magnetic fields created by the permanent magnet systems of the drum separators. In the article, using the example of a magnetic separator for enrichment of highly magnetic ores, the method of analytical calculation of the magnetic fields of systems of permanent magnets based on the Biot-Savart-Laplace law, the equivalent solenoid method, and the superposition principle of fields is considered.

  8. High gradient magnetic field microstructures for magnetophoretic cell separation.

    PubMed

    Abdel Fattah, Abdel Rahman; Ghosh, Suvojit; Puri, Ishwar K

    2016-08-01

    Microfluidics has advanced magnetic blood fractionation by making integrated miniature devices possible. A ferromagnetic microstructure array that is integrated with a microfluidic channel rearranges an applied magnetic field to create a high gradient magnetic field (HGMF). By leveraging the differential magnetic susceptibilities of cell types contained in a host medium, such as paramagnetic red blood cells (RBCs) and diamagnetic white blood cells (WBCs), the resulting HGMF can be used to continuously separate them without attaching additional labels, such as magnetic beads, to them. We describe the effect of these ferromagnetic microstructure geometries have on the blood separation efficacy by numerically simulating the influence of microstructure height and pitch on the HGMF characteristics and resulting RBC separation. Visualizations of RBC trajectories provide insight into how arrays can be optimized to best separate these cells from a host fluid. Periodic microstructures are shown to moderate the applied field due to magnetic interference between the adjacent teeth of an array. Since continuous microstructures do not similarly weaken the resultant HGMF, they facilitate significantly higher RBC separation. Nevertheless, periodic arrays are more appropriate for relatively deep microchannels since, unlike continuous microstructures, their separation effectiveness is independent of depth. The results are relevant to the design of microfluidic devices that leverage HGMFs to fractionate blood by separating RBCs and WBCs. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Magnetofluidic concentration and separation of non-magnetic particles using two magnet arrays

    PubMed Central

    Hejazian, Majid

    2016-01-01

    The present paper reports the use of diluted ferrofluid and two arrays of permanent magnets for the size-selective concentration of non-magnetic particles. The micro magnetofluidic device consists of a straight channels sandwiched between two arrays of permanent magnets. The permanent magnets create multiple capture zones with minimum magnetic field strength along the channel. The complex interaction between magnetic forces and hydrodynamic force allows the device to operate in different regimes suitable for concentration of non-magnetic particles with small difference in size. Our experimental results show that non-magnetic particles with diameters of 3.1 μm and 4.8 μm can be discriminated and separated with this method. The results from this study could be used as a guide for the design of size-sensitive separation devices for particle and cell based on negative magnetophoresis. PMID:27478527

  10. Tessellated permanent magnet circuits for flow-through, open gradient separations of weakly magnetic materials

    PubMed Central

    Moore, Lee R.; Williams, P. Stephen; Chalmers, Jeffrey J.; Zborowski, Maciej

    2017-01-01

    Emerging microfluidic-based cell assays favor label-free red blood cell (RBC) depletion. Magnetic separation of RBC is possible because of the paramagnetism of deoxygenated hemoglobin but the process is slow for open-gradient field configurations. In order to increase the throughput, periodic arrangements of the unit magnets were considered, consisting of commercially available Nd-Fe-B permanent magnets and soft steel flux return pieces. The magnet design is uniquely suitable for multiplexing by magnet tessellation, here meaning the tiling of the magnet assembly cross-sectional plane by periodic repetition of the magnet and the flow channel shapes. The periodic pattern of magnet magnetizations allows a reduction of the magnetic material per channel with minimal distortion of the field cylindrical symmetry inside the magnet apertures. A number of such magnet patterns are investigated for separator performance, size and economy with the goal of designing an open-gradient magnetic separator capable of reducing the RBC number concentration a hundred-fold in 1 mL whole blood per hour. PMID:29104346

  11. Microstructural observation of fuel cell catalyst inks by Cryo-SEM and Cryo-TEM.

    PubMed

    Shimanuki, Junichi; Takahashi, Shinichi; Tohma, Hajime; Ohma, Atsushi; Ishihara, Ayumi; Ito, Yoshiko; Nishino, Yuri; Miyazawa, Atsuo

    2017-06-01

    In order to improve the electricity generation performance of fuel cell electric vehicles, it is necessary to optimize the microstructure of the catalyst layer of a polymer electrolyte fuel cell. The catalyst layer is formed by a wet coating process using catalyst inks. Therefore, it is very important to observe the microstructure of the catalyst ink. In this study, the morphology of carbon-supported platinum (Pt/C) particles in catalyst inks with a different solvent composition was investigated by cryogenic scanning electron microscopy (cryo-SEM). In addition, the morphology of the ionomer, which presumably influences the formation of agglomerated Pt/C particles in a catalyst ink, was investigated by cryogenic transmission electron microscopy (cryo-TEM). The results of a cryo-SEM observation revealed that the agglomerated Pt/C particles tended to become coarser with a higher 1-propanol (NPA) weight fraction. The results of a cryo-TEM observation indicated that the actual ionomer dispersion in a catalyst ink formed a network structure different from that of the ionomer in the solvent. © The Author 2017. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Magnetic separation of coal fly ash from Bulgarian power plants.

    PubMed

    Shoumkova, Annie S

    2011-10-01

    Fly ash from three coal-burning power plants in Bulgaria: 'Maritza 3', 'Republika' and 'Rousse East' were subjected to wet low-intensity magnetic separation. The tests were performed at different combinations of magnetic field intensity, flow velocity and diameter of matrix elements. It was found that all parameters investigated affected the separation efficiency, but their influence was interlinked and was determined by the properties of the material and the combination of other conditions. Among the fly ash characteristics, the most important parameters, determining the magnetic separation applicability, were mineralogical composition and distribution of minerals in particles. The main factors limiting the process were the presence of paramagnetic Fe-containing mineral and amorphous matter, and the existence of poly-mineral particles and aggregates of magnetic and non-magnetic particles. It was demonstrated that the negative effect of both factors could be considerably limited by the selection of a proper set of separation conditions. The dependences between concentration of ferromagnetic iron in the ash, their magnetic properties and magnetic fraction yields were studied. It was experimentally proved that, for a certain set of separation conditions, the yields of magnetic fractions were directly proportional to the saturation magnetization of the ferromagnetic components of the ash. The main properties of typical magnetic and non-magnetic fractions were studied.

  13. ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

    PubMed Central

    ZHOU, Z. HONG

    2013-01-01

    Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

  14. Cryo-electron tomography of bacterial viruses

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Guerrero-Ferreira, Ricardo C.; Wright, Elizabeth R., E-mail: erwrigh@emory.edu

    2013-01-05

    Bacteriophage particles contain both simple and complex macromolecular assemblages and machines that enable them to regulate the infection process under diverse environmental conditions with a broad range of bacterial hosts. Recent developments in cryo-electron tomography (cryo-ET) make it possible to observe the interactions of bacteriophages with their host cells under native-state conditions at unprecedented resolution and in three-dimensions. This review describes the application of cryo-ET to studies of bacteriophage attachment, genome ejection, assembly and egress. Current topics of investigation and future directions in the field are also discussed.

  15. Agglomeration, colloidal stability, and magnetic separation of magnetic nanoparticles: collective influences on environmental engineering applications

    NASA Astrophysics Data System (ADS)

    Yeap, Swee Pin; Lim, JitKang; Ooi, Boon Seng; Ahmad, Abdul Latif

    2017-11-01

    Magnetic nanoparticles (MNPs) which exhibit magnetic and catalytic bifunctionalities have been widely accepted as one of the most promising nanoagents used in water purification processes. However, due to the magnetic dipole-dipole interaction, MNPs can easily lose their colloidal stability and tend to agglomerate. Thus, it is necessary to enhance their colloidal stability in order to maintain the desired high specific surface area. Meanwhile, in order to successfully utilize MNPs for environmental engineering applications, an effective magnetic separation technology has to be developed. This step is to ensure the MNPs that have been used for pollutant removal can be fully reharvested back. Unfortunately, it was recently highlighted that there exists a conflicting role between colloidal stability and magnetic separability of the MNPs, whereby the more colloidally stable the particle is, the harder for it to be magnetically separated. In other words, attaining a win-win scenario in which the MNPs possess both good colloidal stability and fast magnetic separation rate becomes challenging. Such phenomenon has to be thoroughly understood as the colloidal stability and the magnetic separability of MNPs play a pivotal role on affecting their effective implementation in water purification processes. Accordingly, it is the aim of this paper to provide reviews on (i) the colloidal stability and (ii) the magnetic separation of MNPs, as well as to provide insights on (iii) their conflicting relationship based on recent research findings. [Figure not available: see fulltext.

  16. An improved cryo-FIB method for fabrication of frozen hydrated lamella.

    PubMed

    Zhang, Jianguo; Ji, Gang; Huang, Xiaojun; Xu, Wei; Sun, Fei

    2016-05-01

    Cryo-electron tomography (cryo-ET) provides great insights into the ultrastructure of cells and tissues in their native state and provides a promising way to study the in situ 3D structures of macromolecular complexes. However, this technique has been limited on the very thin specimen, which is not applicable for most cells and tissues. Besides cryo-sectioning approach, cryo focused ion beam (cryo-FIB) appeared recently to achieve 'artifact-free' thin frozen hydrated lamella via fabrication. Considering that the current cryo-FIB methods need modified holders or cartridges, here, with a "D-shaped" molybdenum grid and a specific shutter system, we developed a simple cryo-FIB approach for thin frozen hydrated lamella fabrication, which fits both standard transmission cryo-electron microscopes with side-entry cryo-holders and state-of-the-art ones with AutoGrids. Our approach will expand the usage of cryo-FIB approach in many labs. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  17. Development of magnetic separation system of magnetoliposomes

    NASA Astrophysics Data System (ADS)

    Nakao, R.; Matuo, Y.; Mishima, F.; Taguchi, T.; Maenosono, S.; Nishijima, S.

    2009-10-01

    The magnetic separation technology using sub-microsized ferromagnetic particle is indispensable in many areas of medical biosciences. For example, ferromagnetic particles (200-500 nm) are widely used for cell sorting in stem cell research with the use of cell surface-specific antigens. Nanosized ferromagnetic particles (10-20 nm) have been suggested as more suitable in drug delivery studies given their efficiency of tissue penetration, however, the magnetic separation method for them has not been established. One of the major reasons is that magnetic force acting on the object particles decreases drastically as a particle diameter becomes small. In this study, magnetic force acting on the targets was enhanced by the combination of superconducting magnet and the filter consisting of ferromagnetic particle. By doing so, we confirmed that Fe 3O 4 of 20 nm in diameter was trapped in the magnetic filter under an external magnetic field of 0.5 T. Fe 3O 4 encapsulated with phospholipid liposomes of 200 nm in diameter was also shown to be trapped as external magnetic field of 1.5 T, but not of 0.5 T. We also showed the result of particle trajectory calculation which emulated well the experimental data.

  18. Multistage Magnetic Separator of Cells and Proteins

    NASA Technical Reports Server (NTRS)

    Barton, Ken; Ainsworth, Mark; Daily, Bruce; Dunn, Scott; Metz, Bill; Vellinger, John; Taylor, Brock; Meador, Bruce

    2005-01-01

    The multistage electromagnetic separator for purifying cells and magnetic particles (MAGSEP) is a laboratory apparatus for separating and/or purifying particles (especially biological cells) on the basis of their magnetic susceptibility and magnetophoretic mobility. Whereas a typical prior apparatus based on similar principles offers only a single stage of separation, the MAGSEP, as its full name indicates, offers multiple stages of separation; this makes it possible to refine a sample population of particles to a higher level of purity or to categorize multiple portions of the sample on the basis of magnetic susceptibility and/or magnetophoretic mobility. The MAGSEP includes a processing unit and an electronic unit coupled to a personal computer. The processing unit includes upper and lower plates, a plate-rotation system, an electromagnet, an electromagnet-translation system, and a capture-magnet assembly. The plates are bolted together through a roller bearing that allows the plates to rotate with respect to each other. An interface between the plates acts as a seal for separating fluids. A lower cuvette can be aligned with as many as 15 upper cuvette stations for fraction collection during processing. A two-phase stepping motor drives the rotation system, causing the upper plate to rotate for the collection of each fraction of the sample material. The electromagnet generates a magnetic field across the lower cuvette, while the translation system translates the electromagnet upward along the lower cuvette. The current supplied to the electromagnet, and thus the magnetic flux density at the pole face of the electromagnet, can be set at a programmed value between 0 and 1,400 gauss (0.14 T). The rate of translation can be programmed between 5 and 2,000 m/s so as to align all sample particles in the same position in the cuvette. The capture magnet can be a permanent magnet. It is mounted on an arm connected to a stepping motor. The stepping motor rotates the arm to

  19. Collection of Ni-bearing material from electroless plating waste by magnetic separation with HTS bulk magnet

    NASA Astrophysics Data System (ADS)

    Oka, T.; Fukazawa, H.; Fukui, S.; Ogawa, J.; Sato, T.; Ooizumi, M.; Tsujimura, M.; Yokoyama, K.

    2014-01-01

    The magnetic separation experiment to collect the Ni compounds from the waste liquid of electroless plating processes was conducted in the open-gradient magnetic separation process with the high temperature superconducting bulk magnet system. The magnetic pole containing Gd-based bulk superconductors was activated to 3.45 T at 35 K in the static magnetic field of 5 T with use of a superconducting solenoid magnet. The coarse Ni-sulfate crystals were formed by adding the concentrated sulfuric acid to the Ni-phosphite precipitates which yielded from the plating waste liquid by controlling the temperature and the pH value. The open-gradient magnetic separation technique was employed to separate the Ni-sulfate crystals from the mixture of the Ni-sulfate and Ni-phosphite compounds by the difference between their magnetic properties. And we succeeded in collecting Ni-sulfate crystals preferentially to the Ni-phosphite by attracting them to the magnetic pole soon after the Ni-sulfate crystals began to grow.

  20. CryoSat Plus For Oceans: an ESA Project for CryoSat-2 Data Exploitation Over Ocean

    NASA Astrophysics Data System (ADS)

    Benveniste, J.; Cotton, D.; Clarizia, M.; Roca, M.; Gommenginger, C. P.; Naeije, M. C.; Labroue, S.; Picot, N.; Fernandes, J.; Andersen, O. B.; Cancet, M.; Dinardo, S.; Lucas, B. M.

    2012-12-01

    The ESA CryoSat-2 mission is the first space mission to carry a space-borne radar altimeter that is able to operate in the conventional pulsewidth-limited (LRM) mode and in the novel Synthetic Aperture Radar (SAR) mode. Although the prime objective of the Cryosat-2 mission is dedicated to monitoring land and marine ice, the SAR mode capability of the Cryosat-2 SIRAL altimeter also presents the possibility of demonstrating significant potential benefits of SAR altimetry for ocean applications, based on expected performance enhancements which include improved range precision and finer along track spatial resolution. With this scope in mind, the "CryoSat Plus for Oceans" (CP4O) Project, dedicated to the exploitation of CryoSat-2 Data over ocean, supported by the ESA STSE (Support To Science Element) programme, brings together an expert European consortium comprising: DTU Space, isardSAT, National Oceanography Centre , Noveltis, SatOC, Starlab, TU Delft, the University of Porto and CLS (supported by CNES),. The objectives of CP4O are: - to build a sound scientific basis for new scientific and operational applications of Cryosat-2 data over the open ocean, polar ocean, coastal seas and for sea-floor mapping. - to generate and evaluate new methods and products that will enable the full exploitation of the capabilities of the Cryosat-2 SIRAL altimeter , and extend their application beyond the initial mission objectives. - to ensure that the scientific return of the Cryosat-2 mission is maximised. In particular four themes will be addressed: -Open Ocean Altimetry: Combining GOCE Geoid Model with CryoSat Oceanographic LRM Products for the retrieval of CryoSat MSS/MDT model over open ocean surfaces and for analysis of mesoscale and large scale prominent open ocean features. Under this priority the project will also foster the exploitation of the finer resolution and higher SNR of novel CryoSat SAR Data to detect short spatial scale open ocean features. -High Resolution Polar

  1. Rare Cell Separation and Analysis by Magnetic Sorting

    PubMed Central

    Zborowski, Maciej; Chalmers, Jeffrey J.

    2011-01-01

    Summary The separation and or isolation of rare cells using magnetic forces is commonly used and growing in use ranging from simple sample prep for further studies to a FDA approved, clinical diagnostic test. This grown is the result of both the demand to obtain homogeneous rare cells for molecular analysis and the dramatic increases in the power of permanent magnets that even allow the separation of some unlabeled cells based on intrinsic magnetic moments, such as malaria parasite-infected red blood cells. PMID:21812408

  2. Operational CryoSat Product Quality Assessment

    NASA Astrophysics Data System (ADS)

    Mannan, Rubinder; Webb, Erica; Hall, Amanda; Bouzinac, Catherine

    2013-12-01

    The performance and quality of the CryoSat data products are routinely assessed by the Instrument Data quality Evaluation and Analysis Service (IDEAS). This information is then conveyed to the scientific and user community in order to allow them to utilise CryoSat data with confidence. This paper presents details of the Quality Control (QC) activities performed for CryoSat products under the IDEAS contract. Details of the different QC procedures and tools deployed by IDEAS to assess the quality of operational data are presented. The latest updates to the Instrument Processing Facility (IPF) for the Fast Delivery Marine (FDM) products and the future update to Baseline-C are discussed.

  3. Feasibility of turbidity removal by high-gradient superconducting magnetic separation.

    PubMed

    Zeng, Hua; Li, Yiran; Xu, Fengyu; Jiang, Hao; Zhang, Weimin

    2015-01-01

    Several studies have focused on pollutant removal by magnetic seeding and high-gradient superconducting magnetic separation (HGSMS). However, few works reported the application of HGSMS for treating non-magnetic pollutants by an industrial large-scale system. The feasibility of turbidity removal by a 600 mm bore superconducting magnetic separation system was evaluated in this study. The processing parameters were evaluated by using a 102 mm bore superconducting magnetic separation system that was equipped with the same magnetic separation chamber that was used in the 600 mm bore system. The double-canister system was used to process water pollutants. Analytical grade magnetite was used as a magnetic seed and the turbidity of the simulated raw water was approximately 110 NTU, and the effects of polyaluminum chloride (PAC) and magnetic seeds on turbidity removal were evaluated. The use of more PAC and magnetic seeds had few advantages for the HGSMS at doses greater than 8 and 50 mg/l, respectively. A magnetic intensity of 5.0 T was beneficial for HGSMS, and increasing the flow rate through the steel wool matrix decreased the turbidity removal efficiency. In the breakthrough experiments, 90% of the turbidity was removed when 100 column volumes were not reached. The processing capacity of the 600 mm bore industry-scale superconducting magnetic separator for turbidity treatment was approximately 78.0 m(3)/h or 65.5 × 10(4) m(3)/a. The processing cost per ton of water for the 600 mm bore system was 0.1 $/t. Thus, the HGSMS separator could be used in the following special circumstances: (1) when adequate space is not available for traditional water treatment equipment, especially the sedimentation tank, and (2) when decentralized sewage treatment HGSMS systems are easier to transport and install.

  4. Rapid Characterization of Magnetic Moment of Cells for Magnetic Separation

    PubMed Central

    Ooi, Chinchun; Earhart, Christopher M.; Wilson, Robert J.; Wang, Shan X.

    2014-01-01

    NCI-H1650 lung cancer cell lines labeled with magnetic nanoparticles via the Epithelial Cell Adhesion Molecule (EpCAM) antigen were previously shown to be captured at high efficiencies by a microfabricated magnetic sifter. If fine control and optimization of the magnetic separation process is to be achieved, it is vital to be able to characterize the labeled cells’ magnetic moment rapidly. We have thus adapted a rapid prototyping method to obtain the saturation magnetic moment of these cells. This method utilizes a cross-correlation algorithm to analyze the cells’ motion in a simple fluidic channel to obtain their magnetophoretic velocity, and is effective even when the magnetic moments of cells are small. This rapid characterization is proven useful in optimizing our microfabricated magnetic sifter procedures for magnetic cell capture. PMID:24771946

  5. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    PubMed Central

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  6. The rate of separation of magnetic lines of force in a random magnetic field.

    NASA Technical Reports Server (NTRS)

    Jokipii, J. R.

    1973-01-01

    The mixing of magnetic lines of force, as represented by their rate of separation, as a function of distance along the magnetic field, is considered with emphasis on neighboring lines of force. This effect is particularly important in understanding the transport of charged particles perpendicular to the average magnetic field. The calculation is carried out in the approximation that the separation changes by an amount small compared with the correlation scale normal to the field, in a distance along the field of a few correlation scales. It is found that the rate of separation is very sensitive to the precise form of the power spectrum. Application to the interplanetary and interstellar magnetic fields is discussed, and it is shown that in some cases field lines, much closer together than the correlation scale, separate at a rate which is effectively as rapid as if they were many correlation lengths apart.

  7. Disaggregation and separation dynamics of magnetic particles in a microfluidic flow under an alternating gradient magnetic field

    NASA Astrophysics Data System (ADS)

    Cao, Quanliang; Li, Zhenhao; Wang, Zhen; Qi, Fan; Han, Xiaotao

    2018-05-01

    How to prevent particle aggregation in the magnetic separation process is of great importance for high-purity separation, while it is a challenging issue in practice. In this work, we report a novel method to solve this problem for improving the selectivity of size-based separation by use of a gradient alternating magnetic field. The specially designed magnetic field is capable of dynamically adjusting the magnetic field direction without changing the direction of magnetic gradient force acting on the particles. Using direct numerical simulations, we show that particles within a certain center-to-center distance are inseparable under a gradient static magnetic field since they are easy aggregated and then start moving together. By contrast, it has been demonstrated that alternating repulsive and attractive interaction forces between particles can be generated to avoid the formation of aggregations when the alternating gradient magnetic field with a given alternating frequency is applied, enabling these particles to be continuously separated based on size-dependent properties. The proposed magnetic separation method and simulation results have the significance for fundamental understanding of particle dynamic behavior and improving the separation efficiency.

  8. High-resolution structure of the Shigella type-III secretion needle by solid-state NMR and cryo-electron microscopy

    NASA Astrophysics Data System (ADS)

    Demers, Jean-Philippe; Habenstein, Birgit; Loquet, Antoine; Kumar Vasa, Suresh; Giller, Karin; Becker, Stefan; Baker, David; Lange, Adam; Sgourakis, Nikolaos G.

    2014-09-01

    We introduce a general hybrid approach for determining the structures of supramolecular assemblies. Cryo-electron microscopy (cryo-EM) data define the overall envelope of the assembly and rigid-body orientation of the subunits while solid-state nuclear magnetic resonance (ssNMR) chemical shifts and distance constraints define the local secondary structure, protein fold and inter-subunit interactions. Finally, Rosetta structure calculations provide a general framework to integrate the different sources of structural information. Combining a 7.7-Å cryo-EM density map and 996 ssNMR distance constraints, the structure of the type-III secretion system needle of Shigella flexneri is determined to a precision of 0.4 Å. The calculated structures are cross-validated using an independent data set of 691 ssNMR constraints and scanning transmission electron microscopy measurements. The hybrid model resolves the conformation of the non-conserved N terminus, which occupies a protrusion in the cryo-EM density, and reveals conserved pore residues forming a continuous pattern of electrostatic interactions, thereby suggesting a mechanism for effector protein translocation.

  9. Cryo-balloon catheter localization in fluoroscopic images

    NASA Astrophysics Data System (ADS)

    Kurzendorfer, Tanja; Brost, Alexander; Jakob, Carolin; Mewes, Philip W.; Bourier, Felix; Koch, Martin; Kurzidim, Klaus; Hornegger, Joachim; Strobel, Norbert

    2013-03-01

    Minimally invasive catheter ablation has become the preferred treatment option for atrial fibrillation. Although the standard ablation procedure involves ablation points set by radio-frequency catheters, cryo-balloon catheters have even been reported to be more advantageous in certain cases. As electro-anatomical mapping systems do not support cryo-balloon ablation procedures, X-ray guidance is needed. However, current methods to provide support for cryo-balloon catheters in fluoroscopically guided ablation procedures rely heavily on manual user interaction. To improve this, we propose a first method for automatic cryo-balloon catheter localization in fluoroscopic images based on a blob detection algorithm. Our method is evaluated on 24 clinical images from 17 patients. The method successfully detected the cryoballoon in 22 out of 24 images, yielding a success rate of 91.6 %. The successful localization achieved an accuracy of 1.00 mm +/- 0.44 mm. Even though our methods currently fails in 8.4 % of the images available, it still offers a significant improvement over manual methods. Furthermore, detecting a landmark point along the cryo-balloon catheter can be a very important step for additional post-processing operations.

  10. Magnetic separation techniques in sample preparation for biological analysis: a review.

    PubMed

    He, Jincan; Huang, Meiying; Wang, Dongmei; Zhang, Zhuomin; Li, Gongke

    2014-12-01

    Sample preparation is a fundamental and essential step in almost all the analytical procedures, especially for the analysis of complex samples like biological and environmental samples. In past decades, with advantages of superparamagnetic property, good biocompatibility and high binding capacity, functionalized magnetic materials have been widely applied in various processes of sample preparation for biological analysis. In this paper, the recent advancements of magnetic separation techniques based on magnetic materials in the field of sample preparation for biological analysis were reviewed. The strategy of magnetic separation techniques was summarized. The synthesis, stabilization and bio-functionalization of magnetic nanoparticles were reviewed in detail. Characterization of magnetic materials was also summarized. Moreover, the applications of magnetic separation techniques for the enrichment of protein, nucleic acid, cell, bioactive compound and immobilization of enzyme were described. Finally, the existed problems and possible trends of magnetic separation techniques for biological analysis in the future were proposed. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Separation of mixed waste plastics via magnetic levitation.

    PubMed

    Zhao, Peng; Xie, Jun; Gu, Fu; Sharmin, Nusrat; Hall, Philip; Fu, Jianzhong

    2018-06-01

    Separation becomes a bottleneck of dealing with the enormous stream of waste plastics, as most of the extant methods can only handle binary mixtures. In this paper, a novel method that based on magnetic levitation was proposed for separating multiple mixed plastics. Six types of plastics, i.e., polypropylene (PP), acrylonitrile butadiene styrene (ABS), polyamide 6 (PA6), polycarbonate (PC), polyethylene terephthalate (PET), and polytetrafluoroethylene (PTFE), were used to simulate the mixed waste plastics. The samples were mixed and immersed into paramagnetic medium that placed into a magnetic levitation configuration with two identical NdFeB magnets with like-poles facing each other, and Fourier transform infrared (FTIR) spectroscopy was employed to verify the separation outputs. Unlike any conventional separation methods such as froth flotation and hydrocyclone, this method is not limited by particle sizes, as mixtures of different size fractions reached their respective equilibrium positions in the initial tests. The two-stage separation tests demonstrated that the plastics can be completely separated with purities reached 100%. The method has the potential to be industrialised into an economically-viable and environmentally-friendly mass production procedure, since quantitative correlations are determined, and the paramagnetic medium can be reused indefinitely. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

    PubMed

    Zhang, Kaiming; Keane, Sarah C; Su, Zhaoming; Irobalieva, Rossitza N; Chen, Muyuan; Van, Verna; Sciandra, Carly A; Marchant, Jan; Heng, Xiao; Schmid, Michael F; Case, David A; Ludtke, Steven J; Summers, Michael F; Chiu, Wah

    2018-03-06

    Cryoelectron microscopy (cryo-EM) and nuclear magnetic resonance (NMR) spectroscopy are routinely used to determine structures of macromolecules with molecular weights over 65 and under 25 kDa, respectively. We combined these techniques to study a 30 kDa HIV-1 dimer initiation site RNA ([DIS] 2 ; 47 nt/strand). A 9 Å cryo-EM map clearly shows major groove features of the double helix and a right-handed superhelical twist. Simulated cryo-EM maps generated from time-averaged molecular dynamics trajectories (10 ns) exhibited levels of detail similar to those in the experimental maps, suggesting internal structural flexibility limits the cryo-EM resolution. Simultaneous inclusion of the cryo-EM map and 2 H-edited NMR-derived distance restraints during structure refinement generates a structure consistent with both datasets and supporting a flipped-out base within a conserved purine-rich bulge. Our findings demonstrate the power of combining global and local structural information from these techniques for structure determination of modest-sized RNAs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Exploiting Size-Dependent Drag and Magnetic Forces for Size-Specific Separation of Magnetic Nanoparticles

    PubMed Central

    Rogers, Hunter B.; Anani, Tareq; Choi, Young Suk; Beyers, Ronald J.; David, Allan E.

    2015-01-01

    Realizing the full potential of magnetic nanoparticles (MNPs) in nanomedicine requires the optimization of their physical and chemical properties. Elucidation of the effects of these properties on clinical diagnostic or therapeutic properties, however, requires the synthesis or purification of homogenous samples, which has proved to be difficult. While initial simulations indicated that size-selective separation could be achieved by flowing magnetic nanoparticles through a magnetic field, subsequent in vitro experiments were unable to reproduce the predicted results. Magnetic field-flow fractionation, however, was found to be an effective method for the separation of polydisperse suspensions of iron oxide nanoparticles with diameters greater than 20 nm. While similar methods have been used to separate magnetic nanoparticles before, no previous work has been done with magnetic nanoparticles between 20 and 200 nm. Both transmission electron microscopy (TEM) and dynamic light scattering (DLS) analysis were used to confirm the size of the MNPs. Further development of this work could lead to MNPs with the narrow size distributions necessary for their in vitro and in vivo optimization. PMID:26307980

  14. Real-Time MRI-Guided Cardiac Cryo-Ablation: A Feasibility Study.

    PubMed

    Kholmovski, Eugene G; Coulombe, Nicolas; Silvernagel, Joshua; Angel, Nathan; Parker, Dennis; Macleod, Rob; Marrouche, Nassir; Ranjan, Ravi

    2016-05-01

    MRI-based ablation provides an attractive capability of seeing ablation-related tissue changes in real time. Here we describe a real-time MRI-based cardiac cryo-ablation system. Studies were performed in canine model (n = 4) using MR-compatible cryo-ablation devices built for animal use: focal cryo-catheter with 8 mm tip and 28 mm diameter cryo-balloon. The main steps of MRI-guided cardiac cryo-ablation procedure (real-time navigation, confirmation of tip-tissue contact, confirmation of vessel occlusion, real-time monitoring of a freeze zone formation, and intra-procedural assessment of lesions) were validated in a 3 Tesla clinical MRI scanner. The MRI compatible cryo-devices were advanced to the right atrium (RA) and right ventricle (RV) and their position was confirmed by real-time MRI. Specifically, contact between catheter tip and myocardium and occlusion of superior vena cava (SVC) by the balloon was visually validated. Focal cryo-lesions were created in the RV septum. Circumferential ablation of SVC-RA junction with no gaps was achieved using the cryo-balloon. Real-time visualization of freeze zone formation was achieved in all studies when lesions were successfully created. The ablations and presence of collateral damage were confirmed by T1-weighted and late gadolinium enhancement MRI and gross pathological examination. This study confirms the feasibility of a MRI-based cryo-ablation system in performing cardiac ablation procedures. The system allows real-time catheter navigation, confirmation of catheter tip-tissue contact, validation of vessel occlusion by cryo-balloon, real-time monitoring of a freeze zone formation, and intra-procedural assessment of ablations including collateral damage. © 2016 Wiley Periodicals, Inc.

  15. Improving the technique of vitreous cryo-sectioning for cryo-electron tomography: electrostatic charging for section attachment and implementation of an anti-contamination glove box.

    PubMed

    Pierson, Jason; Fernández, José Jesús; Bos, Erik; Amini, Shoaib; Gnaegi, Helmut; Vos, Matthijn; Bel, Bennie; Adolfsen, Freek; Carrascosa, José L; Peters, Peter J

    2010-02-01

    Cryo-electron tomography of vitreous cryo-sections is the most suitable method for exploring the 3D organization of biological samples that are too large to be imaged in an intact state. Producing good quality vitreous cryo-sections, however, is challenging. Here, we focused on the major obstacles to success: contamination in and around the microtome, and attachment of the ribbon of sections to an electron microscopic grid support film. The conventional method for attaching sections to the grid has involved mechanical force generated by a crude stamping or pressing device, but this disrupts the integrity of vitreous cryo-sections. Furthermore, attachment is poor, and parts of the ribbon of sections are often far from the support film. This results in specimen instability during image acquisition and subsequent difficulty with aligning projection images. Here, we have implemented a protective glove box surrounding the cryo-ultramicrotome that reduces the humidity around and within the microtome during sectioning. We also introduce a novel way to attach vitreous cryo-sections to an EM grid support film using electrostatic charging. The ribbon of vitreous cryo-sections remains in place during transfer and storage and is devoid of stamping related artefacts. We illustrate these improvements by exploring the structure of putative cellular 80S ribosomes within 50nm, vitreous cryo-sections of Saccharomyces cerevisiae.

  16. Exploring an optimal wavelet-based filter for cryo-ET imaging.

    PubMed

    Huang, Xinrui; Li, Sha; Gao, Song

    2018-02-07

    Cryo-electron tomography (cryo-ET) is one of the most advanced technologies for the in situ visualization of molecular machines by producing three-dimensional (3D) biological structures. However, cryo-ET imaging has two serious disadvantages-low dose and low image contrast-which result in high-resolution information being obscured by noise and image quality being degraded, and this causes errors in biological interpretation. The purpose of this research is to explore an optimal wavelet denoising technique to reduce noise in cryo-ET images. We perform tests using simulation data and design a filter using the optimum selected wavelet parameters (three-level decomposition, level-1 zeroed out, subband-dependent threshold, a soft-thresholding and spline-based discrete dyadic wavelet transform (DDWT)), which we call a modified wavelet shrinkage filter; this filter is suitable for noisy cryo-ET data. When testing using real cryo-ET experiment data, higher quality images and more accurate measures of a biological structure can be obtained with the modified wavelet shrinkage filter processing compared with conventional processing. Because the proposed method provides an inherent advantage when dealing with cryo-ET images, it can therefore extend the current state-of-the-art technology in assisting all aspects of cryo-ET studies: visualization, reconstruction, structural analysis, and interpretation.

  17. Novel platform for minimizing cell loss on separation process: Droplet-based magnetically activated cell separator

    NASA Astrophysics Data System (ADS)

    Kim, Youngho; Hong, Su; Lee, Sang Ho; Lee, Kangsun; Yun, Seok; Kang, Yuri; Paek, Kyeong-Kap; Ju, Byeong-Kwon; Kim, Byungkyu

    2007-07-01

    To reduce the problem of cell loss due to adhesion, one of the basic phenomena in microchannel, we proposed the droplet-based magnetically activated cell separator (DMACS). Based on the platform of the DMACS—which consists of permanent magnets, a coverslip with a circle-shaped boundary, and an injection tube—we could collect magnetically (CD45)-labeled (positive) cells with high purity and minimize cell loss due to adhesion. To compare separation efficiency between the MACS and the DMACS, the total number of cells before and after separation with both the separators was counted by flow cytometry. We could find that the number (3241/59940) of cells lost in the DMACS is much less than that (22360/59940) in the MACS while the efficiency of cell separation in the DMACS (96.07%) is almost the same as that in the MACS (96.72%). Practically, with fluorescent images, it was visually confirmed that the statistical data are reliable. From the viability test by using Hoechst 33 342, it was also demonstrated that there was no cell damage on a gas-liquid interface. Conclusively, DMACS will be a powerful tool to separate rare cells and applicable as a separator, key component of lab-on-a-chip.

  18. Low-cost cryo-light microscopy stage fabrication for correlated light/electron microscopy.

    PubMed

    Carlson, David B; Evans, James E

    2011-06-05

    The coupling of cryo-light microscopy (cryo-LM) and cryo-electron microscopy (cryo-EM) poses a number of advantages for understanding cellular dynamics and ultrastructure. First, cells can be imaged in a near native environment for both techniques. Second, due to the vitrification process, samples are preserved by rapid physical immobilization rather than slow chemical fixation. Third, imaging the same sample with both cryo-LM and cryo-EM provides correlation of data from a single cell, rather than a comparison of "representative samples". While these benefits are well known from prior studies, the widespread use of correlative cryo-LM and cryo-EM remains limited due to the expense and complexity of buying or building a suitable cryogenic light microscopy stage. Here we demonstrate the assembly, and use of an inexpensive cryogenic stage that can be fabricated in any lab for less than $40 with parts found at local hardware and grocery stores. This cryo-LM stage is designed for use with reflected light microscopes that are fitted with long working distance air objectives. For correlative cryo-LM and cryo-EM studies, we adapt the use of carbon coated standard 3-mm cryo-EM grids as specimen supports. After adsorbing the sample to the grid, previously established protocols for vitrifying the sample and transferring/handling the grid are followed to permit multi-technique imaging. As a result, this setup allows any laboratory with a reflected light microscope to have access to direct correlative imaging of frozen hydrated samples.

  19. Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.

    PubMed

    Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy; He, Jing

    2017-01-01

    Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.

  20. Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix

    PubMed Central

    Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy

    2017-01-01

    Abstract Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4–7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map–model pairs. PMID:27936925

  1. Experimental cryo-irrigation of the knee joint.

    PubMed

    Chen, S C; Helal, B; Revell, P A; Brocklehurst, R; Currey, H L

    1986-10-01

    Experiments have been carried out to test the feasibility of using cryo-irrigation as a means of ablating the synovium in the rheumatoid knee joint. Cryo-irrigation was performed by a cooling machine and pump, which circulated cold 200/10 centistoke (cSt) silicone through the knee joint of rabbits anaesthetised with intravenous (IV) 'Saffan'. Fluid left the joint at -5 to -10 degrees C. Sixteen normal New Zealand rabbits received cryo-irrigation of one knee joint for 10-20 minutes and were killed at one day, and one, two, and 12 weeks thereafter. Judged by radioactive sulphate incorporation there was no impairment of chondrocyte function in the articular cartilage of irrigated joints. Histological examination showed mild synovitis and some loss of staining of superficial cartilage in 6/16 irrigated joints (v 1/16 control joints). Similar treatment of rabbit joints in which the Glynn model of synovitis had been induced showed marked reduction of synovitis 14-45 days after silicone treatment. Nine of 26 animals in which synovitis was induced in both knees and cryo-irrigation performed in one knee died either immediately postoperatively or during the next week. These deaths remain unexplained. A single dog received cryo-irrigation of one knee (-6 to -9 degrees C for 22 min) and remained perfectly well up to sacrifice at six months, when the joint appeared histologically completely normal.

  2. Laser-Induced Skyrmion Writing and Erasing in an Ultrafast Cryo-Lorentz Transmission Electron Microscope

    NASA Astrophysics Data System (ADS)

    Berruto, G.; Madan, I.; Murooka, Y.; Vanacore, G. M.; Pomarico, E.; Rajeswari, J.; Lamb, R.; Huang, P.; Kruchkov, A. J.; Togawa, Y.; LaGrange, T.; McGrouther, D.; Rønnow, H. M.; Carbone, F.

    2018-03-01

    We demonstrate that light-induced heat pulses of different duration and energy can write Skyrmions in a broad range of temperatures and magnetic field in FeGe. Using a combination of camera-rate and pump-probe cryo-Lorentz transmission electron microscopy, we directly resolve the spatiotemporal evolution of the magnetization ensuing optical excitation. The Skyrmion lattice was found to maintain its structural properties during the laser-induced demagnetization, and its recovery to the initial state happened in the sub-μ s to μ s range, depending on the cooling rate of the system.

  3. Magnetic resonance separation imaging using a divided inversion recovery technique (DIRT).

    PubMed

    Goldfarb, James W

    2010-04-01

    The divided inversion recovery technique is an MRI separation method based on tissue T(1) relaxation differences. When tissue T(1) relaxation times are longer than the time between inversion pulses in a segmented inversion recovery pulse sequence, longitudinal magnetization does not pass through the null point. Prior to additional inversion pulses, longitudinal magnetization may have an opposite polarity. Spatial displacement of tissues in inversion recovery balanced steady-state free-precession imaging has been shown to be due to this magnetization phase change resulting from incomplete magnetization recovery. In this paper, it is shown how this phase change can be used to provide image separation. A pulse sequence parameter, the time between inversion pulses (T180), can be adjusted to provide water-fat or fluid separation. Example water-fat and fluid separation images of the head, heart, and abdomen are presented. The water-fat separation performance was investigated by comparing image intensities in short-axis divided inversion recovery technique images of the heart. Fat, blood, and fluid signal was suppressed to the background noise level. Additionally, the separation performance was not affected by main magnetic field inhomogeneities.

  4. Magnetic separation of algae genetically modified for increased intracellular iron uptake

    NASA Astrophysics Data System (ADS)

    Buck, Amy; Moore, Lee R.; Lane, Christopher D.; Kumar, Anil; Stroff, Clayton; White, Nicolas; Xue, Wei; Chalmers, Jeffrey J.; Zborowski, Maciej

    2015-04-01

    Algae were investigated in the past as a potential source of biofuel and other useful chemical derivatives. Magnetic separation of algae by iron oxide nanoparticle binding to cells has been proposed by others for dewatering of cellular mass prior to lipid extraction. We have investigated feasibility of magnetic separation based on the presence of natural iron stores in the cell, such as the ferritin in Auxenochlorella protothecoides (A. protothecoides) strains. The A. protothecoides cell constructs were tested for inserted genes and for increased intracellular iron concentration by inductively coupled plasma atomic absorption (ICP-AA). They were grown in Sueoka's modified high salt media with added vitamin B1 and increasing concentration of soluble iron compound (FeCl3 EDTA, from 1× to 8× compared to baseline). The cell magnetic separation conditions were tested using a thin rectangular flow channel pressed against interpolar gaps of a permanent magnet forming a separation system of a well-defined fluid flow and magnetic fringing field geometry (up to 2.2 T and 1000 T/m) dubbed "magnetic deposition microscopy", or MDM. The presence of magnetic cells in suspension was detected by formation of characteristic deposition bands at the edges of the magnet interpolar gaps, amenable to optical scanning and microscopic examination. The results demonstrated increasing cellular Fe uptake with increasing Fe concentration in the culture media in wild type strain and in selected genetically-modified constructs, leading to magnetic separation without magnetic particle binding. The throughput in this study is not sufficient for an economical scale harvest.

  5. Magnetic separation of algae genetically modified for increased intracellular iron uptake.

    PubMed

    Buck, Amy; Moore, Lee R; Lane, Christopher D; Kumar, Anil; Stroff, Clayton; White, Nicolas; Xue, Wei; Chalmers, Jeffrey J; Zborowski, Maciej

    2015-04-15

    Algae were investigated in the past as a potential source of biofuel and other useful chemical derivatives. Magnetic separation of algae by iron oxide nanoparticle binding to cells has been proposed by others for dewatering of cellular mass prior to lipid extraction. We have investigated feasibility of magnetic separation based on the presence of natural iron stores in the cell, such as the ferritin in Auxenochlorella protothecoides ( A. p. ) strains. The A. p. cell constructs were tested for inserted genes and for increased intracellular iron concentration by inductively coupled plasma atomic absorption (ICP-AA). They were grown in Sueoka's modified high salt media with added vitamin B1 and increasing concentration of soluble iron compound (FeCl 3 EDTA, from 1× to 8× compared to baseline). The cell magnetic separation conditions were tested using a thin rectangular flow channel pressed against interpolar gaps of a permanent magnet forming a separation system of a well-defined fluid flow and magnetic fringing field geometry (up to 2.2 T and 1,000 T/m) dubbed "magnetic deposition microscopy", or MDM. The presence of magnetic cells in suspension was detected by formation of characteristic deposition bands at the edges of the magnet interpolar gaps, amenable to optical scanning and microscopic examination. The results demonstrated increasing cellular Fe uptake with increasing Fe concentration in the culture media in wild type strain and in selected genetically-modified constructs, leading to magnetic separation without magnetic particle binding. The throughput in this study is not sufficient for an economical scale harvest.

  6. Magnetic separation of algae genetically modified for increased intracellular iron uptake

    PubMed Central

    Buck, Amy; Moore, Lee R.; Lane, Christopher D.; Kumar, Anil; Stroff, Clayton; White, Nicolas; Xue, Wei; Chalmers, Jeffrey J.; Zborowski, Maciej

    2017-01-01

    Algae were investigated in the past as a potential source of biofuel and other useful chemical derivatives. Magnetic separation of algae by iron oxide nanoparticle binding to cells has been proposed by others for dewatering of cellular mass prior to lipid extraction. We have investigated feasibility of magnetic separation based on the presence of natural iron stores in the cell, such as the ferritin in Auxenochlorella protothecoides (A. p.) strains. The A. p. cell constructs were tested for inserted genes and for increased intracellular iron concentration by inductively coupled plasma atomic absorption (ICP-AA). They were grown in Sueoka's modified high salt media with added vitamin B1 and increasing concentration of soluble iron compound (FeCl3 EDTA, from 1× to 8× compared to baseline). The cell magnetic separation conditions were tested using a thin rectangular flow channel pressed against interpolar gaps of a permanent magnet forming a separation system of a well-defined fluid flow and magnetic fringing field geometry (up to 2.2 T and 1,000 T/m) dubbed “magnetic deposition microscopy”, or MDM. The presence of magnetic cells in suspension was detected by formation of characteristic deposition bands at the edges of the magnet interpolar gaps, amenable to optical scanning and microscopic examination. The results demonstrated increasing cellular Fe uptake with increasing Fe concentration in the culture media in wild type strain and in selected genetically-modified constructs, leading to magnetic separation without magnetic particle binding. The throughput in this study is not sufficient for an economical scale harvest. PMID:29353957

  7. An Open-Source Storage Solution for Cryo-Electron Microscopy Samples.

    PubMed

    Ultee, Eveline; Schenkel, Fred; Yang, Wen; Brenzinger, Susanne; Depelteau, Jamie S; Briegel, Ariane

    2018-02-01

    Cryo-electron microscopy (cryo-EM) enables the study of biological structures in situ in great detail and to solve protein structures at Ångstrom level resolution. Due to recent advances in instrumentation and data processing, the field of cryo-EM is a rapidly growing. Access to facilities and national centers that house the state-of-the-art microscopes is limited due to the ever-rising demand, resulting in long wait times between sample preparation and data acquisition. To improve sample storage, we have developed a cryo-storage system with an efficient, high storage capacity that enables sample storage in a highly organized manner. This system is simple to use, cost-effective and easily adaptable for any type of grid storage box and dewar and any size cryo-EM laboratory.

  8. Peptide inhibitor modified magnetic particles for pepsin separation.

    PubMed

    Filuszová, Michaela; Kucerová, Zdenka; Tichá, Marie

    2009-06-01

    Synthetic heptapeptide containing D-amino acid residues (Val-D-Leu-Pro-Phe-Phe-Val-D-Leu) was coupled to glyoxal-activated magnetic agarose particles via the free peptide amino group. The peptide-modified magnetic particles were used for the separation of pepsins. Porcine pepsin A and human pepsin A were adsorbed to the magnetic peptide-modified affinity carrier, while the rat pepsin C and human pepsin C did not interact with the immobilized ligand. Conditions of pepsin adsorption to peptide-modified magnetic particles, as well as elution buffers were optimized. Porcine pepsin A did not interact with the immobilized peptide in the presence of pepsin inhibitor pepstatin A, indicating that the enzyme binding site is involved in the studied interaction. The elaborated method represents a rapid and simple technique not only for the separation of pepsins but also, in combination with MS, for the enzyme detection and determination.

  9. Magnetic separation: its application in mining, waste purification, medicine, biochemistry and chemistry.

    PubMed

    Iranmanesh, M; Hulliger, J

    2017-10-02

    The use of strong magnetic field gradients and high magnetic fields generated by permanent magnets or superconducting coils has found applications in many fields such as mining, solid state chemistry, biochemistry and medical research. Lab scale or industrial implementations involve separation of macro- and nanoparticles, cells, proteins, and macromolecules down to small molecules and ions. Most promising are those attempts where the object to be separated is attached to a strong magnetic nanoparticle. Here, all kinds of specific affinity interactions are used to attach magnetic carrier particles to mainly objects of biological interest. Other attempts use a strong paramagnetic suspension for the separation of purely diamagnetic objects, such as bio-macromolecules or heavy metals. The application of magnetic separation to superconducting inorganic phases is of particular interest in combination with ceramic combinatorial chemistry to generate a library of e.g. cuprate superconductors.

  10. Correlated fluorescence microscopy and cryo-electron tomography of virus-infected or transfected mammalian cells

    PubMed Central

    Hampton, Cheri M; Strauss, Joshua D; Ke, Zunlong; Dillard, Rebecca S; Hammonds, Jason E; Alonas, Eric; Desai, Tanay M; Marin, Mariana; Storms, Rachel E; Leon, Fredrick; Melikyan, Gregory B; Santangelo, Philip J; Spearman, Paul W; Wright, Elizabeth R

    2016-01-01

    Correlative light and electron microscopy (CLEM) combines spatiotemporal information from fluorescence light microscopy (fLM) with high-resolution structural data from cryo-electron tomography (cryo-ET). These technologies provide opportunities to bridge knowledge gaps between cell and structural biology. Here we describe our protocol for correlated cryo-fLM, cryo-electron microscopy (cryo-EM), and cryo-ET (i.e., cryo-CLEM) of virus-infected or transfected mammalian cells. Mammalian-derived cells are cultured on EM substrates, using optimized conditions that ensure that the cells are spread thinly across the substrate and are not physically disrupted. The cells are then screened by fLM and vitrified before acquisition of cryo-fLM and cryo-ET images, which is followed by data processing. A complete session from grid preparation through data collection and processing takes 5–15 d for an individual experienced in cryo-EM. PMID:27977021

  11. Microfluidic separation of magnetic nanoparticles on an ordered array of magnetized micropillars

    NASA Astrophysics Data System (ADS)

    Orlandi, G.; Kuzhir, P.; Izmaylov, Y.; Alves Marins, J.; Ezzaier, H.; Robert, L.; Doutre, F.; Noblin, X.; Lomenech, C.; Bossis, G.; Meunier, A.; Sandoz, G.; Zubarev, A.

    2016-06-01

    Microfluidic separation of magnetic particles is based on their capture by magnetized microcollectors while the suspending fluid flows past the microcollectors inside a microchannel. Separation of nanoparticles is often challenging because of strong Brownian motion. Low capture efficiency of nanoparticles limits their applications in bioanalysis. However, at some conditions, magnetic nanoparticles may undergo field-induced aggregation that amplifies the magnetic attractive force proportionally to the aggregate volume and considerably increases nanoparticle capture efficiency. In this paper, we have demonstrated the role of such aggregation on an efficient capture of magnetic nanoparticles (about 80 nm in diameter) in a microfluidic channel equipped with a nickel micropillar array. This array was magnetized by an external uniform magnetic field, of intensity as low as 6-10 kA/m, and experiments were carried out at flow rates ranging between 0.3 and 30 μ L /min . Nanoparticle capture is shown to be mostly governed by the Mason number Ma, while the dipolar coupling parameter α does not exhibit a clear effect in the studied range, 1.4 < α < 4.5. The capture efficiency Λ shows a strongly decreasing Mason number behavior, Λ ∝M a-1.78 within the range 32 ≤ Ma ≤ 3250. We have proposed a simple theoretical model which considers destructible nanoparticle chains and gives the scaling behavior, Λ ∝M a-1.7 , close to the experimental findings.

  12. Magnetic separator having a multilayer matrix, method and apparatus

    DOEpatents

    Kelland, David R.

    1980-01-01

    A magnetic separator having multiple staggered layers of porous magnetic material positioned to intercept a fluid stream carrying magnetic particles and so placed that a bypass of each layer is effected as the pores of the layer become filled with material extracted from the fluid stream.

  13. Processing of Cryo-EM Movie Data.

    PubMed

    Ripstein, Z A; Rubinstein, J L

    2016-01-01

    Direct detector device (DDD) cameras dramatically enhance the capabilities of electron cryomicroscopy (cryo-EM) due to their improved detective quantum efficiency (DQE) relative to other detectors. DDDs use semiconductor technology that allows micrographs to be recorded as movies rather than integrated individual exposures. Movies from DDDs improve cryo-EM in another, more surprising, way. DDD movies revealed beam-induced specimen movement as a major source of image degradation and provide a way to partially correct the problem by aligning frames or regions of frames to account for this specimen movement. In this chapter, we use a self-consistent mathematical notation to explain, compare, and contrast several of the most popular existing algorithms for computationally correcting specimen movement in DDD movies. We conclude by discussing future developments in algorithms for processing DDD movies that would extend the capabilities of cryo-EM even further. © 2016 Elsevier Inc. All rights reserved.

  14. Model-based local density sharpening of cryo-EM maps

    PubMed Central

    Jakobi, Arjen J; Wilmanns, Matthias

    2017-01-01

    Atomic models based on high-resolution density maps are the ultimate result of the cryo-EM structure determination process. Here, we introduce a general procedure for local sharpening of cryo-EM density maps based on prior knowledge of an atomic reference structure. The procedure optimizes contrast of cryo-EM densities by amplitude scaling against the radially averaged local falloff estimated from a windowed reference model. By testing the procedure using six cryo-EM structures of TRPV1, β-galactosidase, γ-secretase, ribosome-EF-Tu complex, 20S proteasome and RNA polymerase III, we illustrate how local sharpening can increase interpretability of density maps in particular in cases of resolution variation and facilitates model building and atomic model refinement. PMID:29058676

  15. Cryo-EM in drug discovery: achievements, limitations and prospects.

    PubMed

    Renaud, Jean-Paul; Chari, Ashwin; Ciferri, Claudio; Liu, Wen-Ti; Rémigy, Hervé-William; Stark, Holger; Wiesmann, Christian

    2018-06-08

    Cryo-electron microscopy (cryo-EM) of non-crystalline single particles is a biophysical technique that can be used to determine the structure of biological macromolecules and assemblies. Historically, its potential for application in drug discovery has been heavily limited by two issues: the minimum size of the structures it can be used to study and the resolution of the images. However, recent technological advances - including the development of direct electron detectors and more effective computational image analysis techniques - are revolutionizing the utility of cryo-EM, leading to a burst of high-resolution structures of large macromolecular assemblies. These advances have raised hopes that single-particle cryo-EM might soon become an important tool for drug discovery, particularly if they could enable structural determination for 'intractable' targets that are still not accessible to X-ray crystallographic analysis. This article describes the recent advances in the field and critically assesses their relevance for drug discovery as well as discussing at what stages of the drug discovery pipeline cryo-EM can be useful today and what to expect in the near future.

  16. Chiral magnetic microspheres purified by centrifugal field flow fractionation and microspheres magnetic chiral chromatography for benzoin racemate separation

    PubMed Central

    Tian, Ailin; Qi, Jing; Liu, Yating; Wang, Fengkang; Ito, Yoichiro; Wei, Yun

    2013-01-01

    Separation of enantiomers still remains a challenge due to their identical physical and chemical properties in a chiral environment, and the research on specific chiral selector along with separation techniques continues to be conducted to resolve individual enantiomers. In our laboratory the promising magnetic chiral microspheres Fe3O4@SiO2@cellulose-2, 3-bis (3, 5-dimethylphenylcarbamate) have been developed to facilitate the resolution using both its magnetic property and chiral recognition ability. In our present studies this magnetic chiral selector was first purified by centrifuge field flow fractionation, and then used to separate benzoin racemate by a chromatographic method. Uniform-sized and masking-impurity-removed magnetic chiral selector was first obtained by field flow fractionation with ethanol through a spiral column mounted on the type-J planetary centrifuge, and using the purified magnetic chiral selector, the final chromatographic separation of benzoin racemate was successfully performed by eluting with ethanol through a coiled tube (wound around the cylindrical magnet to retain the magnetic chiral selector as a stationary phase) submerged in dry ice. In addition, an external magnetic field facilitates the recycling of the magnetic chiral selector. PMID:23891368

  17. Chiral magnetic microspheres purified by centrifugal field flow fractionation and microspheres magnetic chiral chromatography for benzoin racemate separation.

    PubMed

    Tian, Ailin; Qi, Jing; Liu, Yating; Wang, Fengkang; Ito, Yoichiro; Wei, Yun

    2013-08-30

    Separation of enantiomers still remains a challenge due to their identical physical and chemical properties in a chiral environment, and the research on specific chiral selector along with separation techniques continues to be conducted to resolve individual enantiomers. In our laboratory the promising magnetic chiral microspheres Fe3O4@SiO2@cellulose-2, 3-bis (3,5-dimethylphenylcarbamate) have been developed to facilitate the resolution using both its magnetic property and chiral recognition ability. In our present studies this magnetic chiral selector was first purified by centrifuge field flow fractionation, and then used to separate benzoin racemate by a chromatographic method. Uniform-sized and masking-impurity-removed magnetic chiral selector was first obtained by field flow fractionation with ethanol through a spiral column mounted on the type-J planetary centrifuge, and using the purified magnetic chiral selector, the final chromatographic separation of benzoin racemate was successfully performed by eluting with ethanol through a coiled tube (wound around the cylindrical magnet to retain the magnetic chiral selector as a stationary phase) submerged in dry ice. In addition, an external magnetic field facilitates the recycling of the magnetic chiral selector. Copyright © 2013 Elsevier B.V. All rights reserved.

  18. Vapor-liquid phase separator studies

    NASA Technical Reports Server (NTRS)

    Yuan, S. W. K.; Lee, J. M.; Kim, Y. I.; Hepler, W. A.; Frederking, T. H. K.

    1983-01-01

    Porous plugs serve as both entropy rejection devices and phase separation components separating the vapor phase on the downstream side from liquid Helium 2 upstream. The liquid upstream is the cryo-reservoir fluid needed for equipment cooling by means of Helium 2, i.e Helium-4 below its lambda temperature in near-saturated states. The topics outlined are characteristic lengths, transport equations and plug results.

  19. Magnetic filtration of phase separating ferrofluids: From basic concepts to microfluidic device

    NASA Astrophysics Data System (ADS)

    Kuzhir, P.; Magnet, C.; Ezzaier, H.; Zubarev, A.; Bossis, G.

    2017-06-01

    In this work, we briefly review magnetic separation of ferrofluids composed of large magnetic particles (60 nm of the average size) possessing an induced dipole moment. Such ferrofluids exhibit field-induced phase separation at relatively low particle concentrations (∼0.8 vol%) and magnetic fields (∼10 kA/m). Particle aggregates appearing during the phase separation are extracted from the suspending fluid by magnetic field gradients much easier than individual nanoparticles in the absence of phase separation. Nanoparticle capture by a single magnetized microbead and by multi-collector systems (packed bed of spheres and micro-pillar array) has been studied both experimentally and theoretically. Under flow and magnetic fields, the particle capture efficiency Λ decreases with an increasing Mason number for all considered geometries. This decrease may become stronger for aggregated magnetic particles (Λ ∝Ma-1.7) than for individual ones (Λ ∝Ma-1) if the shear fields are strong enough to provoke aggregate rupture. These results can be useful for development of new magneto-microfluidic immunoassays based on magnetic nanoparticles offering a much better sensitivity as compared to presently used magnetic microbeads.

  20. Launch and Early Orbit Operations for CryoSat-2

    NASA Astrophysics Data System (ADS)

    Mardel, Nic; Marchese, Franco

    2010-12-01

    CryoSat-2 was launched from Baikonur on 8th of April 2010 aboard a modified Dnepr ICBM, the so-called SS18 Satan. Following the ascent and separation from the launch vehicle the Flight Operations Segment (FOS) in ESOC, Darmstadt started the operations to configure the satellite into the correct mode to acquire science; switching on units, configuring software and ensuring that the satellite health and performance was as expected. This paper will describe the operations performed by the FOS during the first weeks in orbit, including the unexpected problems encountered, their implications and solutions.

  1. Magnetic Separator Enhances Treatment Possibilities

    NASA Technical Reports Server (NTRS)

    2008-01-01

    Since the earliest missions in space, NASA specialists have performed experiments in low gravity. Protein crystal growth, cell and tissue cultures, and separation technologies such as electrophoresis and magnetophoresis have been studied on Apollo 14, Apollo 16, STS-107, and many other missions. Electrophoresis and magnetophoresis, respectively, are processes that separate substances based on the electrical charge and magnetic field of a molecule or particle. Electrophoresis has been studied on over a dozen space shuttle flights, leading to developments in electrokinetics, which analyzes the effects of electric fields on mass transport (atoms, molecules, and particles) in fluids. Further studies in microgravity will continue to improve these techniques, which researchers use to extract cells for various medical treatments and research.

  2. On-chip free-flow magnetophoresis: continuous flow separation of magnetic particles and agglomerates.

    PubMed

    Pamme, Nicole; Manz, Andreas

    2004-12-15

    The separation of magnetic microparticles was achieved by on-chip free-flow magnetophoresis. In continuous flow, magnetic particles were deflected from the direction of laminar flow by a perpendicular magnetic field depending on their magnetic susceptibility and size and on the flow rate. Magnetic particles could thus be separated from each other and from nonmagnetic materials. Magnetic and nonmagnetic particles were introduced into a microfluidic separation chamber, and their deflection was studied under the microscope. The magnetic particles were 2.0 and 4.5 microm in diameter with magnetic susceptibilities of 1.12 x 10(-4) and 1.6 x 10(-4) m(3) kg(-1), respectively. The 4.5-microm particles with the larger susceptibility were deflected further from the direction of laminar flow than the 2.0-microm magnetic particles. Nonmagnetic 6-microm polystyrene beads, however, were not deflected at all. Furthermore, agglomerates of magnetic particles were found to be deflected to a larger extent than single magnetic particles. The applied flow rate and the strength and gradient of the applied magnetic field were the key parameters in controlling the deflection. This separation method has a wide applicability since magnetic particles are commonly used in bioanalysis as a solid support material for antigens, antibodies, DNA, and even cells. Free-flow magnetophoretic separations could be hyphenated with other microfluidic devices for reaction and analysis steps to form a micro total analysis system.

  3. Continuous Changes in Structure Mapped by Manifold Embedding of Single-Particle Data in Cryo-EM

    PubMed Central

    Fran, Joachim; Ourmazd, Abbas

    2016-01-01

    Cryo-electron microscopy, when combined with single-particle reconstruction, is a powerful method for studying macromolecular structure. Recent developments in detector technology have pushed the resolution into a range comparable to that of X-ray crystallography. However, cryo-EM is able to separate and thus recover the structure of each of several discrete structures present in the sample. For the more general case involving continuous structural changes, a novel technique employing manifold embedding has been recently demonstrated. Potentially, the entire work-cycle of a molecular machine may be observed as it passes through a continuum of states, and its free-energy landscape may be mapped out. This technique will be outlined and discussed in the context of its application to a large single-particle dataset of yeast ribosomes. PMID:26884261

  4. Cryo-EM visualization of the protein machine that replicates the chromosome

    NASA Astrophysics Data System (ADS)

    Li, Huilin

    Structural knowledge is key to understanding biological functions. Cryo-EM is a physical method that uses transmission electron microscopy to visualize biological molecules that are frozen in vitreous ice. Due to recent advances in direct electron detector and image processing algorithm, cryo-EM has become a high-resolution technique. Cryo-EM field is undergoing a rapid expansion and vast majority research institutions and research universities around the world are setting up cryo-EM research. Indeed, the method is revolutionizing structural and molecular biology. We have been using cryo-EM to study the structure and mechanism of eukaryotic chromosome replication. Despite an abundance of cartoon drawings found in review articles and biology textbooks, the structure of the eukaryotic helicase that unwinds the double stranded DNA has been unknown. It has also been unknown how the helicase works with DNA polymerases to accomplish the feat of duplicating the genome. In my presentation, I will show how we have used cryo-EM to derive at structures of the eukaryotic chromosome replication machinery and describe mechanistic insights we have gleaned from the structures.

  5. A simple cryo-holder facilitates specimen observation under a conventional scanning electron microscope.

    PubMed

    Tang, Chih-Yuan; Huang, Rong-Nan; Kuo-Huang, Ling-Long; Kuo, Tai-Chih; Yang, Ya-Yun; Lin, Ching-Yeh; Jane, Wann-Neng; Chen, Shiang-Jiuun

    2012-02-01

    A pre-cryogenic holder (cryo-holder) facilitating cryo-specimen observation under a conventional scanning electron microscope (SEM) is described. This cryo-holder includes a specimen-holding unit (the stub) and a cryogenic energy-storing unit (a composite of three cylinders assembled with a screw). After cooling, the cryo-holder can continue supplying cryogenic energy to extend the observation time for the specimen in a conventional SEM. Moreover, the cryogenic energy-storing unit could retain appropriate liquid nitrogen that can evaporate to prevent frost deposition on the surface of the specimen. This device is proved feasible for various tissues and cells, and can be applied to the fields of both biology and material science. We have employed this novel cryo-holder for observation of yeast cells, trichome, and epidermal cells in the leaf of Arabidopsis thaliana, compound eyes of insects, red blood cells, filiform papillae on the surface of rat tongue, agar medium, water molecules, penicillium, etc. All results suggested that the newly designed cryo-holder is applicable for cryo-specimen observation under a conventional SEM without cooling system. Most importantly, the design of this cryo-holder is simple and easy to operate and could adapt a conventional SEM to a plain type cryo-SEM affordable for most laboratories. Copyright © 2011 Wiley Periodicals, Inc.

  6. Active CryoCubeSat

    NASA Technical Reports Server (NTRS)

    Swenson, Charles

    2016-01-01

    The Active CryoCubeSat project will demonstrate an advanced thermal control system for a 6-Unit (6U) CubeSat platform. A miniature, active thermal control system, in which a fluid is circulated in a closed loop from thermal loads to radiators, will be developed. A miniature cryogenic cooler will be integrated with this system to form a two-stage thermal control system. Key components will be miniaturized by using advanced additive manufacturing techniques resulting in a thermal testbed for proving out these technologies. Previous CubeSat missions have not tackled the problem of active thermal control systems nor have any past or current CubeSat missions included cryogenic instrumentation. This Active CryoCubeSat development effort will provide completely new capacities for CubeSats and constitutes a major advancement over the state-of-the-art in CubeSat thermal control.

  7. High efficiency protein separation with organosilane assembled silica coated magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Chang, Jeong Ho; Kang, Ki Ho; Choi, Jinsub; Jeong, Young Keun

    2008-10-01

    This work describes the development of high efficiency protein separation with functionalized organosilanes on the surface of silica coated magnetic nanoparticles. The magnetic nanoparticles were synthesized with average particle size of 9 nm and silica coated magnetic nanoparticles were obtained by controlling the coating thicknesses on magnetic nanoparticles. The silica coating thickness could be uniformly sized with a diameter of 10-40 nm by a sol-gel approach. The surface modification was performed with four kinds of functionalized organosilanes such as carboxyl, aldehyde, amine, and thiol groups. The protein separation work with organosilane assembled silica coated magnetic nanoparticles was achieved for model proteins such as bovine serum albumin (BSA) and lysozyme (LSZ) at different pH conditions. Among the various functionalities, the thiol group showed good separation efficiency due to the change of electrostatic interactions and protein conformational structure. The adsorption efficiency of BSA and LSZ was up to 74% and 90% corresponding pH 4.65 and pH 11.

  8. Process to remove actinides from soil using magnetic separation

    DOEpatents

    Avens, Larry R.; Hill, Dallas D.; Prenger, F. Coyne; Stewart, Walter F.; Tolt, Thomas L.; Worl, Laura A.

    1996-01-01

    A process of separating actinide-containing components from an admixture including forming a slurry including actinide-containing components within an admixture, said slurry including a dispersion-promoting surfactant, adjusting the pH of the slurry to within a desired range, and, passing said slurry through a pretreated matrix material, said matrix material adapted to generate high magnetic field gradients upon the application of a strong magnetic field exceeding about 0.1 Tesla whereupon a portion of said actinide-containing components are separated from said slurry and remain adhered upon said matrix material is provided.

  9. Separation of magnetic susceptibility components from magnetization curves

    NASA Astrophysics Data System (ADS)

    Kosareva, L.; Nourgaliev, D.; Kuzina, D.; Spassov, S.; Fattakhov, A.

    2014-12-01

    Modern lake sediments are a unique source of information for climate changes, regionally and globally, because all environmental variations are recorded by these sediments with high resolution. The magnetic properties of Chernyshov Bay (Aral Sea) sediments we investigated from core number 4 (N45o57'04.2''; E59o17'14.3'') are taken at far water depth of 9.5 m. The length of the core is 4.16 m. Samples for measurements were taken to plastic sample boxes with internal dimensions 2x2x2 cm. Remanent magnetization curves were measured by coercivity spectrometer for the separate determination of the different contributions to the total bulk magnetic susceptibility. There was measured also magnetic susceptibility using MS2 susceptibility meter. Those operations were done for data comparison between 2 susceptibilities obtained from different equipment. Our goal is to decipher the magnetic susceptibility signal in lake sediments by decomposing the bulk susceptibility signal of a lake sediment sequence into ferromagnetic (χf), dia-/paramagnetic (χp) and superparamagnetic (χsp) components using data from remanent and indused magnetization curves Each of these component has a different origin: paramagnetic minerals are usually attributed to terrigenous sediment input, ferromagnetics are of biogenic origin, and superparamagnetic minerals may be of either biogenic or terrigenous origin. Comparison between susceptibility measurements of MS2-Bartington susceptometer and of the coercivity spectrometer has shown good correlation. The susceptibility values measured in two different equipment are fairly close and indicate thus the reliability the proposed method. In research also has shown water level changes in Aral Sea based on magnetic susceptibility. The work is performed according to the Russian Government Program of Competitive Growth of Kazan Federal University also by RFBR research projects No. 14-05-31376 - а, 14-05-00785- а.

  10. Dynamics of magnetic particles in cylindrical Halbach array: implications for magnetic cell separation and drug targeting.

    PubMed

    Babinec, Peter; Krafcík, Andrej; Babincová, Melánia; Rosenecker, Joseph

    2010-08-01

    Magnetic nanoparticles for therapy and diagnosis are at the leading edge of the rapidly developing field of bionanotechnology. In this study, we have theoretically studied motion of magnetic nano- as well as micro-particles in the field of cylindrical Halbach array of permanent magnets. Magnetic flux density was modeled as magnetostatic problem by finite element method and particle motion was described using system of ordinary differential equations--Newton law. Computations were done for nanoparticles Nanomag-D with radius 65 nm, which are often used in magnetic drug targeting, as well as microparticles DynaBeads-M280 with radius 1.4 microm, which can be used for magnetic separation. Analyzing snapshots of trajectories of hundred magnetite particles of each size in the water as well as in the air, we have found that optimally designed magnetic circuits of permanent magnets in quadrupolar Halbach array have substantially shorter capture time than simple blocks of permanent magnets commonly used in experiments, therefore, such a Halbach array may be useful as a potential source of magnetic field for magnetic separation and targeting of magnetic nanoparticles as well as microparticles for delivery of drugs, genes, and cells in various biomedical applications.

  11. The 2017 Nobel Prize in Chemistry: cryo-EM comes of age.

    PubMed

    Shen, Peter S

    2018-03-01

    The 2017 Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson for "developing cryo-electron microscopy (cryo-EM) for the high-resolution structure determination of biomolecules in solution." This feature article summarizes some of the major achievements leading to the development of cryo-EM and recent technological breakthroughs that have transformed the method into a mainstream tool for structure determination.

  12. Combining image processing and modeling to generate traces of beta-strands from cryo-EM density images of beta-barrels.

    PubMed

    Si, Dong; He, Jing

    2014-01-01

    Electron cryo-microscopy (Cryo-EM) technique produces 3-dimensional (3D) density images of proteins. When resolution of the images is not high enough to resolve the molecular details, it is challenging for image processing methods to enhance the molecular features. β-barrel is a particular structure feature that is formed by multiple β-strands in a barrel shape. There is no existing method to derive β-strands from the 3D image of a β-barrel at medium resolutions. We propose a new method, StrandRoller, to generate a small set of possible β-traces from the density images at medium resolutions of 5-10Å. StrandRoller has been tested using eleven β-barrel images simulated to 10Å resolution and one image isolated from the experimentally derived cryo-EM density image at 6.7Å resolution. StrandRoller was able to detect 81.84% of the β-strands with an overall 1.5Å 2-way distance between the detected and the observed β-traces, if the best of fifteen detections is considered. Our results suggest that it is possible to derive a small set of possible β-traces from the β-barrel cryo-EM image at medium resolutions even when no separation of the β-strands is visible in the images.

  13. Cryo-imaging in a toxicological study on mouse fetuses

    NASA Astrophysics Data System (ADS)

    Roy, Debashish; Gargesha, Madhusudhana; Sloter, Eddie; Watanabe, Michiko; Wilson, David

    2010-03-01

    We applied the Case cryo-imaging system to detect signals of developmental toxicity in transgenic mouse fetuses resulting from maternal exposure to a developmental environmental toxicant (2,3,7,8-tetrachlorodibenzo-p-dioxin, TCDD). We utilized a fluorescent transgenic mouse model that expresses Green Fluorescent Protein (GFP) exclusively in smooth muscles under the control of the smooth muscle gamma actin (SMGA) promoter (SMGA/EGFP mice kindly provided by J. Lessard, U. Cincinnati). Analysis of cryo-image data volumes, comprising of very high-resolution anatomical brightfield and molecular fluorescence block face images, revealed qualitative and quantitative morphological differences in control versus exposed fetuses. Fetuses randomly chosen from pregnant females euthanized on gestation day (GD) 18 were either manually examined or cryo-imaged. For cryo-imaging, fetuses were embedded, frozen and cryo-sectioned at 20 μm thickness and brightfield color and fluorescent block-face images were acquired with an in-plane resolution of ~15 μm. Automated 3D volume visualization schemes segmented out the black embedding medium and blended fluorescence and brightfield data to produce 3D reconstructions of all fetuses. Comparison of Treatment groups TCDD GD13, TCDD GD14 and control through automated analysis tools highlighted differences not observable by prosectors performing traditional fresh dissection. For example, severe hydronephrosis, suggestive of irreversible kidney damage, was detected by cryoimaging in fetuses exposed to TCDD. Automated quantification of total fluorescence in smooth muscles revealed suppressed fluorescence in TCDD-exposed fetuses. This application demonstrated that cryo-imaging can be utilized as a routine high-throughput screening tool to assess the effects of potential toxins on the developmental biology of small animals.

  14. Development of external cooling cryo-resistive cable systems. Part 2: Insulation characteristics on 66 kV rated cryo-resistive testing cable

    NASA Astrophysics Data System (ADS)

    Ishihara, Kaoru; Akita, Shige; Suzuki, Hiroshi; Ogata, Junichi; Nemoto, Minoru

    1987-08-01

    Cryo-resistive cable system was tested to demonstrate dielectric characteristics. Dielectric characteristics of 66kV cryo-resistive cable at the start of immersion cooling in the liquid nitrogen were 2.25 specific dielectric constant and 0.18 percent dielectric loss which was less than 0.4 percent , the aimed value. Electrostatic capacity and dielectric loss tangent of dielectric characteristics under the applied voltage did not depend on the voltage and the dielectric loss was less than 0.4 percent through the temperature range from -170 to -190C. These values fulfilled the specifications on 275kV class cryo-resistive cable design. The tested cable passed the cable test on 66kV oil-filled cable (ac 90kV, 10 min), but broken down at ac 110kV on the way to endurance testing voltage 130kV. The breakdown occurred due to the mechanical damage of cable insulator by bending and thermal contraction of the cable. It is necessary from these facts to develop flexible cable terminal and joint which can absorb the contraction to realize 275kV cryo-resistive cable. (19 figs, 7 tabs, 15 refs).

  15. Progressive Stochastic Reconstruction Technique (PSRT) for cryo electron tomography.

    PubMed

    Turoňová, Beata; Marsalek, Lukas; Davidovič, Tomáš; Slusallek, Philipp

    2015-03-01

    Cryo Electron Tomography (cryoET) plays an essential role in Structural Biology, as it is the only technique that allows to study the structure of large macromolecular complexes in their close to native environment in situ. The reconstruction methods currently in use, such as Weighted Back Projection (WBP) or Simultaneous Iterative Reconstruction Technique (SIRT), deliver noisy and low-contrast reconstructions, which complicates the application of high-resolution protocols, such as Subtomogram Averaging (SA). We propose a Progressive Stochastic Reconstruction Technique (PSRT) - a novel iterative approach to tomographic reconstruction in cryoET based on Monte Carlo random walks guided by Metropolis-Hastings sampling strategy. We design a progressive reconstruction scheme to suit the conditions present in cryoET and apply it successfully to reconstructions of macromolecular complexes from both synthetic and experimental datasets. We show how to integrate PSRT into SA, where it provides an elegant solution to the region-of-interest problem and delivers high-contrast reconstructions that significantly improve template-based localization without any loss of high-resolution structural information. Furthermore, the locality of SA is exploited to design an importance sampling scheme which significantly speeds up the otherwise slow Monte Carlo approach. Finally, we design a new memory efficient solution for the specimen-level interior problem of cryoET, removing all associated artifacts. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Viewing Angle Classification of Cryo-Electron Microscopy Images Using Eigenvectors

    PubMed Central

    Singer, A.; Zhao, Z.; Shkolnisky, Y.; Hadani, R.

    2012-01-01

    The cryo-electron microscopy (cryo-EM) reconstruction problem is to find the three-dimensional structure of a macromolecule given noisy versions of its two-dimensional projection images at unknown random directions. We introduce a new algorithm for identifying noisy cryo-EM images of nearby viewing angles. This identification is an important first step in three-dimensional structure determination of macromolecules from cryo-EM, because once identified, these images can be rotationally aligned and averaged to produce “class averages” of better quality. The main advantage of our algorithm is its extreme robustness to noise. The algorithm is also very efficient in terms of running time and memory requirements, because it is based on the computation of the top few eigenvectors of a specially designed sparse Hermitian matrix. These advantages are demonstrated in numerous numerical experiments. PMID:22506089

  17. X-rays in the Cryo-EM Era: Structural Biology’s Dynamic Future

    PubMed Central

    Shoemaker, Susannah C.; Ando, Nozomi

    2018-01-01

    Over the past several years, single-particle cryo-electron microscopy (cryo-EM) has emerged as a leading method for elucidating macromolecular structures at near-atomic resolution, rivaling even the established technique of X-ray crystallography. Cryo-EM is now able to probe proteins as small as hemoglobin (64 kDa), while avoiding the crystallization bottleneck entirely. The remarkable success of cryo-EM has called into question the continuing relevance of X-ray methods, particularly crystallography. To say that the future of structural biology is either cryo-EM or crystallography, however, would be misguided. Crystallography remains better suited to yield precise atomic coordinates of macromolecules under a few hundred kDa in size, while the ability to probe larger, potentially more disordered assemblies is a distinct advantage of cryo-EM. Likewise, crystallography is better equipped to provide high-resolution dynamic information as a function of time, temperature, pressure, and other perturbations, whereas cryo-EM offers increasing insight into conformational and energy landscapes, particularly as algorithms to deconvolute conformational heterogeneity become more advanced. Ultimately, the future of both techniques depends on how their individual strengths are utilized to tackle questions on the frontiers of structural biology. Structure determination is just one piece of a much larger puzzle: a central challenge of modern structural biology is to relate structural information to biological function. In this perspective, we share insight from several leaders in the field and examine the unique and complementary ways in which X-ray methods and cryo-EM can shape the future of structural biology. PMID:29227642

  18. Development of superconducting high gradient magnetic separation system for highly viscous fluid for practical use

    NASA Astrophysics Data System (ADS)

    Hayashi, S.; Mishima, F.; Akiyama, Y.; Nishijima, S.

    2011-11-01

    In the industrial plants processing highly viscous fluid such as foods or industrial products, it is necessary to remove the metallic wear debris originating from pipe in manufacturing line which triggers quality loss. In this study, we developed a high gradient magnetic separation (HGMS) system which consists of superconducting magnet to remove the metallic wear debris. The magnetic separation experiment and the particle trajectory simulation were conducted with polyvinyl alcohol (PVA) as a model material (viscosity coefficient was 10 Pa s, which is 10,000 times higher than that in water). In order to develop a magnetic separation system for practical use, the particle trajectory simulation by using solenoidal superconducting magnet was conducted, and the possibility of the magnetic separation for removing ferromagnetic stainless steel (SUS) particles in highly viscous fluid of 10 Pa s was indicated. Based on the results, the number of filters to obtain required separation efficiency was examined to design the practical separation system.

  19. CryoScout: A Descent Through the Mars Polar Cap

    NASA Technical Reports Server (NTRS)

    Hecht, M. H.; Saunders, R. S.

    2003-01-01

    CryoScout was proposed as a subsurface investigation of the stratigraphic climate record embedded in Mars North Polar cap. After landing on a gentle landscape in the midst of the mild summer season, CryoScout was to use the continuous polar sunlight to power the descent of a cryobot, a thermal probe, into the ice at a rate of about 1 m per day. CryoScout would probe deep enough into this time capsule to see the effects of planetary obliquity variations and discrete events such as dust storms or volcanic eruptions. By penetrating tens of meters of ice, the mission would explore at least one of the dominant "MOC layers" observed in exposed layered terrain.

  20. Working principle and application of magnetic separation for biomedical diagnostic at high- and low-field gradients.

    PubMed

    Leong, Sim Siong; Yeap, Swee Pin; Lim, JitKang

    2016-12-06

    Magnetic separation is a versatile technique used in sample preparation for diagnostic purpose. For such application, an external magnetic field is applied to drive the separation of target entity (e.g. bacteria, viruses, parasites and cancer cells) from a complex raw sample in order to ease the subsequent task(s) for disease diagnosis. This separation process not only can be achieved via the utilization of high magnetic field gradient, but also, in most cases, low magnetic field gradient with magnitude less than 100 T m -1 is equally feasible. It is the aim of this review paper to summarize the usage of both high gradient magnetic separation and low gradient magnetic separation (LGMS) techniques in this area of research. It is noteworthy that effectiveness of the magnetic separation process not only determines the outcome of a diagnosis but also directly influences its accuracy as well as sensing time involved. Therefore, understanding the factors that simultaneously influence the efficiency of both magnetic separation process and target detection is necessary. Moreover, for LGMS, there are several important considerations that should be taken into account in order to ensure its successful implementation. Hence, this review paper aims to provide an overview to relate all this crucial information by linking the magnetic separation theory to biomedical diagnostic applications.

  1. Magnetic separation of Dy(III) ions from homogeneous aqueous solutions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pulko, B., E-mail: Barbara.Pulko@tu-dresden.de; Yang, X.; Lei, Z.

    2014-12-08

    The possibility to enrich paramagnetic dysprosium(III) ions in a magnetic field gradient is proved by means of interferometry, which may open the route for a magnetic separation of rare earth ions from aqueous solutions. The separation dynamics are studied for three different concentrations of DyCl{sub 3} and compared with those found recently in a sulphate solution of the 3d ion Mn(II). In view of the similar-sized hydration spheres for Dy(III) and Mn(II), the slower separation dynamics in DyCl{sub 3} is attributed to both a higher densification coefficient and the strong impact of Brownian motion due to the absence of ion-pairmore » clusters.« less

  2. Removal of algal blooms from freshwater by the coagulation-magnetic separation method.

    PubMed

    Liu, Dan; Wang, Peng; Wei, Guanran; Dong, Wenbo; Hui, Franck

    2013-01-01

    This research investigated the feasibility of changing waste into useful materials for water treatment and proposed a coagulation-magnetic separation technique. This technique was rapid and highly effective for clearing up harmful algal blooms in freshwater and mitigating lake eutrophication. A magnetic coagulant was synthesized by compounding acid-modified fly ash with magnetite (Fe(3)O(4)). Its removal effects on algal cells and dissolved organics in water were studied. After mixing, coagulation, and magnetic separation, the flocs obtained from the magnet surface were examined by SEM. Treated samples were withdrawn for the content determination of chlorophyll-a, turbidity, chemical oxygen demand (COD), total nitrogen, and total phosphorus. More than 99 % of algal cells were removed within 5 min after the addition of magnetic coagulant at optimal loadings (200 mg L(-1)). The removal efficiencies of COD, total nitrogen, and phosphorus were 93, 91, and 94 %, respectively. The mechanism of algal removal explored preliminarily showed that the magnetic coagulant played multiple roles in mesoporous adsorption, netting and bridging, as well as high magnetic responsiveness to a magnetic field. The magnetic-coagulation separation method can rapidly and effectively remove algae from water bodies and greatly mitigate eutrophication of freshwater using a new magnetic coagulant. The method has good performance, is low cost, can turn waste into something valuable, and provides reference and directions for future pilot and production scale-ups.

  3. Factors that Influence the Formation and Stability of Thin, Cryo-EM Specimens

    DOE PAGES

    Glaeser, Robert M.; Han, Bong-Gyoon; Csencsits, Roseann; ...

    2015-09-17

    Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. We first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. Furthermore, we then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated. In fact, a surfactant layer (of uncontrolled composition and surfacemore » pressure) can hardly be avoided during standard cryo-EM specimen preparation. Thus it is suggested that better control over the composition and properties of the surfactant layer may result in more reliable production of cryo-EM specimens with the desired thickness.« less

  4. Factors that Influence the Formation and Stability of Thin, Cryo-EM Specimens

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Glaeser, Robert M.; Han, Bong-Gyoon; Csencsits, Roseann

    Poor consistency of the ice thickness from one area of a cryo-electron microscope (cryo-EM) specimen grid to another, from one grid to the next, and from one type of specimen to another, motivates a reconsideration of how to best prepare suitably thin specimens. We first review the three related topics of wetting, thinning, and stability against dewetting of aqueous films spread over a hydrophilic substrate. Furthermore, we then suggest that the importance of there being a surfactant monolayer at the air-water interface of thin, cryo-EM specimens has been largely underappreciated. In fact, a surfactant layer (of uncontrolled composition and surfacemore » pressure) can hardly be avoided during standard cryo-EM specimen preparation. Thus it is suggested that better control over the composition and properties of the surfactant layer may result in more reliable production of cryo-EM specimens with the desired thickness.« less

  5. Alignment algorithms and per-particle CTF correction for single particle cryo-electron tomography.

    PubMed

    Galaz-Montoya, Jesús G; Hecksel, Corey W; Baldwin, Philip R; Wang, Eryu; Weaver, Scott C; Schmid, Michael F; Ludtke, Steven J; Chiu, Wah

    2016-06-01

    Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen, the cryo-electron microscopy (cryoEM) grid and/or the carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. Rapid and continuous magnetic separation in droplet microfluidic devices.

    PubMed

    Brouzes, Eric; Kruse, Travis; Kimmerling, Robert; Strey, Helmut H

    2015-02-07

    We present a droplet microfluidic method to extract molecules of interest from a droplet in a rapid and continuous fashion. We accomplish this by first marginalizing functionalized super-paramagnetic beads within the droplet using a magnetic field, and then splitting the droplet into one droplet containing the majority of magnetic beads and one droplet containing the minority fraction. We quantitatively analysed the factors which affect the efficiency of marginalization and droplet splitting to optimize the enrichment of magnetic beads. We first characterized the interplay between the droplet velocity and the strength of the magnetic field and its effect on marginalization. We found that marginalization is optimal at the midline of the magnet and that marginalization is a good predictor of bead enrichment through splitting at low to moderate droplet velocities. Finally, we focused our efforts on manipulating the splitting profile to improve the enrichment provided by asymmetric splitting. We designed asymmetric splitting forks that employ capillary effects to preferentially extract the bead-rich regions of the droplets. Our strategy represents a framework to optimize magnetic bead enrichment methods tailored to the requirements of specific droplet-based applications. We anticipate that our separation technology is well suited for applications in single-cell genomics and proteomics. In particular, our method could be used to separate mRNA bound to poly-dT functionalized magnetic microparticles from single cell lysates to prepare single-cell cDNA libraries.

  7. Rapid and continuous magnetic separation in droplet microfluidic devices

    DOE PAGES

    Brouzes, Eric; Kruse, Travis; Kimmerling, Robert; ...

    2014-12-03

    Here, we present a droplet microfluidic method to extract molecules of interest from a droplet in a rapid and continuous fashion. We accomplish this by first marginalizing functionalized super-paramagnetic beads within the droplet using a magnetic field, and then splitting the droplet into one droplet containing the majority of magnetic beads and one droplet containing the minority fraction. We quantitatively analysed the factors which affect the efficiency of marginalization and droplet splitting to optimize the enrichment of magnetic beads. We first characterized the interplay between the droplet velocity and the strength of the magnetic field and its effect on marginalization.more » We found that marginalization is optimal at the midline of the magnet and that marginalization is a good predictor of bead enrichment through splitting at low to moderate droplet velocities. Finally, we focused our efforts on manipulating the splitting profile to improve the enrichment provided by asymmetric splitting. We designed asymmetric splitting forks that employ capillary effects to preferentially extract the bead-rich regions of the droplets. Our strategy represents a framework to optimize magnetic bead enrichment methods tailored to the requirements of specific droplet-based applications. We anticipate that our separation technology is well suited for applications in single-cell genomics and proteomics. In particular, our method could be used to separate mRNA bound to poly-dT functionalized magnetic microparticles from single cell lysates to prepare single-cell cDNA libraries.« less

  8. Rapid and continuous magnetic separation in droplet microfluidic devices

    PubMed Central

    Brouzes, Eric; Kruse, Travis; Kimmerling, Robert; Strey, Helmut H.

    2015-01-01

    We present a droplet microfluidic method to extract molecules of interest from a droplet in a rapid and continuous fashion. We accomplish this by first marginalizing functionalized super-paramagnetic beads within the droplet using a magnetic field, and then splitting the droplet into one droplet containing the majority of magnetic beads and one droplet containing the minority fraction. We quantitatively analysed the factors which affect the efficiency of marginalization and droplet splitting to optimize the enrichment of magnetic beads. We first characterized the interplay between the droplet velocity and the strength of the magnetic field and its effect on marginalization. We found that marginalization is optimal at the midline of the magnet and that marginalization is a good predictor of bead enrichment through splitting at low to moderate droplet velocities. Finally, we focused our efforts on manipulating the splitting profile to improve the enrichment provided by asymmetric splitting. We designed asymmetric splitting forks that employ capillary effects to preferentially extract the bead-rich regions of the droplets. Our strategy represents a framework to optimize magnetic bead enrichment methods tailored to the requirements of specific droplet-based applications. We anticipate that our separation technology is well suited for applications in single-cell genomics and proteomics. In particular, our method could be used to separate mRNA bound to poly-dT functionalized magnetic microparticles from single cell lysates to prepare single-cell cDNA libraries. PMID:25501881

  9. Nitrogen Separation and Liquefaction Apparatus for Medical Applications and Its Thermodynamic Optimization

    NASA Astrophysics Data System (ADS)

    Chorowski, M.; Piotrowska, A.; Polinski, J.

    2006-04-01

    Low temperature medicine is becoming a widely appreciated method in surgery, dermatology, gynecology and rheumatology. The cryomedical equipment is usually supplied with liquid nitrogen LN2 stored in a dewar and transferred to a tip, where it is evaporated providing a cooling power. LN2 in quantities sufficient for cryo-surgical and cryo-therapeutical applications can be first separated from air and then liquefied using a system combining polymer membrane gas separation technology and a Joule-Thomson closed-cycle refrigerator filled with a nitrogen-hydrocarbons gas mixture. Nitrogen is separated from the compressed air, then liquefied and throttled to atmospheric pressure. The paper analyzes the demanded cooling capacity of the system resulting from cryomedical treatment requirements. Thermal design and flow scheme of the apparatus are given. The system is thermodynamically optimized.

  10. Working principle and application of magnetic separation for biomedical diagnostic at high- and low-field gradients

    PubMed Central

    Yeap, Swee Pin; Lim, JitKang

    2016-01-01

    Magnetic separation is a versatile technique used in sample preparation for diagnostic purpose. For such application, an external magnetic field is applied to drive the separation of target entity (e.g. bacteria, viruses, parasites and cancer cells) from a complex raw sample in order to ease the subsequent task(s) for disease diagnosis. This separation process not only can be achieved via the utilization of high magnetic field gradient, but also, in most cases, low magnetic field gradient with magnitude less than 100 T m−1 is equally feasible. It is the aim of this review paper to summarize the usage of both high gradient magnetic separation and low gradient magnetic separation (LGMS) techniques in this area of research. It is noteworthy that effectiveness of the magnetic separation process not only determines the outcome of a diagnosis but also directly influences its accuracy as well as sensing time involved. Therefore, understanding the factors that simultaneously influence the efficiency of both magnetic separation process and target detection is necessary. Moreover, for LGMS, there are several important considerations that should be taken into account in order to ensure its successful implementation. Hence, this review paper aims to provide an overview to relate all this crucial information by linking the magnetic separation theory to biomedical diagnostic applications. PMID:27920891

  11. Navigation for fluoroscopy-guided cryo-balloon ablation procedures of atrial fibrillation

    NASA Astrophysics Data System (ADS)

    Bourier, Felix; Brost, Alexander; Kleinoeder, Andreas; Kurzendorfer, Tanja; Koch, Martin; Kiraly, Attila; Schneider, Hans-Juergen; Hornegger, Joachim; Strobel, Norbert; Kurzidim, Klaus

    2012-02-01

    Atrial fibrillation (AFib), the most common arrhythmia, has been identified as a major cause of stroke. The current standard in interventional treatment of AFib is the pulmonary vein isolation (PVI). PVI is guided by fluoroscopy or non-fluoroscopic electro-anatomic mapping systems (EAMS). Either classic point-to-point radio-frequency (RF)- catheter ablation or so-called single-shot-devices like cryo-balloons are used to achieve electrically isolation of the pulmonary veins and the left atrium (LA). Fluoroscopy-based systems render overlay images from pre-operative 3-D data sets which are then merged with fluoroscopic imaging, thereby adding detailed 3-D information to conventional fluoroscopy. EAMS provide tracking and visualization of RF catheters by means of electro-magnetic tracking. Unfortunately, current navigation systems, fluoroscopy-based or EAMS, do not provide tools to localize and visualize single shot devices like cryo-balloon catheters in 3-D. We present a prototype software for fluoroscopy-guided ablation procedures that is capable of superimposing 3-D datasets as well as reconstructing cyro-balloon catheters in 3-D. The 3-D cyro-balloon reconstruction was evaluated on 9 clinical data sets, yielded a reprojected 2-D error of 1.72 mm +/- 1.02 mm.

  12. The relationship between the force and separation of miniature magnets used in dentistry.

    PubMed

    Darvell, Brian W; Gilding, Brian H

    2018-06-01

    Miniature magnets are used in dentistry, principally for the retention of prosthetic devices. The relationship between force and separation of a magnet and its keeper, or, equivalently, two such magnets, has been neither defined theoretically nor described practically in any detail suitable for these applications. The present paper addresses this lacuna. A magnet is considered as a conglomeration of magnetic poles distributed over a surface or a solid in three-dimensional space, with the interaction of poles governed by the Coulomb law. This leads to a suite of mathematical models. These models are analysed for their description of the relationship between the force and the separation of two magnets. It is shown that at a large distance of separation, an inverse power law must apply. The power is necessarily integer and at least two. All possibilities are exhausted. Complementarily, under reasonable assumptions, it is shown that at a small distance of separation, the force remains finite. The outcome is in accordance with practical experience, and at odds with the use of simple conceptual models. Consequences relevant to the usage of magnets in dentistry are discussed. Copyright © 2018 The Academy of Dental Materials. Published by Elsevier Inc. All rights reserved.

  13. A novel storage system for cryoEM samples.

    PubMed

    Scapin, Giovanna; Prosise, Winifred W; Wismer, Michael K; Strickland, Corey

    2017-07-01

    We present here a new CryoEM grid boxes storage system designed to simplify sample labeling, tracking and retrieval. The system is based on the crystal pucks widely used by the X-ray crystallographic community for storage and shipping of crystals. This system is suitable for any cryoEM laboratory, but especially for large facilities that will need accurate tracking of large numbers of samples coming from different sources. Copyright © 2017. Published by Elsevier Inc.

  14. Cryo-scanning transmission electron tomography of vitrified cells.

    PubMed

    Wolf, Sharon Grayer; Houben, Lothar; Elbaum, Michael

    2014-04-01

    Cryo-electron tomography (CET) of fully hydrated, vitrified biological specimens has emerged as a vital tool for biological research. For cellular studies, the conventional imaging modality of transmission electron microscopy places stringent constraints on sample thickness because of its dependence on phase coherence for contrast generation. Here we demonstrate the feasibility of using scanning transmission electron microscopy for cryo-tomography of unstained vitrified specimens (CSTET). We compare CSTET and CET for the imaging of whole bacteria and human tissue culture cells, finding favorable contrast and detail in the CSTET reconstructions. Particularly at high sample tilts, the CSTET signals contain more informative data than energy-filtered CET phase contrast images, resulting in improved depth resolution. Careful control over dose delivery permits relatively high cumulative exposures before the onset of observable beam damage. The increase in acceptable specimen thickness broadens the applicability of electron cryo-tomography.

  15. Harnessing mass differential confinement effects in magnetized rotating plasmas to address new separation needs

    NASA Astrophysics Data System (ADS)

    Gueroult, R.; Rax, J.-M.; Zweben, S. J.; Fisch, N. J.

    2018-01-01

    The ability to separate large volumes of mixed species based on atomic mass appears desirable for a variety of emerging applications with high societal impact. One possibility to meet this objective consists in leveraging mass differential effects in rotating plasmas. Beyond conventional centrifugation, rotating plasmas offer in principle additional ways to separate elements based on mass. Single ion orbits show that ion radial mass separation in a uniform magnetized plasma column can be achieved by applying a tailored electric potential profile across the column, or by driving a rotating magnetic field within the column. Furthermore, magnetic pressure and centrifugal effects can be combined in a non-uniform geometry to separate ions based on mass along the field lines. Practical application of these separation schemes hinges on the ability to produce the desirable electric and magnetic field configuration within the plasma column.

  16. Pleomorphism and Viability of the Lyme Disease Pathogen Borrelia burgdorferi Exposed to Physiological Stress Conditions: A Correlative Cryo-Fluorescence and Cryo-Scanning Electron Microscopy Study.

    PubMed

    Vancová, Marie; Rudenko, Nataliia; Vaněček, Jiří; Golovchenko, Maryna; Strnad, Martin; Rego, Ryan O M; Tichá, Lucie; Grubhoffer, Libor; Nebesářová, Jana

    2017-01-01

    To understand the response of the Lyme disease spirochete Borrelia burgdorferi exposed to stress conditions and assess the viability of this spirochete, we used a correlative cryo-fluorescence and cryo-scanning microscopy approach. This approach enables simple exposition of bacteria to various experimental conditions that can be stopped at certain time intervals by cryo-immobilization, examination of cell viability without necessity to maintain suitable culture conditions during viability assays, and visualization of structures in their native state at high magnification. We focused on rare and transient events e.g., the formation of round bodies and the presence of membranous blebs in spirochetes exposed to culture medium, host sera either without or with the bacteriolytic effect and water. We described all crucial steps of the workflow, particularly the influence of freeze-etching and accelerating voltage on the visualization of topography. With the help of newly designed cryo-transport device, we achieved greater reproducibility.

  17. A Unique BSL-3 Cryo-Electron Microscopy Laboratory at UTMB

    PubMed Central

    Sherman, Michael B.; Freiberg, Alexander N.; Razmus, Dennis; Yazuka, Shintaro; Koht, Craig; Hilser, Vincent J.; Lemon, Stanley M.; Brocard, Anne-Sophie; Zimmerman, Dee; Chiu, Wah; Watowich, Stanley J.; Weaver, Scott C.

    2010-01-01

    This article describes a unique cryo-electron microscopy (CryoEM) facility to study the three-dimensional organization of viruses at biological safety level 3 (BSL-3). This facility, the W. M. Keck Center for Virus Imaging, has successfully operated for more than a year without incident and was cleared for select agent studies by the Centers for Disease Control and Prevention (CDC). Standard operating procedures for the laboratory were developed and implemented to ensure its safe and efficient operation. This facility at the University of Texas Medical Branch (Galveston, TX) is the only such BSL-3 CryoEM facility approved for select agent research. PMID:21852942

  18. Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

    PubMed

    DiMaio, F; Chiu, W

    2016-01-01

    Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

  19. A deep convolutional neural network approach to single-particle recognition in cryo-electron microscopy.

    PubMed

    Zhu, Yanan; Ouyang, Qi; Mao, Youdong

    2017-07-21

    Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias. It is critical to develop a highly efficient template-free method for the automatic recognition of particle images from cryo-EM micrographs. We developed a deep learning-based algorithmic framework, DeepEM, for single-particle recognition from noisy cryo-EM micrographs, enabling automated particle picking, selection and verification in an integrated fashion. The kernel of DeepEM is built upon a convolutional neural network (CNN) composed of eight layers, which can be recursively trained to be highly "knowledgeable". Our approach exhibits an improved performance and accuracy when tested on the standard KLH dataset. Application of DeepEM to several challenging experimental cryo-EM datasets demonstrated its ability to avoid the selection of un-wanted particles and non-particles even when true particles contain fewer features. The DeepEM methodology, derived from a deep CNN, allows automated particle extraction from raw cryo-EM micrographs in the absence of a template. It demonstrates an improved performance, objectivity and accuracy. Application of this novel method is expected to free the labor involved in single-particle verification, significantly improving the efficiency of cryo-EM data processing.

  20. Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud.

    PubMed

    Cianfrocco, Michael A; Leschziner, Andres E

    2015-05-08

    The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available 'off-the-shelf' computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16-480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.

  1. Simulating Chiral Magnetic and Separation Effects with Spin-Orbit Coupled Atomic Gases

    PubMed Central

    Huang, Xu-Guang

    2016-01-01

    The chiral magnetic and chiral separation effects—quantum-anomaly-induced electric current and chiral current along an external magnetic field in parity-odd quark-gluon plasma—have received intense studies in the community of heavy-ion collision physics. We show that analogous effects occur in rotating trapped Fermi gases with Weyl-Zeeman spin-orbit coupling where the rotation plays the role of an external magnetic field. These effects can induce a mass quadrupole in the atomic cloud along the rotation axis which may be tested in future experiments. Our results suggest that the spin-orbit coupled atomic gases are potential simulators of the chiral magnetic and separation effects. PMID:26868084

  2. Conceptual design and optimization for JET water detritiation system cryo-distillation facility

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lefebvre, X.; Hollingsworth, A.; Parracho, A.

    2015-03-15

    The aim of the Exhaust Detritiation System (EDS) of the JET Active Gas Handling System (AGHS) is to convert all Q-based species (Q{sub 2}, Q-hydrocarbons) into Q{sub 2}O (Q being indifferently H, D or T) which is then trapped on molecular sieve beds (MSB). Regenerating the saturated MSBs leads to the production of tritiated water which is stored in Briggs drums. An alternative disposal solution to offsite shipping, is to process the tritiated water onsite via the implementation of a Water Detritiation System (WDS) based, in part, on the combination of an electrolyser and a cryo-distillation (CD) facility. The CDmore » system will separate a Q{sub 2} mixture into a de-tritiated hydrogen stream for safe release and a tritiated stream for further processing on existing AGHS subsystems. A sensitivity study of the Souers' model using the simulation program ProSimPlus (edited by ProSim S.A.) has then been undertaken in order to perform an optimised dimensioning of the cryo-distillation system in terms of available cooling technologies, cost of investment, cost of operations, process performance and safety. (authors)« less

  3. Correlation of simulation/finite element analysis to the separation of intrinsically magnetic spores and red blood cells using a microfluidic magnetic deposition system.

    PubMed

    Sun, Jianxin; Moore, Lee; Xue, Wei; Kim, James; Zborowski, Maciej; Chalmers, Jeffrey J

    2018-05-01

    Magnetic separation of cells has been, and continues to be, widely used in a variety of applications, ranging from healthcare diagnostics to detection of food contamination. Typically, these technologies require cells labeled with antibody magnetic particle conjugate and a high magnetic energy gradient created in the flow containing the labeled cells (i.e., a column packed with magnetically inducible material), or dense packing of magnetic particles next to the flow cell. Such designs, while creating high magnetic energy gradients, are not amenable to easy, highly detailed, mathematic characterization. Our laboratories have been characterizing and developing analysis and separation technology that can be used on intrinsically magnetic cells or spores which are typically orders of magnitude weaker than typically immunomagnetically labeled cells. One such separation system is magnetic deposition microscopy (MDM) which not only separates cells, but deposits them in specific locations on slides for further microscopic analysis. In this study, the MDM system has been further characterized, using finite element and computational fluid mechanics software, and separation performance predicted, using a model which combines: 1) the distribution of the intrinsic magnetophoretic mobility of the cells (spores); 2) the fluid flow within the separation device; and 3) accurate maps of the values of the magnetic field (max 2.27 T), and magnetic energy gradient (max of 4.41 T 2 /mm) within the system. Guided by this model, experimental studies indicated that greater than 95% of the intrinsically magnetic Bacillus spores can be separated with the MDM system. Further, this model allows analysis of cell trajectories which can assist in the design of higher throughput systems. © 2018 Wiley Periodicals, Inc.

  4. Fully integrated micro-separator with soft-magnetic micro-pillar arrays for filtrating lymphocytes.

    PubMed

    Dong, Tao; Su, Qianhua; Yang, Zhaochu; Karlsen, Frank; Jakobsen, Henrik; Egeland, Eirik Bentzen; Hjelseth, Snorre

    2010-01-01

    A fully integrated micro-separator with soft-magnetic micro-pillar arrays has been developed, which merely employs one independent Lab-On-Chip to realize the lymphocytes isolation from the human whole blood. The simulation, fabrication and experiment are executed to realize this novel microseparator. The simulation results show that, the soft-magnetic micro-pillars array can amplify and redistribute the electromagnetic field generated by the microcoils. The tests certify desirable separation efficiency can be realized using this new separator at low current. No extra cooling system is required for such a micro-separator. This micro-separator can also be used to separate other target cells or particles with the same principle.

  5. Electron cryo-tomography captures macromolecular complexes in native environments.

    PubMed

    Baker, Lindsay A; Grange, Michael; Grünewald, Kay

    2017-10-01

    Transmission electron microscopy has a long history in cellular biology. Fixed and stained samples have been used for cellular imaging for over 50 years, but suffer from sample preparation induced artifacts. Electron cryo-tomography (cryoET) instead uses frozen-hydrated samples, without chemical modification, to determine the structure of macromolecular complexes in their native environment. Recent developments in electron microscopes and associated technologies have greatly expanded our ability to visualize cellular features and determine the structures of macromolecular complexes in situ. This review highlights the technological improvements and the new areas of biology these advances have made accessible. We discuss the potential of cryoET to reveal novel and significant biological information on the nanometer or subnanometer scale, and directions for further work. Copyright © 2017. Published by Elsevier Ltd.

  6. Study on industrial wastewater treatment using superconducting magnetic separation

    NASA Astrophysics Data System (ADS)

    Zhang, Hao; Zhao, Zhengquan; Xu, Xiangdong; Li, Laifeng

    2011-06-01

    The mechanism of industrial wastewater treatment using superconducting magnetic separation is investigated. Fe 3O 4 nanoparticles were prepared by liquid precipitation and characterized by X-ray diffraction (XRD). Polyacrylic acid (PAA) film was coated on the magnetic particles using plasma coating technique. Transmission electron microscope (TEM) observation and infrared spectrum measurement indicate that the particle surface is well coated with PAA, and the film thickness is around 1 nm. Practical paper factory wastewater treatment using the modified magnetic seeds in a superconducting magnet (SCM) was carried out. The results show that the maximum removal rate of chemical oxygen demand (COD) by SCM method can reach 76%.

  7. Robust w-Estimators for Cryo-EM Class Means.

    PubMed

    Huang, Chenxi; Tagare, Hemant D

    2016-02-01

    A critical step in cryogenic electron microscopy (cryo-EM) image analysis is to calculate the average of all images aligned to a projection direction. This average, called the class mean, improves the signal-to-noise ratio in single-particle reconstruction. The averaging step is often compromised because of the outlier images of ice, contaminants, and particle fragments. Outlier detection and rejection in the majority of current cryo-EM methods are done using cross-correlation with a manually determined threshold. Empirical assessment shows that the performance of these methods is very sensitive to the threshold. This paper proposes an alternative: a w-estimator of the average image, which is robust to outliers and which does not use a threshold. Various properties of the estimator, such as consistency and influence function are investigated. An extension of the estimator to images with different contrast transfer functions is also provided. Experiments with simulated and real cryo-EM images show that the proposed estimator performs quite well in the presence of outliers.

  8. Self-assembled monolayers improve protein distribution on holey carbon cryo-EM supports

    PubMed Central

    Meyerson, Joel R.; Rao, Prashant; Kumar, Janesh; Chittori, Sagar; Banerjee, Soojay; Pierson, Jason; Mayer, Mark L.; Subramaniam, Sriram

    2014-01-01

    Poor partitioning of macromolecules into the holes of holey carbon support grids frequently limits structural determination by single particle cryo-electron microscopy (cryo-EM). Here, we present a method to deposit, on gold-coated carbon grids, a self-assembled monolayer whose surface properties can be controlled by chemical modification. We demonstrate the utility of this approach to drive partitioning of ionotropic glutamate receptors into the holes, thereby enabling 3D structural analysis using cryo-EM methods. PMID:25403871

  9. Integration of carboxyl modified magnetic particles and aqueous two-phase extraction for selective separation of proteins.

    PubMed

    Gai, Qingqing; Qu, Feng; Zhang, Tao; Zhang, Yukui

    2011-07-15

    Both of the magnetic particle adsorption and aqueous two-phase extraction (ATPE) were simple, fast and low-cost method for protein separation. Selective proteins adsorption by carboxyl modified magnetic particles was investigated according to protein isoelectric point, solution pH and ionic strength. Aqueous two-phase system of PEG/sulphate exhibited selective separation and extraction for proteins before and after magnetic adsorption. The two combination ways, magnetic adsorption followed by ATPE and ATPE followed by magnetic adsorption, for the separation of proteins mixture of lysozyme, bovine serum albumin, trypsin, cytochrome C and myloglobin were discussed and compared. The way of magnetic adsorption followed by ATPE was also applied to human serum separation. Copyright © 2011 Elsevier B.V. All rights reserved.

  10. Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

    PubMed Central

    Cianfrocco, Michael A; Leschziner, Andres E

    2015-01-01

    The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16–480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM. DOI: http://dx.doi.org/10.7554/eLife.06664.001 PMID:25955969

  11. JWST Pathfinder Telescope Risk Reduction Cryo Test Program

    NASA Technical Reports Server (NTRS)

    Matthews, Gary W.; Scorse, Thomas R.; Spina, John A.; Noel, Darin M.; Havey, Keith A., Jr.; Huguet, Jesse A.; Whitman, Tony L.; Wells, Conrad; Walker, Chanda B.; Lunt, Sharon; hide

    2015-01-01

    In 2014, the Optical Ground Support Equipment was integrated into the large cryo vacuum chamber at Johnson Space Center (JSC) and an initial Chamber Commissioning Test was completed. This insured that the support equipment was ready for the three Pathfinder telescope cryo tests. The Pathfinder telescope which consists of two primary mirror segment assemblies and the secondary mirror was delivered to JSC in February 2015 in support of this critical risk reduction test program prior to the flight hardware. This paper will detail the Chamber Commissioning and first optical test of the JWST Pathfinder telescope.

  12. Research on magnetic separation for complex nickel deep removal and magnetic seed recycling.

    PubMed

    Qiu, Yiqin; Xiao, Xiao; Ye, Ziwei; Guan, Zhijie; Sun, Shuiyu; Ren, Jie; Yan, Pingfan

    2017-04-01

    This study investigated the deep removal of complex nickel from simulated wastewater using magnetic separation and magnetic seed recycling. Nano-magnetite (Fe 3 O 4 ) was used as the magnetic seed. The flocculant applied was N,N-bis-(dithiocarboxy) ethanediamine (EDTC), a highly efficient heavy metal chelating agent included in dithiocarbamate (DTC). Important investigated parameters included hydraulic retention time, magnetic seed dosage, and magnetic field strength. The study also explored the magnetic flocculation mechanism involved in the reaction. The result indicated that the residual Ni concentration was reduced to less than 0.1 mg/L from the initial concentration of 50 mg/L under optimal conditions. Magnetic seed recovery reached 76.42% after a 3-h stirring period; recycled magnetic seeds were analyzed using scanning electron microscope (SEM) and X-ray diffraction (XRD). The zeta potential results illustrated that magnetic seeds firmly combined with flocs when the pH ranged from 6.5 to 7.5 due to the electrostatic attraction. When the pH was less than 7, magnetic seeds and EDTC were also combined due to electrostatic attraction. Particle size did affect microfloc size; it decreased microfloc size and increased floc volume through magnetic seed loading. The effective binding sites between flocs and magnetic seeds increased when adding the magnetic seeds. This led the majority of magnetic flocs to be integrated with the magnetic seeds, which served as a nucleus to enhance the flocculation property and ultimately improve the nickel complex removal rate.

  13. Low-Field Dynamic Magnetic Separation by Self-Fabricated Magnetic Meshes for Efficient Heavy Metal Removal.

    PubMed

    Wei, Xiangxia; Sugumaran, Pon Janani; Peng, Erwin; Liu, Xiao Li; Ding, Jun

    2017-10-25

    Wastewater contaminated with heavy metals is a worldwide concern due to the toxicity to human and animals. The current study presents an incorporation of adsorption and low-field dynamic magnetic separation technique for the treatment of heavy-metal-contaminated water. The key components are the eco-fabricated magnetic filter with mesh architectures (constituted of a soft magnetic material (Ni,Zn)Fe 2 O 4 ) and poly(acrylic acid) (PAA)-coated quasi-superparamagnetic Fe 3 O 4 nanoparticles (NPs). PAA-coated Fe 3 O 4 NPs possess high adsorption capacity of heavy metal ions including Pb, Ni, Co, and Cu and can be easily regenerated after the adjustment of pH. Moreover, magnetic mesh filter has shown excellent collection ability of quasi-superparamagnetic particles under a magnetic field as low as 0.7 kOe (0.07 T) and can easily release these particles during ultrasonic washing when small magnets are removed. In the end, after one filtration process, the heavy metal concentration can be significantly decreased from 1.0 mg L -1 to below the drinking water standard recommended by the World Health Organization (e.g., less than 0.01 mg L -1 for Pb). Overall, a proof-of-concept adsorption and subsequent low-field dynamic separation technique is demonstrated as an economical and efficient route for heavy metal removal from wastewater.

  14. Routine single particle CryoEM sample and grid characterization by tomography

    PubMed Central

    Noble, Alex J; Brasch, Julia; Chase, Jillian; Acharya, Priyamvada; Tan, Yong Zi; Zhang, Zhening; Kim, Laura Y; Scapin, Giovanna; Rapp, Micah; Eng, Edward T; Rice, William J; Cheng, Anchi; Negro, Carl J; Shapiro, Lawrence; Kwong, Peter D; Jeruzalmi, David; des Georges, Amedee; Potter, Clinton S

    2018-01-01

    Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment. PMID:29809143

  15. Safety of Cryo-Transbronchial Biopsy in Diffuse Lung Diseases: Analysis of Three Hundred Cases.

    PubMed

    Gershman, Evgeni; Fruchter, Oren; Benjamin, Fox; Nader, Abed Rahman; Rosengarten, Dror; Rusanov, Victoria; Fridel, Ludmila; Kramer, Mordechai R

    2015-01-01

    Transbronchial biopsy (TBB) which is performed with metal forceps (forceps TBB) has been accepted as a useful technique in establishing diagnoses of diffuse lung diseases (DLDs). The use of cryoprobes to obtain alveolar tissue (cryo-TBB) is a new method which is currently used by our institute as well as others with excellent results. To assess the safety of cryo-TBB compared with conventional forceps TBB. We performed a retrospective data evaluation of 300 consecutive patients who underwent cryo-TBB between January 2012 and April 2014 and compared them with historical cases treated with forceps TBB between 2010 and 2012. The results of both diagnostic modalities were compared based on pathological reports. The major complications (significant bleeding and pneumothorax) were compared, along with postprocedural hospitalization. Pneumothorax was observed in 15 cases (4.95%) treated with cryo-TBB versus 9 cases (3.15%) treated with forceps TBB, with no significant difference (p = 0.303). The insertion of a chest tube was necessary in 6 (2%) and 4 (1.3%) of the cases having undergone cryo-TBB or forceps TBB, respectively (p = 0.8). In the cryo-TBB group, bleeding was encountered in 16 cases (5.2%), and it occurred in 13 cases (4.5%) of the forceps TBB group, with no significant difference in rates (p = 0.706). Also, there was no significant difference in hospital admission rates between the groups [cryo-TBB: 10 (3.3%); forceps TBB: 4 (1.44%); p = 0.181]. The safety profile of cryo- and forceps TBB remained the same even when stratified according to indications for TBB, i.e. immunocompromised hosts, patients after lung transplantation and those with DLDs. In patients with DLDs, cryo-TBB is as safe as forceps TBB.

  16. Using size-selected gold clusters on graphene oxide films to aid cryo-transmission electron tomography alignment

    PubMed Central

    Arkill, Kenton P.; Mantell, Judith M.; Plant, Simon R.; Verkade, Paul; Palmer, Richard E.

    2015-01-01

    A three-dimensional reconstruction of a nano-scale aqueous object can be achieved by taking a series of transmission electron micrographs tilted at different angles in vitreous ice: cryo-Transmission Electron Tomography. Presented here is a novel method of fine alignment for the tilt series. Size-selected gold clusters of ~2.7 nm (Au561 ± 14), ~3.2 nm (Au923 ± 22), and ~4.3 nm (Au2057 ± 45) in diameter were deposited onto separate graphene oxide films overlaying holes on amorphous carbon grids. After plunge freezing and subsequent transfer to cryo-Transmission Electron Tomography, the resulting tomograms have excellent (de-)focus and alignment properties during automatic acquisition. Fine alignment is accurate when the evenly distributed 3.2 nm gold particles are used as fiducial markers, demonstrated with a reconstruction of a tobacco mosaic virus. Using a graphene oxide film means the fiducial markers are not interfering with the ice bound sample and that automated collection is consistent. The use of pre-deposited size-selected clusters means there is no aggregation and a user defined concentration. The size-selected clusters are mono-dispersed and can be produced in a wide size range including 2–5 nm in diameter. The use of size-selected clusters on a graphene oxide films represents a significant technical advance for 3D cryo-electron microscopy. PMID:25783049

  17. Ferritin conjugates as specific magnetic labels. Implications for cell separation.

    PubMed Central

    Odette, L L; McCloskey, M A; Young, S H

    1984-01-01

    Concanavalin A coupled to the naturally occurring iron storage protein ferritin is used to label rat erythrocytes and increase the cells' magnetic susceptibility. Labeled cells are introduced into a chamber containing spherical iron particles and the chamber is placed in a uniform 5.2 kG (gauss) magnetic field. The trajectory of cells in the inhomogeneous magnetic field around the iron particles and the polar distributions of cells bound to the iron particles compare well with the theoretical predictions for high gradient magnetic systems. On the basis of these findings we suggest that ferritin conjugated ligands can be used for selective magnetic separation of labeled cells. Images FIGURE 2 PMID:6743752

  18. Combined performance of biochar sorption and magnetic separation processes for treatment of chromium-contained electroplating wastewater.

    PubMed

    Wang, Sheng-ye; Tang, Yan-kui; Li, Kun; Mo, Ya-yuan; Li, Hao-feng; Gu, Zhan-qi

    2014-12-01

    Magnetic biochar was prepared with eucalyptus leaf residue remained after essential oil being extracted. Batch experiments were conducted to examine the capacity of the magnetic biochar to remove Cr (VI) from electroplating wastewater and to be separated by an external magnetic field. The results show that the initial solution pH plays an important role on both sorption and separation. The removal rates of Cr (VI), total Cr, Cu (II), and Ni (II) were 97.11%, 97.63%, 100% and 100%, respectively. The turbidity of the sorption-treated solution was reduced to 21.8NTU from 4075NTU after 10min magnetic separation. The study also confirms that the magnetic biochar still retains the original magnetic separation performance after the sorption process. Copyright © 2014 Elsevier Ltd. All rights reserved.

  19. Effect of atomic disorder on the magnetic phase separation

    NASA Astrophysics Data System (ADS)

    Groshev, A. G.; Arzhnikov, A. K.

    2018-05-01

    The effect of disorder on the magnetic phase separation between the antiferromagnetic and incommensurate helical and phases is investigated. The study is based on the quasi-two-dimensional single-band Hubbard model in the presence of atomic disorder (the Anderson–Hubbard model). A model of binary alloy disorder is considered, in which the disorder is determined by the difference in energy between the host and impurity atomic levels at a fixed impurity concentration. The problem is solved within the theory of functional integration in static approximation. Magnetic phase diagrams are obtained as functions of the temperature, the number of electrons and impurity concentration with allowance for phase separation. It is shown that for the model parameters chosen, the disorder caused by impurities whose atomic-level energy is greater than that of the host atomic levels, leads to qualitative changes in the phase diagram of the impurity-free system. In the opposite case, only quantitative changes occur. The peculiarities of the effect of disorder on the phase separation regions of the quasi-two-dimensional Hubbard model are discussed.

  20. Microstructure Evolution and Related Magnetic Properties of Cu-Zr-Al-Gd Phase-Separating Metallic Glasses

    NASA Astrophysics Data System (ADS)

    Kim, Sang Jun; Kim, Jinwoo; Park, Eun Soo

    2018-04-01

    We carefully investigated the correlation between microstructures and magnetic properties of Cu-Zr-Al-Gd phase-separating metallic glasses (PSMGs). The saturation magnetizations of the PSMGs were determined by total Gd contents of the alloys, while their coercivity exhibits a large deviation by the occurrence of phase separation due to the boundary pinning effect of hierarchically separated amorphous phases. Especially, the PSMGs containing Gd-rich amorphous nanoparticles show the highest coercivity which can be attributed to the size effect of the ferromagnetic amorphous phase. Furthermore, the selective crystallization of ferromagnetic amorphous phases can affect the magnetization behavior of the PSMGs. Our results could provide a novel strategy for tailoring unique soft magnetic properties of metallic glasses by introducing hierarchically separated amorphous phases and controlling their crystallinity.

  1. Microstructure Evolution and Related Magnetic Properties of Cu-Zr-Al-Gd Phase-Separating Metallic Glasses

    NASA Astrophysics Data System (ADS)

    Kim, Sang Jun; Kim, Jinwoo; Park, Eun Soo

    2018-06-01

    We carefully investigated the correlation between microstructures and magnetic properties of Cu-Zr-Al-Gd phase-separating metallic glasses (PSMGs). The saturation magnetizations of the PSMGs were determined by total Gd contents of the alloys, while their coercivity exhibits a large deviation by the occurrence of phase separation due to the boundary pinning effect of hierarchically separated amorphous phases. Especially, the PSMGs containing Gd-rich amorphous nanoparticles show the highest coercivity which can be attributed to the size effect of the ferromagnetic amorphous phase. Furthermore, the selective crystallization of ferromagnetic amorphous phases can affect the magnetization behavior of the PSMGs. Our results could provide a novel strategy for tailoring unique soft magnetic properties of metallic glasses by introducing hierarchically separated amorphous phases and controlling their crystallinity.

  2. Fast Switching Magnet for Heavy Ion Beam Separation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hartzell, Josiah

    2017-10-03

    Fast magnets for multiplexing ion beams between different beamlines are technologically challenging and expensive, but there is an ever-growing need to develop such systems for beam separation at research and industrial facilities. For example, The Argonne Tandem Linac Accelerator System (ATLAS) is planning to expand its operations as a multi-user facility and there is a clear need, presently unmet by the industry, for a switching magnet system with the sub-millisecond transient times.In response to this problem, RadiaBeam Technologies is developing a novel pulsed switching magnet system capable of producing a 1.1T peak field over 45 cm length with a shortmore » (<1 ms) rise and fall time. The key enabling innovation in this project is an introduction of a solid-state interposed modulator architecture, which enables to improve magnet performance and reliability and reduce the cost to a practical level.« less

  3. Measurement of the adhesion force between particles for high gradient magnetic separation of pneumatic conveyed powder products

    NASA Astrophysics Data System (ADS)

    Senkawa, K.; Nakai, Y.; Mishima, F.; Akiyama, Y.; Nishijima, S.

    2011-11-01

    In the industrial plants such as foods, medicines or industrial materials, there are big amount of issues on contamination by metallic wear debris originated from pipes of manufacturing lines. In this study, we developed a high gradient magnetic separation system (HGMS) under the dry process by using superconducting magnet to remove the ferromagnetic particles. One of the major problems of dry HGMS systems is, however, the blockage of magnetic filter caused by particle coagulation or deposition. In order to actualize the magnetic separation without blockage, we introduced pneumatic conveyance system as a new method to feed the powder. It is important to increase the drag force acting on the sufficiently dispersed particles, which require strong magnetic fields. To generate the strong magnetic fields, HGMS technique was examined which consists of a magnetic filter and a superconducting solenoid magnet. As a result of the magnetic separation experiment, it was shown that the separation efficiency changes due to the difference of the cohesive property of the particles. On the basis of the result, the adhesion force which acts between the ferromagnetic particles and the medium particles used for the magnetic separation was measured by Atomic Force Microscope (AFM), and cohesion of particles was studied from the aspect of interparticle interaction. We assessed a suitable flow velocity for magnetic separation according to the cohesive property of each particle based on the result.

  4. Robust w-Estimators for Cryo-EM Class Means

    PubMed Central

    Huang, Chenxi; Tagare, Hemant D.

    2016-01-01

    A critical step in cryogenic electron microscopy (cryo-EM) image analysis is to calculate the average of all images aligned to a projection direction. This average, called the “class mean”, improves the signal-to-noise ratio in single particle reconstruction (SPR). The averaging step is often compromised because of outlier images of ice, contaminants, and particle fragments. Outlier detection and rejection in the majority of current cryo-EM methods is done using cross-correlation with a manually determined threshold. Empirical assessment shows that the performance of these methods is very sensitive to the threshold. This paper proposes an alternative: a “w-estimator” of the average image, which is robust to outliers and which does not use a threshold. Various properties of the estimator, such as consistency and influence function are investigated. An extension of the estimator to images with different contrast transfer functions (CTFs) is also provided. Experiments with simulated and real cryo-EM images show that the proposed estimator performs quite well in the presence of outliers. PMID:26841397

  5. Robust estimation for class averaging in cryo-EM Single Particle Reconstruction.

    PubMed

    Huang, Chenxi; Tagare, Hemant D

    2014-01-01

    Single Particle Reconstruction (SPR) for Cryogenic Electron Microscopy (cryo-EM) aligns and averages the images extracted from micrographs to improve the Signal-to-Noise ratio (SNR). Outliers compromise the fidelity of the averaging. We propose a robust cross-correlation-like w-estimator for combating the effect of outliers on the average images in cryo-EM. The estimator accounts for the natural variation of signal contrast among the images and eliminates the need for a threshold for outlier rejection. We show that the influence function of our estimator is asymptotically bounded. Evaluations of the estimator on simulated and real cryo-EM images show good performance in the presence of outliers.

  6. Alignment Algorithms and Per-Particle CTF Correction for Single Particle Cryo-Electron Tomography

    PubMed Central

    Galaz-Montoya, Jesús G.; Hecksel, Corey W.; Baldwin, Philip R.; Wang, Eryu; Weaver, Scott C.; Schmid, Michael F.; Ludtke, Steven J.; Chiu, Wah

    2016-01-01

    Single particle cryo-electron tomography (cryoSPT) extracts features from cryo-electron tomograms, followed by 3D classification, alignment and averaging to generate improved 3D density maps of such features. Robust methods to correct for the contrast transfer function (CTF) of the electron microscope are necessary for cryoSPT to reach its resolution potential. Many factors can make CTF correction for cryoSPT challenging, such as lack of eucentricity of the specimen stage, inherent low dose per image, specimen charging, beam-induced specimen motions, and defocus gradients resulting both from specimen tilting and from unpredictable ice thickness variations. Current CTF correction methods for cryoET make at least one of the following assumptions: that the defocus at the center of the image is the same across the images of a tiltseries, that the particles all lie at the same Z-height in the embedding ice, and/or that the specimen grid and carbon support are flat. These experimental conditions are not always met. We have developed a CTF correction algorithm for cryoSPT without making any of the aforementioned assumptions. We also introduce speed and accuracy improvements and a higher degree of automation to the subtomogram averaging algorithms available in EMAN2. Using motion-corrected images of isolated virus particles as a benchmark specimen, recorded with a DE20 direct detection camera, we show that our CTF correction and subtomogram alignment routines can yield subtomogram averages close to 4/5 Nyquist frequency of the detector under our experimental conditions. PMID:27016284

  7. Cryo-Electron Microscopy of Viruses Infecting Bacterium

    NASA Astrophysics Data System (ADS)

    Chiu, Wah

    2010-03-01

    Single particle cryo-EM can yield structures of infectious bacterial viruses with and without imposed icosahedral symmetry at subnanometer resolution. Reconstructions of infectious and empty phage particles show substantial differences in the portal vertex protein complex at one of the 12 pentameric vertices in the icosahedral virus particle through which the viral genomes are packaged or released. In addition, electron cryo-tomography of viruses during infecting its bacterial host cell displayed multiple conformations of the tail fiber of the virus. Our structural observations by single particle and tomographic reconstructions suggest a mechanism whereby the viral tail fibers, upon binding to the host cell, induce a cascade of structural alterations of the portal vertex protein complex that triggers DNA release.

  8. Removal of less biodegradable dissolved organic matters in water by superconducting magnetic separation with magnetic mesoporous carbon

    NASA Astrophysics Data System (ADS)

    Kondo, K.; Jin, T.; Miura, O.

    2010-11-01

    Less biodegradable dissolved organic matters in water as typified by humic substances are known as precursors of carcinogenic trihalomethanes, and are removed about 60% by current advanced water treatments. However, further increase of the removal ratio is demand. In this study, magnetic mesoporous carbon (MMPC), which can adsorb the substances physically and be efficiently collected by using superconducting high gradient magnetic separation (HGMS), has been synthesized with coconut-shell-based activated carbon and ferric nitrate solution by the gas activation method. The MMPC has the maximum magnetization value of 30.7 emu/g and an adsorption ability of 87% to 10 mg/L humic acid in a short time. The standard MMPC having a magnetization of 6.43 emu/g was able to be separated at magnetic field of 2 T. Used MMPC regained the adsorption ability to 93.1% by N2 reactivation heat treatment. These results show promise for application of current water treatments by superconducting HGMS, which is suitable for high-speed water treatment without secondary wastes.

  9. Protein secondary structure determination by constrained single-particle cryo-electron tomography.

    PubMed

    Bartesaghi, Alberto; Lecumberry, Federico; Sapiro, Guillermo; Subramaniam, Sriram

    2012-12-05

    Cryo-electron microscopy (cryo-EM) is a powerful technique for 3D structure determination of protein complexes by averaging information from individual molecular images. The resolutions that can be achieved with single-particle cryo-EM are frequently limited by inaccuracies in assigning molecular orientations based solely on 2D projection images. Tomographic data collection schemes, however, provide powerful constraints that can be used to more accurately determine molecular orientations necessary for 3D reconstruction. Here, we propose "constrained single-particle tomography" as a general strategy for 3D structure determination in cryo-EM. A key component of our approach is the effective use of images recorded in tilt series to extract high-resolution information and correct for the contrast transfer function. By incorporating geometric constraints into the refinement to improve orientational accuracy of images, we reduce model bias and overrefinement artifacts and demonstrate that protein structures can be determined at resolutions of ∼8 Å starting from low-dose tomographic tilt series. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Application and Prospect of Superconducting High Gradient Magnetic Separation in Disposal of Micro-fine Tailings

    NASA Astrophysics Data System (ADS)

    Yang, Changqiao; Li, Suqin; Guo, Zijie; Kong, Jiawei

    2017-12-01

    Magnetic separation technology is playing an increasingly important role in the field of environmental protection such as waste gas, waste water and solid waste treatment. As a new type of solid waste treatment technology, superconducting high gradient magnetic separation (HGMS) is mainly applied in the separation of micro-fine weakly magnetic particles because of the advantages of high separation efficiency, energy saving, simple equipment and easy automation. In this paper, the basic principle of superconducting HGMS was firstly introduced, then the research status of scholars at home and aboard on the disposal of micro-fine tailings were summarized. Finally, the direction of development for HGMS was put forward.

  11. Amine-functionalized magnetic mesoporous silica nanoparticles for DNA separation

    NASA Astrophysics Data System (ADS)

    Sheng, Wei; Wei, Wei; Li, Junjian; Qi, Xiaoliang; Zuo, Gancheng; Chen, Qi; Pan, Xihao; Dong, Wei

    2016-11-01

    We report a modified approach for the functionalized magnetic mesoporous silica nanoparticles (MMSN) using polymer microspheres incorporated with magnetic nanoparticles in the presence of cetyltrimethylammonium bromide (CTAB) and the core-shell magnetic silica nanoparticles (MSN). These particles were functionalized with amino groups via the addition of aminosilane directly to the particle sol. We then evaluate their DNA separation abilities and find the capacity of DNA binding significantly increased (210.22 μg/mg) compared with normal magnetic silica spheres (138.44 μg/mg) by using an ultraviolet and visible spectrophotometer (UV). The morphologies, magnetic properties, particle size, pore size, core-shell structure and Zeta potential are characterized by Fourier transform infrared spectroscopy (FT-IR), vibrating sample magnetometer (VSM), Transmission electron microscopy (TEM), Powder X-ray diffraction (XRD), and dynamic light scattering (DLS). This work demonstrates that our MMSN own an excellent potential application in bioseparation and drug delivery.

  12. Label-free visualization of ultrastructural features of artificial synapses via cryo-EM.

    PubMed

    Gopalakrishnan, Gopakumar; Yam, Patricia T; Madwar, Carolin; Bostina, Mihnea; Rouiller, Isabelle; Colman, David R; Lennox, R Bruce

    2011-12-21

    The ultrastructural details of presynapses formed between artificial substrates of submicrometer silica beads and hippocampal neurons are visualized via cryo-electron microscopy (cryo-EM). The silica beads are derivatized by poly-d-lysine or lipid bilayers. Molecular features known to exist at presynapses are clearly present at these artificial synapses, as visualized by cryo-EM. Key synaptic features such as the membrane contact area at synaptic junctions, the presynaptic bouton containing presynaptic vesicles, as well as microtubular structures can be identified. This is the first report of the direct, label-free observation of ultrastructural details of artificial synapses.

  13. Airborne surveys in the Arctic and Antarctic for geophysics, sea-ice thickness, and CryoSat validation

    NASA Astrophysics Data System (ADS)

    Forsberg, R.; Olesen, A. V.; Hvidegaard, S.; Skourup, H.

    2010-12-01

    Airborne laser and radar measurements over the Greenland ice sheet, Svalbard, and adjacent parts of the Arctic Ocean have been carried out by DTU-Space in a number of recent Danish/Greenlandic and European project campaigns, with the purpose to monitor ice sheet and sea-ice changes, support of Greenland societal needs (oil exploration and hydropower), and support of CryoSat pre-launch calibration and validation campaigns. The Arctic campaigns have been done using a Twin-Otter aircraft, carrying laser scanners and various radars. Since 2009 a new program of long-range gravity and magnetic surveys have been initiated using a Basler DC3 aircraft for large-scale surveys in the Arctic Ocean and Antarctica, with the 2010 cooperative Danish-Argentinean-Chilean-US ICEGRAV survey of the Antarctic Peninsula additionally including a UTIG 60 MHz ice-penetrating radar. In the paper we outline the recent and upcoming airborne survey activities, outline the usefulness of the airborne data for satellite validation (CryoSat and GOCE), and give examples of measurements and comparisons to satellite and in-situ data.

  14. Cryo-tomography Tilt-series Alignment with Consideration of the Beam-induced Sample Motion

    PubMed Central

    Fernandez, Jose-Jesus; Li, Sam; Bharat, Tanmay A. M.; Agard, David A.

    2018-01-01

    Recent evidence suggests that the beam-induced motion of the sample during tilt-series acquisition is a major resolution-limiting factor in electron cryo-tomography (cryoET). It causes suboptimal tilt-series alignment and thus deterioration of the reconstruction quality. Here we present a novel approach to tilt-series alignment and tomographic reconstruction that considers the beam-induced sample motion through the tilt-series. It extends the standard fiducial-based alignment approach in cryoET by introducing quadratic polynomials to model the sample motion. The model can be used during reconstruction to yield a motion-compensated tomogram. We evaluated our method on various datasets with different sample sizes. The results demonstrate that our method could be a useful tool to improve the quality of tomograms and the resolution in cryoET. PMID:29410148

  15. Automatic Stem Cell Detection in Microscopic Whole Mouse Cryo-imaging

    PubMed Central

    Wuttisarnwattana, Patiwet; Gargesha, Madhusudhana; Hof, Wouter van’t; Cooke, Kenneth R.

    2016-01-01

    With its single cell sensitivity over volumes as large as or larger than a mouse, cryo-imaging enables imaging of stem cell biodistribution, homing, engraftment, and molecular mechanisms. We developed and evaluated a highly automated software tool to detect fluorescently labeled stem cells within very large (~200GB) cryo-imaging datasets. Cell detection steps are: preprocess, remove immaterial regions, spatially filter to create features, identify candidate pixels, classify pixels using bagging decision trees, segment cell patches, and perform 3D labeling. There are options for analysis and visualization. To train the classifier, we created synthetic images by placing realistic digital cell models onto cryo-images of control mice devoid of cells. Very good cell detection results were (precision=98.49%, recall=99.97%) for synthetic cryo-images, (precision=97.81%, recall=97.71%) for manually evaluated, actual cryo-images, and <1% false positives in control mice. An α-multiplier applied to features allows one to correct for experimental variations in cell brightness due to labeling. On dim cells (37% of standard brightness), with correction, we improved recall (49.26%→99.36%) without a significant drop in precision (99.99%→99.75%). With tail vein injection, multipotent adult progenitor cells in a graft-versus-host-disease model in the first days post injection were predominantly found in lung, liver, spleen, and bone marrow. Distribution was not simply related to blood flow. The lung contained clusters of cells while other tissues contained single cells. Our methods provided stem cell distribution anywhere in mouse with single cell sensitivity. Methods should provide a rational means of evaluating dosing, delivery methods, cell enhancements, and mechanisms for therapeutic cells. PMID:26552080

  16. Effect of atomic disorder on the magnetic phase separation.

    PubMed

    Groshev, A G; Arzhnikov, A K

    2018-05-10

    The effect of disorder on the magnetic phase separation between the antiferromagnetic and incommensurate helical [Formula: see text] and [Formula: see text] phases is investigated. The study is based on the quasi-two-dimensional single-band Hubbard model in the presence of atomic disorder (the [Formula: see text] Anderson-Hubbard model). A model of binary alloy disorder is considered, in which the disorder is determined by the difference in energy between the host and impurity atomic levels at a fixed impurity concentration. The problem is solved within the theory of functional integration in static approximation. Magnetic phase diagrams are obtained as functions of the temperature, the number of electrons and impurity concentration with allowance for phase separation. It is shown that for the model parameters chosen, the disorder caused by impurities whose atomic-level energy is greater than that of the host atomic levels, leads to qualitative changes in the phase diagram of the impurity-free system. In the opposite case, only quantitative changes occur. The peculiarities of the effect of disorder on the phase separation regions of the quasi-two-dimensional Hubbard model are discussed.

  17. High Radiation Environment Nuclear Fragment Separator Magnet

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kahn, Stephen; Gupta, Ramesh

    2016-01-31

    Superconducting coils wound with HTS conductor can be used in magnets located in a high radiation environment. NbTi and Nb 3Sn superconductors must operate at 4.5 K or below where removal of heat is less efficient. The HTS conductor can carry significant current at higher temperatures where the Carnot efficiency is significantly more favorable and where the coolant heat capacity is much larger. Using the HTS conductor the magnet can be operated at 40 K. This project examines the use of HTS conductor for the Michigan State University Facility For Rare Isotope Beams (FRIB) fragment separator dipole magnet which bendsmore » the beam by 30° and is located in a high radiation region that will not be easily accessible. Two of these magnets are needed to select the chosen isotope. There are a number of technical challenges to be addressed in the design of this magnet. The separator dipole is 2 m long and subtends a large angle. The magnet should keep a constant transverse field profile along its beam reference path. Winding coils with a curved inner segment is difficult as the conductor will tend to unwind during the process. In the Phase I project two approaches to winding the conductor were examined. The first was to wind the coils with curved sections on the inner and outer segments with the inner segment wound with negative curvature. The alternate approach was to use a straight segment on the inner segment to avoid negative curvature. In Phase I coils with a limited number of turns were successfully wound and tested at 77 K for both coil configurations. The Phase II program concentrated on the design, coil winding procedures, structural analysis, prototyping and testing of an HTS curved dipole coil at 40 K with a heat load representative of the radiation environment. One of the key criteria of the design of this magnet is to avoid the use of organic materials that would degrade rapidly in radiation. The Lorentz forces expected from the coils interacting with the

  18. Cryo-balloon catheter position planning using AFiT

    NASA Astrophysics Data System (ADS)

    Kleinoeder, Andreas; Brost, Alexander; Bourier, Felix; Koch, Martin; Kurzidim, Klaus; Hornegger, Joachim; Strobel, Norbert

    2012-02-01

    Atrial fibrillation (AFib) is the most common heart arrhythmia. In certain situations, it can result in life-threatening complications such as stroke and heart failure. For paroxsysmal AFib, pulmonary vein isolation (PVI) by catheter ablation is the recommended choice of treatment if drug therapy fails. During minimally invasive procedures, electrically active tissue around the pulmonary veins is destroyed by either applying heat or cryothermal energy to the tissue. The procedure is usually performed in electrophysiology labs under fluoroscopic guidance. Besides radio-frequency catheter ablation devices, so-called single-shot devices, e.g., the cryothermal balloon catheters, are receiving more and more interest in the electrophysiology (EP) community. Single-shot devices may be advantageous for certain cases, since they can simplify the creation of contiguous (gapless) lesion sets around the pulmonary vein which is needed to achieve PVI. In many cases, a 3-D (CT, MRI, or C-arm CT) image of a patient's left atrium is available. This data can then be used for planning purposes and for supporting catheter navigation during the procedure. Cryo-thermal balloon catheters are commercially available in two different sizes. We propose the Atrial Fibrillation Planning Tool (AFiT), which visualizes the segmented left atrium as well as multiple cryo-balloon catheters within a virtual reality, to find out how well cryo-balloons fit to the anatomy of a patient's left atrium. First evaluations have shown that AFiT helps physicians in two ways. First, they can better assess whether cryoballoon ablation or RF ablation is the treatment of choice at all. Second, they can select the proper-size cryo-balloon catheter with more confidence.

  19. Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

    PubMed

    Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

    2016-09-26

    Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

  20. Cryopreservation on a cryo-plate of Arundina graminifolia protocorms, dehydrated with silica gel and drying beads.

    PubMed

    Cordova, L B; Thammasiri, K

    2016-01-01

    There are various methods for the cryopreservation of plant material, with each biological specimen potentially requiring protocol optimization to maximize success. The aim of this study is to compare droplet-vitrification, encapsulation-dehydration, and the cryo-plate method for cryopreservation of protocorms of the orchid Arundina graminifolia, using silica gel and drying beads as the desiccation materials. The cryo-plate method included preculture of protocorms, developed from seeds, placed on aluminium cryo-plates and embedded in alginate gel. Cryo-plates were surface dried using sterile filter paper, placed in Petri dishes containing 50 g silica gel or 30 g drying beads in a laminar air-flow cabinet. Specimens on cryo-plates were dehydrated to 25 % moisture content, placed into 2 mL cryotubes and plunged directly into liquid nitrogen for 1 d. For cryopreservation, the cryo-plate method, involving dehydration with 30 g drying beads gave the highest regrowth (77 %), followed by the encapsulation-dehydration method with 30 g drying beads (64 % regrowth) and the droplet-vitrification method, following exposure to PVS2 solution for 20 min (33 % regrowth). Regrowth of cryopreserved protocorms using the cryo-plate method was rapid with the highest survival and regrowth.

  1. Selective binding and magnetic separation of His-tagged proteins using Fe3O4/PAM/NTA-Ni2+ Magnetic Nanoparticles

    NASA Astrophysics Data System (ADS)

    Guo, Huiling; Li, Mengyun; Tu, Shu; Sun, Honghao

    2018-03-01

    Fe3O4 nanoparticles coated with polyacrylamide (PAM) were synthesized. The magnetic core, with an average hydrodynamic size of 235.5 nm, allowed the magnetic nanoparticles (MNPs) rapid separation from solutions under an external magnetic field. NTA-Ni2+ was modified on the surface of Fe3O4/PAM MNPs to selectively trap his-tagged green fluorescent protein (GFP). The results showed that Fe3O4/PAM/NTA-Ni2+ MNPs exhibited remarkable capability of selective binding and separating his-tagged GFP. The adsorption efficiency was 93.37%.

  2. Cryo-electron microscopy of membrane proteins.

    PubMed

    Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning

    2014-01-01

    Electron crystallography is used to study membrane proteins in the form of planar, two-dimensional (2D) crystals, or other crystalline arrays such as tubular crystals. This method has been used to determine the atomic resolution structures of bacteriorhodopsin, tubulin, aquaporins, and several other membrane proteins. In addition, a large number of membrane protein structures were studied at a slightly lower resolution, whereby at least secondary structure motifs could be identified.In order to conserve the structural details of delicate crystalline arrays, cryo-electron microscopy (cryo-EM) allows imaging and/or electron diffraction of membrane proteins in their close-to-native state within a lipid bilayer membrane.To achieve ultimate high-resolution structural information of 2D crystals, meticulous sample preparation for electron crystallography is of outmost importance. Beam-induced specimen drift and lack of specimen flatness can severely affect the attainable resolution of images for tilted samples. Sample preparations that sandwich the 2D crystals between symmetrical carbon films reduce the beam-induced specimen drift, and the flatness of the preparations can be optimized by the choice of the grid material and the preparation protocol.Data collection in the cryo-electron microscope using either the imaging or the electron diffraction mode has to be performed applying low-dose procedures. Spot-scanning further reduces the effects of beam-induced drift. Data collection using automated acquisition schemes, along with improved and user-friendlier data processing software, is increasingly being used and is likely to bring the technique to a wider user base.

  3. Trichoderma sp. spores and Kluyveromyces marxianus cells magnetic separation: Immobilization on chitosan-coated magnetic nanoparticles.

    PubMed

    Palacios-Ponce, Sócrates; Ramos-González, Rodolfo; Ruiz, Héctor A; Aguilar, Miguel A; Martínez-Hernández, José L; Segura-Ceniceros, Elda P; Aguilar, Cristóbal N; Michelena, Georgina; Ilyina, Anna

    2017-07-03

    In the present study, the interactions between chitosan-coated magnetic nanoparticles (C-MNP) and Trichoderma sp. spores as well as Kluyveromyces marxianus cells were studied. By Plackett-Burman design, it was demonstrated that factors which directly influenced on yeast cell immobilization and magnetic separation were inoculum and C-MNP quantity, stirring speed, interaction time, and volume of medium, while in the case of fungal spores, the temperature also was disclosed as an influencing factor. Langmuir and Freundlich models were applied for the mathematical analysis of adsorption isotherms at 30°C. For Trichoderma sp. spore adsorption isotherm, the highest correlation coefficient was observed for lineal function of Langmuir model with a maximum adsorption capacity at 5.00E + 09 spores (C-MNP g -1 ). Adsorption isotherm of K. marxianus cells was better adjusted to Freundlich model with a constant (K f ) estimated as 2.05E + 08 cells (C-MNP g -1 ). Both systems may have a novel application in fermentation processes assisted with magnetic separation of biomass.

  4. CryoCart Restoration and Vacuum Pipe Construction

    NASA Technical Reports Server (NTRS)

    Chaidez, Mariana

    2016-01-01

    first completed at the component level. During this process, the igniter of the main engine and the RCS thrusters will be tested under a vacuum. To complete the testing of the components, the test setup first needed to be finalized. The CryoCart is being used to feed the propellants to the test article. The CryoCart is a movable test set-up that was developed in 2009 to provide a mobile platform for testing oxygen/methane systems with hot-fire capability up to 100 lbf. The CryoCart consists of three different systems: Oxygen, Methane, and liquid Nitrogen. The Oxygen and Methane systems are placed into two different carts while the liquid nitrogen system is mainly located in the methane cart. Over the years, the CryoCart has been utilized for different projects and has undergone deterioration. For this reason, a new phase has been developed to rebuild it to working conditions once again. During my internship, I was aiding in the construction and restoration of the CryoCart. In the initial stages of the process, I updated the fluid and electrical schematics for the oxygen, methane, and test article systems. The original CryoCart consisted of an electrical panel that utilized electromechanical relays and a terminal to drive the igniter power and signal, as well as the main fuel and oxygen valves. This electrical panel connected to the CryoCart through various wire harnesses that could be found exiting from the CryoCart. First, it was determined how these harnesses connected to the electromechanical relays so that they worked correctly. Once the electrical system was understood, an alternative for the electromechanical relays and the Molex connectors used throughout the system was sought since these components can often prove to be unreliable. Solid State relays and MIL connectors were purchased to serve as replacements. Upon arrival of the parts, crimping and wiring was completed to install the new solid state relays and MIL connectors. During the replacement of the relays

  5. EMRinger: side chain–directed model and map validation for 3D cryo-electron microscopy

    DOE PAGES

    Barad, Benjamin A.; Echols, Nathaniel; Wang, Ray Yu-Ruei; ...

    2015-08-17

    Advances in high-resolution cryo-electron microscopy (cryo-EM) require the development of validation metrics to independently assess map quality and model geometry. We report that EMRinger is a tool that assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger (https://github.com/fraser-lab/EMRinger) will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

  6. Limiting factors in atomic resolution cryo electron microscopy: No simple tricks

    PubMed Central

    Zhang, Xing; Zhou, Z. Hong

    2013-01-01

    To bring cryo electron microscopy (cryoEM) of large biological complexes to atomic resolution, several factors – in both cryoEM image acquisition and 3D reconstruction – that may be neglected at low resolution become significantly limiting. Here we present thorough analyses of four limiting factors: (a) electron-beam tilt, (b) inaccurate determination of defocus values, (c) focus gradient through particles, and (d) particularly for large particles, dynamic (multiple) scattering of electrons. We also propose strategies to cope with these factors: (a) the divergence and direction tilt components of electron-beam tilt could be reduced by maintaining parallel illumination and by using a coma-free alignment procedure, respectively. Moreover, the effect of all beam tilt components, including spiral tilt, could be eliminated by use of a spherical aberration corrector. (b) More accurate measurement of defocus value could be obtained by imaging areas adjacent to the target area at high electron dose and by measuring the image shift induced by tilting the electron beam. (c) Each known Fourier coefficient in the Fourier transform of a cryoEM image is the sum of two Fourier coefficients of the 3D structure, one on each of two curved ‘characteristic surfaces’ in 3D Fourier space. We describe a simple model-based iterative method that could recover these two Fourier coefficients on the two characteristic surfaces. (d) The effect of dynamic scattering could be corrected by deconvolution of a transfer function. These analyses and our proposed strategies offer useful guidance for future experimental designs targeting atomic resolution cryoEM reconstruction. PMID:21627992

  7. Beneficiation of Turkish lignites by thermal treatment and magnetic separation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Onal, G.; Renda, D.; Mustafaev, I.

    1999-07-01

    In this paper, the improvement of Turkish lignites by semi-coking and REMS magnetic separation, in two stages, is discussed. The oxidation and decomposition of pyrite through the thermal treatment result in the formation of iron oxide and pyrrhotite on the surface. In addition to pyrite, part of the organic sulfur is also removed. After thermal treatment of lignites at temperatures ranging from 370 to 650 C, the application of REMS magnetic separator produces a product higher in calorific value and lower in sulfur content. The product can be utilized after briquetting. The volatile gases can also be used after sulfurmore » removal. This process appears to be feasible as a clean coal manufacture from the point of energy efficiency. A short economic analysis is also presented.« less

  8. Improved Oceanographic Measurements with CryoSat SAR Altimetry: Applications to the Coastal Zone and Arctic

    NASA Astrophysics Data System (ADS)

    Cotton, D.; Garcia, P. N.; Cancet, M.; Andersen, O.; Stenseng, L.; Martin, F.; Cipollini, P.; Calafat, F. M.; Passaro, M.; Restano, M.; Ambrozio, A.; Benveniste, J.

    2016-08-01

    The ESA CryoSat-2 mission is the first space mission to carry a radar altimeter that can operate in Synthetic Aperture Radar (SAR) mode. Although the prime objective of the CryoSat-2 mission is dedicated to monitoring land and marine ice, the SAR mode capability of the CryoSat-2 SIRAL altimeter also presents significant potential benefits for ocean applications including improved range precision and finer along track spatial resolution.The "CryoSat Plus for Oceans" (CP4O) project, supported by the ESA Support to Science Element (STSE) Programme and by CNES, was dedicated to the exploitation of CryoSat-2 data over the open and coastal ocean. The general objectives of the CP4O project were: to build a sound scientific basis for new oceanographic applications of CryoSat-2 data; to generate and evaluate new methods and products that will enable the full exploitation of the capabilities of the CryoSat-2 SIRAL altimeter, and to ensure that the scientific return of the CryoSat-2 mission is maximised. Cotton et al, (2015) is the final report on this work.However, whilst the results from CP4O were highly promising and confirmed the potential of SAR altimetry to support new scientific and operational oceanographic applications, it was also apparent that further work was needed in some key areas to fully realise the original project objectives. Thus additional work in four areas has been supported by ESA under a Contract Change Notice:• Developments in SARin data processing for Coastal Altimetry (isardSAT).• Implementation of a Regional Tidal Atlas for the Arctic Ocean (Noveltis and DTU Space).• Improvements to the SAMOSA re-tracker: Implementation and Evaluation- Optimised Thermal Noise Estimation. (Starlab and SatOC).• Extended evaluation of CryoSat-2 SAR data for Coastal Applications (NOC).This work was managed by SatOC. The results of this work are summarized here. Detailed information regarding the CP4O project can be found at: http://www.satoc.eu/projects/CP4O/

  9. Method and apparatus for separating materials magnetically. [Patent application; iron pyrite from coal

    DOEpatents

    Hise, E.C. Jr.; Holman, A.S.; Friedlaender, F.J.

    1980-11-06

    Magnetic and nonmagnetic materials are separated by passing stream thereof past coaxial current-carrying coils which produce a magnetic field wherein intensity varies sharply with distance radially of the axis of the coils.

  10. The Concept Of A Potential Operational CryoSat Follow-on Mission

    NASA Astrophysics Data System (ADS)

    Cullen, R.

    2016-12-01

    CryoSat was a planned as a 3 year mission with clear mission objectives to allow the assessment rates of change of thickness in the land and marine ice fields with reduced uncertainties with relation to other non-dedicated missions. Although CryoSat suffered a launch failure in Oct 2005, the mission was recovered with a launch in April 2010 of CryoSat-2. The nominal mission has now been completed, all mission requirements have been fulfilled and CryoSat has been shown to be most successful as a dedicated polar ice sheet measurement system demonstrated by nearly 200 peer reviewed publications within the first four years of launch. Following the completion of the nominal mission in Oct 2013 the platform was shown to be in good health and with a scientific backing provided by the ESA Earth Science Advisory Committee (ESAC) the mission has been extended until Feb 2017 by the ESA Programme Board for Earth Observation. Though not designed to provide data for science and operational services beyond its original mission requirements, a number of services have been developed for exploitation and these are expected to increase over the next few years. Services cover a number of aspects of land and marine ice fields in addition to complementary activities covering glacial monitoring, inland water in addition to coastal and open ocean surface topography science that CryoSat has demonstrated world leading advances with. This paper will present the overall concept for a potential low-cost continuity to the CryoSat mission with the objective to provide both continuity of the existing CryoSat based data sets, i.e., longer term science and operational services that cannot be provided by the existing Copernicus complement of satellites. This is, in part, due to the high inclination (92°) drifting orbit and state of the art Synthetic Aperture Interferometer Radar Altimeter (SIRAL). In addition, further improvements in performance are expected by use of improved modes of operation

  11. A Potential Operational CryoSat Follow-on Mission Concept and Design

    NASA Astrophysics Data System (ADS)

    Cullen, R.

    2015-12-01

    CryoSat was a planned as a 3 year mission with clear mission objectives to allow the assessment rates of change of thickness in the land and marine ice fields with reduced uncertainties with relation to other non-dedicated missions. Although CryoSat suffered a launch failure in Oct 2005, the mission was recovered with a launch in April 2010 of CryoSat-2. The nominal mission has now been completed, all mission requirements have been fulfilled and CryoSat has been shown to be most successful as a dedicated polar ice sheet measurement system demonstrated by nearly 200 peer reviewed publications within the first four years of launch. Following the completion of the nominal mission in Oct 2013 the platform was shown to be in good health and with a scientific backing provided by the ESA Earth Science Advisory Committee (ESAC) the mission has been extended until Feb 2017 by the ESA Programme Board for Earth Observation. Though not designed to provide data for science and operational services beyond its original mission requirements, a number of services have been developed for exploitation and these are expected to increase over the next few years. Services cover a number of aspects of land and marine ice fields in addition to complementary activities covering glacial monitoring, inland water in addition to coastal and open ocean surface topography science that CryoSat has demonstrated world leading advances with. This paper will present the overall concept for a potential low-cost follow-on to the CryoSat mission with the objective to provide both continuity of the existing CryoSat based data sets, i.e., longer term science and operational services that cannot be provided by the existing Copernicus complement of satellites. This is, in part, due to the high inclination (92°) drifting orbit and state of the art Synthetic Aperture Interferometer Radar Altimeter (SIRAL). In addition, further improvements in performance are expected by use of the instrument timing and

  12. Effect of the Hartmann number on phase separation controlled by magnetic field for binary mixture system with large component ratio

    NASA Astrophysics Data System (ADS)

    Heping, Wang; Xiaoguang, Li; Duyang, Zang; Rui, Hu; Xingguo, Geng

    2017-11-01

    This paper presents an exploration for phase separation in a magnetic field using a coupled lattice Boltzmann method (LBM) with magnetohydrodynamics (MHD). The left vertical wall was kept at a constant magnetic field. Simulations were conducted by the strong magnetic field to enhance phase separation and increase the size of separated phases. The focus was on the effect of magnetic intensity by defining the Hartmann number (Ha) on the phase separation properties. The numerical investigation was carried out for different governing parameters, namely Ha and the component ratio of the mixed liquid. The effective morphological evolutions of phase separation in different magnetic fields were demonstrated. The patterns showed that the slant elliptical phases were created by increasing Ha, due to the formation and increase of magnetic torque and force. The dataset was rearranged for growth kinetics of magnetic phase separation in a plot by spherically averaged structure factor and the ratio of separated phases and total system. The results indicate that the increase in Ha can increase the average size of separated phases and accelerate the spinodal decomposition and domain growth stages. Specially for the larger component ratio of mixed phases, the separation degree was also significantly improved by increasing magnetic intensity. These numerical results provide guidance for setting the optimum condition for the phase separation induced by magnetic field.

  13. High-resolution cryo-EM proteasome structures in drug development

    PubMed Central

    da Fonseca, Paula C. A.

    2017-01-01

    With the recent advances in biological structural electron microscopy (EM), protein structures can now be obtained by cryo-EM and single-particle analysis at resolutions that used to be achievable only by crystallographic or NMR methods. We have explored their application to study protein–ligand inter­actions using the human 20S proteasome, a well established target for cancer therapy that is also being investigated as a target for an increasing range of other medical conditions. The map of a ligand-bound human 20S proteasome served as a proof of principle that cryo-EM is emerging as a realistic approach for more general structural studies of protein–ligand interactions, with the potential benefits of extending such studies to complexes that are unfavourable to other methods and allowing structure determination under conditions that are closer to physiological, preserving ligand specificity towards closely related binding sites. Subsequently, the cryo-EM structure of the Plasmodium falciparum 20S proteasome, with a new prototype specific inhibitor bound, revealed the molecular basis for the ligand specificity towards the parasite complex, which provides a framework to guide the development of highly needed new-generation antimalarials. Here, the cryo-EM analysis of the ligand-bound human and P. falciparum 20S proteasomes is reviewed, and a complete description of the methods used for structure determination is provided, including the strategy to overcome the bias orientation of the human 20S proteasome on electron-microscope grids and details of the icr3d software used for three-dimensional reconstruction. PMID:28580914

  14. Volta phase plate data collection facilitates image processing and cryo-EM structure determination.

    PubMed

    von Loeffelholz, Ottilie; Papai, Gabor; Danev, Radostin; Myasnikov, Alexander G; Natchiar, S Kundhavai; Hazemann, Isabelle; Ménétret, Jean-François; Klaholz, Bruno P

    2018-06-01

    A current bottleneck in structure determination of macromolecular complexes by cryo electron microscopy (cryo-EM) is the large amount of data needed to obtain high-resolution 3D reconstructions, including through sorting into different conformations and compositions with advanced image processing. Additionally, it may be difficult to visualize small ligands that bind in sub-stoichiometric levels. Volta phase plates (VPP) introduce a phase shift in the contrast transfer and drastically increase the contrast of the recorded low-dose cryo-EM images while preserving high frequency information. Here we present a comparative study to address the behavior of different data sets during image processing and quantify important parameters during structure refinement. The automated data collection was done from the same human ribosome sample either as a conventional defocus range dataset or with a Volta phase plate close to focus (cfVPP) or with a small defocus (dfVPP). The analysis of image processing parameters shows that dfVPP data behave more robustly during cryo-EM structure refinement because particle alignments, Euler angle assignments and 2D & 3D classifications behave more stably and converge faster. In particular, less particle images are required to reach the same resolution in the 3D reconstructions. Finally, we find that defocus range data collection is also applicable to VPP. This study shows that data processing and cryo-EM map interpretation, including atomic model refinement, are facilitated significantly by performing VPP cryo-EM, which will have an important impact on structural biology. Copyright © 2018 Elsevier Inc. All rights reserved.

  15. [Development of new magnetic bead separation and purification instrument].

    PubMed

    Xu, Yingyuan; Chen, Yi

    2014-05-01

    The article describes the development of new magnetic bead separation and purification instrument. The main application of the instrument is to capture tubercle bacillus from sputum. It is a pretreatment instrument and provides a new platform to help doctors to diagnose bacillary phthisis. Not only could it be used for tubercle bacillus capturing, but also for gene, protein and cell separating and purification. Because the controller of the instrument is 16-bit single chip microcomputer, the cost could be greatly reduced and it will be widely used in China.

  16. Cryo-electron tomography investigation of serum albumin-camouflaged tobacco mosaic virus nanoparticles.

    PubMed

    Gulati, Neetu M; Pitek, Andrzej S; Steinmetz, Nicole F; Stewart, Phoebe L

    2017-03-09

    Nanoparticles offer great potential in drug delivery and imaging, but shielding strategies are necessary to increase circulation time and performance. Structure-function studies are required to define the design rules to achieve effective shielding. With several formulations reaching clinical testing and approval, the ability to assess and detail nanoparticle formulations at the single particle level is becoming increasingly important. To address this need, we use cryo-electron tomography (cryo-ET) to investigate stealth-coated nanoparticles. As a model system, we studied the soft matter nanotubes formed by tobacco mosaic virus (TMV) coated with human serum albumin (SA) stealth proteins. Cryo-ET and subtomogram averaging allow for visualization of individual SA molecules and determination of their orientations relative to the TMV surface, and also for measurement of the surface coverage provided by added stealth proteins. This information fills a critical gap in the understanding of the structural morphology of stealth-coated nanoparticles, and therefore cryo-ET may play an important role in guiding the development of future nanoparticle-based therapeutics.

  17. A Toolkit For CryoSat Investigations By The ESRIN EOP-SER Altimetry Team

    NASA Astrophysics Data System (ADS)

    Dinardo, Salvatore; Bruno, Lucas; Benveniste, Jerome

    2013-12-01

    The scope of this work is to feature the new tool for the exploitation of the CryoSat data, designed and developed entirely by the Altimetry Team at ESRIN EOP-SER (Earth Observation - Exploitation, Research and Development). The tool framework is composed of two separate components: the first one handles the data collection and management, the second one is the processing toolkit. The CryoSat FBR (Full Bit Rate) data is downlinked uncompressed from the satellite, containing un-averaged individual echoes. This data is made available in the Kiruna CalVal server in a 10 day rolling archive. Daily at ESRIN all the CryoSat FBR data, in SAR and SARin Mode, are downloaded (around 30 Gigabytes) catalogued and archived in local ESRIN EOP-SER workstations. As of March 2013, the total amount of FBR data is over 9 Terabytes, with CryoSat acquisition dates spanning January 2011 to February 2013 (with some gaps). This archive was built by merging partial datasets available at ESTEC and NOAA, that have been kindly made available for EOP-SER team. The on-demand access to this low level data is restricted to expert users with validated ESA P.I. credentials. Currently the main users of the archiving functionality are the team members of the Project CP4O (STSE- CryoSat Plus for Ocean), CNES and NOAA. The second component of the service is the processing toolkit. On the EOP-SER workstations there is internally and independently developed software that is able to process the FBR data in SAR/SARin mode to generate multi-looked echoes (Level 1B) and subsequently able to re-track them in SAR and SARin mode (Level 2) over open ocean, exploiting the SAMOSA model and other internally developed models. The processing segment is used for research & development scopes, supporting the development contracts awarded confronting the deliverables to ESA, on site demonstrations/training to selected users, cross- comparison against third part products (CLS/CNES CPP Products for instance), preparation

  18. A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments.

    PubMed

    Comolli, Luis R; Duarte, Robert; Baum, Dennis; Luef, Birgit; Downing, Kenneth H; Larson, David M; Csencsits, Roseann; Banfield, Jillian F

    2012-06-01

    We present a modern, light portable device specifically designed for environmental samples for cryogenic transmission-electron microscopy (cryo-TEM) by on-site cryo-plunging. The power of cryo-TEM comes from preparation of artifact-free samples. However, in many studies, the samples must be collected at remote field locations, and the time involved in transporting samples back to the laboratory for cryogenic preservation can lead to severe degradation artifacts. Thus, going back to the basics, we developed a simple mechanical device that is light and easy to transport on foot yet effective. With the system design presented here we are able to obtain cryo-samples of microbes and microbial communities not possible to culture, in their near-intact environmental conditions as well as in routine laboratory work, and in real time. This methodology thus enables us to bring the power of cryo-TEM to microbial ecology. Copyright © 2011 Wiley Periodicals, Inc.

  19. Beam-induced motion correction for sub-megadalton cryo-EM particles.

    PubMed

    Scheres, Sjors Hw

    2014-08-13

    In electron cryo-microscopy (cryo-EM), the electron beam that is used for imaging also causes the sample to move. This motion blurs the images and limits the resolution attainable by single-particle analysis. In a previous Research article (Bai et al., 2013) we showed that correcting for this motion by processing movies from fast direct-electron detectors allowed structure determination to near-atomic resolution from 35,000 ribosome particles. In this Research advance article, we show that an improved movie processing algorithm is applicable to a much wider range of specimens. The new algorithm estimates straight movement tracks by considering multiple particles that are close to each other in the field of view, and models the fall-off of high-resolution information content by radiation damage in a dose-dependent manner. Application of the new algorithm to four data sets illustrates its potential for significantly improving cryo-EM structures, even for particles that are smaller than 200 kDa. Copyright © 2014, Scheres.

  20. Retrofit implementation of Zernike phase plate imaging for cryo-TEM

    PubMed Central

    Marko, Michael; Leith, ArDean; Hsieh, Chyongere; Danev, Radostin

    2011-01-01

    In-focus phase-plate imaging is particularly beneficial for cryo-TEM because it offers a substantial overall increase in image contrast, without an electron dose penalty, and it simplifies image interpretation. We show how phase-plate cryo-TEM can be implemented with an appropriate existing TEM, and provide a basic practical introduction to use of thin-film (carbon) phase plates. We point out potential pitfalls of phase-plate operation, and discuss solutions. We provide information on evaluating a particular TEM for its suitability. PMID:21272647

  1. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy

    PubMed Central

    Garmann, Rees F.; Gopal, Ajaykumar; Athavale, Shreyas S.; Knobler, Charles M.; Gelbart, William M.; Harvey, Stephen C.

    2015-01-01

    The lifecycle, and therefore the virulence, of single-stranded (ss)-RNA viruses is regulated not only by their particular protein gene products, but also by the secondary and tertiary structure of their genomes. The secondary structure of the entire genomic RNA of satellite tobacco mosaic virus (STMV) was recently determined by selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE). The SHAPE analysis suggested a single highly extended secondary structure with much less branching than occurs in the ensemble of structures predicted by purely thermodynamic algorithms. Here we examine the solution-equilibrated STMV genome by direct visualization with cryo-electron microscopy (cryo-EM), using an RNA of similar length transcribed from the yeast genome as a control. The cryo-EM data reveal an ensemble of branching patterns that are collectively consistent with the SHAPE-derived secondary structure model. Thus, our results both elucidate the statistical nature of the secondary structure of large ss-RNAs and give visual support for modern RNA structure determination methods. Additionally, this work introduces cryo-EM as a means to distinguish between competing secondary structure models if the models differ significantly in terms of the number and/or length of branches. Furthermore, with the latest advances in cryo-EM technology, we suggest the possibility of developing methods that incorporate restraints from cryo-EM into the next generation of algorithms for the determination of RNA secondary and tertiary structures. PMID:25752599

  2. DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.

    PubMed

    Wang, Feng; Gong, Huichao; Liu, Gaochao; Li, Meijing; Yan, Chuangye; Xia, Tian; Li, Xueming; Zeng, Jianyang

    2016-09-01

    Particle picking is a time-consuming step in single-particle analysis and often requires significant interventions from users, which has become a bottleneck for future automated electron cryo-microscopy (cryo-EM). Here we report a deep learning framework, called DeepPicker, to address this problem and fill the current gaps toward a fully automated cryo-EM pipeline. DeepPicker employs a novel cross-molecule training strategy to capture common features of particles from previously-analyzed micrographs, and thus does not require any human intervention during particle picking. Tests on the recently-published cryo-EM data of three complexes have demonstrated that our deep learning based scheme can successfully accomplish the human-level particle picking process and identify a sufficient number of particles that are comparable to those picked manually by human experts. These results indicate that DeepPicker can provide a practically useful tool to significantly reduce the time and manual effort spent in single-particle analysis and thus greatly facilitate high-resolution cryo-EM structure determination. DeepPicker is released as an open-source program, which can be downloaded from https://github.com/nejyeah/DeepPicker-python. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. MOEMS deformable mirror testing in cryo for future optical instrumentation

    NASA Astrophysics Data System (ADS)

    Zamkotsian, Frederic; Lanzoni, Patrick; Barette, Rudy; Grassi, Emmanuel; Vors, Patrick; Helmbrecht, Michael; Marchis, Franck; Teichman, Alex

    2017-02-01

    MOEMS Deformable Mirrors (DM) are key components for next generation optical instruments implementing innovative adaptive optics systems, in existing telescopes as well as in the future ELTs. Due to the wide variety of applications, these DMs must perform at room temperature as well as in cryogenic and vacuum environment. Ideally, the MOEMS-DMs must be designed to operate in such environment. This is unfortunately usually not the case. We will present some major rules for designing / operating DMs in cryo and vacuum. Next step is to characterize with high accuracy the different DM candidates. We chose to use interferometry for the full characterization of these devices, including surface quality measurement in static and dynamical modes, at ambient and in vacuum/cryo. Thanks to our previous set-up developments, we are placing a compact cryo-vacuum chamber designed for reaching 10-6 mbar and 160K, in front of our custom Michelson interferometer, able to measure performances of the DM at actuator/segment level as well as whole mirror level, with a lateral resolution of 2μm and a sub-nanometric zresolution. Using this interferometric bench, we tested the PTT 111 DM from Iris AO: this unique and robust design uses an array of single crystalline silicon hexagonal mirrors with a pitch of 606μm, able to move in tip, tilt and piston with strokes from 5 to 7μm, and tilt angle in the range of +/- 5mrad. They exhibit typically an open-loop flat surface figure as good as < 20nm rms. A specific mount including electronic and opto-mechanical interfaces has been designed for fitting in the test chamber. Segment deformation, mirror shaping, open-loop operation are tested at room and cryo temperature and results are compared. The device could be operated successfully at 160K. An additional, mainly focus-like, 500 nm deformation is measured at 160K; we were able to recover the best flat in cryo by correcting the focus and local tip-tilts on some segments. Tests on DM with

  4. FragFit: a web-application for interactive modeling of protein segments into cryo-EM density maps.

    PubMed

    Tiemann, Johanna K S; Rose, Alexander S; Ismer, Jochen; Darvish, Mitra D; Hilal, Tarek; Spahn, Christian M T; Hildebrand, Peter W

    2018-05-21

    Cryo-electron microscopy (cryo-EM) is a standard method to determine the three-dimensional structures of molecular complexes. However, easy to use tools for modeling of protein segments into cryo-EM maps are sparse. Here, we present the FragFit web-application, a web server for interactive modeling of segments of up to 35 amino acids length into cryo-EM density maps. The fragments are provided by a regularly updated database containing at the moment about 1 billion entries extracted from PDB structures and can be readily integrated into a protein structure. Fragments are selected based on geometric criteria, sequence similarity and fit into a given cryo-EM density map. Web-based molecular visualization with the NGL Viewer allows interactive selection of fragments. The FragFit web-application, accessible at http://proteinformatics.de/FragFit, is free and open to all users, without any login requirements.

  5. Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy

    PubMed Central

    Liao, Hstau Y.; Hashem, Yaser; Frank, Joachim

    2015-01-01

    Summary Single-particle cryogenic electron microscopy (cryo-EM) is a powerful tool for the study of macromolecular structures at high resolution. Classification allows multiple structural states to be extracted and reconstructed from the same sample. One classification approach is via the covariance matrix, which captures the correlation between every pair of voxels. Earlier approaches employ computing-intensive resampling and estimate only the eigenvectors of the matrix, which are then used in a separate fast classification step. We propose an iterative scheme to explicitly estimate the covariance matrix in its entirety. In our approach, the flexibility in choosing the solution domain allows us to examine a part of the molecule in greater detail. 3D covariance maps obtained in this way from experimental data (cryo-EM images of the eukaryotic pre-initiation complex) prove to be in excellent agreement with conclusions derived by using traditional approaches, revealing in addition the interdependencies of ligand bindings and structural changes. PMID:25982529

  6. Efficient estimation of three-dimensional covariance and its application in the analysis of heterogeneous samples in cryo-electron microscopy.

    PubMed

    Liao, Hstau Y; Hashem, Yaser; Frank, Joachim

    2015-06-02

    Single-particle cryogenic electron microscopy (cryo-EM) is a powerful tool for the study of macromolecular structures at high resolution. Classification allows multiple structural states to be extracted and reconstructed from the same sample. One classification approach is via the covariance matrix, which captures the correlation between every pair of voxels. Earlier approaches employ computing-intensive resampling and estimate only the eigenvectors of the matrix, which are then used in a separate fast classification step. We propose an iterative scheme to explicitly estimate the covariance matrix in its entirety. In our approach, the flexibility in choosing the solution domain allows us to examine a part of the molecule in greater detail. Three-dimensional covariance maps obtained in this way from experimental data (cryo-EM images of the eukaryotic pre-initiation complex) prove to be in excellent agreement with conclusions derived by using traditional approaches, revealing in addition the interdependencies of ligand bindings and structural changes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Retrofit implementation of Zernike phase plate imaging for cryo-TEM.

    PubMed

    Marko, Michael; Leith, Ardean; Hsieh, Chyongere; Danev, Radostin

    2011-05-01

    In-focus phase-plate imaging is particularly beneficial for cryo-TEM because it offers a substantial overall increase in image contrast, without an electron dose penalty, and it simplifies image interpretation. We show how phase-plate cryo-TEM can be implemented with an appropriate existing TEM, and provide a basic practical introduction to use of thin-film (carbon) phase plates. We point out potential pitfalls of phase-plate operation, and discuss solutions. We provide information on evaluating a particular TEM for its suitability. Copyright © 2011 Elsevier Inc. All rights reserved.

  8. Efficiency and Impact of Positive and Negative Magnetic Separation on Monocyte Derived Dendritic Cell Generation.

    PubMed

    Kowalewicz-Kulbat, Magdalena; Ograczyk, Elżbieta; Włodarczyk, Marcin; Krawczyk, Krzysztof; Fol, Marek

    2016-06-01

    The immunomagnetic separation technique is the basis of monocyte isolation and further generation of monocyte-derived dendritic cells. To compare the efficiency of monocyte positive and negative separation, concentration of beads, and their impact on generated dendritic cells. Monocytes were obtained using monoclonal antibody-coated magnetic beads followed the Ficoll-Paque gradient separation of mononuclear cell fraction from the peripheral blood of 6 healthy volunteers. CD14 expression was analyzed by flow cytometry. Both types of magnetic separation including recommended and reduced concentrations of beads did not affect the yield and the purity of monocytes and their surface CD14 expression. However, DCs originated from the "positively" separated monocytes had noticeable higher expression of CD80.

  9. The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly

    PubMed Central

    Razi, Aida; Britton, Robert A.

    2017-01-01

    Abstract Cryo-electron microscopy (cryo-EM) had played a central role in the study of ribosome structure and the process of translation in bacteria since the development of this technique in the mid 1980s. Until recently cryo-EM structures were limited to ∼10 Å in the best cases. However, the recent advent of direct electron detectors has greatly improved the resolution of cryo-EM structures to the point where atomic resolution is now achievable. This improved resolution will allow cryo-EM to make groundbreaking contributions in essential aspects of ribosome biology, including the assembly process. In this review, we summarize important insights that cryo-EM, in combination with chemical and genetic approaches, has already brought to our current understanding of the ribosomal assembly process in bacteria using previous detector technology. More importantly, we discuss how the higher resolution structures now attainable with direct electron detectors can be leveraged to propose precise testable models regarding this process. These structures will provide an effective platform to develop new antibiotics that target this fundamental cellular process. PMID:28180306

  10. Comparing IceBridge and CryoSat-2 sea ice observations over the Arctic and the Southern Ocean

    NASA Astrophysics Data System (ADS)

    Yi, D.; Kurtz, N. T.; Harbeck, J.; Hofton, M. A.; Manizade, S.; Cornejo, H.

    2016-12-01

    From 2009 to 2015, CryoSat-2 and IceBridge had 34 coincident lines over sea ice, 23 over the Arctic (20 with ATM, 2 with LVIS, and 1 with both ATM and LVIS) and 11 over the Southern Ocean (9 with ATM and 2 with both ATM and LVIS). In this study, we will compare both surface elevation and sea ice freeboard from CryoSat-2, ATM, and LVIS. We will apply identical ellipsoid, geoid, tide models, and atmospheric corrections to CryoSat-2, ATM, and LVIS data. For CryoSat-2, we will use surface elevation and sea ice freeboard both in the standard CryoSat-2 data product and calculated through a waveform fitting method. For ATM and LVIS, we will use surface elevation and sea ice freeboard in the OIB data product and the elevation and sea ice freeboard calculated through Gaussian waveform fitting method. The results of this study are important for using ATM and LVIS to calibrate/validate CryoSat-2 results and bridging the data gap between ICESat and ICESat-2.

  11. Design and testing of a pilot scale magnetic separator for the treatment of textile dyeing wastewater.

    PubMed

    Salinas, Tobías; Durruty, Ignacio; Arciniegas, Lorena; Pasquevich, Gustavo; Lanfranconi, Matías; Orsi, Isabela; Alvarez, Vera; Bonanni, Sebastian

    2018-07-15

    Iron nanoparticles can be incorporated on the structure of natural clays to obtain magnetic clays, an adsorbent that be easily removed from a wastewater by magnetic means. Magnetic clays have high adsorption capacities of different contaminants such as heavy metals, fungicides, aromatic compounds and colorants and show rapid adsorption kinetics, but crucial data for achieving its full or pilot scale application is still lacking. In this work, magnetic bentonites with different amounts of magnetite (iron fractions on the clay of 0.55, 0.6 and 0.6) were used to remove color from a real textile wastewater. On a first stage the optimal conditions for the adsorption of the dye, including pH, temperature and clay dosage were determined. Also design parameters for the separation process such as residence time, distance from magnet to magnetic clay and magnet strength were obtained. Finally a pilot scale magnetic drum separator was constructed and tested. A removal of 60% of the dye from a wastewater that contained more than 250 ppm of azo dye was achieved with only 10 min of residence time inside the separator. Copyright © 2018 Elsevier Ltd. All rights reserved.

  12. Microscopic validation of whole mouse micro-metastatic tumor imaging agents using cryo-imaging and sliding organ image registration.

    PubMed

    Liu, Yiqiao; Zhou, Bo; Qutaish, Mohammed; Wilson, David L

    2016-01-01

    We created a metastasis imaging, analysis platform consisting of software and multi-spectral cryo-imaging system suitable for evaluating emerging imaging agents targeting micro-metastatic tumor. We analyzed CREKA-Gd in MRI, followed by cryo-imaging which repeatedly sectioned and tiled microscope images of the tissue block face, providing anatomical bright field and molecular fluorescence, enabling 3D microscopic imaging of the entire mouse with single metastatic cell sensitivity. To register MRI volumes to the cryo bright field reference, we used our standard mutual information, non-rigid registration which proceeded: preprocess → affine → B-spline non-rigid 3D registration. In this report, we created two modified approaches: mask where we registered locally over a smaller rectangular solid, and sliding organ . Briefly, in sliding organ , we segmented the organ, registered the organ and body volumes separately and combined results. Though s liding organ required manual annotation, it provided the best result as a standard to measure other registration methods. Regularization parameters for standard and mask methods were optimized in a grid search. Evaluations consisted of DICE, and visual scoring of a checkerboard display. Standard had accuracy of 2 voxels in all regions except near the kidney, where there were 5 voxels sliding. After mask and sliding organ correction, kidneys sliding were within 2 voxels, and Dice overlap increased 4%-10% in mask compared to standard . Mask generated comparable results with sliding organ and allowed a semi-automatic process.

  13. Microscopic validation of whole mouse micro-metastatic tumor imaging agents using cryo-imaging and sliding organ image registration

    NASA Astrophysics Data System (ADS)

    Liu, Yiqiao; Zhou, Bo; Qutaish, Mohammed; Wilson, David L.

    2016-03-01

    We created a metastasis imaging, analysis platform consisting of software and multi-spectral cryo-imaging system suitable for evaluating emerging imaging agents targeting micro-metastatic tumor. We analyzed CREKA-Gd in MRI, followed by cryo-imaging which repeatedly sectioned and tiled microscope images of the tissue block face, providing anatomical bright field and molecular fluorescence, enabling 3D microscopic imaging of the entire mouse with single metastatic cell sensitivity. To register MRI volumes to the cryo bright field reference, we used our standard mutual information, non-rigid registration which proceeded: preprocess --> affine --> B-spline non-rigid 3D registration. In this report, we created two modified approaches: mask where we registered locally over a smaller rectangular solid, and sliding organ. Briefly, in sliding organ, we segmented the organ, registered the organ and body volumes separately and combined results. Though sliding organ required manual annotation, it provided the best result as a standard to measure other registration methods. Regularization parameters for standard and mask methods were optimized in a grid search. Evaluations consisted of DICE, and visual scoring of a checkerboard display. Standard had accuracy of 2 voxels in all regions except near the kidney, where there were 5 voxels sliding. After mask and sliding organ correction, kidneys sliding were within 2 voxels, and Dice overlap increased 4%-10% in mask compared to standard. Mask generated comparable results with sliding organ and allowed a semi-automatic process.

  14. Monitoring the Stability of Perfluorocarbon Nanoemulsions by Cryo-TEM Image Analysis and Dynamic Light Scattering

    PubMed Central

    Grapentin, Christoph; Barnert, Sabine; Schubert, Rolf

    2015-01-01

    Perfluorocarbon nanoemulsions (PFC-NE) are disperse systems consisting of nanoscale liquid perfluorocarbon droplets stabilized by an emulsifier, usually phospholipids. Perfluorocarbons are chemically inert and non-toxic substances that are exhaled after in vivo administration. The manufacture of PFC-NE can be done in large scales by means of high pressure homogenization or microfluidization. Originally investigated as oxygen carriers for cases of severe blood loss, their application nowadays is more focused on using them as marker agents in 19F Magnetic Resonance Imaging (19F MRI). 19F is scarce in organisms and thus PFC-NE are a promising tool for highly specific and non-invasive imaging of inflammation via 19F MRI. Neutrophils, monocytes and macrophages phagocytize PFC-NE and subsequently migrate to inflamed tissues. This technique has proven feasibility in numerous disease models in mice, rabbits and mini pigs. The translation to clinical trials in human needs the development of a stable nanoemulsion whose droplet size is well characterized over a long storage time. Usually dynamic light scattering (DLS) is applied as the standard method for determining particle sizes in the nanometer range. Our study uses a second method, analysis of transmission electron microscopy images of cryo-fixed samples (Cryo-TEM), to evaluate stability of PFC-NE in comparison to DLS. Four nanoemulsions of different composition are observed for one year. The results indicate that DLS alone cannot reveal the changes in particle size, but can even mislead to a positive estimation of stability. The combination with Cryo-TEM images gives more insight in the particulate evolution, both techniques supporting one another. The study is one further step in the development of analytical tools for the evaluation of a clinically applicable perfluorooctylbromide nanoemulsion. PMID:26098661

  15. cryoem-cloud-tools: A software platform to deploy and manage cryo-EM jobs in the cloud.

    PubMed

    Cianfrocco, Michael A; Lahiri, Indrajit; DiMaio, Frank; Leschziner, Andres E

    2018-06-01

    Access to streamlined computational resources remains a significant bottleneck for new users of cryo-electron microscopy (cryo-EM). To address this, we have developed tools that will submit cryo-EM analysis routines and atomic model building jobs directly to Amazon Web Services (AWS) from a local computer or laptop. These new software tools ("cryoem-cloud-tools") have incorporated optimal data movement, security, and cost-saving strategies, giving novice users access to complex cryo-EM data processing pipelines. Integrating these tools into the RELION processing pipeline and graphical user interface we determined a 2.2 Å structure of ß-galactosidase in ∼55 hours on AWS. We implemented a similar strategy to submit Rosetta atomic model building and refinement to AWS. These software tools dramatically reduce the barrier for entry of new users to cloud computing for cryo-EM and are freely available at cryoem-tools.cloud. Copyright © 2018. Published by Elsevier Inc.

  16. A Phos-tag-based magnetic-bead method for rapid and selective separation of phosphorylated biomolecules.

    PubMed

    Tsunehiro, Masaya; Meki, Yuma; Matsuoka, Kanako; Kinoshita-Kikuta, Emiko; Kinoshita, Eiji; Koike, Tohru

    2013-04-15

    A simple and efficient method based on magnetic-bead technology has been developed for the separation of phosphorylated and nonphosphorylated low-molecular-weight biomolecules, such as nucleotides, phosphorylated amino acids, or phosphopeptides. The phosphate-binding site on the bead is an alkoxide-bridged dinuclear zinc(II) complex with 1,3-bis(pyridin-2-ylmethylamino)propan-2-olate (Phos-tag), which is linked to a hydrophilic cross-linked agarose coating on a magnetic core particle. All steps for the phosphate-affinity separation are conducted in buffers of neutral pH with 50 μL of the magnetic beads in a 1.5-mL microtube. The entire separation protocol for phosphomonoester-type compounds, from addition to elution, requires less than 12 min per sample if the buffers and the zinc(II)-bound Phos-tag magnetic beads have been prepared in advance. The phosphate-affinity magnetic beads are reusable at least 15 times without a decrease in their phosphate-binding ability and they are stable for three months in propan-2-ol. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. Directly reconstructing principal components of heterogeneous particles from cryo-EM images.

    PubMed

    Tagare, Hemant D; Kucukelbir, Alp; Sigworth, Fred J; Wang, Hongwei; Rao, Murali

    2015-08-01

    Structural heterogeneity of particles can be investigated by their three-dimensional principal components. This paper addresses the question of whether, and with what algorithm, the three-dimensional principal components can be directly recovered from cryo-EM images. The first part of the paper extends the Fourier slice theorem to covariance functions showing that the three-dimensional covariance, and hence the principal components, of a heterogeneous particle can indeed be recovered from two-dimensional cryo-EM images. The second part of the paper proposes a practical algorithm for reconstructing the principal components directly from cryo-EM images without the intermediate step of calculating covariances. This algorithm is based on maximizing the posterior likelihood using the Expectation-Maximization algorithm. The last part of the paper applies this algorithm to simulated data and to two real cryo-EM data sets: a data set of the 70S ribosome with and without Elongation Factor-G (EF-G), and a data set of the influenza virus RNA dependent RNA Polymerase (RdRP). The first principal component of the 70S ribosome data set reveals the expected conformational changes of the ribosome as the EF-G binds and unbinds. The first principal component of the RdRP data set reveals a conformational change in the two dimers of the RdRP. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Directly Reconstructing Principal Components of Heterogeneous Particles from Cryo-EM Images

    PubMed Central

    Tagare, Hemant D.; Kucukelbir, Alp; Sigworth, Fred J.; Wang, Hongwei; Rao, Murali

    2015-01-01

    Structural heterogeneity of particles can be investigated by their three-dimensional principal components. This paper addresses the question of whether, and with what algorithm, the three-dimensional principal components can be directly recovered from cryo-EM images. The first part of the paper extends the Fourier slice theorem to covariance functions showing that the three-dimensional covariance, and hence the principal components, of a heterogeneous particle can indeed be recovered from two-dimensional cryo-EM images. The second part of the paper proposes a practical algorithm for reconstructing the principal components directly from cryo-EM images without the intermediate step of calculating covariances. This algorithm is based on maximizing the (posterior) likelihood using the Expectation-Maximization algorithm. The last part of the paper applies this algorithm to simulated data and to two real cryo-EM data sets: a data set of the 70S ribosome with and without Elongation Factor-G (EF-G), and a data set of the inluenza virus RNA dependent RNA Polymerase (RdRP). The first principal component of the 70S ribosome data set reveals the expected conformational changes of the ribosome as the EF-G binds and unbinds. The first principal component of the RdRP data set reveals a conformational change in the two dimers of the RdRP. PMID:26049077

  19. In-situ integrity control of frozen-hydrated, vitreous lamellas prepared by the cryo-focused ion beam-scanning electron microscope.

    PubMed

    de Winter, D A Matthijs; Mesman, Rob J; Hayles, Michael F; Schneijdenberg, Chris T W M; Mathisen, Cliff; Post, Jan A

    2013-07-01

    Recently a number of new approaches have been presented with the intention to produce electron beam transparent cryo-sections (lamellas in FIB-SEM terminology) from hydrated vitreously frozen cryo samples with a Focused Ion Beam (FIB) system, suitable for cryo-Transmission Electron Microscopy (cryo-TEM). As the workflow is still challenging and time consuming, it is important to be able to determine the integrity and suitability (cells vs. no cells; vitreous vs. crystalline) of the lamellas. Here we present an in situ method that tests both conditions by using the cryo-Scanning Electron Microscope (cryo-SEM) in transmission mode (TSEM; Transmission Scanning Electron Microscope) once the FIB-made lamella is ready. Cryo-TSEM imaging of unstained cells yields strong contrast, enabling direct imaging of material present in the lamellas. In addition, orientation contrast is shown to be suitable for distinguishing crystalline lamellas from vitreous lamellas. Tilting the stage a few degrees results in changes of contrast between ice grains as a function of the tilt angle, whereas the contrast of areas with vitreous ice remains unchanged as a function of the tilt angle. This orientation contrast has subsequently been validated by cryo-Electron BackScattered Diffraction (EBSD) in transmission mode. Integration of the presented method is discussed and the role it can play in future developments for a new and innovative all-in-one cryo-FIB-SEM life sciences instrument. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Removal of Iron Oxide Scale from Feed-water in Thermal Power Plant by Using Magnetic Separation

    NASA Astrophysics Data System (ADS)

    Nakanishi, Motohiro; Shibatani, Saori; Mishima, Fumihito; Akiyama, Yoko; Nishijima, Shigehiro

    2017-09-01

    One of the factors of deterioration in thermal power generation efficiency is adhesion of the scale to inner wall in feed-water system. Though thermal power plants have employed All Volatile Treatment (AVT) or Oxygen Treatment (OT) to prevent scale formation, these treatments cannot prevent it completely. In order to remove iron oxide scale, we proposed magnetic separation system using solenoidal superconducting magnet. Magnetic separation efficiency is influenced by component and morphology of scale which changes their property depending on the type of water treatment and temperature. In this study, we estimated component and morphology of iron oxide scale at each equipment in the feed-water system by analyzing simulated scale generated in the pressure vessel at 320 K to 550 K. Based on the results, we considered installation sites of the magnetic separation system.

  1. A lysozyme and magnetic bead based method of separating intact bacteria.

    PubMed

    Diler, Ebru; Obst, Ursula; Schmitz, Katja; Schwartz, Thomas

    2011-07-01

    As a response to environmental stress, bacterial cells can enter a physiological state called viable but noncultivable (VBNC). In this state, bacteria fail to grow on routine bacteriological media. Consequently, standard methods of contamination detection based on bacteria cultivation fail. Although they are not growing, the cells are still alive and are able to reactivate their metabolism. The VBNC state and low bacterial densities are big challenges for cultivation-based pathogen detection in drinking water and the food industry, for example. In this context, a new molecular-biological separation method for bacteria using point-mutated lysozymes immobilised on magnetic beads for separating bacteria is described. The immobilised mutated lysozymes on magnetic beads serve as bait for the specific capture of bacteria from complex matrices or water due to their remaining affinity for bacterial cell wall components. Beads with bacteria can be separated using magnetic racks. To avoid bacterial cell lysis by the lysozymes, the protein was mutated at amino acid position 35, leading to the exchange of the catalytic glutamate for alanine (LysE35A) and glutamine (LysE35Q). As proved by turbidity assay with reference bacteria, the muramidase activity was knocked out. The mutated constructs were expressed by the yeast Pichia pastoris and secreted into expression medium. Protein enrichment and purification were carried out by SO(3)-functionalised nanoscale cationic exchanger particles. For a proof of principle, the proteins were biotinylated and immobilised on streptavidin-functionalised, fluorescence dye-labelled magnetic beads. These constructs were used for the successful capture of Syto9-marked Microccocus luteus cells from cell suspension, as visualised by fluorescence microscopy, which confirmed the success of the strategy.

  2. New understanding on separation of Mn and Fe from ferruginous manganese ores by the magnetic reduction roasting process

    NASA Astrophysics Data System (ADS)

    Liu, Bingbing; Zhang, Yuanbo; Wang, Juan; Wang, Jia; Su, Zijian; Li, Guanghui; Jiang, Tao

    2018-06-01

    Magnetic reduction roasting followed by magnetic separation process is reported as a simple route to realize separation of Mn and Fe from ferruginous manganese ores (Fe-Mn ores). However, the separation and recovery of Mn and Fe oxides are not very effective. This work clarified the underlying reason for the poor separation and also proposed some suggestions for the magnetic reduction process. In this work, the effect of temperature on the magnetic reduction roasting - magnetic separation of Fe-Mn ore was investigated firstly. Then the reduction behaviors of MnO2-Fe2O3 system and MnO2-Fe2O3-10 wt.%SiO2 system under 10 vol.% CO-90 vol.% CO2 at 600-1000 °C were investigated by XRD, XPS, SEM-EDS, VSM, DSC and thermodynamics analyses. Reduction and separation tests showed that higher reduction temperature was beneficial to the recovery of iron while it's not in favor of the recovery of manganese when the temperature was over 800 °C. The formation of composite oxide MnxFe3-xO4 with strong magnetism between the interface of the MnO2 and Fe2O3 particles leaded to the poor separation of iron and manganese. In addition, the formation mechanism of MnxFe3-xO4 from MnO2 and Fe2O3 as well as the interface reaction reduced under 10 vol.% CO was discussed in this study. Finally, some suggestions were recommended for the magnetic reduction roasting for utilizing the Fe-Mn ores effectively.

  3. Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem*

    PubMed Central

    Katsevich, E.; Katsevich, A.; Singer, A.

    2015-01-01

    In cryo-electron microscopy (cryo-EM), a microscope generates a top view of a sample of randomly oriented copies of a molecule. The problem of single particle reconstruction (SPR) from cryo-EM is to use the resulting set of noisy two-dimensional projection images taken at unknown directions to reconstruct the three-dimensional (3D) structure of the molecule. In some situations, the molecule under examination exhibits structural variability, which poses a fundamental challenge in SPR. The heterogeneity problem is the task of mapping the space of conformational states of a molecule. It has been previously suggested that the leading eigenvectors of the covariance matrix of the 3D molecules can be used to solve the heterogeneity problem. Estimating the covariance matrix is challenging, since only projections of the molecules are observed, but not the molecules themselves. In this paper, we formulate a general problem of covariance estimation from noisy projections of samples. This problem has intimate connections with matrix completion problems and high-dimensional principal component analysis. We propose an estimator and prove its consistency. When there are finitely many heterogeneity classes, the spectrum of the estimated covariance matrix reveals the number of classes. The estimator can be found as the solution to a certain linear system. In the cryo-EM case, the linear operator to be inverted, which we term the projection covariance transform, is an important object in covariance estimation for tomographic problems involving structural variation. Inverting it involves applying a filter akin to the ramp filter in tomography. We design a basis in which this linear operator is sparse and thus can be tractably inverted despite its large size. We demonstrate via numerical experiments on synthetic datasets the robustness of our algorithm to high levels of noise. PMID:25699132

  4. Application of a Halbach magnetic array for long-range cell and particle separations in biological samples

    NASA Astrophysics Data System (ADS)

    Kang, Joo H.; Driscoll, Harry; Super, Michael; Ingber, Donald E.

    2016-05-01

    Here, we describe a versatile application of a planar Halbach permanent magnet array for an efficient long-range magnetic separation of living cells and microparticles over distances up to 30 mm. A Halbach array was constructed from rectangular bar magnets using 3D-printed holders and compared to a conventional alternating array of identical magnets. We theoretically predicted the superiority of the Halbach array for a long-range magnetic separation and then experimentally validated that the Halbach configuration outperforms the alternating array for isolating magnetic microparticles or microparticle-bound bacterial cells at longer distances. Magnetophoretic velocities (ymag) of magnetic particles (7.9 μm diameter) induced by the Halbach array in a microfluidic device were significantly higher and extended over a larger area than those induced by the alternating magnet array (ymag = 178 versus 0 μm/s at 10 mm, respectively). When applied to 50 ml tubes (˜30 mm diameter), the Halbach array removed >95% of Staphylococcus aureus bacterial cells bound with 1 μm magnetic particles compared to ˜70% removed using the alternating array. In addition, the Halbach array enabled manipulation of 1 μm magnetic beads in a deep 96-well plate for ELISA applications, which was not possible with the conventional magnet arrays. Our analysis demonstrates the utility of the Halbach array for the future design of devices for high-throughput magnetic separations of cells, molecules, and toxins.

  5. Fine Ice Sheet margins topography from swath processing of CryoSat SARIn mode data

    NASA Astrophysics Data System (ADS)

    Gourmelen, N.; Escorihuela, M. J.; Shepherd, A.; Foresta, L.; Muir, A.; Briggs, K.; Hogg, A. E.; Roca, M.; Baker, S.; Drinkwater, M. R.

    2014-12-01

    Reference and repeat-observations of Glacier and Ice Sheet Margin (GISM) topography are critical to identify changes in ice thickness, provide estimates of mass gain or loss and thus quantify the contribution of the cryosphere to sea level change. The lack of such sustained observations was identified in the Integrated Global Observing Strategy (IGOS) Cryosphere Theme Report as a major shortcoming. Conventional altimetry measurements over GISMs exist, but coverage has been sparse and characterized by coarse ground resolution. Additionally, and more importantly, they proved ineffective in the presence of steep slopes, a typical feature of GISM areas. Since the majority of Antarctic and Greenland ice sheet mass loss is estimated to lie within 100 km from the coast, but only about 10% is surveyed, there is the need for more robust and dense observations of GISMs, in both time and space. The ESA Altimetry mission CryoSat aims at gaining better insight into the evolution of the Cryosphere. CryoSat's revolutionary design features a Synthetic Interferometric Radar Altimeter (SIRAL), with two antennas for interferometry. The corresponding SAR Interferometer (SARIn) mode of operation increases spatial resolution while resolving the angular origin of off-nadir echoes occurring over sloping terrain. The SARIn mode is activated over GISMs and the elevation for the Point Of Closest Approach (POCA) is a standard product of the CryoSat mission. Here we present an approach for more comprehensively exploiting the SARIn mode of CryoSat and produce an ice elevation product with enhanced spatial resolution compared to standard CryoSat-2 height products. In this so called L2-swath processing approach, the full CryoSat waveform is exploited under specific conditions of signal and surface characteristics. We will present the rationale, validation exercises and preliminary results from the Eurpean Space Agency's STSE CryoTop study over selected test regions of the margins of the Greenland

  6. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling.

    PubMed

    de Vries, Sjoerd J; Chauvot de Beauchêne, Isaure; Schindler, Christina E M; Zacharias, Martin

    2016-02-23

    Protein-protein interactions carry out a large variety of essential cellular processes. Cryo-electron microscopy (cryo-EM) is a powerful technique for the modeling of protein-protein interactions at a wide range of resolutions, and recent developments have caused a revolution in the field. At low resolution, cryo-EM maps can drive integrative modeling of the interaction, assembling existing structures into the map. Other experimental techniques can provide information on the interface or on the contacts between the monomers in the complex. This inevitably raises the question regarding which type of data is best suited to drive integrative modeling approaches. Systematic comparison of the prediction accuracy and specificity of the different integrative modeling paradigms is unavailable to date. Here, we compare EM-driven, interface-driven, and contact-driven integrative modeling paradigms. Models were generated for the protein docking benchmark using the ATTRACT docking engine and evaluated using the CAPRI two-star criterion. At 20 Å resolution, EM-driven modeling achieved a success rate of 100%, outperforming the other paradigms even with perfect interface and contact information. Therefore, even very low resolution cryo-EM data is superior in predicting heterodimeric and heterotrimeric protein assemblies. Our study demonstrates that a force field is not necessary, cryo-EM data alone is sufficient to accurately guide the monomers into place. The resulting rigid models successfully identify regions of conformational change, opening up perspectives for targeted flexible remodeling. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  7. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling

    PubMed Central

    de Vries, Sjoerd J.; Chauvot de Beauchêne, Isaure; Schindler, Christina E.M.; Zacharias, Martin

    2016-01-01

    Protein-protein interactions carry out a large variety of essential cellular processes. Cryo-electron microscopy (cryo-EM) is a powerful technique for the modeling of protein-protein interactions at a wide range of resolutions, and recent developments have caused a revolution in the field. At low resolution, cryo-EM maps can drive integrative modeling of the interaction, assembling existing structures into the map. Other experimental techniques can provide information on the interface or on the contacts between the monomers in the complex. This inevitably raises the question regarding which type of data is best suited to drive integrative modeling approaches. Systematic comparison of the prediction accuracy and specificity of the different integrative modeling paradigms is unavailable to date. Here, we compare EM-driven, interface-driven, and contact-driven integrative modeling paradigms. Models were generated for the protein docking benchmark using the ATTRACT docking engine and evaluated using the CAPRI two-star criterion. At 20 Å resolution, EM-driven modeling achieved a success rate of 100%, outperforming the other paradigms even with perfect interface and contact information. Therefore, even very low resolution cryo-EM data is superior in predicting heterodimeric and heterotrimeric protein assemblies. Our study demonstrates that a force field is not necessary, cryo-EM data alone is sufficient to accurately guide the monomers into place. The resulting rigid models successfully identify regions of conformational change, opening up perspectives for targeted flexible remodeling. PMID:26846888

  8. Conjugates of magnetic nanoparticle-actinide specific chelator for radioactive waste separation.

    PubMed

    Kaur, Maninder; Zhang, Huijin; Martin, Leigh; Todd, Terry; Qiang, You

    2013-01-01

    A novel nanotechnology for the separation of radioactive waste that uses magnetic nanoparticles (MNPs) conjugated with actinide specific chelators (MNP-Che) is reviewed with a focus on design and process development. The MNP-Che separation process is an effective way of separating heat generating minor actinides (Np, Am, Cm) from spent nuclear fuel solution to reduce the radiological hazard. It utilizes coated MNPs to selectively adsorb the contaminants onto their surfaces, after which the loaded particles are collected using a magnetic field. The MNP-Che conjugates can be recycled by stripping contaminates into a separate, smaller volume of solution, and then become the final waste form for disposal after reusing number of times. Due to the highly selective chelators, this remediation method could be both simple and versatile while allowing the valuable actinides to be recovered and recycled. Key issues standing in the way of large-scale application are stability of the conjugates and their dispersion in solution to maintain their unique properties, especially large surface area, of MNPs. With substantial research progress made on MNPs and their surface functionalization, as well as development of environmentally benign chelators, this method could become very flexible and cost-effective for recycling used fuel. Finally, the development of this nanotechnology is summarized and its future direction is discussed.

  9. The performance of CryoSat-2 as an ocean altimeter

    NASA Astrophysics Data System (ADS)

    Scharroo, R.; Smith, W. H.; Leuliette, E. W.; Lillibridge, J. L.

    2012-12-01

    Two years after the launch of CryoSat-2, oceanographic uses of the CryoSat-2 data have well taken off, after several institutes, NOAA included, have spent a dedicated effort to upgrade the official CryoSat-2 data products to a level that is suitable for monitoring of mesoscale phenomena, as well as wind speed and wave height. But in the coastal areas, this is much less the case. This is mostly the result of the fact that CryoSat-2 is running in SAR or InSAR mode in many of the focus areas, like the Mediterranean Sea. We have shown, however, that the CryoSat data is intrinsically of high quality and for over a year now have been producing "IGDR" type data through FTP and through RADS. These steps include: ● Combine final (LRM) and fast-delivery (FDM) products and split the segmented files into pass files. ● Divide the 369-day repeat cycle into subcycles of 29 or 27 days. ● Retrack the conventional low-rate data to determine range, significant wave height, backscatter (and off-nadir angle). ● Add or replace the usual corrections for ionospheric and atmospheric delays, tides, dynamic atmospheric correction, sea state bias, mean sea surface. ● Update orbits and corrections whenever they become available. This way NOAA produces an "IGDR" product from the fast-delivery FDM and the CNES MOE orbit in about 2 days after real time, and a "GDR" product from the final LRM data and the CNES POE orbit with a delay of about 1 month. In order to extend the data products to the coastal regime, we have developed a process in which the SAR data are first combined to "Pseudo-LRM" or "reduced SAR" wave forms, that are similar to the conventional low-rate wave forms. After this the reduced SAR data are retracked and combined with the conventional data to form a harmonised product. Although this sounds relatively straightforward, many steps were needed to get this done: ● Combine the SAR wave forms to conventional wave forms, without loss of information. ● Reconstruct

  10. Magnetic State of Quasiordered Fe-Al Alloys Doped with Ga and B: Magnetic Phase Separation and Spin Order

    NASA Astrophysics Data System (ADS)

    Voronina, E. V.; Ivanova, A. G.; Arzhnikov, A. K.; Chumakov, A. I.; Chistyakova, N. I.; Pyataev, A. V.; Korolev, A. V.

    2018-04-01

    Results of structural, magnetic, and Mössbauer studies of quasi ordered alloys Fe65Al35 - x M x ( M x = Ga, B; x = 0, 5 at %) are presented. The magnetic state of examined structurally-single-phase alloys at low temperatures is interpreted from the viewpoint of magnetic phase separation. An explanation is proposed for the observed behavior of magnetic characteristics of Fe65Al35 and Fe65Al30Ga5 in the framework of the model of two magnetic phases, a ferromagnetic-type one and a spin density wave. The boron-doped alloy Fe65Al30B5 is shown to demonstrate behavior that is typical of materials with the ferromagnetic type of ordering.

  11. Experimental Investigation of two-phase nitrogen Cryo transfer line

    NASA Astrophysics Data System (ADS)

    Singh, G. K.; Nimavat, H.; Panchal, R.; Garg, A.; Srikanth, GLN; Patel, K.; Shah, P.; Tanna, V. L.; Pradhan, S.

    2017-02-01

    A 6-m long liquid nitrogen based cryo transfer line has been designed, developed and tested at IPR. The test objectives include the thermo-hydraulic characteristics of Cryo transfer line under single phase as well as two phase flow conditions. It is always easy in experimentation to investigate the thermo-hydraulic parameters in case of single phase flow of cryogen but it is real challenge when one deals with the two phase flow of cryogen due to availibity of mass flow measurements (direct) under two phase flow conditions. Established models have been reported in the literature where one of the well-known model of Lockhart-Martenelli relationship has been used to determine the value of quality at the outlet of Cryo transfer line. Under homogenous flow conditions, by taking the ratio of the single-phase pressure drop and the two-phase pressure drop, we estimated the quality at the outlet. Based on these equations, vapor quality at the outlet of the transfer line was predicted at different heat loads. Experimental rresults shown that from inlet to outlet, there is a considerable increment in the pressure drop and vapour quality of the outlet depending upon heat load and mass flow rate of nitrogen flowing through the line.

  12. Comparison of an Atomic Model and Its Cryo-EM Image at the Central Axis of a Helix

    PubMed Central

    He, Jing; Zeil, Stephanie; Hallak, Hussam; McKaig, Kele; Kovacs, Julio; Wriggers, Willy

    2016-01-01

    Cryo-electron microscopy (cryo-EM) is an important biophysical technique that produces three-dimensional (3D) density maps at different resolutions. Because more and more models are being produced from cryo-EM density maps, validation of the models is becoming important. We propose a method for measuring local agreement between a model and the density map using the central axis of the helix. This method was tested using 19 helices from cryo-EM density maps between 5.5 Å and 7.2 Å resolution and 94 helices from simulated density maps. This method distinguished most of the well-fitting helices, although challenges exist for shorter helices. PMID:27280059

  13. High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE

    PubMed Central

    Moriya, Toshio; Saur, Michael; Stabrin, Markus; Merino, Felipe; Voicu, Horatiu; Huang, Zhong; Penczek, Pawel A.; Raunser, Stefan; Gatsogiannis, Christos

    2017-01-01

    SPHIRE (SPARX for High-Resolution Electron Microscopy) is a novel open-source, user-friendly software suite for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. The protocol presented here describes in detail how to obtain a near-atomic resolution structure starting from cryo-EM micrograph movies by guiding users through all steps of the single particle structure determination pipeline. These steps are controlled from the new SPHIRE graphical user interface and require minimum user intervention. Using this protocol, a 3.5 Å structure of TcdA1, a Tc toxin complex from Photorhabdus luminescens, was derived from only 9500 single particles. This streamlined approach will help novice users without extensive processing experience and a priori structural information, to obtain noise-free and unbiased atomic models of their purified macromolecular complexes in their native state. PMID:28570515

  14. On-chip Magnetic Separation and Cell Encapsulation in Droplets

    NASA Astrophysics Data System (ADS)

    Chen, A.; Byvank, T.; Bharde, A.; Miller, B. L.; Chalmers, J. J.; Sooryakumar, R.; Chang, W.-J.; Bashir, R.

    2012-02-01

    The demand for high-throughput single cell assays is gaining importance because of the heterogeneity of many cell suspensions, even after significant initial sorting. These suspensions may display cell-to-cell variability at the gene expression level that could impact single cell functional genomics, cancer, stem-cell research and drug screening. The on-chip monitoring of individual cells in an isolated environment could prevent cross-contamination, provide high recovery yield and ability to study biological traits at a single cell level These advantages of on-chip biological experiments contrast to conventional methods, which require bulk samples that provide only averaged information on cell metabolism. We report on a device that integrates microfluidic technology with a magnetic tweezers array to combine the functionality of separation and encapsulation of objects such as immunomagnetically labeled cells or magnetic beads into pico-liter droplets on the same chip. The ability to control the separation throughput that is independent of the hydrodynamic droplet generation rate allows the encapsulation efficiency to be optimized. The device can potentially be integrated with on-chip labeling and/or bio-detection to become a powerful single-cell analysis device.

  15. OMNY—A tOMography Nano crYo stage

    NASA Astrophysics Data System (ADS)

    Holler, M.; Raabe, J.; Diaz, A.; Guizar-Sicairos, M.; Wepf, R.; Odstrcil, M.; Shaik, F. R.; Panneels, V.; Menzel, A.; Sarafimov, B.; Maag, S.; Wang, X.; Thominet, V.; Walther, H.; Lachat, T.; Vitins, M.; Bunk, O.

    2018-04-01

    For many scientific questions gaining three-dimensional insight into a specimen can provide valuable information. We here present an instrument called "tOMography Nano crYo (OMNY)," dedicated to high resolution 3D scanning x-ray microscopy at cryogenic conditions via hard X-ray ptychography. Ptychography is a lens-less imaging method requiring accurate sample positioning. In OMNY, this in achieved via dedicated laser interferometry and closed-loop position control reaching sub-10 nm positioning accuracy. Cryogenic sample conditions are maintained via conductive cooling. 90 K can be reached when using liquid nitrogen as coolant, and 10 K is possible with liquid helium. A cryogenic sample-change mechanism permits measurements of cryogenically fixed specimens. We compare images obtained with OMNY with older measurements performed using a nitrogen gas cryo-jet of stained, epoxy-embedded retina tissue and of frozen-hydrated Chlamydomonas cells.

  16. High intensity magnetic separation for the clean-up of a site polluted by lead metallurgy.

    PubMed

    Sierra, C; Martínez, J; Menéndez-Aguado, J M; Afif, E; Gallego, J R

    2013-03-15

    The industrial history in the district of Linares (Spain) has had a severe impact on soil quality. Here we examined soil contaminated by lead and other heavy metals in "La Cruz" site, a brownfield affected by metallurgical residues. Initially, the presence of contaminants mainly associated with the presence of lead slag fragments mixed with the soil was evaluated. The subsequent analysis showed a quasi-uniform distribution of the pollution irrespective of the grain-size fractions. This study was accompanied by a characterization of the lead slag behavior under the presence of a magnetic field. Two main magnetic components were detected: first a ferromagnetic and/or ferrimagnetic contribution, second a paramagnetic and/or antiferromagnetic one. It was also established that the slag was composed mainly of lead spherules and iron oxides embedded in a silicate matrix. Under these conditions, the capacity of magnetic separation to remove pollutants was examined. Therefore, two high intensity magnetic separators (dry and wet devices, respectively) were used. Dry separation proved to be successful at decontaminating soil in the first stages of a soil washing plant. In contrast, wet separation was found effective as a post-process for the finer fractions. Copyright © 2013 Elsevier B.V. All rights reserved.

  17. 3D Cryo-Imaging: A Very High-Resolution View of the Whole Mouse

    PubMed Central

    Roy, Debashish; Steyer, Grant J.; Gargesha, Madhusudhana; Stone, Meredith E.; Wilson, David L.

    2009-01-01

    We developed the Case Cryo-imaging system that provides information rich, very high-resolution, color brightfield, and molecular fluorescence images of a whole mouse using a section-and-image block-face imaging technology. The system consists of a mouse-sized, motorized cryo-microtome with special features for imaging, a modified, brightfield/ fluorescence microscope, and a robotic xyz imaging system positioner, all of which is fully automated by a control system. Using the robotic system, we acquired microscopic tiled images at a pixel size of 15.6 µm over the block face of a whole mouse sectioned at 40 µm, with a total data volume of 55 GB. Viewing 2D images at multiple resolutions, we identified small structures such as cardiac vessels, muscle layers, villi of the small intestine, the optic nerve, and layers of the eye. Cryo-imaging was also suitable for imaging embryo mutants in 3D. A mouse, in which enhanced green fluorescent protein was expressed under gamma actin promoter in smooth muscle cells, gave clear 3D views of smooth muscle in the urogenital and gastrointestinal tracts. With cryo-imaging, we could obtain 3D vasculature down to 10 µm, over very large regions of mouse brain. Software is fully automated with fully programmable imaging/sectioning protocols, email notifications, and automatic volume visualization. With a unique combination of field-of-view, depth of field, contrast, and resolution, the Case Cryo-imaging system fills the gap between whole animal in vivo imaging and histology. PMID:19248166

  18. Imaging system for creating 3D block-face cryo-images of whole mice

    NASA Astrophysics Data System (ADS)

    Roy, Debashish; Breen, Michael; Salvado, Olivier; Heinzel, Meredith; McKinley, Eliot; Wilson, David

    2006-03-01

    We developed a cryomicrotome/imaging system that provides high resolution, high sensitivity block-face images of whole mice or excised organs, and applied it to a variety of biological applications. With this cryo-imaging system, we sectioned cryo-preserved tissues at 2-40 μm thickness and acquired high resolution brightfield and fluorescence images with microscopic in-plane resolution (as good as 1.2 μm). Brightfield images of normal and pathological anatomy show exquisite detail, especially in the abdominal cavity. Multi-planar reformatting and 3D renderings allow one to interrogate 3D structures. In this report, we present brightfield images of mouse anatomy, as well as 3D renderings of organs. For BPK mice model of polycystic kidney disease, we compared brightfield cryo-images and kidney volumes to MRI. The color images provided greater contrast and resolution of cysts as compared to in vivo MRI. We note that color cryo-images are closer to what a researcher sees in dissection, making it easier for them to interpret image data. The combination of field of view, depth of field, ultra high resolution and color/fluorescence contrast enables cryo-image volumes to provide details that cannot be found through in vivo imaging or other ex vivo optical imaging approaches. We believe that this novel imaging system will have applications that include identification of mouse phenotypes, characterization of diseases like blood vessel disease, kidney disease, and cancer, assessment of drug and gene therapy delivery and efficacy and validation of other imaging modalities.

  19. Cryo-Vacuum Testing of the JWST Integrated Science Instrument Module

    NASA Technical Reports Server (NTRS)

    Kimble, Randy A.; Vila, M. Begona; Van Campen, Julie M.; Birkmann, Stephen M.; Comber, Brian J.; Fatig, Curtis C.; Glasse, Alistair C. H.; Glazer, Stuart D.; Kelly, Douglas M.; Mann, Steven D.; hide

    2016-01-01

    In late 2015 early 2016, a major cryo-vacuum test was carried out for the Integrated Science Instrument Module (ISIM) of the James Webb Space Telescope. This test comprised the final cryo-certification and calibration test of the ISIM before its delivery for integration with the rest of the JWST observatory. Over the roughly 100-day period of the round-the-clock test program, the full complement of ISIM flight instruments, structure, harness radiator, and electronics were put through a comprehensive program of thermal, optical, electrical, and operational tests. We briefly summarize the goals, setup, execution, and key results for this critical JWST milestone.

  20. Some concepts of the advanced mass spectrometry at the COMBAS magnetic separator of nuclear reaction products

    NASA Astrophysics Data System (ADS)

    Artukh, A. G.; Tarantin, N. I.

    Proposed is an in-flight measurement method of recoil nuclei masses with the help of a Penning trap located behind the COMBAS magnetic separator for nuclear reaction products. The method is based on the following operations: (i) Accepting the recoil nuclear reaction products by the magnetic separator and decreasing their kinetic energy by degraders. (ii) In-flight transportation of the retarded nuclei into the magnetic field of the Penning trap's solenoid and transforming their remaining longitudinal momentum into orbital rotation by the fringing magnetic field of the solenoid. (iii) Cooling the orbital rotation of the ions by the high-frequency azimuthal electric field of the Penning trap's electric hyperboloid.

  1. Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes.

    PubMed

    Judd, Ellen M; Comolli, Luis R; Chen, Joseph C; Downing, Kenneth H; Moerner, W E; McAdams, Harley H

    2005-10-01

    Cryoelectron microscope tomography (cryoEM) and a fluorescence loss in photobleaching (FLIP) assay were used to characterize progression of the terminal stages of Caulobacter crescentus cell division. Tomographic cryoEM images of the cell division site show separate constrictive processes closing first the inner membrane (IM) and then the outer membrane (OM) in a manner distinctly different from that of septum-forming bacteria. FLIP experiments had previously shown cytoplasmic compartmentalization (when cytoplasmic proteins can no longer diffuse between the two nascent progeny cell compartments) occurring 18 min before daughter cell separation in a 135-min cell cycle so the two constrictive processes are separated in both time and space. In the very latest stages of both IM and OM constriction, short membrane tether structures are observed. The smallest observed pre-fission tethers were 60 nm in diameter for both the inner and outer membranes. Here, we also used FLIP experiments to show that both membrane-bound and periplasmic fluorescent proteins diffuse freely through the FtsZ ring during most of the constriction procession.

  2. Preparation and characterization of chemically functionalized silica-coated magnetic nanoparticles as a DNA separator.

    PubMed

    Kang, Kiho; Choi, Jinsub; Nam, Joong Hee; Lee, Sang Cheon; Kim, Kyung Ja; Lee, Sang-Won; Chang, Jeong Ho

    2009-01-15

    The work describes a simple and convenient process for highly efficient and direct DNA separation with functionalized silica-coated magnetic nanoparticles. Iron oxide magnetic nanoparticles and silica-coated magnetic nanoparticles were prepared uniformly, and the silica coating thickness could be easily controlled in a range from 10 to 50 nm by changing the concentration of silica precursor (TEOS) including controlled magnetic strength and particle size. A change in the surface modification on the nanoparticles was introduced by aminosilanization to enhance the selective DNA separation resulting from electrostatic interaction. The efficiency of the DNA separation was explored via the function of the amino-group numbers, particle size, the amount of the nanoparticles used, and the concentration of NaCl salt. The DNA adsorption yields were high in terms of the amount of triamino-functionalized nanoparticles used, and the average particle size was 25 nm. The adsorption efficiency of aminofunctionalized nanoparticles was the 4-5 times (80-100%) higher compared to silica-coated nanoparticles only (10-20%). DNA desorption efficiency showed an optimum level of over 0.7 M of the NaCl concentration. To elucidate the agglomeration of nanoparticles after electrostatic DNA binding, the Guinier plots were calculated from small-angle X-ray diffractions in a comparison of the results of energy diffraction TEM and confocal laser scanning microscopy. Additionally, the direct separation of human genomic DNA was achieved from human saliva and whole blood with high efficiency.

  3. CryoSat Ice Processor: High-Level Overview of Baseline-C Data and Quality-Control

    NASA Astrophysics Data System (ADS)

    Mannan, R.; Webb, E.; Hall, A.; Bouffard, J.; Femenias, P.; Parrinello, T.; Bouffard, J.; Brockley, D.; Baker, S.; Scagliola, M.; Urien, S.

    2016-08-01

    Since April 2015, the CryoSat ice products have been generated with the new Baseline-C Instrument Processing Facilities (IPFs). This represents a major upgrade to the CryoSat ice IPFs and is the baseline for the second CryoSat Reprocessing Campaign. Baseline- C introduces major evolutions with respect to Baseline- B, most notably the release of freeboard data within the L2 SAR products, following optimisation of the SAR retracker. Additional L2 improvements include a new Arctic Mean Sea Surface (MSS) in SAR; a new tuneable land ice retracker in LRM; and a new Digital Elevation Model (DEM) in SARIn. At L1B new attitude fields have been introduced and existing datation and range biases reduced. This paper provides a high level overview of the changes and evolutions implemented at Baseline-C in order to improve CryoSat L1B and L2 data characteristics and exploitation over polar regions. An overview of the main Quality Control (QC) activities performed on operational Baseline-C products is also presented.

  4. Multifunctional magnetic-optical nanoparticle probes for simultaneous detection, separation, and thermal ablation of multiple pathogens.

    PubMed

    Wang, Chungang; Irudayaraj, Joseph

    2010-01-01

    Multifunctional nanoparticles possessing magnetization and near-infrared (NIR) absorption have warranted interest due to their significant applications in magnetic resonance imaging, diagnosis, bioseparation, target delivery, and NIR photothermal ablation. Herein, the site-selective assembly of magnetic nanoparticles onto the ends or ends and sides of gold nanorods with different aspect ratios (ARs) to create multifunctional nanorods decorated with varying numbers of magnetic particles is described for the first time. The resulting hybrid nanoparticles are designated as Fe(3)O(4)-Au(rod)-Fe(3)O(4) nanodumbbells and Fe(3)O(4)-Au(rod) necklacelike constructs with tunable optical and magnetic properties, respectively. These hybrid nanomaterials can be used for multiplex detection and separation because of their tunable magnetic and plasmonic functionality. More specifically, Fe(3)O(4)-Au(rod) necklacelike probes of different ARs are utilized for simultaneous optical detection based on their plasmon properties, magnetic separation, and photokilling of multiple pathogens from a single sample at one time. The combined functionalities of the synthesized probes will open up many exciting opportunities in dual imaging for targeted delivery and photothermal therapy.

  5. Bio-inspired Cryo-ink Preserves Red Blood Cell Phenotype and Function during Nanoliter Vitrification

    PubMed Central

    Assal, Rami El; Guven, Sinan; Gurkan, Umut Atakan; Gozen, Irep; Shafiee, Hadi; Dalbeyber, Sedef; Abdalla, Noor; Thomas, Gawain; Fuld, Wendy; Illigens, Ben M.W.; Estanislau, Jessica; Khoory, Joseph; Kaufman, Richard; Zylberberg, Claudia; Lindeman, Neal; Wen, Qi; Ghiran, Ionita; Demirci, Utkan

    2014-01-01

    Current red blood cell cryopreservation methods utilize bulk volumes, causing cryo-injury of cells, which results in irreversible disruption of cell morphology, mechanics, and function. An innovative approach to preserve human red blood cell morphology, mechanics, and function following vitrification in nanoliter volumes is developed using a novel cryo-ink integrated with a bio-printing approach. PMID:25047246

  6. Accurate model annotation of a near-atomic resolution cryo-EM map.

    PubMed

    Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah

    2017-03-21

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

  7. Accurate model annotation of a near-atomic resolution cryo-EM map

    PubMed Central

    Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D.; King, Jonathan A.; Schmid, Michael F.; Chiu, Wah

    2017-01-01

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages. PMID:28270620

  8. Cryo-comminution of plastic waste.

    PubMed

    Gente, Vincenzo; La Marca, Floriana; Lucci, Federica; Massacci, Paolo; Pani, Eleonora

    2004-01-01

    Recycling of plastics is a big issue in terms of environmental sustainability and of waste management. The development of proper technologies for plastic recycling is recognised as a priority. To achieve this aim, the technologies applied in mineral processing can be adapted to recycling systems. In particular, the improvement of comminution technologies is one of the main actions to improve the quality of recycled plastics. The aim of this work is to point out suitable comminution processes for different types of plastic waste. Laboratory comminution tests have been carried out under different conditions of temperature and sample pre-conditioning adopting as refrigerant agents CO2 and liquid nitrogen. The temperature has been monitored by thermocouples placed in the milling chamber. Also different internal mill screens have been adopted. A proper procedure has been set up in order to obtain a selective comminution and a size reduction suitable for further separation treatment. Tests have been performed on plastics coming from medical plastic waste and from a plant for spent lead batteries recycling. Results coming from different mill devices have been compared taking into consideration different indexes for representative size distributions. The results of the performed tests show as cryo-comminution improves the effectiveness of size reduction of plastics, promotes liberation of constituents and increases specific surface size of comminuted particles in comparison to a comminution process carried out at room temperature. Copyright 2004 Elsevier Ltd.

  9. Challenges and opportunities in the high-resolution cryo-EM visualization of microtubules and their binding partners.

    PubMed

    Nogales, Eva; Kellogg, Elizabeth H

    2017-10-01

    As non-crystallizable polymers, microtubules have been the target of cryo-electron microscopy (cryo-EM) studies since the technique was first established. Over the years, image processing strategies have been developed that take care of the unique, pseudo-helical symmetry of the microtubule. With recent progress in data quality and data processing, cryo-EM reconstructions are now reaching resolutions that allow the generation of atomic models of microtubules and the factors that bind them. These include cellular partners that contribute to microtubule cellular functions, or small ligands that interfere with those functions in the treatment of cancer. The stage is set to generate a family portrait for all identified microtubule interacting proteins and to use cryo-EM as a drug development tool in the targeting of tubulin. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  10. SERS-fluorescence joint spectral encoded magnetic nanoprobes for multiplex cancer cell separation.

    PubMed

    Wang, Zhuyuan; Zong, Shenfei; Chen, Hui; Wang, Chunlei; Xu, Shuhong; Cui, Yiping

    2014-11-01

    A new kind of cancer cell separation method is demonstrated, using surface-enhanced Raman scattering (SERS) and fluorescence dual-encoded magnetic nanoprobes. The designed nanoprobes can realize SERS-fluorescence joint spectral encoding (SFJSE) and greatly improve the multiplexing ability. The nanoprobes have four main components, that is, the magnetic core, SERS generator, fluorescent agent, and targeting antibody. These components are assembled with a multi-layered structure to form the nanoprobes. Specifically, silica-coated magnetic nanobeads (MBs) are used as the inner core. Au core-Ag shell nanorods (Au@Ag NRs) are employed as the SERS generators and attached on the silica-coated MBs. After burying these Au@Ag NRs with another silica layer, CdTe quantum dots (QDs), that is, the fluorescent agent, are anchored onto the silica layer. Finally, antibodies are covalently linked to CdTe QDs. SFJSE is fulfilled by using different Raman molecules and QDs with different emission wavelengths. By utilizing four human cancer cell lines and one normal cell line as the model cells, the nanoprobes can specifically and simultaneously separate target cancer cells from the normal ones. This SFJSE-based method greatly facilitates the multiplex, rapid, and accurate cancer cell separation, and has a prosperous potential in high-throughput analysis and cancer diagnosis. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Assimilation of CryoSat-2 altimetry to a hydrodynamic model of the Brahmaputra river

    NASA Astrophysics Data System (ADS)

    Schneider, Raphael; Nygaard Godiksen, Peter; Ridler, Marc-Etienne; Madsen, Henrik; Bauer-Gottwein, Peter

    2016-04-01

    Remote sensing provides valuable data for parameterization and updating of hydrological models, for example water level measurements of inland water bodies from satellite radar altimeters. Satellite altimetry data from repeat-orbit missions such as Envisat, ERS or Jason has been used in many studies, also synthetic wide-swath altimetry data as expected from the SWOT mission. This study is one of the first hydrologic applications of altimetry data from a drifting orbit satellite mission, namely CryoSat-2. CryoSat-2 is equipped with the SIRAL instrument, a new type of radar altimeter similar to SRAL on Sentinel-3. CryoSat-2 SARIn level 2 data is used to improve a 1D hydrodynamic model of the Brahmaputra river basin in South Asia set up in the DHI MIKE 11 software. CryoSat-2 water levels were extracted over river masks derived from Landsat imagery. After discharge calibration, simulated water levels were fitted to the CryoSat-2 data along the Assam valley by adapting cross section shapes and datums. The resulting hydrodynamic model shows accurate spatio-temporal representation of water levels, which is a prerequisite for real-time model updating by assimilation of CryoSat-2 altimetry or multi-mission data in general. For this task, a data assimilation framework has been developed and linked with the MIKE 11 model. It is a flexible framework that can assimilate water level data which are arbitrarily distributed in time and space. Different types of error models, data assimilation methods, etc. can easily be used and tested. Furthermore, it is not only possible to update the water level of the hydrodynamic model, but also the states of the rainfall-runoff models providing the forcing of the hydrodynamic model. The setup has been used to assimilate CryoSat-2 observations over the Assam valley for the years 2010 to 2013. Different data assimilation methods and localizations were tested, together with different model error representations. Furthermore, the impact of

  12. Optimization of yield in magnetic cell separations using nickel nanowires of different lengths.

    PubMed

    Hultgren, Anne; Tanase, Monica; Felton, Edward J; Bhadriraju, Kiran; Salem, Aliasger K; Chen, Christopher S; Reich, Daniel H

    2005-01-01

    Ferromagnetic nanowires are shown to perform both high yield and high purity single-step cell separations on cultures of NIH-3T3 mouse fibroblast cells. The nanowires are made by electrochemical deposition in nanoporous templates, permitting detailed control of their chemical and physical properties. When added to fibroblast cell cultures, the nanowires are internalized by the cells via the integrin-mediated adhesion pathway. The effectiveness of magnetic cell separations using Ni nanowires 350 nm in diameter and 5-35 micrometers long in field gradients of 40 T/m was compared to commercially available superparamagnetic beads. The percent yield of the separated populations is found to be optimized when the length of the nanowire is matched to the diameter of the cells in the culture. Magnetic cell separations performed under these conditions achieve 80% purity and 85% yield, a 4-fold increase over the beads. This effect is shown to be robust when the diameter of the cell is changed within the same cell line using mitomycin-C.

  13. Hour-glass magnetic excitations induced by nanoscopic phase separation in cobalt oxides.

    PubMed

    Drees, Y; Li, Z W; Ricci, A; Rotter, M; Schmidt, W; Lamago, D; Sobolev, O; Rütt, U; Gutowski, O; Sprung, M; Piovano, A; Castellan, J P; Komarek, A C

    2014-12-23

    The magnetic excitations in the cuprate superconductors might be essential for an understanding of high-temperature superconductivity. In these cuprate superconductors the magnetic excitation spectrum resembles an hour-glass and certain resonant magnetic excitations within are believed to be connected to the pairing mechanism, which is corroborated by the observation of a universal linear scaling of superconducting gap and magnetic resonance energy. So far, charge stripes are widely believed to be involved in the physics of hour-glass spectra. Here we study an isostructural cobaltate that also exhibits an hour-glass magnetic spectrum. Instead of the expected charge stripe order we observe nano phase separation and unravel a microscopically split origin of hour-glass spectra on the nano scale pointing to a connection between the magnetic resonance peak and the spin gap originating in islands of the antiferromagnetic parent insulator. Our findings open new ways to theories of magnetic excitations and superconductivity in cuprate superconductors.

  14. Carotene location in processed food samples measured by cryo In-SEM Raman.

    PubMed

    Lopez-Sanchez, Patricia; Schumm, Stephan; Pudney, Paul D A; Hazekamp, Johan

    2011-09-21

    Cryo In-SEM Raman has been used for the first time to localise carotene compounds in a food matrix. Raman spectra of lycopene and β-carotene have been obtained from sampling oil droplets and plant cell structures visualised with cryo-SEM in tomato and carrot based emulsions containing 5% oil. It was possible to identify the carotenoids in both the oil droplets and the cell walls. Furthermore our results gave some indication that the carotenoids were in the non-crystalline state. It has been suggested that a higher amount of carotenes solubilised into the oil phase of the food matrix would lead to a higher bioaccessibility, thus understanding the effect of processing conditions on micronutrients distribution in a food matrix might help the design of plant based food products with a better nutritional quality. This shows improved structural characterisation of the cryo-SEM with the molecular sensitivity of Raman spectroscopy as a promising approach for complex biological problems.

  15. GraDeR: Membrane Protein Complex Preparation for Single-Particle Cryo-EM.

    PubMed

    Hauer, Florian; Gerle, Christoph; Fischer, Niels; Oshima, Atsunori; Shinzawa-Itoh, Kyoko; Shimada, Satoru; Yokoyama, Ken; Fujiyoshi, Yoshinori; Stark, Holger

    2015-09-01

    We developed a method, named GraDeR, which substantially improves the preparation of membrane protein complexes for structure determination by single-particle cryo-electron microscopy (cryo-EM). In GraDeR, glycerol gradient centrifugation is used for the mild removal of free detergent monomers and micelles from lauryl maltose-neopentyl glycol detergent stabilized membrane complexes, resulting in monodisperse and stable complexes to which standard processes for water-soluble complexes can be applied. We demonstrate the applicability of the method on three different membrane complexes, including the mammalian FoF1 ATP synthase. For this highly dynamic and fragile rotary motor, we show that GraDeR allows visualizing the asymmetry of the F1 domain, which matches the ground state structure of the isolated domain. Therefore, the present cryo-EM structure of FoF1 ATP synthase provides direct structural evidence for Boyer's binding change mechanism in the context of the intact enzyme. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. Cryo-scatter measurements of beryllium

    NASA Astrophysics Data System (ADS)

    Lippey, Barret; Krone-Schmidt, Wilfried

    1991-12-01

    Bi-directional Reflection Distribution Function measurements were performed as a function of cryogenic temperature for various substrates. Substrates investigated include HIPed and sputtered beryllium produced from different powders and by various manufacturing and polishing processes. In some samples investigated, the BRDF at 10.6 microns increased by a factor of 2 to 5 during cooling from 300 to 30 Kelvin. On repeated temperature cycling the change in BRDF appeared to be totally elastic. The cryo-scatter effect does not occur for all types of beryllium.

  17. Elevated Temperature Compressive Strength Properties of Oxide Dispersion Strengthened NiAl After Cryo-milling and Roasting in Nitrogen

    NASA Technical Reports Server (NTRS)

    Whittenberger, J. Daniel; Grahle, Peter; Arzt, Eduard; Hebsur, Mohan

    1998-01-01

    In an effort to superimpose two different elevated temperature strengthening mechanisms in NiAl, several lots of oxide dispersion strengthened (ODS) NiAl powder have been cryo-milled in liquid nitrogen to introduce AlN particles at the grain boundaries. As an alternative to cryo-milling, one lot of ODS NiAl was roasted in nitrogen to produce AlN. Both techniques resulted in hot extruded AlN-strengthened, ODS NiAl alloys which were stronger than the base ODS NiAl between 1200 and 1400 K. However, neither the cryo-milled nor the N2-roasted ODS NiAl alloys were as strong as cryo-milled binary NiAl containing like amounts of AlN. The reason(s) for the relative weakness of cryo-milled ODS NiAl is not certain; however the lack of superior strength in N2-roasted ODS NiAl is probably due to its relatively large AlN particles.

  18. Combining Envisat type and CryoSat-2 altimetry to inform hydrodynamic models

    NASA Astrophysics Data System (ADS)

    Schneider, Raphael; Nygaard Godiksen, Peter; Villadsen, Heidi; Madsen, Henrik; Bauer-Gottwein, Peter

    2015-04-01

    Hydrological models are developed and used for flood forecasting and water resources management. Such models rely on a variety of input and calibration data. In general, and especially in data scarce areas, remote sensing provides valuable data for the parameterization and updating of such models. Satellite radar altimeters provide water level measurements of inland water bodies. So far, many studies making use of satellite altimeters have been based on data from repeat-orbit missions such as Envisat, ERS or Jason or on synthetic wide-swath altimetry data as expected from the SWOT mission. This work represents one of the first hydrologic applications of altimetry data from a drifting orbit satellite mission, using data from CryoSat-2. We present an application where CryoSat-2 data is used to improve a hydrodynamic model of the Ganges and Brahmaputra river basins in South Asia set up in the DHI MIKE 11 software. The model's parameterization and forcing is mainly based on remote sensing data, for example the TRMM 3B42 precipitation product and the SRTM DEM for river and subcatchment delineation. CryoSat-2 water levels were extracted over a river mask derived from Landsat 7 and 8 imagery. After calibrating the hydrological-hydrodynamic model against observed discharge, simulated water levels were fitted to the CryoSat-2 data, with a focus on the Brahmaputra river in the Assam valley: The average simulated water level in the hydrodynamic model was fitted to the average water level along the river's course as observed by CryoSat-2 over the years 2011-2013 by adjusting the river bed elevation. In a second step, the cross section shapes were adjusted so that the simulated water level dynamics matched those obtained from Envisat virtual station time series. The discharge calibration resulted in Nash-Sutcliffe coefficients of 0.86 and 0.94 for the Ganges and Brahmaputra. Using the Landsat river mask, the CryoSat-2 water levels show consistency along the river and are in

  19. Design of microfluidic channels for magnetic separation of malaria-infected red blood cells

    PubMed Central

    Wu, Wei-Tao; Martin, Andrea Blue; Gandini, Alberto; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F.

    2016-01-01

    This study is motivated by the development of a blood cell filtration device for removal of malaria-infected, parasitized red blood cells (pRBCs). The blood was modeled as a multi-component fluid using the computational fluid dynamics discrete element method (CFD-DEM), wherein plasma was treated as a Newtonian fluid and the red blood cells (RBCs) were modeled as soft-sphere solid particles which move under the influence of drag, collisions with other RBCs, and a magnetic force. The CFD-DEM model was first validated by a comparison with experimental data from Han et al. 2006 (Han and Frazier 2006) involving a microfluidic magnetophoretic separator for paramagnetic deoxygenated blood cells. The computational model was then applied to a parametric study of a parallel-plate separator having hematocrit of 40% with a 10% of the RBCs as pRBCs. Specifically, we investigated the hypothesis of introducing an upstream constriction to the channel to divert the magnetic cells within the near-wall layer where the magnetic force is greatest. Simulations compared the efficacy of various geometries upon the stratification efficiency of the pRBCs. For a channel with nominal height of 100 µm, the addition of an upstream constriction of 80% improved the proportion of pRBCs retained adjacent to the magnetic wall (separation efficiency) by almost 2 fold, from 26% to 49%. Further addition of a downstream diffuser reduced remixing, hence improved separation efficiency to 72%. The constriction introduced a greater pressure drop (from 17 to 495 Pa), which should be considered when scaling-up this design for a clinical-sized system. Overall, the advantages of this design include its ability to accommodate physiological hematocrit and high throughput – which is critical for clinical implementation as a blood-filtration system. PMID:27761107

  20. Primary Mouse Myoblast Purification using Magnetic Cell Separation.

    PubMed

    Sincennes, Marie Claude; Wang, Yu Xin; Rudnicki, Michael A

    2017-01-01

    Primary myoblasts can be isolated from mouse muscle cell extracts and cultured in vitro. Muscle cells are usually dissociated manually by mincing with razor blades or scissors in a collagenase/dispase solution. Primary myoblasts are then gradually enriched by pre-plating on collagen-coated plates, based on the observation that mouse fibroblasts attach quickly to collagen-coated plates, and are less adherent. Here, we describe an automated muscle dissociation protocol. We also propose an alternative to pre-plating using magnetic bead separation of primary myoblasts, which improve myoblast purity by minimizing fibroblast contamination.

  1. Cryo-Electron Tomography of Rubella Virus

    PubMed Central

    Battisti, Anthony J.; Yoder, Joshua D.; Plevka, Pavel; Winkler, Dennis C.; Mangala Prasad, Vidya; Kuhn, Richard J.; Frey, Teryl K.; Steven, Alasdair C.

    2012-01-01

    Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses. PMID:22855483

  2. Cryo-electron tomography of rubella virus.

    PubMed

    Battisti, Anthony J; Yoder, Joshua D; Plevka, Pavel; Winkler, Dennis C; Prasad, Vidya Mangala; Kuhn, Richard J; Frey, Teryl K; Steven, Alasdair C; Rossmann, Michael G

    2012-10-01

    Rubella virus is the only member of the Rubivirus genus within the Togaviridae family and is the causative agent of the childhood disease known as rubella or German measles. Here, we report the use of cryo-electron tomography to examine the three-dimensional structure of rubella virions and compare their structure to that of Ross River virus, a togavirus belonging the genus Alphavirus. The ectodomains of the rubella virus glycoproteins, E1 and E2, are shown to be organized into extended rows of density, separated by 9 nm on the viral surface. We also show that the rubella virus nucleocapsid structure often forms a roughly spherical shell which lacks high density at its center. While many rubella virions are approximately spherical and have dimensions similar to that of the icosahedral Ross River virus, the present results indicate that rubella exhibits a large degree of pleomorphy. In addition, we used rotation function calculations and other analyses to show that approximately spherical rubella virions lack the icosahedral organization which characterizes Ross River and other alphaviruses. The present results indicate that the assembly mechanism of rubella virus, which has previously been shown to differ from that of the alphavirus assembly pathway, leads to an organization of the rubella virus structural proteins that is different from that of alphaviruses.

  3. Atomic Resolution Cryo-EM Structure of β-Galactosidase.

    PubMed

    Bartesaghi, Alberto; Aguerrebere, Cecilia; Falconieri, Veronica; Banerjee, Soojay; Earl, Lesley A; Zhu, Xing; Grigorieff, Nikolaus; Milne, Jacqueline L S; Sapiro, Guillermo; Wu, Xiongwu; Subramaniam, Sriram

    2018-05-10

    The advent of direct electron detectors has enabled the routine use of single-particle cryo-electron microscopy (EM) approaches to determine structures of a variety of protein complexes at near-atomic resolution. Here, we report the development of methods to account for local variations in defocus and beam-induced drift, and the implementation of a data-driven dose compensation scheme that significantly improves the extraction of high-resolution information recorded during exposure of the specimen to the electron beam. These advances enable determination of a cryo-EM density map for β-galactosidase bound to the inhibitor phenylethyl β-D-thiogalactopyranoside where the ordered regions are resolved at a level of detail seen in X-ray maps at ∼ 1.5 Å resolution. Using this density map in conjunction with constrained molecular dynamics simulations provides a measure of the local flexibility of the non-covalently bound inhibitor and offers further opportunities for structure-guided inhibitor design. Published by Elsevier Ltd.

  4. Copper Recovery from Yulong Complex Copper Oxide Ore by Flotation and Magnetic Separation

    NASA Astrophysics Data System (ADS)

    Han, Junwei; Xiao, Jun; Qin, Wenqing; Chen, Daixiong; Liu, Wei

    2017-09-01

    A combined process of flotation and high-gradient magnetic separation was proposed to utilize Yulong complex copper oxide ore. The effects of particle size, activators, Na2S dosage, LA (a mixture of ammonium sulfate and ethylenediamine) dosage, activating time, collectors, COC (a combination collector of modified hydroxyl oxime acid and xanthate) dosage, and magnetic intensity on the copper recovery were investigated. The results showed that 74.08% Cu was recovered by flotation, while the average grade of the copper concentrates was 21.68%. Another 17.34% Cu was further recovered from the flotation tailing by magnetic separation at 0.8 T. The cumulative recovery of copper reached 91.42%. The modifier LA played a positive role in facilitating the sulfidation of copper oxide with Na2S, and the combined collector COC was better than other collectors for the copper flotation. This technology has been successfully applied to industrial production, and the results are consistent with the laboratory data.

  5. Apparatus for magnetic separation of paramagnetic and diamagnetic material

    DOEpatents

    Doctor, Richard D.

    1988-01-01

    The present invention relates to methods and apparatus for segregating paramagnetic from diamagnetic particles in particulate material and, in particular, to the open gradient magnetic separation of ash producing components and pyritic sulfur from coal. The apparatus includes a vertical cylinder and a rotatable vertical screw positioned within the cylinder, the screw having a helical blade angled downwardly and outwardly from the axis. Rotation of the vertical screw causes denser particles, which in the case of coal include pyritic sulfur and ash, which are paramagnetic, to migrate to the outside of the screw, and less dense particles, such as the low sulfur organic portion of the coal, which are diamagnetic, to migrate towards the center of the screw. A vibration mechanism attached to the screw causes the screw to vibrate during rotation, agitating and thereby accommodating further segregation of the particles. An open gradient magnetic field is applied circumferentially along the entire length of the screw by a superconducting quadropole magnet. The open gradient magnetic field further segregates the paramagnetic particles from the diamagnetic particles. The paramagnetic particles may then be directed from the cylinder into a first storage bin, and the diamagnetic particles, which are suitable for relatively clean combustion, may be directed into a second storage bin.

  6. Apparatus for magnetic separation of paramagnetic and diamagnetic material

    DOEpatents

    Doctor, R.D.

    1988-10-18

    The present invention relates to methods and apparatus for segregating paramagnetic from diamagnetic particles in particulate material and, in particular, to the open gradient magnetic separation of ash producing components and pyritic sulfur from coal. The apparatus includes a vertical cylinder and a rotatable vertical screw positioned within the cylinder, the screw having a helical blade angled downwardly and outwardly from the axis. Rotation of the vertical screw causes denser particles, which in the case of coal include pyritic sulfur and ash, which are paramagnetic, to migrate to the outside of the screw, and less dense particles, such as the low sulfur organic portion of the coal, which are diamagnetic, to migrate towards the center of the screw. A vibration mechanism attached to the screw causes the screw to vibrate during rotation, agitating and thereby accommodating further segregation of the particles. An open gradient magnetic field is applied circumferentially along the entire length of the screw by a superconducting quadrupole magnet. The open gradient magnetic field further segregates the paramagnetic particles from the diamagnetic particles. The paramagnetic particles may then be directed from the cylinder into a first storage bin, and the diamagnetic particles, which are suitable for relatively clean combustion, may be directed into a second storage bin. 5 figs.

  7. Apparatus for magnetic separation of paramagnetic and diamagnetic material

    DOEpatents

    Doctor, R.D.

    1986-07-24

    The present invention relates to methods and apparatus for segregating paramagnetic from diamagnetic particles in particulate material and, in particular, to the open gradient magnetic separation of ash producing components and pyritic sulfur from coal. The apparatus includes a vertical cylinder and a rotatable vertical screw positioned within the cylinder, the screw having a helical blade angled downwardly and outwardly from the axis. Rotation of the vertical screw causes denser particles, which in the case of coal include pyritic sulfur and ash, which are paramagnetic, to migrate to the outside of the screw, and less dense particles, such as the low sulfur organic portion of the coal, which are diamagnetic, to migrate towards the center of the screw. A vibration mechanism attached to the screw causes the screw to vibrate during rotation, agitating and thereby accommodating further segregation of the particles. An open gradient magnetic field is applied circumferentially along the entire length of the screw by a superconducting quadrupole magnet. The open gradient magnetic field further segregates the paramagnetic-particles from the diamagnetic particles. The paramagnetic particles may then be directed from the cylinder into a first storage bin, and the diamagnetic particles, which are suitable for relatively clean combustion, may be directed into a second storage bin. 5 figs.

  8. Three-dimensional registration of intravascular optical coherence tomography and cryo-image volumes for microscopic-resolution validation.

    PubMed

    Prabhu, David; Mehanna, Emile; Gargesha, Madhusudhana; Brandt, Eric; Wen, Di; van Ditzhuijzen, Nienke S; Chamie, Daniel; Yamamoto, Hirosada; Fujino, Yusuke; Alian, Ali; Patel, Jaymin; Costa, Marco; Bezerra, Hiram G; Wilson, David L

    2016-04-01

    Evidence suggests high-resolution, high-contrast, [Formula: see text] intravascular optical coherence tomography (IVOCT) can distinguish plaque types, but further validation is needed, especially for automated plaque characterization. We developed experimental and three-dimensional (3-D) registration methods to provide validation of IVOCT pullback volumes using microscopic, color, and fluorescent cryo-image volumes with optional registered cryo-histology. A specialized registration method matched IVOCT pullback images acquired in the catheter reference frame to a true 3-D cryo-image volume. Briefly, an 11-parameter registration model including a polynomial virtual catheter was initialized within the cryo-image volume, and perpendicular images were extracted, mimicking IVOCT image acquisition. Virtual catheter parameters were optimized to maximize cryo and IVOCT lumen overlap. Multiple assessments suggested that the registration error was better than the [Formula: see text] spacing between IVOCT image frames. Tests on a digital synthetic phantom gave a registration error of only [Formula: see text] (signed distance). Visual assessment of randomly presented nearby frames suggested registration accuracy within 1 IVOCT frame interval ([Formula: see text]). This would eliminate potential misinterpretations confronted by the typical histological approaches to validation, with estimated 1-mm errors. The method can be used to create annotated datasets and automated plaque classification methods and can be extended to other intravascular imaging modalities.

  9. Optimizing Frozen Sample Preparation for Laser Microdissection: Assessment of CryoJane Tape-Transfer System®

    PubMed Central

    Golubeva, Yelena G.; Smith, Roberta M.; Sternberg, Lawrence R.

    2013-01-01

    Laser microdissection is an invaluable tool in medical research that facilitates collecting specific cell populations for molecular analysis. Diversity of research targets (e.g., cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, etc.) and varied scientific objectives, however, present challenges toward establishing standard laser microdissection protocols. Sample preparation is crucial for quality RNA, DNA and protein retrieval, where it often determines the feasibility of a laser microdissection project. The majority of microdissection studies in clinical and animal model research are conducted on frozen tissues containing native nucleic acids, unmodified by fixation. However, the variable morphological quality of frozen sections from tissues containing fat, collagen or delicate cell structures can limit or prevent successful harvest of the desired cell population via laser dissection. The CryoJane Tape-Transfer System®, a commercial device that improves cryosectioning outcomes on glass slides has been reported superior for slide preparation and isolation of high quality osteocyte RNA (frozen bone) during laser dissection. Considering the reported advantages of CryoJane for laser dissection on glass slides, we asked whether the system could also work with the plastic membrane slides used by UV laser based microdissection instruments, as these are better suited for collection of larger target areas. In an attempt to optimize laser microdissection slide preparation for tissues of different RNA stability and cryosectioning difficulty, we evaluated the CryoJane system for use with both glass (laser capture microdissection) and membrane (laser cutting microdissection) slides. We have established a sample preparation protocol for glass and membrane slides including manual coating of membrane slides with CryoJane solutions, cryosectioning, slide staining and dissection procedure, lysis and RNA extraction that facilitated

  10. Separation of enantiomers by their enantiospecific interaction with achiral magnetic substrates.

    PubMed

    Banerjee-Ghosh, Koyel; Ben Dor, Oren; Tassinari, Francesco; Capua, Eyal; Yochelis, Shira; Capua, Amir; Yang, See-Hun; Parkin, Stuart S P; Sarkar, Soumyajit; Kronik, Leeor; Baczewski, Lech Tomasz; Naaman, Ron; Paltiel, Yossi

    2018-06-22

    It is commonly assumed that recognition and discrimination of chirality, both in nature and in artificial systems, depend solely on spatial effects. However, recent studies have suggested that charge redistribution in chiral molecules manifests an enantiospecific preference in electron spin orientation. We therefore reasoned that the induced spin polarization may affect enantiorecognition through exchange interactions. Here we show experimentally that the interaction of chiral molecules with a perpendicularly magnetized substrate is enantiospecific. Thus, one enantiomer adsorbs preferentially when the magnetic dipole is pointing up, whereas the other adsorbs faster for the opposite alignment of the magnetization. The interaction is not controlled by the magnetic field per se, but rather by the electron spin orientations, and opens prospects for a distinct approach to enantiomeric separations. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  11. Bio-inspired cryo-ink preserves red blood cell phenotype and function during nanoliter vitrification.

    PubMed

    El Assal, Rami; Guven, Sinan; Gurkan, Umut Atakan; Gozen, Irep; Shafiee, Hadi; Dalbeyler, Sedef; Abdalla, Noor; Thomas, Gawain; Fuld, Wendy; Illigens, Ben M W; Estanislau, Jessica; Khoory, Joseph; Kaufman, Richard; Zylberberg, Claudia; Lindeman, Neal; Wen, Qi; Ghiran, Ionita; Demirci, Utkan

    2014-09-03

    Current red-blood-cell cryopreservation methods utilize bulk volumes, causing cryo-injury of cells, which results in irreversible disruption of cell morphology, mechanics, and function. An innovative approach to preserve human red-blood-cell morphology, mechanics, and function following vitrification in nanoliter volumes is developed using a novel cryo-ink integrated with a bioprinting approach. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Capture and separation of l-histidine through optimized zinc-decorated magnetic silica spheres.

    PubMed

    Cardoso, Vanessa F; Sebastián, Víctor; Silva, Carlos J R; Botelho, Gabriela; Lanceros-Méndez, Senentxu

    2017-09-01

    Zinc-decorated magnetic silica spheres were developed, optimized and tested for the capture and separation of l-histidine. The magnetic silica spheres were prepared using a simple sol-gel method and show excellent magnetic characteristics, adsorption capacity toward metal ions, and stability in aqueous solution in a wide pH range. The binding capacity of zinc-decorated magnetic silica spheres to histidine proved to be strongly influenced by the morphology, composition and concentration of metal at the surface of the magnetic silica spheres and therefore these parameters should be carefully controlled in order to maximize the performance for protein purification purposes. Optimized zinc-decorated magnetic silica spheres demonstrate a binding capacity to l-histidine of approximately 44mgg -1 at the optimum binding pH buffer. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. 100J-level nanosecond pulsed Yb:YAG cryo-cooled DPSSL amplifier

    NASA Astrophysics Data System (ADS)

    Smith, J. M.; Butcher, T. J.; Mason, P. D.; Ertel, K.; Phillips, P. J.; Banerjee, S.; De Vido, M.; Chekhlov, O.; Divoky, M.; Pilar, J.; Shaikh, W.; Hooker, C.; Lucianetti, A.; Hernandez Gomez, C.; Mocek, T.; Edwards, C.; Collier, J. L.

    2018-02-01

    We report on the successful demonstration of the world's first kW average power, 100 Joule-class, high-energy, nanosecond pulsed diode-pumped solid-state laser (DPSSL), DiPOLE100. Results from the first long-term test for amplification will be presented; the system was operated for 1 hour with 10 ns duration pulses at 10 Hz pulse repetition rate and an average output energy of 105 J and RMS energy stability of approximately 1%. The laser system is based on scalable cryogenic gas-cooled multi-slab ceramic Yb:YAG amplifier technology. The DiPOLE100 system comprises three major sub-systems, a spatially and temporally shaped front end, a 10 J cryo-amplifier and a 100 J cryo-amplifier. The 10 J cryo-amplifier contain four Yb:YAG ceramic gain media slabs, which are diode pumped from both sides, while a multi-pass architecture configured for seven passes enables 10 J of energy to be extracted at 10 Hz. This seeds the 100 J cryo-amplifier, which contains six Yb:YAG ceramic gain media slabs with the multi-pass configured for four passes. Our future development plans for this architecture will be introduced including closed-loop pulse shaping, increased energy, higher repetition rates and picosecond operation. This laser architecture unlocks the potential for practical applications including new sources for industrial materials processing and high intensity laser matter studies as envisioned for ELI [1], HiLASE [2], and the European XFEL [3]. Alternatively, it can be used as a pump source for higher repetition rate PW-class amplifiers, which can themselves generate high-brightness secondary radiation and ion sources leading to new remote imaging and medical applications.

  14. Magnetic properties and loss separation in iron-silicone-MnZn ferrite soft magnetic composites

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wu, Shen; Sun, Aizhi; Xu, Wenhuan

    This paper investigates the magnetic and structural properties of iron-based soft magnetic composites coated with silicone-MnZn ferrite hybrid. The organic silicone resin was added to improve the flexibility of the insulated iron powder and causes better adhesion between particles to increase the mechanical properties. Scanning electron microscopy and distribution maps show that the iron particle surface is covered with a thin layer of silicone-MnZn ferrite. Silicone-MnZn ferrite coated samples have higher permeability when compared with the non-magnetic silicone resin coated compacts. The real part of permeability increases by 34.18% when compared with the silicone resin coated samples at 20 kHz.more » In this work, a formula for calculating the total loss component by loss separation method is presented and finally the different parts of total losses are calculated. The results show that the eddy current loss coefficient is close to each other for the silicone-MnZn ferrite, silicone resin and MnZn ferrite coated samples (0.0078« less

  15. Accurate model annotation of a near-atomic resolution cryo-EM map

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structuralmore » features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.« less

  16. Accurate model annotation of a near-atomic resolution cryo-EM map

    DOE PAGES

    Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; ...

    2017-03-07

    Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structuralmore » features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.« less

  17. SubspaceEM: A Fast Maximum-a-posteriori Algorithm for Cryo-EM Single Particle Reconstruction

    PubMed Central

    Dvornek, Nicha C.; Sigworth, Fred J.; Tagare, Hemant D.

    2015-01-01

    Single particle reconstruction methods based on the maximum-likelihood principle and the expectation-maximization (E–M) algorithm are popular because of their ability to produce high resolution structures. However, these algorithms are computationally very expensive, requiring a network of computational servers. To overcome this computational bottleneck, we propose a new mathematical framework for accelerating maximum-likelihood reconstructions. The speedup is by orders of magnitude and the proposed algorithm produces similar quality reconstructions compared to the standard maximum-likelihood formulation. Our approach uses subspace approximations of the cryo-electron microscopy (cryo-EM) data and projection images, greatly reducing the number of image transformations and comparisons that are computed. Experiments using simulated and actual cryo-EM data show that speedup in overall execution time compared to traditional maximum-likelihood reconstruction reaches factors of over 300. PMID:25839831

  18. Asynchronous data acquisition and on-the-fly analysis of dose fractionated cryoEM images by UCSFImage

    PubMed Central

    Li, Xueming; Zheng, Shawn; Agard, David A.; Cheng, Yifan

    2015-01-01

    Newly developed direct electron detection cameras have a high image output frame rate that enables recording dose fractionated image stacks of frozen hydrated biological samples by electron cryomicroscopy (cryoEM). Such novel image acquisition schemes provide opportunities to analyze cryoEM data in ways that were previously impossible. The file size of a dose fractionated image stack is 20 ~ 60 times larger than that of a single image. Thus, efficient data acquisition and on-the-fly analysis of a large number of dose-fractionated image stacks become a serious challenge to any cryoEM data acquisition system. We have developed a computer-assisted system, named UCSFImage4, for semi-automated cryo-EM image acquisition that implements an asynchronous data acquisition scheme. This facilitates efficient acquisition, on-the-fly motion correction, and CTF analysis of dose fractionated image stacks with a total time of ~60 seconds/exposure. Here we report the technical details and configuration of this system. PMID:26370395

  19. 2.2 Å resolution cryo-EM structure of β-galactosidase in complex with a cell-permeant inhibitor.

    PubMed

    Bartesaghi, Alberto; Merk, Alan; Banerjee, Soojay; Matthies, Doreen; Wu, Xiongwu; Milne, Jacqueline L S; Subramaniam, Sriram

    2015-06-05

    Cryo-electron microscopy (cryo-EM) is rapidly emerging as a powerful tool for protein structure determination at high resolution. Here we report the structure of a complex between Escherichia coli β-galactosidase and the cell-permeant inhibitor phenylethyl β-D-thiogalactopyranoside (PETG), determined by cryo-EM at an average resolution of ~2.2 angstroms (Å). Besides the PETG ligand, we identified densities in the map for ~800 water molecules and for magnesium and sodium ions. Although it is likely that continued advances in detector technology may further enhance resolution, our findings demonstrate that preparation of specimens of adequate quality and intrinsic protein flexibility, rather than imaging or image-processing technologies, now represent the major bottlenecks to routinely achieving resolutions close to 2 Å using single-particle cryo-EM. Copyright © 2015, American Association for the Advancement of Science.

  20. Magnetically Separable Fe2O3/g-C3N4 Nanocomposites with Cocoon-Like Shape: Magnetic Properties and Photocatalytic Activities

    NASA Astrophysics Data System (ADS)

    Yu, Xiaojia; Yang, Xiaoyu; Li, Guang

    2018-01-01

    We report magnetically separable Fe2O3/g-C3N4 nanocomposites as a photocatalyst under visible-light irradiation in this study. The Fe2O3/g-C3N4 nanocomposites were synthesized through a two-step hydrothermal method. The Fe2O3 with cocoon-like shape was obviously dispersed on the surface of g-C3N4 with porous and layered nanostructure as seen from micrographs of the particles. Furthermore, the magnetic conversion of the samples was studied via vibrating sample magnetometer technology. It was found that the saturated magnetization Ms of the Fe2O3/g-C3N4 nanoparticles obviously decreased in the presence of g-C3N4, and the photocatalytic activity of the samples investigated by degrading Rhodamine B suggested that the Fe2O3/g-C3N4 photocatalyst was prior to the pure Fe2O3 and g-C3N4 samples. In addition, the magnetically separable ability of Fe2O3/g-C3N4 nanocomposites was efficiently exhibited by an external magnet.

  1. Zernike phase contrast cryo-electron tomography of whole bacterial cells.

    PubMed

    Guerrero-Ferreira, Ricardo C; Wright, Elizabeth R

    2014-01-01

    Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution. Copyright © 2013 Elsevier Inc. All rights reserved.

  2. Zernike phase contrast cryo-electron tomography of whole bacterial cells

    PubMed Central

    Guerrero-Ferreira, Ricardo C.; Wright, Elizabeth R.

    2014-01-01

    Cryo-electron tomography (cryo-ET) provides three-dimensional (3D) structural information of bacteria preserved in a native, frozen-hydrated state. The typical low contrast of tilt-series images, a result of both the need for a low electron dose and the use of conventional defocus phase-contrast imaging, is a challenge for high-quality tomograms. We show that Zernike phase-contrast imaging allows the electron dose to be reduced. This limits movement of gold fiducials during the tilt series, which leads to better alignment and a higher-resolution reconstruction. Contrast is also enhanced, improving visibility of weak features. The reduced electron dose also means that more images at more tilt angles could be recorded, further increasing resolution. PMID:24075950

  3. A Temperature-Stable Cryo-System for High-Temperature Superconducting MR In-Vivo Imaging

    PubMed Central

    Lin, In-Tsang; Yang, Hong-Chang; Chen, Jyh-Horng

    2013-01-01

    To perform a rat experiment using a high-temperature superconducting (HTS) surface resonator, a cryostat is essential to maintain the rat's temperature. In this work, a compact temperature-stable HTS cryo-system, keeping animal rectal temperature at 37.4°C for more than 3 hours, was successfully developed. With this HTS cryo-system, a 40-mm-diameter Bi2Sr2Ca2Cu3Ox (Bi-2223) surface resonator at 77 K was demonstrated in a 3-Tesla MRI system. The proton resonant frequency (PRF) method was employed to monitor the rat's temperature. Moreover, the capacity of MR thermometry in the HTS experiments was evaluated by correlating with data from independent fiber-optic sensor temperature measurements. The PRF thermal coefficient was derived as 0.03 rad/°C and the temperature-monitoring architecture can be implemented to upgrade the quality and safety in HTS experiments. The signal-to-noise ratio (SNR) of the HTS surface resonator at 77 K was higher than that of a professionally made copper surface resonator at 300 K, which has the same geometry, by a 3.79-fold SNR gain. Furthermore, the temperature-stable HTS cryo-system we developed can obtain stable SNR gain in every scan. A temperature-stable HTS cryo-system with an external air-blowing circulation system is demonstrated. PMID:23637936

  4. 3D registration of intravascular optical coherence tomography and cryo-image volumes for microscopic-resolution validation

    NASA Astrophysics Data System (ADS)

    Prabhu, David; Mehanna, Emile; Gargesha, Madhusudhana; Wen, Di; Brandt, Eric; van Ditzhuijzen, Nienke S.; Chamie, Daniel; Yamamoto, Hirosada; Fujino, Yusuke; Farmazilian, Ali; Patel, Jaymin; Costa, Marco; Bezerra, Hiram G.; Wilson, David L.

    2016-03-01

    High resolution, 100 frames/sec intravascular optical coherence tomography (IVOCT) can distinguish plaque types, but further validation is needed, especially for automated plaque characterization. We developed experimental and 3D registration methods, to provide validation of IVOCT pullback volumes using microscopic, brightfield and fluorescent cryoimage volumes, with optional, exactly registered cryo-histology. The innovation was a method to match an IVOCT pullback images, acquired in the catheter reference frame, to a true 3D cryo-image volume. Briefly, an 11-parameter, polynomial virtual catheter was initialized within the cryo-image volume, and perpendicular images were extracted, mimicking IVOCT image acquisition. Virtual catheter parameters were optimized to maximize cryo and IVOCT lumen overlap. Local minima were possible, but when we started within reasonable ranges, every one of 24 digital phantom cases converged to a good solution with a registration error of only +1.34+/-2.65μm (signed distance). Registration was applied to 10 ex-vivo cadaver coronary arteries (LADs), resulting in 10 registered cryo and IVOCT volumes yielding a total of 421 registered 2D-image pairs. Image overlays demonstrated high continuity between vascular and plaque features. Bland- Altman analysis comparing cryo and IVOCT lumen area, showed mean and standard deviation of differences as 0.01+/-0.43 mm2. DICE coefficients were 0.91+/-0.04. Finally, visual assessment on 20 representative cases with easily identifiable features suggested registration accuracy within one frame of IVOCT (+/-200μm), eliminating significant misinterpretations introduced by 1mm errors in the literature. The method will provide 3D data for training of IVOCT plaque algorithms and can be used for validation of other intravascular imaging modalities.

  5. A facile method for emulsified oil-water separation by using polyethylenimine-coated magnetic nanoparticles

    NASA Astrophysics Data System (ADS)

    Lü, Ting; Qi, Dongming; Zhang, Dong; Lü, Yulan; Zhao, Hongting

    2018-04-01

    Oil spills and oily wastewater discharges from ships and industrial activities have serious impacts on the environment and human health. In this study, a class of easy-to-synthesize polyethylenimine (PEI)-coated Fe3O4 magnetic nanoparticles (MNPs) was successfully synthesized via a one-step coprecipitation method. The synthesized PEI-coated Fe3O4 MNPs were characterized by using multiple technologies and applied in emulsified oil-water separation for the first time. It was found that the PEI effectively tuned the surface charge and wettability of MNPs. As a result, the PEI-coated MNPs could successfully assemble at the oil-water interface and promote the coalescence of oil droplets, thereby facilitating the subsequent magnetic separation. Results showed that the oil-water separation performance was superior and enhanced with the increase of ionic strength. Recycling experiment indicated that the PEI-coated MNPs could be reused up to six times without showing a significant decrease in separation efficiency. All of these results suggested that the PEI-coated MNP could potentially be used as a class of promising nanomaterials for emulsified oil-water separation. [Figure not available: see fulltext.

  6. Detection of isolated protein-bound metal ions by single-particle cryo-STEM.

    PubMed

    Elad, Nadav; Bellapadrona, Giuliano; Houben, Lothar; Sagi, Irit; Elbaum, Michael

    2017-10-17

    Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography.

  7. Detection of isolated protein-bound metal ions by single-particle cryo-STEM

    PubMed Central

    Elad, Nadav; Bellapadrona, Giuliano; Houben, Lothar; Sagi, Irit; Elbaum, Michael

    2017-01-01

    Metal ions play essential roles in many aspects of biological chemistry. Detecting their presence and location in proteins and cells is important for understanding biological function. Conventional structural methods such as X-ray crystallography and cryo-transmission electron microscopy can identify metal atoms on protein only if the protein structure is solved to atomic resolution. We demonstrate here the detection of isolated atoms of Zn and Fe on ferritin, using cryogenic annular dark-field scanning transmission electron microscopy (cryo-STEM) coupled with single-particle 3D reconstructions. Zn atoms are found in a pattern that matches precisely their location at the ferroxidase sites determined earlier by X-ray crystallography. By contrast, the Fe distribution is smeared along an arc corresponding to the proposed path from the ferroxidase sites to the mineral nucleation sites along the twofold axes. In this case the single-particle reconstruction is interpreted as a probability distribution function based on the average of individual locations. These results establish conditions for detection of isolated metal atoms in the broader context of electron cryo-microscopy and tomography. PMID:28973937

  8. Separation and enrichment of enantiopure from racemic compounds using magnetic levitation.

    PubMed

    Yang, Xiaochuan; Wong, Shin Yee; Bwambok, David K; Atkinson, Manza B J; Zhang, Xi; Whitesides, George M; Myerson, Allan S

    2014-07-18

    Crystallization of a solution with high enantiomeric excess can generate a mixture of crystals of the desired enantiomer and the racemic compound. Using a mixture of S-/RS-ibuprofen crystals as a model, we demonstrated that magnetic levitation (MagLev) is a useful technique for analysis, separation and enantioenrichment of chiral/racemic products.

  9. Evaluation of multi-mode CryoSat-2 altimetry data over the Po River against in situ data and a hydrodynamic model

    NASA Astrophysics Data System (ADS)

    Schneider, Raphael; Tarpanelli, Angelica; Nielsen, Karina; Madsen, Henrik; Bauer-Gottwein, Peter

    2018-02-01

    Coverage of in situ observations to monitor surface waters is insufficient on the global scale, and decreasing across the globe. Satellite altimetry has become an increasingly important monitoring technology for continental surface waters. The ESA CryoSat-2 altimetry mission, launched in 2010, has two novel features. (i) The radar altimeter instrument on board of CryoSat-2 is operated in three modes; two of them reduce the altimeter footprint by using Delay-Doppler processing. (ii) CryoSat-2 is placed on a distinct orbit with a repeat cycle of 369 days, leading to a drifting ground track pattern. The drifting ground track pattern challenges many common methods of processing satellite altimetry data over rivers. This study evaluates the observation error of CryoSat-2 water level observations over the Po River, Italy, against in situ observations. The average RMSE between CryoSat-2 and in situ observations was found to be 0.38 meters. CryoSat-2 was also shown to be useful for channel roughness calibration in a hydrodynamic model of the Po River. The small across-track distance of CryoSat-2 means that observations are distributed almost continuously along the river. This allowed resolving channel roughness with higher spatial resolution than possible with in situ or virtual station altimetry data. Despite the Po River being extensively monitored, CryoSat-2 still provides added value thanks to its unique spatio-temporal sampling pattern.

  10. Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling.

    PubMed

    Rizzo, Alessandro A; Suhanovsky, Margaret M; Baker, Matthew L; Fraser, LaTasha C R; Jones, Lisa M; Rempel, Don L; Gross, Michael L; Chiu, Wah; Alexandrescu, Andrei T; Teschke, Carolyn M

    2014-06-10

    Some capsid proteins built on the ubiquitous HK97-fold have accessory domains imparting specific functions. Bacteriophage P22 coat protein has a unique insertion domain (I-domain). Two prior I-domain models from subnanometer cryoelectron microscopy (cryoEM) reconstructions differed substantially. Therefore, the I-domain's nuclear magnetic resonance structure was determined and also used to improve cryoEM models of coat protein. The I-domain has an antiparallel six-stranded β-barrel fold, not previously observed in HK97-fold accessory domains. The D-loop, which is dynamic in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. The S-loop is important for capsid size determination, likely through intrasubunit interactions. Ten of 18 coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. The synthesis, characterization and application of iron oxide nanocrystals in magnetic separations for arsenic and uranium removal

    NASA Astrophysics Data System (ADS)

    Mayo, John Thomas

    Arsenic and uranium in the environment are hazardous to human health and require better methods for detection and remediation. Nanocrystalline iron oxides offer a number of advantages as sorbents for water purification and environmental remediation. First, highly uniform and crystalline iron oxide nanocrystals (nMAG) were prepared using thermal decomposition of iron salts in organic solutions; for the applications of interest in this thesis, a central challenge was the adaptation of these conventional synthetic methods to the needs of low infrastructure and economically disadvantaged settings. We show here that it is possible to form highly uniform and magnetically responsive nanomaterials using starting reagents and equipment that are readily available and economical. The products of this approach, termed the 'Kitchen Synthesis', are of comparable quality and effectiveness to laboratory materials. The narrow size distributions of the iron oxides produced in the laboratory synthesis made it possible to study the size-dependence of the magnetic separation efficiency of nanocrystals; generally as the diameter of particles increased they could be removed under lower applied magnetic fields. In this work we take advantage of this size-dependence to use magnetic separation as a tool to separate broadly distributed populations of magnetic materials. Such work makes it possible to use these materials in multiplexed separation and sensing schemes. With the synthesis and magnetic separation studies of these materials completed, it was possible to optimize their applications in water purification and environmental remediation. These materials removed both uranium and arsenic from contaminated samples, and had remarkably high sorption capacities --- up to 12 wt% for arsenic and 30 wt% for uranium. The contaminated nMAG is removed from the drinking water by either retention in a sand column, filter, or by magnetic separation. The uranium adsorption process was also utilized

  12. Cryo-thermal therapy elicits potent anti-tumor immunity by inducing extracellular Hsp70-dependent MDSC differentiation

    NASA Astrophysics Data System (ADS)

    Zhu, Jun; Zhang, Yan; Zhang, Aili; He, Kun; Liu, Ping; Xu, Lisa X.

    2016-06-01

    Achieving control of metastatic disease is a long-sought goal in cancer therapy. Treatments that encourage a patient’s own immune system are bringing new hopes in reaching such a goal. In clinic, local hyperthermia and cryoablation have been explored to induce anti-tumor immune responses against tumors. We have also developed a novel therapeutic modality of cryo-thermal treatment by alternating liquid nitrogen (LN2) cooling and radio frequency (RF) heating, and better therapeutic effect was achieved in treating metastatic cancer in animal model. In this study, we investigated the mechanism of systemic immune response elicited by cryo-thermal therapy. In the 4T1 murine mammary carcinoma model, we found that local cryo-thermal therapy resulted in a considerable reduction of distant lung metastases, and improved long-term survival. Moreover, results of tumor re-challenge experiments indicated generation of a strong tumor-specific immune memory after the local treatment of primary tumors. Our further study indicated that cryo-thermal therapy caused an elevated extracellular release of Hsp70. Subsequently, Hsp70 induced differentiation of MDSCs into mature DCs, contributing to the relief of MDSCs-mediated immunosuppression and ultimately the activation of strong anti-tumor immune response. Our findings reveal new insight into the mechanism of robust therapeutic effects of cryo-thermal therapy against metastatic cancers.

  13. A rational design for the separation of metallic and semiconducting single-walled carbon nanotubes using a magnetic field

    NASA Astrophysics Data System (ADS)

    Luo, Chengzhi; Wan, Da; Jia, Junji; Li, Delong; Pan, Chunxu; Liao, Lei

    2016-06-01

    The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm2 V-1 s-1 and an on/off ratio of 106. We also established a model to quantitatively calculate the percentage of m-SWNTs on the substrate and this model shows a good match with the experimental data. Furthermore, our rational design also provides a new avenue for the growth of SWNTs with specific chirality and manipulated arrangement due to the difference of magnetic susceptibilities between different diameters, chiralities, and types.The separation of metallic (m-) and semiconducting (s-) single-walled carbon nanotubes (SWNTs) without causing contamination and damage is a major challenge for SWNT-based devices. As a facile and nondestructive tool, the use of a magnetic field could be an ideal strategy to separate m-/s-SWNTs, based on the difference of magnetic susceptibilities. Here, we designed a novel magnetic field-assisted floating catalyst chemical vapor deposition system to separate m-/s-SWNTs. Briefly, m-SWNTs are attracted toward the magnetic pole, leaving s-SWNTs on the substrate. By using this strategy, s-SWNTs with a purity of 99% could be obtained, which is enough to construct high-performance transistors with a mobility of 230 cm2 V-1 s-1 and an on/off ratio of 106. We also established a model to quantitatively calculate the percentage of m

  14. Speciation of inorganic tellurium from seawater by ICP-MS following magnetic SPE separation and preconcentration.

    PubMed

    Huang, Chaozhang; Hu, Bin

    2008-03-01

    A new method was developed for the speciation of inorganic tellurium species in seawater by inductively coupled plasma-MS (ICP-MS) following selective magnetic SPE (MSPE) separation. Within the pH range of 2-9, tellurite (Te(IV)) could be quantitatively adsorbed on gamma-mercaptopropyltrimethoxysilane (gamma-MPTMS) modified silica-coated magnetic nanoparticles (MNPs), while the tellurate (Te(VI)) was not retained and remained in solution. Without filtration or centrifugation, these tellurite-loaded MNPs could be separated easily from the aqueous solution by simply applying external magnetic field. The Te(IV) adsorbed on the MNPs could be recovered quantitatively using a solution containing 2 mol/L HCl and 0.03 mol/L K2Cr2O7. Te(VI) was reduced to Te(IV) by L-cysteine prior to the determination of total tellurium, and its assay was based on subtracting Te(IV) from total tellurium. The parameters affecting the separation were investigated systematically and the optimal separation conditions were established. Under the optimal conditions, the LOD obtained for Te(IV) was 0.079 ng/L, while the precision was 7.0% (C = 10 ng/L, n = 7). The proposed method was successfully applied to the speciation of inorganic tellurium in seawater.

  15. Yeast Inner-Subunit PA-NZ-1 Labeling Strategy for Accurate Subunit Identification in a Macromolecular Complex through Cryo-EM Analysis.

    PubMed

    Wang, Huping; Han, Wenyu; Takagi, Junichi; Cong, Yao

    2018-05-11

    Cryo-electron microscopy (cryo-EM) has been established as one of the central tools in the structural study of macromolecular complexes. Although intermediate- or low-resolution structural information through negative staining or cryo-EM analysis remains highly valuable, we lack general and efficient ways to achieve unambiguous subunit identification in these applications. Here, we took advantage of the extremely high affinity between a dodecapeptide "PA" tag and the NZ-1 antibody Fab fragment to develop an efficient "yeast inner-subunit PA-NZ-1 labeling" strategy that when combined with cryo-EM could precisely identify subunits in macromolecular complexes. Using this strategy combined with cryo-EM 3D reconstruction, we were able to visualize the characteristic NZ-1 Fab density attached to the PA tag inserted into a surface-exposed loop in the middle of the sequence of CCT6 subunit present in the Saccharomyces cerevisiae group II chaperonin TRiC/CCT. This procedure facilitated the unambiguous localization of CCT6 in the TRiC complex. The PA tag was designed to contain only 12 amino acids and a tight turn configuration; when inserted into a loop, it usually has a high chance of maintaining the epitope structure and low likelihood of perturbing the native structure and function of the target protein compared to other tagging systems. We also found that the association between PA and NZ-1 can sustain the cryo freezing conditions, resulting in very high occupancy of the Fab in the final cryo-EM images. Our study demonstrated the robustness of this strategy combined with cryo-EM in efficient and accurate subunit identification in challenging multi-component complexes. Copyright © 2018 Elsevier Ltd. All rights reserved.

  16. Calibration And Validation Of CryoSat-2 Low Resolution Mode Data

    NASA Astrophysics Data System (ADS)

    Naeije, M.; Schrama, E.; Scharroo, R.

    2011-02-01

    Running ahead of the continuously growing need for operational use of sea level products, TUDelft started off the Radar Altimeter Database System RADS many years ago. This system attends to a global international sea- level service. It supports, on one hand, science, like studies on ocean circulation, El Nio, sea level change, and ice topography, and on the other hand (offshore) operations, like delivery of ocean current information, wind and wave statistics, ice detection and ice classification. At present, the database is used by a large scientific community throughout the world, and is daily maintained and developed by Altimetrics LLC, TUDelft and NOAA. It contains all historic altimeter data, and now has to be up- dated with the data from ESAs ice mission CryoSat-2, which was launched successfully in April 2010. These new data are important to augment the data set and by that to improve the estimates of sea level change and its contributors. For this the data have to be validated and calibrated, necessary corrections added and improved (including modelling of corrections that are not directly available from the CryoSat-2 platform), and the orbit ac- curacy verified and if possible the orbits brushed up. Subsequently, value-added ocean and ice products need to be developed in synergy with all the other satellite altimeter data. During the commissioning phase we primarily looked at the sanity of the available level-1b and level-2 Low Resolution Mode (LRM) data. Here, for the 2011 CryoSat Validation Workshop, we present the results of our calibration and validation of LRM L2 data by internal comparison of CryoSat-2 and external comparison with other satellites. We have established a range bias of 3.77 (measurement range too long) and a timing bias of 8.2ms (measurement range too late).

  17. Standardized combined cryotherapy and compression using Cryo/Cuff after wrist arthroscopy.

    PubMed

    Meyer-Marcotty, M; Jungling, O; Vaske, B; Vogt, P M; Knobloch, Karsten

    2011-02-01

    cryotherapy and compression as integral part of the RICE regimen are thought to improve treatment outcome after sport injuries. Using standardized cryotherapy and compression perioperatively has been reported with conflicting clinical results. The impact of combined cryotherapy and compression is compared to standard care among patients undergoing wrist arthroscopy. fifty-six patients undergoing wrist arthroscopy were assessed, 54 patients were randomized to either Cryo/Cuff (3 × 10 min twice daily) or standard care over 3 weeks. Follow-up clinical visits were at postoperative days 1, 8, and 21. One patient in each group was lost during follow-up. Fifty-two patients were analyzed. Statistics were performed as Intention-to-treat analysis. Outcome parameters were pain, three-dimensional volume of the wrist, range of motion, and DASH score. the Cryo/Cuffgroup had a 49% reduction in pain level (VAS 3.5 ± 0.4 vs. VAS 1.8 ± 0.2 on the 21st postoperative day) when compared to a reduction of 41% in the control group (VAS 5.1 ± 0.6 preoperatively vs. VAS 3.0 ± 0.5 on the 21st postoperative day). Swelling and range of motion were not as significantly different between the two groups as were DASH scores (DASH-score Cryo/Cuff group preoperatively 37.3 ± 3.5 and postoperatively 36.9 ± 3.5; DASH-score control group preoperatively 42.8 ± 4.3 and postoperatively 41.9 ± 4.9). The CONSORT score reached 17 out of 22. there was no significant effect of additional home-based combined cryotherapy and compression using the Cryo/Cuff wrist bandage, following wrist arthroscopy regarding pain, swelling, range of motion, and subjective impairment assessed using the DASH score over 3 weeks in comparison with the control group.

  18. Removal of malaria-infected red blood cells using magnetic cell separators: A computational study

    PubMed Central

    Kim, Jeongho; Massoudi, Mehrdad; Antaki, James F.; Gandini, Alberto

    2012-01-01

    High gradient magnetic field separators have been widely used in a variety of biological applications. Recently, the use of magnetic separators to remove malaria-infected red blood cells (pRBCs) from blood circulation in patients with severe malaria has been proposed in a dialysis-like treatment. The capture efficiency of this process depends on many interrelated design variables and constraints such as magnetic pole array pitch, chamber height, and flow rate. In this paper, we model the malaria-infected RBCs (pRBCs) as paramagnetic particles suspended in a Newtonian fluid. Trajectories of the infected cells are numerically calculated inside a micro-channel exposed to a periodic magnetic field gradient. First-order stiff ordinary differential equations (ODEs) governing the trajectory of particles under periodic magnetic fields due to an array of wires are solved numerically using the 1st –5th order adaptive step Runge-Kutta solver. The numerical experiments show that in order to achieve a capture efficiency of 99% for the pRBCs it is required to have a longer length than 80 mm; this implies that in principle, using optimization techniques the length could be adjusted, i.e., shortened to achieve 99% capture efficiency of the pRBCs. PMID:22345827

  19. Improving chemical shift encoding‐based water–fat separation based on a detailed consideration of magnetic field contributions

    PubMed Central

    Ruschke, Stefan; Eggers, Holger; Meineke, Jakob; Rummeny, Ernst J.; Karampinos, Dimitrios C.

    2018-01-01

    Purpose To improve the robustness of existing chemical shift encoding‐based water–fat separation methods by incorporating a priori information of the magnetic field distortions in complex‐based water–fat separation. Methods Four major field contributions are considered: inhomogeneities of the scanner magnet, the shim field, an object‐based field map estimate, and a residual field. The former two are completely determined by spherical harmonic expansion coefficients directly available from the magnetic resonance (MR) scanner. The object‐based field map is forward simulated from air–tissue interfaces inside the field of view (FOV). The missing residual field originates from the object outside the FOV and is investigated by magnetic field simulations on a numerical whole body phantom. In vivo the spatially linear first‐order component of the residual field is estimated by measuring echo misalignments after demodulation of other field contributions resulting in a linear residual field. Gradient echo datasets of the cervical and the ankle region without and with shimming were acquired, where all four contributions were incorporated in the water–fat separation with two algorithms from the ISMRM water–fat toolbox and compared to water–fat separation with less incorporated field contributions. Results Incorporating all four field contributions as demodulation steps resulted in reduced temporal and spatial phase wraps leading to almost swap‐free water–fat separation results in all datasets. Conclusion Demodulating estimates of major field contributions reduces the phase evolution to be driven by only small differences in local tissue susceptibility, which supports the field smoothness assumption of existing water–fat separation techniques. PMID:29424458

  20. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

    PubMed

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

  1. CryoSat-2: Post launch performance of SIRAL-2 and its calibration/validation

    NASA Astrophysics Data System (ADS)

    Cullen, Robert; Francis, Richard; Davidson, Malcolm; Wingham, Duncan

    2010-05-01

    1. INTRODUCTION The main payload of CryoSat-2 [1], SIRAL (Synthetic interferometric radar altimeter), is a Ku band pulse-width limited radar altimeter which transmits pulses at a high pulse repetition frequency thus making received echoes phase coherent and suitable for azimuth processing [2]. The azimuth processing in conjunction with correction for slant range improves along track resolution to about 250 meters which is a significant improvement over traditional pulse-width limited systems such as Envisat RA-2, [3]. CryoSat-2 will be launched on 25th February 2010 and this paper describes the pre and post launch measures of CryoSat/SIRAL performance and the status of mission validation planning. 2. SIRAL PERFORMANCE: INTERNAL AND EXTERNAL CALIBRATION Phase coherent pulse-width limited radar altimeters such as SIRAL-2 pose a new challenge when considering a strategy for calibration. Along with the need to generate the well understood corrections for transfer function amplitude with respect to frequency, gain and instrument path delay there is also a need to provide corrections for transfer function phase with respect to frequency and AGC setting, phase variation across bursts of pulses. Furthermore, since some components of these radars are temperature sensitive one needs to be careful when the deciding how often calibrations are performed whilst not impacting mission performance. Several internal calibration ground processors have been developed to model imperfections within the CryoSat-2 radar altimeter (SIRAL-2) hardware and reduce their effect from the science data stream via the use of calibration correction auxiliary products within the ground segment. We present the methods and results used to model and remove imperfections and describe the baseline for usage of SIRAL-2 calibration modes during the commissioning phase and the operational exploitation phases of the mission. Additionally we present early results derived from external calibration of SIRAL via

  2. Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin.

    PubMed

    Afanasyev, Pavel; Seer-Linnemayr, Charlotte; Ravelli, Raimond B G; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V; Pannu, Navraj S; Schatz, Michael; van Heel, Marin

    2017-09-01

    Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

  3. A data assimilation system combining CryoSat-2 data and hydrodynamic river models

    NASA Astrophysics Data System (ADS)

    Schneider, Raphael; Ridler, Marc-Etienne; Godiksen, Peter Nygaard; Madsen, Henrik; Bauer-Gottwein, Peter

    2018-02-01

    There are numerous hydrologic studies using satellite altimetry data from repeat-orbit missions such as Envisat or Jason over rivers. This study is one of the first examples for the combination of altimetry from drifting-ground track satellite missions, namely CryoSat-2, with a river model. CryoSat-2 SARIn Level 2 data is used to improve a 1D hydrodynamic model of the Brahmaputra River in South Asia, which is based on the Saint-Venant equations for unsteady flow and set up in the MIKE HYDRO River software. After calibration of discharge and water level the hydrodynamic model can accurately and bias-free represent the spatio-temporal variations of water levels. A data assimilation framework has been developed and linked with the model. It is a flexible framework that can assimilate water level data which are arbitrarily distributed in time and space. The setup has been used to assimilate CryoSat-2 water level observations over the Assam valley for the years 2010-2015, using an Ensemble Transform Kalman Filter (ETKF). Performance improvement in terms of discharge forecasting skill was then evaluated. For experiments with synthetic CryoSat-2 data the continuous ranked probability score (CRPS) was improved by up to 32%, whilst for experiments assimilating real data it could be improved by up to 10%. The developed methods are expected to be transferable to other rivers and altimeter missions. The model setup and calibration is based almost entirely on globally available remote sensing data.

  4. Cryo-Imaging and Software Platform for Analysis of Molecular MR Imaging of Micrometastases

    PubMed Central

    Qutaish, Mohammed Q.; Zhou, Zhuxian; Prabhu, David; Liu, Yiqiao; Busso, Mallory R.; Izadnegahdar, Donna; Gargesha, Madhusudhana; Lu, Hong; Lu, Zheng-Rong

    2018-01-01

    We created and evaluated a preclinical, multimodality imaging, and software platform to assess molecular imaging of small metastases. This included experimental methods (e.g., GFP-labeled tumor and high resolution multispectral cryo-imaging), nonrigid image registration, and interactive visualization of imaging agent targeting. We describe technological details earlier applied to GFP-labeled metastatic tumor targeting by molecular MR (CREKA-Gd) and red fluorescent (CREKA-Cy5) imaging agents. Optimized nonrigid cryo-MRI registration enabled nonambiguous association of MR signals to GFP tumors. Interactive visualization of out-of-RAM volumetric image data allowed one to zoom to a GFP-labeled micrometastasis, determine its anatomical location from color cryo-images, and establish the presence/absence of targeted CREKA-Gd and CREKA-Cy5. In a mouse with >160 GFP-labeled tumors, we determined that in the MR images every tumor in the lung >0.3 mm2 had visible signal and that some metastases as small as 0.1 mm2 were also visible. More tumors were visible in CREKA-Cy5 than in CREKA-Gd MRI. Tape transfer method and nonrigid registration allowed accurate (<11 μm error) registration of whole mouse histology to corresponding cryo-images. Histology showed inflammation and necrotic regions not labeled by imaging agents. This mouse-to-cells multiscale and multimodality platform should uniquely enable more informative and accurate studies of metastatic cancer imaging and therapy. PMID:29805438

  5. G-mode magnetic force microscopy: Separating magnetic and electrostatic interactions using big data analytics

    DOE PAGES

    Collins, Liam; Belianinov, Alex; Proksch, Roger; ...

    2016-05-09

    We develop a full information capture approach for Magnetic Force Microscopy (MFM), referred to as generalized mode (G-Mode) MFM. G-Mode MFM acquires and stores the full data stream from the photodetector at sampling rates approaching the intrinsic photodiode limit. The data can be subsequently compressed, denoised, and analyzed, without information loss. Also, 3 G-Mode MFM is implemented and compared to traditional heterodyne based MFM on model systems including domain structures in ferromagnetic Yttrium Iron Garnet (YIG) and electronically and magnetically inhomogeneous high entropy alloy, CoFeMnNiSn. We investigate the use of information theory to mine the G-Mode MFM data and demonstratemore » its usefulness for extracting information which may be hidden in traditional MFM modes, including signatures of nonlinearities and mode coupling phenomena. Finally we demonstrate detection and separation of magnetic and electrostatic tip-sample interactions from a single G-Mode image, by analyzing the entire frequency response of the cantilever. G-Mode MFM is immediately implementable on any AFM platform and as such is expected to be a useful technique for probing spatiotemporal cantilever dynamics and mapping material properties as well as their mutual interactions.« less

  6. Recovery of iron from cyanide tailings with reduction roasting-water leaching followed by magnetic separation.

    PubMed

    Zhang, Yali; Li, Huaimei; Yu, Xianjin

    2012-04-30

    Cyanide tailing is a kind of solid waste produced in the process of gold extraction from gold ore. In this paper, recovery of iron from cyanide tailings was studied with reduction roasting-water leaching process followed by magnetic separation. After analysis of chemical composition and crystalline phase, the effects of different parameters on recovery of iron were chiefly introduced. Systematic studies indicate that the high recovery rate and grade of magnetic concentrate of iron can be achieved under the following conditions: weight ratios of cyanide tailings/activated carbon/sodium carbonate/sodium sulfate, 100:10:3:10; temperature, 50 °C; time, 60 min at the reduction roasting stage; the liquid to solid ratio is 15:1 (ml/g), leaching at 60 °C for 5 min and stirring speed at 20 r/min at water-leaching; exciting current is 2A at magnetic separation. The iron grade of magnetic concentrate was 59.11% and the recovery ratio was 75.12%. The mineralography of cyanide tailings, roasted product, water-leached sample, magnetic concentrate and magnetic tailings were studied by X-ray powder diffraction (XRD) technique. The microstructures of above products except magnetic tailings were also analyzed by scanning electron microscope (SEM) and energy disperse spectroscopy (EDS) to help understand the mechanism. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Cryogenic coherent X-ray diffraction imaging of biological samples at SACLA: a correlative approach with cryo-electron and light microscopy.

    PubMed

    Takayama, Yuki; Yonekura, Koji

    2016-03-01

    Coherent X-ray diffraction imaging at cryogenic temperature (cryo-CXDI) allows the analysis of internal structures of unstained, non-crystalline, whole biological samples in micrometre to sub-micrometre dimensions. Targets include cells and cell organelles. This approach involves preparing frozen-hydrated samples under controlled humidity, transferring the samples to a cryo-stage inside a vacuum chamber of a diffractometer, and then exposing the samples to coherent X-rays. Since 2012, cryo-coherent diffraction imaging (CDI) experiments have been carried out with the X-ray free-electron laser (XFEL) at the SPring-8 Ångstrom Compact free-electron LAser (SACLA) facility in Japan. Complementary use of cryo-electron microscopy and/or light microscopy is highly beneficial for both pre-checking samples and studying the integrity or nature of the sample. This article reports the authors' experience in cryo-XFEL-CDI of biological cells and organelles at SACLA, and describes an attempt towards reliable and higher-resolution reconstructions, including signal enhancement with strong scatterers and Patterson-search phasing.

  8. On-chip Magnetic Separation and Cell Encapsulation in Droplets†

    PubMed Central

    Chen, Aaron; Byvank, Tom; Chang, Woo-Jin; Bharde, Atul; Vieira, Greg; Miller, Brandon; Chalmers, Jeffrey J.; Bashir, Rashid; Sooryakumar, Ratnasingham

    2014-01-01

    The demand for high-throughput single cell assays is gaining importance because of the heterogeneity of many cell suspensions, even after significant initial sorting. These suspensions may display cell-to-cell variability at the gene expression level that could impact single cell functional genomics, cancer, stem-cell research and drug screening. The on-chip monitoring of individual cells in an isolated environment would prevent cross-contamination, provide high recovery yield, and enable study of biological traits at a single cell level. These advantages of on-chip biological experiments is a significant improvement for myriad of cell analyses over conventional methods, which require bulk samples providing only averaged information on cell metabolism. We report on a device that integrates mobile magnetic trap array with microfluidic technology to provide, combined functionality of separation of immunomagnetically labeled cells or magnetic beads and their encapsulation with reagents into pico-liter droplets. This scheme of simultaneous reagent delivery and compartmentalization of the cells immediately after sorting, all performed seamlessly within the same chip, offers unique advantages such as the ability to capture cell traits as originated from its native environment, reduced chance of contamination, minimal use and freshness of the reagent solution that reacts only with separated objects, and tunable encapsulation characteristics independent of the input flow. In addition to the demonstrated preliminary cell viability assay, the device can potentially be integrated with other up- or downstream on-chip modules to become a powerful single-cell analysis tool. PMID:23370785

  9. The CryoSat Interferometer after 6 years in orbit: calibration and achievable performance

    NASA Astrophysics Data System (ADS)

    Scagliola, Michele; Fornari, Marco; De Bartolomei, Maurizio; Bouffard, Jerome; Parrinello, Tommaso

    2016-04-01

    The main payload of CryoSat is a Ku-band pulse width limited radar altimeter, called SIRAL (Synthetic interferometric radar altimeter). When commanded in SARIn (synthetic aperture radar interferometry) mode, through coherent along-track processing of the returns received from two antennas, the interferometric phase related to the first arrival of the echo is used to retrieve the angle of arrival of the scattering in the across-track direction. In fact, the across-track echo direction can be derived by exploiting the precise knowledge of the baseline vector (i.e. the vector between the two antennas centers of phase) and simple geometry. The end-to-end calibration strategy for the CryoSat interferometer consists on in-orbit calibration campaigns following the approach described in [1]. From the beginning of the CryoSat mission, about once a year the interferometer calibration campaigns have been periodically performed by rolling left and right the spacecraft of about ±0.4 deg. This abstract is aimed at presenting our analysis of the calibration parameters and of the achievable performance of the CryoSat interferometer over the 6 years of mission. Additionally, some further studies have been performed to assess the accuracy of the roll angle computed on ground as function of the aberration (the apparent displacement of a celestial object from its true position, caused by the relative motion of the observer and the object) correction applied to the attitude quaternions, provided by the Star Tracker mounted on-board. In fact, being the roll information crucial to obtain an accurate estimate of the angle of arrival, the data from interferometer calibration campaigns have been used to verify how the application of the aberration correction affects the roll information and, in turns, the measured angle of arrival. [1] Galin, N.; Wingham, D.J.; Cullen, R.; Fornari, M.; Smith, W.H.F.; Abdalla, S., "Calibration of the CryoSat-2 Interferometer and Measurement of Across

  10. Magnetic deep eutectic solvents molecularly imprinted polymers for the selective recognition and separation of protein.

    PubMed

    Liu, Yanjin; Wang, Yuzhi; Dai, Qingzhou; Zhou, Yigang

    2016-09-14

    A novel and facile magnetic deep eutectic solvents (DES) molecularly imprinted polymers (MIPs) for the selective recognition and separation of Bovine hemoglobin (BHb) was prepared. The new-type DES was adopted as the functional monomer which would bring molecular imprinted technology to a new direction. The amounts of DES were optimized. The obtained magnetic DES-MIPs were characterized with fourier transform infrared spectrometry (FT-IR), thermogravimetric analysis (TGA), field emission scanning electron microscope (FESEM), dynamic light scattering (DLS), elemental analysis and vibrating sample magnetometer (VSM). The results suggested that the imprinted polymers were successfully formed and possessed a charming magnetism. The maximum adsorption capability (Qmax) and dissociation constant (KL) were analyzed by Langmuir isotherms (R(2) = 0.9983) and the value were estimated to be 175.44 mg/g and 0.035 mg/mL for the imprinted particles. And the imprinted particles showed a high imprinting factor of 4.77. In addition, the magnetic DES-MIPs presented outstanding recognition specificity and selectivity so that it can be utilized to separate template protein from the mixture of proteins and real samples. Last but not least, the combination of deep eutectic solvents and molecular imprinted technology in this paper provides a new perspective for the recognition and separation of proteins. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Environmental friendly crush-magnetic separation technology for recycling metal-plated plastics from end-of-life vehicles.

    PubMed

    Xue, Mianqiang; Li, Jia; Xu, Zhenming

    2012-03-06

    Metal-plated plastics (MPP), which are important from the standpoint of aesthetics or even performance, are increasingly employed in a wide variety of situations in the automotive industry. Serious environmental problems will be caused if they are not treated appropriately. Therefore, recycling of MPP is an important subject not only for resource recycling but also for environmental protection. This work represents a novel attempt to deal with the MPP. A self-designed hammer crusher was used to liberate coatings from the plastic substrate. The size distribution of particles was analyzed and described by the Rosin-Rammler function model. The optimum retaining time of materials in the crusher is 3 min. By this time, the liberation rate of the materials can reach 87.3%. When the density of the suspension is 31,250 g/m(3), the performance of liberation is the best. Two-step magnetic separation was adopted to avoid excessive crushing and to guarantee the quality of products. Concerning both the separation efficiency and grade of products, the optimum rotational speed of the magnetic separator is 50-70 rpm. On the basis of the above studies about the liberating and separating behavior of the materials, a continuous recycling system (the technology of crush-magnetic separation) is developed. This recycling system provides a feasible method for recycling MPP efficiently, economically, and environmentally.

  12. Breast cancer cells synchronous labeling and separation based on aptamer and fluorescence-magnetic silica nanoparticles

    NASA Astrophysics Data System (ADS)

    Wang, Qiu-Yue; Huang, Wei; Jiang, Xing-Lin; Kang, Yan-Jun

    2018-01-01

    In this work, an efficient method based on biotin-labeled aptamer and streptavidin-conjugated fluorescence-magnetic silica nanoprobes (FITC@Fe3O4@SiNPs-SA) has been established for human breast carcinoma MCF-7 cells synchronous labeling and separation. Carboxyl-modified fluorescence-magnetic silica nanoparticles (FITC@Fe3O4@SiNPs-COOH) were first synthesized using the Stöber method. Streptavidin (SA) was then conjugated to the surface of FITC@Fe3O4@SiNPs-COOH. The MCF-7 cell suspension was incubated with biotin-labeled MUC-1 aptamer. After centrifugation and washing, the cells were then treated with FITC@Fe3O4@SiNPs-SA. Afterwards, the mixtures were separated by a magnet. The cell-probe conjugates were then imaged using fluorescent microscopy. The results show that the MUC-1 aptamer could recognize and bind to the targeted cells with high affinity and specificity, indicating the prepared FITC@Fe3O4@SiNPs-SA with great photostability and superparamagnetism could be applied effectively in labeling and separation for MCF-7 cell in suspension synchronously. In addition, the feasibility of MCF-7 cells detection in peripheral blood was assessed. The results indicate that the method above is also applicable for cancer cells synchronous labeling and separation in complex biological system.

  13. Improvement in gold grade from iron-oxide mineral using reduction roasting and magnetic separation

    NASA Astrophysics Data System (ADS)

    Kim, Hyun-soo; On, Hyun-sung; Lim, Dae-hack; Myung, Eun-ji; Park, Cheon-young

    2017-04-01

    Microwave has a wide range of applications in mineral technology, metallurgy, etc. It is an established fact that microwave energy has potential for the speedy and efficient heating of minerals and in a commercial context may provide savings in both time and energy. Microwave heating is being developed as a potential thermal pre-treatment process, because of its unique advantages over the differences of ore minerals in absorbing microwaves. The aim of this study was to investigate the improvement in Au grade from iron-oxide mineral using reduction roasting and magnetic separation. The characteristics of iron-oxide mineral were analyzed using chemical, XRD and reflected light microscopy. The reduction roasting using microwave and magnetic separation experiments were examined under various conditions (reducing agent and chemical additive). The results of XRD and reflected light microscopy showed that the iron-oxide mineral mainly composed of illite, quartz and hematite. The iron-oxide mineral had an Au, Ag, Fe contents of 6.4, 35.1 and 155,441.1 mg/kg, respectively. The results demonstrated that the improvement in Au by reduction roasting using microwave (frequency of 2.45GHz, intensity of 5kW) and magnetic separation (magnetic field intensity of 9,000 Gauss) were effective processes. The Au content in iron-oxide mineral from 6.4 mg/kg to 14.2 mg/kg was achieved within microwave exposure time of 10min (reducing agent(PAC) ratio = 50 : 50, 5% of chemical additive(Soda ash)). Acknowledgment : This subject is supported by Korea Ministry of Environment as "Advanced Technology Program for Environmental Industry"

  14. Single-particle cryo-electron microscopy of Rift Valley fever virus

    PubMed Central

    Sherman, Michael B.; Freiberg, Alexander N.; Holbrook, Michael R.; Watowich, Stanley J.

    2009-01-01

    Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human veterinary pathogen causing acute hepatitis in ruminants and has the potential to Single-particle cryo-EM reconstruction of RVFV MP-12 hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T=12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit-vaccines. PMID:19304307

  15. Site-Specific Preparation of Intact Solid–Liquid Interfaces by Label-Free In Situ Localization and Cryo-Focused Ion Beam Lift-Out

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zachman, Michael J.; Asenath-Smith, Emily; Estroff, Lara A.

    Abstract Scanning transmission electron microscopy (STEM) allows atomic scale characterization of solid–solid interfaces, but has seen limited applications to solid–liquid interfaces due to the volatility of liquids in the microscope vacuum. Although cryo-electron microscopy is routinely used to characterize hydrated samples stabilized by rapid freezing, sample thinning is required to access the internal interfaces of thicker specimens. Here, we adapt cryo-focused ion beam (FIB) “lift-out,” a technique recently developed for biological specimens, to prepare intact internal solid–liquid interfaces for high-resolution structural and chemical analysis by cryo-STEM. To guide the milling process we introduce a label-freein situmethod of localizing subsurface structuresmore » in suitable materials by energy dispersive X-ray spectroscopy (EDX). Monte Carlo simulations are performed to evaluate the depth-probing capability of the technique, and show good qualitative agreement with experiment. We also detail procedures to produce homogeneously thin lamellae, which enable nanoscale structural, elemental, and chemical analysis of intact solid–liquid interfaces by analytical cryo-STEM. This work demonstrates the potential of cryo-FIB lift-out and cryo-STEM for understanding physical and chemical processes at solid–liquid interfaces.« less

  16. Cryo-Vacuum Testing of JWST's Integrated Telescope & Scientific Instrument Suite (OTIS)

    NASA Astrophysics Data System (ADS)

    Kimble, Randy; Apollo, Peter; Feinberg, Lee; Glazer, Stuart; Hanley, Jeffrey; Keski-Kuha, Ritva; Kirk, Jeffrey; Knight, J. Scott; Lambros, Scott; Lander, Juli; McGuffey, Douglas; Mehalick, Kimberly; Ohl, Raymond; Ousley, Wes; Reis, Carl; Reynolds, Paul; Begoña Vila, Maria; Waldman, Mark; Whitman, Tony

    2018-01-01

    A year ago we reported on the planning for a major test in the James Webb Space Telescope (JWST) program: cryo-vacuum testing of the combination of the Optical Telescope Element (OTE) and the Integrated Science Instrument Module (ISIM). The cryo-vacuum testing of that scientific heart of the JWST observatory, known as OTIS (= OTE + ISIM), has now been completed in historic chamber A at NASA’s Johnson Space Center. From July through October 2017, the flight payload was cooled to its operating temperatures, put through a comprehensive suite of optical, thermal, and operational tests, and then safely warmed back to room temperature. We report here on the execution and top-level results from this milestone event in the JWST program.

  17. 3D structure of eukaryotic flagella/cilia by cryo-electron tomography

    PubMed Central

    Ishikawa, Takashi

    2013-01-01

    Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

  18. Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

    PubMed Central

    Seer-Linnemayr, Charlotte; Ravelli, Raimond B. G.; Matadeen, Rishi; De Carlo, Sacha; Alewijnse, Bart; Portugal, Rodrigo V.; Pannu, Navraj S.; Schatz, Michael; van Heel, Marin

    2017-01-01

    Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the ‘Einstein from random noise’ problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous (‘four-dimensional’) cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, ‘random-startup’ three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external ‘starting models’. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive ‘ABC-4D’ pipeline is based on the two-dimensional reference-free ‘alignment by classification’ (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure. PMID:28989723

  19. Magnetically separable nanoferrite-anchored glutathione: Aqueous homocoupling of arylboronic acids under microwave irradiation

    EPA Science Inventory

    A highly active, stable and magnetically separable glutathione based organocatalyst provided good to excellent yields to symmetric biaryls in the homocoupling of arylboronic acids under microwave irradiation. Symmetrical biaryl motifs are present in a wide range of natural p...

  20. Development of high gradient magnetic separation system for removing the metallic wear debris to be present in highly viscous fluid

    NASA Astrophysics Data System (ADS)

    Hayashi, S.; Mishima, F.; Akiyama, Y.; Nishijima, S.

    2010-11-01

    In the industrial plants processing highly viscous fluid such as foods or industrial materials, there is an issue of contamination by metallic wear debris originating from pipe of manufacturing line. It is necessary to remove the metallic wear debris in highly viscous fluid, since these debris causes quality loss. In this study, we developed a high gradient magnetic separation system by using superconducting magnet to remove the metallic wear debris. The particle trajectory simulation and the magnetic separation experiment were conducted with polyvinyl alcohol as a model material. As a result, ca. 100% and 92.2% of the separation efficiency was achieved respectively for the highly viscous fluid of 1 Pa s and 6 Pa s in viscosity, with 14 and 30 mesh magnetic filters.

  1. Superior lithium adsorption and required magnetic separation behavior of iron-doped lithium ion-sieves

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Shulei; Zheng, Shili; Wang, Zheming

    The recent research on adsorption-based lithium recovery from lithium-containing solutions has been centred on adsorption capacity and separation of lithium ion-sieves powder from solutions. Herein, an effective iron-doped lithium titanium oxide (Fe-doped Li 2TiO 3) was synthesized by Fe-doping via solid state reactions followed by acid treatment to form iron-doped lithium ion-sieves (Fe/Ti-x(H)). The resulting solid powder displays both superior adsorption capacity of lithium and high separation efficiency of the adsorbent from the solutions. SEM imaging and BET surface area measurement results showed that at Fe doping levels x ≤ 0.15, Fe-doping led to grain shrinkage as compared to Limore » 2TiO 3 and at the same time the BET surface area increased. The Fe/Ti-0.15(H) exhibited saturated magnetization values of 13.76 emu g -1, allowing effective separation of the material from solid suspensions through the use of a magnet. Consecutive magnetic separation results suggested that the Fe/Ti-0.15(H) powders could be applied at large-scale and continuously removed from LiOH solutions with separation efficiency of 96% or better. Lithium adsorption studies indicated that the equilibrium adsorption capacity of Fe/Ti-0.15(H) in LiOH solutions (1.8 g L -1 Li, pH 12) reached 53.3 mg g -1 within 24 h, which was higher than that of pristine Li 2TiO 3 (50.5 mg g-1) without Fe doping. Competitive adsorption and regeneration results indicated that the Fe/Ti-0.15(H) possessed a high selectivity for Li with facile regeneration. Therefore, it could be expected that the iron-doped lithium ion-sieves have practical applicability potential for large scale lithium extraction and recovery from lithium-bearing solutions.« less

  2. Superior lithium adsorption and required magnetic separation behavior of iron-doped lithium ion-sieves

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Shulei; Zheng, Shili; Wang, Zheming

    The recent research on adsorption-based lithium recovery from lithium-containing solutions has been centred on adsorption capacity and separation of lithium ion-sieves powder from solutions. Herein, an effective iron-doped lithium titanium oxide (Fe-doped Li2TiO3) was synthesized by Fe-doping via solid state reactions followed by acid treatment to form iron-doped lithium ion-sieves (Fe/Ti-x(H)). The resulting solid powder displays both superior adsorption capacity of lithium and high separation efficiency of the adsorbent from the solutions. SEM imaging and BET surface area measurement results showed that at Fe doping levels x0.15, Fe-doping led to grain shrinkage as compared to Li2TiO3 and at the samemore » time the BET surface area increased. The Fe/Ti-0.15(H) exhibited saturated magnetization values of 13.76 emu g-1, allowing effective separation of the material from solid suspensions through the use of a magnet. Consecutive magnetic separation results suggested that the Fe/Ti-0.15(H) powders could be applied at large-scale and continuously removed from LiOH solutions with separation efficiency of 96% or better. Lithium adsorption studies indicated that the equilibrium adsorption capacity of Fe/Ti-0.15(H) in LiOH 2 solutions (1.8 g L-1 Li, pH 12) reached 53.3 mg g-1 within 24 h, which was higher than that of pristine Li2TiO3 (50.5 mg g-1) without Fe doping. Competitive adsorption and regeneration results indicated that the Fe/Ti-0.15(H) possessed a high selectivity for Li with facile regeneration. Therefore, it could be expected that the iron-doped lithium ion-sieves have practical applicability potential for large scale lithium extraction and recovery from lithium-bearing solutions.« less

  3. Superior lithium adsorption and required magnetic separation behavior of iron-doped lithium ion-sieves

    DOE PAGES

    Wang, Shulei; Zheng, Shili; Wang, Zheming; ...

    2018-09-09

    The recent research on adsorption-based lithium recovery from lithium-containing solutions has been centred on adsorption capacity and separation of lithium ion-sieves powder from solutions. Herein, an effective iron-doped lithium titanium oxide (Fe-doped Li 2TiO 3) was synthesized by Fe-doping via solid state reactions followed by acid treatment to form iron-doped lithium ion-sieves (Fe/Ti-x(H)). The resulting solid powder displays both superior adsorption capacity of lithium and high separation efficiency of the adsorbent from the solutions. SEM imaging and BET surface area measurement results showed that at Fe doping levels x ≤ 0.15, Fe-doping led to grain shrinkage as compared to Limore » 2TiO 3 and at the same time the BET surface area increased. The Fe/Ti-0.15(H) exhibited saturated magnetization values of 13.76 emu g -1, allowing effective separation of the material from solid suspensions through the use of a magnet. Consecutive magnetic separation results suggested that the Fe/Ti-0.15(H) powders could be applied at large-scale and continuously removed from LiOH solutions with separation efficiency of 96% or better. Lithium adsorption studies indicated that the equilibrium adsorption capacity of Fe/Ti-0.15(H) in LiOH solutions (1.8 g L -1 Li, pH 12) reached 53.3 mg g -1 within 24 h, which was higher than that of pristine Li 2TiO 3 (50.5 mg g-1) without Fe doping. Competitive adsorption and regeneration results indicated that the Fe/Ti-0.15(H) possessed a high selectivity for Li with facile regeneration. Therefore, it could be expected that the iron-doped lithium ion-sieves have practical applicability potential for large scale lithium extraction and recovery from lithium-bearing solutions.« less

  4. Temperature-Switchable Agglomeration of Magnetic Particles Designed for Continuous Separation Processes in Biotechnology.

    PubMed

    Paulus, Anja S; Heinzler, Raphael; Ooi, Huey Wen; Franzreb, Matthias

    2015-07-08

    The purpose of this work was the synthesis and characterization of thermally switchable magnetic particles for use in biotechnological applications such as protein purification and enzymatic conversions. Reversible addition-fragmentation chain-transfer polymerization was employed to synthesize poly(N-isopropylacrylamide) brushes via a "graft-from" approach on the surface of magnetic microparticles. The resulting particles were characterized by infrared spectroscopy and thermogravimetric analysis and their temperature-dependent agglomeration behavior was assessed. The influence of several factors on particle agglomeration (pH, temperature, salt type, and particle concentration) was evaluated. The results showed that a low pH value (pH 3-4), a kosmotropic salt (ammonium sulfate), and a high particle concentration (4 g/L) resulted in improved agglomeration at elevated temperature (40 °C). Recycling of particles and reversibility of the temperature-switchable agglomeration were successfully demonstrated for ten heating-cooling cycles. Additionally, enhanced magnetic separation was observed for the modified particles. Ionic monomers were integrated into the polymer chain to create end-group functionalized particles as well as two- and three-block copolymer particles for protein binding. The adsorption of lactoferrin, bovine serum albumin, and lysozyme to these ion exchange particles was evaluated and showed a binding capacity of up to 135 mg/g. The dual-responsive particles combined magnetic and thermoresponsive properties for switchable agglomeration, easy separability, and efficient protein adsorption.

  5. Using Cryo-EM to Map Small Ligands on Dynamic Metabolic Enzymes: Studies with Glutamate Dehydrogenase

    PubMed Central

    Borgnia, Mario J.; Banerjee, Soojay; Merk, Alan; Matthies, Doreen; Bartesaghi, Alberto; Rao, Prashant; Pierson, Jason; Earl, Lesley A.; Falconieri, Veronica

    2016-01-01

    Cryo-electron microscopy (cryo-EM) methods are now being used to determine structures at near-atomic resolution and have great promise in molecular pharmacology, especially in the context of mapping the binding of small-molecule ligands to protein complexes that display conformational flexibility. We illustrate this here using glutamate dehydrogenase (GDH), a 336-kDa metabolic enzyme that catalyzes the oxidative deamination of glutamate. Dysregulation of GDH leads to a variety of metabolic and neurologic disorders. Here, we report near-atomic resolution cryo-EM structures, at resolutions ranging from 3.2 Å to 3.6 Å for GDH complexes, including complexes for which crystal structures are not available. We show that the binding of the coenzyme NADH alone or in concert with GTP results in a binary mixture in which the enzyme is in either an “open” or “closed” state. Whereas the structure of NADH in the active site is similar between the open and closed states, it is unexpectedly different at the regulatory site. Our studies thus demonstrate that even in instances when there is considerable structural information available from X-ray crystallography, cryo-EM methods can provide useful complementary insights into regulatory mechanisms for dynamic protein complexes. PMID:27036132

  6. Magnetic separation of heavy metal ions and evaluation based on surface-enhanced Raman spectroscopy: copper(II) ions as a case study.

    PubMed

    Yan, Xue; Zhang, Xue-Jiao; Yuan, Ya-Xian; Han, San-Yang; Xu, Min-Min; Gu, Ren'ao; Yao, Jian-Lin

    2013-11-01

    A new approach was developed for the magnetic separation of copper(II) ions with easy operation and high efficiency. p-Mercaptobenzoic acid served as the modified tag of Fe2O3@Au nanoparticles both for the chelation ligand and Raman reporter. Through the chelation between the copper(II) ions and carboxyl groups on the gold shell, the Fe2O3@Au nanoparticles aggregated to form networks that were enriched and separated from the solution by a magnet. A significant decrease in the concentration of copper(II) ions in the supernatant solution was observed. An extremely sensitive method based on surface-enhanced Raman spectroscopy was employed to detect free copper(II) ions that remained after the magnetic separation, and thus to evaluate the separation efficiency. The results indicated the intensities of the surface-enhanced Raman spectroscopy bands from p-mercaptobenzoic acid were dependent on the concentration of copper(II) ions, and the concentration was decreased by several orders of magnitude after the magnetic separation. The present protocol effectively decreased the total amount of heavy metal ions in the solution. This approach opens a potential application in the magnetic separation and highly sensitive detection of heavy metal ions. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Single-step synthesis and magnetic separation of graphene and carbon nanotubes in arc discharge plasmas.

    PubMed

    Volotskova, O; Levchenko, I; Shashurin, A; Raitses, Y; Ostrikov, K; Keidar, M

    2010-10-01

    The unique properties of graphene and carbon nanotubes made them the most promising nanomaterials attracting enormous attention, due to the prospects for applications in various nanodevices, from nanoelectronics to sensors and energy conversion devices. Here we report on a novel deterministic, single-step approach to simultaneous production and magnetic separation of graphene flakes and carbon nanotubes in an arc discharge by splitting the high-temperature growth and low-temperature separation zones using a non-uniform magnetic field and tailor-designed catalyst alloy, and depositing nanotubes and graphene in different areas. Our results are very relevant to the development of commercially-viable, single-step production of bulk amounts of high-quality graphene.

  8. Never at rest: insights into the conformational dynamics of ion channels from cryo-electron microscopy.

    PubMed

    Lau, Carus; Hunter, Mark J; Stewart, Alastair; Perozo, Eduardo; Vandenberg, Jamie I

    2018-04-01

    The tightly regulated opening and closure of ion channels underlies the electrical signals that are vital for a wide range of physiological processes. Two decades ago the first atomic level view of ion channel structures led to a detailed understanding of ion selectivity and conduction. In recent years, spectacular developments in the field of cryo-electron microscopy have resulted in cryo-EM superseding crystallography as the technique of choice for determining near-atomic resolution structures of ion channels. Here, we will review the recent developments in cryo-EM and its specific application to the study of ion channel gating. We will highlight the advantages and disadvantages of the current technology and where the field is likely to head in the next few years. © 2018 The Authors. The Journal of Physiology © 2018 The Physiological Society.

  9. Monte Carlo simulations of magnetic properties of Kekulene structure bilayers separate by a nonmagnetic with RKKY interactions

    NASA Astrophysics Data System (ADS)

    Jabar, A.; Masrour, R.

    2018-05-01

    The magnetic properties of magnetic bilayers of Kekulene structure separate by a nonmagnetic layer with Ruderman-Kittel-Kasuya-Yosida (RKKY) exchange interactions with Ising spin model have been studied using Monte Carlo simulations. The RKKY interaction between the bilayers of Kekulene is considered for different distances. The transition temperature has been deduced from the magnetizations and magnetic susceptibilities partial for a fixed value of nonmagnetic layer. The reduced transition temperatures are also deduced from the total magnetization and total magnetic susceptibilities with different values of L. The magnetic hysteresis cycles of systems have been determined.

  10. Lipid-Based Immuno-Magnetic Separation of Archaea from a Mixed Community

    NASA Astrophysics Data System (ADS)

    Frickle, C. M.; Bailey, J.; Lloyd, K. G.; Shumaker, A.; Flood, B.

    2014-12-01

    Despite advancing techniques in microbiology, an estimated 98% of all microbial species on Earth have yet to be isolated in pure culture. Natural samples, once transferred to the lab, are commonly overgrown by "weed" species whose metabolic advantages enable them to monopolize available resources. Developing new methods for the isolation of thus-far uncultivable microorganisms would allow us to better understand their ecology, physiology and genetic potential. Physically separating target organisms from a mixed community is one approach that may allow enrichment and growth of the desired strain. Here we report on a novel method that uses known physiological variations between taxa, in this case membrane lipids, to segregate the desired organisms while keeping them alive and viable for reproduction. Magnetic antibodies bound to the molecule squalene, which is found in the cell membranes of certain archaea, but not bacteria, enable separation of archaea from bacteria in mixed samples. Viability of cells was tested by growing the separated fractions in batch culture. Efficacy and optimization of the antibody separation technique are being evaluated using qPCR and cell counts. Future work will apply this new separation technique to natural samples.

  11. A Novel Approach to Identifying Physical Markers of Cryo-Damage in Bull Spermatozoa

    PubMed Central

    Yoon, Sung-Jae; Kwon, Woo-Sung; Rahman, Md Saidur; Lee, June-Sub; Pang, Myung-Geol

    2015-01-01

    Cryopreservation is an efficient way to store spermatozoa and plays a critical role in the livestock industry as well as in clinical practice. During cryopreservation, cryo-stress causes substantial damage to spermatozoa. In present study, the effects of cryo-stress at various cryopreservation steps, such as dilution / cooling, adding cryoprtectant, and freezing were studied in spermatozoa collected from 9 individual bull testes. The motility (%), motion kinematics, capacitation status, mitochondrial activity, and viability of bovine spermatozoa at each step of the cryopreservation process were assessed using computer-assisted sperm analysis, Hoechst 33258/chlortetracycline fluorescence, rhodamine 123 staining, and hypo-osmotic swelling test, respectively. The results demonstrate that the cryopreservation steps reduced motility (%), rapid speed (%), and mitochondrial activity, whereas medium/slow speed (%), and the acrosome reaction were increased (P < 0.05). Differences (Δ) of the acrosome reaction were higher in dilution/cooling step (P < 0.05), whereas differences (Δ) of motility, rapid speed, and non-progressive motility were higher in cryoprotectant and freezing as compared to dilution/cooling (P < 0.05). On the other hand, differences (Δ) of mitochondrial activity, viability, and progressive motility were higher in freezing step (P < 0.05) while the difference (Δ) of the acrosome reaction was higher in dilution/cooling (P < 0.05). Based on these results, we propose that freezing / thawing steps are the most critical in cryopreservation and may provide a logical ground of understanding on the cryo-damage. Moreover, these sperm parameters might be used as physical markers of sperm cryo-damage. PMID:25938413

  12. Performance analysis of a microfluidic mixer based on high gradient magnetic separation principles

    NASA Astrophysics Data System (ADS)

    Liu, Mengyu; Han, Xiaotao; Cao, Quanliang; Li, Liang

    2017-09-01

    To achieve a rapid mixing between a water-based ferrofluid and DI water in a microfluidic environment, a magnetically actuated mixing system based on high gradient magnetic separation principles is proposed in this work. The microfluidic system consists of a T-shaped mirochannel and an array of integrated soft-magnetic elements at the sidewall of the channel. With the aid of an external magnetic bias field, these elements are magnetized to produce a magnetic volume force acting on the fluids containing magnetic nanoparticles, and then to induce additional flows for improving the mixing performance. The mixing process is numerically investigated through analyzing the concentration distribution of magnetic nanoparticles using a coupled particle-fluid transport model, and mixing performances under different parametrical conditions are investigated in detail. Numerical results show that a high mixing efficiency around 97.5% can be achieved within 2 s under an inlet flow rate of 1 mm s-1 and a relatively low magnetic bias field of 50 mT. Meanwhile, it has been found that there is an optimum number of magnetic elements used for obtaining the best mixing performance. These results show the potential of the proposed mixing method in lab-on-a-chip system and could be helpful in designing and optimizing system performance.

  13. Phase transition of AISI type 304L stainless steel induced by severe plastic deformation via cryo-rolling

    NASA Astrophysics Data System (ADS)

    Shit, Gopinath; Bhaskar, Pragna; Ningshen, S.; Dasgupta, A.; Mudali, U. Kamachi; Bhaduri, A. Kumar

    2017-05-01

    The phase transition induced by Severe Plastic Deformation (SPD) was confirmed in metastable AISI type 304L austenitic stainless steel (SS). SPD via cryo-rolling in liquid nitrogen (L-N2) temperature is the adopted route for correlating the phase transition and corrosion resistance. The thickness of the annealed AISI type 304L SS at 1050°C sheet was reduced step by step from 15% to 50% of its initial thickness. The phase changes and phase transformation are qualitatively analyzed by X-Ray Diffraction (XRD) method. During the process, the XRD of each Cryo-Rolled and annealed sample was analyzed and different phases and phase transitions are measured. The investigated AISI type 304L SS by SPD reveals a microstructure of γ-austenite; α'-marternsite and ɛ-martensite formation depending on the percentage of cryo-rolling. The Vickers hardness (HV) of the samples is also measured. The corrosion rate of the annealed sheet and cryo rolled sample was estimated in boiling nitric acid as per ASTM A-262 practice-C test.

  14. The high Beta cryo-modules and the associated cryogenic system for the HIE-ISOLDE upgrade at CERN

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Delruelle, N.; Leclercq, Y.; Pirotte, O.

    2014-01-29

    The major upgrade of the energy and intensity of the existing ISOLDE and REX-ISOLDE radioactive ion beam facilities at CERN requires the replacement of most of the existing ISOLDE post-acceleration equipment by a superconducting linac based on quarter-wave resonators housed together with superconducting solenoids in a series of four high-β and two low-β cryo-modules. As well as providing optimum conditions for physics, the cryo-modules need to function under stringent vacuum and cryogenic conditions. We present the detail design and expected cryogenic performance of the high- β cryo-module together with the cryogenic supply and distribution system destined to service the completemore » superconducting linac.« less

  15. First Cryo-Vacuum Test of the JWST Integrated Science Instrument Module

    NASA Astrophysics Data System (ADS)

    Kimble, Randy A.; Antonille, S. R.; Balzano, V.; Comber, B. J.; Davila, P. S.; Drury, M. D.; Glasse, A.; Glazer, S. D.; Lundquist, R.; Mann, S. D.; McGuffey, D. B.; Novo-Gradac, K. J.; Penanen, K.; Ramey, D. D.; Sullivan, J.; Van Campen, J.; Vila, M. B.

    2014-01-01

    The integration and test program for the Integrated Science Instrument Module (ISIM) of the James Webb Space Telescope (JWST) calls for three cryo-vacuum tests of the ISIM hardware. The first is a risk-reduction test aimed at checking out the test hardware and procedures; this will be followed by two formal verification tests that will bracket other key aspects of the environmental test program (e.g. vibration and acoustics, EMI/EMC). The first of these cryo-vacuum tests, the risk-reduction test, was executed at NASA’s Goddard Space Flight Center starting in late August, 2013. Flight hardware under test included two (of the eventual four) flight instruments, the Mid-Infrared Instrument (MIRI) and the Fine Guidance Sensor/Near-Infrared Imager and Slitless Spectrograph (FGS/NIRISS), mounted to the ISIM structure, as well as the ISIM Electronics Compartment (IEC). The instruments were cooled to their flight operating temperatures 40K for FGS/NIRISS, ~6K for MIRI) and optically tested against a cryo-certified telescope simulator. Key goals for the risk reduction test included: 1) demonstration of controlled cooldown and warmup, stable control at operating temperature, and measurement of heat loads, 2) operation of the science instruments with ISIM electronics systems at temperature, 3) health trending of the science instruments against instrument-level test results, 4) measurement of the pupil positions and six degree of freedom alignment of the science instruments against the simulated telescope focal surface, 5) detailed optical characterization of the NIRISS instrument, 6) verification of the signal-to-noise performance of the MIRI, and 7) exercise of the Onboard Script System that will be used to operate the instruments in flight. In addition, the execution of the test is expected to yield invaluable logistical experience - development and execution of procedures, communications, analysis of results - that will greatly benefit the subsequent verification tests

  16. Cryo-EM structure of haemoglobin at 3.2 Å determined with the Volta phase plate

    NASA Astrophysics Data System (ADS)

    Khoshouei, Maryam; Radjainia, Mazdak; Baumeister, Wolfgang; Danev, Radostin

    2017-06-01

    With the advent of direct electron detectors, the perspectives of cryo-electron microscopy (cryo-EM) have changed in a profound way. These cameras are superior to previous detectors in coping with the intrinsically low contrast and beam-induced motion of radiation-sensitive organic materials embedded in amorphous ice, and hence they have enabled the structure determination of many macromolecular assemblies to atomic or near-atomic resolution. Nevertheless, there are still limitations and one of them is the size of the target structure. Here, we report the use of a Volta phase plate in determining the structure of human haemoglobin (64 kDa) at 3.2 Å. Our results demonstrate that this method can be applied to complexes that are significantly smaller than those previously studied by conventional defocus-based approaches. Cryo-EM is now close to becoming a fast and cost-effective alternative to crystallography for high-resolution protein structure determination.

  17. CryoSat SAR/SARin Level1b products: assessment of BaselineC and improvements towards BaselineD

    NASA Astrophysics Data System (ADS)

    Scagliola, Michele; Fornari, Marco; Bouffard, Jerome; Parrinello, Tommaso

    2017-04-01

    CryoSat was launched on the 8th April 2010 and is the first European ice mission dedicated to the monitoring of precise changes in the thickness of polar ice sheets and floating sea ice. Cryosat carries an innovative radar altimeter called the Synthetic Aperture Interferometric Altimeter (SIRAL), that transmits pulses at a high pulse repetition frequency thus making the received echoes phase coherent and suitable for azimuth processing. This allows to reach a significantly improved along track resolution with respect to traditional pulse-width limited altimeters. CryoSat is the first altimetry mission operating in SAR mode and continuous improvements in the Level1 Instrument Processing Facility (IPF1) are being identified, tested and validated in order to improve the quality of the Level1b products. The current IPF, Baseline C, was released in operation in April 2015 and the second CryoSat reprocessing campaign was jointly initiated, taking benefit of the upgrade implemented in the IPF1 processing chain but also of some specific configurations for the calibration corrections. In particular, the CryoSat Level1b BaselineC products generated in the framework of the second reprocessing campaign include refined information for what concerns the mispointing angles and the calibration corrections. This poster will thus detail thus the evolutions that are currently planned for the CryoSat BaselineD SAR/SARin Level1b products and the corresponding quality improvements that are expected.

  18. Cryo-mediated exfoliation and fracturing of layered materials into 2D quantum dots

    PubMed Central

    Wang, Yan; Liu, Yang; Zhang, Jianfang; Wu, Jingjie; Xu, Hui; Wen, Xiewen; Zhang, Xiang; Tiwary, Chandra Sekhar; Yang, Wei; Vajtai, Robert; Zhang, Yong; Chopra, Nitin; Odeh, Ihab Nizar; Wu, Yucheng; Ajayan, Pulickel M.

    2017-01-01

    Atomically thin quantum dots from layered materials promise new science and applications, but their scalable synthesis and separation have been challenging. We demonstrate a universal approach for the preparation of quantum dots from a series of materials, such as graphite, MoS2, WS2, h-BN, TiS2, NbS2, Bi2Se3, MoTe2, Sb2Te3, etc., using a cryo-mediated liquid-phase exfoliation and fracturing process. The method relies on liquid nitrogen pretreatment of bulk layered materials before exfoliation and breakdown into atomically thin two-dimensional quantum dots of few-nanometer lateral dimensions, exhibiting size-confined optical properties. This process is efficient for a variety of common solvents with a wide range of surface tension parameters and eliminates the use of surfactants, resulting in pristine quantum dots without surfactant covering or chemical modification. PMID:29250597

  19. From CryoSat-2 to Sentinel-3 and Beyond

    NASA Astrophysics Data System (ADS)

    Francis, R.

    2011-12-01

    CryoSat-2 carried into Earth orbit the first altimeter using SAR principles, although similar techniques had been used on earlier Venusian missions. Furthermore, it carries a second antenna and receive chain, and has been very carefully calibrated, allowing interferometry between these antennas. The results of the SAR mode and of the interferometer have met all expectations, with handsome margins. Even before the launch of CryoSat-2 the further development of this concept was underway with the radar for the oceanography mission Sentinel-3. While this radar, named SRAL (SAR Radar Altimeter) does not have the interferometer capability of CryoSat-2's SIRAL (SAR Interferometric Radar Altimeter), it does have a second frequency, to enable direct measurement of the delay induced by the ionospheric electron content. Sentinel-3 will have a sun-synchronous orbit, like ERS and EnviSat, and will have a similar latitudinal range: about 82° north and south, compared to CryoSat's 88°. Sentinel-3 will operate its radar altimeter in the high-resolution SAR mode over coastal oceans and inland water, and will revert to the more classical pulse-width limited mode over the open oceans. The SAR mode generates data at a high rate, so the major limiting factor is the amount of on-board storage. The power consumption is also higher, imposing less critical constraints. For sizing purposes the coastal oceans are defined as waters within 300 km of the continental shorelines. Sentinel-3 is expected to be launched in 2013 and be followed 18 months later by a second satellite of the same design. The next step in the development of this family of radar altimeters is Jason-CS, which will provide Continuity of Service to the existing Jason series of operational oceanography missions. Jason-CS has a very strong heritage from CryoSat but will fly the traditional Jason orbit, which covers latitudes up to 66° from a high altitude of 1330 km. The new radar is called Poseidon-4, to emphasise the

  20. Ice elevation change from Swath Processing of CryoSat SARIn Mode Data

    NASA Astrophysics Data System (ADS)

    Foresta, Luca; Gourmelen, Noel; Shepherd, Andrew; Muir, Alan; Nienow, Pete

    2015-04-01

    Reference and repeat-observations of Glacier and Ice Sheet Margin (GISM) topography are critical to identify changes in ice elevation, provide estimates of mass gain or loss and thus quantify the contribution of the cryosphere to sea level rise (e.g. McMillan et al., 2014). The Synthetic Interferometric Radar Altimeter (SIRAL) onboard the ESA radar altimetry CryoSat (CS) mission has collected ice elevation measurements since 2010. The corresponding SARIn mode of operation, activated over GISM areas, provides high spatial resolution in the along-track direction while resolving the angular origin of echoes (i.e. across-track). The current ESA SARIn processor calculates the elevation of the Point Of Closest Approach (POCA) within each waveform and maps of elevation change in Antarctica and Greenland have been produced using the regular CS height product (McMillan et al., 2014; Helm et al., 2014). Data from the CS-SARIn mode has also been used to produce measurements of ice elevation beyond the POCA, also known as swath elevation (Hawley et al. 2009; Gray et al., 2013; ESA-STSE CryoTop project). Here we use the swath processing approach to generate maps of ice elevation change from selected regions around the margins of the Greenland and Antarctic Ice Sheets. We discuss the impact of the swath processing on the spatial resolution and precision of the resulting ice elevation field and compare our results to current dh/dt estimates. References: ESA STSE CryoTop project - http://www.stse-cryotop.org/ Gray L., Burgess D., Copland L., Cullen R., Galin N., Hawley R. and Helm V. Interferometric swath processing of Cryosat data for glacial ice topography. The Cryosphere, 7(6):1857-1867, December 2013. Hawley R.L., Shepherd A., Cullen R., Helm V. and WIngham D.J. Ice-sheet elevations from across-track processing of airborne interferometric radar altimetry. Geophysical Research Letters, 36(22):L22501, November 2009. Helm V., Humbert A. and Miller H. Elevation and elevation

  1. Estimation of Arctic Sea Ice Freeboard and Thickness Using CryoSat-2

    NASA Astrophysics Data System (ADS)

    Lee, Sanggyun; Im, Jungho; yoon, Hyeonjin; Shin, Minso; Kim, Miae

    2014-05-01

    Arctic sea ice is one of the significant components of the global climate system as it plays a significant role in driving global ocean circulation, provides a continuous insulating layer at air-sea interface, and reflects a large portion of the incoming solar radiation in Polar Regions. Sea ice extent has constantly declined since 1980s. Its area was the lowest ever recorded on 16 September 2012 since the satellite record began in 1979. Arctic sea ice thickness has also been diminishing along with the decreasing sea ice extent. Because extent and thickness, two main characteristics of sea ice, are important indicators of the polar response to on-going climate change, there has been a great effort to quantify them using various approaches. Sea ice thickness has been measured with numerous field techniques such as surface drilling and deploying buoys. These techniques provide sparse and discontinuous data in spatiotemporal domain. Spaceborne radar and laser altimeters can overcome these limitations and have been used to estimate sea ice thickness. Ice Cloud and land Elevation Satellite (ICEsat), a laser altimeter from National Aeronautics and Space Administration (NASA), provided data to detect polar area elevation change between 2003 and 2009. CryoSat-2 launched with Synthetic Aperture Radar (SAR)/Interferometric Radar Altimeter (SIRAL) on April 2010 can provide data to estimate time-series of Arctic sea ice thickness. In this study, Arctic sea ice freeboard and thickness in 2012 and 2013 were estimated using CryoSat-2 SAR mode data that has sea ice surface height relative to the reference ellipsoid WGS84. In order to estimate sea ice thickness, freeboard height, elevation difference between the top of sea ice surface and leads should be calculated. CryoSat-2 profiles such as pulse peakiness, backscatter sigma-0, number of echoes, and significant wave height were examined to distinguish leads from sea ice. Several near-real time cloud-free MODIS images as CryoSat-2

  2. Magnetic Separation Methods for the Detection of Mycobacterium avium subsp. paratuberculosis in Various Types of Matrices: A Review

    PubMed Central

    Dziedzinska, Radka

    2017-01-01

    The main reasons to improve the detection of Mycobacterium avium subsp. paratuberculosis (MAP) are animal health and monitoring of MAP entering the food chain via meat, milk, and/or dairy products. Different approaches can be used for the detection of MAP, but the use of magnetic separation especially in conjunction with PCR as an end-point detection method has risen in past years. However, the extraction of DNA which is a crucial step prior to PCR detection can be complicated due to the presence of inhibitory substances. Magnetic separation methods involving either antibodies or peptides represent a powerful tool for selective separation of target bacteria from other nontarget microorganisms and inhibitory sample components. These methods enable the concentration of pathogens present in the initial matrix into smaller volume and facilitate the isolation of sufficient quantities of pure DNA. The purpose of this review was to summarize the methods based on the magnetic separation approach that are currently available for the detection of MAP in a broad range of matrices. PMID:28642876

  3. Magnetic separation of carbon-encapsulated Fe nanoparticles from thermally-treated wood char

    Treesearch

    Sung Phil Mun; Zhiyong Cai; Jilei Zhang

    2013-01-01

    Wood char,a by-product from the fast-pyrolysis process of southern yellow pine wood for bio-oil production, was carbonized with Fenano particles (FeNPs) as a catalyst to prepare carbon-encapsulated Fe nanoparticles. A magnetic separation method was tested to isolate carbon-encapsulated Fe nano particles from the carbonized char. X-ray diffraction pattern clearly shows...

  4. CryoSat Processing Prototype, how to generate LRM like echoes with SAR data and a Comparison to DUACS SLA over high latitudes

    NASA Astrophysics Data System (ADS)

    Picot, N.; Boy, F.; Desjonqueres, J.

    2012-12-01

    Like CryoSat, Sentinel3 embarks a doppler altimeter. While there is a long experience of LRM processing, SAR nadir looking data are new and will need in depth validation. Thanks to CryoSat data, the processing of SAR data can be experienced in orbit. The continuity to current altimeter data set (based on LRM acquisitions) has also to be analysed with details. A Cryosat Processing Prototype (C2P) has been developed on CNES side to prepare the CNES SAR ocean retracking study. this prototype allows to process SAR data in order to generate LRM like echoes on ground. Those CryoSat ocean products are routinely processed on CNES side and ingested in the SALP/DUACS system. CryoSat data have proved to be very accurate and very valuable for the ocean user community in the past monthes. For example, it has allowed to largely reduce the impact of the lost of the ESA ENVISAT mission as well as the long non availability of Jason-1 data. This paper will describe the system set up in place early 2012 to feed CryoSat data in the SALP/DUACS products and will present the routine data analysis . C2P CryoSat products will be compared with DUACS SLA estimates and a specific focus will be given over high latitudes knowing that CryoSat is the oinly mission providing sea surface estimates over latitudes above 66 degrees since the lost of the ESA ENVISAT mission.

  5. 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: A pilot study

    PubMed Central

    Klementieva, Oxana; Werner, Stephan; Guttmann, Peter; Pratsch, Christoph; Cladera, Josep

    2017-01-01

    Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state. This paper reports a new tool to segment and quantify structural changes of biological membranes in 3D from cryo-TXM images by tracking an initial 2D contour along the third axis of the microscope, through a multi-scale ridge detection followed by an active contours-based model, with a subsequent refinement along the other two axes. A quantitative metric that assesses the grayscale profiles perpendicular to the membrane surfaces is introduced and shown to be linearly related to the membrane thickness. Our methodology has been validated on synthetic phantoms using realistic microscope properties and structure dimensions, as well as on real cryo-TXM data. Results demonstrate the validity of our algorithms for cryo-TXM data analysis. PMID:28376110

  6. A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data.

    PubMed

    Larivière, Damien; Galindo-Murillo, Rodrigo; Fourmentin, Eric; Hornus, Samuel; Lévy, Bruno; Papillon, Julie; Ménétret, Jean-François; Lamour, Valérie

    2017-01-01

    The structural modeling of a macromolecular machine is like a "Lego" approach that is challenged when blocks, like proteins imported from the Protein Data Bank, are to be assembled with an element adopting a serpentine shape, such as DNA templates. DNA must then be built ex nihilo, but modeling approaches are either not user-friendly or very long and fastidious. In this method chapter we show how to use GraphiteLifeExplorer, a software with a simple graphical user interface that enables the sketching of free forms of DNA, of any length, at the atomic scale, as fast as drawing a line on a sheet of paper. We took as an example the nucleoprotein complex of DNA gyrase, a bacterial topoisomerase whose structure has been determined using cryo-electron microscopy (Cryo-EM). Using GraphiteLifeExplorer, we could model in one go a 155 bp long and twisted DNA duplex that wraps around DNA gyrase in the cryo-EM map, improving the quality and interpretation of the final model compared to the initially published data.

  7. CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin

    PubMed Central

    van Pee, Katharina; Neuhaus, Alexander; D'Imprima, Edoardo; Mills, Deryck J; Kühlbrandt, Werner; Yildiz, Özkan

    2017-01-01

    Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain 3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane. DOI: http://dx.doi.org/10.7554/eLife.23644.001 PMID:28323617

  8. Droplet-based magnetically activated cell separation: analysis of separation efficiency based on the variation of flow-induced circulation in a pendent drop.

    PubMed

    Kim, Youngho; Lee, Sang Ho; Kim, Byungkyu

    2009-12-01

    Under the assumption that separation efficiencies are mainly affected by the velocity of flow-induced circulation due to buffer injection in a pendent drop, this paper describes an analysis of the separation efficiency of a droplet-based magnetically activated cell separation (DMACS) system. To investigate the velocity of the flow-induced circulation, we supposed that numerous flows in a pendent drop could be considered as a "theoretically normalized" flow (or conceptually normalized flow, CNF) based on the Cauchy-Goursat theorem. With the morphological characteristics (length and duration time) of a pendent drop depending on the initial volume, we obtained the velocities of the CNF. By measuring the separation efficiencies for different initial volumes and by analyzing the separation efficiency in terms of the velocity of the CNF, we found that the separation efficiencies (in the case of a low rate of buffer injection; 5 and 15 microl x min(-1)) are mainly affected by the velocity of the CNF. Moreover, we confirmed that the phenomenological features of a pendent drop cause a fluctuation of its separation efficiencies over a range of specific volumes (initial volumes ranging from 40 to 80 microl), because of the "sweeping-off" phenomenon, that is, positive cells gathered into the positive fraction are forced to move away from the magnetic side by flow-induced circulation due to buffer injection. In addition, from the variation of the duration time, that is, the interval between the beginning of injection of the buffer solution and the time at which a pendent drop detaches, it could also be confirmed that a shorter duration time leads to decrease of the number of positive cells in negative fraction regardless of the rate of buffer injection (5, 15, and 50 microl x min(-1)). Therefore, if a DMACS system is operated with a 15 microl x min(-1) buffer injection flow rate and an initial volume of 80 microl or more, we would have the best efficiency of separation in the

  9. Validation of cryo-EM structure of IP₃R1 channel.

    PubMed

    Murray, Stephen C; Flanagan, John; Popova, Olga B; Chiu, Wah; Ludtke, Steven J; Serysheva, Irina I

    2013-06-04

    About a decade ago, three electron cryomicroscopy (cryo-EM) single-particle reconstructions of IP3R1 were reported at low resolution. It was disturbing that these structures bore little similarity to one another, even at the level of quaternary structure. Recently, we published an improved structure of IP3R1 at ∼1 nm resolution. However, this structure did not bear any resemblance to any of the three previously published structures, leading to the question of why the structure should be considered more reliable than the original three. Here, we apply several methods, including class-average/map comparisons, tilt-pair validation, and use of multiple refinement software packages, to give strong evidence for the reliability of our recent structure. The map resolution and feature resolvability are assessed with the gold standard criterion. This approach is generally applicable to assessing the validity of cryo-EM maps of other molecular machines. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Water activity and mobility in solutions of glycerol and small molecular weight sugars: Implication for cryo- and lyopreservation

    NASA Astrophysics Data System (ADS)

    He, Xiaoming; Fowler, Alex; Toner, Mehmet

    2006-10-01

    In this study, the free volume models, originally developed for large molecular weight polymer-solvent systems, were used to study the water activity and mobility in solutions of four small molecular weight cryo-/lyoprotectants, viz., glycerol, a monosaccharide (fructose), and two disaccharides (sucrose and trehalose). The free volume model parameters were determined by fitting the models to available experimental data using a nonlinear optimization procedure. It was found that free volume models could accurately predict the available experimental data, which suggests that the free volume models might be generally applicable to aqueous solutions of small molecular weight cryo-/lyoprotectants. Furthermore, several models for estimating the mutual diffusion coefficient were tested using available experimental data for aqueous solutions of glycerol and a better method to estimate the mutual diffusion coefficient was proposed. Free volume models were used to predict and analyze the water activity and mobility in solutions of four cryo-/lyoprotectants under conditions frequently encountered in cryo-/lyopreservation applications. It was found that the water mobility in the glassy state of the above four solutions is essentially negligible in the case of cryopreservation with storage temperature lower than -110°C. However, the water mobility in a glass at higher temperature (>-80°C) may be significant. As a result, a subcooling of up to 50°C may be necessary for the long-term cryo-/lyopreservation of biomaterials depending on the water content and the type of cryo-/lyoprotectants. It was further shown that trehalose might be the best of the four protectants studied for lyopreservation (water mass fraction ⩽0.1) when the storage temperature is above the room temperature. The results from this study might be useful for the development of more effective protocols for both cryopreservation and lyopreservation of living cells and other biomaterials.

  11. Electrospun magnetically separable calcium ferrite nanofibers for photocatalytic water purification

    NASA Astrophysics Data System (ADS)

    EL-Rafei, A. M.; El-Kalliny, Amer S.; Gad-Allah, Tarek A.

    2017-04-01

    Three-dimensional random calcium ferrite, CaFe2O4, nanofibers (NFs) were successfully prepared via the electrospinning method. The effect of calcination temperature on the characteristics of the as-spun NFs was investigated. X-ray diffraction analysis showed that CaFe2O4 phase crystallized as a main phase at 700 °C and as a sole phase at 1000 °C. Field emission scanning electron microscopy emphasized that CaFe2O4 NFs were fabricated with diameters in the range of 50-150 nm and each fiber was composed of 20-50 nm grains. Magnetic hysteresis loops revealed superparamagnetic behavior for the prepared NFs. These NFs produced active hydroxyl radicals under simulated solar light irradiation making them recommendable for photocatalysis applications in water purification. In the meantime, these NFs can be easily separated from the treated water by applying an external magnetic field.

  12. CryoSat: ready to launch (again)

    NASA Astrophysics Data System (ADS)

    Francis, R.; Wingham, D.; Cullen, R.

    2009-12-01

    Over the last ten years the relationship between climate change and the cryosphere has become increasingly important. Evidence of change in the polar regions is widespread, and the subject of public discussion. During this same ten years ESA has been preparing its CryoSat mission, specifically designed to provide measurements to determine the overall change in the mass balance of all of the ice caps and of change in the volume of sea-ice (rather than simply its extent). In fact the mission was ready for launch in October 2005, but a failure in the launch vehicle led to a loss of the satellite some 6 minutes after launch. The determination to rebuild the satellite and complete the mission was widespread in the relevant scientific, industrial and political entities, and the decision to redirect financial resources to the rebuild was sealed with a scientific report confirming that the mission was even more important in 2005 than at its original selection in 1999. The evolution of the cryosphere since then has emphasised that conclusion. In order to make a meaningful measurement of the secular change of the surface legation of ice caps and the thickness of sea-ice, the accuracy required has been specified as about half of the variation expected due to natural variability, over reasonable scales for the surfaces concerned. The selected technique is radar altimetry. Previous altimeter missions have pioneered the method: the CryoSat instrument has been modified to provide the enhanced capabilities needed to significantly extend the spatial coverage of these earlier missions. Thus the radar includes a synthetic aperture mode which enables the along-track resolution to be improved to about 250 m. This will will allow detection of leads in sea-ice which are narrower than those detected hitherto, so that operation deeper into pack-ice can be achieved with a consequent reduction in errors due to omission. Altimetry over the steep edges of ice caps is hampered by the irregular

  13. Nanoparticle targeting of Gram-positive and Gram-negative bacteria for magnetic-based separations of bacterial pathogens

    NASA Astrophysics Data System (ADS)

    Lu, Hoang D.; Yang, Shirley S.; Wilson, Brian K.; McManus, Simon A.; Chen, Christopher V. H.-H.; Prud'homme, Robert K.

    2017-04-01

    Antimicrobial resistance is a healthcare problem of increasing significance, and there is increasing interest in developing new tools to address bacterial infections. Bacteria-targeting nanoparticles hold promise to improve drug efficacy, compliance, and safety. In addition, nanoparticles can also be used for novel applications, such as bacterial imaging or bioseperations. We here present the use of a scalable block-copolymer-directed self-assembly process, Flash NanoPrecipitation, to form zinc(II)-bis(dipicolylamine) modified nanoparticles that bind to both Gram-positive and Gram-negative bacteria with specificity. Particles have tunable surface ligand densities that change particle avidity and binding efficacy. A variety of materials can be encapsulated into the core of the particles, such as optical dyes or iron oxide colloids, to produce imageable and magnetically active bacterial targeting constructs. As a proof-of-concept, these particles are used to bind and separate bacteria from solution in a magnetic column. Magnetic manipulation and separation would translate to a platform for pathogen identification or removal. These magnetic and targeted nanoparticles enable new methods to address bacterial infections.

  14. Continuous Quadrupole Magnetic Separation of Islets during Digestion Improves Purified Porcine Islet Viability.

    PubMed

    Weegman, Bradley P; Kumar Sajja, Venkata Sunil; Suszynski, Thomas M; Rizzari, Michael D; Scott Iii, William E; Kitzmann, Jennifer P; Mueller, Kate R; Hanley, Thomas R; Kennedy, David J; Todd, Paul W; Balamurugan, Appakalai N; Hering, Bernhard J; Papas, Klearchos K

    2016-01-01

    Islet transplantation (ITx) is an emerging and promising therapy for patients with uncontrolled type 1 diabetes. The islet isolation and purification processes require exposure to extended cold ischemia, warm-enzymatic digestion, mechanical agitation, and use of damaging chemicals for density gradient separation (DG), all of which reduce viable islet yield. In this paper, we describe initial proof-of-concept studies exploring quadrupole magnetic separation (QMS) of islets as an alternative to DG to reduce exposure to these harsh conditions. Three porcine pancreata were split into two parts, the splenic lobe (SPL) and the combined connecting/duodenal lobes (CDL), for paired digestions and purifications. Islets in the SPL were preferentially labeled using magnetic microparticles (MMPs) that lodge within the islet microvasculature when infused into the pancreas and were continuously separated from the exocrine tissue by QMS during the collection phase of the digestion process. Unlabeled islets from the CDL were purified by conventional DG. Islets purified by QMS exhibited significantly improved viability (measured by oxygen consumption rate per DNA, p < 0.03) and better morphology relative to control islets. Islet purification by QMS can reduce the detrimental effects of prolonged exposure to toxic enzymes and density gradient solutions and substantially improve islet viability after isolation.

  15. Continuous Quadrupole Magnetic Separation of Islets during Digestion Improves Purified Porcine Islet Viability

    PubMed Central

    Kumar Sajja, Venkata Sunil; Rizzari, Michael D.; Scott III, William E.; Kitzmann, Jennifer P.; Kennedy, David J.; Todd, Paul W.; Balamurugan, Appakalai N.; Hering, Bernhard J.

    2016-01-01

    Islet transplantation (ITx) is an emerging and promising therapy for patients with uncontrolled type 1 diabetes. The islet isolation and purification processes require exposure to extended cold ischemia, warm-enzymatic digestion, mechanical agitation, and use of damaging chemicals for density gradient separation (DG), all of which reduce viable islet yield. In this paper, we describe initial proof-of-concept studies exploring quadrupole magnetic separation (QMS) of islets as an alternative to DG to reduce exposure to these harsh conditions. Three porcine pancreata were split into two parts, the splenic lobe (SPL) and the combined connecting/duodenal lobes (CDL), for paired digestions and purifications. Islets in the SPL were preferentially labeled using magnetic microparticles (MMPs) that lodge within the islet microvasculature when infused into the pancreas and were continuously separated from the exocrine tissue by QMS during the collection phase of the digestion process. Unlabeled islets from the CDL were purified by conventional DG. Islets purified by QMS exhibited significantly improved viability (measured by oxygen consumption rate per DNA, p < 0.03) and better morphology relative to control islets. Islet purification by QMS can reduce the detrimental effects of prolonged exposure to toxic enzymes and density gradient solutions and substantially improve islet viability after isolation. PMID:27843954

  16. Cryo-vacuum testing of the JWST Integrated Science Instrument Module (SPIE)

    NASA Technical Reports Server (NTRS)

    Kimble, Randy A.; Vila, M. Begona; Van Campen, Julie; Birkmann, Stephan M.; Comber, Brian J.; Fatig, Curtis C.; Glasse, Alistair C. H.; Glazer, Stuart D.; Kelly, Douglas M.; Mann, Steven D.; hide

    2016-01-01

    In late 2015/early 2016, a major cryo-vacuum test was carried out for the Integrated Science Instrument Module (ISIM) of the James Webb Space Telescope (JWST). This test comprised the final cryo-certification and calibration test of the ISIM, after its ambient environmental test program (vibration, acoustics, EMI/EMC), and before its delivery for integration with the rest of the JWST observatory. Over the 108-day period of the round-the-clock test program, the full complement of ISIM flight instruments, structure, harness radiator, and electronics were put through a comprehensive program of thermal, optical, electrical, and operational tests. The test verified the health and excellent performance of the instruments and ISIM systems, proving the ISIM element's readiness for integration with the telescope. We report here on the context, goals, setup, execution, and key results for this critical JWST milestone.

  17. How cryo-electron microscopy and X-ray crystallography complement each other.

    PubMed

    Wang, Hong-Wei; Wang, Jia-Wei

    2017-01-01

    With the ability to resolve structures of macromolecules at atomic resolution, X-ray crystallography has been the most powerful tool in modern structural biology. At the same time, recent technical improvements have triggered a resolution revolution in the single particle cryo-EM method. While the two methods are different in many respects, from sample preparation to structure determination, they both have the power to solve macromolecular structures at atomic resolution. It is important to understand the unique advantages and caveats of the two methods in solving structures and to appreciate the complementary nature of the two methods in structural biology. In this review we provide some examples, and discuss how X-ray crystallography and cryo-EM can be combined in deciphering structures of macromolecules for our full understanding of their biological mechanisms. © 2016 The Protein Society.

  18. Ablation of atrial-ventricular junction tissues via the coronary sinus using cryo balloon technology.

    PubMed

    Avitall, Boaz; Lafontaine, Daniel; Rozmus, Grzegorz; Adoni, Naveed; Dehnee, Abed; Urbonas, Arvydas; Le, Khoi M; Aleksonis, Dinas

    2005-04-01

    The coronary sinus (CS) can provide access to targets across and within the atrioventricular (AV) junction. In 12 dogs (32 +/- 3 Kg), cryo balloons (10-19 mm) were applied to regions of the AV junction for 3 minutes at a temperature of -75.9( composite function) +/- 9(composite function)C (ranging -57 to -83). Electrical activity and pacing within the CS were assessed pre and post ablation and at least 3 months later in 9 dogs. In the 3 other dogs, hearts were examined immediately after cryo ablation. CS and circumflex angiography was performed pre and post ablation. The hearts, CS, and Cx were then examined for structural injury. The AV junction was sectioned and the hearts were immersed in Tetrazolium, and the lesions were inspected for transmurality across the AV groove. In 3/12 dogs the distal CS cryo lesions resulted in inferior ST segment depression that resolved within 5 minutes. There was no arrhythmia or hemodynamic changes. No CS electrical activity was noted post ablation. The pacing threshold increased from 2 +/- 2.3 mA to 7.4 +/- 3.6 mA (p < 0.001). Pathological examination of 3 acute hearts revealed hematomas. There was no pericardial effusion. No evidence of stenosis or thrombosis was seen within the CS and the circumflex artery. After 3 months of recovery, transmural lesions across the AV groove were present in all of the targeted AV regions. Intra-CS cryo balloon ablation is safe and can potentially replace endocardial RF ablation targeting the AV junction and the CS muscular sleeve.

  19. Monitoring Snow and Land Ice Using Satellite data in the GMES Project CryoLand

    NASA Astrophysics Data System (ADS)

    Bippus, Gabriele; Nagler, Thomas

    2013-04-01

    The main objectives of the project "CryoLand - GMES Service Snow and Land Ice" are to develop, implement and validate services for snow, glaciers and lake and river ice products as a Downstream Service within the Global Monitoring for Environment and Security (GMES) program of the European Commission. CryoLand exploits Earth Observation data from current optical and microwave sensors and of the upcoming GMES Sentinel satellite family. The project prepares also the basis for the cryospheric component of the GMES Land Monitoring services. The CryoLand project team consists of 10 partner organisations from Austria, Finland, Norway, Sweden, Switzerland and Romania and is funded by the 7th Framework Program of the European Commission. The CryoLand baseline products for snow include fractional snow extent from optical satellite data, the extent of melting snow from SAR data, and coarse resolution snow water equivalent maps from passive microwave data. Experimental products include maps of snow surface wetness and temperature. The products range from large scale coverage at medium resolution to regional products with high resolution, in order to address a wide user community. Medium resolution optical data (e.g. MODIS, in the near future Sentinel-3) and SAR (ENVISAT ASAR, in the near future Sentinel-1) are the main sources of EO data for generating large scale products in near real time. For generation of regional products high resolution satellite data are used. Glacier products are based on high resolution optical (e.g. SPOT-5, in the near future Sentinel-2) and SAR (TerraSAR-X, in the near future Sentinel-1) data and include glacier outlines, mapping of glacier facies, glacier lakes and ice velocity. The glacier products are generated on users demand. Current test areas are located in the Alps, Norway, Greenland and the Himalayan Mountains. The lake and river ice products include ice extent and its temporal changes and snow extent on ice. The algorithms for these

  20. Development of a High-Throughput Magnetic Separation Device for Malaria-infected Erythrocytes

    PubMed Central

    Martin, A. Blue; Wu, Wei-Tao; Kameneva, Marina V.; Antaki, James F.

    2017-01-01

    This study describes a non-dilutive high-gradient magnetic separation (HGMS) device intended to continuously remove malaria-infected red blood cells (iRBCs) from the circulation. A mesoscale prototype device with disposable photo-etched ferromagnetic grid and reusable permanent magnet was designed with a computationally-optimized magnetic force. The prototype device was evaluated in-vitro using a non-pathogenic analog for malaria-infected blood, comprised of 24% healthy RBCs, 6% human methemoglobin RBCs (metRBCs), and 70% phosphate buffer solution (PBS). The device provided a 27.0 ± 2.2% reduction of metRBCs in a single pass at a flow rate of 77 μL min−1. This represents a clearance rate over 380 times greater throughput than microfluidic devices reported previously. These positive results encourage development of a clinical scale system that would economize time and donor blood for treating severe malaria. PMID:28924724

  1. Development of a High-Throughput Magnetic Separation Device for Malaria-Infected Erythrocytes.

    PubMed

    Blue Martin, A; Wu, Wei-Tao; Kameneva, Marina V; Antaki, James F

    2017-12-01

    This study describes a non-dilutive high-gradient magnetic separation (HGMS) device intended to continuously remove malaria-infected red blood cells (iRBCs) from the circulation. A mesoscale prototype device with disposable photo-etched ferromagnetic grid and reusable permanent magnet was designed with a computationally-optimized magnetic force. The prototype device was evaluated in vitro using a non-pathogenic analog for malaria-infected blood, comprised of 24% healthy RBCs, 6% human methemoglobin RBCs (metRBCs), and 70% phosphate buffer solution (PBS). The device provided a 27.0 ± 2.2% reduction of metRBCs in a single pass at a flow rate of 77 μL min -1 . This represents a clearance rate over 380 times greater throughput than microfluidic devices reported previously. These positive results encourage development of a clinical scale system that would economize time and donor blood for treating severe malaria.

  2. Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography.

    PubMed

    Norlén, Lars; Masich, Sergej; Goldie, Kenneth N; Hoenger, Andreas

    2007-06-10

    Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly alpha-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

  3. Cryo-EM structure of the large subunit of the spinach chloroplast ribosome

    PubMed Central

    Ahmed, Tofayel; Yin, Zhan; Bhushan, Shashi

    2016-01-01

    Protein synthesis in the chloroplast is mediated by the chloroplast ribosome (chloro-ribosome). Overall architecture of the chloro-ribosome is considerably similar to the Escherichia coli (E. coli) ribosome but certain differences are evident. The chloro-ribosome proteins are generally larger because of the presence of chloroplast-specific extensions in their N- and C-termini. The chloro-ribosome harbours six plastid-specific ribosomal proteins (PSRPs); four in the small subunit and two in the large subunit. Deletions and insertions occur throughout the rRNA sequence of the chloro-ribosome (except for the conserved peptidyl transferase center region) but the overall length of the rRNAs do not change significantly, compared to the E. coli. Although, recent advancements in cryo-electron microscopy (cryo-EM) have provided detailed high-resolution structures of ribosomes from many different sources, a high-resolution structure of the chloro-ribosome is still lacking. Here, we present a cryo-EM structure of the large subunit of the chloro-ribosome from spinach (Spinacia oleracea) at an average resolution of 3.5 Å. High-resolution map enabled us to localize and model chloro-ribosome proteins, chloroplast-specific protein extensions, two PSRPs (PSRP5 and 6) and three rRNA molecules present in the chloro-ribosome. Although comparable to E. coli, the polypeptide tunnel and the tunnel exit site show chloroplast-specific features. PMID:27762343

  4. Haloing in bimodal magnetic colloids: The role of field-induced phase separation

    NASA Astrophysics Data System (ADS)

    Magnet, C.; Kuzhir, P.; Bossis, G.; Meunier, A.; Suloeva, L.; Zubarev, A.

    2012-07-01

    If a suspension of magnetic micrometer-sized and nanosized particles is subjected to a homogeneous magnetic field, the nanoparticles are attracted to the microparticles and form thick anisotropic halos (clouds) around them. Such clouds can hinder the approach of microparticles and result in effective repulsion between them [M. T. López-López, A. Yu. Zubarev, and G. Bossis, Soft Matter10.1039/c0sm00261e 6, 4346 (2010)]. In this paper, we present detailed experimental and theoretical studies of nanoparticle concentration profiles and of the equilibrium shapes of nanoparticle clouds around a single magnetized microsphere, taking into account interactions between nanoparticles. We show that at a strong enough magnetic field, the ensemble of nanoparticles experiences a gas-liquid phase transition such that a dense liquid phase is condensed around the magnetic poles of a microsphere while a dilute gas phase occupies the rest of the suspension volume. Nanoparticle accumulation around a microsphere is governed by two dimensionless parameters—the initial nanoparticle concentration (φ0) and the magnetic-to-thermal energy ratio (α)—and the three accumulation regimes are mapped onto a α-φ0 phase diagram. Our local thermodynamic equilibrium approach gives a semiquantitative agreement with the experiments on the equilibrium shapes of nanoparticle clouds. The results of this work could be useful for the development of the bimodal magnetorheological fluids and of the magnetic separation technologies used in bioanalysis and water purification systems.

  5. Enhancing the Arctic Mean Sea Surface and Mean Dynamic Topography with CryoSat-2 Data

    NASA Astrophysics Data System (ADS)

    Stenseng, Lars; Andersen, Ole B.; Knudsen, Per

    2014-05-01

    A reliable mean sea surface (MSS) is essential to derive a good mean dynamic topography (MDT) and for the estimation of short and long-term changes in the sea surface. The lack of satellite radar altimetry observations above 82 degrees latitude means that existing mean sea surface models have been unreliable in the Arctic Ocean. We here present the latest DTU mean sea surface and mean dynamic topography models that includes CryoSat-2 data to improve the reliability in the Arctic Ocean. In an attempt to extrapolate across the gap above 82 degrees latitude the previously models included ICESat data, gravimetrical geoids, ocean circulation models and various combinations hereof. Unfortunately cloud cover and the short periods of operation has a negative effect on the number of ICESat sea surface observations. DTU13MSS and DTU13MDT are the new generation of state of the art global high-resolution models that includes CryoSat-2 data to extend the satellite radar altimetry coverage up to 88 degrees latitude. Furthermore the SAR and SARin capability of CryoSat-2 dramatically increases the amount of useable sea surface returns in sea-ice covered areas compared to conventional radar altimeters like ENVISAT and ERS-1/2. With the inclusion of CryoSat-2 data the new mean sea surface is improved by more than 20 cm above 82 degrees latitude compared with the previous generation of mean sea surfaces.

  6. Development of a TES based Cryo-Anticoincidence for a large array of microcalorimeters

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Colasanti, L.; Macculi, C.; Piro, L.

    2009-12-16

    The employment of large arrays of microcalorimeters in space missions (IXO, EDGE/XENIA), requires the presence of an anticoincidence detector to remove the background due to the particles, with a rejection efficiency at least equal to Suzaku (98%). A new concept of anticoincidence is under development to match the very tight thermal requirements and to simplify the design of the electronic chain. The idea is to produce a Cryo-AntiCoincidence (Cryo-AC) based on a silicon absorber and read by a TES (Transition-Edge Sensor). This configuration would ensure very good performances in terms of efficiency, time response and signal to noise ratio. Wemore » present the results of estimations, simulations and preliminary measurement.« less

  7. Big data in cryoEM: automated collection, processing and accessibility of EM data.

    PubMed

    Baldwin, Philip R; Tan, Yong Zi; Eng, Edward T; Rice, William J; Noble, Alex J; Negro, Carl J; Cianfrocco, Michael A; Potter, Clinton S; Carragher, Bridget

    2018-06-01

    The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Construction and Organization of a BSL-3 Cryo-Electron Microscopy Laboratory at UTMB

    PubMed Central

    Sherman, Michael B.; Trujillo, Juan; Leahy, Ian; Razmus, Dennis; DeHate, Robert; Lorcheim, Paul; Czarneski, Mark A.; Zimmerman, Domenica; Newton, Je T’Aime M.; Haddow, Andrew D.; Weaver, Scott C.

    2013-01-01

    A unique cryo-electron microscopy facility has been designed and constructed at the University of Texas Medical Branch (UTMB) to study the three-dimensional organization of viruses and bacteria classified as select agents at biological safety level (BSL)-3, and their interactions with host cells. A 200 keV high-end cryo-electron microscope was installed inside a BSL-3 containment laboratory and standard operating procedures were developed and implemented to ensure its safe and efficient operation. We also developed a new microscope decontamination protocol based on chlorine dioxide gas with a continuous flow system, which allowed us to expand the facility capabilities to study bacterial agents including spore-forming species. The new unified protocol does not require agent-specific treatment in contrast to the previously used heat decontamination. To optimize the use of the cryo-electron microscope and to improve safety conditions, it can be remotely controlled from a room outside of containment, or through a computer network world-wide. Automated data collection is provided by using JADAS (single particle imaging) and SerialEM (tomography). The facility has successfully operated for more than a year without an incident and was certified as a select agent facility by the Centers for Disease Control. PMID:23274136

  9. Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning

    PubMed Central

    Wu, Jiayi; Ma, Yong-Bei; Congdon, Charles; Brett, Bevin; Chen, Shuobing; Xu, Yaofang; Ouyang, Qi

    2017-01-01

    Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR) in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM). We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC) environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization. PMID:28786986

  10. Massively parallel unsupervised single-particle cryo-EM data clustering via statistical manifold learning.

    PubMed

    Wu, Jiayi; Ma, Yong-Bei; Congdon, Charles; Brett, Bevin; Chen, Shuobing; Xu, Yaofang; Ouyang, Qi; Mao, Youdong

    2017-01-01

    Structural heterogeneity in single-particle cryo-electron microscopy (cryo-EM) data represents a major challenge for high-resolution structure determination. Unsupervised classification may serve as the first step in the assessment of structural heterogeneity. However, traditional algorithms for unsupervised classification, such as K-means clustering and maximum likelihood optimization, may classify images into wrong classes with decreasing signal-to-noise-ratio (SNR) in the image data, yet demand increased computational costs. Overcoming these limitations requires further development of clustering algorithms for high-performance cryo-EM data processing. Here we introduce an unsupervised single-particle clustering algorithm derived from a statistical manifold learning framework called generative topographic mapping (GTM). We show that unsupervised GTM clustering improves classification accuracy by about 40% in the absence of input references for data with lower SNRs. Applications to several experimental datasets suggest that our algorithm can detect subtle structural differences among classes via a hierarchical clustering strategy. After code optimization over a high-performance computing (HPC) environment, our software implementation was able to generate thousands of reference-free class averages within hours in a massively parallel fashion, which allows a significant improvement on ab initio 3D reconstruction and assists in the computational purification of homogeneous datasets for high-resolution visualization.

  11. Construction and organization of a BSL-3 cryo-electron microscopy laboratory at UTMB.

    PubMed

    Sherman, Michael B; Trujillo, Juan; Leahy, Ian; Razmus, Dennis; Dehate, Robert; Lorcheim, Paul; Czarneski, Mark A; Zimmerman, Domenica; Newton, Je T'aime M; Haddow, Andrew D; Weaver, Scott C

    2013-03-01

    A unique cryo-electron microscopy facility has been designed and constructed at the University of Texas Medical Branch (UTMB) to study the three-dimensional organization of viruses and bacteria classified as select agents at biological safety level (BSL)-3, and their interactions with host cells. A 200keV high-end cryo-electron microscope was installed inside a BSL-3 containment laboratory and standard operating procedures were developed and implemented to ensure its safe and efficient operation. We also developed a new microscope decontamination protocol based on chlorine dioxide gas with a continuous flow system, which allowed us to expand the facility capabilities to study bacterial agents including spore-forming species. The new unified protocol does not require agent-specific treatment in contrast to the previously used heat decontamination. To optimize the use of the cryo-electron microscope and to improve safety conditions, it can be remotely controlled from a room outside of containment, or through a computer network world-wide. Automated data collection is provided by using JADAS (single particle imaging) and SerialEM (tomography). The facility has successfully operated for more than a year without an incident and was certified as a select agent facility by the Centers for Disease Control. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. New National Cryo-EM Facility Provides Access to Cutting-Edge Technology for Cancer Research Community | Frederick National Laboratory for Cancer Research

    Cancer.gov

    Cancer researchers nationwide now have access to the latest technology in the field of cryo-electron microscopy (cryo-EM)—the study of protein structures at atomic resolution—at the Frederick National Lab for Cancer Research. The emerging technol

  13. Characteristics of the new AtriCure cryoFORM® cryoablation probe for the surgical treatment of cardiac arrhythmias.

    PubMed

    Schroeter, Thomas; Misfeld, Martin

    2017-04-01

    Atrial fibrillation has a significant impact on patient mortality and morbidity. In particular, stroke is a frequent complication associated with atrial fibrillation. In recent years, various treatment options have been developed that are based on the elimination of atypical electrically active atrial areas. Areas covered: This manuscript presents a new cryoablation probe from AtriCure Inc. In addition to describing the characteristics of the probe, we also discuss atrial fibrillation and its surgical therapy options as well as the basics of cryosurgery. The cryoFORM® cryoablation probe is an ablation system developed for cardiothoracic surgeons that utilizes nitrous oxide (N 2 O) to create continuous transmural lesions that block propagation of atrial activation. The main features of the probe are an excellent working capacity due to the use of N 2 O, high flexibility, and, in combination with the cryoICE® Box V6, an active defrost mode for quick detachment. Expert commentary: The cryoFORM® ablation probe is a new device for the treatment of atrial fibrillation using N 2 O as an energy source. The probe is made from stainless steel and has a corrugated surface, a design that provides a higher flexibility than the cryoICE probe.

  14. Streptavidin-coated magnetic beads for DNA strand separation implicate a multitude of problems during cell-SELEX.

    PubMed

    Paul, Angela; Avci-Adali, Meltem; Ziemer, Gerhard; Wendel, Hans P

    2009-09-01

    Using whole living cells as a target for SELEX (systematic evolution of ligands by exponential enrichment) experiments represents a promising method to generate cell receptor-specific aptamers. These aptamers have a huge potential in diagnostics, therapeutics, imaging, regenerative medicine, and target validation. During the SELEX for selecting DNA aptamers, one important step is the separation of 2 DNA strands to yield one of the 2 strands as single-stranded DNA aptamer. This is being done routinely by biotin labeling of the complementary DNA strand to the desired aptamer and then separating the DNA strand by using streptavidin-coated magnetic beads. After immobilization of the double-stranded DNA on these magnetic beads and alkaline denaturation, the non-biotinylated strand is being eluted and the biotinylated strand is retarded. Using Western blot analysis, we demonstrated the detachment of covalent-bonded streptavidin from the bead surface after alkaline treatment. The eluates were also contaminated with undesired biotinylated strands. Furthermore, a streptavidin-induced aggregation of target cells was demonstrated by flow cytometry and microscopic methods. Cell-specific enrichment of aptamers was not possible due to clustering and patching effects triggered by streptavidin. Therefore, the use of streptavidin-coated magnetic beads for DNA strand separation should be examined thoroughly, especially for cell-SELEX applications.

  15. Design of a single magnet separator with mass resolving power m/Δm ≈ 20, 000

    NASA Astrophysics Data System (ADS)

    Breitenfeldt, Martin; Augustin, Mathieu; Catherall, Richard; Giles, Tim; Schoerling, Daniel; Tveten, Gry M.

    2016-06-01

    ISOLDE at CERN is a leading radioactive ion beam facility. With its upgrade, the HIE-ISOLDE project, an increase in primary beam intensity and energy is envisaged and the aim is a significant increase in intensity of the exotic beams. The high resolution separator (HRS) after the upgrade is required to suppress contaminations almost completely when the masses differ to the beam of interest by Δm / m > 1 / 20, 000 . Here a 120° magnet with a bending radius of 1.25 m has been chosen. The magnetic rigidity is 0.625 Tm (B-field of 0.5 T) to allow for separation of molecules of up to a mass of 300 u. The magnet comprises a yoke in wedged H-type configuration for stability and precision and pole face conductors for focusing and compensation of aberrations. The concept was derived analytically, refined with the OPERA 2D software and tested with the ray-tracing module of OPERA 3D.

  16. Characterization of zeolites synthesized from porous wastes using hydrothermal agitational leaching assisted by magnetic separation

    NASA Astrophysics Data System (ADS)

    Top, Soner; Vapur, Huseyin; Ekicibil, Ahmet

    2018-07-01

    In this study, zeolite Na-P1 synthesis from the fly ashes (FA) taken from dust catcher in Sugözü thermic power plant was researched. The structural and magnetic characteristics of the synthesized materials were studied by using the XRD, SEM, EDS, CEC, TGA, DTA, DSC and M-H techniques. High intensity wet magnetic separation was applied to the ashes at different magnetic field intensities. 61% of the iron oxide impurity (Fe2O3) was removed by single-stage high intensity wet magnetic separation at 1.5 T. Non-magnetic phase was accumulated in order to leach in alkali medium. 2 M NaOH was used as the synthesizing solution. Solid-liquid ratio was 0.3 kg:1 L. It was determined that the zeolitization degrees of the products depend on the reaction time. Zeolite Na-P1 (Na6Al6Si10O32·12H2O) which is the member of the group P zeolites was the dominant species after 10 h reaction time. Additionally, gismondine (Ca2Al4Si4O16·9H2O) presence was observed in the products. It was found out that the ferromagnetisms of the products were weakened by elapsed time. The CEC values of the synthesized products were the superior grades ranging from 269.63 meq/100 g to 388.85 meq/100 g.

  17. Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging.

    PubMed

    Hagen, Wim J H; Wan, William; Briggs, John A G

    2017-02-01

    Cryo-electron tomography (cryoET) allows 3D structural information to be obtained from cells and other biological samples in their close-to-native state. In combination with subtomogram averaging, detailed structures of repeating features can be resolved. CryoET data is collected as a series of images of the sample from different tilt angles; this is performed by physically rotating the sample in the microscope between each image. The angles at which the images are collected, and the order in which they are collected, together are called the tilt-scheme. Here we describe a "dose-symmetric tilt-scheme" that begins at low tilt and then alternates between increasingly positive and negative tilts. This tilt-scheme maximizes the amount of high-resolution information maintained in the tomogram for subsequent subtomogram averaging, and may also be advantageous for other applications. We describe implementation of the tilt-scheme in combination with further data-collection refinements including setting thresholds on acceptable drift and improving focus accuracy. Requirements for microscope set-up are introduced, and a macro is provided which automates the application of the tilt-scheme within SerialEM. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Selective fluorescence response and magnetic separation probe for 2,4,6-trinitrotoluene based on iron oxide magnetic nanoparticles.

    PubMed

    Zou, Wen-Sheng; Wang, Ya-Qin; Wang, Feng; Shao, Qun; Zhang, Jun; Liu, Jin

    2013-05-01

    Despite the rapid development of nanomaterials and nanotechnology, it is still desirable to develop novel nanoparticle-based techniques which are cost-effective, timesaving, and environment-friendly, and with ease of operation and procedural simplicity, for assay of target analytes. In the work discussed in this paper, the dye fluorescein isothiocyanate (FITC) was conjugated to 1,6-hexanediamine (HDA)-capped iron oxide magnetic nanoparticles (FITC-HDA Fe3O4 MNPs), and the product was characterized. HDA ligands on the surface of Fe3O4 MNPs can bind 2,4,6-trinitrotoluene (TNT) to form TNT anions by acid-base pairing interaction. Formation of TNT anions, and captured TNT substantially affect the emission of FITC on the surface of the Fe3O4 MNPs, resulting in quenching of the fluorescence at 519 nm. A novel FITC-HDA Fe3O4 MNPs-based probe featuring chemosensing and magnetic separation has therefore been constructed. i.e. FITC-HDA Fe3O4 MNPs had a highly selective fluorescence response and enabled magnetic separation of TNT from other nitroaromatic compounds by quenching of the emission of FITC and capture of TNT in aqueous solution. Very good linearity was observed for TNT concentrations in the range 0.05-1.5 μmol L(-1), with a detection limit of 37.2 nmol L(-1) and RSD of 4.7 % (n = 7). Approximately 12 % of the total amount of TNT was captured. The proposed methods are well-suited to trace detection and capture of TNT in aqueous solution.

  19. Magnetically Separable Fe3O4@DOPA-Pd: A Heterogeneous Catalyst for Aqueous Heck Reaction

    EPA Science Inventory

    Magnetically separable Fe3O4@DOPA-Pd catalyst has been synthesized via anchoring of palladium over dopamine-coated magnetite via non-covalent interaction and the catalyst is utilized for expeditious Heck coupling in aqueous media.

  20. ISOTOPE SEPARATORS

    DOEpatents

    Bacon, C.G.

    1958-08-26

    An improvement is presented in the structure of an isotope separation apparatus and, in particular, is concerned with a magnetically operated shutter associated with a window which is provided for the purpose of enabling the operator to view the processes going on within the interior of the apparatus. The shutier is mounted to close under the force of gravity in the absence of any other force. By closing an electrical circuit to a coil mouated on the shutter the magnetic field of the isotope separating apparatus coacts with the magnetic field of the coil to force the shutter to the open position.

  1. Enhanced Arctic Mean Sea Surface and Mean Dynamic Topography including retracked CryoSat-2 Data

    NASA Astrophysics Data System (ADS)

    Andersen, O. B.; Jain, M.; Stenseng, L.; Knudsen, P.

    2014-12-01

    A reliable mean sea surface (MSS) is essential to derive a good mean dynamic topography (MDT) and for the estimation of short and long-term changes in the sea surface. The lack of satellite radar altimetry observations above 82 degrees latitude means that existing mean sea surface models have been unreliable in the Arctic Ocean. We here present the latest DTU mean sea surface and mean dynamic topography models combining conventional altimetry with retracked CryoSat-2 data to improve the reliability in the Arctic Ocean. For the derivation of a mean dynamic topography the ESA GOCE derived geoid model have been used to constrain the longer wavelength. We present the retracking of C2 SAR data using various retrackes and how we have been able to combine data from various retrackers under various sea ice conditions. DTU13MSS and DTU13MDT are the newest state of the art global high-resolution models including CryoSat-2 data to extend the satellite radar altimetry coverage up to 88 degrees latitude and through combination with a GOCE geoid model completes coverage all the way to the North Pole. Furthermore the SAR and SARin capability of CryoSat-2 dramatically increases the amount of useable sea surface returns in sea-ice covered areas compared to conventional radar altimeters like ENVISAT and ERS-1/2. With the inclusion of CryoSat-2 data the new mean sea surface is improved by more than 20 cm above 82 degrees latitude compared with the previous generation of mean sea surfaces.

  2. A Fast and Effective Microfluidic Spraying-Plunging Method for High-Resolution Single-Particle Cryo-EM.

    PubMed

    Feng, Xiangsong; Fu, Ziao; Kaledhonkar, Sandip; Jia, Yuan; Shah, Binita; Jin, Amy; Liu, Zheng; Sun, Ming; Chen, Bo; Grassucci, Robert A; Ren, Yukun; Jiang, Hongyuan; Frank, Joachim; Lin, Qiao

    2017-04-04

    We describe a spraying-plunging method for preparing cryoelectron microscopy (cryo-EM) grids with vitreous ice of controllable, highly consistent thickness using a microfluidic device. The new polydimethylsiloxane (PDMS)-based sprayer was tested with apoferritin. We demonstrate that the structure can be solved to high resolution with this method of sample preparation. Besides replacing the conventional pipetting-blotting-plunging method, one of many potential applications of the new sprayer is in time-resolved cryo-EM, as part of a PDMS-based microfluidic reaction channel to study short-lived intermediates on the timescale of 10-1,000 ms. Published by Elsevier Ltd.

  3. Cryo-transmission electron tomography of native casein micelles from bovine milk

    PubMed Central

    Trejo, R.; Dokland, T.; Jurat-Fuentes, J.; Harte, F.

    2013-01-01

    Caseins are the principal protein components in milk and an important ingredient in the food industry. In liquid milk, caseins are found as micelles of casein proteins and colloidal calcium nanoclusters. Casein micelles were isolated from raw skim milk by size exclusion chromatography and suspended in milk protein-free serum produced by ultrafiltration (molecular weight cut-off of 3 kDa) of raw skim milk. The micelles were imaged by cryo-electron microscopy and subjected to tomographic reconstruction methods to visualize the 3-dimensional and internal organization of native casein micelles. This provided new insights into the internal architecture of the casein micelle that had not been apparent from prior cryo-transmission electron microscopy studies. This analysis demonstrated the presence of water-filled cavities (~20 to 30 nm in diameter), channels (diameter greater than ~5 nm), and several hundred high-density nanoclusters (6 to 12 nm in diameter) within the interior of the micelles. No spherical protein submicellar structures were observed. PMID:22118067

  4. Building the atomic model of a boreal lake virus of unknown fold in a 3.9 Å cryo-EM map.

    PubMed

    De Colibus, Luigi; Stuart, David I

    2018-04-01

    We report here the protocol adopted to build the atomic model of the newly discovered virus FLiP (Flavobacterium infecting, lipid-containing phage) into 3.9 Å cryo-electron microscopy (cryo-EM) maps. In particular, this report discusses the combination of density modification procedures, automatic model building and bioinformatics tools applied to guide the tracing of the major capsid protein (MCP) of this virus. The protocol outlined here may serve as a reference for future structural determination by cryo-EM of viruses lacking detectable structural homologues. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  5. Method and apparatus for separating gases based on electrically and magnetically enhanced monolithic carbon fiber composite sorbents

    DOEpatents

    Judkins, Roddie R.; Burchell, Timothy D.

    1999-01-01

    A method for separating gases or other fluids involves placing a magnetic field on a monolithic carbon fiber composite sorption material to more preferentially attract certain gases or other fluids to the sorption material to which a magnetic field is applied. This technique may be combined with the known "pressure swing adsorption" technique utilizing the same sorption material.

  6. Measurement of the magnetic interaction between two bound electrons of two separate ions.

    PubMed

    Kotler, Shlomi; Akerman, Nitzan; Navon, Nir; Glickman, Yinnon; Ozeri, Roee

    2014-06-19

    Electrons have an intrinsic, indivisible, magnetic dipole aligned with their internal angular momentum (spin). The magnetic interaction between two electronic spins can therefore impose a change in their orientation. Similar dipolar magnetic interactions exist between other spin systems and have been studied experimentally. Examples include the interaction between an electron and its nucleus and the interaction between several multi-electron spin complexes. The challenge in observing such interactions for two electrons is twofold. First, at the atomic scale, where the coupling is relatively large, it is often dominated by the much larger Coulomb exchange counterpart. Second, on scales that are substantially larger than the atomic, the magnetic coupling is very weak and can be well below the ambient magnetic noise. Here we report the measurement of the magnetic interaction between the two ground-state spin-1/2 valence electrons of two (88)Sr(+) ions, co-trapped in an electric Paul trap. We varied the ion separation, d, between 2.18 and 2.76 micrometres and measured the electrons' weak, millihertz-scale, magnetic interaction as a function of distance, in the presence of magnetic noise that was six orders of magnitude larger than the magnetic fields the electrons apply on each other. The cooperative spin dynamics was kept coherent for 15 seconds, during which spin entanglement was generated, as verified by a negative measured value of -0.16 for the swap entanglement witness. The sensitivity necessary for this measurement was provided by restricting the spin evolution to a decoherence-free subspace that is immune to collective magnetic field noise. Our measurements show a d(-3.0(4)) distance dependence for the coupling, consistent with the inverse-cube law.

  7. Synthesis of pH-sensitive and recyclable magnetic nanoparticles for efficient separation of emulsified oil from aqueous environments

    NASA Astrophysics Data System (ADS)

    Lü, Ting; Zhang, Shuang; Qi, Dongming; Zhang, Dong; Vance, George F.; Zhao, Hongting

    2017-02-01

    Emulsified oil wastewaters, arisen from oil industry and oil spill accidents, cause severe environmental and ecological problems. In this study, a series of pH-sensitive magnetic nanomaterials (MNPs) were synthesized and characterized for their evaluation in separation of emulsified oil from aqueous environments. A coprecipitation method was used to produce Fe3O4 magnetic nanoparticles that were coated in a 2-step process with first silica to form a surface for anchoring an (3-aminopropyl)triethoxysilane (APTES) molecular layer. Detailed studies were conducted on effects of MNPs dosage, APTES anchoring density (DA) and pH on oil-water separation performance of the synthetic MNPs. Results showed that, under both acidic and neutral conditions, MNPs with high DA exhibited enhanced oil-water separation performance, while under alkaline condition, the oil-water separation process was minimal. Alkaline conditions allowed the MNPs to be recycled up to 9 cycles without showing any significant decrease in oil-water separation efficiency. An examination of the oil-water separation mechanism found that electrostatic interaction and interfacial activity both played important roles in oil-water separation. In conclusion, pH-sensitive MNPs can be easily synthesized and recycled, providing a promising, cost-effective and environmentally-friendly process for the efficient treatment of emulsified oil wastewater.

  8. Micro-fabric damages in Boom Clay inferred from cryo-BIB-SEM experiment: recent results

    NASA Astrophysics Data System (ADS)

    Desbois, Guillaume; Schmatz, Joyce; Klaver, Jop; Urai, Janos L.

    2017-04-01

    The Boom Clay is considered as a potential host rock in Belgium for nuclear waste disposal in a deep geological formation. One of the keys to understand the long-term performance of such a host rock is the fundamental understanding of coupling between microstructural evolution, poromechanical behaviour and the state of hydration of the system. At in situ conditions, Boom Clay is a nearly water-saturated (>94%) clay-rich geomaterial. Subsequently, for measurement of mechanical and transport properties in laboratory, cores of Boom Clay are vacuum-packed in Al-coated-poly-ethylene barrier foil to be best preserved at original hydric state. Because clay microstructures are very sensitive to dehydration, the validity of investigations done on such preserved or/and dried samples is often questionable. Desbois et al. (2009, 2013, 2014) showed the possibility to image fluid-filled porosity in Boom Clay, by using the FIB-cryo-SEM (FIB: Focussed Ion Beam) and FIB-cryo-SEM (BIB: Broad Ion Beam) techniques. However, surprisingly in Desbois et al. (2014), BIB-cryo-SEM experiments on Boom Clay, shown that the majority of the pores were fluid-free, contrasting with result in Desbois et al. (2009). In Desbois et al. (2014), several reasons were discussed to explain such discrepancies. The likely ones are the sealing efficiency of the Al-barrier foil at long term and the volume expansion due to the release of in-situ stress after core extraction, contributing both to dehydration and microfabric damage. This contribution presents the newest results based on cryo-BIB-SEM. Small pieces (30 mm3) of Boom Clay were preserved in liquid nitrogen after the core extraction at the MOL/Dessel Underground Research Laboratory in Belgium. A maximum of ten minutes time span was achieved between opening the core, the sub-sample extraction and the quenching of sub-samples in liquid nitrogen. First results show that all pores visible at cryo-SEM resolution are water saturated. However, water

  9. Arctic and Antarctic sea-ice thickness from CryoSat and Envisat radar altimetry

    NASA Astrophysics Data System (ADS)

    Hendricks, S.; Rinne, E. J.; Paul, S.; Ricker, R.; Skourup, H.; Kern, S.; Sandven, S.

    2017-12-01

    One objective of the ESA Climate Change Initiative (CCI) on Sea Ice is the generation of a climate data record of sea-ice thickness from satellite radar altimetry in both hemispheres. We report on the results of the second phase of the CCI project, which are based on the15-year (2002-2017) monthly data record from Envisat and CryoSat-2 radar altimeter data. The data records needs to maintain consistency in the freeboard retrieval, freeboard to thickness conversion and uncertainty estimation for the full observational period. The main challenge has been to maintain consistency in the sea-ice freeboard retrieval due to the different radar altimeter concepts and footprints between Envisat and CryoSat-2. We have developed a novel empirical algorithm for both missions to minimize inter-mission biases for surface type classification as well as freeboard retrieval based on CryoSat reference data for the overlap period from November 2010 to March 2012. The parametrization takes differences between sea-ice surface properties in both hemisphere and the seasonal cycle into account. We report on the changes of sea-ice thickness in the Arctic winter seasons since 2002 and the comparison to independent freeboard and thickness observations. Far less validation data exists for the southern hemisphere and we provide an overview of changes and the expected skill of Antarctic sea ice thickness of the full seasonal cycle.

  10. Effective preparation of magnetic superhydrophobic Fe3O4/PU sponge for oil-water separation

    NASA Astrophysics Data System (ADS)

    Li, Zeng-Tian; Lin, Bo; Jiang, Li-Wang; Lin, En-Chao; Chen, Jian; Zhang, Shi-Jie; Tang, Yi-Wen; He, Fu-An; Li, De-Hao

    2018-01-01

    Fe3O4 nanoparticles were modified by tetraethoxysilane and different amounts of trimethoxy (1H,1H,2H,2H-heptadecafluorodecyl) silane in sequence to obtain the magnetic nanoparticles with low surface energy, which could be used to construct the superhydrophobic surfaces for PU sponge, cotton fabric, and filter paper by a simple drop-coating method. Particularly, all the resultant Fe3O4/PU sponges containing different fluoroalkylsilane-modified Fe3O4 nanoparticles possessed both high water repellency with contact angle in the range of 150.2-154.7° and good oil affinity, which could not only effectively remove oil from water followed by convenient magnetic recovery but also easily realize the oil-water separation as a filter only driven by gravity. The Fe3O4/PU sponges showed high absorption capability of peanut oil, pump oil, and silicone oil with the maximum absorptive capacities of 40.3, 39.3, and 46.3 g/g, respectively. Such novel sponges might be a potential candidate for oil-water separation as well as oil absorption and transportation accompanied by the advantages of simple process, remote control by magnetic field, and low energy consumption.

  11. CryoSat Plus for Oceans - analysis of the state-of-the-art

    NASA Astrophysics Data System (ADS)

    Naeije, Marc; Gommenginger, Christine; Moreau, Thomas; Cotton, David; Benveniste, Jerome; Dinardo Dinardo, Salvatore

    2013-04-01

    The CryoSat Plus for Oceans (CP4O) project is an ESA initiative carried out by a European wide consortium of altimetry experts. It aims to build a sound scientific basis for new scientific and operational applications of data coming from CryoSat-2 over the open ocean, polar ocean, coastal seas and for seafloor mapping. It also generates and evaluates new methods and products that will enable the full exploitation of the capabilities of the CryoSat-2 SIRAL altimeter, and extend their application beyond the initial mission objectives. It therefore also acts as a preparation for the upcoming Sentinel and Jason SAR enabled altimetry missions. In this paper we address the review of the CryoSat state-of-the-art, relevant current initiatives, algorithms, models and Earth Observation based products and datasets that are relevant in the Cryosat+ ocean theme. Compared to conventional (pulse-limited) altimeter missions, Cryosat-2 is not a dedicated platform for ocean research: typically the microwave radiometer (MWR) for wet tropospheric corrections is lacking, as is the direct measurement of the first order ionospheric effect by means of a dual-frequency altimeter. Also the orbit of Cryosat-2 has a rather long repetition period, unsuited for collinear tracks analyses. These three particular features have been studied already in the HERACLES project on the eve of the first CryoSat launch. We revisit the outcome of this study, update to current understanding and perception, and ultimately develop what was, is and will be proposed in these problem areas. Clearly, we question the standard ionosphere corrections, the wet troposphere corrections and the accuracy of the mean sea surface (MSS) underlying the accuracy of derived sea level anomalies. In addition, Cryosat-2 provides the first innovative altimeter with SAR and SARIn modes. This raises the direct problem of "how to process these data", simply because this has not been done before. Compared to pulse-limited altimetry it

  12. Magnetic design and field optimization of a superferric dipole for the RISP fragment separator

    NASA Astrophysics Data System (ADS)

    Zaghloul, A.; Kim, J. Y.; Kim, D. G.; Jo, H. C.; Kim, M. J.

    2015-10-01

    The in-flight fragment separator of the Rare Isotope Science Project requires eight dipole magnets to produce a gap field of 1.7 T in a deflection sector of 30 degree with a 6-m central radius. If the beam-optics requirements are to be met, an integral field homogeneity of a few units (1 unit = 10-4) must be achieved. A superferric dipole magnet has been designed by using the Low-Temperature Superconducting wire NbTi and soft iron of grade SAE1010. The 3D magnetic design and field optimization have been performed using the Opera code. The length and the width of the air slots in the poles have been determined in an optimization process that considered not only the uniformity of the field in the straight section but also the field errors in the end regions. The field uniformity has also been studied for a range of operation of the dipole magnet from 0.4 T to 1.7 T. The magnetic design and field uniformity are discussed.

  13. NASA IN-STEP Cryo System Experiment flight test

    NASA Astrophysics Data System (ADS)

    Russo, S. C.; Sugimura, R. S.

    The Cryo System Experiment (CSE), a NASA In-Space Technology Experiments Program (IN-STEP) flight experiment, was flown on Space Shuttle Discovery (STS 63) in February 1995. The experiment was developed by Hughes Aircraft Company to validate in zero- g space a 65 K cryogenic system for focal planes, optics, instruments or other equipment (gamma-ray spectrometers and infrared and submillimetre imaging instruments) that requires continuous cryogenic cooling. The CSE is funded by the NASA Office of Advanced Concepts and Technology's IN-STEP and managed by the Jet Propulsion Laboratory (JPL). The overall goal of the CSE was to validate and characterize the on-orbit performance of the two thermal management technologies that comprise a hybrid cryogenic system. These thermal management technologies consist of (1) a second-generation long-life, low-vibration, Stirling-cycle 65 K cryocooler that was used to cool a simulated thermal energy storage device (TRP) and (2) a diode oxygen heat pipe thermal switch that enables physical separation between a cryogenic refrigerator and a TRP. All CSE experiment objectives and 100% of the experiment success criteria were achieved. The level of confidence provided by this flight experiment is an important NASA and Department of Defense (DoD) milestone prior to multi-year mission commitment. Presented are generic lessons learned from the system integration of cryocoolers for a flight experiment and the recorded zero- g performance of the Stirling cryocooler and the diode oxygen heat pipe.

  14. The innovation of cryo-SEM freeze-fracturing methodology demonstrated on high pressure frozen biofilm.

    PubMed

    Hrubanova, Kamila; Nebesarova, Jana; Ruzicka, Filip; Krzyzanek, Vladislav

    2018-07-01

    In this study we present an innovative method for the preparation of fully hydrated samples of microbial biofilms of cultures Staphylococcus epidermidis, Candida parapsilosis and Candida albicans. Cryo-scanning electron microscopy (cryo-SEM) and high-pressure freezing (HPF) rank among cutting edge techniques in the electron microscopy of hydrated samples such as biofilms. However, the combination of these techniques is not always easily applicable. Therefore, we present a method of combining high-pressure freezing using EM PACT2 (Leica Microsystems), which fixes hydrated samples on small sapphire discs, with a high resolution SEM equipped with the widely used cryo-preparation system ALTO 2500 (Gatan). Using a holder developed in house, a freeze-fracturing technique was applied to image and investigate microbial cultures cultivated on the sapphire discs. In our experiments, we focused on the ultrastructure of the extracellular matrix produced during cultivation and the relationships among microbial cells in the biofilm. The main goal of our investigations was the detailed visualization of areas of the biofilm where the microbial cells adhere to the substrate/surface. We show the feasibility of this technique, which is clearly demonstrated in experiments with various freeze-etching times. Copyright © 2018 Elsevier Ltd. All rights reserved.

  15. States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM.

    PubMed

    Serwer, Philip; Wright, Elena T; Demeler, Borries; Jiang, Wen

    2018-04-01

    Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.

  16. Method and apparatus for separating gases based on electrically and magnetically enhanced monolithic carbon fiber composite sorbents

    DOEpatents

    Judkins, R.R.; Burchell, T.D.

    1999-07-20

    A method for separating gases or other fluids involves placing a magnetic field on a monolithic carbon fiber composite sorption material to more preferentially attract certain gases or other fluids to the sorption material to which a magnetic field is applied. This technique may be combined with the known pressure swing adsorption'' technique utilizing the same sorption material. 1 fig.

  17. Estimation of Arctic Sea Ice Freeboard and Thickness Using CryoSat-2

    NASA Astrophysics Data System (ADS)

    Lee, S.; Im, J.; Kim, J. W.; Kim, M.; Shin, M.

    2014-12-01

    Arctic sea ice is one of the significant components of the global climate system as it plays a significant role in driving global ocean circulation. Sea ice extent has constantly declined since 1980s. Arctic sea ice thickness has also been diminishing along with the decreasing sea ice extent. Because extent and thickness, two main characteristics of sea ice, are important indicators of the polar response to on-going climate change. Sea ice thickness has been measured with numerous field techniques such as surface drilling and deploying buoys. These techniques provide sparse and discontinuous data in spatiotemporal domain. Spaceborne radar and laser altimeters can overcome these limitations and have been used to estimate sea ice thickness. Ice Cloud and land Elevation Satellite (ICEsat), a laser altimeter provided data to detect polar area elevation change between 2003 and 2009. CryoSat-2 launched with Synthetic Aperture Radar (SAR)/Interferometric Radar Altimeter (SIRAL) in April 2010 can provide data to estimate time-series of Arctic sea ice thickness. In this study, Arctic sea ice freeboard and thickness between 2011 and 2014 were estimated using CryoSat-2 SAR and SARIn mode data that have sea ice surface height relative to the reference ellipsoid WGS84. In order to estimate sea ice thickness, freeboard, i.e., elevation difference between the top of sea ice surface should be calculated. Freeboard can be estimated through detecting leads. We proposed a novel lead detection approach. CryoSat-2 profiles such as pulse peakiness, backscatter sigma-0, stack standard deviation, skewness and kurtosis were examined to distinguish leads from sea ice. Near-real time cloud-free MODIS images corresponding to CryoSat-2 data measured were used to visually identify leads. Rule-based machine learning approaches such as See5.0 and random forest were used to identify leads. The proposed lead detection approach better distinguished leads from sea ice than the existing approaches

  18. Separation of superparamagnetic particles through ratcheted Brownian motion and periodically switching magnetic fields.

    PubMed

    Liu, Fan; Jiang, Li; Tan, Huei Ming; Yadav, Ashutosh; Biswas, Preetika; van der Maarel, Johan R C; Nijhuis, Christian A; van Kan, Jeroen A

    2016-11-01

    Brownian ratchet based particle separation systems for application in lab on chip devices have drawn interest and are subject to ongoing theoretical and experimental investigations. We demonstrate a compact microfluidic particle separation chip, which implements an extended on-off Brownian ratchet scheme that actively separates and sorts particles using periodically switching magnetic fields, asymmetric sawtooth channel sidewalls, and Brownian motion. The microfluidic chip was made with Polydimethylsiloxane (PDMS) soft lithography of SU-8 molds, which in turn was fabricated using Proton Beam Writing. After bonding of the PDMS chip to a glass substrate through surface activation by oxygen plasma treatment, embedded electromagnets were cofabricated by the injection of InSn metal into electrode channels. This fabrication process enables rapid production of high resolution and high aspect ratio features, which results in parallel electrodes accurately aligned with respect to the separation channel. The PDMS devices were tested with mixtures of 1.51  μ m, 2.47  μ m, and 2.60  μ m superparamagnetic particles suspended in water. Experimental results show that the current device design has potential for separating particles with a size difference around 130 nm. Based on the promising results, we will be working towards extending this design for the separation of cells or biomolecules.

  19. Separation of superparamagnetic particles through ratcheted Brownian motion and periodically switching magnetic fields

    PubMed Central

    Liu, Fan; Jiang, Li; Tan, Huei Ming; Yadav, Ashutosh; Biswas, Preetika; van der Maarel, Johan R. C.; Nijhuis, Christian A.; van Kan, Jeroen A.

    2016-01-01

    Brownian ratchet based particle separation systems for application in lab on chip devices have drawn interest and are subject to ongoing theoretical and experimental investigations. We demonstrate a compact microfluidic particle separation chip, which implements an extended on-off Brownian ratchet scheme that actively separates and sorts particles using periodically switching magnetic fields, asymmetric sawtooth channel sidewalls, and Brownian motion. The microfluidic chip was made with Polydimethylsiloxane (PDMS) soft lithography of SU-8 molds, which in turn was fabricated using Proton Beam Writing. After bonding of the PDMS chip to a glass substrate through surface activation by oxygen plasma treatment, embedded electromagnets were cofabricated by the injection of InSn metal into electrode channels. This fabrication process enables rapid production of high resolution and high aspect ratio features, which results in parallel electrodes accurately aligned with respect to the separation channel. The PDMS devices were tested with mixtures of 1.51 μm, 2.47 μm, and 2.60 μm superparamagnetic particles suspended in water. Experimental results show that the current device design has potential for separating particles with a size difference around 130 nm. Based on the promising results, we will be working towards extending this design for the separation of cells or biomolecules. PMID:27917252

  20. Ion mass separation modeling inside a plasma separator

    NASA Astrophysics Data System (ADS)

    Gavrikov, A. V.; Sidorov, V. S.; Smirnov, V. P.; Tarakanov, V. P.

    2018-01-01

    The results have been obtained in a continuation of the work for ion trajectories calculation in crossed electric and magnetic fields and also in a close alignment with the plasma separation study development. The main task was to calculate trajectories of ions of the substance imitating spent nuclear fuel in order to find a feasible plasma separator configuration. The three-dimensional modeling has been made with KARAT code in a single-particle approximation. The calculations have been performed under the following conditions. Magnetic field is produced by 2 coils of wire, the characteristic field strength in a uniform area is 1.4 kG. Electric field is produced by several electrodes (axial ones, anode shell and capacitor sheets) with electric potential up to 500 V. The characteristic linear size of the cylindrical separator area is ∼ 100 cm. The characteristic size of injection region is ∼ 1 cm. Spatial position of the injection region is inside the separator. The injection direction is along magnetic lines. Injected particles are single-charged ions with energies from 0 to 20 eV with atomic masses A = 150 and 240. Wide spreading angle range was investigated. As a result of simulation a feasible separator configuration was found. This configuration allows to achieve more than 10 cm spatial division distance for the separated ions and is fully compliant with and supplementary to the vacuum arc-based ion source research.

  1. Magnetic biochar combining adsorption and separation recycle for removal of chromium in aqueous solution.

    PubMed

    Xin, Ouyang; Yitong, Han; Xi, Cao; Jiawei, Chen

    2017-03-01

    Biochar has been developed in recent years for the removal of contaminants such as Cr (VI) in water. The enhancement of the adsorption capacity of biochar and its recyclable use are still challenges. In this study, magnetic biochar derived from corncobs and peanut hulls was synthesized under different pyrolysis temperatures after pretreating the biomass with a low concentration of 0.5 M FeCl 3 solution. The morphology, specific surface area, saturation magnetization and Fourier transform infrared spectroscopy (FT-IR) spectra were characterized for biochar. The magnetic biochar performed well in combining adsorption and separation recycle for the removal of Cr (VI) in water. The Cr (VI) adsorbance of the biochar was increased with the increase in pyrolysis temperature, and the magnetic biochar derived from corncobs showed better performance for both magnetization and removal of Cr (VI) than that from peanut hulls. The Langmuir model was used for the isothermal adsorption and the maximum Cr (VI) adsorption capacity of corncob magnetic biochar pyrolyzed at 650 °C reached 61.97 mg/g. An alkaline solution (0.1 M NaOH) favored the desorption of Cr (VI) from the magnetic biochar, and the removal of Cr (VI) still remained around 77.6% after four cycles of adsorption-desorption. The results showed that corncob derived magnetic biochar is a potentially efficient and recoverable adsorbent for remediation of heavy metals in water.

  2. Delivery of femtolitre droplets using surface acoustic wave based atomisation for cryo-EM grid preparation.

    PubMed

    Ashtiani, Dariush; Venugopal, Hari; Belousoff, Matthew; Spicer, Bradley; Mak, Johnson; Neild, Adrian; de Marco, Alex

    2018-04-06

    Cryo-Electron Microscopy (cryo-EM) has become an invaluable tool for structural biology. Over the past decade, the advent of direct electron detectors and automated data acquisition has established cryo-EM as a central method in structural biology. However, challenges remain in the reliable and efficient preparation of samples in a manner which is compatible with high time resolution. The delivery of sample onto the grid is recognized as a critical step in the workflow as it is a source of variability and loss of material due to the blotting which is usually required. Here, we present a method for sample delivery and plunge freezing based on the use of Surface Acoustic Waves to deploy 6-8 µm droplets to the EM grid. This method minimises the sample dead volume and ensures vitrification within 52.6 ms from the moment the sample leaves the microfluidics chip. We demonstrate a working protocol to minimize the atomised volume and apply it to plunge freeze three different samples and provide proof that no damage occurs due to the interaction between the sample and the acoustic waves. Copyright © 2018 Elsevier Inc. All rights reserved.

  3. Effect of fringe-artifact correction on sub-tomogram averaging from Zernike phase-plate cryo-TEM

    PubMed Central

    Kishchenko, Gregory P.; Danev, Radostin; Fisher, Rebecca; He, Jie; Hsieh, Chyongere; Marko, Michael; Sui, Haixin

    2015-01-01

    Zernike phase-plate (ZPP) imaging greatly increases contrast in cryo-electron microscopy, however fringe artifacts appear in the images. A computational de-fringing method has been proposed, but it has not been widely employed, perhaps because the importance of de-fringing has not been clearly demonstrated. For testing purposes, we employed Zernike phase-plate imaging in a cryo-electron tomographic study of radial-spoke complexes attached to microtubule doublets. We found that the contrast enhancement by ZPP imaging made nonlinear denoising insensitive to the filtering parameters, such that simple low-frequency band-pass filtering made the same improvement in map quality. We employed sub-tomogram averaging, which compensates for the effect of the “missing wedge” and considerably improves map quality. We found that fringes (caused by the abrupt cut-on of the central hole in the phase plate) can lead to incorrect representation of a structure that is well-known from the literature. The expected structure was restored by amplitude scaling, as proposed in the literature. Our results show that de-fringing is an important part of image-processing for cryo-electron tomography of macromolecular complexes with ZPP imaging. PMID:26210582

  4. Comparison of CryoSat-2 and ENVISAT radar freeboard over Arctic sea ice: toward an improved Envisat freeboard retrieval

    NASA Astrophysics Data System (ADS)

    Guerreiro, Kevin; Fleury, Sara; Zakharova, Elena; Kouraev, Alexei; Rémy, Frédérique; Maisongrande, Philippe

    2017-09-01

    Over the past decade, sea-ice freeboard has been monitored with various satellite altimetric missions with the aim of producing long-term time series of ice thickness. While recent studies have demonstrated the capacity of the CryoSat-2 mission (2010-present) to provide accurate freeboard measurements, the current estimates obtained with the Envisat mission (2002-2012) still require some large improvements. In this study, we first estimate Envisat and CryoSat-2 radar freeboard by using the exact same processing algorithms. We then analyse the freeboard difference between the two estimates over the common winter periods (November 2010-April 2011 and November 2011-March 2012). The analysis of along-track data and gridded radar freeboard in conjunction with Envisat pulse-peakiness (PP) maps suggests that the discrepancy between the two sensors is related to the surface properties of sea-ice floes and to the use of a threshold retracker. Based on the relation between the Envisat pulse peakiness and the radar freeboard difference between Envisat and CryoSat-2, we produce a monthly CryoSat-2-like version of Envisat freeboard. The improved Envisat data set freeboard displays a similar spatial distribution to CryoSat-2 (RMSD = 1.5 cm) during the two ice growth seasons and for all months of the period of study. The comparison of the altimetric data sets with in situ ice draught measurements during the common flight period shows that the improved Envisat data set (RMSE = 12-28 cm) is as accurate as CryoSat-2 (RMSE = 15-21 cm) and much more accurate than the uncorrected Envisat data set (RMSE = 178-179 cm). The comparison of the improved Envisat radar freeboard data set is then extended to the rest of the Envisat mission to demonstrate the validity of PP correction from the calibration period. The good agreement between the improved Envisat data set and the in situ ice draught data set (RMSE = 13-32 cm) demonstrates the potential of the PP correction to produce accurate

  5. Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study.

    PubMed

    Huang, Rui; Ripstein, Zev A; Augustyniak, Rafal; Lazniewski, Michal; Ginalski, Krzysztof; Kay, Lewis E; Rubinstein, John L

    2016-07-19

    The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded.

  6. The separated electric and magnetic field responses of luminescent bacteria exposed to pulsed microwave irradiation

    NASA Astrophysics Data System (ADS)

    Williams, Catrin F.; Geroni, Gilles M.; Pirog, Antoine; Lloyd, David; Lees, Jonathan; Porch, Adrian

    2016-08-01

    Electromagnetic fields (EMFs) are ubiquitous in the digital world we inhabit, with microwave and millimetre wave sources of non-ionizing radiation employed extensively in electronics and communications, e.g., in mobile phones and Wi-Fi. Indeed, the advent of 5G systems and the "internet of things" is likely to lead to massive densification of wireless networks. Whilst the thermal effects of EMFs on biological systems are well characterised, their putative non-thermal effects remain a controversial subject. Here, we use the bioluminescent marine bacterium, Vibrio fischeri, to monitor the effects of pulsed microwave electromagnetic fields, of nominal frequency 2.5 GHz, on light emission. Separated electric and magnetic field effects were investigated using a resonant microwave cavity, within which the maxima of each field are separated. For pulsed electric field exposure, the bacteria gave reproducible responses and recovery in light emission. At the lowest pulsed duty cycle (1.25%) and after short durations (100 ms) of exposure to the electric field at power levels of 4.5 W rms, we observed an initial stimulation of bioluminescence, whereas successive microwave pulses became inhibitory. Much of this behaviour is due to thermal effects, as the bacterial light output is very sensitive to the local temperature. Conversely, magnetic field exposure gave no measurable short-term responses even at the highest power levels of 32 W rms. Thus, we were able to detect, de-convolute, and evaluate independently the effects of separated electric and magnetic fields on exposure of a luminescent biological system to microwave irradiation.

  7. Cesium separation from contaminated milk using magnetic particles containing crystalline silicotitantes.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nunez, L.; Kaminski, M.; Chemical Engineering

    2000-11-01

    The Chernobyl nuclear reactor disaster in 1986 contaminated vast regions of prime grazing land. Subsequently, milk produced in the region has been contaminated with small amounts of the long-lived fission product cesium-137, and the Ukraine is seeking to deploy a simple separation process that will remove the Cs and preserve the nutritional value of the milk. Tiny magnetic particles containing crystalline silicotitanates (CST) have been manufactured and tested to this end. The results show that partitioning efficiency is optimized with low ratios of particle mass to volume. To achieve 90% Cs decontamination in a single-stage process, <3 g of magneticmore » CST per l milk is sufficient with a 30-min mixing time. A two-stage process would utilize <0.4 g/l per stage. The modeling of the magnetic CST system described herein can be achieved rather simply which is important for deployment in the affected Ukraine region.« less

  8. EMHP: an accurate automated hole masking algorithm for single-particle cryo-EM image processing.

    PubMed

    Berndsen, Zachary; Bowman, Charles; Jang, Haerin; Ward, Andrew B

    2017-12-01

    The Electron Microscopy Hole Punch (EMHP) is a streamlined suite of tools for quick assessment, sorting and hole masking of electron micrographs. With recent advances in single-particle electron cryo-microscopy (cryo-EM) data processing allowing for the rapid determination of protein structures using a smaller computational footprint, we saw the need for a fast and simple tool for data pre-processing that could run independent of existing high-performance computing (HPC) infrastructures. EMHP provides a data preprocessing platform in a small package that requires minimal python dependencies to function. https://www.bitbucket.org/chazbot/emhp Apache 2.0 License. bowman@scripps.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  9. Monolithic Microfluidic Mixing-Spraying Devices for Time-Resolved Cryo-Electron Microscopy

    PubMed Central

    Lu, Zonghuan; Shaikh, Tanvir R.; Barnard, David; Meng, Xing; Mohamed, Hisham; Yassin, Aymen; Mannella, Carmen A.; Agrawal, Rajendra K.; Lu, Toh-Ming

    2009-01-01

    The goal of time-resolved cryo-electron microscopy is to determine structural models for transient functional states of large macromolecular complexes such as ribosomes and viruses. The challenge of time-resolved cryo-electron microscopy is to rapidly mix reactants, and then, following a defined time interval, to rapidly deposit them as a thin film and freeze the sample to the vitreous state. Here we describe a methodology in which reaction components are mixed and allowed to react, and are then sprayed onto an EM grid as it is being plunged into cryogen. All steps are accomplished by a monolithic, microfabricated silicon device that incorporates a mixer, reaction channel, and pneumatic sprayer in a single chip. We have found that microdroplets produced by air atomization spread to sufficiently thin films on a millisecond time scale provided that the carbon supporting film is made suitably hydrophilic. The device incorporates two T-mixers flowing into a single channel of four butterfly-shaped mixing elements that ensure effective mixing, followed by a microfluidic reaction channel whose length can be varied to achieve the desired reaction time. The reaction channel is flanked by two ports connected to compressed humidified nitrogen gas (at 50 psi) to generate the spray. The monolithic mixer-sprayer is incorporated into a computer-controlled plunging apparatus. To test the mixing performance and the suitability of the device for preparation of biological macromolecules for cryo-EM, ribosomes and ferritin were mixed in the device and sprayed onto grids. Three-dimensional reconstructions of the ribosomes demonstrated retention of native structure, and 30S and 50S subunits were shown to be capable of reassociation into ribosomes after passage through the device. PMID:19683579

  10. Cryo-transmission electron tomography of native casein micelles from bovine milk.

    PubMed

    Trejo, R; Dokland, T; Jurat-Fuentes, J; Harte, F

    2011-12-01

    Caseins are the principal protein components in milk and an important ingredient in the food industry. In liquid milk, caseins are found as micelles of casein proteins and colloidal calcium nanoclusters. Casein micelles were isolated from raw skim milk by size exclusion chromatography and suspended in milk protein-free serum produced by ultrafiltration (molecular weight cut-off of 3 kDa) of raw skim milk. The micelles were imaged by cryo-electron microscopy and subjected to tomographic reconstruction methods to visualize the 3-dimensional and internal organization of native casein micelles. This provided new insights into the internal architecture of the casein micelle that had not been apparent from prior cryo-transmission electron microscopy studies. This analysis demonstrated the presence of water-filled cavities (∼20 to 30 nm in diameter), channels (diameter greater than ∼5 nm), and several hundred high-density nanoclusters (6 to 12 nm in diameter) within the interior of the micelles. No spherical protein submicellar structures were observed. Copyright © 2011 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  11. Cryo-EM structure of a herpesvirus capsid at 3.1 Å.

    PubMed

    Yuan, Shuai; Wang, Jialing; Zhu, Dongjie; Wang, Nan; Gao, Qiang; Chen, Wenyuan; Tang, Hao; Wang, Junzhi; Zhang, Xinzheng; Liu, Hongrong; Rao, Zihe; Wang, Xiangxi

    2018-04-06

    Structurally and genetically, human herpesviruses are among the largest and most complex of viruses. Using cryo-electron microscopy (cryo-EM) with an optimized image reconstruction strategy, we report the herpes simplex virus type 2 (HSV-2) capsid structure at 3.1 angstroms, which is built up of about 3000 proteins organized into three types of hexons (central, peripentonal, and edge), pentons, and triplexes. Both hexons and pentons contain the major capsid protein, VP5; hexons also contain a small capsid protein, VP26; and triplexes comprise VP23 and VP19C. Acting as core organizers, VP5 proteins form extensive intermolecular networks, involving multiple disulfide bonds (about 1500 in total) and noncovalent interactions, with VP26 proteins and triplexes that underpin capsid stability and assembly. Conformational adaptations of these proteins induced by their microenvironments lead to 46 different conformers that assemble into a massive quasisymmetric shell, exemplifying the structural and functional complexity of HSV. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  12. Magnetic separation - Advanced nanotechnology for future nuclear fuel recycle

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kaur, M.; Zhang, H.; Qiang, Y.

    2013-07-01

    The unique properties of magnetic nanoparticles (MNPs), such as their extremely small size and high surface area to volume ratio, provide better kinetics for the adsorption of metal ions from aqueous solutions. In this work, we demonstrated the separation of minor actinides using complex conjugates of MNPs with diethylenetriamine-pentaacetic acid (DTPA) chelator. The sorption results show the strong affinity of DTPA towards Am (III) and Pu (IV) by extracting 97% and 80% of actinides, respectively. It is shown that the extraction process is highly dependent on the pH of the solution. If these long-term heat generating actinides can be efficientlymore » removed from the used fuel raffinates, the volume of material that can be placed in a given amount of repository space can be significantly increased. (authors)« less

  13. Unmanned Aircraft Systems For CryoSat-2 Validation

    NASA Astrophysics Data System (ADS)

    Crocker, Roger Ian; Maslanik, James A.

    2011-02-01

    A suite of sensors has been assembled to map surface elevation with fine-resolution from small unmanned aircraft systems (UAS). The sensor package consists of a light detecting and ranging (LIDAR) instrument, an inertial measurement unit (IMU), a GPS module, and digital still and video cameras. It has been utilized to map ice sheet topography in Greenland and to measure sea ice freeboard and roughness in Fram Strait. Data collected during these campaigns illustrate its potential to compliment ongoing CryoSat-2 (CS-2) calibration and validation efforts.

  14. Large-scale HTS bulks for magnetic application

    NASA Astrophysics Data System (ADS)

    Werfel, Frank N.; Floegel-Delor, Uta; Riedel, Thomas; Goebel, Bernd; Rothfeld, Rolf; Schirrmeister, Peter; Wippich, Dieter

    2013-01-01

    ATZ Company has constructed about 130 HTS magnet systems using high-Tc bulk magnets. A key feature in scaling-up is the fabrication of YBCO melts textured multi-seeded large bulks with three to eight seeds. Except of levitation, magnetization, trapped field and hysteresis, we review system engineering parameters of HTS magnetic linear and rotational bearings like compactness, cryogenics, power density, efficiency and robust construction. We examine mobile compact YBCO bulk magnet platforms cooled with LN2 and Stirling cryo-cooler for demonstrator use. Compact cryostats for Maglev train operation contain 24 pieces of 3-seed bulks and can levitate 2500-3000 N at 10 mm above a permanent magnet (PM) track. The effective magnetic distance of the thermally insulated bulks is 2 mm only; the stored 2.5 l LN2 allows more than 24 h operation without refilling. 34 HTS Maglev vacuum cryostats are manufactured tested and operate in Germany, China and Brazil. The magnetic levitation load to weight ratio is more than 15, and by group assembling the HTS cryostats under vehicles up to 5 t total loads levitated above a magnetic track is achieved.

  15. Popcorn-shaped magnetic core-plasmonic shell multifunctional nanoparticles for the targeted magnetic separation and enrichment, label-free SERS imaging, and photothermal destruction of multidrug-resistant bacteria.

    PubMed

    Fan, Zhen; Senapati, Dulal; Khan, Sadia Afrin; Singh, Anant Kumar; Hamme, Ashton; Yust, Brian; Sardar, Dhiraj; Ray, Paresh Chandra

    2013-02-18

    Over the last few years, one of the most important and complex problems facing our society is treating infectious diseases caused by multidrug-resistant bacteria (MDRB), by using current market-existing antibiotics. Driven by this need, we report for the first time the development of the multifunctional popcorn-shaped iron magnetic core-gold plasmonic shell nanotechnology-driven approach for targeted magnetic separation and enrichment, label-free surface-enhanced Raman spectroscopy (SERS) detection, and the selective photothermal destruction of MDR Salmonella DT104. Due to the presence of the "lightning-rod effect", the core-shell popcorn-shaped gold-nanoparticle tips provided a huge field of SERS enhancement. The experimental data show that the M3038 antibody-conjugated nanoparticles can be used for targeted separation and SERS imaging of MDR Salmonella DT104. A targeted photothermal-lysis experiment, by using 670 nm light at 1.5 W cm(-2) for 10 min, results in selective and irreparable cellular-damage to MDR Salmonella. We discuss the possible mechanism and operating principle for the targeted separation, label-free SERS imaging, and photothermal destruction of MDRB by using the popcorn-shaped magnetic/plasmonic nanotechnology. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Do's and don'ts of cryo-electron microscopy: a primer on sample preparation and high quality data collection for macromolecular 3D reconstruction.

    PubMed

    Cabra, Vanessa; Samsó, Montserrat

    2015-01-09

    Cryo-electron microscopy (cryoEM) entails flash-freezing a thin layer of sample on a support, and then visualizing the sample in its frozen hydrated state by transmission electron microscopy (TEM). This can be achieved with very low quantity of protein and in the buffer of choice, without the use of any stain, which is very useful to determine structure-function correlations of macromolecules. When combined with single-particle image processing, the technique has found widespread usefulness for 3D structural determination of purified macromolecules. The protocol presented here explains how to perform cryoEM and examines the causes of most commonly encountered problems for rational troubleshooting; following all these steps should lead to acquisition of high quality cryoEM images. The technique requires access to the electron microscope instrument and to a vitrification device. Knowledge of the 3D reconstruction concepts and software is also needed for computerized image processing. Importantly, high quality results depend on finding the right purification conditions leading to a uniform population of structurally intact macromolecules. The ability of cryoEM to visualize macromolecules combined with the versatility of single particle image processing has proven very successful for structural determination of large proteins and macromolecular machines in their near-native state, identification of their multiple components by 3D difference mapping, and creation of pseudo-atomic structures by docking of x-ray structures. The relentless development of cryoEM instrumentation and image processing techniques for the last 30 years has resulted in the possibility to generate de novo 3D reconstructions at atomic resolution level.

  17. Fluorescent, Magnetic Multifunctional Carbon Dots for Selective Separation, Identification, and Eradication of Drug-Resistant Superbugs

    PubMed Central

    2017-01-01

    The emergence of drug-resistant superbugs remains a major burden to society. As the mortality rate caused by sepsis due to superbugs is more than 40%, accurate identification of blood infections during the early stage will have a huge significance in the clinical setting. Here, we report the synthesis of red/blue fluorescent carbon dot (CD)-attached magnetic nanoparticle-based multicolor multifunctional CD-based nanosystems, which can be used for selective separation and identification of superbugs from infected blood samples. The reported data show that multifunctional fluorescent magneto-CD nanoparticles are capable of isolating Methicillin-resistant Staphylococcus aureus (MRSA) and Salmonella DT104 superbug from whole blood samples, followed by accurate identification via multicolor fluorescence imaging. As multidrug-resistant (MDR) superbugs are resistant to antibiotics available in the market, this article also reports the design of antimicrobial peptide-conjugated multicolor fluorescent magneto-CDs for effective separation, accurate identification, and complete disinfection of MDR superbugs from infected blood. The reported data demonstrate that by combining pardaxin antimicrobial peptides, magnetic nanoparticles, and multicolor fluorescent CDs into a single system, multifunctional CDs represent a novel material for efficient separation, differentiation, and eradication of superbugs. This material shows great promise for use in clinical settings. PMID:28261690

  18. Fluorescent, Magnetic Multifunctional Carbon Dots for Selective Separation, Identification, and Eradication of Drug-Resistant Superbugs.

    PubMed

    Pramanik, Avijit; Jones, Stacy; Pedraza, Francisco; Vangara, Aruna; Sweet, Carrie; Williams, Mariah S; Ruppa-Kasani, Vikram; Risher, Sean Edward; Sardar, Dhiraj; Ray, Paresh Chandra

    2017-02-28

    The emergence of drug-resistant superbugs remains a major burden to society. As the mortality rate caused by sepsis due to superbugs is more than 40%, accurate identification of blood infections during the early stage will have a huge significance in the clinical setting. Here, we report the synthesis of red/blue fluorescent carbon dot (CD)-attached magnetic nanoparticle-based multicolor multifunctional CD-based nanosystems, which can be used for selective separation and identification of superbugs from infected blood samples. The reported data show that multifunctional fluorescent magneto-CD nanoparticles are capable of isolating Methicillin-resistant Staphylococcus aureus (MRSA) and Salmonella DT104 superbug from whole blood samples, followed by accurate identification via multicolor fluorescence imaging. As multidrug-resistant (MDR) superbugs are resistant to antibiotics available in the market, this article also reports the design of antimicrobial peptide-conjugated multicolor fluorescent magneto-CDs for effective separation, accurate identification, and complete disinfection of MDR superbugs from infected blood. The reported data demonstrate that by combining pardaxin antimicrobial peptides, magnetic nanoparticles, and multicolor fluorescent CDs into a single system, multifunctional CDs represent a novel material for efficient separation, differentiation, and eradication of superbugs. This material shows great promise for use in clinical settings.

  19. Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate.

    PubMed

    Karuppasamy, Manikandan; Karimi Nejadasl, Fatemeh; Vulovic, Milos; Koster, Abraham J; Ravelli, Raimond B G

    2011-05-01

    Radiation damage is an important resolution limiting factor both in macromolecular X-ray crystallography and cryo-electron microscopy. Systematic studies in macromolecular X-ray crystallography greatly benefited from the use of dose, expressed as energy deposited per mass unit, which is derived from parameters including incident flux, beam energy, beam size, sample composition and sample size. In here, the use of dose is reintroduced for electron microscopy, accounting for the electron energy, incident flux and measured sample thickness and composition. Knowledge of the amount of energy deposited allowed us to compare doses with experimental limits in macromolecular X-ray crystallography, to obtain an upper estimate of radical concentrations that build up in the vitreous sample, and to translate heat-transfer simulations carried out for macromolecular X-ray crystallography to cryo-electron microscopy. Stroboscopic exposure series of 50-250 images were collected for different incident flux densities and integration times from Lumbricus terrestris extracellular hemoglobin. The images within each series were computationally aligned and analyzed with similarity metrics such as Fourier ring correlation, Fourier ring phase residual and figure of merit. Prior to gas bubble formation, the images become linearly brighter with dose, at a rate of approximately 0.1% per 10 MGy. The gradual decomposition of a vitrified hemoglobin sample could be visualized at a series of doses up to 5500 MGy, by which dose the sample was sublimed. Comparison of equal-dose series collected with different incident flux densities showed a dose-rate effect favoring lower flux densities. Heat simulations predict that sample heating will only become an issue for very large dose rates (50 e(-)Å(-2) s(-1) or higher) combined with poor thermal contact between the grid and cryo-holder. Secondary radiolytic effects are likely to play a role in dose-rate effects. Stroboscopic data collection combined with

  20. Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate

    PubMed Central

    Karuppasamy, Manikandan; Karimi Nejadasl, Fatemeh; Vulovic, Milos; Koster, Abraham J.; Ravelli, Raimond B. G.

    2011-01-01

    Radiation damage is an important resolution limiting factor both in macromolecular X-ray crystallography and cryo-electron microscopy. Systematic studies in macromolecular X-ray crystallography greatly benefited from the use of dose, expressed as energy deposited per mass unit, which is derived from parameters including incident flux, beam energy, beam size, sample composition and sample size. In here, the use of dose is reintroduced for electron microscopy, accounting for the electron energy, incident flux and measured sample thickness and composition. Knowledge of the amount of energy deposited allowed us to compare doses with experimental limits in macromolecular X-ray crystallography, to obtain an upper estimate of radical concentrations that build up in the vitreous sample, and to translate heat-transfer simulations carried out for macromolecular X-ray crystallography to cryo-electron microscopy. Stroboscopic exposure series of 50–250 images were collected for different incident flux densities and integration times from Lumbricus terrestris extracellular hemoglobin. The images within each series were computationally aligned and analyzed with similarity metrics such as Fourier ring correlation, Fourier ring phase residual and figure of merit. Prior to gas bubble formation, the images become linearly brighter with dose, at a rate of approximately 0.1% per 10 MGy. The gradual decomposition of a vitrified hemoglobin sample could be visualized at a series of doses up to 5500 MGy, by which dose the sample was sublimed. Comparison of equal-dose series collected with different incident flux densities showed a dose-rate effect favoring lower flux densities. Heat simulations predict that sample heating will only become an issue for very large dose rates (50 e−Å−2 s−1 or higher) combined with poor thermal contact between the grid and cryo-holder. Secondary radiolytic effects are likely to play a role in dose-rate effects. Stroboscopic data collection

  1. Arctic and Antarctic Sea-Ice Freeboard and Thickness Retrievals from CryoSat-2 and EnviSat

    NASA Astrophysics Data System (ADS)

    Ricker, Robert; Hendricks, Stefan; Schwegmann, Sandra; Helm, Veit; Rinne, Eero

    2016-04-01

    The CryoSat-2 satellite is now in the 6th year of data acquisition. With its synthetic aperture radar altimeter, CryoSat-2 achieves great improvements in the along track resolution compared to previous radar altimeter missions like ERS or Envisat. The latitudinal coverage contains major parts of the Arctic marine ice fields where previous missions left a big data gap around the North Pole and especially over the multiyear ice zone north of Greenland. With this unique data set, changes in sea-ice thickness can be investigated in the context of the rapid reduction of the Arctic sea-ice cover which has been observed during the last decades. We present the current state of the CryoSat-2 Arctic sea-ice thickness retrieval that is processed at the Alfred Wegener Institute and available via seaiceportal.de (originally: meereisportal.de). Though biases in sea-ice thickness may occur due to the interpretation of waveforms, airborne and ground-based validation measurements give confidence that the retrieval algorithm enables us to capture the actual distributions of sea-ice regimes. Nevertheless, long time series of data retrievals are essential to estimate trends in sea-ice thickness and volume. Today, more than 20 years of radar altimeter data are potentially available and capable to derive sea ice thickness. However, data originate from satellites with different sensor characteristics. Therefore, it is crucial to study the consistency between single sensors to derive long and consistent time series. We present results from the tested consistency between Antarctic freeboard measurements of the radar altimeters on-board of Envisat and CryoSat-2 for their overlap period in 2011.

  2. Adsorption mechanism of magnetically separable Fe3O4/graphene oxide hybrids

    NASA Astrophysics Data System (ADS)

    Ouyang, Ke; Zhu, Chuanhe; Zhao, Ya; Wang, Leichao; Xie, Shan; Wang, Qun

    2015-11-01

    A reclaimable Fe3O4/graphene oxide (GO) magnetic hybrid was successfully synthesized via a facile one-pot polyol approach and employed as a recyclable adsorbent for Bisphenol A (BPA) in aqueous solutions. The maximum adsorption capacity (qm) of the Fe3O4/GO hybrid for BPA was 72.80 mg/g at 273 K. The kinetics of the adsorption process and the adsorption isotherm data were fitted using the Freundlich equation and a pseudo-second-order kinetic model. The results of the thermodynamic parameters ΔH°, ΔS° and ΔG° showed that the adsorption process was exothermic and spontaneous. Furthermore, the reusability of the samples was investigated, and the results indicated that the samples exhibited high stability. The magnetic characterization demonstrated that hybrids were superparamagnetic and could be recovered conveniently by magnetic separation. The strong π-π interaction was determined to be the predominant driving force behind the adsorption of BPA onto the Fe3O4/GO hybrid. Therefore, the Fe3O4/GO hybrid could be regarded as a potential adsorbent for wastewater treatment and purification processes.

  3. Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study

    PubMed Central

    Huang, Rui; Ripstein, Zev A.; Augustyniak, Rafal; Lazniewski, Michal; Ginalski, Krzysztof; Kay, Lewis E.; Rubinstein, John L.

    2016-01-01

    The AAA+ (ATPases associated with a variety of cellular activities) enzymes play critical roles in a variety of homeostatic processes in all kingdoms of life. Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), the archaeal homolog of the ubiquitous AAA+ protein Cdc48/p97, functions in concert with the 20S proteasome by unfolding substrates and passing them on for degradation. Here, we present electron cryomicroscopy (cryo-EM) maps showing that VAT undergoes large conformational rearrangements during its ATP hydrolysis cycle that differ dramatically from the conformational states observed for Cdc48/p97. We validate key features of the model with biochemical and solution methyl-transverse relaxation optimized spectroscopY (TROSY) NMR experiments and suggest a mechanism for coupling the energy of nucleotide hydrolysis to substrate unfolding. These findings illustrate the unique complementarity between cryo-EM and solution NMR for studies of molecular machines, showing that the structural properties of VAT, as well as the population distributions of conformers, are similar in the frozen specimens used for cryo-EM and in the solution phase where NMR spectra are recorded. PMID:27402735

  4. Allosteric effects in bacteriophage HK97 procapsids revealed directly from covariance analysis of cryo EM data.

    PubMed

    Xu, Nan; Veesler, David; Doerschuk, Peter C; Johnson, John E

    2018-05-01

    The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways. First, instead of imposing icosahedral symmetry on every particle in the data set during the variance analysis, we only assume that the data set as a whole has icosahedral symmetry. This change removes artifacts of high variance along icosahedral symmetry axes, but retains all of the features previously reported in the HK97 data set. Second we present a covariance analysis that reveals correlations in structural dynamics (variance) between the interior of the HK97 procapsid with the protease and regions of the exterior (not seen in the absence of the protease). The latter analysis corresponds well with hydrogen deuterium exchange studies previously published that reveal the same correlation. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Separation of variables in anisotropic models: anisotropic Rabi and elliptic Gaudin model in an external magnetic field

    NASA Astrophysics Data System (ADS)

    Skrypnyk, T.

    2017-08-01

    We study the problem of separation of variables for classical integrable Hamiltonian systems governed by non-skew-symmetric non-dynamical so(3)\\otimes so(3) -valued elliptic r-matrices with spectral parameters. We consider several examples of such models, and perform separation of variables for classical anisotropic one- and two-spin Gaudin-type models in an external magnetic field, and for Jaynes-Cummings-Dicke-type models without the rotating wave approximation.

  6. A Review Of CryoSat-2/SIRAL Applications For The Monitoring Of River Water Levels

    NASA Astrophysics Data System (ADS)

    Bercher, Nicolas; Dinardo, Salvatore; Lucas, Bruno Manuel; Fleury, Sara; Calmant, Stephane; Femenias, Pierre; Boy, Francois; Picot, Nicolas; Benveniste, Jerome

    2013-12-01

    Regarding hydrology applications and particularly the monitoring of river water levels from space, the CryoSat- 2 ice mission has two main valuable characteristics: (1) its geodetic orbit and (2) the altimeter's SAR and SARin modes. The benefits of the geodetic orbit of the satellite have been illustrated in the frame of the ”20 years of progress in radar altimetry” symposium (Venice, 2012) [2]. It has been shown that, with such an orbit, the way river water level was monitored using conventional altimeters had to be revisited. In particular, using LRM mode only, CryoSat-2 allowed us to build spatio-temporal time series of the river water level, to map river's topography and eventually derive pseudo-time series and pseudo-profiles of the river. This paper focuses on the new ways to use altimetry for the monitoring of river water levels. SIRAL's (CryoSat-2 altimeter) SAR and SARin modes have the ability to deliver surface heights with an unprecedented along-track resolution of about 300 m. Moreover, using the SARin mode (involving the satellite's two antennas), the cross- track angle of the retracked echo is also available in routine. These two aspects of the SARin mode (high resolution and cross-track angle) make it a new tool to distinguish whether the retracked echo came from the sur- face of interest (e.g., a river) or any other reflective object nearby the surface of interest (e.g., another river section, lakes or temporary lake after flooding events or any other specular surfaces). We introduce the multiple benefits of using the intermediate multi-look matrix (also known as stack matrix), among them: (1) to refine and select among the multiple Doppler-beam waveforms before averaging and retracking them, and (2) to be able to study the surfaces response according to their view angle. Custom products processed at ESA (ESRIN) by Dinardo et al. [7], in the perspective of Sentinel-3, as well as official CryoSat-2 L1b and L2 products were used to illustrate

  7. Electron Tomography of Cryo-Immobilized Plant Tissue: A Novel Approach to Studying 3D Macromolecular Architecture of Mature Plant Cell Walls In Situ

    PubMed Central

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G.; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H.; Auer, Manfred

    2014-01-01

    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the

  8. Graphene supported silver@silver chloride & ferroferric oxide hybrid, a magnetically separable photocatalyst with high performance under visible light irradiation

    NASA Astrophysics Data System (ADS)

    Zhong, Suting; Jiang, Wei; Han, Mei; Liu, Gongzong; Zhang, Na; Lu, Yue

    2015-08-01

    A stable magnetic separable plasmonic photocatalyst was successfully fabricated by grafting silver@silver chloride (Ag@AgCl) and ferroferric oxide (Fe3O4) nanoparticles on graphene sheets. The composite exhibited high activity degrading methylene blue (MB) and rhodamine B (RB) under visible light irradiation: decomposition 97.4% of MB in 100 min and 97.9% of RB in 120 min. The enhanced photocatalytic activities can be attributed to synergistic effect between Ag@AgCl and graphene: the effective charge transfer from Ag@AgCl to graphene thus promotes the separation of electron-hole pairs. Moreover, the excellent magnetic property gives a more convenient way to recycle the photocatalysts.

  9. Nitride Fuel Development Using Cryo-process Technique

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    O'Brien, Brandi M; Windes, William E

    A new cryo-process technique has been developed for the fabrication of advanced fuel for nuclear systems. The process uses a new cryo-processing technique whereby small, porous microspheres (<2000 µm) are formed from sub-micron oxide powder. A simple aqueous particle slurry of oxide powder is pumped through a microsphere generator consisting of a vibrating needle with controlled amplitude and frequency. As the water-based droplets are formed and pass through the microsphere generator they are frozen in a bath of liquid nitrogen and promptly vacuum freeze-dried to remove the water. The resulting porous microspheres consist of half micron sized oxide particles heldmore » together by electrostatic forces and mechanical interlocking of the particles. Oxide powder microspheres ranging from 750 µm to 2000 µm are then converted into a nitride form using a high temperature fluidized particle bed. Carbon black can be added to the oxide powder before microsphere formation to augment the carbothermic reaction during conversion to a nitride. Also, the addition of ethyl alcohol to the aqueous slurry reduces the surface tension energy of the droplets resulting in even smaller droplets forming in the microsphere generator. Initial results from this new process indicate a lower impurity contamination in the final nitrides due to the single feed stream of particles, material handling and conversion are greatly simplified, a minimum of waste and personnel exposure are anticipated, and finally the conversion kinetics may be greatly increased because of the small oxide powder size (sub-micron) forming the porous microsphere. Thus far the fabrication process has been successful in demonstrating all of these improvements with surrogate ZrO2 powder. Further tests will be conducted in the future using the technique on UO2 powders.« less

  10. Upgrading nickel content of limonite nickel ore through pelletization, selective reduction and magnetic separation

    NASA Astrophysics Data System (ADS)

    Mayangsari, W.; Prasetyo, A. B.; Prasetiyo, Puguh

    2018-04-01

    Limonite nickel ore has potency to utilize as raw material for ferronickel or nickel matte, since it has low grade nickel content, thus process development is needed to find the acceptable process for upgrading nickel. The aim of this research is to determine upgrading of Ni content as result of selective reduction of limonite nickel pellet continued by magnetic separation as effect of temperature and time reduction as well as coal and CaSO4 addition. There are four steps to perform this research, such as preparation including characterization of raw ore and pelletization, selective reduction, magnetic separation and characterization of products by using AAS, XRD and SEM. Based on the result study, pellet form can upgrade 77.78% higher than powder form. Upgrading of Ni and Fe content was up to 3fold and 1.5fold respectively from raw ore used when reduced at 1100°C for 60 minutes with composition of coal and CaSO4, both 10%. The excess of CaSO4 addition caused fayalite formation. Moreover, S2 from CaSO4 also support to reach low melting point and enlardge particle size of metal formed.

  11. Cryo-EM structures of two bovine adenovirus type 3 intermediates

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cheng, Lingpeng; Huang, Xiaoxing; Li, Xiaomin

    2014-02-15

    Adenoviruses (Ads) infect hosts from all vertebrate species and have been investigated as vaccine vectors. We report here near-atomic structures of two bovine Ad type 3 (BAd3) intermediates obtained by cryo-electron microscopy. A comparison between the two intermediate structures reveals that the differences are localized in the fivefold vertex region, while their facet structures are identical. The overall facet structure of BAd3 exhibits a similar structure to human Ads; however, BAd3 protein IX has a unique conformation. Mass spectrometry and cryo-electron tomography analyses indicate that one intermediate structure represents the stage during DNA encapsidation, whilst the other intermediate structure representsmore » a later stage. These results also suggest that cleavage of precursor protein VI occurs during, rather than after, the DNA encapsidation process. Overall, our results provide insights into the mechanism of Ad assembly, and allow the first structural comparison between human and nonhuman Ads at backbone level. - Highlights: • First structure of bovine adenovirus type 3. • Some channels are located at the vertex of intermediate during DNA encapsidation. • Protein IX exhibits a unique conformation of trimeric coiled–coiled structure. • Cleavage of precursor protein VI occurs during the DNA encapsidation process.« less

  12. Mouse Sperm Cryopreservation and Recovery using the I·Cryo Kit

    PubMed Central

    Liu, Ling; Sansing, Steven R.; Morse, Iva S.; Pritchett-Corning, Kathleen R.

    2011-01-01

    Thousands of new genetically modified (GM) strains of mice have been created since the advent of transgenesis and knockout technologies. Many of these valuable animals exist only as live animals, with no backup plan in case of emergency. Cryopreservation of embryos can provide this backup, but is costly, can be a lengthy procedure, and generally requires a large number of animals for success. Since the discovery that mouse sperm can be successfully cryopreserved with a basic cryoprotective agent (CPA) consisting of 18% raffinose and 3% skim milk, sperm cryopreservation has become an acceptable and cost-effective procedure for archiving, distributing and recovery of these valuable strains. Here we demonstrate a newly developed I•Cryo kit for mouse sperm cryopreservation. Sperm from five commonly-used strains of inbred mice were frozen using this kit and then recovered. Higher protection ratios of sperm motility (> 60%) and rapid progressive motility (> 45%) compared to the control (basic CPA) were seen for sperm frozen with this kit in 5 inbred mouse strains. Two cell stage embryo development after IVF with the recovered sperm was improved consistently in all 5 mouse strains examined. Over a 1.5 year period, 49 GM mouse lines were archived by sperm cryopreservation with the I•Cryo kit and later recovered by IVF. PMID:22214993

  13. Tools for model-building with cryo-EM maps

    DOE PAGES

    Terwilliger, Thomas Charles

    2018-01-01

    There are new tools available to you in Phenix for interpreting cryo-EM maps. You can automatically sharpen (or blur) a map with phenix.auto_sharpen and you can segment a map with phenix.segment_and_split_map. If you have overlapping partial models for a map, you can merge them with phenix.combine_models. If you have a protein-RNA complex and protein chains have been accidentally built in the RNA region, you can try to remove them with phenix.remove_poor_fragments. You can put these together and automatically sharpen, segment and build a map with phenix.map_to_model.

  14. Tools for model-building with cryo-EM maps

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Terwilliger, Thomas Charles

    There are new tools available to you in Phenix for interpreting cryo-EM maps. You can automatically sharpen (or blur) a map with phenix.auto_sharpen and you can segment a map with phenix.segment_and_split_map. If you have overlapping partial models for a map, you can merge them with phenix.combine_models. If you have a protein-RNA complex and protein chains have been accidentally built in the RNA region, you can try to remove them with phenix.remove_poor_fragments. You can put these together and automatically sharpen, segment and build a map with phenix.map_to_model.

  15. Microcystin-LR removal from aqueous solutions using a magnetically separable N-doped TiO2 nanocomposite under visible light irradiation

    EPA Science Inventory

    The performance of magnetically separable N-doped TiO2 was found to be significantly improved when compared with a non-magnetic N-doped TiO2 for the aqueous removal of cyanotoxin Microcystin-LR. The observed enhanced photocatalytic activity may be related to the presence of ferri...

  16. Electron beam control for barely separated beams

    DOEpatents

    Douglas, David R.; Ament, Lucas J. P.

    2017-04-18

    A method for achieving independent control of multiple beams in close proximity to one another, such as in a multi-pass accelerator where coaxial beams are at different energies, but moving on a common axis, and need to be split into spatially separated beams for efficient recirculation transport. The method for independent control includes placing a magnet arrangement in the path of the barely separated beams with the magnet arrangement including at least two multipole magnets spaced closely together and having a multipole distribution including at least one odd multipole and one even multipole. The magnetic fields are then tuned to cancel out for a first of the barely separated beams to allow independent control of the second beam with common magnets. The magnetic fields may be tuned to cancel out either the dipole component or tuned to cancel out the quadrupole component in order to independently control the separate beams.

  17. Magnetically separable mesoporous Fe{sub 3}O{sub 4}/silica catalysts with very low Fe{sub 3}O{sub 4} content

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Grau-Atienza, A.; Serrano, E.; Linares, N.

    2016-05-15

    Two magnetically separable Fe{sub 3}O{sub 4}/SiO{sub 2} (aerogel and MSU-X) composites with very low Fe{sub 3}O{sub 4} content (<1 wt%) have been successfully prepared at room temperature by co-condensation of MPTES-functionalized Fe{sub 3}O{sub 4} nanoparticles (NPs) with a silicon alkoxide. This procedure yields a homogeneous incorporation of the Fe{sub 3}O{sub 4} NPs on silica supports, leading to magnetic composites that can be easily recovered using an external magnetic field, despite their very low Fe{sub 3}O{sub 4} NPs content (ca. 1 wt%). These novel hybrid Fe{sub 3}O{sub 4}/SiO{sub 2} materials have been tested for the oxidation reaction of 3,3′,5,5′-tetramethylbenzidine (TMB) withmore » hydrogen peroxide showing an enhancement of the stability of the NPs in the Fe{sub 3}O{sub 4}/silica aerogel as compared to the Fe{sub 3}O{sub 4} NPs alone, even after five catalytic cycles, no leaching or agglomeration of the Fe{sub 3}O{sub 4}/SiO{sub 2} systems. - Graphical abstract: Novel magnetically separable mesoporous silica-based composites with very low magnetite content. - Highlights: • An innovative way to prepare magnetically separable composites with <1 wt% NPs. • The Fe{sub 3}O{sub 4}/silica composites are readily magnetized/demagnetized. • The Fe{sub 3}O{sub 4}/silica composites can be easily recovered using an external magnetic field. • Excellent catalytic performance and recyclability despite the low Fe{sub 3}O{sub 4} NPs content.« less

  18. Morphology of the pore space in claystones - evidence from BIB/FIB ion beam sectioning and cryo-SEM observations

    NASA Astrophysics Data System (ADS)

    Desbois, G.; Urai, J. L.; Kukla, P. A.

    2009-12-01

    Mudrocks and clay-rich fault gouges are important mechanical elements in the Earth’s crust and form seals for crustal fluids such as groundwater and hydrocarbons. Other fields of interest are the storage of anthropogenic carbon dioxide and radioactive waste in geologic formations. In addition, coupled flows, capillary processes, and associated deformation are of importance in many applied fields. A key factor to understanding these processes is a detailed understanding of the morphology of the pore space. Classic studies of porosity in fine grained materials are performed on dried or freeze dried samples and include metal injection methods, magnetic susceptibility measurement, SEM and TEM imaging, neutron scattering, NMR spectroscopy, and ESEM. Confocal microscopy and X-ray tomography are used to image porosity in coarse grained sediments but the resolution of these techniques is not sufficient at present for applications to mudrocks or clay-rich fault gouges. Therefore, observations and interpretations remain difficult because none of these approaches is able to directly describe the in-situ porosity at the pore scale. In addition, some methods require dried samples in which the natural structure of pores may have been damaged to some extent due to desiccation and dehydration of the clay minerals. A recently developed alternative is to study wet samples using a cryo-SEM, which allows stabilization of wet media at cryo-temperature, in-situ sample preparation by ion beam cross-sectioning (BIB, FIB) and observations of the stabilized microstructure at high resolution. We report on a study of Boom clay from a proposed disposal site of radioactive waste (Mol site, Belgium) using cryo-SEM at cryogenic temperature, with ion beam cross-sectioning to prepare smooth, damage free surfaces. Pores commonly have crack-like tips, preferred orientation parallel to bedding and power law size distribution. We define a number of pore types depending on shape and location in the

  19. 76 FR 4338 - Research and Development Strategies for Compressed & Cryo-Compressed Hydrogen Storage Workshops

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-25

    ... DEPARTMENT OF ENERGY Research and Development Strategies for Compressed & Cryo- Compressed Hydrogen Storage Workshops AGENCY: Fuel Cell Technologies Program, Office of Energy Efficiency and Renewable Energy, Department of Energy. ACTION: Notice of meeting. SUMMARY: The Systems Integration group of...

  20. CryoSat Ice Processor: Known Processor Anomalies and Potential Future Product Evolutions

    NASA Astrophysics Data System (ADS)

    Mannan, R.; Webb, E.; Hall, A.; Bouffard, J.; Femenias, P.; Parrinello, T.; Bouffard, J.; Brockley, D.; Baker, S.; Scagliola, M.; Urien, S.

    2016-08-01

    Launched in 2010, CryoSat was designed to measure changes in polar sea ice thickness and ice sheet elevation. To reach this goal the CryoSat data products have to meet the highest performance standards and are subjected to a continual cycle of improvement achieved through upgrades to the Instrument Processing Facilities (IPFs). Following the switch to the Baseline-C Ice IPFs there are already planned evolutions for the next processing Baseline, based on recommendations from the Scientific Community, Expert Support Laboratory (ESL), Quality Control (QC) Centres and Validation campaigns. Some of the proposed evolutions, to be discussed with the scientific community, include the activation of freeboard computation in SARin mode, the potential operation of SARin mode over flat-to-slope transitory land ice areas, further tuning of the land ice retracker, the switch to NetCDF format and the resolution of anomalies arising in Baseline-C. This paper describes some of the anomalies known to affect Baseline-C in addition to potential evolutions that are planned and foreseen for Baseline-D.

  1. Single-particle cryo-EM-Improved ab initio 3D reconstruction with SIMPLE/PRIME.

    PubMed

    Reboul, Cyril F; Eager, Michael; Elmlund, Dominika; Elmlund, Hans

    2018-01-01

    Cryogenic electron microscopy (cryo-EM) and single-particle analysis now enables the determination of high-resolution structures of macromolecular assemblies that have resisted X-ray crystallography and other approaches. We developed the SIMPLE open-source image-processing suite for analysing cryo-EM images of single-particles. A core component of SIMPLE is the probabilistic PRIME algorithm for identifying clusters of images in 2D and determine relative orientations of single-particle projections in 3D. Here, we extend our previous work on PRIME and introduce new stochastic optimization algorithms that improve the robustness of the approach. Our refined method for identification of homogeneous subsets of images in accurate register substantially improves the resolution of the cluster centers and of the ab initio 3D reconstructions derived from them. We now obtain maps with a resolution better than 10 Å by exclusively processing cluster centers. Excellent parallel code performance on over-the-counter laptops and CPU workstations is demonstrated. © 2017 The Protein Society.

  2. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM.

    PubMed

    Zhou, Anna; Rohou, Alexis; Schep, Daniel G; Bason, John V; Montgomery, Martin G; Walker, John E; Grigorieff, Nikolaus; Rubinstein, John L

    2015-10-06

    Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases.

  3. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM

    PubMed Central

    Zhou, Anna; Rohou, Alexis; Schep, Daniel G; Bason, John V; Montgomery, Martin G; Walker, John E; Grigorieff, Nikolaus; Rubinstein, John L

    2015-01-01

    Adenosine triphosphate (ATP), the chemical energy currency of biology, is synthesized in eukaryotic cells primarily by the mitochondrial ATP synthase. ATP synthases operate by a rotary catalytic mechanism where proton translocation through the membrane-inserted FO region is coupled to ATP synthesis in the catalytic F1 region via rotation of a central rotor subcomplex. We report here single particle electron cryomicroscopy (cryo-EM) analysis of the bovine mitochondrial ATP synthase. Combining cryo-EM data with bioinformatic analysis allowed us to determine the fold of the a subunit, suggesting a proton translocation path through the FO region that involves both the a and b subunits. 3D classification of images revealed seven distinct states of the enzyme that show different modes of bending and twisting in the intact ATP synthase. Rotational fluctuations of the c8-ring within the FO region support a Brownian ratchet mechanism for proton-translocation-driven rotation in ATP synthases. DOI: http://dx.doi.org/10.7554/eLife.10180.001 PMID:26439008

  4. Comparative study on histological structures of the vitelline membrane of hen and duck egg observed by cryo-scanning electron microscopy.

    PubMed

    Chung, Wen-Hsin; Lai, Kung-Ming; Hsu, Kuo-chiang

    2010-02-10

    The histological structures of the vitelline membranes (VM) of hen and duck eggs were observed by cryo-scanning electron microscopy (cryo-SEM), and the chemical characteristics were also compared. The outer layer surface (OLS) of duck egg VM showed networks constructed by fibrils and sheets (0.1-5.2 microm in width), and that of hen egg presented networks formed only by sheets (2-6 microm in width). Thicker fibrils (0.5-1.5 microm in width) with different arrangement were observed on the inner layer surface (ILS) of duck egg VM as compared to those (0.3-0.7 microm in width) of hen egg VM. Upon separation, the outer surface of the outer layer (OSOL) and the inner surface of the inner layer (ISIL) of hen and duck egg VMs were quite similar to fresh VM except that the OSOL of duck egg VM showed networks constructed only by sheets. Thin fibrils interlaced above a bumpy or flat structure were observed at the exposed surface of the outer layer (ESOL) of hen and duck egg VMs. The exposed surfaces of inner layers (ESIL) of hen and duck egg VMs showed similar structures of fibrils, which joined, branched, and ran in straight lines for long distances up to 30 microm; however, the widths of the fibrils shown in ESOL and ESIL of duck egg VM were 0.1 and 0.7-1.4 microm, respectively, and were greater than those (<0.1 and 0.5-0.8 microm) of hen egg VM. The continuous membranes of both hen and duck egg VMs were still attached to the outer layers when separated. The content of protein, the major component of VM, was higher in duck egg VM (88.6%) than in hen egg VM (81.6%). Four and six major SDS-soluble protein patterns with distinct localization were observed in hen and duck egg VMs, respectively. Overall, the different histological structures of hen and duck egg VMs were suggested to be majorly attributable to the diverse protein components.

  5. A Magnetically Separable, Highly Stable Enzyme System Based on Nanocomposites of Enzymes and Magnetic Nanoparticles Shipped in Hierarchically Ordered, Mesocellular, Mesoporous Silica

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kim, Jungbae; Lee, Jinwoo; Na, Hyon Bin

    2005-12-01

    Enzymes are versatile nanoscale biocatalysts, and find increasing applications in many areas, including organic synthesis[1-3] and bioremediation.[4-5] However, the application of enzymes is often hampered by the short catalytic lifetime of enzymes and by the difficulty in recovery and recycling. To solve these problems, there have been a lot of efforts to develop effective enzyme immobilization techniques. Recent advances in nanotechnology provide more diverse materials and approaches for enzyme immobilization. For example, mesoporous materials offer potential advantages as a host of enzymes due to their well-controlled porosity and large surface area for the immobilization of enzymes.[6,7] On the other hand,more » it has been demonstrated that enzymes attached on magnetic iron oxide nanoparticles can be easily recovered using a magnet and recycled for iterative uses.[8] In this paper, we report the development of magnetically-separable and highly-stable enzyme system by the combined use of two different kinds of nanostructured materials: magnetic nanoparticles and mesoporous silica.« less

  6. Cryo-imaging of fluorescently labeled single cells in a mouse

    NASA Astrophysics Data System (ADS)

    Steyer, Grant J.; Roy, Debashish; Salvado, Olivier; Stone, Meredith E.; Wilson, David L.

    2009-02-01

    We developed a cryo-imaging system to provide single-cell detection of fluorescently labeled cells in mouse, with particular applicability to stem cells and metastatic cancer. The Case cryoimaging system consists of a fluorescence microscope, robotic imaging positioner, customized cryostat, PC-based control system, and visualization/analysis software. The system alternates between sectioning (10-40 μm) and imaging, collecting color brightfield and fluorescent blockface image volumes >60GB. In mouse experiments, we imaged quantum-dot labeled stem cells, GFP-labeled cancer and stem cells, and cell-size fluorescent microspheres. To remove subsurface fluorescence, we used a simplified model of light-tissue interaction whereby the next image was scaled, blurred, and subtracted from the current image. We estimated scaling and blurring parameters by minimizing entropy of subtracted images. Tissue specific attenuation parameters were found [uT : heart (267 +/- 47.6 μm), liver (218 +/- 27.1 μm), brain (161 +/- 27.4 μm)] to be within the range of estimates in the literature. "Next image" processing removed subsurface fluorescence equally well across multiple tissues (brain, kidney, liver, adipose tissue, etc.), and analysis of 200 microsphere images in the brain gave 97+/-2% reduction of subsurface fluorescence. Fluorescent signals were determined to arise from single cells based upon geometric and integrated intensity measurements. Next image processing greatly improved axial resolution, enabled high quality 3D volume renderings, and improved enumeration of single cells with connected component analysis by up to 24%. Analysis of image volumes identified metastatic cancer sites, found homing of stem cells to injury sites, and showed microsphere distribution correlated with blood flow patterns. We developed and evaluated cryo-imaging to provide single-cell detection of fluorescently labeled cells in mouse. Our cryo-imaging system provides extreme (>60GB), micron

  7. Tyloses and Phenolic Deposits in Xylem Vessels Impede Water Transport in Low-Lignin Transgenic Poplars: A Study by Cryo-Fluorescence Microscopy1[W][OA

    PubMed Central

    Kitin, Peter; Voelker, Steven L.; Meinzer, Frederick C.; Beeckman, Hans; Strauss, Steven H.; Lachenbruch, Barbara

    2010-01-01

    Of 14 transgenic poplar genotypes (Populus tremula × Populus alba) with antisense 4-coumarate:coenzyme A ligase that were grown in the field for 2 years, five that had substantial lignin reductions also had greatly reduced xylem-specific conductivity compared with that of control trees and those transgenic events with small reductions in lignin. For the two events with the lowest xylem lignin contents (greater than 40% reduction), we used light microscopy methods and acid fuchsin dye ascent studies to clarify what caused their reduced transport efficiency. A novel protocol involving dye stabilization and cryo-fluorescence microscopy enabled us to visualize the dye at the cellular level and to identify water-conducting pathways in the xylem. Cryo-fixed branch segments were planed in the frozen state on a sliding cryo-microtome and observed with an epifluorescence microscope equipped with a cryo-stage. We could then distinguish clearly between phenolic-occluded vessels, conductive (stain-filled) vessels, and nonconductive (water- or gas-filled) vessels. Low-lignin trees contained areas of nonconductive, brown xylem with patches of collapsed cells and patches of noncollapsed cells filled with phenolics. In contrast, phenolics and nonconductive vessels were rarely observed in normal colored wood of the low-lignin events. The results of cryo-fluorescence light microscopy were supported by observations with a confocal microscope after freeze drying of cryo-planed samples. Moreover, after extraction of the phenolics, confocal microscopy revealed that many of the vessels in the nonconductive xylem were blocked with tyloses. We conclude that reduced transport efficiency of the transgenic low-lignin xylem was largely caused by blockages from tyloses and phenolic deposits within vessels rather than by xylem collapse. PMID:20639405

  8. Isolation of osteoprogenitors from human jaw periosteal cells: a comparison of two magnetic separation methods.

    PubMed

    Olbrich, Marcus; Rieger, Melanie; Reinert, Siegmar; Alexander, Dorothea

    2012-01-01

    Human jaw periosteum tissue contains osteoprogenitors that have potential for tissue engineering applications in oral and maxillofacial surgeries. To isolate osteoprogenitor cells from heterogeneous cell populations, we used the specific mesenchymal stem cell antigen-1 (MSCA-1) antibody and compared two magnetic separation methods. We analyzed the obtained MSCA-1(+) and MSCA-1(-) fractions in terms of purity, yield of positive/negative cells and proliferative and mineralization potentials. The analysis of cell viability after separation revealed that the EasySep method yielded higher viability rates, whereas the flow cytometry results showed a higher purity for the MACS-separated cell fractions. The mineralization capacity of the osteogenic induced MSCA-1(+) cells compared with the MSCA-1(-) controls using MACS was 5-fold higher, whereas the same comparison after EasySep showed no significant differences between both fractions. By analyzing cell proliferation, we detected a significant difference between the proliferative potential of the osteogenic cells versus untreated cells after the MACS and EasySep separations. The differentiated cells after MACS separation adjusted their proliferative capacity, whereas the EasySep-separated cells failed to do so. The protein expression analysis showed small differences between the two separation methods. Our findings suggest that MACS is a more suitable separation method to isolate osteoprogenitors from the entire jaw periosteal cell population.

  9. Preparation of Fe2O3-TiO2 composite from Sukabumi iron sand through magnetic separation, pyrometallurgy, and hydrometallurgy

    NASA Astrophysics Data System (ADS)

    Wahyuningsih, S.; Ramelan, A. H.; Pranata, H. P.; Hanif, Q. A.; Ismoyo, Y. A.; Ichsan, K. F.

    2016-11-01

    Preparation of Fe2O3/TiO2 composite from Sukabumi iron sand by magnetic separation, roasting, leaching and precipitation treatment has been carried out. Magnetic separation can separate magnetic particles and non-magnetic particles of iron sand content, while the non-magnetic particles (wustite (FeO), hematite (α-Fe2O3), maghemite (γ-Fe2O3) and magnetite (Fe3O4)) was washing with oxalic acid 1 M. The result product then was roasted at 800 °C treated by sodium carbonate (Na2CO3) addition of 1:1; 2:1 and 1:2 (w/w) of iron sand to Na2CO3 weight ratio, respectively. The X-Ray Fluorescence (XRF) analysis result shown that Sukabumi iron sand have hematite (Fe2O3) and titanium dioxide (TiO2) content about 72.17% dan 14.42%. XRD analysis of roasted iron sand shown the rutile (TiO2), Hematite (Fe2O3), NaFeO2, FeO, and Na2TiO3. Leaching of roasted iron sand using sulphuric acid (H2SO4) have influenced by concentrations of the H2SO4 solution. The optimum iron sand dissolution occurred in H2SO4 9 M, which condensation product of the leachant have a weight ratio of Fe:Ti = 1:1 (w/w). Meanwhile, the settling back-filtrate result of second condensation was obtained a ratio of Fe2O3: TiO2 of 3: 1 (w/w).

  10. Integration of single-molecule detection with magnetic separation for multiplexed detection of DNA glycosylases.

    PubMed

    Li, Chen-Chen; Zhang, Yan; Tang, Bo; Zhang, Chun-Yang

    2018-06-05

    We combine single-molecule detection with magnetic separation for simultaneous measurement of human 8-oxoG DNA glycosylase 1 (hOGG1) and uracil DNA glycosylase (UDG) based on excision repair-initiated endonuclease IV (Endo IV)-assisted signal amplification. This method can sensitively detect multiple DNA glycosylases, and it can be further applied for the simultaneous measurement of enzyme kinetic parameters and screening of both hOGG1 and UDG inhibitors.

  11. Reducing Relaxation of Hyperpolarized ^129 Xe during Cryogenic Separation

    NASA Astrophysics Data System (ADS)

    Patton, B.; Kuzma, N. N.; Happer, W.

    2004-05-01

    Recent experimental results^1 indicate that the T1 relaxation time of solid ^129Xe is much shorter than previous models had predicted^2 near the xenon melting point of 161 K and at low magnetic fields. This enhanced relaxation is detrimental to commercial xenon polarizers, which cryogenically distill hyperpolarized ^129Xe from a buffer gas mixture. We have measured the fraction of xenon polarization lost during a typical cryogenic collection, using different permanent magnets to vary the holding field from 700 gauss to over a tesla. The results indicate that using a stronger permanent magnet around the cryo-trap is a simple way to increase the final polarization of the pure xenon gas. An additional experiment was conducted in order to determine whether the majority of the xenon relaxation occurs throughout accumulation (possibly as a result of temperature inhomogeneities within the frozen sample) or during the brief thawing time. In pinpointing the polarization loss, this research may suggest new designs for xenon polarizers. 1. Kuzma et al., Phys. Rev. Lett. 88, 147602 (2002). 2. Fitzgerald et al., Phys. Rev. B 59, 8795 (1999).

  12. Visualization of the herpes simplex virus portal in situ by cryo-electron tomography

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cardone, Giovanni; Winkler, Dennis C.; Trus, Benes L.

    2007-05-10

    Herpes simplex virus type 1 (HSV-1), the prototypical herpesvirus, has an icosahedral nucleocapsid surrounded by a proteinaceous tegument and a lipoprotein envelope. As in tailed bacteriophages, the icosahedral symmetry of the capsid is broken at one of the 12 vertices, which is occupied by a dodecameric ring of portal protein, UL6, instead of a pentamer of the capsid protein, UL19. The portal ring serves as a conduit for DNA entering and exiting the capsid. From a cryo-EM reconstruction of capsids immuno-gold-labeled with anti-UL6 antibodies, we confirmed that UL6 resides at a vertex. To visualize the portal in the context ofmore » the assembled capsid, we used cryo-electron tomography to determine the three-dimensional structures of individual A-capsids (empty, mature capsids). The similarity in size and overall shape of the portal and a UL19 pentamer - both are cylinders of {approx} 800 kDa - combined with residual noise in the tomograms, prevented us from identifying the portal vertices directly; however, this was accomplished by a computational classification procedure. Averaging the portal-containing subtomograms produced a structure that tallies with the isolated portal, as previously reconstructed by cryo-EM. The portal is mounted on the outer surface of the capsid floor layer, with its narrow end pointing outwards. This disposition differs from that of known phage portals in that the bulk of its mass lies outside, not inside, the floor. This distinction may be indicative of divergence at the level of portal-related functions other than its role as a DNA channel.« less

  13. CryoSat-2 SAR and SARin Inland Water Heights from the CRUCIAL project

    NASA Astrophysics Data System (ADS)

    Benveniste, J.; Restano, M.; Ambrózio, A.; Moore, P.; Birkinshaw, S.

    2017-12-01

    CRUCIAL was an ESA/STSE funded project investigating innovative land and inland water applications from CryoSat-2 with a forward-look component to the Sentinel-3 and Jason-CS/Sentinel-6 missions. The high along-track sampling of CryoSat-2 in its SAR and SARin modes offers the opportunity to recover high frequency signals over inland waters. A methodology was developed to process the FBR L1A Doppler beams to form a waveform product using ground cell gridding, beam steering and beam stacking. Inland water heights from CryoSat-2 are derived by using a set of empirical retrackers formulated for inland water applications. Results of the processing strategy include a comparison of waveforms and heights from the burst echoes (80 m along-track) and from multi-look waveforms (320 m along-track). SAR and SARin FBR data are available for the Amazon, Brahmaputra and Mekong for 2011-2015. FBR SAR results are compared against stage data from the nearest gauge. Heights from Tonlé Sap are also compared against Jason-2 data from the United States Department of Agriculture. A strategy to select the number of multi-looks over rivers was designed based on the rms of heights across Tonlé Sap. Comparisons include results from the empirical retrackers and from waveforms and heights obtained via ESA's Grid Processing on Demand (G-POD/SARvatore) using the SAMOSA2 retracker. Results of FBR SARin processing for the Amazon and Brahmaputra are presented including comparison of heights from the two antennae, extraction of slope of the ground surface and validation against ground data where appropriate.

  14. Cationized Magnetoferritin Enables Rapid Labeling and Concentration of Gram-Positive and Gram-Negative Bacteria in Magnetic Cell Separation Columns

    PubMed Central

    Spencer, J.; Schwarzacher, W.

    2016-01-01

    ABSTRACT In order to identify pathogens rapidly and reliably, bacterial capture and concentration from large sample volumes into smaller ones are often required. Magnetic labeling and capture of bacteria using a magnetic field hold great promise for achieving this goal, but the current protocols have poor capture efficiency. Here, we present a rapid and highly efficient approach to magnetic labeling and capture of both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria using cationized magnetoferritin (cat-MF). Magnetic labeling was achieved within a 1-min incubation period with cat-MF, and 99.97% of the labeled bacteria were immobilized in commercially available magnetic cell separation (MACS) columns. Longer incubation times led to more efficient capture, with S. aureus being immobilized to a greater extent than E. coli. Finally, low numbers of magnetically labeled E. coli bacteria (<100 CFU per ml) were immobilized with 100% efficiency and concentrated 7-fold within 15 min. Therefore, our study provides a novel protocol for rapid and highly efficient magnetic labeling, capture, and concentration of both Gram-positive and Gram-negative bacteria. IMPORTANCE Antimicrobial resistance (AMR) is a significant global challenge. Rapid identification of pathogens will retard the spread of AMR by enabling targeted treatment with suitable agents and by reducing inappropriate antimicrobial use. Rapid detection methods based on microfluidic devices require that bacteria are concentrated from large volumes into much smaller ones. Concentration of bacteria is also important to detect low numbers of pathogens with confidence. Here, we demonstrate that magnetic separation columns capture small amounts of bacteria with 100% efficiency. Rapid magnetization was achieved by exposing bacteria to cationic magnetic nanoparticles, and magnetized bacteria were concentrated 7-fold inside the column. Thus, bacterial capture and concentration were achieved

  15. Cationized Magnetoferritin Enables Rapid Labeling and Concentration of Gram-Positive and Gram-Negative Bacteria in Magnetic Cell Separation Columns.

    PubMed

    Correia Carreira, S; Spencer, J; Schwarzacher, W; Seddon, A M

    2016-06-15

    In order to identify pathogens rapidly and reliably, bacterial capture and concentration from large sample volumes into smaller ones are often required. Magnetic labeling and capture of bacteria using a magnetic field hold great promise for achieving this goal, but the current protocols have poor capture efficiency. Here, we present a rapid and highly efficient approach to magnetic labeling and capture of both Gram-negative (Escherichia coli) and Gram-positive (Staphylococcus aureus) bacteria using cationized magnetoferritin (cat-MF). Magnetic labeling was achieved within a 1-min incubation period with cat-MF, and 99.97% of the labeled bacteria were immobilized in commercially available magnetic cell separation (MACS) columns. Longer incubation times led to more efficient capture, with S. aureus being immobilized to a greater extent than E. coli Finally, low numbers of magnetically labeled E. coli bacteria (<100 CFU per ml) were immobilized with 100% efficiency and concentrated 7-fold within 15 min. Therefore, our study provides a novel protocol for rapid and highly efficient magnetic labeling, capture, and concentration of both Gram-positive and Gram-negative bacteria. Antimicrobial resistance (AMR) is a significant global challenge. Rapid identification of pathogens will retard the spread of AMR by enabling targeted treatment with suitable agents and by reducing inappropriate antimicrobial use. Rapid detection methods based on microfluidic devices require that bacteria are concentrated from large volumes into much smaller ones. Concentration of bacteria is also important to detect low numbers of pathogens with confidence. Here, we demonstrate that magnetic separation columns capture small amounts of bacteria with 100% efficiency. Rapid magnetization was achieved by exposing bacteria to cationic magnetic nanoparticles, and magnetized bacteria were concentrated 7-fold inside the column. Thus, bacterial capture and concentration were achieved within 15 min. This

  16. ScipionCloud: An integrative and interactive gateway for large scale cryo electron microscopy image processing on commercial and academic clouds.

    PubMed

    Cuenca-Alba, Jesús; Del Cano, Laura; Gómez Blanco, Josué; de la Rosa Trevín, José Miguel; Conesa Mingo, Pablo; Marabini, Roberto; S Sorzano, Carlos Oscar; Carazo, Jose María

    2017-10-01

    New instrumentation for cryo electron microscopy (cryoEM) has significantly increased data collection rate as well as data quality, creating bottlenecks at the image processing level. Current image processing model of moving the acquired images from the data source (electron microscope) to desktops or local clusters for processing is encountering many practical limitations. However, computing may also take place in distributed and decentralized environments. In this way, cloud is a new form of accessing computing and storage resources on demand. Here, we evaluate on how this new computational paradigm can be effectively used by extending our current integrative framework for image processing, creating ScipionCloud. This new development has resulted in a full installation of Scipion both in public and private clouds, accessible as public "images", with all the required preinstalled cryoEM software, just requiring a Web browser to access all Graphical User Interfaces. We have profiled the performance of different configurations on Amazon Web Services and the European Federated Cloud, always on architectures incorporating GPU's, and compared them with a local facility. We have also analyzed the economical convenience of different scenarios, so cryoEM scientists have a clearer picture of the setup that is best suited for their needs and budgets. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  17. CryoSat Level1b SAR/SARin BaselineC: Product Format and Algorithm Improvements

    NASA Astrophysics Data System (ADS)

    Scagliola, Michele; Fornari, Marco; Di Giacinto, Andrea; Bouffard, Jerome; Féménias, Pierre; Parrinello, Tommaso

    2015-04-01

    CryoSat was launched on the 8th April 2010 and is the first European ice mission dedicated to the monitoring of precise changes in the thickness of polar ice sheets and floating sea ice. Cryosat carries an innovative radar altimeter called the Synthetic Aperture Interferometric Altimeter (SIRAL), that transmits pulses at a high pulse repetition frequency thus making the received echoes phase coherent and suitable for azimuth processing. This allows to reach a significantly improved along track resolution with respect to traditional pulse-width limited altimeters. CryoSat is the first altimetry mission operating in SAR mode and continuous improvements in the Level1 Instrument Processing Facility (IPF1) are being identified, tested and validated in order to improve the quality of the Level1b products. The current IPF, Baseline B, was released in operation in February 2012. A reprocessing campaign followed, in order to reprocess the data since July 2010. After more than 2 years of development, the release in operations of Baseline C is expected in the first half of 2015. BaselineC Level1b products will be distributed in an updated format, including for example the attitude information (roll, pitch and yaw) and, for SAR/SARIN, the waveform length doubled with respect to Baseline B. Moreveor, various algorithm improvements have been identified: • a datation bias of about -0.5195 ms will be corrected (SAR/SARIn) • a range bias of about 0.6730 m will be corrected (SAR/SARIn) • a roll bias of 0.1062 deg and a pitch bias of 0.0520 deg • Surface sample stack weighting to filter out the single look echoes acquired at highest look angle, that results in a sharpening of the 20Hz waveforms With the operational release of BaselineC, the second CryoSat reprocessing campaign will be initiated, taking benefit of the upgrade implemented in the IPF1 processing chain but also at IPF2 level. The reprocessing campaign will cover the full Cryosat mission starting on 16th July 2010

  18. A New Technique for Preparation of High-Grade Titanium Slag from Titanomagnetite Concentrate by Reduction-Melting-Magnetic Separation Processing

    NASA Astrophysics Data System (ADS)

    Lv, Chao; Yang, Kun; Wen, Shu-ming; Bai, Shao-jun; Feng, Qi-cheng

    2017-10-01

    This paper proposes a new technique for preparation of high-grade titanium slag from Panzhihua vanadium titanomagnetite concentrate by reduction-melting-magnetic separation processing. Chemical analysis, x-ray diffraction, and scanning electron microscopy in conjunction with energy-dispersive spectroscopy were used to characterize the samples. The effective separation of iron and titanium slag could be realized by melting metallized pellets at 1550°C for 60 min with the addition of 1% CaO (basicity of 1.1) and 2% graphite powder. The small iron particles embedded in the slag could be removed by fine grinding and magnetic separation process. The grade of TiO2 in the obtained high-grade titanium slag reached 60.68% and the total recovery of TiO2 was 91.25%, which could be directly applied for producing titanium white by the sulfuric acid process. This technique provides an alternative method to use vanadium titanomagnetite concentrate of the Panzhihua area in China.

  19. Effects of pH and Magnetic Material on Immunomagnetic Separation of Cryptosporidium Oocysts from Concentrated Water Samples

    PubMed Central

    Kuhn, Ryan C.; Rock, Channah M.; Oshima, Kevin H.

    2002-01-01

    In this study, we examined the effect that magnetic materials and pH have on the recoveries of Cryptosporidium oocysts by immunomagnetic separation (IMS). We determined that particles that were concentrated on a magnet during bead separation have no influence on oocyst recovery; however, removal of these particles did influence pH values. The optimal pH of the IMS was determined to be 7.0. The numbers of oocysts recovered from deionized water at pH 7.0 were 26.3% higher than those recovered from samples that were not at optimal pH. The results indicate that the buffers in the IMS kit did not adequately maintain an optimum pH in some water samples. By adjusting the pH of concentrated environmental water samples to 7.0, recoveries of oocysts increased by 26.4% compared to recoveries from samples where the pH was not adjusted. PMID:11916735

  20. eCryo SHIIVER Customer/Stakeholder Checkpoint Briefing

    NASA Technical Reports Server (NTRS)

    Zoeckler, Joseph G.; Guzik, Monica; Van Dresar, Neil

    2015-01-01

    Given the wide diversity of cryogenic fluid management technology that had been developed at the research level, there was a need for eCryo to prioritize and focus on a limited subset of the possibilities in order to set a practical scope. As part of the effort to determine that focus, a survey was conducted in May of 2014 to solicit opinions of members of the aerospace industry as to what they considered the most important and beneficial cryogenic technologies to be developed in the near term. The project was also directed to consider the SLS exploration upper stage (EUS) as a potential infusion target, and to focus on technology that would provide the most immediate benefit to a cryogenic system of that type.

  1. 3D image reconstruction algorithms for cryo-electron-microscopy images of virus particles

    NASA Astrophysics Data System (ADS)

    Doerschuk, Peter C.; Johnson, John E.

    2000-11-01

    A statistical model for the object and the complete image formation process in cryo electron microscopy of viruses is presented. Using this model, maximum likelihood reconstructions of the 3D structure of viruses are computed using the expectation maximization algorithm and an example based on Cowpea mosaic virus is provided.

  2. Estimating loop length from CryoEM images at medium resolutions.

    PubMed

    McKnight, Andrew; Si, Dong; Al Nasr, Kamal; Chernikov, Andrey; Chrisochoides, Nikos; He, Jing

    2013-01-01

    De novo protein modeling approaches utilize 3-dimensional (3D) images derived from electron cryomicroscopy (CryoEM) experiments. The skeleton connecting two secondary structures such as α-helices represent the loop in the 3D image. The accuracy of the skeleton and of the detected secondary structures are critical in De novo modeling. It is important to measure the length along the skeleton accurately since the length can be used as a constraint in modeling the protein. We have developed a novel computational geometric approach to derive a simplified curve in order to estimate the loop length along the skeleton. The method was tested using fifty simulated density images of helix-loop-helix segments of atomic structures and eighteen experimentally derived density data from Electron Microscopy Data Bank (EMDB). The test using simulated density maps shows that it is possible to estimate within 0.5 Å of the expected length for 48 of the 50 cases. The experiments, involving eighteen experimentally derived CryoEM images, show that twelve cases have error within 2 Å. The tests using both simulated and experimentally derived images show that it is possible for our proposed method to estimate the loop length along the skeleton if the secondary structure elements, such as α-helices, can be detected accurately, and there is a continuous skeleton linking the α-helices.

  3. Towards an electro-magnetic field separation of deposited material implemented in an ion beam sputter process

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Malobabic, Sina; Jupe, Marco; Ristau, Detlev

    Nowadays, Ion Beam Sputter (IBS) processes are very well optimized on an empirical basis. To achieve further progresses, a modification of the IBS process by guiding the coating material using an axial magnetic field and an additional electrical field has been studied. The electro-magnetic (EM) field leads to a significant change in plasma properties and deposition rate distributions, whereas an increase in deposition rate along the centerline of the axial EM field around 150% was observed. These fundamental studies on the prototype are the basis for the development of an applicable and workable design of a separation device.

  4. Spotiton: A prototype for an integrated inkjet dispense and vitrification system for cryo-TEM

    PubMed Central

    Jain, Tilak; Sheehan, Patrick; Crum, John; Carragher, Bridget; Potter, Clinton S.

    2012-01-01

    Over the last three decades, Cryo-TEM has developed into a powerful technique for high-resolution imaging of biological macromolecules in their native vitrified state. However, the technique for vitrifying specimens onto EM grids is essentially unchanged – application of ~ 3 µL sample to a grid, followed by blotting and rapid plunge freezing into liquid ethane. Several trials are often required to obtain suitable thin (few hundred nanometers or less) vitrified layers amenable for cryo-TEM imaging, which results in waste of precious sample and resources. While commercially available instruments provide some level of automation to control the vitrification process in an effort to increase quality and reproducibility, obtaining satisfactory vitrified specimens remains a bottleneck in the Cryo-TEM pipeline. We describe here a completely novel method for EM specimen preparation based on small volume (picoliter to nanoliter) dispensing using inkjet technology. A first prototype system (Spotiton v0.5) demonstrates feasibility of this new approach for specimen vitrification. A piezo-electric inkjet dispenser is integrated with optical real-time cameras (100 Hz frame rate) to analyze picoliter to nanoliter droplet profiles in-flight and spreading dynamics on the grid, and thus provides a method to optimize timing of the process. Using TEM imaging and biochemical assays we demonstrate that the piezo-electric inkjet mechanism does not disrupt the structural or functional integrity of macromolecules. These preliminary studies provide insight into the factors and components that will need further development to enable a robust and repeatable technique for specimen vitrification using this novel approach. PMID:22569522

  5. Interleukin-6 Induced "Acute" Phenotypic Microenvironment Promotes Th1 Anti-Tumor Immunity in Cryo-Thermal Therapy Revealed By Shotgun and Parallel Reaction Monitoring Proteomics.

    PubMed

    Xue, Ting; Liu, Ping; Zhou, Yong; Liu, Kun; Yang, Li; Moritz, Robert L; Yan, Wei; Xu, Lisa X

    2016-01-01

    Cryo-thermal therapy has been emerged as a promising novel therapeutic strategy for advanced breast cancer, triggering higher incidence of tumor regression and enhanced remission of metastasis than routine treatments. To better understand its anti-tumor mechanism, we utilized a spontaneous metastatic mouse model and quantitative proteomics to compare N-glycoproteome changes in 94 serum samples with and without treatment. We quantified 231 highly confident N-glycosylated proteins using iTRAQ shotgun proteomics. Among them, 53 showed significantly discriminated regulatory patterns over the time course, in which the acute phase response emerged as the most enhanced pathway. The anti-tumor feature of the acute response was further investigated using parallel reaction monitoring target proteomics and flow cytometry on 23 of the 53 significant proteins. We found that cryo-thermal therapy reset the tumor chronic inflammation to an "acute" phenotype, with up-regulation of acute phase proteins including IL-6 as a key regulator. The IL-6 mediated "acute" phenotype transformed IL-4 and Treg-promoting ICOSL expression to Th1-promoting IFN-γ and IL-12 production, augmented complement system activation and CD86(+)MHCII(+) dendritic cells maturation and enhanced the proliferation of Th1 memory cells. In addition, we found an increased production of tumor progression and metastatic inhibitory proteins under such "acute" environment, favoring the anti-metastatic effect. Moreover, cryo-thermal on tumors induced the strongest "acute" response compared to cryo/hyperthermia alone or cryo-thermal on healthy tissues, accompanying by the most pronounced anti-tumor immunological effect. In summary, we demonstrated that cryo-thermal therapy induced, IL-6 mediated "acute" microenvironment shifted the tumor chronic microenvironment from Th2 immunosuppressive and pro-tumorigenic to Th1 immunostimulatory and tumoricidal state. Moreover, the magnitude of "acute" and "danger" signals play a key

  6. Modeling Cryotherapy Ice Ball Dimensions and Isotherms in a Novel Gel-based Model to Determine Optimal Cryo-needle Configurations and Settings for Potential Use in Clinical Practice

    PubMed Central

    Shah, Taimur T.; Arbel, Uri; Foss, Sonja; Zachman, Andrew; Rodney, Simon; Ahmed, Hashim U.; Arya, Manit

    2016-01-01

    Objective To gain a better understanding of ice ball dimensions and temperature isotherms relevant for cell kill when using combinations of cryo-needles we set out to answer 4 questions: (1) what type of cryo-needle? (2) how many needles? (3) best spatial configuration? and (4) correct duty cycle percentage? Methods We conducted laboratory experiments to monitor ice ball dimensions and create multi-needle planar isotherm maps for 17G and 10G cryo-needles using a novel multi-needle thermocouple fixture within gel at body temperature. We tested configurations of 1-4 cryo-needles at duty cycles of 20%-100% with 1-2.5 cm spacing. Results Analysis of various combinations shows that a central core of ≤−40°C develops at a distance of ~1 cm around the cryo-needles. Temperature increases linearly from this point to the ice ball leading edge (0°C), which is a further ≈1 cm away. Thus, the −40°C isotherm is approximately 1 cm inside the leading edge of the ice ball. The optimum distance between cryo-needles was 1.5-2 cm, at duty cycle settings of 70%-100%. At distances further apart or with lower duty cycle settings, ice balls either had a central core >−40°C or had an hourglass shape. Conclusion In answer to questions 1-3, tumor length, diameter, and shape will ultimately determine the number of needles and their configuration. However, we propose a conservative distance for cryo-needle placement between 1 and 1.5 cm should be adopted for clinical practice. In answer to question 4, using low duty cycle settings runs the risk of incomplete −40°C isotherm coverage of the tumor, and thus in routine practice we suggest that settings of 70%-100% are most appropriate. PMID:26902833

  7. [Detection of Plasmodium falciparum by using magnetic nanoparticles separation-based quantitative real-time PCR assay].

    PubMed

    Wang, Fei; Tian, Yin; Yang, Jing; Sun, Fu-Jun; Sun, Ning; Liu, Bi-Yong; Tian, Rui; Ge, Guang-Lu; Zou, Ming-qiang; Deng, Cong-liang; Liu, Yi

    2014-10-01

    To establish a magnetic nanoparticles separation-based quantitative real-time PCR (RT-PCR) assay for fast and accurate detection of Plasmodium falciparum and providing a technical support for improving the control and prevention of imported malaria. According to the conserved sequences of the P. falciparum genome 18SrRNA, the species-specific primers and probe were designed and synthetized. The RT-PCR was established by constructing the plasmid standard, fitting the standard curve and using magnetic nanoparticles separation. The sensitivity and specificity of the assay were evaluated. The relationship between the threshold cycle (Ct) and logarithm of initial templates copies was linear over a range of 2.5 x 10(1) to 2.5 x 10(8) copies/μl (R2 = 0.999). Among 13 subjects of entry frontier, a P. falciparum carrier with low load was detected by using the assay and none was detected with the conventional examinations (microscopic examinations and rapid tests). This assay shows a high sensitivity in detection of P. falciparum, with rapid and accurate characteristics, and is especially useful in diagnosis of P. falciparum infectors with low parasitaemia at entry-exit frontier ports.

  8. Magnetically separable maghemite/montmorillonite composite as an efficient heterogeneous Fenton-like catalyst for phenol degradation.

    PubMed

    Jin, Mingjie; Long, Mingce; Su, Hanrui; Pan, Yue; Zhang, Qiuzhuo; Wang, Juan; Zhou, Baoxue; Zhang, Yanwu

    2017-01-01

    To develop highly efficient and conveniently separable iron containing catalysts is crucial to remove recalcitrant organic pollutants in wastewater through a heterogeneous Fenton-like reaction. A maghemite/montmorillonite composite was synthesized by a coprecipitation and calcination method. The physiochemical properties of catalysts were characterized by XRD, TEM, nitrogen physisorption, thermogravimetric analysis/differential scanning calorimetry (TG/DSC), zeta potential, and magnetite susceptibility measurements. The influence of calcination temperatures and reaction parameters was investigated. The calcined composites retain magnetism because the presence of montmorillonite inhibited the growth of γ-Fe 2 O 3 nanoparticles, as well as their phase transition. The catalytic activities for phenol degradation were significantly enhanced by calcinations, which strengthen the interaction between iron oxides and aluminosilicate framework and result in more negatively charged surface. The composite (73 m 2 /g) calcined at 350 °C had the highest catalytic activities, with more than 99 % phenol reduction after only 35 min reaction at pH 3.6. Simultaneously, this catalyst exhibited high stability, low iron leaching, and magnetically separable ability for consecutive usage, making it promising for the removal of recalcitrant organic pollutants in wastewater.

  9. Microfluidic immunomagnetic cell separation from whole blood.

    PubMed

    Bhuvanendran Nair Gourikutty, Sajay; Chang, Chia-Pin; Puiu, Poenar Daniel

    2016-02-01

    Immunomagnetic-based separation has become a viable technique for the separation of cells and biomolecules. Here we report on the design and analysis of a simple and efficient microfluidic device for high throughput and high efficiency capture of cells tagged with magnetic particles. This is made possible by using a microfluidic chip integrated with customized arrays of permanent magnets capable of creating large magnetic field gradients, which determine the effective capturing of the tagged cells. This method is based on manipulating the cells which are under the influence of a combination of magnetic and fluid dynamic forces in a fluid under laminar flow through a microfluidic chip. A finite element analysis (FEA) model is developed to analyze the cell separation process and predict its behavior, which is validated subsequently by the experimental results. The magnetic field gradients created by various arrangements of magnetic arrays have been simulated using FEA and the influence of these field gradients on cell separation has been studied with the design of our microfluidic chip. The proof-of-concept for the proposed technique is demonstrated by capturing white blood cells (WBCs) from whole human blood. CD45-conjugated magnetic particles were added into whole blood samples to label WBCs and the mixture was flown through our microfluidic device to separate the labeled cells. After the separation process, the remaining WBCs in the elute were counted to determine the capture efficiency, and it was found that more than 99.9% WBCs have been successfully separated from whole blood. The proposed design can be used for positive selection as well as for negative enrichment of rare cells. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. CryoEM structure of a prokaryotic cyclic nucleotide-gated ion channel

    PubMed Central

    James, Zachary M.; Borst, Andrew J.; Haitin, Yoni; Frenz, Brandon; DiMaio, Frank; Zagotta, William N.; Veesler, David

    2017-01-01

    Cyclic nucleotide-gated (CNG) and hyperpolarization-activated cyclic nucleotide-regulated (HCN) ion channels play crucial physiological roles in phototransduction, olfaction, and cardiac pace making. These channels are characterized by the presence of a carboxyl-terminal cyclic nucleotide-binding domain (CNBD) that connects to the channel pore via a C-linker domain. Although cyclic nucleotide binding has been shown to promote CNG and HCN channel opening, the precise mechanism underlying gating remains poorly understood. Here we used cryoEM to determine the structure of the intact LliK CNG channel isolated from Leptospira licerasiae—which shares sequence similarity to eukaryotic CNG and HCN channels—in the presence of a saturating concentration of cAMP. A short S4–S5 linker connects nearby voltage-sensing and pore domains to produce a non–domain-swapped transmembrane architecture, which appears to be a hallmark of this channel family. We also observe major conformational changes of the LliK C-linkers and CNBDs relative to the crystal structures of isolated C-linker/CNBD fragments and the cryoEM structures of related CNG, HCN, and KCNH channels. The conformation of our LliK structure may represent a functional state of this channel family not captured in previous studies. PMID:28396445

  11. A new challenge: in-situ investigation of the elusive nanostructures in wet halite and clay using BIB/FIB-cryo-SEM methods

    NASA Astrophysics Data System (ADS)

    Desbois, G.; Urai, J. L.

    2009-04-01

    Mudrocks and saltrocks form seals for hydrocarbon accumulations, aquitards and chemical barriers. The sealing capacity is controlled either by the rock microstructure or by chemical interactions between minerals and the permeating fluid. A detailed knowledge about the sealing characteristics is of particular interest in Petroleum Sciences. Other fields of interest are the storage of anthropogenic carbon dioxide and radioactive waste in geologic formations. A key factor to the understanding of sealing by mudstones and saltrocks is the study of their porosity. However, Halite and clay are so fluids sensitive that investigation on dried samples required by traditional methods of investigations (metal injection methods [6],[3]; magnetic susceptibility measurement [4]; SEM imaging of broken surfaces [5] and CT scanner computing [7]) are critical for robust interpretation. In one hand, none of these methods is able to directly describe the in-situ porosity at the pore scale and on the other hand, most of these methods require dried samples in which the natural structure of pores could be damaged due to the desiccation, dehydration and dissolution-recrystallisation of the fabric. SEM imaging is certainly the most direct approach to investigate the porosity but it is generally limited by the poor quality of the mechanically prepared surfaces. This problem is solved by the recent development of ion milling tools (FIB: Focussed Ion Beam or BIB: Broad Ion Beam, which allows producing in-situ high quality polished cross-sections suitable for high resolution pores SEM imaging at nano-scale. More over, new and innovative developments of the cryo-SEM approach in the Geosciences allow investigating samples under wet natural conditions. Thus, we are developing the combination of FIB/BIB-cryo-SEM methods ([1],[2]), which combine in one machine the vitrification of the pore fluids by very rapid cooling, the excavation of the sample by ion milling tool and SEM imaging. By these, we

  12. Adding the Third Dimension to Virus Life Cycles: Three-Dimensional Reconstruction of Icosahedral Viruses from Cryo-Electron Micrographs

    PubMed Central

    Baker, T. S.; Olson, N. H.; Fuller, S. D.

    1999-01-01

    Viruses are cellular parasites. The linkage between viral and host functions makes the study of a viral life cycle an important key to cellular functions. A deeper understanding of many aspects of viral life cycles has emerged from coordinated molecular and structural studies carried out with a wide range of viral pathogens. Structural studies of viruses by means of cryo-electron microscopy and three-dimensional image reconstruction methods have grown explosively in the last decade. Here we review the use of cryo-electron microscopy for the determination of the structures of a number of icosahedral viruses. These studies span more than 20 virus families. Representative examples illustrate the use of moderate- to low-resolution (7- to 35-Å) structural analyses to illuminate functional aspects of viral life cycles including host recognition, viral attachment, entry, genome release, viral transcription, translation, proassembly, maturation, release, and transmission, as well as mechanisms of host defense. The success of cryo-electron microscopy in combination with three-dimensional image reconstruction for icosahedral viruses provides a firm foundation for future explorations of more-complex viral pathogens, including the vast number that are nonspherical or nonsymmetrical. PMID:10585969

  13. Improved cryoEM-Guided Iterative Molecular Dynamics–Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction

    PubMed Central

    2016-01-01

    Many excellent methods exist that incorporate cryo-electron microscopy (cryoEM) data to constrain computational protein structure prediction and refinement. Previously, it was shown that iteration of two such orthogonal sampling and scoring methods – Rosetta and molecular dynamics (MD) simulations – facilitated exploration of conformational space in principle. Here, we go beyond a proof-of-concept study and address significant remaining limitations of the iterative MD–Rosetta protein structure refinement protocol. Specifically, all parts of the iterative refinement protocol are now guided by medium-resolution cryoEM density maps, and previous knowledge about the native structure of the protein is no longer necessary. Models are identified solely based on score or simulation time. All four benchmark proteins showed substantial improvement through three rounds of the iterative refinement protocol. The best-scoring final models of two proteins had sub-Ångstrom RMSD to the native structure over residues in secondary structure elements. Molecular dynamics was most efficient in refining secondary structure elements and was thus highly complementary to the Rosetta refinement which is most powerful in refining side chains and loop regions. PMID:25883538

  14. MASS SEPARATION OF HIGH ENERGY PARTICLES

    DOEpatents

    Marshall, L.

    1962-09-25

    An apparatus and method are described for separating charged, high energy particles of equal momentum forming a beam where the particles differ slightly in masses. Magnetic lenses are utilized to focus the beam and maintain that condition while electrostatic fields located between magnetic lenses are utilized to cause transverse separation of the particles into two beams separated by a sufficient amount to permit an aperture to block one beam. (AEC)

  15. Accurate modelling of single-particle cryo-EM images quantifies the benefits expected from using Zernike phase contrast

    PubMed Central

    Hall, R. J.; Nogales, E.; Glaeser, R. M.

    2011-01-01

    The use of a Zernike-type phase plate in biological cryo-electron microscopy allows the imaging, without using defocus, of what are predominantly phase objects. It is thought that such phase-plate implementations might result in higher quality images, free from the problems of CTF correction that occur when images must be recorded at extremely high values of defocus. In single-particle cryo-electron microscopy it is hoped that these improvements in image quality will facilitate work on structures that have proved difficult to study, either because of their relatively small size or because the structures are not completely homogeneous. There is still a need, however, to quantify how much improvement can be gained by using a phase plate for single-particle cryo-electron microscopy. We present a method for quantitatively modelling the images recorded with 200 keV electrons, for single particles embedded in vitreous ice. We then investigate what difference the use of a phase-plate device could have on the processing of single-particle data. We confirm that using a phase plate results in single-particle datasets in which smaller molecules can be detected, particles can be more accurately aligned and problems of heterogeneity can be more easily addressed. PMID:21463690

  16. Tailoring transport properties of phase-separated manganite films with ordered magnetic nanostructures

    DOE PAGES

    Vlaminck, V.; Yanez, W.; Hoffman, J.; ...

    2016-08-02

    Here, the magnetotransport properties of thin manganite films (La 0.7Ca 0.3MnO 3) coupled with arrays of permalloy (Py) nanodots deposited on the surface of the film are studied as a function of temperature, magnetic field, and the size of the dots. In the presence of the magnetic dots, a reduction of the electrical resistivity is observed, especially at the insulator-to-metal transition, as well as a shift of the transition peak towards higher temperatures. This indicates that, due to local interface exchange coupling, highly conductive ferromagnetic domains are nucleated in the manganite film underneath the Py nanodots. The use of amore » simplified resistor network model allows us to estimate the size of the metallic regions induced by exchange coupling. At low temperatures, these regions extend ~70 nm beyond the edge of the nanodots, a length scale comparable to the correlation length of the ferromagnetic clusters in the phase-separated state of La 0.7Ca 0.3MnO 3.« less

  17. Cryo-electron microscopy study of bacteriophage T4 displaying anthrax toxin proteins

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fokine, Andrei; Bowman, Valorie D.; Battisti, Anthony J.

    2007-10-25

    The bacteriophage T4 capsid contains two accessory surface proteins, the small outer capsid protein (Soc, 870 copies) and the highly antigenic outer capsid protein (Hoc, 155 copies). As these are dispensable for capsid formation, they can be used for displaying proteins and macromolecular complexes on the T4 capsid surface. Anthrax toxin components were attached to the T4 capsid as a fusion protein of the N-terminal domain of the anthrax lethal factor (LFn) with Soc. The LFn-Soc fusion protein was complexed in vitro with Hoc{sup -}Soc{sup -}T4 phage. Subsequently, cleaved anthrax protective antigen heptamers (PA63){sub 7} were attached to the exposedmore » LFn domains. A cryo-electron microscopy study of the decorated T4 particles shows the complex of PA63 heptamers with LFn-Soc on the phage surface. Although the cryo-electron microscopy reconstruction is unable to differentiate on its own between different proposed models of the anthrax toxin, the density is consistent with a model that had predicted the orientation and position of three LFn molecules bound to one PA63 heptamer.« less

  18. Visualization of water transport into soybean nodules by Tof-SIMS cryo system.

    PubMed

    Iijima, Morio; Watanabe, Toshimasa; Yoshida, Tomoharu; Kawasaki, Michio; Kato, Toshiyuki; Yamane, Koji

    2015-04-15

    This paper examined the route of water supply into soybean nodules through the new visualization technique of time of flight secondary ion mass spectrometry (Tof-SIMS) cryo system, and obtained circumstantial evidence for the water inflow route. The maximum resolution of the Tof-SIMS imaging used by this study was 1.8 μm (defined as the three pixel step length), which allowed us to detect water movement at the cellular level. Deuterium-labeled water was supplied to soybean plants for 4h and the presence of deuterium in soybean nodules was analyzed by the Tof-SIMS cryo system. Deuterium ions were found only in the endodermis tissue surrounding the central cylinder in soybean nodules. Neither xylem vessels nor phloem complex itself did not indicate any deuterium accumulation. Deuterium-ion counts in the endodermis tissue were not changed by girdling treatment, which restricted water movement through the phloem complex. The results strongly indicated that nodule tissues did not receive water directly from the phloem complex, but received water through root cortex apoplastic pathway from the root axis. Copyright © 2015 Elsevier GmbH. All rights reserved.

  19. Structural dynamics of ribosome subunit association studied by mixing-spraying time-resolved cryo-EM

    PubMed Central

    Chen, Bo; Kaledhonkar, Sandip; Sun, Ming; Shen, Bingxin; Lu, Zonghuan; Barnard, David; Lu, Toh-Ming; Gonzalez, Ruben L.; Frank, Joachim

    2015-01-01

    Ribosomal subunit association is a key checkpoint in translation initiation, but its structural dynamics are poorly understood. Here, we used a recently developed mixing-spraying, time-resolved, cryogenic electron microscopy (cryo-EM) method to study ribosomal subunit association in the sub-second time range. We have improved this method and increased the cryo-EM data yield by tenfold. Pre-equilibrium states of the association reaction were captured by reacting the mixture of ribosomal subunits for 60 ms and 140 ms. We also identified three distinct ribosome conformations in the associated ribosomes. The observed proportions of these conformations are the same in these two time points, suggesting that ribosomes equilibrate among the three conformations within less than 60 ms upon formation. Our results demonstrate that the mixing-spraying method can capture multiple states of macromolecules during a sub-second reaction. Other fast processes, such as translation initiation, decoding and ribosome recycling, are amenable to study with this method. PMID:26004440

  20. A Protocol for the Preparation of Cryoprecipitate and Cryo-depleted Plasma for Proteomic Studies.

    PubMed

    Sparrow, Rosemary L; Simpson, Richard J; Greening, David W

    2017-01-01

    Cryoprecipitate is a concentrate of high-molecular-weight plasma proteins that precipitate when frozen plasma is slowly thawed at 1-6 °C. The concentrate contains factor VIII (antihemophilic factor), von Willebrand factor (vWF), fibrinogen, factor XIII, fibronectin, and small amounts of other plasma proteins. Clinical grade preparations of cryoprecipitate are mainly used to treat fibrinogen deficiency caused by acute bleeding or functional abnormalities of the fibrinogen protein. In the past, cryoprecipitate was used to treat von Willebrand disease and hemophilia A (factor VIII deficiency), but the availability of more highly purified coagulation factor concentrates or recombinant protein preparations has superseded the use of cryoprecipitate for these coagulopathies. Cryo-depleted plasma ("cryosupernatant") is the plasma supernatant remaining following removal of the cryoprecipitate from frozen-thawed plasma. It contains all the other plasma proteins and clotting factors present in plasma that remain soluble during cold-temperature thawing of the plasma. This protocol describes the clinical-scale preparation of cryoprecipitate and cryo-depleted plasma for proteomic studies.

  1. Native architecture of the Chlamydomonas chloroplast revealed by in situ cryo-electron tomography

    PubMed Central

    Engel, Benjamin D; Schaffer, Miroslava; Kuhn Cuellar, Luis; Villa, Elizabeth; Plitzko, Jürgen M; Baumeister, Wolfgang

    2015-01-01

    Chloroplast function is orchestrated by the organelle's intricate architecture. By combining cryo-focused ion beam milling of vitreous Chlamydomonas cells with cryo-electron tomography, we acquired three-dimensional structures of the chloroplast in its native state within the cell. Chloroplast envelope inner membrane invaginations were frequently found in close association with thylakoid tips, and the tips of multiple thylakoid stacks converged at dynamic sites on the chloroplast envelope, implicating lipid transport in thylakoid biogenesis. Subtomogram averaging and nearest neighbor analysis revealed that RuBisCO complexes were hexagonally packed within the pyrenoid, with ∼15 nm between their centers. Thylakoid stacks and the pyrenoid were connected by cylindrical pyrenoid tubules, physically bridging the sites of light-dependent photosynthesis and light-independent carbon fixation. Multiple parallel minitubules were bundled within each pyrenoid tubule, possibly serving as conduits for the targeted one-dimensional diffusion of small molecules such as ATP and sugars between the chloroplast stroma and the pyrenoid matrix. DOI: http://dx.doi.org/10.7554/eLife.04889.001 PMID:25584625

  2. Precision orbit determination performance for CryoSat-2

    NASA Astrophysics Data System (ADS)

    Schrama, Ernst

    2018-01-01

    In this paper we discuss our efforts to perform precision orbit determination (POD) of CryoSat-2 which depends on Doppler and satellite laser ranging tracking data. A dynamic orbit model is set-up and the residuals between the model and the tracking data is evaluated. The average r.m.s. of the 10 s averaged Doppler tracking pass residuals is approximately 0.39 mm/s; and the average of the laser tracking pass residuals becomes 1.42 cm. There are a number of other tests to verify the quality of the orbit solution, we compare our computed orbits against three independent external trajectories provided by the CNES. The CNES products are part of the CryoSat-2 products distributed by ESA. The radial differences of our solution relative to the CNES precision orbits shows an average r.m.s. of 1.25 cm between Jun-2010 and Apr-2017. The SIRAL altimeter crossover difference statistics demonstrate that the quality of our orbit solution is comparable to that of the POE solution computed by the CNES. In this paper we will discuss three important changes in our POD activities that have brought the orbit performance to this level. The improvements concern the way we implement temporal gravity accelerations observed by GRACE; the implementation of ITRF2014 coordinates and velocities for the DORIS beacons and the SLR tracking sites. We also discuss an adjustment of the SLR retroreflector position within the satellite reference frame. An unexpected result is that we find a systematic difference between the median of the 10 s Doppler tracking residuals which displays a statistically significant pattern in the South Atlantic Anomaly (SSA) area where the median of the velocity residuals varies in the range of -0.15 to +0.15 mm/s.

  3. Boundary-value problem for a counterrotating electrical discharge in an axial magnetic field. [plasma centrifuge for isotope separation

    NASA Technical Reports Server (NTRS)

    Hong, S. H.; Wilhelm, H. E.

    1978-01-01

    An electrical discharge between two ring electrodes embedded in the mantle of a cylindrical chamber is considered, in which the plasma in the anode and cathode regions rotates in opposite directions under the influence of an external axial magnetic field. The associated boundary-value problem for the coupled partial differential equations describing the azimuthal velocity and radial current-density fields is solved in closed form. The velocity, current density, induced magnetic induction, and electric fields are presented for typical Hartmann numbers, magnetic Reynolds numbers, and geometry parameters. The discharge is shown to produce anodic and cathodic plasma sections rotating at speeds of the order 1,000,000 cm/sec for conventional magnetic field intensities. Possible application of the magnetoactive discharge as a plasma centrifuge for isotope separation is discussed.

  4. Magnetic Reconnection at a Thin Current Sheet Separating Two Interlaced Flux Tubes at the Earth's Magnetopause

    NASA Astrophysics Data System (ADS)

    Kacem, I.; Jacquey, C.; Génot, V.; Lavraud, B.; Vernisse, Y.; Marchaudon, A.; Le Contel, O.; Breuillard, H.; Phan, T. D.; Hasegawa, H.; Oka, M.; Trattner, K. J.; Farrugia, C. J.; Paulson, K.; Eastwood, J. P.; Fuselier, S. A.; Turner, D.; Eriksson, S.; Wilder, F.; Russell, C. T.; Øieroset, M.; Burch, J.; Graham, D. B.; Sauvaud, J.-A.; Avanov, L.; Chandler, M.; Coffey, V.; Dorelli, J.; Gershman, D. J.; Giles, B. L.; Moore, T. E.; Saito, Y.; Chen, L.-J.; Penou, E.

    2018-03-01

    The occurrence of spatially and temporally variable reconnection at the Earth's magnetopause leads to the complex interaction of magnetic fields from the magnetosphere and magnetosheath. Flux transfer events (FTEs) constitute one such type of interaction. Their main characteristics are (1) an enhanced core magnetic field magnitude and (2) a bipolar magnetic field signature in the component normal to the magnetopause, reminiscent of a large-scale helicoidal flux tube magnetic configuration. However, other geometrical configurations which do not fit this classical picture have also been observed. Using high-resolution measurements from the Magnetospheric Multiscale mission, we investigate an event in the vicinity of the Earth's magnetopause on 7 November 2015. Despite signatures that, at first glance, appear consistent with a classic FTE, based on detailed geometrical and dynamical analyses as well as on topological signatures revealed by suprathermal electron properties, we demonstrate that this event is not consistent with a single, homogenous helicoidal structure. Our analysis rather suggests that it consists of the interaction of two separate sets of magnetic field lines with different connectivities. This complex three-dimensional interaction constructively conspires to produce signatures partially consistent with that of an FTE. We also show that, at the interface between the two sets of field lines, where the observed magnetic pileup occurs, a thin and strong current sheet forms with a large ion jet, which may be consistent with magnetic flux dissipation through magnetic reconnection in the interaction region.

  5. The separated electric and magnetic field responses of luminescent bacteria exposed to pulsed microwave irradiation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Williams, Catrin F., E-mail: williamscf@cardiff.ac.uk; School of Biosciences, Cardiff University, Main Building, Cathays Park, Cardiff, CF10 3AT Wales; Geroni, Gilles M.

    Electromagnetic fields (EMFs) are ubiquitous in the digital world we inhabit, with microwave and millimetre wave sources of non-ionizing radiation employed extensively in electronics and communications, e.g., in mobile phones and Wi-Fi. Indeed, the advent of 5G systems and the “internet of things” is likely to lead to massive densification of wireless networks. Whilst the thermal effects of EMFs on biological systems are well characterised, their putative non-thermal effects remain a controversial subject. Here, we use the bioluminescent marine bacterium, Vibrio fischeri, to monitor the effects of pulsed microwave electromagnetic fields, of nominal frequency 2.5 GHz, on light emission. Separatedmore » electric and magnetic field effects were investigated using a resonant microwave cavity, within which the maxima of each field are separated. For pulsed electric field exposure, the bacteria gave reproducible responses and recovery in light emission. At the lowest pulsed duty cycle (1.25%) and after short durations (100 ms) of exposure to the electric field at power levels of 4.5 W rms, we observed an initial stimulation of bioluminescence, whereas successive microwave pulses became inhibitory. Much of this behaviour is due to thermal effects, as the bacterial light output is very sensitive to the local temperature. Conversely, magnetic field exposure gave no measurable short-term responses even at the highest power levels of 32 W rms. Thus, we were able to detect, de-convolute, and evaluate independently the effects of separated electric and magnetic fields on exposure of a luminescent biological system to microwave irradiation.« less

  6. Preparation of anti-CD4 monoclonal antibody-conjugated magnetic poly(glycidyl methacrylate) particles and their application on CD4+ lymphocyte separation.

    PubMed

    Pimpha, Nuttaporn; Chaleawlert-umpon, Saowaluk; Chruewkamlow, Nuttapol; Kasinrerk, Watchara

    2011-03-15

    Novel immunomagnetic particles have been prepared for separation of CD4(+) lymphocytes. The magnetic nanoparticles with a diameter of approximately 5-6 nm were first synthesized by co-precipitation from ferrous and ferric iron solutions and subsequently encapsulated with poly(glycidyl methacrylate) (PGMA) by precipitation polymerization. Monoclonal antibody specific to CD4 molecules expressed on CD4(+) lymphocytes was conjugated to the surface of magnetic PGMA particles through covalent bonding between epoxide functional groups on the particle surface and primary amine groups of the antibodies. The generated immunomagnetic particles have successfully separated CD4(+) lymphocytes from whole blood with over 95% purity. The results indicated that these particles can be employed for cell separation and provide a strong potential to be applied in various biomedical applications including diagnosis, and monitoring of human diseases. Copyright © 2010 Elsevier B.V. All rights reserved.

  7. Distribution of coniferin in freeze-fixed stem of Ginkgo biloba L. by cryo-TOF-SIMS/SEM

    NASA Astrophysics Data System (ADS)

    Aoki, Dan; Hanaya, Yuto; Akita, Takuya; Matsushita, Yasuyuki; Yoshida, Masato; Kuroda, Katsushi; Yagami, Sachie; Takama, Ruka; Fukushima, Kazuhiko

    2016-08-01

    To clarify the role of coniferin in planta, semi-quantitative cellular distribution of coniferin in quick-frozen Ginkgo biloba L. (ginkgo) was visualized by cryo time-of-flight secondary ion mass spectrometry and scanning electron microscopy (cryo-TOF-SIMS/SEM) analysis. The amount and rough distribution of coniferin were confirmed through quantitative chromatography measurement using serial tangential sections of the freeze-fixed ginkgo stem. The lignification stage of the sample was estimated using microscopic observations. Coniferin distribution visualized at the transverse and radial surfaces of freeze-fixed ginkgo stem suggested that coniferin is stored in the vacuoles, and showed good agreement with the assimilation timing of coniferin to lignin in differentiating xylem. Consequently, it is suggested that coniferin is stored in the tracheid cells of differentiating xylem and is a lignin precursor.

  8. Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome

    PubMed Central

    Abeyrathne, Priyanka D; Koh, Cha San; Grant, Timothy; Grigorieff, Nikolaus; Korostelev, Andrei A

    2016-01-01

    Internal ribosome entry sites (IRESs) mediate cap-independent translation of viral mRNAs. Using electron cryo-microscopy of a single specimen, we present five ribosome structures formed with the Taura syndrome virus IRES and translocase eEF2•GTP bound with sordarin. The structures suggest a trajectory of IRES translocation, required for translation initiation, and provide an unprecedented view of eEF2 dynamics. The IRES rearranges from extended to bent to extended conformations. This inchworm-like movement is coupled with ribosomal inter-subunit rotation and 40S head swivel. eEF2, attached to the 60S subunit, slides along the rotating 40S subunit to enter the A site. Its diphthamide-bearing tip at domain IV separates the tRNA-mRNA-like pseudoknot I (PKI) of the IRES from the decoding center. This unlocks 40S domains, facilitating head swivel and biasing IRES translocation via hitherto-elusive intermediates with PKI captured between the A and P sites. The structures suggest missing links in our understanding of tRNA translocation. DOI: http://dx.doi.org/10.7554/eLife.14874.001 PMID:27159452

  9. Evaluation of CryoSat-2 SARIn vs. SAR Arctic Sea Ice Freeboard

    NASA Astrophysics Data System (ADS)

    Di Bella, A.; Skourup, H.; Forsberg, R.

    2017-12-01

    Earth climate is a complex system which behaviour is dictated by the interaction among many components. Sea ice, one of these fundamental components, interacts directly with the oceans and the atmosphere playing an important role in defining heat exchange processes and, thus, impacting weather patterns on a global scale. Sea ice thickness estimates have notably improved in the last couple of decades, however, the uncertainty of such estimates is still significant. For the past 7 years, the ESA CryoSat-2 (CS2) mission has provided a unique opportunity to observe polar regions due to its extended coverage up to 88° N/S. The SIRAL radar altimeter on board CS2 enables the sea ice community to estimate sea ice thickness by measuring the sea ice freeboard. Studies by Armitage and Davidson [2014] and Di Bella et al. [submitted] showed that the interferometric capabilities of SIRAL can be used to retrieve an increased number of valid sea surface heights in sea ice covered regions and thus reduce the random uncertainty of the estimated freeboards, especially in areas with a sparse lead distribution. This study focuses on the comparison between sea ice freeboard estimates obtained by processing L1B SARIn data inside the Wingham box - an area in the Arctic Ocean where SIRAL has acquired SARIn data for 4 years - and those obtained by processing L1B SAR data in the area surrounding the box. This comparison evaluates CS2 performance on Arctic sea ice from a statistical perspective by analysing the continuity of freeboard estimates in areas where SIRAL switches between SAR and SARIn acquisition modes. Data collected during the Operation IceBridge and CryoVEx field campaigns are included in the study as an additional validation. Besides investigating the possibility of including the phase information from SIRAL in currently available freeboard estimates, this results provide valuable information for a possible SARIn CryoSat follow-on mission.

  10. Selective separation of lambdacyhalothrin by porous/magnetic molecularly imprinted polymers prepared by Pickering emulsion polymerization.

    PubMed

    Hang, Hui; Li, Chunxiang; Pan, Jianming; Li, Linzi; Dai, Jiangdong; Dai, Xiaohui; Yu, Ping; Feng, Yonghai

    2013-10-01

    Porous/magnetic molecularly imprinted polymers (PM-MIPs) were prepared by Pickering emulsion polymerization. The reaction was carried out in an oil/water emulsion using magnetic halloysite nanotubes as the stabilizer instead of a toxic surfactant. In the oil phase, the imprinting process was conducted by radical polymerization of functional and cross-linked monomers, and porogen chloroform generated steam under the high reaction temperature, which resulted in some pores decorated with easily accessible molecular binding sites within the as-made PM-MIPs. The characterization demonstrated that the PM-MIPs were porous and magnetic inorganic-polymer composite microparticles with magnetic sensitivity (M(s) = 0.7448 emu/g), thermal stability (below 473 K) and magnetic stability (over the pH range of 2.0-8.0). The PM-MIPs were used as a sorbent for the selective binding of lambdacyhalothrin (LC) and rapidly separated under an external magnetic field. The Freundlich isotherm model gave a good fit to the experimental data. The adsorption kinetics of the PM-MIPs was well described by pseudo-second-order kinetics, indicating that the chemical process could be the rate-limiting step in the adsorption of LC. The selective recognition experiments exhibited the outstanding selective adsorption effect of the PM-MIPs for target LC. Moreover, the PM-MIPs regeneration without significant loss in adsorption capacity was demonstrated by at least four repeated cycles. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Stack Characterization in CryoSat Level1b SAR/SARin Baseline C

    NASA Astrophysics Data System (ADS)

    Scagliola, Michele; Fornari, Marco; Di Giacinto, Andrea; Bouffard, Jerome; Féménias, Pierre; Parrinello, Tommaso

    2015-04-01

    CryoSat was launched on the 8th April 2010 and is the first European ice mission dedicated to the monitoring of precise changes in the thickness of polar ice sheets and floating sea ice. CryoSat is the first altimetry mission operating in SAR mode and it carries an innovative radar altimeter called the Synthetic Aperture Interferometric Altimeter (SIRAL), that transmits pulses at a high pulse repetition frequency thus making the received echoes phase coherent and suitable for azimuth processing. The current CryoSat IPF (Instrument Processing Facility), Baseline B, was released in operation in February 2012. After more than 2 years of development, the release in operations of the Baseline C is expected in the first half of 2015. It is worth recalling here that the CryoSat SAR/SARin IPF1 generates 20Hz waveforms in correspondence of an approximately equally spaced set of ground locations on the Earth surface, i.e. surface samples, and that a surface sample gathers a collection of single-look echoes coming from the processed bursts during the time of visibility. Thus, for a given surface sample, the stack can be defined as the collection of all the single-look echoes pointing to the current surface sample, after applying all the necessary range corrections. The L1B product contains the power average of all the single-look echoes in the stack: the multi-looked L1B waveform. This reduces the data volume, while removing some information contained in the single looks, useful for characterizing the surface and modelling the L1B waveform. To recover such information, a set of parameters has been added to the L1B product: the stack characterization or beam behaviour parameters. The stack characterization, already included in previous Baselines, has been reviewed and expanded in Baseline C. This poster describes all the stack characterization parameters, detailing what they represent and how they have been computed. In details, such parameters can be summarized in: - Stack

  12. 3D structure of eukaryotic flagella in a quiescent state revealed by cryo-electron tomography

    PubMed Central

    Nicastro, Daniela; McIntosh, J. Richard; Baumeister, Wolfgang

    2005-01-01

    We have used cryo-electron tomography to investigate the 3D structure and macromolecular organization of intact, frozen-hydrated sea urchin sperm flagella in a quiescent state. The tomographic reconstructions provide information at a resolution better than 6 nm about the in situ arrangements of macromolecules that are key for flagellar motility. We have visualized the heptameric rings of the motor domains in the outer dynein arm complex and determined that they lie parallel to the plane that contains the axes of neighboring flagellar microtubules. Both the material associated with the central pair of microtubules and the radial spokes display a plane of symmetry that helps to explain the planar beat pattern of these flagella. Cryo-electron tomography has proven to be a powerful technique for helping us understand the relationships between flagellar structure and function and the design of macromolecular machines in situ. PMID:16246999

  13. Separating hyperfine from spin-orbit interactions in organic semiconductors by multi-octave magnetic resonance using coplanar waveguide microresonators

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Joshi, G.; Miller, R.; Ogden, L.

    2016-09-05

    Separating the influence of hyperfine from spin-orbit interactions in spin-dependent carrier recombination and dissociation processes necessitates magnetic resonance spectroscopy over a wide range of frequencies. We have designed compact and versatile coplanar waveguide resonators for continuous-wave electrically detected magnetic resonance and tested these on organic light-emitting diodes. By exploiting both the fundamental and higher-harmonic modes of the resonators, we cover almost five octaves in resonance frequency within a single setup. The measurements with a common π-conjugated polymer as the active material reveal small but non-negligible effects of spin-orbit interactions, which give rise to a broadening of the magnetic resonance spectrummore » with increasing frequency.« less

  14. Southern hemisphere sand furrows: spatial patterning and implications for the cryo-venting process.

    NASA Astrophysics Data System (ADS)

    Nash, Ciaran; Bourke, Mary

    2015-04-01

    Carbon dioxide is an important volatile on Mars. Seasonally, atmospheric CO2 condenses as ice on to the Martian surface and sublimates during the spring. Links have been made between a suite of observed surface features and the sublimation of surface CO2 ice; these include spider-like araneiform, gullies, and fans. Sand furrows are one such feature; suggested to form due to the erosive action of pressurised CO2 gas as it escapes through cracks in surficial ice (i.e. cryo-venting, Bourke, 2013). There are significant and important differences between the North and South Hemispheres, particularly in the seasonal CO2 deposits. Previous investigations into the formation and distribution of sand furrows on Mars have concentrated solely on the northern hemisphere. We present a study of furrows in the southern hemisphere which has yielded new data on their distribution and spatial patterning as well as providing insights into the cryo-venting process. A total of 221 dune sites were surveyed over the three Martian years' of available HiRISE data to establish the overall distribution of sand furrows. A more detailed study was carried out at eight sites using data from Mars Year 30. These sites represent a latitudinal sample of dunefields located between 40°S to 72°S. Surficial CO2 ice thickness was estimated using the Mars Climate Database (Millour et al., 2014). Our data show that sand furrows are significantly less numerous in the study region than in the northern hemisphere where data show they occur in 95% of surveyed sites. We found a strong correlation between latitude and furrow distribution. As one progresses polewards from 40°S, furrows become more numerous until 68°S. Furrows were not detected south of 72°S. Carbon dioxide ice thickness has been highlighted as a potentially important factor controlling furrow distribution in the northern hemisphere (Bourke and McGaley-Towle, 2014). Results from our investigation suggest there is a feedback mechanism between

  15. Retrieving improved multi-temporal CryoSat elevations over ice caps and glaciers - a case study of Barnes ice cap

    NASA Astrophysics Data System (ADS)

    Nilsson, Johan; Burgess, David

    2014-05-01

    The CryoSat mission was launched in 2010 to observe the Earth's cryosphere. In contrast to previous satellite radar altimeters, this mission is expected to monitor the elevation of small ice caps and glaciers, which according to the IPCC will be the largest contributor to 21st century sea level rise. To date the ESA CryoSat SARiN level-2 (L2) elevation product is not yet fully optimized for use over these types of glaciated regions, as its processed with a more universal algorithm. Thus the aim of this study is to demonstrate that with the use of improved processing CryoSat SARiN data can be used for more accurate topography mapping and elevation change detection for ice caps and glaciers. To demonstrate this, elevations and elevation changes over Barnes ice cap, located on Baffin Island in the Canadian Arctic, have been estimated from available data from the years 2010-2013. ESA's CryoSat level-1b (L1b) SARiN baseline "B" data product was used and processed in-house to estimate surface elevations. The resulting product is referred to as DTU-L2. The processing focused on improving the retracker, reducing phase noise and correcting phase ambiguities. The accuracy of the DTU-L2 and the ESA-L2 product was determined by comparing the measured elevations against NASA's IceBridge Airborne Topographic Mapper (ATM) elevations from May 2011. The resulting difference in accuracy was determined by comparing their associated errors. From the multi-temporal measurements spanning the period 2010-2013, elevation changes where estimated and compared to ICESat derived changes from 2003-2009. The result of the study shows good agreement between the NASA measured ATM elevations and the DTU-L2 data. It also shows that the pattern of elevation change is similar to that derived from ICESat data. The accuracy of the DTU-L2 estimated elevations is on average several factors higher compared to the ESA-L2 elevation product. These preliminary results demonstrates that CryoSat elevation data

  16. Smart Energy Cryo-refrigerator Technology for the next generation Very Large Array

    NASA Astrophysics Data System (ADS)

    Spagna, Stefano

    2018-01-01

    We describe a “smart energy” cryocooler technology architecture for the next generation Very Large Array that makes use of multiple variable frequency cold heads driven from a single variable speed air cooled compressor. Preliminary experiments indicate that the compressor variable flow control, advanced diagnostics, and the cryo-refrigerator low vibration, provide a unique energy efficient capability for the very large number of antennas that will be employed in this array.

  17. Tailored functionalization of iron oxide nanoparticles for MRI, drug delivery, magnetic separation and immobilization of biosubstances.

    PubMed

    Hola, Katerina; Markova, Zdenka; Zoppellaro, Giorgio; Tucek, Jiri; Zboril, Radek

    2015-11-01

    In this critical review, we outline various covalent and non-covalent approaches for the functionalization of iron oxide nanoparticles (IONPs). Tuning the surface chemistry and design of magnetic nanoparticles are described in relation to their applicability in advanced medical technologies and biotechnologies including magnetic resonance imaging (MRI) contrast agents, targeted drug delivery, magnetic separations and immobilizations of proteins, enzymes, antibodies, targeting agents and other biosubstances. We review synthetic strategies for the controlled preparation of IONPs modified with frequently used functional groups including amine, carboxyl and hydroxyl groups as well as the preparation of IONPs functionalized with other species, e.g., epoxy, thiol, alkane, azide, and alkyne groups. Three main coupling strategies for linking IONPs with active agents are presented: (i) chemical modification of amine groups on the surface of IONPs, (ii) chemical modification of bioactive substances (e.g. with fluorescent dyes), and (iii) the activation of carboxyl groups mainly for enzyme immobilization. Applications for drug delivery using click chemistry linking or biodegradable bonds are compared to non-covalent methods based on polymer modified condensed magnetic nanoclusters. Among many challenges, we highlight the specific surface engineering allowing both therapeutic and diagnostic applications (theranostics) of IONPs and magnetic/metallic hybrid nanostructures possessing a huge potential in biocatalysis, green chemistry, magnetic bioseparations and bioimaging. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Inactivation and magnetic separation of bacteria from liquid suspensions using electrosprayed and nonelectrosprayed nZVI particles: observations and mechanisms.

    PubMed

    Chen, Qi; Gao, Min; Li, Jing; Shen, Fangxia; Wu, Yan; Xu, Zhenqiang; Yao, Maosheng

    2012-02-21

    Here, nonelectrosprayed nanoscale zerovalent iron (NE-nZVI), electrosprayed nZVI (E-nZVI) and preoxidized nZVI (O-nZVI) particles were applied to inactivating Bacillus subtilis, Escherichia coli as well as bacteria in various wastewater samples. In addition, magnetic separation was applied to the mixture of 0.2 mL bacterial sample and 1.8 mL E-nZVI or NE-nZVI suspensions. Bacterial concentrations and optical density of the supernatants were analyzed using culturing, optical adsorption and qPCR tests. In general, for wastewater samples the inactivations were shown to range from 1-log to 3-log. PCR-DGGE analysis indicated that no gene mutation occurred when bacteria were treated with nZVI. Using magnetic separation, significant physical removals, revealed as a function of nZVI type (NE-,E- and O-nZVI) and bacterial concentration, up to 6-log were obtained. E-nZVI and NE-nZVI were shown to react differently with B. subtilis and E. coli, although exhibiting similar inactivation rates. qPCR tests detected higher amount of DNA in the supernatants from mixing E. coli with NE-nZVI, but less for E-nZVI. However, the opposite was observed with B. subtilis. Our data together with optical adsorption analysis suggested that the inactivation and magnetic separation mainly depend on Fe(0)/Fe(3)O(4) shell compositions, the type of bacteria (aerobic and anaerobic) and their concentrations.

  19. Extraction of remanent magnetization from magnetization vector inversions of airborne full tensor magnetic gradiometry data

    NASA Astrophysics Data System (ADS)

    Queitsch, M.; Schiffler, M.; Stolz, R.; Meyer, M.; Kukowski, N.

    2017-12-01

    Measurements of the Earth's magnetic field are one of the most used methods in geophysical exploration. The ambiguity of the method, especially during modeling and inversion of magnetic field data sets, is one of its biggest challenges. Additional directional information, e.g. gathered by gradiometer systems based on Superconducting Quantum Interference Devices (SQUIDs), will positively influence the inversion results and will thus lead to better subsurface magnetization models. This is especially beneficial, regarding the shape and direction of magnetized structures, especially when a significant remanent magnetization of the underlying sources is present. The possibility to separate induced and remanent contributions to the total magnetization may in future also open up advanced ways for geological interpretation of the data, e.g. a first estimation of diagenesis processes. In this study we present the results of airborne full tensor magnetic gradiometry (FTMG) surveys conducted over a dolerite intrusion in central Germany and the results of two magnetization vector inversions (MVI) of the FTMG and a conventional total field anomaly data set. A separation of the two main contributions of the acquired total magnetization will be compared with information of the rock magnetization measured on orientated rock samples. The FTMG inversion results show a much better agreement in direction and strength of both total and remanent magnetization compared to the inversion using only total field anomaly data. To enhance the separation process, the application of additional geophysical methods, i.e. frequency domain electromagnetics (FDEM), in order to gather spatial information of subsurface rock susceptibility will also be discussed. In this approach, we try to extract not only information on subsurface conductivity but also the induced magnetization. Using the total magnetization from the FTMG data and the induced magnetization from the FDEM data, the full separation of

  20. Magnetic separation of encapsulated islet cells labeled with superparamagnetic iron oxide nano particles.

    PubMed

    Mettler, Esther; Trenkler, Anja; Feilen, Peter J; Wiegand, Frederik; Fottner, Christian; Ehrhart, Friederike; Zimmermann, Heiko; Hwang, Yong Hwa; Lee, Dong Yun; Fischer, Stefan; Schreiber, Laura M; Weber, Matthias M

    2013-01-01

    Islet cell transplantation is a promising option for the restoration of normal glucose homeostasis in patients with type 1 diabetes. Because graft volume is a crucial issue in islet transplantations for patients with diabetes, we evaluated a new method for increasing functional tissue yield in xenogeneic grafts of encapsulated islets. Islets were labeled with three different superparamagnetic iron oxide nano particles (SPIONs; dextran-coated SPION, siloxane-coated SPION, and heparin-coated SPION). Magnetic separation was performed to separate encapsulated islets from the empty capsules, and cell viability and function were tested. Islets labeled with 1000 μg Fe/ml dextran-coated SPIONs experienced a 69.9% reduction in graft volume, with a 33.2% loss of islet-containing capsules. Islets labeled with 100 μg Fe/ml heparin-coated SPIONs showed a 46.4% reduction in graft volume, with a 4.5% loss of capsules containing islets. No purification could be achieved using siloxane-coated SPIONs due to its toxicity to the primary islets. SPION labeling of islets is useful for transplant purification during islet separation as well as in vivo imaging after transplantation. Furthermore, purification of encapsulated islets can also reduce the volume of the encapsulated islets without impairing their function by removing empty capsules. © 2013 John Wiley & Sons A/S.