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Sample records for afm images reveal

  1. AFM imaging reveals the tetrameric structure of the TRPC1 channel

    SciTech Connect

    Barrera, Nelson P.; Shaifta, Yasin; McFadzean, Ian; Ward, Jeremy P.T.; Henderson, Robert M.; Edwardson, J. Michael . E-mail: jme1000@cam.ac.uk

    2007-07-13

    We have determined the subunit stoichiometry of the transient receptor potential C1 (TRPC1) channel by imaging isolated channels using atomic force microscopy (AFM). A frequency distribution of the molecular volumes of individual channel particles had two peaks, at 170 and 720 nm{sup 3}, corresponding with the expected sizes of TRPC1 monomers and tetramers, respectively. Complexes were formed between TRPC1 channels and antibodies against a V5 epitope tag present on each subunit. The frequency distribution of angles between pairs of bound antibodies had two peaks, at 88{sup o} and 178{sup o}. This result again indicates that the channel assembles as a tetramer.

  2. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

    PubMed Central

    Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; Norton, Malgorzata G.; Teckman, Jeffrey H.; Marszal, Ewa; Osmulski, Pawel A.

    2016-01-01

    α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found in WT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo

  3. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

    DOE PAGES

    Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; ...

    2016-03-23

    α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemicalmore » data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found inWT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in vivo

  4. AFM Imaging Reveals Topographic Diversity of Wild Type and Z Variant Polymers of Human α1-Proteinase Inhibitor

    SciTech Connect

    Gaczynska, Maria; Karpowicz, Przemyslaw; Stuart, Christine E.; Norton, Malgorzata G.; Teckman, Jeffrey H.; Marszal, Ewa; Osmulski, Pawel A.

    2016-03-23

    α1-Proteinase inhibitor (antitrypsin) is a canonical example of the serpin family member that binds and inhibits serine proteases. The natural metastability of serpins is crucial to carry out structural rearrangements necessary for biological activity. However, the enhanced metastability of the mutant Z variant of antitrypsin, in addition to folding defect, may substantially contribute to its polymerization, a process leading to incurable serpinopathy. The metastability also impedes structural studies on the polymers. There are no crystal structures of Z monomer or any kind of polymers larger than engineered wild type (WT) trimer. Our understanding of polymerization mechanisms is based on biochemical data using in vitro generated WT oligomers and molecular simulations. Here we applied atomic force microscopy (AFM) to compare topography of monomers, in vitro formed WT oligomers, and Z type polymers isolated from transgenic mouse liver. We found the AFM images of monomers closely resembled an antitrypsin outer shell modeled after the crystal structure. We confirmed that the Z variant demonstrated higher spontaneous propensity to dimerize than WT monomers. We also detected an unexpectedly broad range of different types of polymers with periodicity and topography depending on the applied method of polymerization. Short linear oligomers of unit arrangement similar to the Z polymers were especially abundant in heat-treated WT preparations. Long linear polymers were a prominent and unique component of liver extracts. However, the liver preparations contained also multiple types of oligomers of topographies undistinguishable from those found inWT samples polymerized with heat, low pH or guanidine hydrochloride treatments. In conclusion, we established that AFM is an excellent technique to assess morphological diversity of antitrypsin polymers, which is important for etiology of serpinopathies. These data also support previous, but controversial models of in

  5. Nanomechanics of Yeast Surfaces Revealed by AFM

    NASA Astrophysics Data System (ADS)

    Dague, Etienne; Beaussart, Audrey; Alsteens, David

    Despite the large and well-documented characterization of the microbial cell wall in terms of chemical composition, the determination of the mechanical properties of surface molecules in relation to their function remains a key challenge in cell biology.The emergence of powerful tools allowing molecular manipulations has already revolutionized our understanding of the surface properties of fungal cells. At the frontier between nanophysics and molecular biology, atomic force microscopy (AFM), and more specifically single-molecule force spectroscopy (SMFS), has strongly contributed to our current knowledge of the cell wall organization and nanomechanical properties. However, due to the complexity of the technique, measurements on live cells are still at their infancy.In this chapter, we describe the cell wall composition and recapitulate the principles of AFM as well as the main current methodologies used to perform AFM measurements on live cells, including sample immobilization and tip functionalization.The current status of the progress in probing nanomechanics of the yeast surface is illustrated through three recent breakthrough studies. Determination of the cell wall nanostructure and elasticity is presented through two examples: the mechanical response of mannoproteins from brewing yeasts and elasticity measurements on lacking polysaccharide mutant strains. Additionally, an elegant study on force-induced unfolding and clustering of adhesion proteins located at the cell surface is also presented.

  6. Vibration signature analysis of AFM images

    SciTech Connect

    Joshi, G.A.; Fu, J.; Pandit, S.M.

    1995-12-31

    Vibration signature analysis has been commonly used for the machine condition monitoring and the control of errors. However, it has been rarely employed for the analysis of the precision instruments such as an atomic force microscope (AFM). In this work, an AFM was used to collect vibration data from a sample positioning stage under different suspension and support conditions. Certain structural characteristics of the sample positioning stage show up as a result of the vibration signature analysis of the surface height images measured using an AFM. It is important to understand these vibration characteristics in order to reduce vibrational uncertainty, improve the damping and structural design, and to eliminate the imaging imperfections. The choice of method applied for vibration analysis may affect the results. Two methods, the data dependent systems (DDS) analysis and the Welch`s periodogram averaging method were investigated for application to this problem. Both techniques provide smooth spectrum plots from the data. Welch`s periodogram provides a coarse resolution as limited by the number of samples and requires a choice of window to be decided subjectively by the user. The DDS analysis provides sharper spectral peaks at a much higher resolution and a much lower noise floor. A decomposition of the signal variance in terms of the frequencies is provided as well. The technique is based on an objective model adequacy criterion.

  7. Combination STM/AFM and AFM Images of Magnetic Domains

    NASA Astrophysics Data System (ADS)

    Yi, L.; Gallagher, M.; Howells, S.; Chen, T.; Sarid, D.

    1991-12-01

    By employing a cantilevered tip in a scanning tunneling microscope, one obtains images that show an enhancement of features associated with forces whose derivatives vary along the direction of scanning. The theory of this process is described together with experimental results showing magnetic domains on a gold coated floppy disk. Also shown are atomic force microscopy images of a ferrofluid-developed magnetic tape.

  8. Preparation of DNA and nucleoprotein samples for AFM imaging

    PubMed Central

    Lyubchenko, Yuri L.

    2010-01-01

    Sample preparation techniques allowing reliable and reproducible imaging of DNA with various structures, topologies and complexes with proteins are reviewed. The major emphasis is given to methods utilizing chemical functionalization of mica, enabling preparation of the surfaces with required characteristics. The methods are illustrated by examples of imaging of different DNA structures. Special attention is given to the possibility of AFM to image the dynamics of DNA at the nanoscale. The capabilities of time-lapse AFM in aqueous solutions are illustrated by imaging of dynamic processes as transitions of local alternative structures (transition of DNA between H and B forms). The application of AFM to studies of protein-DNA complexes is illustrated by a few examples of imaging site-specific complexes, as well as such systems as chromatin. The time-lapse AFM studies of protein-DNA complexes including very recent advances with the use of high-speed AFM are reviewed. PMID:20864349

  9. AFM imaging of fenestrated liver sinusoidal endothelial cells.

    PubMed

    Braet, F; Wisse, E

    2012-12-01

    Each microscope with its dedicated sample preparation technique provides the investigator with a specific set of data giving an instrument-determined (or restricted) insight into the structure and function of a tissue, a cell or parts thereof. Stepwise improvements in existing techniques, both instrumental and preparative, can sometimes cross barriers in resolution and image quality. Of course, investigators get really excited when completely new principles of microscopy and imaging are offered in promising new instruments, such as the AFM. The present paper summarizes a first phase of studies on the thin endothelial cells of the liver. It describes the preparation-dependent differences in AFM imaging of these cells after isolation. Special point of interest concerned the dynamics of the fenestrae, thought to filter lipid-carrying particles during their transport from the blood to the liver cells. It also describes the attempts to image the details of these cells when alive in cell cultures. It explains what physical conditions, mainly contributed to the scanning stylus, are thought to play a part in the limitations in imaging these cells. The AFM also offers promising specifications to those interested in cell surface details, such as membrane-associated structures, receptors, coated pits, cellular junctions and molecular aggregations or domains. The AFM also offers nano-manipulation possibilities, strengths and elasticity measurements, force interactions, affinity measurements, stiffness and other physical aspects of membranes and cytoskeleton. The potential for molecular approaches is there. New developments in cantilever construction and computer software promise to bring real time video imaging to the AFM. Home made accessories for the first generation of AFM are now commodities in commercial instruments and make the life of the AFM microscopist easier. Also, the combination of different microscopies, such as AFM and TEM, or AFM and SEM find their way to the

  10. Mounting of Escherichia coli spheroplasts for AFM imaging.

    SciTech Connect

    Sullivan, Claretta J; Morrell-Falvey, Jennifer L; Allison, David P; Doktycz, Mitchel John

    2005-11-01

    The cytoplasmic membrane of Escherichia coli (E. coli) is the location of numerous, chemically specific transporters and recognition elements. Investigation of this membrane in vivo by atomic force microscopy (AFM) requires removal of the cell wall and stable immobilization of the spheroplast. AFM images demonstrate that spheroplasts can be secured with warm gelatin applied to the mica substrate just before the addition of a spheroplast suspension. The resulting preparation can be repeatedly imaged by AFM over the course of several hours. Confocal fluorescence imaging confirms the association of the spheroplasts with the gelatin layer. Gelatin molecules are known to reorder into a network after heating. Entrapment within this gelatin network is believed to be responsible for the immobilization of spheroplasts on mica.

  11. Mapping individual cosmid DNAs by direct AFM imaging.

    PubMed

    Allison, D P; Kerper, P S; Doktycz, M J; Thundat, T; Modrich, P; Larimer, F W; Johnson, D K; Hoyt, P R; Mucenski, M L; Warmack, R J

    1997-05-01

    Individual cosmid clones have been restriction mapped by directly imaging, with the atomic force microscope (AFM), a mutant EcoRI endonuclease site-specifically bound to DNA. Images and data are presented that locate six restriction sites, predicted from gel electrophoresis, on a 35-kb cosmid isolated from mouse chromosome 7. Measured distances between endonuclease molecules bound to lambda DNA, when compared to known values, demonstrate the accuracy of AFM mapping to better than 1%. These results may be extended to identify other important site-specific protein-DNA interactions, such as transcription factor and mismatch repair enzyme binding, difficult to resolve by current techniques.

  12. Probing the Double Layer: Effect of Image Forces on AFM

    PubMed Central

    Sachs, Frederick

    2006-01-01

    Force probes such as AFM tips or laser trap latex beads have a dielectric constant much less than that of the water that they displace. Thus when a probe approaches a charged surface under water it will be repelled simply based upon the image forces, and these can be of nN magnitude. PMID:16714346

  13. Fractal analysis of AFM images of the surface of Bowman's membrane of the human cornea.

    PubMed

    Ţălu, Ştefan; Stach, Sebastian; Sueiras, Vivian; Ziebarth, Noël Marysa

    2015-04-01

    The objective of this study is to further investigate the ultrastructural details of the surface of Bowman's membrane of the human cornea, using atomic force microscopy (AFM) images. One representative image acquired of Bowman's membrane of a human cornea was investigated. The three-dimensional (3-D) surface of the sample was imaged using AFM in contact mode, while the sample was completely submerged in optisol solution. Height and deflection images were acquired at multiple scan lengths using the MFP-3D AFM system software (Asylum Research, Santa Barbara, CA), based in IGOR Pro (WaveMetrics, Lake Oswego, OR). A novel approach, based on computational algorithms for fractal analysis of surfaces applied for AFM data, was utilized to analyze the surface structure. The surfaces revealed a fractal structure at the nanometer scale. The fractal dimension, D, provided quantitative values that characterize the scale properties of surface geometry. Detailed characterization of the surface topography was obtained using statistical parameters, in accordance with ISO 25178-2: 2012. Results obtained by fractal analysis confirm the relationship between the value of the fractal dimension and the statistical surface roughness parameters. The surface structure of Bowman's membrane of the human cornea is complex. The analyzed AFM images confirm a fractal nature of the surface, which is not taken into account by classical surface statistical parameters. Surface fractal dimension could be useful in ophthalmology to quantify corneal architectural changes associated with different disease states to further our understanding of disease evolution.

  14. Tissue section AFM: In situ ultrastructural imaging of native biomolecules

    PubMed Central

    Graham, Helen K.; Hodson, Nigel W.; Hoyland, Judith A.; Millward-Sadler, Sarah J.; Garrod, David; Scothern, Anthea; Griffiths, Christopher E.M.; Watson, Rachel E.B.; Cox, Thomas R.; Erler, Janine T.; Trafford, Andrew W.; Sherratt, Michael J.

    2010-01-01

    Conventional approaches for ultrastructural high-resolution imaging of biological specimens induce profound changes in bio-molecular structures. By combining tissue cryo-sectioning with non-destructive atomic force microscopy (AFM) imaging we have developed a methodology that may be applied by the non-specialist to both preserve and visualize bio-molecular structures (in particular extracellular matrix assemblies) in situ. This tissue section AFM technique is capable of: i) resolving nm–µm scale features of intra- and extracellular structures in tissue cryo-sections; ii) imaging the same tissue region before and after experimental interventions; iii) combining ultrastructural imaging with complimentary microscopical and micromechanical methods. Here, we employ this technique to: i) visualize the macro-molecular structures of unstained and unfixed fibrillar collagens (in skin, cartilage and intervertebral disc), elastic fibres (in aorta and lung), desmosomes (in nasal epithelium) and mitochondria (in heart); ii) quantify the ultrastructural effects of sequential collagenase digestion on a single elastic fibre; iii) correlate optical (auto fluorescent) with ultrastructural (AFM) images of aortic elastic lamellae. PMID:20144712

  15. Image Analysis and Length Estimation of Biomolecules Using AFM

    PubMed Central

    Sundstrom, Andrew; Cirrone, Silvio; Paxia, Salvatore; Hsueh, Carlin; Kjolby, Rachel; Gimzewski, James K.; Reed, Jason; Mishra, Bud

    2014-01-01

    There are many examples of problems in pattern analysis for which it is often possible to obtain systematic characterizations, if in addition a small number of useful features or parameters of the image are known a priori or can be estimated reasonably well. Often, the relevant features of a particular pattern analysis problem are easy to enumerate, as when statistical structures of the patterns are well understood from the knowledge of the domain. We study a problem from molecular image analysis, where such a domain-dependent understanding may be lacking to some degree and the features must be inferred via machine-learning techniques. In this paper, we propose a rigorous, fully automated technique for this problem. We are motivated by an application of atomic force microscopy (AFM) image processing needed to solve a central problem in molecular biology, aimed at obtaining the complete transcription profile of a single cell, a snapshot that shows which genes are being expressed and to what degree. Reed et al. (“Single molecule transcription profiling with AFM,” Nanotechnology, vol. 18, no. 4, 2007) showed that the transcription profiling problem reduces to making high-precision measurements of biomolecule backbone lengths, correct to within 20–25 bp (6–7.5 nm). Here, we present an image processing and length estimation pipeline using AFM that comes close to achieving these measurement tolerances. In particular, we develop a biased length estimator on trained coefficients of a simple linear regression model, biweighted by a Beaton–Tukey function, whose feature universe is constrained by James–Stein shrinkage to avoid overfitting. In terms of extensibility and addressing the model selection problem, this formulation subsumes the models we studied. PMID:22759526

  16. AFM-IR: Technology and Applications in Nanoscale Infrared Spectroscopy and Chemical Imaging.

    PubMed

    Dazzi, Alexandre; Prater, Craig B

    2016-12-13

    Atomic force microscopy-based infrared spectroscopy (AFM-IR) is a rapidly emerging technique that provides chemical analysis and compositional mapping with spatial resolution far below conventional optical diffraction limits. AFM-IR works by using the tip of an AFM probe to locally detect thermal expansion in a sample resulting from absorption of infrared radiation. AFM-IR thus can provide the spatial resolution of AFM in combination with the chemical analysis and compositional imaging capabilities of infrared spectroscopy. This article briefly reviews the development and underlying technology of AFM-IR, including recent advances, and then surveys a wide range of applications and investigations using AFM-IR. AFM-IR applications that will be discussed include those in polymers, life sciences, photonics, solar cells, semiconductors, pharmaceuticals, and cultural heritage. In the Supporting Information , the authors provide a theoretical section that reviews the physics underlying the AFM-IR measurement and detection mechanisms.

  17. Intrinsically High-Q Dynamic AFM Imaging in Liquid with a Significantly Extended Needle Tip

    PubMed Central

    Minary-Jolandan, Majid; Tajik, Arash; Wang, Ning; Yu, Min-Feng

    2012-01-01

    Atomic force microscope (AFM) probe with a long and rigid needle tip was fabricated and studied for high Q factor dynamic (tapping mode) AFM imaging of samples submersed in liquid. The extended needle tip over a regular commercially-available tapping mode AFM cantilever was sufficiently long to keep the AFM cantilever from submersed in liquid, which significantly minimized the hydrodynamic damping involved in dynamic AFM imaging of samples in liquid. Dynamic AFM imaging of samples in liquid at an intrinsic Q factor of over 100 and an operation frequency of over 200 kHz was demonstrated. The method has the potential to be extended to acquire viscoelastic materials properties and provide truly gentle imaging of soft biological samples in physiological environments. PMID:22595833

  18. Combined force spectroscopy, AFM and calorimetric studies to reveal the nanostructural organization of biomimetic membranes.

    PubMed

    Suárez-Germà, C; Morros, A; Montero, M T; Hernández-Borrell, J; Domènech, Ò

    2014-10-01

    In this work we studied a binary lipid matrix of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) (POPG), a composition that mimics the inner membrane of Escherichia coli. More specifically, liposomes with varying fractions of POPG were analysed by differential scanning calorimetry (DSC) and a binary phase diagram of the system was created. Additionally, we performed atomic force microscopy (AFM) imaging of supported lipid bilayers (SLBs) of similar compositions at different temperatures, in order to create a pseudo-binary phase diagram specific to this membrane model. AFM study of SLBs is of particular interest, as it is conceived as the most adequate technique not only for studying lipid bilayer systems but also for imaging and even nanomanipulating inserted membrane proteins. The construction of the above-mentioned phase diagram enabled us to grasp better the thermodynamics of the thermal lipid transition from a gel-like POPE:POPG phase system to a more fluid phase system. Finally, AFM force spectroscopy (FS) was used to determine the nanomechanics of these two lipid phases at 27°C and at different POPG fractions. The resulting data correlated with the specific composition of each phase was calculated from the AFM phase diagram obtained. All the experiments were done in the presence of 10 mM of Ca(2+), as this ion is commonly used when performing AFM with negatively charged phospholipids.

  19. In-plane information from tapping mode AFM images

    NASA Astrophysics Data System (ADS)

    Marcus, Matthew

    2003-03-01

    Phase contrast in intermittent-contact atomic force microscopy is shown to reveal in-plane structural and mechanical properties of poly(diacetylene) monolayer films. This is surprising because measurements of in-plane properties typically require a contact mode of microscopy. Such measurements are possible because the tilt in the oscillating cantilever provides components of motion not just perpendicular to the surface, but also parallel to the sample surface. Lateral tip displacement is virtually universal in AFM, implying that any oscillating tip-AFM technique is sensitive to in-plane material properties. Although the tilt in the cantilever is small ( 10^o) it produces a component of motion that is 20% of the total tip displacement, and this motion accounts for 5-10% of dissipated energy through the tip-sample interaction[1]. The data is used in conjunction with a numerical model to extract in-plane material parameters. The effect of the cantilever tilt on phase measurements is directly verified through measurements on silicon samples tilted at a variety of angles with respect to the cantilever. The lateral tip displacement we make use of allows measurements of in-plane properties of soft samples such as polymer and biological samples. This work was done in collaboration with M. D'Amato, R.W. Carpick, and M.A. Eriksson, and was supported by the NSF CAREER and MRSEC programs and the Research Corporation. 1. M.S. Marcus, R.W. Carpick, D.Y. Sasaki, M.A. Eriksson, Phys. Rev. Lett. 88, 226103 (2002)

  20. Structure and Dynamics of Four-way DNA Junctions Dynamics Revealed by Single-Molecule AFM

    NASA Astrophysics Data System (ADS)

    Lyubchenko, Yuri

    2004-03-01

    For-way DNA junctions (Holliday junctions) are critical intermediates for homologous, site-specific recombination, DNA repair and replication. A wealth of structural information is available for immobile four-way junctions. However, these data cannot give the answer on the mechanism of branch migration, the major property of the Holliday junction. Two models for the mechanism of branch migration were suggested. According to the early model of Alberts-Meselson-Sigal, exchanging DNA strands around the junction remain parallel during branch migration. Kinetic studies of branch migration suggest an alternative model in which the junction adopts an extended conformation. We tested these models using a Holliday junction undergoing branch migration. Note that it was the first time when the dynamics of the four-way DNA junction capable of branch migration had been analyzed. We applied time-lapse atomic force microscopy (single molecule dynamics AFM) to image directly loosely bound DNA at liquid-surface interface. These experiments show that mobile Holliday junctions adopt an unfolded conformation during branch migration. This conformation of the junction remains unchanged until strand separation. The data obtained support the model for branch migration having the extended conformation of the Holliday junction. The analysis of the Holliday junctions dynamics at conditions limiting branch migration revealed a broad movement of the arms suggesting that the range of mobility of these junctions is much wider than detected before. Further applications of the time-lapse AFM approach in attempt to resolve the subpopulations of the junctions conformers and the prospects for analyses of dynamics of complex biological systems will be discussed.

  1. High-speed AFM images of thermal motion provide stiffness map of interfacial membrane protein moieties.

    PubMed

    Preiner, Johannes; Horner, Andreas; Karner, Andreas; Ollinger, Nicole; Siligan, Christine; Pohl, Peter; Hinterdorfer, Peter

    2015-01-14

    The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges.

  2. High-Speed AFM Images of Thermal Motion Provide Stiffness Map of Interfacial Membrane Protein Moieties

    PubMed Central

    2014-01-01

    The flexibilities of extracellular loops determine ligand binding and activation of membrane receptors. Arising from fluctuations in inter- and intraproteinaceous interactions, flexibility manifests in thermal motion. Here we demonstrate that quantitative flexibility values can be extracted from directly imaging the thermal motion of membrane protein moieties using high-speed atomic force microscopy (HS-AFM). Stiffness maps of the main periplasmic loops of single reconstituted water channels (AqpZ, GlpF) revealed the spatial and temporal organization of loop-stabilizing intraproteinaceous H-bonds and salt bridges. PMID:25516527

  3. Molecular shape and binding force of Mycoplasma mobile's leg protein Gli349 revealed by an AFM study

    SciTech Connect

    Lesoil, Charles; Nonaka, Takahiro; Sekiguchi, Hiroshi; Osada, Toshiya; Miyata, Makoto; Afrin, Rehana; Ikai, Atsushi

    2010-01-15

    Recent studies of the gliding bacteria Mycoplasma mobile have identified a family of proteins called the Gli family which was considered to be involved in this novel and yet fairly unknown motility system. The 349 kDa protein called Gli349 was successfully isolated and purified from the bacteria, and electron microscopy imaging and antibody experiments led to the hypothesis that it acts as the 'leg' of M. mobile, responsible for attachment to the substrate as well as for gliding motility. However, more precise evidence of the molecular shape and function of this protein was required to asses this theory any further. In this study, an atomic force microscope (AFM) was used both as an imaging and a force measurement device to provide new information about Gli349 and its role in gliding motility. AFM images of the protein were obtained revealing a complex structure with both rigid and flexible parts, consistent with previous electron micrographs of the protein. Single-molecular force spectroscopy experiments were also performed, revealing that Gli349 is able to specifically bind to sialyllactose molecules and withstand unbinding forces around 70 pN. These findings strongly support the idea that Gli349 is the 'leg' protein of M. mobile, responsible for binding and also most probably force generation during gliding motility.

  4. Investigation of the influence of UV irradiation on collagen thin films by AFM imaging.

    PubMed

    Stylianou, Andreas; Yova, Dido; Alexandratou, Eleni

    2014-12-01

    Collagen is the major fibrous extracellular matrix protein and due to its unique properties, it has been widely used as biomaterial, scaffold and cell-substrate. The aim of the paper was to use Atomic Force Microscopy (AFM) in order to investigate well-characterized collagen thin films after ultraviolet light (UV) irradiation. The films were also used as in vitro culturing substrates in order to investigate the UV-induced alterations to fibroblasts. A special attention was given in the alteration on collagen D-periodicity. For short irradiation times, spectroscopy (fluorescence/absorption) studies demonstrated that photodegradation took place and AFM imaging showed alterations in surface roughness. Also, it was highlighted that UV-irradiation had different effects when it was applied on collagen solution than on films. Concerning fibroblast culturing, it was shown that fibroblast behavior was affected after UV irradiation of both collagen solution and films. Furthermore, after a long irradiation time, collagen fibrils were deformed revealing that collagen fibrils are consisting of multiple shells and D-periodicity occurred on both outer and inner shells. The clarification of the effects of UV light on collagen and the induced modifications of cell behavior on UV-irradiated collagen-based surfaces will contribute to the better understanding of cell-matrix interactions in the nanoscale and will assist in the appropriate use of UV light for sterilizing and photo-cross-linking applications.

  5. Multiparametric high-resolution imaging of native proteins by force-distance curve-based AFM.

    PubMed

    Pfreundschuh, Moritz; Martinez-Martin, David; Mulvihill, Estefania; Wegmann, Susanne; Muller, Daniel J

    2014-05-01

    A current challenge in the life sciences is to understand how the properties of individual molecular machines adjust in order to meet the functional requirements of the cell. Recent developments in force-distance (FD) curve-based atomic force microscopy (FD-based AFM) enable researchers to combine sub-nanometer imaging with quantitative mapping of physical, chemical and biological properties. Here we present a protocol to apply FD-based AFM to the multiparametric imaging of native proteins under physiological conditions. We describe procedures for experimental FD-based AFM setup, high-resolution imaging of proteins in the native unperturbed state with simultaneous quantitative mapping of multiple parameters, and data interpretation and analysis. The protocol, which can be completed in 1-3 d, enables researchers to image proteins and protein complexes in the native unperturbed state and to simultaneously map their biophysical and biochemical properties at sub-nanometer resolution.

  6. Mechanism of high-resolution STM, AFM and IETS-STM imaging with functionalized tips

    NASA Astrophysics Data System (ADS)

    Temirov, R.; Hapala, P.; Tautz, F. S.; Jelinek, P.

    2015-03-01

    High-resolution AFM and STM with functionalized tips is well established, but a detailed understanding of the image mechanism is still missing. Moreover, recently this family of imaging techniques has been complemented by a method based on inelastic electron tunneling spectroscopy. Here we present a comprehensive mechanical and transport simulation model that explains essentially all image features in functionalized tip STM, AFM and IETS-STM. Important aspects of the mechanism are: (i) Images are dominantly determined by Pauli repulsion, (ii) in STM and IETS STM this force signal is transduced into an elastic or inelastic conductance signal, (iii) probe particle relaxation leads to image sharpening, (iv) the apparent imaging of hydrogen bonds can be explained by a relaxation effect, and (v) electrostatic forces may also influence the image contrast.

  7. New insights into morphology of high performance BHJ photovoltaics revealed by high resolution AFM.

    PubMed

    Wang, Dong; Liu, Feng; Yagihashi, Noritoshi; Nakaya, Masafumi; Ferdous, Sunzida; Liang, Xiaobin; Muramatsu, Atsushi; Nakajima, Ken; Russell, Thomas P

    2014-10-08

    Direct imaging of the bulk heterojunction (BHJ) thin film morphology in polymer-based solar cells is essential to understand device function and optimize efficiency. The morphology of the BHJ active layer consists of bicontinuous domains of the donor and acceptor materials, having characteristic length scales of several tens of nanometers, that reduces charge recombination, enhances charge separation, and enables electron and hole transport to their respective electrodes. Direct imaging of the morphology from the molecular to macroscopic level, though, is lacking. Though transmission electron tomography provides a 3D, real-space image of the morphology, quantifying the structure is not possible. Here we used high-resolution atomic force microscopy (AFM) in the tapping and nanomechanical modes to investigate the BHJ active layer morphology that, when combined with Ar(+) etching, provided unique insights with unparalleled spatial resolution. PCBM was seen to form a network that interpenetrated into the fibrillar network of the hole-conducting polymer, both being imbedded in a mixture of the two components. The free surface was found to be enriched with polymer crystals having a "face-on" orientation and the morphology at the anode interface was markedly different.

  8. A rapid and automated relocation method of an AFM probe for high-resolution imaging.

    PubMed

    Zhou, Peilin; Yu, Haibo; Shi, Jialin; Jiao, Niandong; Wang, Zhidong; Wang, Yuechao; Liu, Lianqing

    2016-09-30

    The atomic force microscope (AFM) is one of the most powerful tools for high-resolution imaging and high-precision positioning for nanomanipulation. The selection of the scanning area of the AFM depends on the use of the optical microscope. However, the resolution of an optical microscope is generally no larger than 200 nm owing to wavelength limitations of visible light. Taking into consideration the two determinants of relocation-relative angular rotation and positional offset between the AFM probe and nano target-it is therefore extremely challenging to precisely relocate the AFM probe to the initial scan/manipulation area for the same nano target after the AFM probe has been replaced, or after the sample has been moved. In this paper, we investigate a rapid automated relocation method for the nano target of an AFM using a coordinate transformation. The relocation process is both simple and rapid; moreover, multiple nano targets can be relocated by only identifying a pair of reference points. It possesses a centimeter-scale location range and nano-scale precision. The main advantages of this method are that it overcomes the limitations associated with the resolution of optical microscopes, and that it is label-free on the target areas, which means that it does not require the use of special artificial markers on the target sample areas. Relocation experiments using nanospheres, DNA, SWCNTs, and nano patterns amply demonstrate the practicality and efficiency of the proposed method, which provides technical support for mass nanomanipulation and detection based on AFM for multiple nano targets that are widely distributed in a large area.

  9. Imaging and force measurement of LDL and HDL by AFM in air and liquid

    PubMed Central

    Gan, Chaoye; Ao, Meiying; Liu, Zhanghua; Chen, Yong

    2015-01-01

    The size and biomechanical properties of lipoproteins are tightly correlated with their structures/functions. While atomic force microscopy (AFM) has been used to image lipoproteins the force measurement of these nano-sized particles is missing. We detected that the sizes of LDL and HDL in liquid are close to the commonly known values. The Young’s modulus of LDL or HDL is ∼0.4 GPa which is similar to that of some viral capsids or nanovesicles but greatly larger than that of various liposomes. The adhesive force of LDL or HDL is small (∼200 pN). The comparison of AFM detection in air and liquid was also performed which is currently lacking. Our data may provide useful information for better understanding and AFM detection of lipoproteins. PMID:25893163

  10. Imaging and force measurement of LDL and HDL by AFM in air and liquid.

    PubMed

    Gan, Chaoye; Ao, Meiying; Liu, Zhanghua; Chen, Yong

    2015-01-01

    The size and biomechanical properties of lipoproteins are tightly correlated with their structures/functions. While atomic force microscopy (AFM) has been used to image lipoproteins the force measurement of these nano-sized particles is missing. We detected that the sizes of LDL and HDL in liquid are close to the commonly known values. The Young's modulus of LDL or HDL is ∼0.4 GPa which is similar to that of some viral capsids or nanovesicles but greatly larger than that of various liposomes. The adhesive force of LDL or HDL is small (∼200 pN). The comparison of AFM detection in air and liquid was also performed which is currently lacking. Our data may provide useful information for better understanding and AFM detection of lipoproteins.

  11. First-principles AFM image simulation with frozen density embedding theory

    NASA Astrophysics Data System (ADS)

    Sakai, Yuki; Lee, Alex J.; Chelikowsky, James R.

    We present efficient first-principles method of non-contact atomic force microscopy (nc-AFM). Ordinary nc-AFM simulations based on density functional theory (DFT) require exhaustive computational cost because it involves thousands of total energy calculations. Regarding the sample as a fixed external potential can reduce the computational cost, and we adopt frozen density embedding theory (FDET) for this purpose. Simulated nc-AFM images with FDET using a carbon monoxide tip well reproduces the full DFT images of benzene, pentacene, and graphene, although optimized tip-sample distances and interaction energies in FDET are underestimated and overestimated, respectively. The FDET-based simulation method is promising for AFM image simulation of surfaces and two-dimensional materials. This work was supported by U.S. DOE under Grant No. DE-FG02-06ER46286 and Award No. DE-SC0008877, and by Welch Foundation under Grant F-1837. Computational resources are provided by NERSC and TACC.

  12. SEM and AFM imaging of solar cells defects

    NASA Astrophysics Data System (ADS)

    Škarvada, Pavel; Macků, Robert; Dallaeva, Dinara S.; Sedlák, Petr; Grmela, Lubomír.; Tománek, Pavel

    2015-01-01

    The paper deals with the successive localization and imaging of solar cell defects, going from macroscale to microscale. For the purpose of localization, the light emission from reversed bias samples is used. After rough macroscopic localization, microscopic localization by scanning probe microscopy combined with a photomultiplier (shadow mapping) is performed. The type of microscopic defects are discernable from their current-voltage plot or from noise measurements. Two specific defects, both of the avalanche type, with different voltage threshold, are presented in this paper. Current voltage plots and radiant flux versus voltage characteristics for two temperatures, topography, shadow map and corresponding SEM micrographs are shown for both samples.

  13. Investigation of surface changes of nanoparticles using TM-AFM phase imaging.

    PubMed

    Dong, Rong; Yu, Liya E

    2003-06-15

    Tapping-mode AFM (TM-AFM) phase imaging was utilized to characterize the surface changes of nanosize particles, in regard to the effects of different amounts of condensed water and organic coatings on particle surfaces. Model nanoparticles were continuously examined under various relative humidity (RH) levels by concurrently obtaining both topographic and phase images. The condensed water appeared to soften particle surfaces and to increase tip-sample attractive interaction over relatively stiff surfaces, which were shown with dark phase contrasts and negative phase shift values in phase images. Under high RH, a massive amount of water gave the particles a droplet-like surface, which reversed the original negative phase shifts to positive values with bright contrasts. Glutaric-acid coatings provided a compliant surface with high viscosity resulting in a dark phase contrast, whereas water droplets containing relatively low viscosity gave a bright phase contrast and positive phase shift. Overall, our results show that it is essential to describe the physical properties of a sample surface as solid, soft, or droplet-like material in order to derive a meaningful understanding of the surface changes of nanosize particles based on TM-AFM phase images. In contrast to other phase imaging studies, this work clearly correlates continuous surface changes with phase images, demonstrating a promising approach to characterize environmental nanoparticles.

  14. AFM tip characterization by using FFT filtered images of step structures.

    PubMed

    Yan, Yongda; Xue, Bo; Hu, Zhenjiang; Zhao, Xuesen

    2016-01-01

    The measurement resolution of an atomic force microscope (AFM) is largely dependent on the radius of the tip. Meanwhile, when using AFM to study nanoscale surface properties, the value of the tip radius is needed in calculations. As such, estimation of the tip radius is important for analyzing results taken using an AFM. In this study, a geometrical model created by scanning a step structure with an AFM tip was developed. The tip was assumed to have a hemispherical cone shape. Profiles simulated by tips with different scanning radii were calculated by fast Fourier transform (FFT). By analyzing the influence of tip radius variation on the spectra of simulated profiles, it was found that low-frequency harmonics were more susceptible, and that the relationship between the tip radius and the low-frequency harmonic amplitude of the step structure varied monotonically. Based on this regularity, we developed a new method to characterize the radius of the hemispherical tip. The tip radii estimated with this approach were comparable to the results obtained using scanning electron microscope imaging and blind reconstruction methods.

  15. Graphene Nanopore Support System for Simultaneous High-Resolution AFM Imaging and Conductance Measurements

    PubMed Central

    2015-01-01

    Accurately defining the nanoporous structure and sensing the ionic flow across nanoscale pores in thin films and membranes has a wide range of applications, including characterization of biological ion channels and receptors, DNA sequencing, molecule separation by nanoparticle films, sensing by block co-polymers films, and catalysis through metal–organic frameworks. Ionic conductance through nanopores is often regulated by their 3D structures, a relationship that can be accurately determined only by their simultaneous measurements. However, defining their structure–function relationships directly by any existing techniques is still not possible. Atomic force microscopy (AFM) can image the structures of these pores at high resolution in an aqueous environment, and electrophysiological techniques can measure ion flow through individual nanoscale pores. Combining these techniques is limited by the lack of nanoscale interfaces. We have designed a graphene-based single-nanopore support (∼5 nm thick with ∼20 nm pore diameter) and have integrated AFM imaging and ionic conductance recording using our newly designed double-chamber recording system to study an overlaid thin film. The functionality of this integrated system is demonstrated by electrical recording (<10 pS conductance) of suspended lipid bilayers spanning a nanopore and simultaneous AFM imaging of the bilayer. PMID:24581087

  16. Robust deposition of lambda DNA on mica for imaging by AFM in air.

    PubMed

    Cervantes, Nancy Anabel Gerling; Gutiérrez-Medina, Braulio

    2014-01-01

    Long DNA molecules remain difficult to image by atomic force microscopy (AFM) because of their tendency to entanglement and spontaneous formation of networks. We present a comparison of two different DNA deposition methods operating at room temperature and humidity conditions, aimed at reproducible imaging of isolated and relaxed λ DNA conformations by AFM in air. We first demonstrate that a standard deposition procedure, consisting in adsorption of DNA in the presence of divalent cations followed by washing and air-drying steps, yields a coexistence of different types of λ DNA networks with a only a few isolated DNA chains. In contrast, deposition using a spin-coating-based technique results in reproducible coverage of a significant fraction of the substrate area by isolated and relaxed λ DNA molecules, with the added benefit of a reduction in the effect of a residual layer that normally embeds DNA strands and leads to an apparent DNA height closer to the expected value. Furthermore, we show that deposition by spin-coating is also well-suited to visualize DNA-protein complexes. These results indicate that spin-coating is a simple, powerful alternative for reproducible sample preparation for AFM imaging.

  17. Quantitative description of collagen fibre network on trabecular bone surfaces based on AFM imaging.

    PubMed

    Hua, W-D; Chen, P-P; Xu, M-Q; Ao, Z; Liu, Y; Han, D; He, F

    2016-04-01

    The collagen fibre network is an important part of extracellular matrix (ECM) on trabecular bone surface. The geometry features of the network can provide us insights into its physical and physiological properties. However, previous researches have not focused on the geometry and the quantitative description of the collagen fibre network on trabecular bone surface. In this study,we developed a procedure to quantitatively describe the network and verified the validity of the procedure. The experiment proceeds as follow. Atomic force microscopy (AFM) was used to acquire submicron resolution images of the trabecular surface. Then, an image analysing procedure was built to extract important parameters, including, fibre orientation, fibre density, fibre width, fibre crossing numbers, the number of holes formed by fibre s, and the area of holes from AFM images. In order to verify the validity of the parameters extracted by image analysing methods, we adopted two other methods, which are statistical geometry model and computer simulation, to calculate those same parameters and check the consistency of the three methods' results. Statistical tests indicate that there is no significant difference between three groups. We conclude that, (a) the ECM on trabecular surface mainly consists of random collagen fibre network with oriented fibres; (b) our method based on image analysing can be used to characterize quantitative geometry features of the collagen fibre network effectively. This method may provide a basis for quantitative investigating the architecture and function of collagen fibre network.

  18. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging

    PubMed Central

    Dukic, Maja; Adams, Jonathan D.; Fantner, Georg E.

    2015-01-01

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air. PMID:26574164

  19. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging

    NASA Astrophysics Data System (ADS)

    Dukic, Maja; Adams, Jonathan D.; Fantner, Georg E.

    2015-11-01

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air.

  20. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging.

    PubMed

    Dukic, Maja; Adams, Jonathan D; Fantner, Georg E

    2015-11-17

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air.

  1. Identifying and quantifying two ligand-binding sites while imaging native human membrane receptors by AFM

    NASA Astrophysics Data System (ADS)

    Pfreundschuh, Moritz; Alsteens, David; Wieneke, Ralph; Zhang, Cheng; Coughlin, Shaun R.; Tampé, Robert; Kobilka, Brian K.; Müller, Daniel J.

    2015-11-01

    A current challenge in life sciences is to image cell membrane receptors while characterizing their specific interactions with various ligands. Addressing this issue has been hampered by the lack of suitable nanoscopic methods. Here we address this challenge and introduce multifunctional high-resolution atomic force microscopy (AFM) to image human protease-activated receptors (PAR1) in the functionally important lipid membrane and to simultaneously localize and quantify their binding to two different ligands. Therefore, we introduce the surface chemistry to bifunctionalize AFM tips with the native receptor-activating peptide and a tris-N-nitrilotriacetic acid (tris-NTA) group binding to a His10-tag engineered to PAR1. We further introduce ways to discern between the binding of both ligands to different receptor sites while imaging native PAR1s. Surface chemistry and nanoscopic method are applicable to a range of biological systems in vitro and in vivo and to concurrently detect and localize multiple ligand-binding sites at single receptor resolution.

  2. Hydrocarbons in phlogopite from Kasenyi kamafugitic rocks (SW Uganda): cross-correlated AFM, confocal microscopy and Raman imaging

    NASA Astrophysics Data System (ADS)

    Moro, Daniele; Valdrè, Giovanni; Mesto, Ernesto; Scordari, Fernando; Lacalamita, Maria; Ventura, Giancarlo Della; Bellatreccia, Fabio; Scirè, Salvatore; Schingaro, Emanuela

    2017-01-01

    This study presents a cross-correlated surface and near surface investigation of two phlogopite polytypes from Kasenyi kamafugitic rocks (SW Uganda) by means of advanced Atomic Force Microscopy (AFM), confocal microscopy and Raman micro-spectroscopy. AFM revealed comparable nanomorphology and electrostatic surface potential for the two mica polytypes. A widespread presence of nano-protrusions located on the mica flake surface was also observed, with an aspect ratio (maximum height/maximum width) from 0.01 to 0.09. Confocal microscopy showed these features to range from few nm to several μm in dimension, and shapes from perfectly circular to ellipsoidic and strongly elongated. Raman spectra collected across the bubbles showed an intense and convolute absorption in the range 3000–2800 cm‑1, associated with weaker bands at 1655, 1438 and 1297 cm‑1, indicating the presence of fluid inclusions consisting of aliphatic hydrocarbons, alkanes and cycloalkanes, with minor amounts of oxygenated compounds, such as carboxylic acids. High-resolution Raman images provided evidence that these hydrocarbons are confined within the bubbles. This work represents the first direct evidence that phlogopite, a common rock-forming mineral, may be a possible reservoir for hydrocarbons.

  3. Hydrocarbons in phlogopite from Kasenyi kamafugitic rocks (SW Uganda): cross-correlated AFM, confocal microscopy and Raman imaging.

    PubMed

    Moro, Daniele; Valdrè, Giovanni; Mesto, Ernesto; Scordari, Fernando; Lacalamita, Maria; Ventura, Giancarlo Della; Bellatreccia, Fabio; Scirè, Salvatore; Schingaro, Emanuela

    2017-01-18

    This study presents a cross-correlated surface and near surface investigation of two phlogopite polytypes from Kasenyi kamafugitic rocks (SW Uganda) by means of advanced Atomic Force Microscopy (AFM), confocal microscopy and Raman micro-spectroscopy. AFM revealed comparable nanomorphology and electrostatic surface potential for the two mica polytypes. A widespread presence of nano-protrusions located on the mica flake surface was also observed, with an aspect ratio (maximum height/maximum width) from 0.01 to 0.09. Confocal microscopy showed these features to range from few nm to several μm in dimension, and shapes from perfectly circular to ellipsoidic and strongly elongated. Raman spectra collected across the bubbles showed an intense and convolute absorption in the range 3000-2800 cm(-1), associated with weaker bands at 1655, 1438 and 1297 cm(-1), indicating the presence of fluid inclusions consisting of aliphatic hydrocarbons, alkanes and cycloalkanes, with minor amounts of oxygenated compounds, such as carboxylic acids. High-resolution Raman images provided evidence that these hydrocarbons are confined within the bubbles. This work represents the first direct evidence that phlogopite, a common rock-forming mineral, may be a possible reservoir for hydrocarbons.

  4. Hydrocarbons in phlogopite from Kasenyi kamafugitic rocks (SW Uganda): cross-correlated AFM, confocal microscopy and Raman imaging

    PubMed Central

    Moro, Daniele; Valdrè, Giovanni; Mesto, Ernesto; Scordari, Fernando; Lacalamita, Maria; Ventura, Giancarlo Della; Bellatreccia, Fabio; Scirè, Salvatore; Schingaro, Emanuela

    2017-01-01

    This study presents a cross-correlated surface and near surface investigation of two phlogopite polytypes from Kasenyi kamafugitic rocks (SW Uganda) by means of advanced Atomic Force Microscopy (AFM), confocal microscopy and Raman micro-spectroscopy. AFM revealed comparable nanomorphology and electrostatic surface potential for the two mica polytypes. A widespread presence of nano-protrusions located on the mica flake surface was also observed, with an aspect ratio (maximum height/maximum width) from 0.01 to 0.09. Confocal microscopy showed these features to range from few nm to several μm in dimension, and shapes from perfectly circular to ellipsoidic and strongly elongated. Raman spectra collected across the bubbles showed an intense and convolute absorption in the range 3000–2800 cm−1, associated with weaker bands at 1655, 1438 and 1297 cm−1, indicating the presence of fluid inclusions consisting of aliphatic hydrocarbons, alkanes and cycloalkanes, with minor amounts of oxygenated compounds, such as carboxylic acids. High-resolution Raman images provided evidence that these hydrocarbons are confined within the bubbles. This work represents the first direct evidence that phlogopite, a common rock-forming mineral, may be a possible reservoir for hydrocarbons. PMID:28098185

  5. BOREAS AFM-6 NOAA/ETL 35 GHz Cloud/Turbulence Radar GIF Images

    NASA Technical Reports Server (NTRS)

    Martner, Brooks E.; Newcomer, Jeffrey A. (Editor); Hall, Forrest G.; Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Administration/Environment Technology Laboratory (NOAA/ETL) operated a 35-GHz cloud-sensing radar in the Northern Study Area (NSA) near the Old Jack Pine (OJP) tower from 16 Jul 1994 to 08 Aug 1994. This data set contains a time series of GIF images that show the structure of the lower atmosphere. The NOAA/ETL 35-GHz cloud/turbulence radar GIF images are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  6. Graphite, graphene on SiC, and graphene nanoribbons: Calculated images with a numerical FM-AFM

    PubMed Central

    Castanié, Fabien; Nony, Laurent; Gauthier, Sébastien

    2012-01-01

    Summary Background: Characterization at the atomic scale is becoming an achievable task for FM-AFM users equipped, for example, with a qPlus sensor. Nevertheless, calculations are necessary to fully interpret experimental images in some specific cases. In this context, we developed a numerical AFM (n-AFM) able to be used in different modes and under different usage conditions. Results: Here, we tackled FM-AFM image calculations of three types of graphitic structures, namely a graphite surface, a graphene sheet on a silicon carbide substrate with a Si-terminated surface, and finally, a graphene nanoribbon. We compared static structures, meaning that all the tip and sample atoms are kept frozen in their equilibrium position, with dynamic systems, obtained with a molecular dynamics module allowing all the atoms to move freely during the probe oscillations. Conclusion: We found a very good agreement with experimental graphite and graphene images. The imaging process for the deposited nanoribbon demonstrates the stability of our n-AFM to image a non-perfectly planar substrate exhibiting a geometrical step as well as a material step. PMID:22497004

  7. Computational simulation of subatomic-resolution AFM and STM images for graphene/hexagonal boron nitride heterostructures with intercalated defects

    NASA Astrophysics Data System (ADS)

    Lee, Junsu; Kim, Minjung; Chelikowsky, James R.; Kim, Gunn

    2016-07-01

    Using ab initio density functional calculations, we predict subatomic-resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) images of vertical heterostructures of graphene/hexagonal boron nitride (h-BN) with an intercalated metal atom (Li, K, Cr, Mn, Co, or Cu), and study the effects of the extrinsic metal defect on the interfacial coupling. We find that the structural deformation of the graphene/h-BN layer caused by the metal defect strongly affects the AFM images, whereas orbital hybridization between the metal defect and the graphene/h-BN layer characterizes the STM images.

  8. Multiparametric AFM reveals turgor-responsive net-like peptidoglycan architecture in live streptococci

    NASA Astrophysics Data System (ADS)

    Saar Dover, Ron; Bitler, Arkady; Shimoni, Eyal; Trieu-Cuot, Patrick; Shai, Yechiel

    2015-05-01

    Cell-wall peptidoglycan (PG) of Gram-positive bacteria is a strong and elastic multi-layer designed to resist turgor pressure and determine the cell shape and growth. Despite its crucial role, its architecture remains largely unknown. Here using high-resolution multiparametric atomic force microscopy (AFM), we studied how the structure and elasticity of PG change when subjected to increasing turgor pressure in live Group B Streptococcus. We show a new net-like arrangement of PG, which stretches and stiffens following osmotic challenge. The same structure also exists in isogenic mutants lacking surface appendages. Cell aging does not alter the elasticity of the cell wall, yet destroys the net architecture and exposes single segmented strands with the same circumferential orientation as predicted for intact glycans. Together, we show a new functional PG architecture in live Gram-positive bacteria.

  9. tRNA conjugation with chitosan nanoparticles: An AFM imaging study.

    PubMed

    Agudelo, D; Kreplak, L; Tajmir-Riahi, H A

    2016-04-01

    The conjugation of tRNA with chitosan nanoparticles of different sizes 15,100 and 200 kDa was investigated in aqueous solution using multiple spectroscopic methods and atomic force microscopy (AFM). Structural analysis showed that chitosan binds tRNA via G-C and A-U base pairs as well as backbone PO2 group, through electrostatic, hydrophilic and H-bonding contacts with overall binding constants of KCh-15-tRNA=4.1 (±0.60)×10(3)M(-1), KCh-100-tRNA=5.7 (±0.8)×10(3)M(-1) and KCh-200-tRNA=1.2 (±0.3)×10(4)M(-1). As chitosan size increases more stable polymer-tRNA conjugate is formed. AFM images showed major tRNA aggregation and particle formation occurred as chitosan concentration increased. Even though chitosan induced major biopolymer structural changes, tRNA remains in A-family structure.

  10. Atomic force microscopy for analyzing metaphase chromosomes: comparison of AFM images with fluorescence labeling images of banding patterns.

    PubMed

    Hoshi, Osamu; Ushiki, Tatsuo

    2014-01-01

    The combined use of fluorescence microscopy with atomic force microscopy (AFM) has been introduced to analyze the replication-banding patterns of human chromosomes. Human lymphocytes synchronized with excess thymidine are treated with 5-ethynyl-2'-deoxyuridine (EdU) during the late S phase. EdU-labeled DNA is detected in metaphase chromosomes using Alexa Fluor 488(®) azide, through the 1,3-dipolar cycloaddition reaction of organic azides with the terminal acetylene group of EdU. Chromosomes with EdU incorporated during the late S phase show a banding pattern similar to the G-banding pattern of normal human chromosomes. The comparison between the fluorescence and AFM image of the same chromosome indicates the presence of ridges and grooves in the chromatid arms, which correspond to G-positive and G-negative bands, respectively. This technique of EdU-labeled replication bands combined with AFM is useful to analyze the structure of chromosomes in relation to the banding pattern.

  11. The synthesis and STM/AFM imaging of 'olympicene' benzo[cd]pyrenes.

    PubMed

    Mistry, Anish; Moreton, Ben; Schuler, Bruno; Mohn, Fabian; Meyer, Gerhard; Gross, Leo; Williams, Antony; Scott, Peter; Costantini, Giovanni; Fox, David J

    2015-01-26

    H-Benzo[cd]pyrene ('Olympicene') is a polyaromatic hydrocarbon and non-Kekulé fragment of graphene. A new synthetic method has been developed for the formation of 6H-benzo[cd]pyrene and related ketones including the first time isolation of the unstable alcohol 6H-benzo[cd]pyren-6-ol. Molecular imaging of the reaction products with scanning tunnelling microscopy (STM) and non-contact atomic force microscopy (NC-AFM) characterised the 6H-benzo[cd]pyrene as well as the previously intangible and significantly less stable 5H-benzo[cd]pyrene, the fully conjugated benzo[cd]pyrenyl radical and the ketones as oxidation products.

  12. AFM/TIRF force clamp measurements of neurosecretory vesicle tethers reveal characteristic unfolding steps

    PubMed Central

    Harris, Mark C.; Cislo, Dillon; Lenz, Joan S.; Umbach, Christopher

    2017-01-01

    Although several proteins have been implicated in secretory vesicle tethering, the identity and mechanical properties of the components forming the physical vesicle-plasma membrane link remain unknown. Here we present the first experimental measurements of nanomechanical properties of secretory vesicle-plasma membrane tethers using combined AFM force clamp and TIRF microscopy on membrane sheets from PC12 cells expressing the vesicle marker ANF-eGFP. Application of pulling forces generated tether extensions composed of multiple steps with variable length. The frequency of short (<10 nm) tether extension events was markedly higher when a fluorescent vesicle was present at the cantilever tip and increased in the presence of GTPγS, indicating that these events reflect specifically the properties of vesicle-plasma membrane tethers. The magnitude of the short tether extension events is consistent with extension lengths expected from progressive unfolding of individual helices of the exocyst complex, supporting its direct role in forming the physical vesicle-plasma membrane link. PMID:28323853

  13. Absorption Spectroscopy and Imaging from the Visible through Mid-IR with 20 nm Resolution Using AFM probes

    NASA Astrophysics Data System (ADS)

    Centrone, Andrea

    2015-03-01

    Correlated nanoscale composition and optical property maps are important to engineer nanomaterials in applications ranging from photovoltaics to sensing and therapeutics. Wavelengths (λs) from the visible to near-IR probe electronic transitions in materials, providing information regarding band gap and defects while light in mid-IR probes vibrational transitions and provide chemical composition. However, light diffraction limits the lateral resolution of conventional micro-spectroscopic techniques to approximately λ/2, which is insufficient to image nanomaterials. Additionally, the λ-dependent resolution impedes direct comparison of spectral maps from different spectral ranges. Photo Thermal Induced Resonance (PTIR) is a novel technique that circumvents light diffraction by employing an AFM tip as a local detector for measuring light absorption with λ-independent nanoscale resolution. Our PTIR setup combines an AFM microscope with three lasers providing λ-tunability from 500 nm to 16000 nm continuously. The AFM tip transduces locally the sample thermal expansion induced by light absorption into large cantilever oscillations. Local absorption spectra (electronic or vibrational) and maps are obtained recording the amplitude of the tip deflection as a function of λ and position, respectively. The working principles of the PTIR technique will be described first, and nano-patterned polymer samples will be used to evaluate its lateral resolution, sensitivity and linearity. Results show that the PTIR signal intensity is proportional to the local absorbed energy suggesting applicability of this technique for quantitative chemical analysis at nanoscale, at least for thin (less than 1000 nm thick) samples. Additionally, a λ-independent resolution as high as 20 nm is demonstrated across the whole spectral range. In the second part of the talk, PTIR will be applied to image the dark plasmonic resonance of gold Asymmetric Split Ring Resonators (A-SRRs) in the mid

  14. Tracer kinetic modeling of [11C]AFM, a new PET imaging agent for the serotonin transporter

    PubMed Central

    Naganawa, Mika; Nabulsi, Nabeel; Planeta, Beata; Gallezot, Jean-Dominique; Lin, Shu-Fei; Najafzadeh, Soheila; Williams, Wendol; Ropchan, Jim; Labaree, David; Neumeister, Alexander; Huang, Yiyun; Carson, Richard E

    2013-01-01

    [11C]AFM, or [11C]2-[2-(dimethylaminomethyl)phenylthio]-5-fluoromethylphenylamine, is a new positron emission tomography (PET) radioligand with high affinity and selectivity for the serotonin transporter (SERT). The purpose of this study was to determine the most appropriate kinetic model to quantify [11C]AFM binding in the healthy human brain. Positron emission tomography data and arterial input functions were acquired from 10 subjects. Compartmental modeling and the multilinear analysis-1(MA1) method were tested using the arterial input functions. The one-tissue model showed a lack of fit in low-binding regions, and the two-tissue model failed to estimate parameters reliably. Regional time–activity curves were well described by MA1. The rank order of [11C]AFM binding potential (BPND) matched well with the known regional SERT densities. For routine use of [11C]AFM, several noninvasive methods for quantification of regional binding were evaluated, including simplified reference tissue models (SRTM and SRTM2), and multilinear reference tissue models (MRTM and MRTM2). The best methods for region of interest (ROI) analysis were MA1, MRTM2, and SRTM2, with fixed population kinetic values ( or b′) for the reference methods. The MA1 and MRTM2 methods were best for parametric imaging. These results showed that [11C]AFM is a suitable PET radioligand to image and quantify SERT in humans. PMID:23921898

  15. Lower nanometer-scale size limit for the deformation of a metallic glass by shear transformations revealed by quantitative AFM indentation.

    PubMed

    Caron, Arnaud; Bennewitz, Roland

    2015-01-01

    We combine non-contact atomic force microscopy (AFM) imaging and AFM indentation in ultra-high vacuum to quantitatively and reproducibly determine the hardness and deformation mechanisms of Pt(111) and a Pt57.5Cu14.7Ni5.3P22.5 metallic glass with unprecedented spatial resolution. Our results on plastic deformation mechanisms of crystalline Pt(111) are consistent with the discrete mechanisms established for larger scales: Plasticity is mediated by dislocation gliding and no rate dependence is observed. For the metallic glass we have discovered that plastic deformation at the nanometer scale is not discrete but continuous and localized around the indenter, and does not exhibit rate dependence. This contrasts with the observation of serrated, rate-dependent flow of metallic glasses at larger scales. Our results reveal a lower size limit for metallic glasses below which shear transformation mechanisms are not activated by indentation. In the case of metallic glass, we conclude that the energy stored in the stressed volume during nanometer-scale indentation is insufficient to account for the interfacial energy of a shear band in the glassy matrix.

  16. Combined quantitative ultrasonic and time-resolved interaction force AFM imaging

    NASA Astrophysics Data System (ADS)

    Parlak, Z.; Degertekin, F. L.

    2011-01-01

    The authors describe a method where quantitative ultrasonic atomic force microscopy (UAFM) is achieved during time-resolved interaction force (TRIF) imaging in intermittent contact mode. The method uses a calibration procedure for quantitative UAFM. It improves elasticity measurements of stiff regions of surfaces while retaining the capabilities of the TRIF mode for topography, adhesion, dissipation, and elasticity measurements on soft regions of sample surfaces. This combination is especially advantageous when measuring and imaging samples with broad stiffness range in a nondestructive manner. The experiments utilize an active AFM probe with high bandwidth and the UAFM calibration is performed by measuring the magnitude of the time-resolved UAFM signal at a judiciously chosen frequency for different contact stiffness values during individual taps. Improved sensitivity to stiff surface elasticity is demonstrated on a special sample. The results show that combining UAFM with TRIF provides 2.5 GPa (5%) standard deviation on the silicon surface reduced Young's modulus, representing 5× improvement over using only TRIF mode imaging.

  17. Study on effects of scan parameters on the image quality and tip wear in AFM tapping mode.

    PubMed

    Xue, Bo; Yan, Yongda; Hu, Zhenjiang; Zhao, Xuesen

    2014-01-01

    Due to the tip-sample interaction which is the measurement principle of Atomic Force Microscope (AFM), tip wear constantly occurs during scanning. The blunt tip caused by the wear process makes more tip geometry information involved in the image, and correspondingly it increases the measurement error. In the present study, the scan parameters of AFM in tapping mode which affect the wear of single crystal silicon tips, such as the approaching rate, the scan rate, the scan amplitude, and the integral gain are investigated. By proposing a parameter reflecting the imaging quality, the tip state tracing the sample surface is evaluated quantitatively. The influences of scan parameters on this imaging quality parameter are obtained by experiments. Finally, in order to achieve the perfect images with little tip wear influence, tip wear experiments are carried out and then the optimal parameter settings which can lighten the tip wear are obtained.

  18. Single Cell Wall Nonlinear Mechanics Revealed by a Multiscale Analysis of AFM Force-Indentation Curves.

    PubMed

    Digiuni, Simona; Berne-Dedieu, Annik; Martinez-Torres, Cristina; Szecsi, Judit; Bendahmane, Mohammed; Arneodo, Alain; Argoul, Françoise

    2015-05-05

    Individual plant cells are rather complex mechanical objects. Despite the fact that their wall mechanical strength may be weakened by comparison with their original tissue template, they nevertheless retain some generic properties of the mother tissue, namely the viscoelasticity and the shape of their walls, which are driven by their internal hydrostatic turgor pressure. This viscoelastic behavior, which affects the power-law response of these cells when indented by an atomic force cantilever with a pyramidal tip, is also very sensitive to the culture media. To our knowledge, we develop here an original analyzing method, based on a multiscale decomposition of force-indentation curves, that reveals and quantifies for the first time the nonlinearity of the mechanical response of living single plant cells upon mechanical deformation. Further comparing the nonlinear strain responses of these isolated cells in three different media, we reveal an alteration of their linear bending elastic regime in both hyper- and hypotonic conditions.

  19. Combination of ToF-SIMS imaging and AFM to study the early stages of corrosion in Al-Cu thin films

    SciTech Connect

    Seyeux, A.; Missert, Nancy; Frankel, Gerald; Unocic, Kinga A; Klein, L. H.; Galtayries, A.; Marcus, P

    2011-01-01

    The pitting corrosion of Al-Cu thin film alloys was investigated using samples that were heat treated in air to form through-thickness Al2Cu particles within an Al-0.5%Cu matrix. Time-of-Flight SIMS (ToF-SIMS) analysis revealed Cu-rich regions 250 - 800 nm in lateral extent near the metal/oxide interface. Following exposure that generated pitting corrosion, secondary electron, secondary ion, and AFM images showed pits with size and density similar to those of the Cu-rich regions. The role of the Cu-rich regions is addressed.

  20. Hubble Images Reveal Jupiter's Auroras

    NASA Technical Reports Server (NTRS)

    1996-01-01

    These images, taken by the Hubble Space Telescope, reveal changes in Jupiter's auroral emissions and how small auroral spots just outside the emission rings are linked to the planet's volcanic moon, Io. The images represent the most sensitive and sharply-detailed views ever taken of Jovian auroras.

    The top panel pinpoints the effects of emissions from Io, which is about the size of Earth's moon. The black-and-white image on the left, taken in visible light, shows how Io and Jupiter are linked by an invisible electrical current of charged particles called a 'flux tube.' The particles - ejected from Io (the bright spot on Jupiter's right) by volcanic eruptions - flow along Jupiter's magnetic field lines, which thread through Io, to the planet's north and south magnetic poles. This image also shows the belts of clouds surrounding Jupiter as well as the Great Red Spot.

    The black-and-white image on the right, taken in ultraviolet light about 15 minutes later, shows Jupiter's auroral emissions at the north and south poles. Just outside these emissions are the auroral spots. Called 'footprints,' the spots are created when the particles in Io's 'flux tube' reach Jupiter's upper atmosphere and interact with hydrogen gas, making it fluoresce. In this image, Io is not observable because it is faint in the ultraviolet.

    The two ultraviolet images at the bottom of the picture show how the auroral emissions change in brightness and structure as Jupiter rotates. These false-color images also reveal how the magnetic field is offset from Jupiter's spin axis by 10 to 15 degrees. In the right image, the north auroral emission is rising over the left limb; the south auroral oval is beginning to set. The image on the left, obtained on a different date, shows a full view of the north aurora, with a strong emission inside the main auroral oval.

    The images were taken by the telescope's Wide Field and Planetary Camera 2 between May 1994 and September 1995.

    This image and

  1. Increased imaging speed and force sensitivity for bio-applications with small cantilevers using a conventional AFM setup

    PubMed Central

    Leitner, Michael; Fantner, Georg E.; Fantner, Ernest J.; Ivanova, Katerina; Ivanov, Tzvetan; Rangelow, Ivo; Ebner, Andreas; Rangl, Martina; Tang, Jilin; Hinterdorfer, Peter

    2012-01-01

    In this study, we demonstrate the increased performance in speed and sensitivity achieved by the use of small AFM cantilevers on a standard AFM system. For this, small rectangular silicon oxynitride cantilevers were utilized to arrive at faster atomic force microscopy (AFM) imaging times and more sensitive molecular recognition force spectroscopy (MRFS) experiments. The cantilevers we used had lengths between 13 and 46 μm, a width of about 11 μm, and a thickness between 150 and 600 nm. They were coated with chromium and gold on the backside for a better laser reflection. We characterized these small cantilevers through their frequency spectrum and with electron microscopy. Due to their small size and high resonance frequency we were able to increase the imaging speed by a factor of 10 without any loss in resolution for images from several μm scansize down to the nanometer scale. This was shown on bacterial surface layers (s-layer) with tapping mode under aqueous, near physiological conditions and on nuclear membranes in contact mode in ambient environment. In addition, we showed that single molecular forces can be measured with an up to 5 times higher force sensitivity in comparison to conventional cantilevers with similar spring constants. PMID:22721963

  2. Comparison of the ability of quantitative parameters to differentiate surface texture of Atomic Force Microscope (AFM) images

    NASA Astrophysics Data System (ADS)

    Niedzielski, Bethany; Caragianis Broadbridge, Christine; DaPonte, John S.; Gherasimova, Maria

    2010-01-01

    The purpose of this study was to compare the ability of several texture analysis parameters to differentiate textured samples from a smooth control on images obtained with an Atomic Force Microscope (AFM). Surface roughness plays a major role in the realm of material science, especially in integrated electronic devices. As these devices become smaller and smaller, new materials with better electrical properties are needed. New materials with smoother surface morphology have been found to have superior electrical properties than their rougher counterparts. Therefore, in many cases surface texture is indicative of the electrical properties that material will have. Physical vapor deposition techniques such as Jet Vapor Deposition and Molecular Beam Epitaxy are being utilized to synthesize these materials as they have been found to create pure and uniform thin layers. For the current study, growth parameters were varied to produce a spectrum of textured samples. The focus of this study was the image processing techniques associated with quantifying surface texture. As a result of the limited sample size, there was no attempt to draw conclusions about specimen processing methods. The samples were imaged using an AFM in tapping mode. In the process of collecting images, it was discovered that roughness data was much better depicted in the microscope's "height" mode as opposed to "equal area" mode. The AFM quantified the surface texture of each image by returning RMS roughness and the first order histogram statistics of mean roughness, standard deviation, skewness, and kurtosis. Color images from the AFM were then processed on an off line computer running NIH ImageJ with an image texture plug in. This plug in produced another set of first order statistics computed from each images' histogram as well as second order statistics computed from each images' cooccurrence matrix. The second order statistics, which were originally proposed by Haralick, include contrast, angular

  3. AFM imaging of ligand binding to platelet integrin alphaIIbbeta3 receptors reconstituted into planar lipid bilayers.

    PubMed

    Hussain, Mohammad A; Agnihotri, Aashiish; Siedlecki, Christopher A

    2005-07-19

    The platelet integrin alphaIIbbeta3 plays a key role in platelet adhesion, activation, and aggregation at the subendothelium and at protein-coated synthetic biomaterials. In this study, interactions between alphaIIbbeta3 and both protein and peptide ligands for the receptor were imaged under physiological conditions by high-resolution atomic force microscopy (AFM). To directly image the ligand-receptor interactions, alphaIIbbeta3 receptors were reconstituted into a supported lipid bilayer formed on a mica surface in the AFM fluid cell assembly and subsequently activated with Mn2+. Fibrinogen, the natural protein ligand for the integrin, as well as a nanogold-labeled peptide ligand (an RGD-containing heptamer) were infused into the AFM fluid cell, incubated with the reconstituted and activated receptors, and imaged under buffer. Height images illustrating topographical features showed the integrin reconstituted in the bilayer. Fibrinogen molecules binding to the receptors were easily observed in the height images, with fibrinogen showing its characteristic trinodular structure and occasionally bridging integrin receptors. Fibrinogen was observed to bind to integrins at the D-domain consistent with the location of the gamma-chain dodecapeptide, while fibrinogen bridging integrins bound to receptors on opposite sides of the protein consistent with a 2-fold axis of symmetry. Peptide ligands were not visible in height images; however, phase images that map the mechanical properties detected the nanogold labels and demonstrated the presence of peptide ligands bound to the receptors. The results demonstrate the ability of this high-resolution microscopy technique to directly visualize single ligand/receptor interactions in a dynamic and physiologically relevant environment, and establish a framework for future fundamental studies of single protein/receptor interactions during normal pathological processes as well as biomaterial surface-induced thrombosis.

  4. Bi-stability of amplitude modulation AFM in air: deterministic and stochastic outcomes for imaging biomolecular systems.

    PubMed

    Santos, Sergio; Barcons, Victor; Font, Josep; Thomson, Neil H

    2010-06-04

    The dynamics of the oscillating microcantilever for amplitude modulation atomic force microscopy (AM AFM) operating in air is well understood theoretically but the experimental outcomes are still emerging. We use double-stranded DNA on mica as a model biomolecular system for investigating the connection between theory and experiment. A demonstration that the switching between the two cantilever oscillation states is stochastic in nature is achieved, and it can be induced by means of topographical anomalies on the surface. Whether one or the other attractor basin is accessed depends on the tip-sample separation history used to achieve the imaging conditions, and we show that the behaviour is reproducible when the tip is stable and well characterized. Emergence of background noise occurs in certain regions of parameter space regardless of whether two cantilever oscillation states coexist. The low state has been explored in detail and we note that at low to intermediate values of the free amplitude, noise-free imaging is achieved. The outcomes shown here are general and demonstrate that a thorough and systematic experimental approach in conjunction with standard modelling gives insight into the mechanisms behind image contrast formation in AM AFM in air.

  5. Unspecific membrane protein-lipid recognition: combination of AFM imaging, force spectroscopy, DSC and FRET measurements.

    PubMed

    Borrell, Jordi H; Montero, M Teresa; Morros, Antoni; Domènech, Òscar

    2015-11-01

    In this work, we will describe in quantitative terms the unspecific recognition between lactose permease (LacY) of Escherichia coli, a polytopic model membrane protein, and one of the main components of the inner membrane of this bacterium. Supported lipid bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) (3:1, mol/mol) in the presence of Ca(2+) display lateral phase segregation that can be distinguished by atomic force microscopy (AFM) as well as force spectroscopy. LacY shows preference for fluid (Lα) phases when it is reconstituted in POPE : POPG (3:1, mol/mol) proteoliposomes at a lipid-to-protein ratio of 40. When the lipid-to-protein ratio is decreased down to 0.5, two domains can be distinguished by AFM. While the upper domain is formed by self-segregated units of LacY, the lower domain is constituted only by phospholipids in gel (Lβ) phase. On the one hand, classical differential scanning calorimetry (DSC) measurements evidenced the segregation of a population of phospholipids and point to the existence of a boundary region at the lipid-protein interface. On the other hand, Förster Resonance Energy Transfer (FRET) measurements in solution evidenced that POPE is selectively recognized by LacY. A binary pseudophase diagram of POPE : POPG built from AFM observations enables to calculate the composition of the fluid phase where LacY is inserted. These results are consistent with a model where POPE constitutes the main component of the lipid-LacY interface segregated from the fluid bulk phase where POPG predominates.

  6. A review of the application of atomic force microscopy (AFM) in food science and technology.

    PubMed

    Liu, Shaoyang; Wang, Yifen

    2011-01-01

    Atomic force microscopy (AFM) is a powerful nanoscale analysis technique used in food area. This versatile technique can be used to acquire high-resolution sample images and investigate local interactions in air or liquid surroundings. In this chapter, we explain the principles of AFM and review representative applications of AFM in gelatin, casein micelle, carrageenan, gellan gum, starch, and interface. We elucidate new knowledge revealed with AFM as well as ways to use AFM to obtain morphology and rheology information in different food fields.

  7. Single molecule detection of PARP1 and PARP2 interaction with DNA strand breaks and their poly(ADP-ribosyl)ation using high-resolution AFM imaging

    PubMed Central

    Sukhanova, Maria V.; Abrakhi, Sanae; Joshi, Vandana; Pastre, David; Kutuzov, Mikhail M.; Anarbaev, Rashid O.; Curmi, Patrick A.; Hamon, Loic; Lavrik, Olga I.

    2016-01-01

    PARP1 and PARP2 are implicated in the synthesis of poly(ADP-ribose) (PAR) after detection of DNA damage. The specificity of PARP1 and PARP2 interaction with long DNA fragments containing single- and/or double-strand breaks (SSBs and DSBs) have been studied using atomic force microscopy (AFM) imaging in combination with biochemical approaches. Our data show that PARP1 localizes mainly on DNA breaks and exhibits a slight preference for nicks over DSBs, although the protein has a moderately high affinity for undamaged DNA. In contrast to PARP1, PARP2 is mainly detected at a single DNA nick site, exhibiting a low level of binding to undamaged DNA and DSBs. The enhancement of binding affinity of PARP2 for DNA containing a single nick was also observed using fluorescence titration. AFM studies reveal that activation of both PARPs leads to the synthesis of highly branched PAR whose size depends strongly on the presence of SSBs and DSBs for PARP1 and of SSBs for PARP2. The initial affinity between the PARP1, PARP2 and the DNA damaged site appears to influence both the size of the PAR synthesized and the time of residence of PARylated PARP1 and PARP2 on DNA damages. PMID:26673720

  8. Supramolecular self-assembly of linear oligosilsesquioxanes on mica--AFM surface imaging and hydrophilicity studies.

    PubMed

    Kowalewska, Anna; Nowacka, Maria; Tracz, Adam; Makowski, Tomasz

    2015-06-28

    Linear oligomeric [2-(carboxymethylthio)ethylsilsesquioxanes] (LPSQ-COOH) adsorb spontaneously on muscovite mica and form smooth, well-ordered lamellar structures at the liquid-solid interface. Side carboxylic groups, having donor-acceptor character with regard to hydrogen bonds, are engaged both in multipoint molecule-to-substrate interactions and intermolecular cross-linking. The unique arrangement of silsesquioxane macromolecules, with COOH groups situated at the interface with air, produces highly hydrophilic surfaces of good thermal and solvolytic stability. Supramolecular assemblies of LPSQ-COOH were studied using atomic force microscopy (AFM), angle-resolved X-ray photoelectron spectroscopy (ARXPS) and attenuated total reflectance (ATR) FTIR spectroscopy. Comparative height profile analysis combined with ATR-FTIR studies of the spectral regions characteristic of carboxylic groups and C1s core level envelope by XPS confirmed specific interactions between LPSQ-COOH and mica.

  9. Nanoscale structural features determined by AFM for single virus particles

    NASA Astrophysics Data System (ADS)

    Chen, Shu-Wen W.; Odorico, Michael; Meillan, Matthieu; Vellutini, Luc; Teulon, Jean-Marie; Parot, Pierre; Bennetau, Bernard; Pellequer, Jean-Luc

    2013-10-01

    In this work, we propose ``single-image analysis'', as opposed to multi-image averaging, for extracting valuable information from AFM images of single bio-particles. This approach allows us to study molecular systems imaged by AFM under general circumstances without restrictions on their structural forms. As feature exhibition is a resolution correlation, we have performed AFM imaging on surfaces of tobacco mosaic virus (TMV) to demonstrate variations of structural patterns with probing resolution. Two AFM images were acquired with the same tip at different probing resolutions in terms of pixel width, i.e., 1.95 and 0.49 nm per pixel. For assessment, we have constructed an in silico topograph based on the three-dimensional crystal structure of TMV as a reference. The prominent artifacts observed in the AFM-determined shape of TMV were attributed to tip convolutions. The width of TMV rod was systematically overestimated by ~10 nm at both probing resolutions of AFM. Nevertheless, the effects of tip convolution were less severe in vertical orientation so that the estimated height of TMV by AFM imaging was in close agreement with the in silico X-ray topograph. Using dedicated image processing algorithms, we found that at low resolution (i.e., 1.95 nm per pixel), the extracted surface features of TMV can be interpreted as a partial or full helical repeat (three complete turns with ~7.0 nm in length), while individual protein subunits (~2.5 nm) were perceivable only at high resolution. The present study shows that the scales of revealed structural features in AFM images are subject to both probing resolution and processing algorithms for image analysis.

  10. Adsorption of modified dextrins to a hydrophobic surface: QCM-D studies, AFM imaging, and dynamic contact angle measurements.

    PubMed

    Sedeva, Iliana G; Fetzer, Renate; Fornasiero, Daniel; Ralston, John; Beattie, David A

    2010-05-15

    The adsorption of three dextrin-based polymers, regular wheat dextrin (Dextrin TY), phenyl succinate dextrin (PS Dextrin), and styrene oxide dextrin (SO Dextrin) on a model hydrophobic surface, consisting of a mixed alkanethiol layer on gold, has been characterized using the quartz crystal microbalance with dissipation monitoring (QCM-D). The three polymers exhibited varying affinities and capacity for adsorption on the hydrophobic substrate. Atomic force microscope (AFM) imaging of the polymer layers indicates that all three polymers fully cover the surface. The effect of the three polymers on the static contact angle of the surface was studied using captive bubble contact angle measurements. The three polymers were seen to reduce the receding contact angle by similar amounts (approximately 14°) in spite of having varying adsorbed amounts and differences in adsorbed layer water content. Although no differences were observed in the ability of the polymers to reduce the static contact angle, measurements of the dynamic contact angle between a rising air bubble and the polymer covered substrate yielded stark differences between the polymers, with one polymer (SO Dextrin) slowing the dewetting by an order of magnitude more than the other two polymers. The differences in dewetting behavior correlate with the adsorbed layer characteristics determined by QCM-D and AFM. The role of the dynamic and static contact angle in the performance of a polymer as depressant is discussed.

  11. Zeta potential, contact angles, and AFM imaging of protein conformation adsorbed on hybrid nanocomposite surfaces.

    PubMed

    Pinho, Ana C; Piedade, Ana P

    2013-08-28

    The sputtering deposition of gold (Au) and poly(tetrafluoroethylene) (PTFE) was used to prepare a nanocomposite hybrid thin film suitable for protein adsorption while maintaining the native conformation of the biological material. The monolithic PTFE and the nanocomposite PTFE/Au thin films, with Au content up to 1 at %, were co-deposited by r.f. magnetron sputtering using argon as a discharge gas and deposited onto 316L stainless steel substrates, the most commonly used steel in biomaterials. The deposited thin films, before and after bovine serum albumin (BSA) adsorption, were thoroughly characterized with special emphasis on the surface properties/characteristics by atomic force microscopy (AFM), zeta potential, and static and dynamic contact angle measurements, in order to assess the relationship between structure and conformational changes. The influence of a pre-adsorbed peptide (RGD) was also evaluated. The nanotopographic and chemical changes induced by the presence of gold in the nanocomposite thin films enable RGD bonding, which is critical for the maintenance of the BSA native conformation after adsorption.

  12. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    PubMed Central

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-01-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed. PMID:28194036

  13. Indications of chemical bond contrast in AFM images of a hydrogen-terminated silicon surface

    NASA Astrophysics Data System (ADS)

    Labidi, Hatem; Koleini, Mohammad; Huff, Taleana; Salomons, Mark; Cloutier, Martin; Pitters, Jason; Wolkow, Robert A.

    2017-02-01

    The origin of bond-resolved atomic force microscope images remains controversial. Moreover, most work to date has involved planar, conjugated hydrocarbon molecules on a metal substrate thereby limiting knowledge of the generality of findings made about the imaging mechanism. Here we report the study of a very different sample; a hydrogen-terminated silicon surface. A procedure to obtain a passivated hydrogen-functionalized tip is defined and evolution of atomic force microscopy images at different tip elevations are shown. At relatively large tip-sample distances, the topmost atoms appear as distinct protrusions. However, on decreasing the tip-sample distance, features consistent with the silicon covalent bonds of the surface emerge. Using a density functional tight-binding-based method to simulate atomic force microscopy images, we reproduce the experimental results. The role of the tip flexibility and the nature of bonds and false bond-like features are discussed.

  14. Tendon exhibits complex poroelastic behavior at the nanoscale as revealed by high-frequency AFM-based rheology.

    PubMed

    Connizzo, Brianne K; Grodzinsky, Alan J

    2017-03-21

    Tendons transmit load from muscle to bone by utilizing their unique static and viscoelastic tensile properties. These properties are highly dependent on the composition and structure of the tissue matrix, including the collagen I hierarchy, proteoglycans, and water. While the role of matrix constituents in the tensile response has been studied, their role in compression, particularly in matrix pressurization via regulation of fluid flow, is not well understood. Injured or diseased tendons and tendon regions that naturally experience compression are known to have alterations in glycosaminoglycan content, which could modulate fluid flow and ultimately mechanical function. While recent theoretical studies have predicted tendon mechanics using poroelastic theory, no experimental data have directly demonstrated such behavior. In this study, we use high-bandwidth AFM-based rheology to determine the dynamic response of tendons to compressive loading at the nanoscale and to determine the presence of poroelastic behavior. Tendons are found to have significant characteristic dynamic relaxation behavior occurring at both low and high frequencies. Classic poroelastic behavior is observed, although we hypothesize that the full dynamic response is caused by a combination of flow-dependent poroelasticity as well as flow-independent viscoelasticity. Tendons also demonstrate regional dependence in their dynamic response, particularly near the junction of tendon and bone, suggesting that the structural and compositional heterogeneity in tendon may be responsible for regional poroelastic behavior. Overall, these experiments provide the foundation for understanding fluid-flow-dependent poroelastic mechanics of tendon, and the methodology is valuable for assessing changes in tendon matrix compressive behavior at the nanoscale.

  15. Adsorption of modified dextrins on molybdenite: AFM imaging, contact angle, and flotation studies.

    PubMed

    Beaussart, Audrey; Parkinson, Luke; Mierczynska-Vasilev, Agnieszka; Beattie, David A

    2012-02-15

    The adsorption of three dextrins (a regular wheat dextrin, Dextrin TY, carboxymethyl (CM) Dextrin, and hydroxypropyl (HP) Dextrin) on molybdenite has been investigated using adsorption isotherms, tapping mode atomic force microscopy (TMAFM), contact angle measurements, and dynamic bubble-surface collisions. In addition, the effect of the polymers on the flotation recovery of molybdenite has been determined. The isotherms revealed the importance of molecular weight in determining the adsorbed amounts of the polymers on molybdenite at plateau coverage. TMAFM revealed the morphology of the three polymers, which consisted of randomly dispersed domains with a higher area fraction of surface coverage for the substituted dextrins. The contact angle of polymer-treated molybdenite indicated that polymer layer coverage and hydration influenced the mineral surface hydrophobicity. Bubble-surface collisions indicated that the polymers affected thin film rupture and dewetting rate differently, correlating with differences in the adsorbed layer morphology. Direct correlations were found between the surface coverage of the adsorbed layers, their impact on thin film rupture time, and their impact on flotation recovery, highlighting the paramount role of the polymer morphology in the bubble/particle attachment process and subsequent flotation.

  16. Contrast mechanisms on nanoscale subsurface imaging in ultrasonic AFM: scattering of ultrasonic waves and contact stiffness of the tip-sample.

    PubMed

    Sharahi, Hossein Jiryaei; Shekhawat, Gajendra; Dravid, Vinayak; Park, Simon; Egberts, Philip; Kim, Seonghwan

    2017-02-09

    Ultrasonic atomic force microscopy (AFM) and its associated derivatives are nondestructive techniques that can elucidate subsurface nanoscale structures and properties. Despite the usefulness of these techniques, the physical contrast mechanisms responsible for the reported subsurface features observed in ultrasonic AFM are not well defined. In this study, we present a comprehensive model combining ultrasonic wave scattering and tip-sample contact stiffness to better reproduce the experimentally measured phase variations over subsurface features in two model systems. These model systems represent the two extreme sample types typically imaged by ultrasonic AFM, one being a hard material and the other a soft polymeric material. The theoretical analysis presented and associated comparisons with experimental results suggest that the image contrast depends on the combination of two contrast mechanisms: the perturbation of the scattered ultrasonic waves and the local variation of the contact stiffness at the tip-sample contact. The results of this study open up a new door for the depth estimation of buried nanoscale features into hard (engineering structures) and soft (polymers and biological structures) materials, and eventually lead to non-invasive, high-resolution 3D nano-tomography by ultrasonic AFM.

  17. Revealing the topography of cellular membrane domains by combined atomic force microscopy/fluorescence imaging.

    PubMed

    Frankel, D J; Pfeiffer, J R; Surviladze, Z; Johnson, A E; Oliver, J M; Wilson, B S; Burns, A R

    2006-04-01

    Simultaneous atomic force microscopy (AFM) and confocal fluorescence imaging were used to observe in aqueous buffer the three-dimensional landscape of the inner surface of membrane sheets stripped from fixed tumor mast cells. The AFM images reveal prominent, irregularly shaped raised domains that label with fluorescent markers for both resting and activated immunoglobin E receptors (FcepsilonRI), as well as with cholera toxin-aggregated GM1 and clathrin. The latter suggests that coated pits bud from these regions. These features are interspersed with flatter regions of membrane and are frequently surrounded and interconnected by cytoskeletal assemblies. The raised domains shrink in height by approximately 50% when cholesterol is extracted with methyl-beta-cyclodextrin. Based on composition, the raised domains seen by AFM correspond to the cholesterol-enriched dark patches observed in transmission electron microscopy (TEM). These patches were previously identified as sites of signaling and endocytosis based on their localization of activated FcepsilonRI, at least 10 associated signaling molecules, and the presence of clathrin-coated pits. Overall the data suggest that signaling and endocytosis occur in mast cells from raised membrane regions that depend on cholesterol for their integrity and may be organized in specific relationship with the cortical cytoskeleton.

  18. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    SciTech Connect

    Warren, Jeffrey; Bilheux, Hassina Z; Kang, Misun; Voisin, Sophie; Cheng, Chu-Lin; Horita, Jusuke; Perfect, Edmund

    2013-01-01

    Many terrestrial ecosystem processes are constrained by water availability and transport within the soil. Knowledge of plant water fluxes is thus critical for assessing mechanistic processes linked to biogeochemical cycles, yet resolution of root structure and xylem water transport dynamics has been a particularly daunting task for the ecologist. Through neutron imaging, we demonstrate the ability to non-invasively monitor individual root functionality and water fluxes within Zea mays L. (maize) and Panicum virgatum L. (switchgrass) seedlings growing in a sandy medium. Root structure and growth were readily imaged by neutron radiography and neutron computed tomography. Seedlings were irrigated with water or deuterium oxide and imaged through time as a growth lamp was cycled on to alter leaf demand for water. Sub-millimeter scale resolution reveals timing and magnitudes of root water uptake, redistribution within the roots, and root-shoot hydraulic linkages, relationships not well characterized by other techniques.

  19. AFM Structural Characterization of Drinking Water Biofilm ...

    EPA Pesticide Factsheets

    Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

  20. Revealing Invisible Photonic Inscriptions: Images from Strain

    PubMed Central

    2015-01-01

    Photonic structural materials have received intensive interest and have been strongly developed over the past few years for image displays, sensing, and anticounterfeit materials. Their “smartness” arises from their color responsivity to changes of environment, strain, or external fields. Here, we introduce a novel invisible photonic system that reveals encrypted images or characters by simply stretching, or immersing in solvents. This type of intriguing photonic material is composed of regularly arranged core–shell particles that are selectively cross-linked by UV irradiation, giving different strain response compared to un-cross-linked regions. The images reversibly appear and disappear when cycling the strain and releasing it. The unique advantages of this soft polymer opal system compared with other types of photonic gels are that it can be produced in roll to roll quantities, can be vigorously deformed to achieve strong color changes, and has no solvent evaporation issues because it is a photonic rubber system. We demonstrate potential applications together with a fabrication procedure which is straightforward and scalable, vital for user take-up. Our work deepens understanding of this rubbery photonic system based on core–shell nanospheres. PMID:26039279

  1. In vivo characterization of protein uptake by yeast cell envelope: single cell AFM imaging and μ-tip-enhanced Raman scattering study.

    PubMed

    Naumenko, Denys; Snitka, Valentinas; Serviene, Elena; Bruzaite, Ingrida; Snopok, Boris

    2013-09-21

    Direct detection of biological transformations of single living cells in vivo has been performed by the advanced combination of local topographic imaging by Atomic Force Microscopy (AFM) and label-free sub-surface chemical characterization using new μ-Tip-Enhanced Raman Spectroscopy (μ-TERS). The enhancing mechanism for μ-TERS tips with micrometre range radius differs significantly to that of the conventional tapered structures terminated by a sharp apex and conditioned by the effects of propagating instead of localizing surface plasmon resonance phenomena. Sub-wavelength light confinement in the form of a nonradiative evanescent wave near the tip surface with penetration depth in the sub-micrometre range opens the way for monitoring of subsurface processes near or within the cell wall, inaccessible by other methods. The efficiency of the approach has been demonstrated by the analysis of the cell envelope of genetically modified (by glucose dehydrogenase (GDH) gene bearing Kluyveromyces lactis toxin signal sequence) yeast cells enriched by GDH protein. The presence of trans-membrane fragments in GDH together with the tendency to form active dimers and tetramers causes the accumulation of the proteins within the periplasmic space. These results demonstrate that the advanced combination of AFM imaging and subsurface chemical characterization by the novel μ-TERS technique provides a new analytical tool for the investigation of single living cells in vivo.

  2. Savinase action on bovine serum albumin (BSA) monolayers demonstrated with measurements at the air-water interface and liquid Atomic Force Microscopy (AFM) imaging.

    PubMed

    Balashev, Konstantin; Callisen, Thomas H; Svendsen, Allan; Bjørnholm, Thomas

    2011-12-01

    We studied the enzymatic action of Savinase on bovine serum albumin (BSA) organized in a monolayer spread at the air/water interface or adsorbed at the mica surface. We carried out two types of experiments. In the first one we followed the degradation of the protein monolayer by measuring the surface pressure and surface area decrease versus time. In the second approach we applied AFM imaging of the supported BSA monolayers adsorbed on mica solid supports and extracted information for the enzyme action by analyzing the obtained images of the surface topography in the course of enzyme action. In both cases we obtained an estimate for the turnover number (TON) of the enzyme reaction.

  3. Neutron Imaging Reveals Internal Plant Hydraulic Dynamics

    NASA Astrophysics Data System (ADS)

    Warren, J.; Bilheux, H.; Kang, M.; Voisin, S.; Cheng, C.; Horita, J.; Perfect, E.

    2011-12-01

    In situ quantification of soil-plant water fluxes have not been fully successful due to a lack of non-destructive techniques capable of revealing roots or water fluxes at relevant spatial scales. Neutron imaging is a unique non-invasive tool that can assess sub-millimeter scale material properties and transport in situ, and which has been successfully applied to characterize soil and plant water status. Here, we have applied neutron radiography and tomography to quantify water transport through individual maize roots in response to internal plant demand. Zea mays seedlings were grown for 10 days in Flint silica sand within 2.6 cm diameter Al chambers. Using a reactor-based neutron source at Oak Ridge National Laboratory (HFIR), water fluxes were tracked through the maize soil-root systems by collecting consecutive neutron radiographs over a 12 h period following irrigation with D2O. D has a much lower neutron attenuation than H, thus D2O displacement of existing H2O within the plant vascular system, or influx of D2O into previously dry tissue or soil is readily tracked by changes in image intensity through time. Plant water release and uptake was regulated by periodically cycling on a high-intensity grow light. From each maize replicate, selected regions of interest (ROI) were delineated around individual roots, root free soil, stem and leaf segments. Changes in ROI were tracked through time to reveal patterns of water flux. The hydration of root and stem tissue cycled in response to illumination; root water content often increased during darkness, then decreased with illumination as water was transported from the root into the stem. Relative root-shoot hydration through time illustrates the balance between demand, storage capacity and uptake, which varies depending on root characteristics and its localized soil environment. The dynamic transport of water between soil, individual roots, stems and leaves was readily visualized and quantified illustrating the value

  4. PREFACE: Non-contact AFM Non-contact AFM

    NASA Astrophysics Data System (ADS)

    Giessibl, Franz J.; Morita, Seizo

    2012-02-01

    This special issue is focussed on high resolution non-contact atomic force microscopy (AFM). Non-contact atomic force microscopy was established approximately 15 years ago as a tool to image conducting and insulating surfaces with atomic resolution. Since 1998, an annual international conference has taken place, and although the proceedings of these conferences are a useful source of information, several key developments warrant devoting a special issue to this subject. In the theoretic field, the possibility of supplementing established techniques such as scanning tunneling microscopy (STM) and Kelvin probe microscopy with atomically resolved force micrsoscopy poses many challenges in the calculation of contrast and contrast reversal. The surface science of insulators, self-assembled monolayers and adsorbates on insulators is a fruitful field for the application of non-contact AFM: several articles in this issue are devoted to these subjects. Atomic imaging and manipulation have been pioneered using STM, but because AFM allows the measurement of forces, AFM has had a profound impact in this field as well. Three-dimensional force spectroscopy has allowed many important insights into surface science. In this issue a combined 3D tunneling and force microscopy is introduced. Non-contact AFM typically uses frequency modulation to measure force gradients and was initially used mainly in a vacuum. As can be seen in this issue, frequency modulation is now also used in ambient conditions, allowing better spatial and force resolution. We thank all of the contributors for their time and efforts in making this special issue possible. We are also very grateful to the staff of IOP Publishing for handling the administrative aspects and for steering the refereeing process. Non-contact AFM contents Relation between the chemical force and the tunnelling current in atomic point contacts: a simple model Pavel Jelínek, Martin Ondrácek and Fernando Flores Theoretical simulation of

  5. Fabrication of homogeneously cross-linked, functional alginate microcapsules validated by NMR-, CLSM- and AFM-imaging.

    PubMed

    Zimmermann, H; Hillgärtner, M; Manz, B; Feilen, P; Brunnenmeier, F; Leinfelder, U; Weber, M; Cramer, H; Schneider, S; Hendrich, C; Volke, F; Zimmermann, U

    2003-05-01

    Cross-linked alginate microcapsules of sufficient mechanical strength can immunoisolate cells for the long-term treatment of hormone and other deficiency diseases in human beings. However, gelation of alginate by external Ba(2+) (or other divalent cations) produces non-homogeneous cross-linking of the polymeric mannuronic (M) and guluronic (G) acid chains. The stability of such microcapsules is rather limited. Here, we show that homogeneous cross-linking can be achieved by injecting BaCl(2) crystals into alginate droplets before they come into contact with external BaCl(2). The high effectiveness of this crystal gun method is demonstrated by confocal laser scanning microscopy and by advanced nuclear magnetic resonance imaging. Both techniques gave clear-cut evidence that homogeneous cross-linkage throughout the microcapsule is only obtained with simultaneous internal and external gelation. Atomic force microscopy showed a very smooth surface topography for microcapsules made by the crystal gun method, provided that excess Ba(2+) ions were removed immediately after gelation. In vitro experiments showed greatly suppressed swelling for crystal gun microcapsules. Even alginate extracted from Lessonia nigrescens (highly biocompatible) yielded microcapsules with long-term mechanical stability not hitherto possible. Encapsulation of rat islets, human monoclonal antibodies secreting hybridoma cells and murine mesenchymal stem cells transfected with cDNA encoding for bone morphogenetic protein (BMP-4) revealed that injection of BaCl(2) crystals has no adverse side effects on cell viability and function. However, the release of low-molecular weight factors (such as insulin) may be delayed when using alginate concentrations in the usual range.

  6. Images Revealing More Than a Thousand Words

    NASA Technical Reports Server (NTRS)

    2003-01-01

    A unique sensor developed by ProVision Technologies, a NASA Commercial Space Center housed by the Institute for Technology Development, produces hyperspectral images with cutting-edge applications in food safety, skin health, forensics, and anti-terrorism activities. While hyperspectral imaging technology continues to make advances with ProVision Technologies, it has also been transferred to the commercial sector through a spinoff company, Photon Industries, Inc.

  7. High Deformability and Particle Size Distribution of Monodisperse Phytoglycogen Nanoparticles Revealed By Atomic Force Microscopy Imaging

    NASA Astrophysics Data System (ADS)

    Baylis, Benjamin; Dutcher, John

    We have used atomic force microscopy (AFM) imaging in water to determine the volume of hydrated monodisperse phytoglycogen nanoparticles adsorbed onto mica surfaces. By significantly reducing the interaction between the AFM tip and the ``sticky'' nanoparticles, we were able to obtain high quality images. We found that the adsorbed particles are highly deformed, forming pancake-like objects on the hydrophilic mica surface. By measuring the distribution of particle volumes, we calculated the average effective spherical radius of the hydrated particles, and compared this value with that measured in solution using small angle neutron scattering. These measurements illustrate the distinct advantages of AFM imaging over other imaging techniques, namely the ability to measure the height of objects in a liquid environment.

  8. Molecular-level insights of early-stage prion protein aggregation on mica and gold surface determined by AFM imaging and molecular simulation.

    PubMed

    Lou, Zhichao; Wang, Bin; Guo, Cunlan; Wang, Kun; Zhang, Haiqian; Xu, Bingqian

    2015-11-01

    By in situ time-lapse AFM, we investigated early-stage aggregates of PrP formed at low concentration (100 ng/mL) on mica and Au(111) surfaces in acetate buffer (pH 4.5). Remarkably different PrP assemblies were observed. Oligomeric structures of PrP aggregates were observed on mica surface, which was in sharp contrast to the multi-layer PrP aggregates yielding parallel linear patterns observed Au(111) surface. Combining molecular dynamics and docking simulations, PrP monomers, dimers and trimers were revealed as the basic units of the observed aggregates. Besides, the mechanisms of the observed PrP aggregations and the corresponding molecular-substrate and intermolecular interactions were suggested. These interactions involved gold-sulfur interaction, electrostatic interaction, hydrophobic interaction, and hydrogen binding interaction. In contrast, the PrP aggregates observed in pH 7.2 PBS buffer demonstrated similar large ball-like structures on both mica and Au(111) surfaces. The results indicate that the pH of a solution and the surface of the system can have strong effects on supramolecular assemblies of prion proteins. This study provides in-depth understanding on the structural and mechanistic nature of PrP aggregation, and can be used to study the aggregation mechanisms of other proteins with similar misfolding properties.

  9. Atomic force microscopy imaging reveals the formation of ASIC/ENaC cross-clade ion channels

    SciTech Connect

    Jeggle, Pia; Smith, Ewan St. J.; Stewart, Andrew P.; Haerteis, Silke; Korbmacher, Christoph; Edwardson, J. Michael

    2015-08-14

    ASIC and ENaC are co-expressed in various cell types, and there is evidence for a close association between them. Here, we used atomic force microscopy (AFM) to determine whether ASIC1a and ENaC subunits are able to form cross-clade hybrid ion channels. ASIC1a and ENaC could be co-isolated from detergent extracts of tsA 201 cells co-expressing the two subunits. Isolated proteins were incubated with antibodies against ENaC and Fab fragments against ASIC1a. AFM imaging revealed proteins that were decorated by both an antibody and a Fab fragment with an angle of ∼120° between them, indicating the formation of ASIC1a/ENaC heterotrimers. - Highlights: • There is evidence for a close association between ASIC and ENaC. • We used AFM to test whether ASIC1a and ENaC subunits form cross-clade ion channels. • Isolated proteins were incubated with subunit-specific antibodies and Fab fragments. • Some proteins were doubly decorated at ∼120° by an antibody and a Fab fragment. • Our results indicate the formation of ASIC1a/ENaC heterotrimers.

  10. Anomalies in nanostructure size measurements by AFM

    NASA Astrophysics Data System (ADS)

    Mechler, Ádám; Kopniczky, Judit; Kokavecz, János; Hoel, Anders; Granqvist, Claes-Göran; Heszler, Peter

    2005-09-01

    Anomalies in atomic force microscopy (AFM) based size determination of nanoparticles were studied via comparative analysis of experiments and numerical calculations. Single tungsten oxide nanoparticles with a mean diameter of 3nm were deposited on mica and graphite substrates and were characterised by AFM. The size (height) of the nanoparticles, measured by tapping mode AFM, was found to be sensitive to the free amplitude of the oscillating tip, thus indicating that the images were not purely topographical. By comparing the experimental results to model calculations, we demonstrate that the dependence of the nanoparticle size on the oscillation amplitude of the tip is an inherent characteristic of the tapping mode AFM; it is also a function of physical properties such as elasticity and surface energy of the nanoparticle and the sample surface, and it depends on the radius of curvature of the tip. We show that good approximation of the real size can easily be obtained from plots of particle height vs free amplitude of the oscillating tip, although errors might persist for individual experiments. The results are valid for size (height) determination of any nanometer-sized objects imaged by tapping mode AFM.

  11. Visualization of internal structure of banana starch granule through AFM.

    PubMed

    Peroni-Okita, Fernanda H G; Gunning, A Patrick; Kirby, Andrew; Simão, Renata A; Soares, Claudinéia A; Cordenunsi, Beatriz R

    2015-09-05

    Atomic force microscopy (AFM) is a high resolution technique for studying the external and internal structures of starch granules. For this purpose granules were isolated from bananas and embedded in a non-penetrating resin. To achieve image contrast of the ultrastructure, the face of the cut blocks were wetted in steam and force modulation mode imaging was used. Images of starch from green bananas showed large variation of height across the granule due to a locational specific absorption of water and swelling of amorphous regions; the data reveal that the center of the granules are structurally different and have different viscoelastic properties. Images of starches from ripe bananas showed an even greater different level of organization: absence of growth rings around the hilum; the central region of the granule is richer in amylose; very porous surface with round shaped dark structures; the size of blocklets are larger than the green fruits.

  12. High-speed AFM of human chromosomes in liquid

    NASA Astrophysics Data System (ADS)

    Picco, L. M.; Dunton, P. G.; Ulcinas, A.; Engledew, D. J.; Hoshi, O.; Ushiki, T.; Miles, M. J.

    2008-09-01

    Further developments of the previously reported high-speed contact-mode AFM are described. The technique is applied to the imaging of human chromosomes at video rate both in air and in water. These are the largest structures to have been imaged with high-speed AFM and the first imaging in liquid to be reported. A possible mechanism that allows such high-speed contact-mode imaging without significant damage to the sample is discussed in the context of the velocity dependence of the measured lateral force on the AFM tip.

  13. AFM-Based Mechanical Nanomanipulation

    NASA Astrophysics Data System (ADS)

    Landolsi, Fakhreddine

    2011-12-01

    Advances in several research areas increase the need for more sophisticated fabrication techniques and better performing materials. Tackling this problem from a bottom-up perspective is currently an active field of research. The bottom-up fabrication procedure offers sub-nanometer accurate manipulation. At this time, candidates to achieve nanomanipulation include chemical (self-assembly), biotechnology methods (DNA-based), or using controllable physical forces (e.g. electrokinetic forces, mechanical forces). In this thesis, new methods and techniques for mechanical nanomanipulation using probe force interaction are developed. The considered probes are commonly used in Atomic Force Microscopes (AFMs) for high resolution imaging. AFM-based mechanical nanomanipulation will enable arranging nanoscale entities such as nanotubes and molecules in a precise and controlled manner to assemble and produce novel devices and systems at the nanoscale. The novelty of this research stems from the development of new modeling of the physics and mechanics of the tip interaction with nanoscale entities, coupled with the development of new smart cantilevers with multiple degrees of freedom. The gained knowledge from the conducted simulations and analysis is expected to enable true precision and repeatability of nanomanipulation tasks which is not feasible with existing methods and technologies.

  14. AFM characterization of nonwoven material functionalized by ZnO sputter coating

    SciTech Connect

    Deng Bingyao; Yan Xiong; Wei Qufu Gao Weidong

    2007-10-15

    Sputter coatings provide new approaches to the surface functionalization of textile materials. In this study, polyethylene terephthalate (PET) nonwoven material was used as a substrate for creating functional nanostructures on the fiber surfaces. A magnetron sputter coating was used to deposit functional zinc oxide (ZnO) nanostructures onto the nonwoven substrate. The evolution of the surface morphology of the fibers in the nonwoven web was examined using atomic force microscopy (AFM). The AFM observations revealed a significant difference in the morphology of the fibers before and after the sputter coating. The AFM images also indicated the effect of the sputtering conditions on the surface morphology of the fibers. The increase in the sputtering time led to the growth of the ZnO grains on the fiber surfaces. The higher pressure in the sputtering chamber could cause the formation of larger grains on the fiber surfaces. The higher power used also generated larger grains on the fiber surfaces.

  15. Spectral Imaging for Revealing and Preserving World Cultural Heritage

    DTIC Science & Technology

    2011-09-01

    of appearance of the original woodcut features Other signal processing included a PCA spectral separation of an iron gall ink inscription most...likely added by Schöner, 1451 as shown in Figure 3. The image processing clearly illus- trates the iron gall ink writing on top of the printing ink ...Figure 3 – PCA of printing and iron gall ink inscription (sheet 10) Other obscured historical information included revealing the text of a

  16. Contact nanomechanical measurements with the AFM

    NASA Astrophysics Data System (ADS)

    Geisse, Nicholas

    2013-03-01

    The atomic force microscope (AFM) has found broad use in the biological sciences largely due to its ability to make measurements on unfixed and unstained samples under liquid. In addition to imaging at multiple spatial scales ranging from micro- to nanometer, AFMs are commonly used as nanomechanical probes. This is pertinent for cell biology, as it has been demonstrated that the geometrical and mechanical properties of the extracellular microenvironment are important in such processes as cancer, cardiovascular disease, muscular dystrophy, and even the control of cell life and death. Indeed, the ability to control and quantify these external geometrical and mechanical parameters arises as a key issue in the field. Because AFM can quantitatively measure the mechanical properties of various biological samples, novel insights to cell function and to cell-substrate interactions are now possible. As the application of AFM to these types of problems is widened, it is important to understand the performance envelope of the technique and its associated data analyses. This talk will discuss the important issues that must be considered when mechanical models are applied to real-world data. Examples of the effect of different model assumptions on our understanding of the measured material properties will be shown. Furthermore, specific examples of the importance of mechanical stimuli and the micromechanical environment to the structure and function of biological materials will be presented.

  17. Introduction to atomic force microscopy (AFM) in biology.

    PubMed

    Goldsbury, Claire S; Scheuring, Simon; Kreplak, Laurent

    2009-11-01

    The atomic force microscope (AFM) has the unique capability of imaging biological samples with molecular resolution in buffer solution. In addition to providing topographical images of surfaces with nanometer- to angstrom-scale resolution, forces between single molecules and mechanical properties of biological samples can be investigated from the nanoscale to the microscale. Importantly, the measurements are made in buffer solutions, allowing biological samples to "stay alive" within a physiological-like environment while temporal changes in structure are measured-e.g., before and after addition of chemical reagents. These qualities distinguish AFM from conventional imaging techniques of comparable resolution, e.g., electron microscopy (EM). This unit provides an introduction to AFM on biological systems and describes specific examples of AFM on proteins, cells, and tissues. The physical principles of the technique and methodological aspects of its practical use and applications are also described.

  18. [Application of atomic force microscopy (AFM) in ophthalmology].

    PubMed

    Milka, Michał; Mróz, Iwona; Jastrzebska, Maria; Wrzalik, Roman; Dobrowolski, Dariusz; Roszkowska, Anna M; Moćko, Lucyna; Wylegała, Edward

    2012-01-01

    Atomic force microscopy (AFM) allows to examine surface of different biological objects in the nearly physiological conditions at the nanoscale. The purpose of this work is to present the history of introduction and the potential applications of the AFM in ophthalmology research and clinical practice. In 1986 Binnig built the AFM as a next generation of the scanning tunnelling microscope (STM). The functional principle of AFM is based on the measurement of the forces between atoms on the sample surface and the probe. As a result, the three-dimensional image of the surface with the resolution on the order of nanometres can be obtained. Yamamoto used as the first the AFM on a wide scale in ophthalmology. The first investigations used the AFM method to study structure of collagen fibres of the cornea and of the sclera. Our research involves the analysis of artificial intraocular lenses (IOLs). According to earlier investigations, e.g. Lombardo et al., the AFM was used to study only native IOLs. Contrary to the earlier investigations, we focused our measurements on lenses explanted from human eyes. The surface of such lenses is exposed to the influence of the intraocular aqueous environment, and to the related impacts of biochemical processes. We hereby present the preliminary results of our work in the form of AFM images depicting IOL surface at the nanoscale. The images allowed us to observe early stages of the dye deposit formation as well as local calcinosis. We believe that AFM is a very promising tool for studying the structure of IOL surface and that further observations will make it possible to explain the pathomechanism of artificial intraocular lens opacity formation.

  19. Raman and AFM study of gamma irradiated plastic bottle sheets

    NASA Astrophysics Data System (ADS)

    Ali, Yasir; Kumar, Vijay; Sonkawade, R. G.; Dhaliwal, A. S.

    2013-02-01

    In this investigation, the effects of gamma irradiation on the structural properties of plastic bottle sheet are studied. The Plastic sheets were exposed with 1.25MeV 60Co gamma rays source at various dose levels within the range from 0-670 kGy. The induced modifications were followed by micro-Raman and atomic force microscopy (AFM). The Raman spectrum shows the decrease in Raman intensity and formation of unsaturated bonds with an increase in the gamma dose. AFM image displays rough surface morphology after irradiation. The detailed Raman analysis of plastic bottle sheets is presented here, and the results are correlated with the AFM observations.

  20. AFM studies of the crystallization and habit modification of an excipient material, adipic acid.

    PubMed

    Keel, T R; Thompson, C; Davies, M C; Tendler, S J B; Roberts, C J

    2004-08-06

    Atomic force microscopy (AFM) has been used to investigate the (1 0 0) face of crystalline adipic acid, both in air and liquid environments. In air, surface reorganization occurred during scanning of the AFM probe, which has been investigated using single point force-distance analysis under a controlled relative humidity (RH) environment. We suggest such reorganization can be attributed to the influence of a network of water molecules bound to the hydrophilic (1 0 0) surface permitting local AFM tip-enhanced dissolution and reorganization of the solute. In situ imaging was also carried out on the crystals, revealing etch-pit formation during dissolution, and rapid growth at higher levels of supersaturation (sigma), both of which are direct consequences of the hydrophilic nature of the (1 0 0) face. Also presented here are nanoscale observations of the effect of octanoic acid, a structurally-related habit modifier, on crystalline adipic acid. Using AFM, we have been able to show that the presence of octanoic acid at low concentration has little observable affect on the development of the (1 0 0) face; however, as this concentration is increased, there are clear changes in step morphology and growth mode on the (1 0 0) face of the crystal. At a concentration of 1.26 mmol dm(-3) (a concentration corresponding to a molar ratio of approximately 1:175 octanoic acid:adipic acid), growth on the (1 0 0) face is inhibited, with in situ AFM imaging indicating this is a direct consequence of octanoic acid binding to the surface, and pinning the monomolecular growth steps.

  1. Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging

    PubMed Central

    Bergmann, U.; Morton, R. W.; Manning, P. L.; Sellers, W. I.; Farrar, S.; Huntley, K. G.; Wogelius, R. A.; Larson, P.

    2010-01-01

    Evolution of flight in maniraptoran dinosaurs is marked by the acquisition of distinct avian characters, such as feathers, as seen in Archaeopteryx from the Solnhofen limestone. These rare fossils were pivotal in confirming the dinosauria-avian lineage. One of the key derived avian characters is the possession of feathers, details of which were remarkably preserved in the Lagerstätte environment. These structures were previously simply assumed to be impressions; however, a detailed chemical analysis has, until now, never been completed on any Archaeopteryx specimen. Here we present chemical imaging via synchrotron rapid scanning X-ray fluorescence (SRS-XRF) of the Thermopolis Archaeopteryx, which shows that portions of the feathers are not impressions but are in fact remnant body fossil structures, maintaining elemental compositions that are completely different from the embedding geological matrix. Our results indicate phosphorous and sulfur retention in soft tissue as well as trace metal (Zn and Cu) retention in bone. Other previously unknown chemical details of Archaeopteryx are also revealed in this study including: bone chemistry, taphonomy (fossilization process), and curation artifacts. SRS-XRF represents a major advancement in the study of the life chemistry and fossilization processes of Archaeopteryx and other extinct organisms because it is now practical to image the chemistry of large specimens rapidly at concentration levels of parts per million. This technique has wider application to the archaeological, forensic, and biological sciences, enabling the mapping of “unseen” compounds critical to understanding biological structures, modes of preservation, and environmental context. PMID:20457935

  2. Archaeopteryx feathers and bone chemistry fully revealed via synchrotron imaging.

    PubMed

    Bergmann, U; Morton, R W; Manning, P L; Sellers, W I; Farrar, S; Huntley, K G; Wogelius, R A; Larson, P

    2010-05-18

    Evolution of flight in maniraptoran dinosaurs is marked by the acquisition of distinct avian characters, such as feathers, as seen in Archaeopteryx from the Solnhofen limestone. These rare fossils were pivotal in confirming the dinosauria-avian lineage. One of the key derived avian characters is the possession of feathers, details of which were remarkably preserved in the Lagerstätte environment. These structures were previously simply assumed to be impressions; however, a detailed chemical analysis has, until now, never been completed on any Archaeopteryx specimen. Here we present chemical imaging via synchrotron rapid scanning X-ray fluorescence (SRS-XRF) of the Thermopolis Archaeopteryx, which shows that portions of the feathers are not impressions but are in fact remnant body fossil structures, maintaining elemental compositions that are completely different from the embedding geological matrix. Our results indicate phosphorous and sulfur retention in soft tissue as well as trace metal (Zn and Cu) retention in bone. Other previously unknown chemical details of Archaeopteryx are also revealed in this study including: bone chemistry, taphonomy (fossilization process), and curation artifacts. SRS-XRF represents a major advancement in the study of the life chemistry and fossilization processes of Archaeopteryx and other extinct organisms because it is now practical to image the chemistry of large specimens rapidly at concentration levels of parts per million. This technique has wider application to the archaeological, forensic, and biological sciences, enabling the mapping of "unseen" compounds critical to understanding biological structures, modes of preservation, and environmental context.

  3. New insights into the mucoadhesion of pectins by AFM roughness parameters in combination with SPR.

    PubMed

    Joergensen, Lars; Klösgen, Beate; Simonsen, Adam Cohen; Borch, Jonas; Hagesaether, Ellen

    2011-06-15

    The object of this study was to assess the mucoadhesion of the three main commercially available types of pectin by atomic force microscopy (AFM) and surface Plasmon resonance (SPR). Polyacrylic acid and polyvinyl pyrrolidone were used as positive and negative control, respectively. Image analysis of the AFM scans revealed a significant change of roughness parameters when low-ester pectin was introduced to mica supported bovine submaxillarymucin, indicating a high mucoadhesion for this type of pectin. Only minor changes were observed with high-ester and amidated pectin. The same ranking order of adhesion affinity was confirmed by SPR. In conclusion, a high specific mucin interaction of pectin with a high charge density was demonstrated directly on a molecular scale without interference from the viscoelastic properties or the intra-molecular interactions between the polymer chains themselves, using two independent methods.

  4. Tip in-light on: Advantages, challenges, and applications of combining AFM and Raman microscopy on biological samples.

    PubMed

    Prats-Mateu, Batirtze; Gierlinger, Notburga

    2017-01-01

    Scanning probe microscopies and spectroscopies, especially AFM and Confocal Raman microscopy are powerful tools to characterize biological materials. They are both non-destructive methods and reveal mechanical and chemical properties on the micro and nano-scale. In the last years the interest for increasing the lateral resolution of optical and spectral images has driven the development of new technologies that overcome the diffraction limit of light. The combination of AFM and Raman reaches resolutions of about 50-150 nm in near-field Raman and 1.7-50 nm in tip enhanced Raman spectroscopy (TERS) and both give a molecular information of the sample and the topography of the scanned surface. In this review, the mentioned approaches are introduced, the main advantages and problems for application on biological samples discussed and some examples for successful experiments given. Finally the potential of colocated AFM and Raman measurements is shown on a case study of cellulose-lignin films: the topography structures revealed by AFM can be related to a certain chemistry by the colocated Raman scan and additionally the mechanical properties be revealed by using the digital pulsed force mode. Microsc. Res. Tech. 80:30-40, 2017. © 2016 Wiley Periodicals, Inc.

  5. Tip in–light on: Advantages, challenges, and applications of combining AFM and Raman microscopy on biological samples

    PubMed Central

    Gierlinger, Notburga

    2016-01-01

    Abstract Scanning probe microscopies and spectroscopies, especially AFM and Confocal Raman microscopy are powerful tools to characterize biological materials. They are both non‐destructive methods and reveal mechanical and chemical properties on the micro and nano‐scale. In the last years the interest for increasing the lateral resolution of optical and spectral images has driven the development of new technologies that overcome the diffraction limit of light. The combination of AFM and Raman reaches resolutions of about 50–150 nm in near‐field Raman and 1.7–50 nm in tip enhanced Raman spectroscopy (TERS) and both give a molecular information of the sample and the topography of the scanned surface. In this review, the mentioned approaches are introduced, the main advantages and problems for application on biological samples discussed and some examples for successful experiments given. Finally the potential of colocated AFM and Raman measurements is shown on a case study of cellulose‐lignin films: the topography structures revealed by AFM can be related to a certain chemistry by the colocated Raman scan and additionally the mechanical properties be revealed by using the digital pulsed force mode. Microsc. Res. Tech. 80:30–40, 2017. © 2016 Wiley Periodicals, Inc. PMID:27514318

  6. Fractal properties of macrophage membrane studied by AFM.

    PubMed

    Bitler, A; Dover, R; Shai, Y

    2012-12-01

    Complexity of cell membrane poses difficulties to quantify corresponding morphology changes during cell proliferation and damage. We suggest using fractal dimension of the cell membrane to quantify its complexity and track changes produced by various treatments. Glutaraldehyde fixed mouse RAW 264.7 macrophage membranes were chosen as model system and imaged in PeakForce QNM (quantitative nanomechanics) mode of AFM (atomic force microscope). The morphology of the membranes was characterized by fractal dimension. The parameter was calculated for set of AFM images by three different methods. The same calculations were done for the AFM images of macrophages treated with colchicine, an inhibitor of the microtubule polymerization, and microtubule stabilizing agent taxol. We conclude that fractal dimension can be additional and useful parameter to characterize the cell membrane complexity and track the morphology changes produced by different treatments.

  7. Ancient Pb and Ti mobilization revealed by Scanning Ion Imaging

    NASA Astrophysics Data System (ADS)

    Kusiak, Monika A.; Whitehouse, Martin J.; Wilde, Simon A.

    2014-05-01

    Zircons from strongly layered early Archean ortho- and paragneisses in ultra-high temperature (UHT) metamorphic rocks of the Napier Complex, Enderby Land, East Antarctica are characterized by complex U-Th-Pb systematics [1,2,3]. A large number of zircons from three samples, Gage Ridge, Mount Sones and Dallwitz Nunatak, are reversely discordant (U/Pb ages older than 207Pb/206Pb ages) with the oldest date of 3.9 Ga [4] (for the grain from Gage Ridge orthogneiss). To further investigate this process, we utilized a novel high spatial resolution Scanning Ion Imaging technique on the CAMECA IMS 1280 at the Natural History Museum in Stockholm. Areas of 70 μm x 70 μm were selected for imaging in mono- and multicollection modes using a ~2 μm rastered primary beam to map out the distribution of 48Ti, 89Y, 180Hf, 232Th, 238U, 204Pb, 206Pb and 207Pb. The ion maps reveal variable distribution of certain elements within analysed grains that can be compared to their CL response. Yttrium, together with U and Th, exhibits zonation visible on the CL images, Hf shows expected minimal variation. Unusual patchiness is visible in the map for Ti and Pb distribution. The bright patches with enhanced signal do not correspond to any zones or to crystal imperfections (e.g. cracks). The presence of patchy titanium is likely to affect Ti-in-zircon thermometry, and patchy Pb affecting 207Pb/206Pb ages, usually considered as more robust for Archean zircons. Using the WinImage program, we produced 207Pb/206Pb ratio maps that allow calculation of 207Pb/206Pb ages for spots of any size within the frame of the picture and at any time after data collection. This provides a new and unique method for obtaining age information from zircon. These maps show areas of enhanced brightness where the 207Pb/206Pb ratio is higher and demonstrate that within these small areas (μm scale) the apparent 207Pb/206Pb age is older, in some of these patches even > 4 Ga. These data are a result of ancient Pb

  8. APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies

    NASA Astrophysics Data System (ADS)

    Shlyakhtenko, Luda S.; Dutta, Samrat; Banga, Jaspreet; Li, Ming; Harris, Reuben S.; Lyubchenko, Yuri L.

    2015-10-01

    APOBEC3G (A3G) protein has antiviral activity against HIV and other pathogenic retroviruses. A3G has two domains: a catalytic C-terminal domain (CTD) that deaminates cytidine, and a N-terminal domain (NTD) that binds to ssDNA. Although abundant information exists about the biological activities of A3G protein, the interplay between sequence specific deaminase activity and A3G binding to ssDNA remains controversial. We used the topographic imaging and force spectroscopy modalities of Atomic Force Spectroscopy (AFM) to characterize the interaction of A3G protein with deaminase specific and nonspecific ssDNA substrates. AFM imaging demonstrated that A3G has elevated affinity for deaminase specific ssDNA than for nonspecific ssDNA. AFM force spectroscopy revealed two distinct binding modes by which A3G interacts with ssDNA. One mode requires sequence specificity, as demonstrated by stronger and more stable complexes with deaminase specific ssDNA than with nonspecific ssDNA. Overall these observations enforce prior studies suggesting that both domains of A3G contribute to the sequence specific binding of ssDNA.

  9. HUBBLE IMAGES REVEAL A YOUNG STAR'S DYNAMIC DISK AND JETS

    NASA Technical Reports Server (NTRS)

    2002-01-01

    These images of HH 30 show changes over only a five-year period in the disk and jets of this newborn star, which is about half a million years old. The pictures were taken between 1995 and 2000 with the Wide Field and Planetary Camera 2 aboard NASA's Hubble Space Telescope. Astronomers are interested in the disk because it is probably similar to the one from which the Sun and the planets in our solar system formed. Hubble reveals an edge-on disk (located at the bottom of the images), which appears as a flattened cloud of dust split into two halves by a dark lane. The disk blocks light from the central star. All that is visible is the reflection of the star's light by dust above and below the plane of the disk. The disk's diameter is 450 astronomical units (one astronomical unit equals the Earth-Sun distance). Shadows billions of miles in size can be seen moving across the disk. In 1995 and 2000, the left and right sides of the disk were about the same brightness, but in 1998 the right side was brighter. These patterns may be caused by bright spots on the star or variations in the disk near the star. The dust cloud near the top of these frames is illuminated by the star and reflects changes in its brightness. The star's magnetic field plays a major role in forming the jets (located above and below the disk), which look like streams of water from a fire hose. The powerful magnetic field creates the jets by channeling gas from the disk along the magnetic poles above and below the star. The gaps between the compact knots of gas seen in the jet above the disk indicate that this is a sporadic process. By tracking the motion of these knots over time, astronomers have measured the jet's speed at between 200,000 to 600,000 miles per hour (160,000 and 960,000 kilometers per hour). Oddly, the jet below the disk is moving twice as fast as the one above it. Credits: NASA, Alan Watson (Universidad Nacional Autonoma de Mexico), Karl Stapelfeldt (Jet Propulsion Laboratory), John

  10. Optimization of phase contrast in bimodal amplitude modulation AFM

    PubMed Central

    Damircheli, Mehrnoosh; Payam, Amir F

    2015-01-01

    Summary Bimodal force microscopy has expanded the capabilities of atomic force microscopy (AFM) by providing high spatial resolution images, compositional contrast and quantitative mapping of material properties without compromising the data acquisition speed. In the first bimodal AFM configuration, an amplitude feedback loop keeps constant the amplitude of the first mode while the observables of the second mode have not feedback restrictions (bimodal AM). Here we study the conditions to enhance the compositional contrast in bimodal AM while imaging heterogeneous materials. The contrast has a maximum by decreasing the amplitude of the second mode. We demonstrate that the roles of the excited modes are asymmetric. The operational range of bimodal AM is maximized when the second mode is free to follow changes in the force. We also study the contrast in trimodal AFM by analyzing the kinetic energy ratios. The phase contrast improves by decreasing the energy of second mode relative to those of the first and third modes. PMID:26114079

  11. Low tip damage AFM technique development for nano structures characterization

    NASA Astrophysics Data System (ADS)

    Liu, Biao; Wang, Charles C.; Huang, Po-Fu; Uritsky, Yuri

    2010-06-01

    Ambient dynamic mode (tapping mode or intermittent-contact mode) AFM imaging has been used extensively for the characterization of the topography of nano structures. However, the results are beset with artifacts, because hard tapping of the AFM tip on sample surface usually causes premature tip damage. Through careful study of the cantilever amplitude and phase signals as functions of tip-to-sample distance, principle of non-contact AFM operation was discovered to enable high resolution and low tip damage AFM image acquisition [1, 2]. However, current study discovers that the conventional way of acquiring amplitude and phase versus distance curves gives erroneous non-contact operating range, because the tip gets damaged during the data acquisition process. A new technique is developed to reliably map the operating parameters of an intact tip that ensures the AFM be operated with the correct non-contact settings. Two examples are given to illustrate the successful applications of this new technique. The first example involves the size characterization of polystyrene latex (PSL) nano particles used for light scattering tool calibration. The second example is the development of robust recipes for the measurement of the depth of phase-shift mask trenches.

  12. Determining surface properties with bimodal and multimodal AFM.

    PubMed

    Forchheimer, D; Borysov, Stanislav S; Platz, D; Haviland, David B

    2014-12-05

    Conventional dynamic atomic force microscopy (AFM) can be extended to bimodal and multimodal AFM in which the cantilever is simultaneously excited at two or more resonance frequencies. Such excitation schemes result in one additional amplitude and phase images for each driven resonance, and potentially convey more information about the surface under investigation. Here we present a theoretical basis for using this information to approximate the parameters of a tip-surface interaction model. The theory is verified by simulations with added noise corresponding to room-temperature measurements.

  13. AFM Structural Characterization of Drinking Water Biofilm under Physiological Conditions

    EPA Science Inventory

    Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air...

  14. 3D Color Digital Elevation Map of AFM Sample

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This color image is a three dimensional (3D) view of a digital elevation map of a sample collected by NASA's Phoenix Mars Lander's Atomic Force Microscope (AFM).

    The image shows four round pits, only 5 microns in depth, that were micromachined into the silicon substrate, which is the background plane shown in red. This image has been processed to reflect the levelness of the substrate.

    A Martian particle only one micrometer, or one millionth of a meter, across is held in the upper left pit.

    The rounded particle shown at the highest magnification ever seen from another world is a particle of the dust that cloaks Mars. Such dust particles color the Martian sky pink, feed storms that regularly envelop the planet and produce Mars' distinctive red soil.

    The particle was part of a sample informally called 'Sorceress' delivered to the AFM on the 38th Martian day, or sol, of the mission (July 2, 2008). The AFM is part of Phoenix's microscopic station called MECA, or the Microscopy, Electrochemistry, and Conductivity Analyzer.

    The AFM was developed by a Swiss-led consortium, with Imperial College London producing the silicon substrate that holds sampled particles.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  15. AFM of biological complexes: what can we learn?

    PubMed Central

    Gaczynska, Maria; Osmulski, Pawel A.

    2009-01-01

    The term “biological complexes” broadly encompasses particles as diverse as multisubunit enzymes, viral capsids, transport cages, molecular nets, ribosomes, nucleosomes, biological membrane components and amyloids. The complexes represent a broad range of stability and composition. Atomic force microscopy offers a wealth of structural and functional data about such assemblies. For this review, we choose to comment on the significance of AFM to study various aspects of biology of selected nonmembrane protein assemblies. Such particles are large enough to reveal many structural details under the AFM probe. Importantly, the specific advantages of the method allow for gathering dynamic information about their formation, stability or allosteric structural changes critical for their function. Some of them have already found their way to nanomedical or nanotechnological applications. Here we present examples of studies where the AFM provided pioneering information about the biology of complexes, and examples of studies where the simplicity of the method is used toward the development of potential diagnostic applications. PMID:19802337

  16. Inside Out: Modern Imaging Techniques to Reveal Animal Anatomy

    PubMed Central

    Lauridsen, Henrik; Hansen, Kasper; Wang, Tobias; Agger, Peter; Andersen, Jonas L.; Knudsen, Peter S.; Rasmussen, Anne S.; Uhrenholt, Lars; Pedersen, Michael

    2011-01-01

    Animal anatomy has traditionally relied on detailed dissections to produce anatomical illustrations, but modern imaging modalities, such as MRI and CT, now represent an enormous resource that allows for fast non-invasive visualizations of animal anatomy in living animals. These modalities also allow for creation of three-dimensional representations that can be of considerable value in the dissemination of anatomical studies. In this methodological review, we present our experiences using MRI, CT and μCT to create advanced representation of animal anatomy, including bones, inner organs and blood vessels in a variety of animals, including fish, amphibians, reptiles, mammals, and spiders. The images have a similar quality to most traditional anatomical drawings and are presented together with interactive movies of the anatomical structures, where the object can be viewed from different angles. Given that clinical scanners found in the majority of larger hospitals are fully suitable for these purposes, we encourage biologists to take advantage of these imaging techniques in creation of three-dimensional graphical representations of internal structures. PMID:21445356

  17. Granite petrogenesis revealed by combined gravimetric and radiometric imaging

    NASA Astrophysics Data System (ADS)

    Tartèse, Romain; Boulvais, Philippe; Poujol, Marc; Vigneresse, Jean-Louis

    2011-03-01

    In peneplaned terranes, it is often impossible to get a full 3D view of geological objects. In the case of granitic plutons, for which intrusive relationships between constituent units can provide first order information regarding their petrogenesis, this lack of 3D field evidence is a major issue. Indirect observations can be provided by geophysical surveys. Here, we interpret field gravity data and airborne gamma ray radiometric maps with whole rock geochemistry data in order to obtain information on granite petrogenesis. First, we test our proposed combined geophysical and geochemical approach on the Huelgoat Variscan intrusion (Armorican Massif, France) and we show that ternary radiometric maps are a good proxy for the distribution of K, U and Th radioelements. Then, we apply our method to the Lizio and Questembert Variscan granitic intrusions (Armorican Massif) and show that some features characteristic of the intrusions, such as the feeding zones, can be localised by geophysical imaging. Indeed, radiometric maps constitute a frozen image of the latest stage of the magmatic building of plutons.

  18. AFM imaging of natural optical structures

    NASA Astrophysics Data System (ADS)

    Dallaeva, Dinara; Tománek, Pavel; Prokopyeva, Elena; Kaspar, Pavel; Grmela, Lubomír.; Škarvada, Pavel

    2015-01-01

    The colors of some living organisms assosiated with the surface structure. Irridesence butterfly wings is an example of such coloration. Optical effects such as interference, diffraction, polarization are responsible for physical colors appearance. Alongside with amazing beauty this structure represent interest for design of optical devices. Here we report the results of morphology investigation by atomic force microscopy. The difference in surface structure of black and blue wings areas is clearly observed. It explains the angle dependence of the wing blue color, since these micrometer and sub-micrometer quasiperiodical structures could control the light propagation, absorption and reflection.

  19. Image analysis of weaverbird nests reveals signature weave textures.

    PubMed

    Bailey, Ida E; Backes, André; Walsh, Patrick T; Morgan, Kate V; Meddle, Simone L; Healy, Susan D

    2015-06-01

    In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual weaverbird that built them. We found that a computer-aided texture analysis approach does allow the assignment of a signature to weaverbirds' nests. We suggest that this approach will be a useful tool with which to examine individual variation across a range of animal constructions, not just for nests.

  20. Image analysis of weaverbird nests reveals signature weave textures

    PubMed Central

    Bailey, Ida E.; Backes, André; Walsh, Patrick T.; Morgan, Kate V.; Meddle, Simone L.; Healy, Susan D.

    2015-01-01

    In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual weaverbird that built them. We found that a computer-aided texture analysis approach does allow the assignment of a signature to weaverbirds' nests. We suggest that this approach will be a useful tool with which to examine individual variation across a range of animal constructions, not just for nests. PMID:26543586

  1. Fully Quantified Spectral Imaging Reveals in Vivo Membrane Protein Interactions

    PubMed Central

    King, Christopher; Stoneman, Michael; Raicu, Valerica; Hristova, Kalina

    2016-01-01

    Here we introduce the Fully Quantified Spectral Imaging (FSI) method as a new tool to probe the stoichiometry and stability of protein complexes in biological membranes. The FSI method yields two dimensional membrane concentrations and FRET efficiencies in native plasma membranes. It can be used to characterize the association of membrane proteins: to differentiate between monomers, dimers, or oligomers, to produce binding (association) curves, and to measure the free energies of association in the membrane. We use the FSI method to study the lateral interactions of Vascular Endothelial Growth Factor Receptor 2 (VEGFR2), a member of the receptor tyrosine kinase (RTK) superfamily, in plasma membranes, in vivo. The knowledge gained through the use of the new method challenges the current understanding of VEGFR2 signaling. PMID:26787445

  2. Terahertz Lasers Reveal Information for 3D Images

    NASA Technical Reports Server (NTRS)

    2013-01-01

    After taking off her shoes and jacket, she places them in a bin. She then takes her laptop out of its case and places it in a separate bin. As the items move through the x-ray machine, the woman waits for a sign from security personnel to pass through the metal detector. Today, she was lucky; she did not encounter any delays. The man behind her, however, was asked to step inside a large circular tube, raise his hands above his head, and have his whole body scanned. If you have ever witnessed a full-body scan at the airport, you may have witnessed terahertz imaging. Terahertz wavelengths are located between microwave and infrared on the electromagnetic spectrum. When exposed to these wavelengths, certain materials such as clothing, thin metal, sheet rock, and insulation become transparent. At airports, terahertz radiation can illuminate guns, knives, or explosives hidden underneath a passenger s clothing. At NASA s Kennedy Space Center, terahertz wavelengths have assisted in the inspection of materials like insulating foam on the external tanks of the now-retired space shuttle. "The foam we used on the external tank was a little denser than Styrofoam, but not much," says Robert Youngquist, a physicist at Kennedy. The problem, he explains, was that "we lost a space shuttle by having a chunk of foam fall off from the external fuel tank and hit the orbiter." To uncover any potential defects in the foam covering, such as voids or air pockets, that could keep the material from staying in place, NASA employed terahertz imaging to see through the foam. For many years, the technique ensured the integrity of the material on the external tanks.

  3. White Matter Change Revealed by Diffusion Tensor Imaging in Gliomas

    PubMed Central

    Won, Young Il; Kim, Chi Heon; Park, Chul-Kee; Koo, Bang-Bon; Lee, Jong-Min; Jung, Hee-Won

    2016-01-01

    Background Tumor-related white matter change is detected at late stages with magnetic resonance imaging (MRI), when mass effect or prominent edema is present. We analyzed if diffusion tensor imaging (DTI) white matter change earlier than conventional MRI. Methods Twenty-six patients with gliomas (World Health Organization grade II, 5; grade III, 12; and grade IV, 9) within 2 cm from the posterior limb of the internal capsule (IC) were studied. Fifteen normal adults were enrolled as controls. Fluid attenuation inversion recovery MRI showed a high signal change at the posterior limb of the IC (HSIC) in 9 patients with grade III or IV gliomas. We classified the gliomas as WHO grade II (gliomas II), grade III or IV without HSIC [gliomas III/IV(-)] and grade III or IV with HSIC [gliomas III/IV(+)], as an indicator of the increase in the severity of the white matter changes. Fractional anisotropy (FA) and apparent diffusion coefficients (ADC) were calculated for the pyramidal tract. Tumor progression along pyramidal tract was evaluated by follow-up MRI in 16 patients at 40±18 months. Results FA showed no significant difference between gliomas II and control (p=0.694), but was lower in gliomas III/IV(-) and gliomas III/IV(+) (p<0.001). ADCs were higher in gliomas II, gliomas III/IV(-) and gliomas III/IV(+) than control (p<0.001). Tumor progression was detected in 2/16 patients. Conclusion DTI detected white matter changes that appeared to be normal in MRI. ADC changed even in low grade glioma, indicating ADC may be a better parameter for the early detection of white matter change. PMID:27867919

  4. Cryogenic AFM-STM for mesoscopic physics

    NASA Astrophysics Data System (ADS)

    Le Sueur, H.

    Electronic spectroscopy based on electron tunneling gives access to the electronic density of states (DOS) in conductive materials, and thus provides detailed information about their electronic properties. During this thesis work, we have developed a microscope in order to perform spatially resolved (10 nm) tunneling spectroscopy, with an unprecedented energy resolution (10 μeV), on individual nanocircuits. This machine combines an Atomic Force Microscope (AFM mode) together with a Scanning Tunneling Spectroscope (STS mode) and functions at very low temperatures (30 mK). In the AFM mode, the sample topography is recorded using a piezoelectric quartz tuning fork, which allows us to locate and image nanocircuits. Tunneling can then be performed on conductive areas of the circuit. With this microscope, we have measured the local DOS in a hybrid Superconductor-Normal metal-Superconductor (S-N-S) structure. In such circuit, the electronic properties of N and S are modified by the superconducting proximity effect. In particular, for short N wires, we have observed a minigap independent of position in the DOS of the N wire, as was previously predicted. Moreover, when varying the superconducting phase difference between the S electrodes, we have measured the modification of the minigap and its disappearance when the phase difference equals π. Our experimental results for the DOS, and its dependences (on phase, position, N length), are quantitatively accounted for by the quasiclassical theory of superconductivity. Some predictions of this theory are observed for the first time. La spectroscopie électronique basée sur l'effet tunnel donne accès à la densité d'états des électrons (DOS) dans les matériaux conducteurs, et renseigne ainsi en détail sur leurs propriétés électroniques. Au cours de cette thèse, nous avons développé un microscope permettant d'effectuer la spectroscopie tunnel résolue spatialement (10 nm) de nanocircuits individuels, avec une r

  5. The formation of liquid bridge in different operating modes of AFM

    NASA Astrophysics Data System (ADS)

    Wei, Zheng; Sun, Yan; Ding, WenXuan; Wang, ZaiRan

    2016-09-01

    The liquid bridge is one of the principal factors that cause artifacts in ambient-pressure atomic force microscope (AFM) images. Additionally, it is the main component of the adhesion force in ambient conditions. To understand the AFM imaging mechanism and the sample characteristics, it is essential to study the liquid bridge. This study interprets the physical mechanism involved in liquid bridge formation, which is composed of three different physical processes: the squeezing process, capillary condensation, and liquid film flow. We discuss the contributions of these three mechanisms to the volume and the capillary force of the liquid bridge in different AFM operation modes.

  6. Fine Surface Images That Reflect Cytoskeletal Structures in Cultured Glial Cells by Atomic Force Microscopy

    NASA Astrophysics Data System (ADS)

    Yamane, Yukako; Hatakeyama, Dai; Tojima, Takuro; Kawabata, Kazushige; Ushiki, Tatsuo; Ogura, Shigeaki; Abe, Kazuhiro; Ito, Etsuro

    1998-06-01

    The morphology of cultured glial cells was examined using a combination of atomic force microscopy (AFM) and immunofluorescence staining for cytoskeletons. The meshwork of type-1 astrocytes consisted of thick longitudinal and thin lateral lines on the cell surfaces observed by AFM; the former lines were confirmed to be reflections of actin filaments. The astrocytic processes of type-2 astrocytes were observed to be rugged on AFM. These structures were mainly affected by microtubules. Immunofluorescence imaging of microglia revealed that actin filaments and microtubules were arranged radially and wavily along the cell edge, respectively. AFM could detect these radial and wavy structures clearly. These results show that AFM can provide information on the cytoskeletons of glial cells, indicating that AFM is a useful tool for the morphological characterization of cells.

  7. Scanning hall probe microscopy (SHPM) using quartz crystal AFM feedback.

    PubMed

    Dede, M; Urkmen, K; Girişen, O; Atabak, M; Oral, A; Farrer, I; Ritchie, D

    2008-02-01

    Scanning Hall Probe Microscopy (SHPM) is a quantitative and non-invasive technique for imaging localized surface magnetic field fluctuations such as ferromagnetic domains with high spatial and magnetic field resolution of approximately 50 nm and 7 mG/Hz(1/2) at room temperature. In the SHPM technique, scanning tunneling microscope (STM) or atomic force microscope (AFM) feedback is used to keep the Hall sensor in close proximity of the sample surface. However, STM tracking SHPM requires conductive samples; therefore the insulating substrates have to be coated with a thin layer of gold. This constraint can be eliminated with the AFM feedback using sophisticated Hall probes that are integrated with AFM cantilevers. However it is very difficult to micro fabricate these sensors. In this work, we have eliminated the difficulty in the cantilever-Hall probe integration process, just by gluing a Hall Probe chip to a quartz crystal tuning fork force sensor. The Hall sensor chip is simply glued at the end of a 32.768 kHz or 100 kHz Quartz crystal, which is used as force sensor. An LT-SHPM system is used to scan the samples. The sensor assembly is dithered at the resonance frequency using a digital Phase Locked Loop circuit and frequency shifts are used for AFM tracking. SHPM electronics is modified to detect AFM topography and the frequency shift, along with the magnetic field image. Magnetic domains and topography of an Iron Garnet thin film crystal, NdFeB demagnetised magnet and hard disk samples are presented at room temperature. The performance is found to be comparable with the SHPM using STM feedback.

  8. Microhardness, chemical etching, SEM, AFM and SHG studies of novel nonlinear optical crystal -L-threonine formate

    SciTech Connect

    Hanumantha Rao, Redrothu; Kalainathan, S.

    2012-04-15

    Highlights: Black-Right-Pointing-Pointer Microhardness studies of novel LTF crystal reported first time in the literature. Black-Right-Pointing-Pointer Surface studies are done by AFM, chemical etching and SEM. Black-Right-Pointing-Pointer From SHG studies, it is known that LTF is potential NLO crystal. -- Abstract: The crystal L-threonine formate, an organic NLO crystal was synthesized from aqueous solution by slow evaporation technique. The grown crystal surface has been analyzed by scanning electron microscopy (SEM), chemical etching and atomic force microscopy (AFM). SEM analysis reveals pyramidal shaped minute crystallites on the growth surface. The etching study indicates the occurrence of etch pit patterns like striations and step like pattern. The mechanical properties of LTF crystals were evaluated by mechanical testing which reveals certain mechanical characteristics like elastic stiffness constant (C{sub 11}) and young's modulus (E). The Vickers and Knoop microhardness studies have been carried out on LTF crystals over a range of 10-50 g. Hardness anisotropy has been observed in accordance with the orientation of the crystal. AFM image shows major hillock on growth surface. The second harmonic generation (SHG) efficiency has been tested by the Kurtz powder technique using Nd:YAG laser and found to be about 1.21 times in comparison with standard potassium dihydrogen phosphate (KDP) crystals.

  9. Imaging Sensor Noise as Digital X-Ray for Revealing Forgeries

    NASA Astrophysics Data System (ADS)

    Chen, Mo; Fridrich, Jessica; Lukáš, Jan; Goljan, Miroslav

    In this paper, we describe a new forensic tool for revealing digitally altered images by detecting the presence of photo-response non-uniformity noise (PRNU) in small regions. This method assumes that either the camera that took the image is available to the analyst or at least some other non-tampered images taken by the camera are available. Forgery detection using the PRNU involves two steps - estimation of the PRNU from non-tampered images and its detection in individual image regions. From a simplified model of the sensor output, we design optimal PRNU estimators and detectors. Binary hypothesis testing is used to determine which regions are forged. The method is tested on forged images coming from a variety of digital cameras and with different JPEG quality factors. The approximate probability of falsely identifying a forged region in a non-forged image is estimated by running the algorithm on a large number of non-forged images.

  10. AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

    NASA Technical Reports Server (NTRS)

    Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

    2002-01-01

    Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

  11. Investigation of biopolymer networks by means of AFM

    NASA Astrophysics Data System (ADS)

    Keresztes, Z.; Rigó, T.; Telegdi, J.; Kálmán, E.

    Natural hydrogel alginate was investigated by means of atomic force microscopy (AFM) to gain microscale information on the morphological and rheological properties of the biopolymer network cross-linked by various cations. Local rheological properties of the gels measured by force spectroscopy gave correlation between increasing ion selectivity and increasing polymer elasticity. Adhesive forces acting between the surface of the gel and the probe, and also the intrinsic rheological properties of bulk polymers affect the microscopical image formation.

  12. Structural investigations on native collagen type I fibrils using AFM

    SciTech Connect

    Strasser, Stefan; Zink, Albert; Janko, Marek; Heckl, Wolfgang M.; Thalhammer, Stefan . E-mail: stefan.thalhammer@gsf.de

    2007-03-02

    This study was carried out to determine the elastic properties of single collagen type I fibrils with the use of atomic force microscopy (AFM). Native collagen fibrils were formed by self-assembly in vitro characterized with the AFM. To confirm the inner assembly of the collagen fibrils, the AFM was used as a microdissection tool. Native collagen type I fibrils were dissected and the inner core uncovered. To determine the elastic properties of collagen fibrils the tip of the AFM was used as a nanoindentor by recording force-displacement curves. Measurements were done on the outer shell and in the core of the fibril. The structural investigations revealed the banding of the shell also in the core of native collagen fibrils. Nanoindentation experiments showed the same Young's modulus on the shell as well as in the core of the investigated native collagen fibrils. In addition, the measurements indicate a higher adhesion in the core of the collagen fibrils compared to the shell.

  13. Structure, cell wall elasticity and polysaccharide properties of living yeast cells, as probed by AFM

    NASA Astrophysics Data System (ADS)

    Alsteens, David; Dupres, Vincent; McEvoy, Kevin; Wildling, Linda; Gruber, Hermann J.; Dufrêne, Yves F.

    2008-09-01

    Although the chemical composition of yeast cell walls is known, the organization, assembly, and interactions of the various macromolecules remain poorly understood. Here, we used in situ atomic force microscopy (AFM) in three different modes to probe the ultrastructure, cell wall elasticity and polymer properties of two brewing yeast strains, i.e. Saccharomyces carlsbergensis and S. cerevisiae. Topographic images of the two strains revealed smooth and homogeneous cell surfaces, and the presence of circular bud scars on dividing cells. Nanomechanical measurements demonstrated that the cell wall elasticity of S. carlsbergensis is homogeneous. By contrast, the bud scar of S. cerevisiae was found to be stiffer than the cell wall, presumably due to the accumulation of chitin. Notably, single molecule force spectroscopy with lectin-modified tips revealed major differences in polysaccharide properties of the two strains. Polysaccharides were clearly more extended on S. cerevisiae, suggesting that not only oligosaccharides, but also polypeptide chains of the mannoproteins were stretched. Consistent with earlier cell surface analyses, these findings may explain the very different aggregation properties of the two organisms. This study demonstrates the power of using multiple complementary AFM modalities for probing the organization and interactions of the various macromolecules of microbial cell walls.

  14. Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction.

    PubMed

    Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

    2016-07-25

    The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation.

  15. Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction

    NASA Astrophysics Data System (ADS)

    Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

    2016-07-01

    The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation.

  16. Nano-Wilhelmy investigation of dynamic wetting properties of AFM tips through tip-nanobubble interaction

    PubMed Central

    Wang, Yuliang; Wang, Huimin; Bi, Shusheng; Guo, Bin

    2016-01-01

    The dynamic wetting properties of atomic force microscopy (AFM) tips are of much concern in many AFM-related measurement, fabrication, and manipulation applications. In this study, the wetting properties of silicon and silicon nitride AFM tips are investigated through dynamic contact angle measurement using a nano-Wilhelmy balance based method. This is done by capillary force measurement during extension and retraction motion of AFM tips relative to interfacial nanobubbles. The working principle of the proposed method and mathematic models for dynamic contact angle measurement are presented. Geometric models of AFM tips were constructed using scanning electronic microscopy (SEM) images taken from different view directions. The detailed process of tip-nanobubble interaction was investigated using force-distance curves of AFM on nanobubbles. Several parameters including nanobubble height, adhesion and capillary force between tip and nanobubbles are extracted. The variation of these parameters was studied over nanobubble surfaces. The dynamic contact angles of the AFM tips were calculated from the capillary force measurements. The proposed method provides direct measurement of dynamic contact angles for AFM tips and can also be taken as a general approach for nanoscale dynamic wetting property investigation. PMID:27452115

  17. Quantitative biomolecular imaging by dynamic nanomechanical mapping.

    PubMed

    Zhang, Shuai; Aslan, Hüsnü; Besenbacher, Flemming; Dong, Mingdong

    2014-11-07

    The ability to 'see' down to nanoscale has always been one of the most challenging obstacles for researchers to address fundamental questions. For many years, researchers have been developing scanning probe microscopy techniques to improve imaging capability at nanoscale. Among them, atomic force microscopy (AFM) has received considerable attention, which allows probing topography of biological species at real space under physiological environment. Importantly, force measurements in AFM enable researchers to reveal not only the topography but also the relevant physical-chemical properties. AFM-based dynamic nanomechanical mapping (DNM) provides insights into the functions of biological systems by the interpretation of 'force', which are inaccessible by most of the other analytic techniques. This review is aiming to shed light on these recently developed AFM-based DNM techniques for biomolecular imaging, and discuss the relative applications in biological research from the nanomechanical point of view.

  18. Image manifold revealing for breast lesion segmentation in DCE-MRI.

    PubMed

    Hu, Liang; Cheng, Zhaoning; Wang, Manning; Song, Zhijian

    2015-01-01

    Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is widely used for breast lesion differentiation. Manual segmentation in DCE-MRI is difficult and open to viewer interpretation. In this paper, an automatic segmentation method based on image manifold revealing was introduced to overcome the problems of the currently used method. First, high dimensional datasets were constructed from a dynamic image series. Next, an embedded image manifold was revealed in the feature image by nonlinear dimensionality reduction technique. In the last stage, k-means clustering was performed to obtain final segmentation results. The proposed method was applied in actual clinical cases and compared with the gold standard. Statistical analysis showed that the proposed method achieved an acceptable accuracy, sensitivity, and specificity rates.

  19. Arrangement of rotational domains of the (√31×√31) R±9° reconstruction of Al 2O 3( 0 0 0 1 ) revealed by non-contact AFM

    NASA Astrophysics Data System (ADS)

    Wang, J.; Howard, A.; Egdell, R. G.; Pethica, J. B.; Foord, J. S.

    2002-09-01

    Non-contact atomic force microscopy using a needle sensor with a phase shift feedback mechanism has been used to characterise Al 2O 3(0 0 0 1) surfaces prepared by annealing in 10 -4 mbar partial pressures of oxygen. The preparation procedure leads to flat terraces with lengths in excess of 1000 nm and widths of order 40 nm separated by c/6 steps. The unit cell of the (√31×√31) R±9° reconstruction is resolved, with a single rotational domain on each of the terraces. The 18° rotation between the domains is observed exclusively at step edges. The mechanism of imaging the (√31×√31) R±9° reconstruction is discussed.

  20. AFM Manipulation of Viruses: Substrate Interactions and Mechanical Properties

    NASA Astrophysics Data System (ADS)

    Falvo, M. R.; Superfine, R.; Washburn, S.; Finch, M.; Taylor, R. M.; Chi, V.; Brooks, F. P.; Ferrari, F.; Samulski, R.

    1996-03-01

    Using an AFM tip as a manipulation tool, we have translated, rotated, and dissected individual Tobacco Mosaic Virus (TMV) and Adenovirus particles. We have implemented a teleoperation system which allows manual control of the relative tip-sample position while also allowing conventional AFM operation for imaging resulting structure. Using simple tip trajectories to bend the rod-shaped TMV, we observed a variety of resulting structures and mechanical failures. The distributed adhesive interaction between the virus and the sample surface, as well as the local tip-virus interaction affect the distortion in the shape of the virus. Experiments were performed in air as well as in liquid on graphite and Si substrates. The in-liquid experiments allow tuning of the environmental conditions, including osmolarity and pH, which are known to profoundly affect the virus structure. A continuum mechanical model relating mechanical properties to observations provides insight into the constraints for successful nondestructive manipulation.

  1. High aspect ratio AFM Probe processing by helium-ion-beam induced deposition.

    PubMed

    Onishi, Keiko; Guo, Hongxuan; Nagano, Syoko; Fujita, Daisuke

    2014-11-01

    A Scanning Helium Ion Microscope (SHIM) is a high resolution surface observation instrument similar to a Scanning Electron Microscope (SEM) since both instruments employ finely focused particle beams of ions or electrons [1]. The apparent difference is that SHIMs can be used not only for a sub-nanometer scale resolution microscopic research, but also for the applications of very fine fabrication and direct lithography of surfaces at the nanoscale dimensions. On the other hand, atomic force microscope (AFM) is another type of high resolution microscopy which can measure a three-dimensional surface morphology by tracing a fine probe with a sharp tip apex on a specimen's surface.In order to measure highly uneven and concavo-convex surfaces by AFM, the probe of a high aspect ratio with a sharp tip is much more necessary than the probe of a general quadrangular pyramid shape. In this paper we report the manufacture of the probe tip of the high aspect ratio by ion-beam induced gas deposition using a nanoscale helium ion beam of SHIM.Gas of platinum organic compound was injected into the sample surface neighborhood in the vacuum chamber of SHIM. The decomposition of the gas and the precipitation of the involved metal brought up a platinum nano-object in a pillar shape on the normal commercial AFM probe tip. A SHIM system (Carl Zeiss, Orion Plus) equipped with the gas injection system (OmniProbe, OmniGIS) was used for the research. While the vacuum being kept to work, we injected platinum organic compound ((CH3)3(CH3C5H4)Pt) into the sample neighborhood and irradiated the helium ion beam with the shape of a point on the apex of the AFM probe tip. It is found that we can control the length of the Pt nano-pillar by irradiation time of the helium ion beam. The AFM probe which brought up a Pt nano-pillar is shown in Figure 1. It is revealed that a high-aspect-ratio Pt nano-pillar of ∼40nm diameter and up to ∼2000 nm length can be grown. In addition, for possible heating

  2. Nanomechanics of new materials — AFM and computer modelling studies of trichoptera silk

    NASA Astrophysics Data System (ADS)

    Strzelecki, Janusz; Strzelecka, Joanna; Mikulska, Karolina; Tszydel, Mariusz; Balter, Aleksander; Nowak, Wiesław

    2011-04-01

    Caddisfly (Trichopera) can glue diverse material underwater with a silk fiber. This makes it a particularly interesting subject for biomimetcs. Better understanding of silk composition and structure could lead to an adhesive capable to close bleeding wounds or to new biomaterials. However, while spiderweb or silkworm secretion is well researched, caddisfly silk is still poorly understood. Here we report a first nanomechanical analysis of H. Angustipennis caddisfly silk fiber. An Atomic Force Microscope (AFM) imaging shows dense 150 nm bumps on silk surface, which can be identified as one of features responsible for its outstanding adhesive properties. AFM force spectroscopy at the fiber surface showed, among others, characteristic saw like pattern. This pattern is attributed to sacrificial bond stretching and enhances energy dissipation in mechanical deformation. Similarities of some force curves observed on Tegenaria domestica spiderweb and caddisfly silk are also discussed. Steered Molecular Dynamics simulations revealed that the strength of short components of Fib-H HA species molecules, abundant in Trichoptera silk is critically dependent on calcium presence.

  3. Structural changes of polysulfone membrane use for hemodialysis in the consecutive regime: nanometric analysis by AFM

    NASA Astrophysics Data System (ADS)

    Batina, Nikola; Acosta García, Ma. Cristina; Avalos Pérez, Angélica; Alberto Ramírez, Mario; Franco, Martha; Pérez Gravas, Héctor; Cadena Méndez, Miguel

    2013-08-01

    Nowadays, the hemodialytic treatment of patients with either acute or chronic renal failure has been improved by promoting biocompatibility in the use of new materials and improve membrane surface characteristics. Low and high flux polysulfone membranes (PM) used in dialysis and ultra filtration have been studied in order to understand the geometry and surface chemistry of the pores at inner (nanometric) and outer (micrometric) membrane parts. The surface changes of polysulfone cartridge membrane (PM) during different number of consecutive reuse trials: after 1st, 10th and 23th times of use. The morphology of the hollow fibers surfaces was studied by means of the atomic force microscopy (AFM) imaging and the surface roughness analysis. The roughness of both inner and outer part of PM surface increases with numbers of reuse trails. Thus, small and medium size pores were wiped out when the number of uses changed from zero to 23 on the outer surface. The pore density decreases. The inner part of membrane shows some nanometric size deformation in forms of new openings and raptures. The AFM analysis show differences in the PM morphology at the nanometric level, not previously revealed, which could be important in the evaluation of the PM.

  4. Intravital imaging reveals new ancillary mechanisms co-opted by cancer cells to drive tumor progression

    PubMed Central

    Lucas, Morghan C.; Timpson, Paul

    2016-01-01

    Intravital imaging is providing new insights into the dynamics of tumor progression in native tissues and has started to reveal the layers of complexity found in cancer. Recent advances in intravital imaging have allowed us to look deeper into cancer behavior and to dissect the interactions between tumor cells and the ancillary host niche that promote cancer development. In this review, we provide an insight into the latest advances in cancer biology achieved by intravital imaging, focusing on recently discovered mechanisms by which tumor cells manipulate normal tissue to facilitate disease progression. PMID:27239290

  5. Tip Characterization Method using Multi-feature Characterizer for CD-AFM

    PubMed Central

    Orji, Ndubuisi G.; Itoh, Hiroshi; Wang, Chumei; Dixson, Ronald G.; Walecki, Peter S.; Schmidt, Sebastian W.; Irmer, Bernd

    2016-01-01

    In atomic force microscopy (AFM) metrology, the tip is a key source of uncertainty. Images taken with an AFM show a change in feature width and shape that depends on tip geometry. This geometric dilation is more pronounced when measuring features with high aspect ratios, and makes it difficult to obtain absolute dimensions. In order to accurately measure nanoscale features using an AFM, the tip dimensions should be known with a high degree of precision. We evaluate a new AFM tip characterizer, and apply it to critical dimension AFM (CD-AFM) tips used for high aspect ratio features. The characterizer is made up of comb-shaped lines and spaces, and includes a series of gratings that could be used as an integrated nanoscale length reference. We also demonstrate a simulation method that could be used to specify what range of tip sizes and shapes the characterizer can measure. Our experiments show that for non re-entrant features, the results obtained with this characterizer are consistent to 1 nm with the results obtained by using widely accepted but slower methods that are common practice in CD-AFM metrology. A validation of the integrated length standard using displacement interferometry indicates a uniformity of better than 0.75%, suggesting that the sample could be used as highly accurate and SI traceable lateral scale for the whole evaluation process. PMID:26720439

  6. UV laser ablation of intraocular lenses: SEM and AFM microscopy examination of the biomaterial surface

    NASA Astrophysics Data System (ADS)

    Spyratou, E.; Asproudis, I.; Tsoutsi, D.; Bacharis, C.; Moutsouris, K.; Makropoulou, M.; Serafetinides, A. A.

    2010-02-01

    Several new materials and patterns are studied for the formation and etching of intraocular lenses (IOLs), in order to improve their optical properties, to reduce the diffractive aberrations and to decrease the incidence of posterior capsular opacification. The aim of this study is to investigate the use of UV ( λ = 266 nm) laser pulses to ablate the intraocular lenses materials, and thus to provide an alternative to conventional surface shaping techniques for IOLs fabrication. Ablation experiments were conducted using various polymer substrates of hydrophobic acrylic IOLs and PMMA IOLs. We investigated the ablation efficiency and the morphology of the ablated area by imaging the surface modification with atomic force microscopy (AFM) and scanning electron microscopy (SEM). The morphological appearance of IOL samples reveals the effect of a photochemical and photothermal ablation mechanism.

  7. Morphological and Structural Changes on Human Dental Enamel After Er:YAG Laser Irradiation: AFM, SEM, and EDS Evaluation

    PubMed Central

    Rodríguez-Vilchis, Laura Emma; Olea-Mejìa, Oscar Fernando; Sánchez-Flores, Ignacio; Centeno-Pedraza, Claudia

    2011-01-01

    Abstract Objective: The purpose of this study was to evaluate, using atomic force microscopy (AFM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS), the morphological and structural changes of the enamel after irradiation with the Er:YAG laser. Background data: A previous study showed that subablative Er:YAG laser irradiation produced undesirable morphological changes on the enamel surface, such as craters and cracks; however, the enamel acid resistance was not increased. Methods: Fifty-two samples of human enamel were divided into four groups (n = 13): Group I was the control (no laser irradiation), whereas Groups II, III, and IV were irradiated with the Er:YAG 100 mJ (12.7 J/cm2), 100 mJ (7.5 J/cm2), and 150 mJ (11 J/cm2), respectively, at 10 Hz with water spray. The morphological changes were observed by AFM and SEM. The weight percentages (wt%) of calcium (Ca), phosphorus (P), oxygen (O) and chlorine (Cl) were determined in the resultant craters and their periphery using EDS. Kruskal–Wallis and Mann–Whitney U tests were performed (p ≤ 0.05) to distinguish significant differences among the groups. Results: The AFM images showed cracks with depths between 250 nm and 750 nm for Groups II and IV, respectively, and the widths of these cracks were 5.37 μm and 2.58 μm. The interior of the cracks showed a rough surface. The SEM micrographs revealed morphological changes. Significant differences were detected in Ca, P, and Cl in the crater and its periphery. Conclusions: AFM observations showed triangular-shaped cracks, whereas craters and cracks were evident by SEM in all irradiated samples. It was not possible to establish a characteristic chemical pattern in the craters. PMID:21417912

  8. Nano Mechanical Machining Using AFM Probe

    NASA Astrophysics Data System (ADS)

    Mostofa, Md. Golam

    Complex miniaturized components with high form accuracy will play key roles in the future development of many products, as they provide portability, disposability, lower material consumption in production, low power consumption during operation, lower sample requirements for testing, and higher heat transfer due to their very high surface-to-volume ratio. Given the high market demand for such micro and nano featured components, different manufacturing methods have been developed for their fabrication. Some of the common technologies in micro/nano fabrication are photolithography, electron beam lithography, X-ray lithography and other semiconductor processing techniques. Although these methods are capable of fabricating micro/nano structures with a resolution of less than a few nanometers, some of the shortcomings associated with these methods, such as high production costs for customized products, limited material choices, necessitate the development of other fabricating techniques. Micro/nano mechanical machining, such an atomic force microscope (AFM) probe based nano fabrication, has, therefore, been used to overcome some the major restrictions of the traditional processes. This technique removes material from the workpiece by engaging micro/nano size cutting tool (i.e. AFM probe) and is applicable on a wider range of materials compared to the photolithographic process. In spite of the unique benefits of nano mechanical machining, there are also some challenges with this technique, since the scale is reduced, such as size effects, burr formations, chip adhesions, fragility of tools and tool wear. Moreover, AFM based machining does not have any rotational movement, which makes fabrication of 3D features more difficult. Thus, vibration-assisted machining is introduced into AFM probe based nano mechanical machining to overcome the limitations associated with the conventional AFM probe based scratching method. Vibration-assisted machining reduced the cutting forces

  9. AFM nanoscale indentation in air of polymeric and hybrid materials with highly different stiffness

    NASA Astrophysics Data System (ADS)

    Suriano, Raffaella; Credi, Caterina; Levi, Marinella; Turri, Stefano

    2014-08-01

    In this study, nanomechanical properties of a variety of polymeric materials was investigated by means of AFM. In particular, selecting different AFM probes, poly(methyl methacrylate) (PMMA), polydimethylsiloxane (PDMS) bulk samples, sol-gel hybrid thin films and hydrated hyaluronic acid hydrogels were indented in air to determine the elastic modulus. The force-distance curves and the indentation data were found to be greatly affected by the cantilever stiffness and by tip geometry. AFM indentation tests show that the choice of the cantilever spring constant and of tip shape is crucially influenced by elastic properties of samples. When adhesion-dominated interactions occur between the tip and the surface of samples, force-displacement curves reveal that a suitable functionalization of AFM probes allows the control of such interactions and the extraction of Young' modulus from AFM curves that would be otherwise unfeasible. By applying different mathematical models depending on AFM probes and materials under investigation, the values of Young's modulus were obtained and compared to those measured by rheological and dynamic mechanical analysis or to literature data. Our results show that a wide range of elastic moduli (10 kPa-10 GPa) can be determined by AFM in good agreement with those measured by conventional macroscopic measurements.

  10. Imaging surface and submembranous structures with the atomic force microscope: a study on living cancer cells, fibroblasts and macrophages.

    PubMed

    Braet, F; Seynaeve, C; De Zanger, R; Wisse, E

    1998-06-01

    Atomic force microscopy (AFM) has been used to image a wide variety of cells. Fixed and dried-coated, wet-fixed or living cells were investigated. The major advantage of AFM over SEM is the avoidance of vacuum and electrons, whereas imaging can be done at environmental pressure and in aqueous conditions. Evidence of the successful application of AFM in biological imaging is provided by comparing results of AFM with SEM and/or TEM. In this study, we investigated surface and submembranous structures of living and glutaraldehyde-fixed colon carcinoma cells, skin fibroblasts and liver macrophages by AFM. Special attention was paid to the correct conditions for the acquisition of images of the surface of these cells, because quality SEM examinations have already been abundantly presented. AFM imaging of living cells revealed specific structures, such as the cytoskeleton, which were not observed by SEM. Membrane structures, such as ruffles, lamellipodia, microspikes and microvilli, could only clearly be observed after fixing the cells with 0.1% glutaraldehyde. AFM images of living cells were comparable to SEM images of fixed, dried and coated cells, but contained a number of artefacts due to tip-sample interaction. In addition, AFM imaging allowed the visualization of cytoplasmic submembranous structures without the necessity for further preparative steps, allowing us: (i) to follow cytoskeletal changes in fibroblasts under the influence of the microfilament disrupting agent latrunculin A; (ii) to study particle phagocytosis in macrophages. Therefore, in spite of the slow image acquisition of the AFM, the instrument can be used for high-resolution real-time studies of dynamic changes in submembranous structures.

  11. Complex patterns in fossilized stromatolites revealed by hyperspectral imaging (400-2496 nm).

    PubMed

    Murphy, R J; Van Kranendonk, M J; Kelloway, S J; Wainwright, I E

    2016-09-01

    Hyperspectral imaging (400-2496 nm) was used to quantitatively map surface textures and compositional variations in stromatolites to determine whether complexity of textures could be used as evidence to support biogenicity in the absence of preserved biomarkers. Four samples of 2.72-2.4 Ga stromatolites from a variety of settings, encompassing marine and lacustrine environments, were selected for hyperspectral imaging. Images of the sawn surfaces of samples were processed to identify reflectance and mineral absorption features and quantify their intensity (as an index of mineral abundance) using automated feature extraction. Amounts of ferrous iron were quantified using a ratio of reflectance at 1650 and 1299 nm. Visible near infrared imagery (400-970 nm) did not reveal additional textural patterns to those obtained from visual inspection. Shortwave infrared imagery (1000-2496 nm), however, revealed complex laminar and convoluted patterns, including a distinctive texture of sharp peaks and broad, low troughs in one sample, similar to living tufted microbial mats. Spectral analysis revealed another sample to be composed of dolomite. Two other samples were dominated by calcite or chlorite ± illite. Large variations in amounts of ferrous iron were found, but ferric iron was exclusively located in the oxidation crust. Hyperspectral imaging revealed large differences between parts of a sample of biogenic and non-biogenic origin. The former was characterized by calcite with varying amounts of ferrous iron, distributed in lenticular, convoluted patterns; the latter by Mg-Fe chlorite with large amounts of aluminium silicate, distributed as fine laminar layers. All minerals identified by hyperspectral imaging were confirmed by thin section petrography and XRD analyses. Spatial statistics generated from quantitative minerals maps showed different patterns between these different parts of the sample. Thus, hyperspectral imaging was shown to be a powerful tool for

  12. An AFM study of the chlorite-fluid interface. [Atomic Force Microscopy

    SciTech Connect

    Vrdoljak, G.A.; Henderson, G.S.; Fawcett, J.J. . Dept. of Geology)

    1992-01-01

    Chlorite is a ubiquitous mineral in many geologic environments and plays an important role in elemental adsorption and retention in soils. Chlorite has a 2:1 layer structure consisting of two tetrahedral sheets with an octahedral sheet between them (talc-like layer). The 2:1 layer is charge balanced and hydrogen-bonded by an interlayer of MgOH[sub 6] octahedra (brucite-like layer). The nature of chlorite's structure, its ease of imaging, and perfect 001 cleavage, make this mineral an ideal substrate for use in elemental adsorption studies in solution, with the AFM. The 001 cleavage plane of a 2b polytype with composition (Mg[sub 4.4]Fe[sub 0.6]Al[sub 1.0])[(Si[sub 2.9]Al[sub 1.1])]O[sub 10](OH)[sub g] has been imaged in air, water, and oil by atomic force microscopy. Dissolution features are observed in water, showing sub-micron features dissolving in real-time. Atomic resolution of both the talc-like and brucite-like layers has been obtained in air. However, only the tetrahedral sheet of the talc-like layer has been imaged at atomic resolution in oil and water, which may indicate a structural instability of the brucite-like surface in solution. Measurements of the unit-cell dimensions (a and b) for the talc-like layer in the three different media indicate a structural expansion of the mineral surface in solution. The a unit cell dimension expands by 7.4 [+-] 0.1% when in water; conversely, the b dimension varies greatly when in oil ([minus]10% to +20%), relative to air. The effects of these solution media on the structure of chlorite are revealed by characterization with the AFM. This information should prove useful in future studies of adsorption onto layer silicates.

  13. LET Spectrum Measurements In CR-39 PNTD With AFM

    SciTech Connect

    Johnson, C. E.; DeWitt, J. M.; Benton, E. R.; Yasuda, N.; Benton, E. V.

    2011-06-01

    Energetic protons, neutrons, and heavy ions undergoing collisions with target nuclei of varying Z can produce residual heavy recoil fragments via intra-nuclear cascade/evaporation reactions. The particles produced in these non-elastic collisions generally have such extremely short range ({approx}<10 {mu}m) that they cannot be directly observed by conventional detection methods including CR-39 plastic nuclear track detector (PNTD) that has been chemically etched for analysis by standard visible light microscopy. However, high-LET recoil fragments having range on the order of several cell diameters can be produced in tissue during radiotherapy using proton and carbon beams. We have developed a method to analyze short-range, high-LET tracks in CR-39 plastic nuclear track detector (PNTD) using short duration chemical etching ({approx}<1 {mu}m) following by automated atomic force microscope (AFM) scanning. The post-scan data processing used in this work was based on semi-automated matrix analysis opposed to traditional grey-scale image analysis. This method takes advantage of the 3-D data obtained via AFM to achieve robust discrimination of nuclear tracks from other features inherently present in the post-etch detector surface. Through automation of AFM scanning, sufficient AFM scan frames were obtained to attain an LET spectrum spanning the LET range from 200-1500 keV/{mu}m. In addition to our experiments, simulations were carried out with the Monte Carlo transport code, FLUKA. To demonstrate this method, CR-39 PNTD was exposed to the proton therapy beam at Loma Linda University Medical Center (LLUMC) at 60 and 230 MeV. Additionally, detectors were exposed to 1 GeV protons at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). For these exposures CR-39 PNTD, Al and Cu target foils were used between detector layers.

  14. LET Spectrum Measurements In CR-39 PNTD With AFM

    NASA Astrophysics Data System (ADS)

    Johnson, C. E.; DeWitt, J. M.; Benton, E. R.; Yasuda, N.; Benton, E. V.

    2011-06-01

    Energetic protons, neutrons, and heavy ions undergoing collisions with target nuclei of varying Z can produce residual heavy recoil fragments via intra-nuclear cascade/evaporation reactions. The particles produced in these non-elastic collisions generally have such extremely short range (˜<10 μm) that they cannot be directly observed by conventional detection methods including CR-39 plastic nuclear track detector (PNTD) that has been chemically etched for analysis by standard visible light microscopy. However, high-LET recoil fragments having range on the order of several cell diameters can be produced in tissue during radiotherapy using proton and carbon beams. We have developed a method to analyze short-range, high-LET tracks in CR-39 plastic nuclear track detector (PNTD) using short duration chemical etching (˜<1 μm) following by automated atomic force microscope (AFM) scanning. The post-scan data processing used in this work was based on semi-automated matrix analysis opposed to traditional grey-scale image analysis. This method takes advantage of the 3-D data obtained via AFM to achieve robust discrimination of nuclear tracks from other features inherently present in the post-etch detector surface. Through automation of AFM scanning, sufficient AFM scan frames were obtained to attain an LET spectrum spanning the LET range from 200-1500 keV/μm. In addition to our experiments, simulations were carried out with the Monte Carlo transport code, FLUKA. To demonstrate this method, CR-39 PNTD was exposed to the proton therapy beam at Loma Linda University Medical Center (LLUMC) at 60 and 230 MeV. Additionally, detectors were exposed to 1 GeV protons at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). For these exposures CR-39 PNTD, Al and Cu target foils were used between detector layers.

  15. LET spectrum measurements in Cr-39 PNTD with AFM

    SciTech Connect

    Johnson, Carl Edward; De Witt, Joel M; Benton, Eric R; Yasuda, Nakahiro; Benton, Eugene V

    2010-01-01

    Energetic protons, neutrons, and heavy ions undergoing collisions with target nuclei of varying Z can produce residual heavy recoil fragments via intra-nuclear cascade/evaporation reactions. The particles produced in these non-elastic collisions generally have such extremely short range ({approx}< 10 {mu}m) that they cannot be directly observed by conventional detection methods including CR-39 plastic nuclear track detector (PNTD) that has been chemically etched for analysis by standard visible light microscopy. However, high-LET recoil fragments having range on the order of several cell diameters can be produced in tissue during radiotherapy using proton and carbon beams. We have developed a method to analyze short-range, high-LET tracks in CR-39 plastic nuclear track detector (PNTD) using short duration chemical etching ({approx}< 1 {mu}m) followed by automated atomic force microscope (AFM) scanning. The post-scan data processing used in this work was based on semi-automated matrix analysis opposed to traditional grey-scale image analysis. This method takes advantage of the 3-D data obtained via AFM to achieve robust discrimination of nuclear tracks from other features. Through automation of AFM scanning, sufficient AFM scan frames were obtained to attain an LET spectrum spanning the LET range from 200-1500 keV/{mu}m. In addition to our experiments, simulations were carried out with the Monte Carlo transport code, FLUKA. To demonstrate this method, CR-39 PNTD was exposed to the proton therapy beam at Loma Linda University Medical Center (LLUMC) at 60 and 230 MeV. Additionally, detectors were exposed to I GeV protons at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). For these exposures CR-39 PNTD, Al and Cu target foils were used between detector layers.

  16. Probing Cytoskeletal Structures by Coupling Optical Superresolution and AFM Techniques for a Correlative Approach

    PubMed Central

    Chacko, Jenu Varghese; Zanacchi, Francesca Cella; Diaspro, Alberto

    2013-01-01

    In this article, we describe and show the application of some of the most advanced fluorescence superresolution techniques, STED AFM and STORM AFM microscopy towards imaging of cytoskeletal structures, such as microtubule filaments. Mechanical and structural properties can play a relevant role in the investigation of cytoskeletal structures of interest, such as microtubules, that provide support to the cell structure. In fact, the mechanical properties, such as the local stiffness and the elasticity, can be investigated by AFM force spectroscopy with tens of nanometers resolution. Force curves can be analyzed in order to obtain the local elasticity (and the Young's modulus calculation by fitting the force curves from every pixel of interest), and the combination with STED/STORM microscopy integrates the measurement with high specificity and yields superresolution structural information. This hybrid modality of superresolution-AFM working is a clear example of correlative multimodal microscopy. PMID:24027190

  17. Nanoscale Nucleosome Dynamics Assessed with Time-lapse AFM

    PubMed Central

    Lyubchenko, Yuri L.

    2013-01-01

    A fundamental challenge associated with chromosomal gene regulation is accessibility of DNA within nucleosomes. Recent studies performed by various techniques, including single-molecule approaches, led to the realization that nucleosomes are dynamic structures rather than static systems, as it was once believed. Direct data is required in order to understand the dynamics of nucleosomes more clearly and answer fundamental questions, including: What is the range of nucleosome dynamics? Does a non-ATP dependent unwrapping process of nucleosomes exist? What are the factors facilitating the large scale opening and unwrapping of nucleosomes? This review summarizes the results of nucleosome dynamics obtained with time-lapse AFM, including a high-speed version (HS-AFM) capable of visualizing molecular dynamics on the millisecond time scale. With HS-AFM, the dynamics of nucleosomes at a sub-second time scale was observed allowing one to visualize various pathways of nucleosome dynamics, such as sliding and unwrapping, including complete dissociation. Overall, these findings reveal new insights into the dynamics of nucleosomes and the novel mechanisms controlling spontaneous chromatin dynamics. PMID:24839467

  18. Quantitative nano-mechanics of biological cells with AFM

    NASA Astrophysics Data System (ADS)

    Sokolov, Igor

    2013-03-01

    The importance of study of living cells is hard to overestimate. Cell mechanics is a relatively young, yet not a well-developed area. Besides just a fundamental interest, large practical need has emerged to measure cell mechanics quantitatively. Recent studies revealed a significant correlation between stiffness of biological cells and various human diseases, such as cancer, malaria, arthritis, and even aging. However, really quantitative studies of mechanics of biological cells are virtually absent. It is not even clear if the cell, being a complex and heterogeneous object, can be described by the elastic modulus at all. Atomic force microscopy (AFM) is a natural instrument to study properties of cells in their native environments. Here we will demonstrate that quantitative measurements of elastic modulus of cells with AFM are possible. Specifically, we will show that the ``cell body'' (cell without ``brush'' surface layer, a non-elastic layer surrounding cells) typically demonstrates the response of a homogeneous elastic medium up to the deformation of 10-20%, but if and only if a) the cellular brush layer is taken into account, b) rather dull AFM probes are used. This will be justified with the help of the strong condition of elastic behavior of material: the elastic modulus is shown to be independent on the indentation depth. We will also demonstrate that an attempt either to ignore the brush layer or to use sharp AFM probes will result in the violation of the strong condition, which implies impossibility to use the concept of the elastic modulus to describe cell mechanics in such experiments. Examples of quantitative measurements of the Young's modulus of the cell body and the cell brush parameters will be given for various cells. Address when submitting: Clarkson University, Potsdam, NY 13699

  19. Revealing glacier flow and surge dynamics from animated satellite image sequences: examples from the Karakoram

    NASA Astrophysics Data System (ADS)

    Paul, F.

    2015-04-01

    Although animated images are very popular on the Internet, they have so far found only limited use for glaciological applications. With long time-series of satellite images becoming increasingly available and glaciers being well recognized for their rapid changes and variable flow dynamics, animated sequences of multiple satellite images reveal glacier dynamics in a time-lapse mode, making the otherwise slow changes of glacier movement visible and understandable for a wide public. For this study animated image sequences were created from freely available image quick-looks of orthorectified Landsat scenes for four regions in the central Karakoram mountain range. The animations play automatically in a web-browser and might help to demonstrate glacier flow dynamics for educational purposes. The animations revealed highly complex patterns of glacier flow and surge dynamics over a 15-year time period (1998-2013). In contrast to other regions, surging glaciers in the Karakoram are often small (around 10 km2), steep, debris free, and advance for several years at comparably low annual rates (a few hundred m a-1). The advance periods of individual glaciers are generally out of phase, indicating a limited climatic control on their dynamics. On the other hand, nearly all other glaciers in the region are either stable or slightly advancing, indicating balanced or even positive mass budgets over the past few years to decades.

  20. Hydration states of AFm cement phases

    SciTech Connect

    Baquerizo, Luis G.; Matschei, Thomas; Scrivener, Karen L.; Saeidpour, Mahsa; Wadsö, Lars

    2015-07-15

    The AFm phase, one of the main products formed during the hydration of Portland and calcium aluminate cement based systems, belongs to the layered double hydrate (LDH) family having positively charged layers and water plus charge-balancing anions in the interlayer. It is known that these phases present different hydration states (i.e. varying water content) depending on the relative humidity (RH), temperature and anion type, which might be linked to volume changes (swelling and shrinkage). Unfortunately the stability conditions of these phases are insufficiently reported. This paper presents novel experimental results on the different hydration states of the most important AFm phases: monocarboaluminate, hemicarboaluminate, strätlingite, hydroxy-AFm and monosulfoaluminate, and the thermodynamic properties associated with changes in their water content during absorption/desorption. This data opens the possibility to model the response of cementitious systems during drying and wetting and to engineer systems more resistant to harsh external conditions.

  1. Graphene MEMS: AFM probe performance improvement.

    PubMed

    Martin-Olmos, Cristina; Rasool, Haider Imad; Weiller, Bruce H; Gimzewski, James K

    2013-05-28

    We explore the feasibility of growing a continuous layer of graphene in prepatterned substrates, like an engineered silicon wafer, and we apply this as a mold for the fabrication of AFM probes. This fabrication method proves the fabrication of SU-8 devices coated with graphene in a full-wafer parallel technology and with high yield. It also demonstrates that graphene coating enhances the functionality of SU-8 probes, turning them conductive and more resistant to wear. Furthermore, it opens new experimental possibilities such as studying graphene-graphene interaction at the nanoscale with the precision of an AFM or the exploration of properties in nonplanar graphene layers.

  2. Ultrahigh-resolution imaging of water networks by atomic force microscopy

    PubMed Central

    Shiotari, Akitoshi; Sugimoto, Yoshiaki

    2017-01-01

    Local defects in water layers growing on metal surfaces have a key influence on the wetting process at the surfaces; however, such minor structures are undetectable by macroscopic methods. Here, we demonstrate ultrahigh-resolution imaging of single water layers on a copper(110) surface by using non-contact atomic force microscopy (AFM) with molecular functionalized tips at 4.8 K. AFM with a probe tip terminated by carbon monoxide predominantly images oxygen atoms, whereas the contribution of hydrogen atoms is modest. Oxygen skeletons in the AFM images reveal that the water networks containing local defects and edges are composed of pentagonal and hexagonal rings. The results reinforce the applicability of AFM to characterize atomic structures of weakly bonded molecular assemblies. PMID:28155856

  3. Accelerated design and quality control of impact modifiers for plastics through atomic force microscopy (AFM) analysis

    NASA Astrophysics Data System (ADS)

    Moeller, Gunter

    2011-03-01

    Standard polymer resins are often too brittle or do not meet other mechanical property requirements for typical polymer applications. To achieve desired properties it is common to disperse so called ``impact modifiers'', which are spherical latex particles with diameters of much less than one micrometer, into the pure resin. Understanding and control of the entire process from latex particle formation to subsequent dispersion into polymer resins are necessary to accelerate the development of new materials that meet specific application requirements. In this work AFM imaging and nanoindentation techniques in combination with AFM-based spectroscopic techniques were applied to assess latex formation and dispersion. The size and size distribution of the latex particles can be measured based on AFM amplitude modulation images. AFM phase images provide information about the chemical homogeneity of individual particles. Nanoindentation may be used to estimate their elastic and viscoelastic properties. Proprietary creep and nanoscale Dynamic Mechanical Analysis (DMA) tests that we have developed were used to measure these mechanical properties. The small size of dispersed latex inclusions requires local mechanical and spectroscopic analysis techniques with high lateral and spatial resolution. We applied the CRAVE AFM method, developed at NIST, to perform mechanical analysis of individual latex inclusions and compared results with those obtained using nanoscale DMA. NanoIR, developed by Anasys Inc., and principal component confocal Raman were used for spectroscopic analysis and results from both techniques compared.

  4. Current imaging and electromigration-induced splitting of GaN nanowires as revealed by conductive atomic force microscopy.

    PubMed

    Li, Chun; Bando, Yoshio; Golberg, Dmitri

    2010-04-27

    Current images of electromigration-induced common vapor-liquid-solid-grown GaN nanowires were obtained using a conductive atomic force microscope. Structural characterization indicated that these wurtzite (ZW) [0110] nanowires contained longitudinal zinc blende (ZB) defects as stacking faults. The current was attributed to tunneling current through the Schottky barrier between the AFM tip and a nanowire, which was dominated by the local nanowire surface work function. Due to the electromigration induced by large current densities around the defects, the axial splitting process of the nanowires was directly observed under continuous current scanning. The electromigration was likely enhanced by non-uniformly distributed electrostatic pressure around the axial ZW/ZB domain interfaces.

  5. Conductance of AFM Deformed Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Svizhenko, Alexei; Maiti, Amitesh; Anatram, M. P.; Biegel, Bryan (Technical Monitor)

    2002-01-01

    This viewgraph presentation provides information on the electrical conductivity of carbon nanotubes upon deformation by atomic force microscopy (AFM). The density of states and conductance were computed using four orbital tight-binding method with various parameterizations. Different chiralities develop bandgap that varies with chirality.

  6. Investigation of mussel adhesive protein adsorption on polystyrene and poly(octadecyl methacrylate) using angle dependent XPS, ATR-FTIR, and AFM

    SciTech Connect

    Baty, A.M.; Suci, P.A.; Tyler, B.J.; Geesey, G.G.

    1996-02-10

    Despite many years of research effort, the molecular interactions that are responsible for microbial adhesion and fouling of surfaces remain obscure. An understanding of these interactions would contribute to the development of surfaces that resist colonization of microorganisms. The irreversible adsorption of mussel adhesive proteins (MAP) from the marine mussel Mytilus edulis has been investigated on polystyrene (PS) and poly(octadecyl methacrylate) (POMA) surfaces using angle resolved X-ray photoelectron spectroscopy (XPS), attenuated total reflection Fourier transform infrared (ATR-FTIR) spectrometry, and atomic force microscopy (AFM). Angle resolved XPS was used to quantify the elemental composition with depth of the upper 90 {angstrom} of the surface, and AFM was used to obtain the surface topography. The adsorption pattern of MAP, revealed by AFM images, is distinctly different on the two polymer surfaces and suggests that the substratum influences protein adhesion. The depth profiles of MAP, obtained from angle resolved XPS, show differences in nitrogen composition with depth for MAP adsorbed to PS and POMA. Infrared spectra of hydrated adsorbed MAP revealed significant differences in the amide III region and in two bands which may originate from residues in the tandemly repeated sequences of MAP. This data demonstrates that the chemistry of the polymer film that is present at the protein-polymer interface can influence protein-protein and protein-surface interactions.

  7. High throughput nanofabrication of silicon nanowire and carbon nanotube tips on AFM probes by stencil-deposited catalysts.

    PubMed

    Engstrom, Daniel S; Savu, Veronica; Zhu, Xueni; Bu, Ian Y Y; Milne, William I; Brugger, Juergen; Boggild, Peter

    2011-04-13

    A new and versatile technique for the wafer scale nanofabrication of silicon nanowire (SiNW) and multiwalled carbon nanotube (MWNT) tips on atomic force microscope (AFM) probes is presented. Catalyst material for the SiNW and MWNT growth was deposited on prefabricated AFM probes using aligned wafer scale nanostencil lithography. Individual vertical SiNWs were grown epitaxially by a catalytic vapor-liquid-solid (VLS) process and MWNTs were grown by a plasma-enhanced chemical vapor (PECVD) process on the AFM probes. The AFM probes were tested for imaging micrometers-deep trenches, where they demonstrated a significantly better performance than commercial high aspect ratio tips. Our method demonstrates a reliable and cost-efficient route toward wafer scale manufacturing of SiNW and MWNT AFM probes.

  8. Medial prefrontal cortex pathology in schizophrenia as revealed by convergent findings from multimodal imaging

    PubMed Central

    Pomarol-Clotet, E; Canales-Rodríguez, E J; Salvador, R; Sarró, S; Gomar, J J; Vila, F; Ortiz-Gil, J; Iturria-Medina, Y; Capdevila, A; McKenna, P J

    2010-01-01

    Neuroimaging studies have found evidence of altered brain structure and function in schizophrenia, but have had complex findings regarding the localization of abnormality. We applied multimodal imaging (voxel-based morphometry (VBM), functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) combined with tractography) to 32 chronic schizophrenic patients and matched healthy controls. At a conservative threshold of P=0.01 corrected, structural and functional imaging revealed overlapping regions of abnormality in the medial frontal cortex. DTI found that white matter abnormality predominated in the anterior corpus callosum, and analysis of the anatomical connectivity of representative seed regions again implicated fibres projecting to the medial frontal cortex. There was also evidence of convergent abnormality in the dorsolateral prefrontal cortex, although here the laterality was less consistent across techniques. The medial frontal region identified by these three imaging techniques corresponds to the anterior midline node of the default mode network, a brain system which is believed to support internally directed thought, a state of watchfulness, and/or the maintenance of one's sense of self, and which is of considerable current interest in neuropsychiatric disorders. PMID:20065955

  9. Probing ternary solvent effect in high Voc polymer solar cells using advanced AFM techniques

    DOE PAGES

    Li, Chao; Soleman, Mikhael; Lorenzo, Josie; ...

    2016-01-25

    This work describes a simple method to develop a high Voc low band gap PSCs. In addition, two new atomic force microscopy (AFM)-based nanoscale characterization techniques to study the surface morphology and physical properties of the structured active layer are introduced. With the help of ternary solvent processing of the active layer and C60 buffer layer, a bulk heterojunction PSC with Voc more than 0.9 V and conversion efficiency 7.5% is developed. In order to understand the fundamental properties of the materials ruling the performance of the PSCs tested, AFM-based nanoscale characterization techniques including Pulsed-Force-Mode AFM (PFM-AFM) and Mode-Synthesizing AFMmore » (MSAFM) are introduced. Interestingly, MSAFM exhibits high sensitivity for direct visualization of the donor–acceptor phases in the active layer of the PSCs. Lastly, conductive-AFM (cAFM) studies reveal local variations in conductivity in the donor and acceptor phases as well as a significant increase in photocurrent in the PTB7:ICBA sample obtained with the ternary solvent processing.« less

  10. AFM/MFM hybrid nanocharacterization of martensitic transformation and degradation for Fe-Pd shape memory alloy

    NASA Astrophysics Data System (ADS)

    Suzuki, Takayuki; Nagatani, Kohei; Hirano, Kazumi; Teramoto, Tokuo; Taya, Minoru

    2003-07-01

    Martensitic transformation and degradation characteristics for Fe-Pd ferromagnetic shape memory alloy were investigated by the developed AFM (Atomic Force Microscope)/MFM (Magnetic Force Microscope) hybrid nano-characterization technique. In AFM martensitic transformation was detected by the changes of surface topography of martensite plates. In MFM martensitic transformation was detected by the changes of magnetic domain structures. This technique has an advantage that martensitic transformation characteristics such as martensitic transformation temperature and reverse transformation temperature can be measured at microscopic and nanoscopic small area. Degradation characteristics of martensitic transformation under cyclic loading were also detected by the changes of AFM and MFM images. In AFM images surface topography of martensite plates became flat and in MFM images the morphology of magnetic domain structures became unfocused under cyclic loading. Then it was found that the hybrid nano-characterization was very high sensitive technique to evaluate degradation for Fe-Pd ferromagnetic shape memory alloy.

  11. Revealing glacier flow and surge dynamics from animated satellite image sequences: examples from the Karakoram

    NASA Astrophysics Data System (ADS)

    Paul, F.

    2015-11-01

    Although animated images are very popular on the internet, they have so far found only limited use for glaciological applications. With long time series of satellite images becoming increasingly available and glaciers being well recognized for their rapid changes and variable flow dynamics, animated sequences of multiple satellite images reveal glacier dynamics in a time-lapse mode, making the otherwise slow changes of glacier movement visible and understandable to the wider public. For this study, animated image sequences were created for four regions in the central Karakoram mountain range over a 25-year time period (1990-2015) from freely available image quick-looks of orthorectified Landsat scenes. The animations play automatically in a web browser and reveal highly complex patterns of glacier flow and surge dynamics that are difficult to obtain by other methods. In contrast to other regions, surging glaciers in the Karakoram are often small (10 km2 or less), steep, debris-free, and advance for several years to decades at relatively low annual rates (about 100 m a-1). These characteristics overlap with those of non-surge-type glaciers, making a clear identification difficult. However, as in other regions, the surging glaciers in the central Karakoram also show sudden increases of flow velocity and mass waves travelling down glacier. The surges of individual glaciers are generally out of phase, indicating a limited climatic control on their dynamics. On the other hand, nearly all other glaciers in the region are either stable or slightly advancing, indicating balanced or even positive mass budgets over the past few decades.

  12. Hypothalamic metabolic compartmentation during appetite regulation as revealed by magnetic resonance imaging and spectroscopy methods

    PubMed Central

    Lizarbe, Blanca; Benitez, Ania; Peláez Brioso, Gerardo A.; Sánchez-Montañés, Manuel; López-Larrubia, Pilar; Ballesteros, Paloma; Cerdán, Sebastián

    2013-01-01

    We review the role of neuroglial compartmentation and transcellular neurotransmitter cycling during hypothalamic appetite regulation as detected by Magnetic Resonance Imaging (MRI) and Spectroscopy (MRS) methods. We address first the neurochemical basis of neuroendocrine regulation in the hypothalamus and the orexigenic and anorexigenic feed-back loops that control appetite. Then we examine the main MRI and MRS strategies that have been used to investigate appetite regulation. Manganese-enhanced magnetic resonance imaging (MEMRI), Blood oxygenation level-dependent contrast (BOLD), and Diffusion-weighted magnetic resonance imaging (DWI) have revealed Mn2+ accumulations, augmented oxygen consumptions, and astrocytic swelling in the hypothalamus under fasting conditions, respectively. High field 1H magnetic resonance in vivo, showed increased hypothalamic myo-inositol concentrations as compared to other cerebral structures. 1H and 13C high resolution magic angle spinning (HRMAS) revealed increased neuroglial oxidative and glycolytic metabolism, as well as increased hypothalamic glutamatergic and GABAergic neurotransmissions under orexigenic stimulation. We propose here an integrative interpretation of all these findings suggesting that the neuroendocrine regulation of appetite is supported by important ionic and metabolic transcellular fluxes which begin at the tripartite orexigenic clefts and become extended spatially in the hypothalamus through astrocytic networks becoming eventually MRI and MRS detectable. PMID:23781199

  13. Studying post-etching silicon crystal defects on 300mm wafer by automatic defect review AFM

    NASA Astrophysics Data System (ADS)

    Zandiatashbar, Ardavan; Taylor, Patrick A.; Kim, Byong; Yoo, Young-kook; Lee, Keibock; Jo, Ahjin; Lee, Ju Suk; Cho, Sang-Joon; Park, Sang-il

    2016-03-01

    Single crystal silicon wafers are the fundamental elements of semiconductor manufacturing industry. The wafers produced by Czochralski (CZ) process are very high quality single crystalline materials with known defects that are formed during the crystal growth or modified by further processing. While defects can be unfavorable for yield for some manufactured electrical devices, a group of defects like oxide precipitates can have both positive and negative impacts on the final device. The spatial distribution of these defects may be found by scattering techniques. However, due to limitations of scattering (i.e. light wavelength), many crystal defects are either poorly classified or not detected. Therefore a high throughput and accurate characterization of their shape and dimension is essential for reviewing the defects and proper classification. While scanning electron microscopy (SEM) can provide high resolution twodimensional images, atomic force microscopy (AFM) is essential for obtaining three-dimensional information of the defects of interest (DOI) as it is known to provide the highest vertical resolution among all techniques [1]. However AFM's low throughput, limited tip life, and laborious efforts for locating the DOI have been the limitations of this technique for defect review for 300 mm wafers. To address these limitations of AFM, automatic defect review AFM has been introduced recently [2], and is utilized in this work for studying DOI on 300 mm silicon wafer. In this work, we carefully etched a 300 mm silicon wafer with a gaseous acid in a reducing atmosphere at a temperature and for a sufficient duration to decorate and grow the crystal defects to a size capable of being detected as light scattering defects [3]. The etched defects form a shallow structure and their distribution and relative size are inspected by laser light scattering (LLS). However, several groups of defects couldn't be properly sized by the LLS due to the very shallow depth and low

  14. Noise in NC-AFM measurements with significant tip–sample interaction

    PubMed Central

    Lübbe, Jannis; Temmen, Matthias

    2016-01-01

    The frequency shift noise in non-contact atomic force microscopy (NC-AFM) imaging and spectroscopy consists of thermal noise and detection system noise with an additional contribution from amplitude noise if there are significant tip–sample interactions. The total noise power spectral density D Δ f(f m) is, however, not just the sum of these noise contributions. Instead its magnitude and spectral characteristics are determined by the strongly non-linear tip–sample interaction, by the coupling between the amplitude and tip–sample distance control loops of the NC-AFM system as well as by the characteristics of the phase locked loop (PLL) detector used for frequency demodulation. Here, we measure D Δ f(f m) for various NC-AFM parameter settings representing realistic measurement conditions and compare experimental data to simulations based on a model of the NC-AFM system that includes the tip–sample interaction. The good agreement between predicted and measured noise spectra confirms that the model covers the relevant noise contributions and interactions. Results yield a general understanding of noise generation and propagation in the NC-AFM and provide a quantitative prediction of noise for given experimental parameters. We derive strategies for noise-optimised imaging and spectroscopy and outline a full optimisation procedure for the instrumentation and control loops. PMID:28144538

  15. AN IMAGING AND SPECTROSCOPIC STUDY OF FOUR STRONG Mg II ABSORBERS REVEALED BY GRB 060418

    SciTech Connect

    Pollack, L. K.; Prochaska, J. X.; Chen, H.-W.; Bloom, J. S.

    2009-08-20

    We present results from an imaging and spectroscopic study of four strong Mg II absorbers of W(2796) {approx}> 1 A revealed by the afterglow of GRB 060418 at z{sub GRB} = 1.491. These absorbers, at z = 0.603, 0.656, 1.107, and z {sub GRB}, exhibit large ion abundances that suggest neutral gas columns characteristic of damped Ly{alpha} systems. The imaging data include optical images obtained using Low-Resolution Imaging Spectrometer (LRIS) on the Keck I telescope and using Advanced Camera for Surveys on board Hubble Space Telescope, and near-infrared H-band images obtained using Persson's Auxiliary Nasmyth Infrared Camera on the Magellan Baade Telescope and K'-band images obtained using NIRC2 with laser guide star adaptive optics on the Keck II telescope. These images reveal six distinct objects at {delta} {theta} {approx}< 3.''5 of the afterglow's position, two of which exhibit well-resolved mature disk morphology, one shows red colors, and three are blue compact sources. Follow-up spectroscopic observations using LRIS confirm that one of the disk galaxies coincides with the Mg II absorber at z = 0.656. The observed broadband spectral energy distributions of the second disk galaxy and the red source indicate that they are associated with the absorbers at z = 0.603 and z = 1.107, respectively. These results show that strong Mg II absorbers identified in gamma-ray burst (GRB) afterglow spectra are associated with typical galaxies of luminosity {approx}0.1 - 1 L{sub *} at impact parameter of {rho} {approx}< 10 h {sup -1} kpc. The close angular separation would preclude easy detections toward a bright quasar. Finally, we associate the remaining three blue compact sources with the GRB host galaxy, noting that they are likely star-forming knots located at projected distances of {rho} = 2 - 12 h {sup -1} kpc from the afterglow. At the afterglow's position, we derive a 2{sigma} upper limit to the underlying star-formation rate intensity of 0.0074 M{sub sun} yr{sup -1} kpc

  16. Cryptic microtextures and geological histories of K-rich alkali feldspars revealed by charge contrast imaging

    NASA Astrophysics Data System (ADS)

    Flude, Stephanie; Lee, Martin R.; Sherlock, Sarah C.; Kelley, Simon P.

    2012-06-01

    Charge contrast imaging in the scanning electron microscope can provide new insights into the scale and composition of alkali feldspar microtextures, and such information helps considerably with the interpretation of their geological histories and results of argon isotope thermochronological analyses. The effectiveness of this technique has been illustrated using potassium-rich alkali feldspars from the Dartmoor granite (UK). These feldspars contain strain-controlled lamellar crypto- and microperthites that are cross-cut by strain-free deuteric microperthites. The constituent albite- and orthoclase-rich phases of both microperthite generations can be readily distinguished by atomic number contrast imaging. The charge contrast results additionally show that sub-micrometre-sized albite `platelets' are commonplace between coarser exsolution lamellae and occur together to make cryptoperthites. Furthermore, charge contrast imaging reveals that the orthoclase-rich feldspar is an intergrowth of two phases, one that is featureless with uniform contrast and another that occurs as cross-cutting veins and grains with the {110} adularia habit. Transmission electron microscopy shows that the featureless feldspar is tweed orthoclase, whereas the veins and euhedral grains are composed of irregular microcline that has formed from orthoclase by `unzipping' during deuteric or hydrothermal alteration. The charge contrast imaging results are especially important in demonstrating that deuteric perthites are far more abundant in alkali feldspars than would be concluded from investigations using conventional microscopy techniques. The unexpected presence of such a high volume of replacement products has significant implications for understanding the origins and geological histories of crustal rocks and the use of alkali feldspars in geo- and thermochronology. Whilst the precise properties of feldspars that generate contrast remain unclear, the similarity between charge contrast images

  17. Nanoscale thermal AFM of polymers: transient heat flow effects.

    PubMed

    Duvigneau, Joost; Schönherr, Holger; Vancso, G Julius

    2010-11-23

    Thermal transport around the nanoscale contact area between the heated atomic force microscopy (AFM) probe tip and the specimen under investigation is a central issue in scanning thermal microscopy (SThM). Polarized light microscopy and AFM imaging of the temperature-induced crystallization of poly(ethylene terephthalate) (PET) films in the region near the tip were used in this study to unveil the lateral heat transport. The radius of the observed lateral surface isotherm at 133 °C ranged from 2.2 ± 0.5 to 18.7 ± 0.5 μm for tip-polymer interface temperatures between 200 and 300 °C with contact times varying from 20 to 120 s, respectively. In addition, the heat transport into polymer films was assessed by measurements of the thermal expansion of poly(dimethyl siloxane) (PDMS) films with variable thickness on silicon supports. Our data showed that heat transport in the specimen normal (z) direction occurred to depths exceeding 1000 μm using representative non-steady-state SThM conditions (i.e., heating from 40 to 180 °C at a rate of 10 °C s(-1)). On the basis of the experimental results, a 1D steady-state model for heat transport was developed, which shows the temperature profile close to the tip-polymer contact. The model also indicates that ≤1% of the total power generated in the heater area, which is embedded in the cantilever end, is transported into the polymer through the tip-polymer contact interface. Our results complement recent efforts in the evaluation and improvement of existing theoretical models for thermal AFM, as well as advance further developments of SThM for nanoscale thermal materials characterization and/or manipulation via scanning thermal lithography (SThL).

  18. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids.

    PubMed

    Schmitz, Alexander; Fischer, Sabine C; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H K

    2017-03-03

    Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid's size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 10(5) to 1 × 10(6 )cells/mm(3). Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.

  19. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids

    PubMed Central

    Schmitz, Alexander; Fischer, Sabine C.; Mattheyer, Christian; Pampaloni, Francesco; Stelzer, Ernst H. K.

    2017-01-01

    Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid’s size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 105 to 1 × 106 cells/mm3. Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture. PMID:28255161

  20. Multiparametric, Longitudinal Optical Coherence Tomography Imaging Reveals Acute Injury and Chronic Recovery in Experimental Ischemic Stroke

    PubMed Central

    Srinivasan, Vivek J.; Mandeville, Emiri T.; Can, Anil; Blasi, Francesco; Climov, Mihail; Daneshmand, Ali; Lee, Jeong Hyun; Yu, Esther; Radhakrishnan, Harsha; Lo, Eng H.; Sakadžić, Sava; Eikermann-Haerter, Katharina; Ayata, Cenk

    2013-01-01

    Progress in experimental stroke and translational medicine could be accelerated by high-resolution in vivo imaging of disease progression in the mouse cortex. Here, we introduce optical microscopic methods that monitor brain injury progression using intrinsic optical scattering properties of cortical tissue. A multi-parametric Optical Coherence Tomography (OCT) platform for longitudinal imaging of ischemic stroke in mice, through thinned-skull, reinforced cranial window surgical preparations, is described. In the acute stages, the spatiotemporal interplay between hemodynamics and cell viability, a key determinant of pathogenesis, was imaged. In acute stroke, microscopic biomarkers for eventual infarction, including capillary non-perfusion, cerebral blood flow deficiency, altered cellular scattering, and impaired autoregulation of cerebral blood flow, were quantified and correlated with histology. Additionally, longitudinal microscopy revealed remodeling and flow recovery after one week of chronic stroke. Intrinsic scattering properties serve as reporters of acute cellular and vascular injury and recovery in experimental stroke. Multi-parametric OCT represents a robust in vivo imaging platform to comprehensively investigate these properties. PMID:23940761

  1. Multiparametric, longitudinal optical coherence tomography imaging reveals acute injury and chronic recovery in experimental ischemic stroke.

    PubMed

    Srinivasan, Vivek J; Mandeville, Emiri T; Can, Anil; Blasi, Francesco; Climov, Mihail; Daneshmand, Ali; Lee, Jeong Hyun; Yu, Esther; Radhakrishnan, Harsha; Lo, Eng H; Sakadžić, Sava; Eikermann-Haerter, Katharina; Ayata, Cenk

    2013-01-01

    Progress in experimental stroke and translational medicine could be accelerated by high-resolution in vivo imaging of disease progression in the mouse cortex. Here, we introduce optical microscopic methods that monitor brain injury progression using intrinsic optical scattering properties of cortical tissue. A multi-parametric Optical Coherence Tomography (OCT) platform for longitudinal imaging of ischemic stroke in mice, through thinned-skull, reinforced cranial window surgical preparations, is described. In the acute stages, the spatiotemporal interplay between hemodynamics and cell viability, a key determinant of pathogenesis, was imaged. In acute stroke, microscopic biomarkers for eventual infarction, including capillary non-perfusion, cerebral blood flow deficiency, altered cellular scattering, and impaired autoregulation of cerebral blood flow, were quantified and correlated with histology. Additionally, longitudinal microscopy revealed remodeling and flow recovery after one week of chronic stroke. Intrinsic scattering properties serve as reporters of acute cellular and vascular injury and recovery in experimental stroke. Multi-parametric OCT represents a robust in vivo imaging platform to comprehensively investigate these properties.

  2. Holocord hydrosyringomyelia with terminal myelocystocele revealed by constructive interference in steady-state MR imaging.

    PubMed

    Hashiguchi, Kimiaki; Morioka, Takato; Samura, Kazuhiro; Yoshida, Fumiaki; Miyagi, Yasushi; Nagata, Shinji; Kokubo, Takayuki; Yoshiura, Takashi; Sasaki, Tomio

    2008-01-01

    We report an operated case with terminal myelocystocele and holocord hydrosyringomyelia (syrinx). The patient exhibited a subcutaneous mass at the right lumbosacral region with multiple anomalies including scoliosis and hyperdactylia of the right foot and systemic disease such as hydronephroureter. Neurological examination revealed palsy of the left diaphragm, and left upper and right lower limbs. Constructive interference in steady-state (CISS) images demonstrated a terminal myelocystocele with a huge syrinx extending to the medulla. The curvilinear reconstruction of the CISS sequence depicted continuous cystocele and whole syrinx. At day 37, sac excision and untethering of the spinal cord were performed. The caudal part of the central canal was opened to the subarachnoid space (terminal ventriculostomy), resulting in a slight improvement of limb palsy and shrinkage of the holocord syrinx. CISS imaging is useful to detect the complicated pathology, and terminal ventriculostomy should be performed to improve associated syrinx.

  3. Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers

    PubMed Central

    Pan, Jing; Cha, Tae-Gon; Li, Feiran; Chen, Haorong; Bragg, Nina A.; Choi, Jong Hyun

    2017-01-01

    DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers’ small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s−1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps. PMID:28116353

  4. Large-scale inhomogeneity in sapphire test masses revealed by Rayleigh scattering imaging

    NASA Astrophysics Data System (ADS)

    Yan, Zewu; Ju, Li; Eon, François; Gras, Slawomir; Zhao, Chunnong; Jacob, John; Blair, David G.

    2004-03-01

    Rayleigh scattering in test masses can introduce noise and reduce the sensitivity of laser interferometric gravitational wave detectors. In this paper, we present laser Rayleigh scattering imaging as a technique to investigate sapphire test masses. The system provides three-dimensional Rayleigh scattering mapping of entire test masses and quantitative evaluation of the Rayleigh scattering coefficient. Rayleigh scattering mapping of two sapphire samples reveals point defects as well as inhomogeneous structures in the samples. We present results showing significant non-uniform scattering within two 4.5 kg sapphire test masses manufactured by the heat exchanger method.

  5. Stacking sequence and interlayer coupling in few-layer graphene revealed by in situ imaging

    SciTech Connect

    Wang, Zhu-Jun; Dong, Jichen; Cui, Yi; Eres, Gyula; Timpe, Olaf; Fu, Qiang; Ding, Feng; Willinger, Marc-Georg; Schloegl, R.

    2016-10-19

    In the transition from graphene to graphite, the addition of each individual graphene layer modifies the electronic structure and produces a different material with unique properties. Controlled growth of few-layer graphene is therefore of fundamental interest and will provide access to materials with engineered electronic structure. Here we combine isothermal growth and etching experiments with in situ scanning electron microscopy to reveal the stacking sequence and interlayer coupling strength in few-layer graphene. The observed layer-dependent etching rates reveal the relative strength of the graphene graphene and graphene substrate interaction and the resulting mode of adlayer growth. Scanning tunnelling microscopy and density functional theory calculations confirm a strong coupling between graphene edge atoms and platinum. Simulated etching confirms that etching can be viewed as reversed growth. This work demonstrates that real-time imaging under controlled atmosphere is a powerful method for designing synthesis protocols for sp2 carbon nanostructures in between graphene and graphite.

  6. Stacking sequence and interlayer coupling in few-layer graphene revealed by in situ imaging

    NASA Astrophysics Data System (ADS)

    Wang, Zhu-Jun; Dong, Jichen; Cui, Yi; Eres, Gyula; Timpe, Olaf; Fu, Qiang; Ding, Feng; Schloegl, R.; Willinger, Marc-Georg

    2016-10-01

    In the transition from graphene to graphite, the addition of each individual graphene layer modifies the electronic structure and produces a different material with unique properties. Controlled growth of few-layer graphene is therefore of fundamental interest and will provide access to materials with engineered electronic structure. Here we combine isothermal growth and etching experiments with in situ scanning electron microscopy to reveal the stacking sequence and interlayer coupling strength in few-layer graphene. The observed layer-dependent etching rates reveal the relative strength of the graphene-graphene and graphene-substrate interaction and the resulting mode of adlayer growth. Scanning tunnelling microscopy and density functional theory calculations confirm a strong coupling between graphene edge atoms and platinum. Simulated etching confirms that etching can be viewed as reversed growth. This work demonstrates that real-time imaging under controlled atmosphere is a powerful method for designing synthesis protocols for sp2 carbon nanostructures in between graphene and graphite.

  7. Detection of Pathogens Using AFM and SPR

    NASA Astrophysics Data System (ADS)

    Vaseashta, Ashok

    2005-03-01

    A priori detection of pathogens in food and water has become a subject of paramount importance. Several recent incidents have resulted in the government passing stringent regulations for tolerable amounts of contamination of food products. Identification and/or monitoring of bacterial contamination in food are critical. The conventional methods of pathogen detection require time-consuming steps to arrive disembark at meaningful measurement in a timely manner as the detection time exceeds the time in which perishable food recycles through the food chain distribution. The aim of this presentation is to outline surface plasmon resonance (SPR) and atomic force microscopy (AFM) as two methods for fast detect6ion of pathogens. Theoretical basis of SPR and experimental results of SPR and AFM on E. coli O157:H7 and prion are presented.

  8. Characterizing Cell Mechanics with AFM and Microfluidics

    NASA Astrophysics Data System (ADS)

    Walter, N.; Micoulet, A.; Suresh, S.; Spatz, J. P.

    2007-03-01

    Cell mechanical properties and functionality are mainly determined by the cytoskeleton, besides the cell membrane, the nucleus and the cytosol, and depend on various parameters e.g. surface chemistry and rigidity, surface area and time available for cell spreading, nutrients and drugs provided in the culture medium. Human epithelial pancreatic and mammary cancer cells and their keratin intermediate filaments are the main focus of our work. We use Atomic Force Microscopy (AFM) to study cells adhering to substrates and Microfluidic Channels to probe cells in suspension, respectively. Local and global properties are extracted by varying AFM probe tip size and the available adhesion area for cells. Depth-sensing, instrumented indentation tests with AFM show a clear difference in contact stiffness for cells that are spread of controlled substrates and those that are loosely attached. Microfluidic Channels are utilized in parallel to evaluate cell deformation and ``flow resistance'', which are dependent on channel cross section, flow rate, cell nucleus size and the mechanical properties of cytoskeleton and membrane. The results from the study are used to provide some broad and quantitative assessments of the connections between cellular/subcellular mechanics and biochemical origins of disease states.

  9. The nature of letter crowding as revealed by first- and second-order classification images

    PubMed Central

    Nandy, Anirvan S.; Tjan, Bosco S.

    2009-01-01

    Visual crowding refers to the marked inability to identify an otherwise perfectly identifiable object when it is flanked by other objects. Crowding places a significant limit on form vision in the visual periphery; its mechanism is, however, unknown. Building on the method of signal-clamped classification images (Tjan & Nandy, 2006), we developed a series of first- and second-order classification-image techniques to investigate the nature of crowding without presupposing any model of crowding. Using an “o” versus “x” letter-identification task, we found that (1) crowding significantly reduced the contrast of first-order classification images, although it did not alter the shape of the classification images; (2) response errors during crowding were strongly correlated with the spatial structures of the flankers that resembled those of the erroneously perceived targets; (3) crowding had no systematic effect on intrinsic spatial uncertainty of an observer nor did it suppress feature detection; and (4) analysis of the second-order classification images revealed that crowding reduced the amount of valid features used by the visual system and, at the same time, increased the amount of invalid features used. Our findings strongly support the feature-mislocalization or source-confusion hypothesis as one of the proximal contributors of crowding. Our data also agree with the inappropriate feature-integration account with the requirement that feature integration be a competitive process. However, the feature-masking account and a front-end version of the spatial attention account of crowding are not supported by our data. PMID:18217820

  10. Iron oxide mineral-water interface reactions studied by AFM

    SciTech Connect

    Hawley, M.E.; Rogers, P.S.Z.

    1994-07-01

    Natural iron mineral surfaces have been examined in air by atomic force (AFM) and scanning tunneling (STM) microscopies. A number of different surface features were found to be characteristic of the native surface. Even surfaces freshly exposed by crushing larger crystals were found to have a pebbly surface texture caused by the presence of thin coatings of what might be surface precipitates. This finding is interpreted as evidence for previous exposure to water, probably through an extensive network of microfractures. Surface reactions on the goethite crystals were studied by AFM at size resolutions ranging from microns to atomic resolution before, during, and after reaction with distilled water and 0.lN HCl. Immediate and extensive surface reconfiguration occurred on contact with water. In one case, after equilibration with water for 3 days, surface reprecipitation, etching and pitting were observed. Atomic resolution images taken under water were found to be disordered. The result of surface reaction was generally to increase the surface area substantially through the extension of surface platelet arrays, present prior to reaction. This work is being done in support of the site characterization project at Yucca Mountain.

  11. AFM analysis of bleaching effects on dental enamel microtopography

    NASA Astrophysics Data System (ADS)

    Pedreira de Freitas, Ana Carolina; Espejo, Luciana Cardoso; Botta, Sergio Brossi; Teixeira, Fernanda de Sa; Luz, Maria Aparecida A. Cerqueira; Garone-Netto, Narciso; Matos, Adriana Bona; Salvadori, Maria Cecilia Barbosa da Silveira

    2010-02-01

    The purpose of this in vitro study was to test a new methodology to evaluate the effects of 35% hydrogen peroxide agent on the microtopography of sound enamel using an atomic force microscope (AFM). The buccal sound surfaces of three extracted human lower incisors were used, without polishing the surfaces to maintain them with natural morphology. These unpolished surfaces were subjected to bleaching procedure with 35% hydrogen peroxide that consisted of 4 applications of the bleaching agent on enamel surfaces for 10 min each application. Surface images were obtained in a 15 μm × 15 μm area using an AFM. The roughness (Ra and RMS) and the power spectral density (PSD) were obtained before and after the bleaching treatment. As results we could inquire that the PSD analyses were very suitable to identifying the morphological changes on the surfaces, while the Ra and RMS parameters were insufficient to represent the morphological alterations promoted by bleaching procedure on enamel. The morphological wavelength in the range of visible light spectrum (380-750 nm) was analyzed, showing a considerable increase of the PSD with the bleaching treatment.

  12. Cross-Sectional Nakagami Images in Passive Stretches Reveal Damage of Injured Muscles

    PubMed Central

    Lin, Shih-Ping; Lin, Yi-Hsun; Fan, Shih-Chen; Huang, Bu-Miin; Lin, Wei-Yin; Wang, Shyh-Hau; Shung, K. Kirk; Su, Fong-Chin; Wu, Chia-Ching

    2016-01-01

    Muscle strain is still awanting a noninvasive quantitatively diagnosis tool. High frequency ultrasound (HFU) improves image resolution for monitoring changes of tissue structures, but the biomechanical factors may influence ultrasonography during injury detection. We aim to illustrate the ultrasonic parameters to present the histological damage of overstretched muscle with the consideration of biomechanical factors. Gastrocnemius muscles from mice were assembled and ex vivo passive stretching was performed before or after injury. After injury, the muscle significantly decreased mechanical strength. Ultrasonic images were obtained by HFU at different deformations to scan in cross and longitudinal orientations of muscle. The ultrasonography was quantified by echogenicity and Nakagami parameters (NP) for structural evaluation and correlated with histological results. The injured muscle at its original length exhibited decreased echogenicity and NP from HFU images. Cross-sectional ultrasonography revealed a loss of correlation between NP and passive muscle stretching that suggested a special scatterer pattern in the cross section of injured muscle. The independence of NP during passive stretching of injured muscle was confirmed by histological findings in ruptured collagen fibers, decreased muscle density, and increased intermuscular fiber space. Thus, HFU analysis of NP in cross section represents muscle injury that may benefit the clinical diagnosis. PMID:27034946

  13. Cross-Sectional Nakagami Images in Passive Stretches Reveal Damage of Injured Muscles.

    PubMed

    Lin, Shih-Ping; Lin, Yi-Hsun; Fan, Shih-Chen; Huang, Bu-Miin; Lin, Wei-Yin; Wang, Shyh-Hau; Shung, K Kirk; Su, Fong-Chin; Wu, Chia-Ching

    2016-01-01

    Muscle strain is still awanting a noninvasive quantitatively diagnosis tool. High frequency ultrasound (HFU) improves image resolution for monitoring changes of tissue structures, but the biomechanical factors may influence ultrasonography during injury detection. We aim to illustrate the ultrasonic parameters to present the histological damage of overstretched muscle with the consideration of biomechanical factors. Gastrocnemius muscles from mice were assembled and ex vivo passive stretching was performed before or after injury. After injury, the muscle significantly decreased mechanical strength. Ultrasonic images were obtained by HFU at different deformations to scan in cross and longitudinal orientations of muscle. The ultrasonography was quantified by echogenicity and Nakagami parameters (NP) for structural evaluation and correlated with histological results. The injured muscle at its original length exhibited decreased echogenicity and NP from HFU images. Cross-sectional ultrasonography revealed a loss of correlation between NP and passive muscle stretching that suggested a special scatterer pattern in the cross section of injured muscle. The independence of NP during passive stretching of injured muscle was confirmed by histological findings in ruptured collagen fibers, decreased muscle density, and increased intermuscular fiber space. Thus, HFU analysis of NP in cross section represents muscle injury that may benefit the clinical diagnosis.

  14. Functional magnetic resonance imaging reveals brain regions mediating the response to resistive expiratory loads in humans.

    PubMed Central

    Gozal, D; Omidvar, O; Kirlew, K A; Hathout, G M; Lufkin, R B; Harper, R M

    1996-01-01

    Obstructive lung disease is the most common form of respiratory disturbance. However, the location of brain structures underlying the ventilatory response to resistive expiratory loads is unknown in humans. To study this issue, midsagittal magnetic resonance images were acquired in eight healthy volunteers before and after application of a moderate resistive expiratory load (30 cmH2O/liter/s), using functional magnetic resonance imaging (fMRI) strategies (1.5-T magnetic resonance; repetition time: 72 ms; echo time: 45 ms; flip angle: 30 degrees; field of view: 26 cm; slice thickness: 5 mm; 128 x 256 x 1 number of excitations). Digital image subtractions and region of interest analyses revealed significant increases in fMRI signal intensity in discrete areas of the ventral medulla, ventral and dorsal pontomedullary structures, basal forebrain, and cerebellum. Upon load withdrawal, a rapid fMRI signal off-transient occurred in all activated sites. Application of an identical load immediately after recovery from the initial stimulus resulted in smaller signal increases (P < 0.02). Prolongation of load duration was associated with progressive fMRI signal decrease across activated regions. In three additional subjects, the threshold for significant MRI signal increases was established at expiratory loads > or = 15 cmH2O/liter/s and was dose dependent with increasing loads. We conclude that resistive expiratory loads > or = 15 cmH2O/liter/s elicit regional activation of discrete brain locations in humans. PMID:8550849

  15. Image-Guided Synthesis Reveals Potent Blood-Brain Barrier Permeable Histone Deacetylase Inhibitors

    PubMed Central

    2014-01-01

    Recent studies have revealed that several histone deacetylase (HDAC) inhibitors, which are used to study/treat brain diseases, show low blood-brain barrier (BBB) penetration. In addition to low HDAC potency and selectivity observed, poor brain penetrance may account for the high doses needed to achieve therapeutic efficacy. Here we report the development and evaluation of highly potent and blood-brain barrier permeable HDAC inhibitors for CNS applications based on an image-guided approach involving the parallel synthesis and radiolabeling of a series of compounds based on the benzamide HDAC inhibitor, MS-275 as a template. BBB penetration was optimized by rapid carbon-11 labeling and PET imaging in the baboon model and using the imaging derived data on BBB penetration from each compound to feed back into the design process. A total of 17 compounds were evaluated, revealing molecules with both high binding affinity and BBB permeability. A key element conferring BBB penetration in this benzamide series was a basic benzylic amine. These derivatives exhibited 1–100 nM inhibitory activity against recombinant human HDAC1 and HDAC2. Three of the carbon-11 labeled aminomethyl benzamide derivatives showed high BBB penetration (∼0.015%ID/cc) and regional binding heterogeneity in the brain (high in thalamus and cerebellum). Taken together this approach has afforded a strategy and a predictive model for developing highly potent and BBB permeable HDAC inhibitors for CNS applications and for the discovery of novel candidate molecules for small molecule probes and drugs. PMID:24780082

  16. Interactions of arsenic with calcite surfaces revealed by in-situ nanoscale imaging

    NASA Astrophysics Data System (ADS)

    Renard, Francois; Putnis, Christine; Montes-Hernandez, German; Ruiz-Agudo, Encarnacion; Hövelmann, Jörn; Sarret, Géraldine

    2015-04-01

    Arsenic dissolved in water represents a key environmental and health challenge because several million people are under the threat of contamination. In calcareous environments calcite may play an important role in arsenic solubility and transfer in water. Arsenic-calcite interactions remain controversial, especially for As(III) which was proposed to be either incorporated as such, or as As(V) after oxidation. Here, we provide the first time-lapse in-situ study of calcite dissolution and growth in the presence of solutions with various amounts of As(III) or As(V). This was performed at room temperature and pH range 6-9 using a flow through cell connected to an atomic force microscope (AFM), to study the evolution of the (10-14) calcite cleavage surface morphology. Reaction products were then characterized by Raman spectroscopy. In parallel, co-precipitation experiments with either As(III) or As(V) were performed in batch reactors, and the speciation of arsenic in the resulting solids was studied by X-ray absorption spectroscopy (XAS). For As(V), AFM results showed that it interacts strongly with the calcite surface, and XAS results showed that As(V) was mostly incorporated in the calcite structure. For As(III), AFM results showed much less impact on calcite growth and dissolution and less incorporation was observed. This was confirmed by XAS results that indicate that As(III) was partly oxidized into As(V) before being incorporated into calcite and the resulting calcite contained 36% As(III) and 64% As(V). All these experimental results confirm that As(V) has a much stronger interaction with calcite than As(III) and that calcite may represent an important reservoir for arsenic in various geological environments.

  17. Interactions of arsenic with calcite surfaces revealed by in situ nanoscale imaging

    NASA Astrophysics Data System (ADS)

    Renard, François; Putnis, Christine V.; Montes-Hernandez, German; Ruiz-Agudo, Encarnacion; Hovelmann, Jörn; Sarret, Géraldine

    2015-06-01

    Arsenic dissolved in water represents a key environmental and health challenge because several million people are under the threat of contamination. In calcareous environments calcite may play an important role in arsenic solubility and transfer in water. Arsenic-calcite interactions remain controversial, especially for As(III) which was proposed to be either incorporated as such, or as As(V) after oxidation. Here, we provide the first time-lapse in situ study of the evolution of the (10-14) calcite cleavage surface morphology during dissolution and growth in the presence of solutions with various amounts of As(III) or As(V) at room temperature and pH range 6-11 using a flow-through cell connected to an atomic force microscope (AFM). Reaction products were then characterized by Raman spectroscopy. In parallel, co-precipitation experiments with either As(III) or As(V) were performed in batch reactors, and the speciation of arsenic in the resulting solids was studied by X-ray absorption spectroscopy (XAS). For As(V), AFM results showed that it interacts strongly with the calcite surface, and XAS results showed that As(V) was mostly incorporated in the calcite structure. For As(III), AFM results showed much less impact on calcite growth and dissolution and less incorporation was observed. This was confirmed by XAS results that indicate that As(III) was partly oxidized into As(V) before being incorporated into calcite and the resulting calcite contained 36% As(III) and 64% As(V). All these experimental results confirm that As(V) has a much stronger interaction with calcite than As(III) and that calcite may represent an important reservoir for arsenic in various geological environments.

  18. Custom AFM for X-ray beamlines: in situ biological investigations under physiological conditions

    PubMed Central

    Gumí-Audenis, B.; Carlà, F.; Vitorino, M. V.; Panzarella, A.; Porcar, L.; Boilot, M.; Guerber, S.; Bernard, P.; Rodrigues, M. S.; Sanz, F.; Giannotti, M. I.; Costa, L.

    2015-01-01

    A fast atomic force microscope (AFM) has been developed that can be installed as a sample holder for grazing-incidence X-ray experiments at solid/gas or solid/liquid interfaces. It allows a wide range of possible investigations, including soft and biological samples under physiological conditions (hydrated specimens). The structural information obtained using the X-rays is combined with the data gathered with the AFM (morphology and mechanical properties), providing a unique characterization of the specimen and its dynamics in situ during an experiment. In this work, lipid monolayers and bilayers in air or liquid environment have been investigated by means of AFM, both with imaging and force spectroscopy, and X-ray reflectivity. In addition, this combination allows the radiation damage induced by the beam on the sample to be studied, as has been observed on DOPC and DPPC supported lipid bilayers under physiological conditions. PMID:26524300

  19. Image Restoration and Analysis of Influenza Virions Binding to Membrane Receptors Reveal Adhesion-Strengthening Kinetics

    PubMed Central

    Lee, Donald W.; Hsu, Hung-Lun; Bacon, Kaitlyn B.; Daniel, Susan

    2016-01-01

    With the development of single-particle tracking (SPT) microscopy and host membrane mimics called supported lipid bilayers (SLBs), stochastic virus-membrane binding interactions can be studied in depth while maintaining control over host receptor type and concentration. However, several experimental design challenges and quantitative image analysis limitations prevent the widespread use of this approach. One main challenge of SPT studies is the low signal-to-noise ratio of SPT videos, which is sometimes inevitable due to small particle sizes, low quantum yield of fluorescent dyes, and photobleaching. These situations could render current particle tracking software to yield biased binding kinetic data caused by intermittent tracking error. Hence, we developed an effective image restoration algorithm for SPT applications called STAWASP that reveals particles with a signal-to-noise ratio of 2.2 while preserving particle features. We tested our improvements to the SPT binding assay experiment and imaging procedures by monitoring X31 influenza virus binding to α2,3 sialic acid glycolipids. Our interests lie in how slight changes to the peripheral oligosaccharide structures can affect the binding rate and residence times of viruses. We were able to detect viruses binding weakly to a glycolipid called GM3, which was undetected via assays such as surface plasmon resonance. The binding rate was around 28 folds higher when the virus bound to a different glycolipid called GD1a, which has a sialic acid group extending further away from the bilayer surface than GM3. The improved imaging allowed us to obtain binding residence time distributions that reflect an adhesion-strengthening mechanism via multivalent bonds. We empirically fitted these distributions using a time-dependent unbinding rate parameter, koff, which diverges from standard treatment of koff as a constant. We further explain how to convert these models to fit ensemble-averaged binding data obtained by assays such

  20. Seeing the Invisible: Revealing Atrial Ablation Lesions Using Hyperspectral Imaging Approach

    PubMed Central

    Muselimyan, Narine; Swift, Luther M.; Asfour, Huda; Chahbazian, Tigran; Mazhari, Ramesh; Mercader, Marco A.; Sarvazyan, Narine A.

    2016-01-01

    Background Currently, there are limited means for high-resolution monitoring of tissue injury during radiofrequency ablation procedures. Objective To develop the next generation of visualization catheters that can reveal irreversible atrial muscle damage caused by ablation and identify viability gaps between the lesions. Methods Radiofrequency lesions were placed on the endocardial surfaces of excised human and bovine atria and left ventricles of blood perfused rat hearts. Tissue was illuminated with 365nm light and a series of images were acquired from individual spectral bands within 420-720nm range. By extracting spectral profiles of individual pixels and spectral unmixing, the relative contribution of ablated and unablated spectra to each pixel was then displayed. Results of spectral unmixing were compared to lesion pathology. Results RF ablation caused significant changes in the tissue autofluorescence profile. The magnitude of these spectral changes in human left atrium was relatively small (< 10% of peak fluorescence value), yet highly significant. Spectral unmixing of hyperspectral datasets enabled high spatial resolution, in-situ delineation of radiofrequency lesion boundaries without the need for exogenous markers. Lesion dimensions derived from hyperspectral imaging approach strongly correlated with histological outcomes. Presence of blood within the myocardium decreased the amplitude of the autofluorescence spectra while having minimal effect on their overall shapes. As a result, the ability of hyperspectral imaging to delineate ablation lesions in vivo was not affected. Conclusions Hyperspectral imaging greatly increases the contrast between ablated and unablated tissue enabling visualization of viability gaps at clinically relevant locations. Data supports the possibility for developing percutaneous hyperspectral catheters for high-resolution ablation guidance. PMID:27930718

  1. Inhibition of cold rolled steel corrosion by Tween-20 in sulfuric acid: weight loss, electrochemical and AFM approaches.

    PubMed

    Mu, Guannan; Li, Xianghong

    2005-09-01

    The inhibiting action of a nonionic surfactant of Tween-20 on the corrosion of cold rolled steel (CRS) in 0.5-7.0 M sulfuric acid (H(2)SO(4)) was studied by weight loss and potentiodynamic polarization methods. Atomic force microscope (AFM) provided the surface conditions. The results show that inhibition efficiency increases with the inhibitor concentration, while it decreases with the sulfuric acid concentration. The adsorption of inhibitor on the cold rolled steel surface obeys the Langmuir adsorption isotherm equation. Effect of immersion time was studied and discussed. The effect of temperature on the corrosion behavior of cold rolled steel was also studied at four temperatures ranging from 30 to 60 degrees C, the thermodynamic parameters such as adsorption heat, adsorption free energy, and adsorption entropy were calculated. The results revealed that the adsorption was physisorption mechanism. A kinetic study of cold rolled steel in uninhibited and inhibited acid was also discussed. The kinetic parameters such as apparent activation energy, pre-exponential factor, rate constant, and reaction constant were calculated for the reactions of corrosion. The inhibition effect is satisfactorily explained by both thermodynamic and kinetic models. Polarization curves show that Tween-20 is a cathodic-type inhibitor in sulfuric acid. The results obtained from weight loss and potentiodynamic polarization are in good agreement, and the Tween-20 inhibition action could also be evidenced by surface AFM images.

  2. Non-contact AFM investigation of influence of freezing process on the surface structure of potato starch granule

    NASA Astrophysics Data System (ADS)

    Krok, F.; Szymońska, J.; Tomasik, P.; Szymoński, M.

    2000-04-01

    To assess the influence of the freezing process on the surface structure of a potato starch granule, a non-contact Atomic Force Microscopy (NC-AFM) investigation at ambient conditions has been undertaken. The observations were carried out for dried (oven-dried) and native (air-dried) starch. The obtained AFM images of the native starch granule surface demonstrated it as not uniformly smooth and having rough undulating appearance with layers of adsorbed water which could be removed by oven drying in 130°C. After freezing, the dried starch granule surface still consisted of nodules of about 100 nm in diameter. Significant changes in the granule surface appearance can be seen for dried starch samples frozen with some excess of water as well as for native starch samples frozen with its original water. Then the aggregation and polishing of the granules was observed and their surface revealed a microstructure with distinct ring-like protrusions of about 300 nm in diameter. Our observations tally with the amylopectine "blocket" starch granule structure model proposed in the literature and allowed to conclude that freezing may be a useful tool, among other methods, for modifying starch granule properties.

  3. The morphological and biomechanical changes of keratocytes cultured on modified p (HEMA-MMA) hydrogel studied by AFM.

    PubMed

    Yan, Tuo; Sun, Rong; Deng, Hua; Tan, Baihua; Ao, Ningjian

    2009-01-01

    The poor integration with host cornea tissue and the low mechanical properties of pHEMA hydrogel for artificial cornea remains a difficult problem to solve. A modified pHEMA hydrogel, MMA copolymerized and type-I collagen and bFGF immobilized, was previously prepared in an attempt to solve the problems. In this study, the cytotoxicity of Col/bFGF-p (HEMA-MMA) and p (HEMA-MMA) was studied by cell adhesion assay and atomic force microscopy (AFM). The results of cell adhesion assay show that the attachment of keratocytes on the modified membrane is much higher than that of the unmodified membrane. This indicates that the material after modification have better cell-material interaction. The AFM images reveal that the morphology of keratocytes cultured on different substrate is obviously different. The cell cultured on modified membrane presented a completely elongated and spindle-shape morphology. The force-distance indicates that the biomechanical of keratocytes changes significantly after culturing on different substrates. The adhesion force (2328+/-523 pN) and Young's modulus (0.51+/-0.125 kPa) of the cell cultured on modified membrane are much higher, and the stiffness (0.08+/-0.022 mN/m) is lower than those of the cell cultured on unmodified membrane. These results show that the cytotoxicity of Col/bFGF-p (HEMA-MMA) for keratocytes is much improved.

  4. Mechanistic insights into EGFR membrane clustering revealed by super-resolution imaging

    NASA Astrophysics Data System (ADS)

    Gao, Jing; Wang, Ye; Cai, Mingjun; Pan, Yangang; Xu, Haijiao; Jiang, Junguang; Ji, Hongbin; Wang, Hongda

    2015-01-01

    The clustering of membrane receptors such as EGFR is critical for various biological processes, for example cell signaling and tumorigenesis. However, the mechanism involved remains poorly understood. Here, we used a super resolution imaging technique, which has shattered the longstanding resolution barrier of light diffraction, to investigate the distribution of membrane EGFR on apical or basal surfaces of COS-7 cells and on the surface of suspended COS-7 cells. Our data show that more and larger EGFR clusters are detected on the apical surface in comparison with those on the basal surface and this difference is not affected by the EGFR activation state, whereas suspended COS-7 cells exhibit a moderate clustering state and a homogeneous distribution pattern, indicating that the external environment surrounding the cell membrane is the decisive factor in the EGFR clustering pattern. A dual-color dSTORM image reveals the significant colocalization of EGFR and lipid rafts; interestingly MβCD treatment leads to a dramatic decrease of the amount and size of EGFR clusters on both apical and basal surfaces, highlighting a key role of lipid rafts in EGFR cluster formation. Altogether, our results illustrate the distribution pattern of EGFR in polarized cells and uncover the essential role of lipid rafts in EGFR cluster maintenance.The clustering of membrane receptors such as EGFR is critical for various biological processes, for example cell signaling and tumorigenesis. However, the mechanism involved remains poorly understood. Here, we used a super resolution imaging technique, which has shattered the longstanding resolution barrier of light diffraction, to investigate the distribution of membrane EGFR on apical or basal surfaces of COS-7 cells and on the surface of suspended COS-7 cells. Our data show that more and larger EGFR clusters are detected on the apical surface in comparison with those on the basal surface and this difference is not affected by the EGFR

  5. The AFM Observation of Single Polyethylene Molecules in Coiled State on Mica

    NASA Astrophysics Data System (ADS)

    Prokhorov, V. V.; Yaminsky, I. V.

    2003-12-01

    Single polyethylene molecules and their small aggregates have been deposited on mica from diluted solutions at elevated temperatures and visualized by AFM in coiled and crystalline states. Coils have two-dimensional conformations with both highly tangled sites and locally extended segments with a length much exceeding the persistent length in a solution. The length measurements of coils reveal a wide distribution with the length of a maximum much smaller than the length of fully stretched molecules, moreover the long coils have been observed indicating the existence of linear multimolecular aggregates. Two models have been considered for the explanation of the observed deficit in the coils length, correspondingly the model implying the substantial smoothing of a winding chain trajectory due to the lack of the AFM resolution and the model of locally extended surface conformations with the long intramolecular folds. The roots of the apparent negative AFM height contrast of coils have been discussed.

  6. BOREAS AFM-6 Surface Meteorological Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Adminsitration/Environment Technology Laboratory (NOAA/ETL) collected surface meteorological data from 21 May to 20 Sep 1994 near the Southern Study Area-Old Jack Pine (SSA-OJP) tower site. The data are in tabular ASCII files. The surface meteorological data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  7. Revealing letters in rolled Herculaneum papyri by X-ray phase-contrast imaging

    NASA Astrophysics Data System (ADS)

    Mocella, Vito; Brun, Emmanuel; Ferrero, Claudio; Delattre, Daniel

    2015-01-01

    Hundreds of papyrus rolls, buried by the eruption of Mount Vesuvius in 79 AD and belonging to the only library passed on from Antiquity, were discovered 260 years ago at Herculaneum. These carbonized papyri are extremely fragile and are inevitably damaged or destroyed in the process of trying to open them to read their contents. In recent years, new imaging techniques have been developed to read the texts without unwrapping the rolls. Until now, specialists have been unable to view the carbon-based ink of these papyri, even when they could penetrate the different layers of their spiral structure. Here for the first time, we show that X-ray phase-contrast tomography can reveal various letters hidden inside the precious papyri without unrolling them. This attempt opens up new opportunities to read many Herculaneum papyri, which are still rolled up, thus enhancing our knowledge of ancient Greek literature and philosophy.

  8. Revealing letters in rolled Herculaneum papyri by X-ray phase-contrast imaging.

    PubMed

    Mocella, Vito; Brun, Emmanuel; Ferrero, Claudio; Delattre, Daniel

    2015-01-20

    Hundreds of papyrus rolls, buried by the eruption of Mount Vesuvius in 79 AD and belonging to the only library passed on from Antiquity, were discovered 260 years ago at Herculaneum. These carbonized papyri are extremely fragile and are inevitably damaged or destroyed in the process of trying to open them to read their contents. In recent years, new imaging techniques have been developed to read the texts without unwrapping the rolls. Until now, specialists have been unable to view the carbon-based ink of these papyri, even when they could penetrate the different layers of their spiral structure. Here for the first time, we show that X-ray phase-contrast tomography can reveal various letters hidden inside the precious papyri without unrolling them. This attempt opens up new opportunities to read many Herculaneum papyri, which are still rolled up, thus enhancing our knowledge of ancient Greek literature and philosophy.

  9. The organization of thinking: what functional brain imaging reveals about the neuroarchitecture of complex cognition.

    PubMed

    Just, Marcel Adam; Varma, Sashank

    2007-09-01

    Recent findings in brain imaging, particularly in fMRI, are beginning to reveal some of the fundamental properties of the organization of the cortical systems that underpin complex cognition. We propose an emerging set of operating principles that govern this organization, characterizing the system as a set of collaborating cortical centers that operate as a large-scale cortical network. Two of the network's critical features are that it is resource constrained and dynamically configured, with resource constraints and demands dynamically shaping the network topology. The operating principles are embodied in a cognitive neuroarchitecture, 4CAPS, consisting of a number of interacting computational centers that correspond to activating cortical areas. Each 4CAPS center is a hybrid production system, possessing both symbolic and connectionist attributes. We describe 4CAPS models of sentence comprehension, spatial problem solving, and complex multitasking and compare the accounts of these models with brain activation and behavioral results. Finally, we compare 4CAPS with other proposed neuroarchitectures.

  10. Adenovirus Structure as Revealed by X-Ray Crystallography, Electron Microscopy, and Difference Imaging

    NASA Astrophysics Data System (ADS)

    Stewart, Phoebe L.; Burnett, Roger M.

    1993-03-01

    The three-dimensional structure of human type 2 adenovirus was studied by combining X-ray crystallography and electron microscopy in a novel way. The 2.9 Å crystal structure of the major capsid protein, hexon, was positioned into a three-dimensional image reconstruction of the intact virus that was derived from cryo-electron micrographs. A three-dimensional difference map was generated by subtracting 240 copies of the crystallographic hexon from the density of the intact virus. This map revealed several minor structural proteins acting as “cement” to stabilize the assembly. The current state of structural knowledge concerning the location of the polypeptide components and the viral DNA is presented.

  11. Fragmentation process during Ho:YAG laser lithotripsy revealed by time-resolved imaging

    NASA Astrophysics Data System (ADS)

    Beghuin, Didier; Delacretaz, Guy P.; Schmidlin, Franz R.; Rink, Klaus

    1998-01-01

    The stone fragmentation process induced during Ho:YAG laser lithotripsy was observed by time-resolved flash video imaging. Possible acoustic transient occurrence was simultaneously monitored with a PVDF needle hydrophone. We used artificial and cystine kidney stones. We observed that, although the fragmentation process is accompanied with the formation of a cavitation bubble, cavitation has a minimal incidence on stone fragmentation. Fragment ejection is mainly due to a direct laser stone heating and vaporization of stone organic constituents and interstitial water. The minimal effect of the cavitation bubble for fragmentation is confirmed by acoustic transients measurements, which reveal weak pressure transients. This is in contrast with the fragmentation mechanisms induced by laser of shorter pulse duration.

  12. Adaptive optics retinal imaging reveals S-cone dystrophy in tritan color-vision deficiency

    NASA Astrophysics Data System (ADS)

    Baraas, Rigmor C.; Carroll, Joseph; Gunther, Karen L.; Chung, Mina; Williams, David R.; Foster, David H.; Neitz, Maureen

    2007-05-01

    Tritan color-vision deficiency is an autosomal dominant disorder associated with mutations in the short-wavelength-sensitive- (S-) cone-pigment gene. An unexplained feature of the disorder is that individuals with the same mutation manifest different degrees of deficiency. To date, it has not been possible to examine whether any loss of S-cone function is accompanied by physical disruption in the cone mosaic. Two related tritan subjects with the same novel mutation in their S-cone-opsin gene, but different degrees of deficiency, were examined. Adaptive optics was used to obtain high-resolution retinal images, which revealed distinctly different S-cone mosaics consistent with their discrepant phenotypes. In addition, a significant disruption in the regularity of the overall cone mosaic was observed in the subject completely lacking S-cone function. These results taken together with other recent findings from molecular genetics indicate that, with rare exceptions, tritan deficiency is progressive in nature.

  13. Probing ternary solvent effect in high Voc polymer solar cells using advanced AFM techniques

    SciTech Connect

    Li, Chao; Soleman, Mikhael; Lorenzo, Josie; Dhasmana, Nitesh; Chantharasupawong, Panit; Ievlev, Anton; Gesquiere, Andre; Tetard, Laurene; Thomas, Jayan

    2016-01-25

    This work describes a simple method to develop a high Voc low band gap PSCs. In addition, two new atomic force microscopy (AFM)-based nanoscale characterization techniques to study the surface morphology and physical properties of the structured active layer are introduced. With the help of ternary solvent processing of the active layer and C60 buffer layer, a bulk heterojunction PSC with Voc more than 0.9 V and conversion efficiency 7.5% is developed. In order to understand the fundamental properties of the materials ruling the performance of the PSCs tested, AFM-based nanoscale characterization techniques including Pulsed-Force-Mode AFM (PFM-AFM) and Mode-Synthesizing AFM (MSAFM) are introduced. Interestingly, MSAFM exhibits high sensitivity for direct visualization of the donor–acceptor phases in the active layer of the PSCs. Lastly, conductive-AFM (cAFM) studies reveal local variations in conductivity in the donor and acceptor phases as well as a significant increase in photocurrent in the PTB7:ICBA sample obtained with the ternary solvent processing.

  14. Automated image analysis reveals the dynamic 3-dimensional organization of multi-ciliary arrays.

    PubMed

    Galati, Domenico F; Abuin, David S; Tauber, Gabriel A; Pham, Andrew T; Pearson, Chad G

    2015-12-23

    Multi-ciliated cells (MCCs) use polarized fields of undulating cilia (ciliary array) to produce fluid flow that is essential for many biological processes. Cilia are positioned by microtubule scaffolds called basal bodies (BBs) that are arranged within a spatially complex 3-dimensional geometry (3D). Here, we develop a robust and automated computational image analysis routine to quantify 3D BB organization in the ciliate, Tetrahymena thermophila. Using this routine, we generate the first morphologically constrained 3D reconstructions of Tetrahymena cells and elucidate rules that govern the kinetics of MCC organization. We demonstrate the interplay between BB duplication and cell size expansion through the cell cycle. In mutant cells, we identify a potential BB surveillance mechanism that balances large gaps in BB spacing by increasing the frequency of closely spaced BBs in other regions of the cell. Finally, by taking advantage of a mutant predisposed to BB disorganization, we locate the spatial domains that are most prone to disorganization by environmental stimuli. Collectively, our analyses reveal the importance of quantitative image analysis to understand the principles that guide the 3D organization of MCCs.

  15. Voltage-Sensitive Dyes And Imaging Techniques Reveal New Patterns Of Electrical Activity In Heart Cortex

    NASA Astrophysics Data System (ADS)

    Salama, Guy

    1988-04-01

    Voltage-sensitive dyes bind to the plasms membrane of excitable cells (ie., muscle or nerve cells) and exhibit fluorescence and/or absorption changes that vary linearly with changes in transmembrane electrical potential. These potentiometric optical probes can be used to measure local changes in transmembrane potential by monitoring optical signals from dye molecules bound to the surface membrane. Consequently, when excitable cells are stained with such a dye and are stimulated to fire an electrical impulse (ie., an action potential (AP)), the changes in dye fluorescence have the characteristic shape and time course of APs recorded with an intracellular micro-electrode. Potentiometric dyes in conjuction with imaging techniques can now be used to visualize complex patterns and propagation of electrical activity. With photodiode arrays on video imaging techniques, patterns of biological electrical activity can be obtained with high temporal and spatial resolution which could not be obtained by conventional micro-electrodes. These methods reveal new details and offer powerful approaches to study fundamental problem in cardiac electrophysiology, communication in nerve networks, and the organization of cortical neurons.

  16. Synthesis and folding of a mirror-image enzyme reveals ambidextrous chaperone activity

    PubMed Central

    Weinstock, Matthew T.; Jacobsen, Michael T.; Kay, Michael S.

    2014-01-01

    Mirror-image proteins (composed of d-amino acids) are promising therapeutic agents and drug discovery tools, but as synthesis of larger d-proteins becomes feasible, a major anticipated challenge is the folding of these proteins into their active conformations. In vivo, many large and/or complex proteins require chaperones like GroEL/ES to prevent misfolding and produce functional protein. The ability of chaperones to fold d-proteins is unknown. Here we examine the ability of GroEL/ES to fold a synthetic d-protein. We report the total chemical synthesis of a 312-residue GroEL/ES-dependent protein, DapA, in both l- and d-chiralities, the longest fully synthetic proteins yet reported. Impressively, GroEL/ES folds both l- and d-DapA. This work extends the limits of chemical protein synthesis, reveals ambidextrous GroEL/ES folding activity, and provides a valuable tool to fold d-proteins for drug development and mirror-image synthetic biology applications. PMID:25071217

  17. Lateral and Medial Ventral Occipitotemporal Regions Interact During the Recognition of Images Revealed from Noise

    PubMed Central

    Nordhjem, Barbara; Ćurčić-Blake, Branislava; Meppelink, Anne Marthe; Renken, Remco J.; de Jong, Bauke M.; Leenders, Klaus L.; van Laar, Teus; Cornelissen, Frans W.

    2016-01-01

    Several studies suggest different functional roles for the medial and the lateral sections of the ventral visual cortex in object recognition. Texture and surface information is processed in medial sections, while shape information is processed in lateral sections. This begs the question whether and how these functionally specialized sections interact with each other and with early visual cortex to facilitate object recognition. In the current research, we set out to answer this question. In an fMRI study, 13 subjects viewed and recognized images of objects and animals that were gradually revealed from noise while their brains were being scanned. We applied dynamic causal modeling (DCM)—a method to characterize network interactions—to determine the modulatory effect of object recognition on a network comprising the primary visual cortex (V1), the lingual gyrus (LG) in medial ventral cortex and the lateral occipital cortex (LO). We found that object recognition modulated the bilateral connectivity between LG and LO. Moreover, the feed-forward connectivity from V1 to LG and LO was modulated, while there was no evidence for feedback from these regions to V1 during object recognition. In particular, the interaction between medial and lateral areas supports a framework in which visual recognition of objects is achieved by networked regions that integrate information on image statistics, scene content and shape—rather than by a single categorically specialized region—within the ventral visual cortex. PMID:26778997

  18. Lithium Accumulates in Neurogenic Brain Regions as Revealed by High Resolution Ion Imaging

    PubMed Central

    Zanni, Giulia; Michno, Wojciech; Di Martino, Elena; Tjärnlund-Wolf, Anna; Pettersson, Jean; Mason, Charlotte Elizabeth; Hellspong, Gustaf; Blomgren, Klas; Hanrieder, Jörg

    2017-01-01

    Lithium (Li) is a potent mood stabilizer and displays neuroprotective and neurogenic properties. Despite extensive investigations, the mechanisms of action have not been fully elucidated, especially in the juvenile, developing brain. Here we characterized lithium distribution in the juvenile mouse brain during 28 days of continuous treatment that result in clinically relevant serum concentrations. By using Time-of-Flight Secondary Ion Mass Spectrometry- (ToF-SIMS) based imaging we were able to delineate temporospatial lithium profile throughout the brain and concurrent distribution of endogenous lipids with high chemical specificity and spatial resolution. We found that Li accumulated in neurogenic regions and investigated the effects on hippocampal neurogenesis. Lithium increased proliferation, as judged by Ki67-immunoreactivity, but did not alter the number of doublecortin-positive neuroblasts at the end of the treatment period. Moreover, ToF-SIMS revealed a steady depletion of sphingomyelin in white matter regions during 28d Li-treatment, particularly in the olfactory bulb. In contrast, cortical levels of cholesterol and choline increased over time in Li-treated mice. This is the first study describing ToF-SIMS imaging for probing the brain-wide accumulation of supplemented Li in situ. The findings demonstrate that this technique is a powerful approach for investigating the distribution and effects of neuroprotective agents in the brain. PMID:28098178

  19. Lithium Accumulates in Neurogenic Brain Regions as Revealed by High Resolution Ion Imaging.

    PubMed

    Zanni, Giulia; Michno, Wojciech; Di Martino, Elena; Tjärnlund-Wolf, Anna; Pettersson, Jean; Mason, Charlotte Elizabeth; Hellspong, Gustaf; Blomgren, Klas; Hanrieder, Jörg

    2017-01-18

    Lithium (Li) is a potent mood stabilizer and displays neuroprotective and neurogenic properties. Despite extensive investigations, the mechanisms of action have not been fully elucidated, especially in the juvenile, developing brain. Here we characterized lithium distribution in the juvenile mouse brain during 28 days of continuous treatment that result in clinically relevant serum concentrations. By using Time-of-Flight Secondary Ion Mass Spectrometry- (ToF-SIMS) based imaging we were able to delineate temporospatial lithium profile throughout the brain and concurrent distribution of endogenous lipids with high chemical specificity and spatial resolution. We found that Li accumulated in neurogenic regions and investigated the effects on hippocampal neurogenesis. Lithium increased proliferation, as judged by Ki67-immunoreactivity, but did not alter the number of doublecortin-positive neuroblasts at the end of the treatment period. Moreover, ToF-SIMS revealed a steady depletion of sphingomyelin in white matter regions during 28d Li-treatment, particularly in the olfactory bulb. In contrast, cortical levels of cholesterol and choline increased over time in Li-treated mice. This is the first study describing ToF-SIMS imaging for probing the brain-wide accumulation of supplemented Li in situ. The findings demonstrate that this technique is a powerful approach for investigating the distribution and effects of neuroprotective agents in the brain.

  20. Surface phenomena revealed by in situ imaging: studies from adhesion, wear and cutting

    NASA Astrophysics Data System (ADS)

    Viswanathan, Koushik; Mahato, Anirban; Yeung, Ho; Chandrasekar, Srinivasan

    2017-03-01

    Surface deformation and flow phenomena are ubiquitous in mechanical processes. In this work we present an in situ imaging framework for studying a range of surface mechanical phenomena at high spatial resolution and across a range of time scales. The in situ framework is capable of resolving deformation and flow fields quantitatively in terms of surface displacements, velocities, strains and strain rates. Three case studies are presented demonstrating the power of this framework for studying surface deformation. In the first, the origin of stick-slip motion in adhesive polymer interfaces is investigated, revealing a intimate link between stick-slip and surface wave propagation. Second, the role of flow in mediating formation of surface defects and wear particles in metals is analyzed using a prototypical sliding process. It is shown that conventional post-mortem observation and inference can lead to erroneous conclusions with regard to formation of surface cracks and wear particles. The in situ framework is shown to unambiguously capture delamination wear in sliding. Third, material flow and surface deformation in a typical cutting process is analyzed. It is shown that a long-standing problem in the cutting of annealed metals is resolved by the imaging, with other benefits such as estimation of energy dissipation and power from the flow fields. In closure, guidelines are provided for profitably exploiting in situ observations to study large-strain deformation, flow and friction phenomena at surfaces that display a variety of time-scales.

  1. Automated image analysis reveals the dynamic 3-dimensional organization of multi-ciliary arrays

    PubMed Central

    Galati, Domenico F.; Abuin, David S.; Tauber, Gabriel A.; Pham, Andrew T.; Pearson, Chad G.

    2016-01-01

    ABSTRACT Multi-ciliated cells (MCCs) use polarized fields of undulating cilia (ciliary array) to produce fluid flow that is essential for many biological processes. Cilia are positioned by microtubule scaffolds called basal bodies (BBs) that are arranged within a spatially complex 3-dimensional geometry (3D). Here, we develop a robust and automated computational image analysis routine to quantify 3D BB organization in the ciliate, Tetrahymena thermophila. Using this routine, we generate the first morphologically constrained 3D reconstructions of Tetrahymena cells and elucidate rules that govern the kinetics of MCC organization. We demonstrate the interplay between BB duplication and cell size expansion through the cell cycle. In mutant cells, we identify a potential BB surveillance mechanism that balances large gaps in BB spacing by increasing the frequency of closely spaced BBs in other regions of the cell. Finally, by taking advantage of a mutant predisposed to BB disorganization, we locate the spatial domains that are most prone to disorganization by environmental stimuli. Collectively, our analyses reveal the importance of quantitative image analysis to understand the principles that guide the 3D organization of MCCs. PMID:26700722

  2. Systematic imaging reveals features and changing localization of mRNAs in Drosophila development.

    PubMed

    Jambor, Helena; Surendranath, Vineeth; Kalinka, Alex T; Mejstrik, Pavel; Saalfeld, Stephan; Tomancak, Pavel

    2015-04-02

    mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types-the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3'UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, http://tomancak-srv1.mpi-cbg.de/DOT/main.html) enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells.

  3. Systematic imaging reveals features and changing localization of mRNAs in Drosophila development

    PubMed Central

    Jambor, Helena; Surendranath, Vineeth; Kalinka, Alex T; Mejstrik, Pavel; Saalfeld, Stephan; Tomancak, Pavel

    2015-01-01

    mRNA localization is critical for eukaryotic cells and affects numerous transcripts, yet how cells regulate distribution of many mRNAs to their subcellular destinations is still unknown. We combined transcriptomics and systematic imaging to determine the tissue-specific expression and subcellular distribution of 5862 mRNAs during Drosophila oogenesis. mRNA localization is widespread in the ovary and detectable in all of its cell types—the somatic epithelial, the nurse cells, and the oocyte. Genes defined by a common RNA localization share distinct gene features and differ in expression level, 3′UTR length and sequence conservation from unlocalized mRNAs. Comparison of mRNA localizations in different contexts revealed that localization of individual mRNAs changes over time in the oocyte and between ovarian and embryonic cell types. This genome scale image-based resource (Dresden Ovary Table, DOT, http://tomancak-srv1.mpi-cbg.de/DOT/main.html) enables the transition from mechanistic dissection of singular mRNA localization events towards global understanding of how mRNAs transcribed in the nucleus distribute in cells. DOI: http://dx.doi.org/10.7554/eLife.05003.001 PMID:25838129

  4. Multispectral imaging reveals the tissue distribution of tetraspanins in human lymphoid organs.

    PubMed

    de Winde, Charlotte M; Zuidscherwoude, Malou; Vasaturo, Angela; van der Schaaf, Alie; Figdor, Carl G; van Spriel, Annemiek B

    2015-08-01

    Multispectral imaging is a novel microscopy technique that combines imaging with spectroscopy to obtain both quantitative expression data and tissue distribution of different cellular markers. Tetraspanins CD37 and CD53 are four-transmembrane proteins involved in cellular and humoral immune responses. However, comprehensive immunohistochemical analyses of CD37 and CD53 in human lymphoid organs have not been performed so far. We investigated CD37 and CD53 protein expression on primary human immune cell subsets in blood and in primary and secondary lymphoid organs. Both tetraspanins were prominently expressed on antigen-presenting cells, with highest expression of CD37 on B lymphocytes. Analysis of subcellular distribution showed presence of both tetraspanins on the plasma membrane and on endosomes. In addition, CD53 was also present on lysosomes. Quantitative analysis of expression and localization of CD37 and CD53 on lymphocytes within lymphoid tissues by multispectral imaging revealed high expression of both tetraspanins on CD20(+) cells in B cell follicles in human spleen and appendix. CD3(+) T cells within splenic T cell zones expressed lower levels of CD37 and CD53 compared to T cells in the red pulp of human spleen. B cells in human bone marrow highly expressed CD37, whereas the expression of CD53 was low. In conclusion, we demonstrate differential expression of CD37 and CD53 on primary human immune cells, their subcellular localization and their quantitative distribution in human lymphoid organs. This study provides a solid basis for better insight into the function of tetraspanins in the human immune response.

  5. GAPS IN THE HD 169142 PROTOPLANETARY DISK REVEALED BY POLARIMETRIC IMAGING: SIGNS OF ONGOING PLANET FORMATION?

    SciTech Connect

    Quanz, Sascha P.; Avenhaus, Henning; Garufi, Antonio; Schmid, Hans Martin; Buenzli, Esther; Wolf, Sebastian

    2013-03-20

    We present H-band Very Large Telescope/NACO polarized light images of the Herbig Ae/Be star HD 169142 probing its protoplanetary disk as close as {approx}0.''1 to the star. Our images trace the face-on disk out to {approx}1.''7 ({approx}250 AU) and reveal distinct substructures for the first time: (1) the inner disk ({approx}<20 AU) appears to be depleted in scattering dust grains; (2) an unresolved disk rim is imaged at {approx}25 AU; (3) an annular gap extends from {approx}40 to 70 AU; (4) local brightness asymmetries are found on opposite sides of the annular gap. We discuss different explanations for the observed morphology among which ongoing planet formation is a tempting, but yet to be proven, one. Outside of {approx}85 AU the surface brightness drops off roughly {proportional_to}r {sup -3.3}, but describing the disk regions between 85-120 AU and 120-250 AU separately with power laws {proportional_to}r {sup -2.6} and {proportional_to}r {sup -3.9} provides a better fit hinting toward another discontinuity in the disk surface. The flux ratio between the disk-integrated polarized light and the central star is {approx}4.1 Multiplication-Sign 10{sup -3}. Finally, combining our results with those from the literature, {approx}40% of the scattered light in the H band appears to be polarized. Our results emphasize that HD 169142 is an interesting system for future planet formation or disk evolution studies.

  6. Ratiometric high-resolution imaging of JC-1 fluorescence reveals the subcellular heterogeneity of astrocytic mitochondria.

    PubMed

    Keil, Vera C; Funke, Frank; Zeug, Andre; Schild, Detlev; Müller, Michael

    2011-11-01

    Using the mitochondrial potential (ΔΨ(m)) marker JC-1 (5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidazolylcarbocyanine iodide) and high-resolution imaging, we functionally analyzed mitochondria in cultured rat hippocampal astrocytes. Ratiometric detection of JC-1 fluorescence identified mitochondria with high and low ΔΨ(m). Mitochondrial density was highest in the perinuclear region, whereas ΔΨ(m) tended to be higher in peripheral mitochondria. Spontaneous ΔΨ(m) fluctuations, representing episodes of increased energization, appeared in individual mitochondria or synchronized in mitochondrial clusters. They continued upon withdrawal of extracellular Ca(2+), but were antagonized by dantrolene or 2-aminoethoxydiphenylborate (2-APB). Fluo-3 imaging revealed local cytosolic Ca(2+) transients with similar kinetics that also were depressed by dantrolene and 2-APB. Massive cellular Ca(2+) load or metabolic impairment abolished ΔΨ(m) fluctuations, occasionally evoking heterogeneous mitochondrial depolarizations. The detected diversity and ΔΨ(m) heterogeneity of mitochondria confirms that even in less structurally polarized cells, such as astrocytes, specialized mitochondrial subpopulations coexist. We conclude that ΔΨ(m) fluctuations are an indication of mitochondrial viability and are triggered by local Ca(2+) release from the endoplasmic reticulum. This spatially confined organelle crosstalk contributes to the functional heterogeneity of mitochondria and may serve to adapt the metabolism of glial cells to the activity and metabolic demand of complex neuronal networks. The established ratiometric JC-1 imaging-especially combined with two-photon microscopy-enables quantitative functional analyses of individual mitochondria as well as the comparison of mitochondrial heterogeneity in different preparations and/or treatment conditions.

  7. Stacking sequence and interlayer coupling in few-layer graphene revealed by in situ imaging

    PubMed Central

    Wang, Zhu-Jun; Dong, Jichen; Cui, Yi; Eres, Gyula; Timpe, Olaf; Fu, Qiang; Ding, Feng; Schloegl, R.; Willinger, Marc-Georg

    2016-01-01

    In the transition from graphene to graphite, the addition of each individual graphene layer modifies the electronic structure and produces a different material with unique properties. Controlled growth of few-layer graphene is therefore of fundamental interest and will provide access to materials with engineered electronic structure. Here we combine isothermal growth and etching experiments with in situ scanning electron microscopy to reveal the stacking sequence and interlayer coupling strength in few-layer graphene. The observed layer-dependent etching rates reveal the relative strength of the graphene–graphene and graphene–substrate interaction and the resulting mode of adlayer growth. Scanning tunnelling microscopy and density functional theory calculations confirm a strong coupling between graphene edge atoms and platinum. Simulated etching confirms that etching can be viewed as reversed growth. This work demonstrates that real-time imaging under controlled atmosphere is a powerful method for designing synthesis protocols for sp2 carbon nanostructures in between graphene and graphite. PMID:27759024

  8. Stacking sequence and interlayer coupling in few-layer graphene revealed by in situ imaging

    DOE PAGES

    Wang, Zhu-Jun; Dong, Jichen; Cui, Yi; ...

    2016-10-19

    In the transition from graphene to graphite, the addition of each individual graphene layer modifies the electronic structure and produces a different material with unique properties. Controlled growth of few-layer graphene is therefore of fundamental interest and will provide access to materials with engineered electronic structure. Here we combine isothermal growth and etching experiments with in situ scanning electron microscopy to reveal the stacking sequence and interlayer coupling strength in few-layer graphene. The observed layer-dependent etching rates reveal the relative strength of the graphene graphene and graphene substrate interaction and the resulting mode of adlayer growth. Scanning tunnelling microscopy andmore » density functional theory calculations confirm a strong coupling between graphene edge atoms and platinum. Simulated etching confirms that etching can be viewed as reversed growth. This work demonstrates that real-time imaging under controlled atmosphere is a powerful method for designing synthesis protocols for sp2 carbon nanostructures in between graphene and graphite.« less

  9. Oxidant Signaling in Cells Revealed by Single Rare-Earth Based Nanoparticle Imaging

    NASA Astrophysics Data System (ADS)

    Bouzigues, Cedric; Abdesselem, Mouna; Ramodiharilafy, Rivo; Gacoin, Thierry; Tharaux, Pierre-Louis; Alexandrou, Antigoni

    The spatio-temporal organization of signaling pathways controls the cell response. Reactive oxygen species (ROS) are second messengers involved in the control of numerous normal and pathological processes and their local concentration is thus tightly regulated. However, the dynamics of ROS production and organization is mostly unknown, due to the lack of efficient probes. We developed single ROS sensitive Eu3+-doped nanoparticle imaging to quantitatively probed the intracellular ROS response. We revealed specific temporal patterns of ROS production under different types of stimulation (PDGF and ET-1) and quantitatively identified mechanisms of transactivation, which notably control the dynamics of the cell response. By using a microfluidic system, we apply spatially controlled stimulations and displayed the maintenance of asymmetric ROS concentration in the cell under a PDGF gradient. We then developed a ratiometric method using a nanoparticle mix, to quantitatively detect ROS with a 500 ms temporal resolution. We thus elucidate molecular mechanisms responsible for the control of the oxidant production kinetics. Altogether, our results reveal regulation mechanisms controlling ROS spatio-temporal organization, which can be crucial for the buildup of the cell response.

  10. Superresolution Fluorescence Imaging of Mitochondrial Nucleoids Reveals Their Spatial Range, Limits, and Membrane Interaction ▿ †

    PubMed Central

    Brown, Timothy A.; Tkachuk, Ariana N.; Shtengel, Gleb; Kopek, Benjamin G.; Bogenhagen, Daniel F.; Hess, Harald F.; Clayton, David A.

    2011-01-01

    A fundamental objective in molecular biology is to understand how DNA is organized in concert with various proteins, RNA, and biological membranes. Mitochondria maintain and express their own DNA (mtDNA), which is arranged within structures called nucleoids. Their functions, dimensions, composition, and precise locations relative to other mitochondrial structures are poorly defined. Superresolution fluorescence microscopy techniques that exceed the previous limits of imaging within the small and highly compartmentalized mitochondria have been recently developed. We have improved and employed both two- and three-dimensional applications of photoactivated localization microscopy (PALM and iPALM, respectively) to visualize the core dimensions and relative locations of mitochondrial nucleoids at an unprecedented resolution. PALM reveals that nucleoids differ greatly in size and shape. Three-dimensional volumetric analysis indicates that, on average, the mtDNA within ellipsoidal nucleoids is extraordinarily condensed. Two-color PALM shows that the freely diffusible mitochondrial matrix protein is largely excluded from the nucleoid. In contrast, nucleoids are closely associated with the inner membrane and often appear to be wrapped around cristae or crista-like inner membrane invaginations. Determinations revealing high packing density, separation from the matrix, and tight association with the inner membrane underscore the role of mechanisms that regulate access to mtDNA and that remain largely unknown. PMID:22006021

  11. Integrated live imaging and molecular profiling of embryoid bodies reveals a synchronized progression of early differentiation

    PubMed Central

    Boxman, Jonathan; Sagy, Naor; Achanta, Sirisha; Vadigepalli, Rajanikanth; Nachman, Iftach

    2016-01-01

    Embryonic stem cells can spontaneously differentiate into cell types of all germ layers within embryoid bodies (EBs) in a highly variable manner. Whether there exists an intrinsic differentiation program common to all EBs is unknown. Here, we present a novel combination of high-throughput live two-photon imaging and gene expression profiling to study early differentiation dynamics spontaneously occurring within developing EBs. Onset timing of Brachyury-GFP was highly variable across EBs, while the spatial patterns as well as the dynamics of mesendodermal progression following onset were remarkably similar. We therefore defined a ‘developmental clock’ using the Brachyury-GFP signal onset timing. Mapping snapshot gene expression measurements to this clock revealed their temporal trends, indicating that loss of pluripotency, formation of primitive streak and mesodermal lineage progression are synchronized in EBs. Exogenous activation of Wnt or BMP signaling accelerated the intrinsic clock. CHIR down-regulated Wnt3, allowing insights into dependency mechanisms between canonical Wnt signaling and multiple genes. Our findings reveal a developmental clock characteristic of an early differentiation program common to all EBs, further establishing them as an in vitro developmental model. PMID:27530599

  12. Locations and types of ruptures involved in the 2008 Wenchuan earthquake revealed by SAR image matching

    NASA Astrophysics Data System (ADS)

    Kobayashi, T.; Takada, Y.; Furuya, M.; Murakami, M.

    2009-12-01

    Introduction: A catastrophic earthquake with a moment magnitude of 7.9 struck China’s Sichuan area on 12 May 2008. The rupture was thought to proceed northeastward along the Longmen Shan fault zone (LMSFZ), but it remained uncertain where and how the faults were involved in the seismic event. Interferometric SAR (InSAR) analysis has an advantage of detecting ground deformation in a vast region with high precision. However, for the Sichuan event, the standard InSAR approach was not helpful in knowing the faults directly related to the seismic rupture, due to a wide coherent loss area in the proximity of the fault zone. Thus, in order to reveal the unknown surface displacements, we conducted a SAR image matching procedure that enables us to robustly detect large ground deformation even in an incoherent area. Although similar approaches can be taken with optical images to detect surface displacements, SAR images are advantageous because of the radar’s all-weather detection capability. In this presentation we will show a strong advantage of SAR data for inland large earthquakes. Analysis Method: We use ALOS/PALSAR data on the ascending orbital paths. We process the SAR data from a level-1.0 product using a software package Gamma. After conducting coregistration between two images acquired before and after the mainshock, we divide the single-look SAR amplitude images into patches and calculate an offset between the corresponding patches by an intensity tracking method. This method is performed by cross-correlating samples of backscatter intensity of a master image with those of a slave image. To reduce the artificial offsets in range component, we apply an elevation dependent correction incorporating SRTM3 DEM data. Results: We have successfully obtained the surface deformation in range component: A sharp displacement discontinuity with a relative motion of 1-2 m appears over a length of 200 km along the LMSFZ, which demonstrates that the main rupture has proceeded

  13. Applications of AFM in semiconductor R&D and manufacturing at 45 nm technology node and beyond

    NASA Astrophysics Data System (ADS)

    Lee, Moon-Keun; Shin, Minjung; Bao, Tianming; Song, Chul-Gi; Dawson, Dean; Ihm, Dong-Chul; Ukraintsev, Vladimir

    2009-03-01

    Continuing demand for high performance microelectronic products propelled integrated circuit technology into 45 nm node and beyond. The shrinking device feature geometry created unprecedented challenges for dimension metrology in semiconductor manufacturing and research and development. Automated atomic force microscope (AFM) has been used to meet the challenge and characterize narrower lines, trenches and holes at 45nm technology node and beyond. AFM is indispensable metrology techniques capable of non-destructive full three-dimensional imaging, surface morphology characterization and accurate critical dimension (CD) measurements. While all available dimensional metrology techniques approach their limits, AFM continues to provide reliable information for development and control of processes in memory, logic, photomask, image sensor and data storage manufacturing. In this paper we review up-todate applications of automated AFM in every mentioned above semiconductor industry sector. To demonstrate benefits of AFM at 45 nm node and beyond we compare capability of automated AFM with established in-line and off-line metrologies like critical dimension scanning electron microscopy (CDSEM), optical scatterometry (OCD) and transmission electronic microscopy (TEM).

  14. New AFM Techniques for Investigating Molecular Growth Mechanisms of Protein Crystals

    NASA Technical Reports Server (NTRS)

    Li, Huayu; Nadarajah, Arunan; Konnert, John H.; Pusey, Marc L.

    1998-01-01

    Atomic Force Microscopy (AFM) has emerged as a powerful technique for investigating protein crystal growth. Earlier AFM studies were among the first to demonstrate that these crystals grew by dislocation and 2D nucleation growth mechanisms [1]. These investigations were restricted to the micron range where only surface features, such as dislocation hillocks and 2D islands are visible. Most AFM instruments can scan at higher resolutions and have the potential to resolve individual protein molecules at nanometer ranges. Such scans are essential for determining the molecular packing arrangements on crystal faces and for probing the growth process at the molecular level. However, at this resolution the AFM tip influences the image produced, with the resulting image being a convolution of the tip shape and the surface morphology [2]. In most studies this problem is resolved by deconvoluting the image to obtain the true surface morphology. Although deconvolution routines work reasonably well for simple one- dimensional shapes, for complex surfaces this approach does not produce accurate results. In this study we devised a new approach which takes advantage of the precise molecular order of crystal surfaces, combined with the knowledge of individual molecular shapes from the crystallographic data of the protein and the AFM tip shape. This information is used to construct expected theoretical AFM images by convoluting the tip shape with the constructed crystal surface shape for a given surface packing arrangement. By comparing the images from actual AFM scans with the constructed ones for different possible surface packing arrangements, the correct packing arrangement can be conclusively determined. This approach was used in this study to determine the correct one from two possible packing arrangements on (I 10) faces of tetragonal lysozyme crystals. Another novel AFM technique was also devised to measure the dimension of individual growth units of the crystal faces

  15. Implications of the contact radius to line step (CRLS) ratio in AFM for nanotribology measurements.

    PubMed

    Helt, James M; Batteas, James D

    2006-07-04

    Investigating the mechanisms of defect generation and growth at surfaces on the nanometer scale typically requires high-resolution tools such as the atomic force microscope (AFM). To accurately assess the kinetics and activation parameters of defect production over a wide range of loads (F(z)), the AFM data should be properly conditioned. Generally, AFM wear trials are performed over an area defined by the length of the slow (L(sscan)) and fast scan axes. The ratio of L(sscan) to image resolution (res, lines per image) becomes an important experimental parameter in AFM wear trials because it defines the magnitude of the line step (LS = L(sscan)/res), the distance the AFM tip steps along the slow scan axis. Comparing the contact radius (a) to the line step (LS) indicates that the overlap of successive scans will result unless the contact radius-line step ratio (CRLS) is < or =(1)/(2). If this relationship is not considered, then the scan history (e.g., contact frequency) associated with a single scan is not equivalent at different loads owing to the scaling of contact radius with load (a proportional variant F(z)(1/3)). Here, we present a model in conjunction with empirical wear tests on muscovite mica to evaluate the effects of scan overlap on surface wear. Using the Hertz contact mechanics definition of a, the CRLS model shows that scan overlap pervades AFM wear trials even under low loads. Such findings indicate that simply counting the number of scans (N(scans)) in an experiment underestimates the full history conveyed to the surface by the tip and translates into an error in the actual extent to which a region on the surface is contacted. Utilizing the CRLS method described here provides an approach to account for image scan history accurately and to predict the extent of surface wear. This general model also has implications for any AFM measurement where one wishes to correlate scan-dependent history to image properties as well as feature resolution in scanned

  16. Cloud top structure of Venus revealed by Subaru/COMICS mid-infrared images

    NASA Astrophysics Data System (ADS)

    Sato, T. M.; Sagawa, H.; Kouyama, T.; Mitsuyama, K.; Satoh, T.; Ohtsuki, S.; Ueno, M.; Kasaba, Y.; Nakamura, M.; Imamura, T.

    2014-11-01

    We have investigated the cloud top structure of Venus by analyzing ground-based images taken at the mid-infrared wavelengths of 8.66 μm and 11.34 μm. Venus at a solar phase angle of ∼90°, with the morning terminator in view, was observed by the Cooled Mid-Infrared Camera and Spectrometer (COMICS), mounted on the 8.2-m Subaru Telescope, during the period October 25-29, 2007. The disk-averaged brightness temperatures for the observation period are ∼230 K and ∼238 K at 8.66 μm and 11.34 μm, respectively. The obtained images with good signal-to-noise ratio and with high spatial resolution (∼200 km at the sub-observer point) provide several important findings. First, we present observational evidence, for the first time, of the possibility that the westward rotation of the polar features (the hot polar spots and the surrounding cold collars) is synchronized between the northern and southern hemispheres. Second, after high-pass filtering, the images reveal that streaks and mottled and patchy patterns are distributed over the entire disk, with typical amplitudes of ∼0.5 K, and vary from day to day. The detected features, some of which are similar to those seen in past UV images, result from inhomogeneities of both the temperature and the cloud top altitude. Third, the equatorial center-to-limb variations of brightness temperatures have a systematic day-night asymmetry, except those on October 25, that the dayside brightness temperatures are higher than the nightside brightness temperatures by 0-4 K under the same viewing geometry. Such asymmetry would be caused by the propagation of the migrating semidiurnal tide. Finally, by applying the lapse rates deduced from previous studies, we demonstrate that the equatorial center-to-limb curves in the two spectral channels give access to two parameters: the cloud scale height H and the cloud top altitude zc. The acceptable models for data on October 25 are obtained at H = 2.4-4.3 km and zc = 66-69 km; this supports

  17. An AFM-based pit-measuring method for indirect measurements of cell-surface membrane vesicles

    SciTech Connect

    Zhang, Xiaojun; Chen, Yuan; Chen, Yong

    2014-03-28

    Highlights: • Air drying induced the transformation of cell-surface membrane vesicles into pits. • An AFM-based pit-measuring method was developed to measure cell-surface vesicles. • Our method detected at least two populations of cell-surface membrane vesicles. - Abstract: Circulating membrane vesicles, which are shed from many cell types, have multiple functions and have been correlated with many diseases. Although circulating membrane vesicles have been extensively characterized, the status of cell-surface membrane vesicles prior to their release is less understood due to the lack of effective measurement methods. Recently, as a powerful, micro- or nano-scale imaging tool, atomic force microscopy (AFM) has been applied in measuring circulating membrane vesicles. However, it seems very difficult for AFM to directly image/identify and measure cell-bound membrane vesicles due to the similarity of surface morphology between membrane vesicles and cell surfaces. Therefore, until now no AFM studies on cell-surface membrane vesicles have been reported. In this study, we found that air drying can induce the transformation of most cell-surface membrane vesicles into pits that are more readily detectable by AFM. Based on this, we developed an AFM-based pit-measuring method and, for the first time, used AFM to indirectly measure cell-surface membrane vesicles on cultured endothelial cells. Using this approach, we observed and quantitatively measured at least two populations of cell-surface membrane vesicles, a nanoscale population (<500 nm in diameter peaking at ∼250 nm) and a microscale population (from 500 nm to ∼2 μm peaking at ∼0.8 μm), whereas confocal microscopy only detected the microscale population. The AFM-based pit-measuring method is potentially useful for studying cell-surface membrane vesicles and for investigating the mechanisms of membrane vesicle formation/release.

  18. Earthquakes' local site effects in Christchurch revealed by Cosmo-Skymed and Envisat radar images

    NASA Astrophysics Data System (ADS)

    Closson, Damien; Abou Karaki, N.; Pasquali, P.; Holecz, P.; Riccardi, P.; Milisavljevic, N.; Bouaraba, A.

    2012-04-01

    In September 4th, 2010, and February 22nd, 2011, a 7.1 and 6.3 earthquakes have strongly affected the city of Chirstchurch, New Zealand. The hypocenters were located 40 km westwards and 10 km southwards respectively. The shallow depths of the epicenter were estimated to 10 and 5 km. The deformation field associated with the first event was mapped with Envisat data (C band). One month later, the Italian Space Agency started the surveillance of the city of Chirstchurch. Cosmo-Skymed images (X band) in spotlight mode (pixel of about one meter) were collected from November onwards with a minimum of four days between repeated acquisitions. In that framework, it was possible to study with great accuracy and precision the ground deformations caused by the aftershock that took place on February 22nd, 2011. One image was acquired three days before and another scene one day after. Moreover, two days after this event that killed 181 persons; an aerial survey was performed leading to an orthophoto of the city having a pixel size of 20 cm. An interferometric processing was applied to the Cosmo-Skymed scenes. The interferogram revealed the fringes of the major displacement with a precision of 1.5 cm (half of the wavelenght). At closer look, the general dislocation pattern shown numerous irregularities that have been interpreted as local sites effects. One of the most obvious evidence of local site effects can be seen in the kilometric abandoned landfill of Barwood. Field observations and interviews of local people support the observations regarding the limits of specific zones in the urban area. This research is still in progress and comparisons are currently performed with other earthquakes in Chili and Turkey. This work suggests that an independent method could provide new original data in the frame of the mapping of earthquakes local sites effects.

  19. 3-D Radar Imaging Reveals Deep Structures and Buried Craters Within the Martian Polar Caps

    NASA Astrophysics Data System (ADS)

    Putzig, N. E.; Foss, F. J., II; Campbell, B. A.; Phillips, R. J.; Smith, I. B.

    2015-12-01

    We use Shallow Radar (SHARAD) observations on thousands of orbital passes by the Mars Reconnaissance Orbiter to produce fully imaged 3-D data volumes encompassing both polar ice caps of Mars. Greatly clarifying the view of subsurface features, a completed volume for Planum Boreum provides new constraints on the nature and timing of emplacement of the northern polar deposits and their relationship to climate. The standard method of mapping subsurface features with single-pass 2-D radargrams has been very fruitful (see Brothers et al. 2015, JGR 120 in press, and references therein), but a full assessment of internal structures has been hindered by interfering off-nadir echoes from spiral troughs and other variable topography prevalent on both caps. By assembling the SHARAD radargrams into a volume and applying a 3-D imaging process (migration) borrowed from seismic processing techniques, we enhance the signal-to-noise ratio while repositioning the echoes to their proper locations, thereby unraveling the interference. As part of the process, we correct ionospheric distortions and delays of the radar echoes (Campbell et al. 2014, IEEE GRSL 11 #3). Interfaces painstakingly mapped in radargrams (e.g., the basal-unit surface, a buried chasma) are clearly visible in the 3-D volume, and new features are revealed. Structures may now be mapped through trough-rich regions, including a widespread sequence that provides corroborative evidence of recent ice ages (Smith et al. 2015, LPSC XLVI #2574). Distinctive radar signatures associated with known, partially buried craters also occur elsewhere in the volume but without surface expression. Presumably, these are fully buried craters that may provide a new means to estimate the age of the deposits. Preliminary work for Planum Australe demonstrates that the 3-D processing currently underway will illuminate deep structures that are broadly obfuscated in 2-D radargrams by a shallow scatterer (Campbell et al. 2015, LPSC XLVI #2366).

  20. Dynamic auxin transport patterns preceding vein formation revealed by live-imaging of Arabidopsis leaf primordia

    PubMed Central

    Marcos, Danielle; Berleth, Thomas

    2014-01-01

    Self-regulatory patterning mechanisms capable of generating biologically meaningful, yet unpredictable cellular patterns offer unique opportunities for obtaining mathematical descriptions of underlying patterning systems properties. The networks of higher-order veins in leaf primordia constitute such a self-regulatory system. During the formation of higher-order veins, vascular precursors are selected from a homogenous field of subepidermal cells in unpredictable positions to eventually connect in complex cellular networks. Auxin transport routes have been implicated in this selection process, but understanding of their role in vascular patterning has been limited by our inability to monitor early auxin transport dynamics in vivo. Here we describe a live-imaging system in emerging Arabidopsis thaliana leaves that uses a PIN1:GFP reporter to visualize auxin transport routes and an Athb8:YFP reporter as a marker for vascular commitment. Live-imaging revealed common features initiating the formation of all higher-order veins. The formation of broad PIN1 expression domains is followed by their restriction, leading to sustained, elevated PIN1 expression in incipient procambial cells files, which then express Athb8. Higher-order PIN1 expression domains (hPEDs) are initiated as freely ending domains that extend toward each other and sometimes fuse with them, creating connected domains. During the restriction and specification phase, cells in wider hPEDs are partitioned into vascular and non-vascular fates: Central cells acquire a coordinated cell axis and express elevated PIN1 levels as well as the pre-procambial marker Athb8, while edge cells downregulate PIN1 and remain isodiametric. The dynamic nature of the early selection process is underscored by the instability of early hPEDs, which can result in dramatic changes in vascular network architecture prior to Athb8 expression, which is correlated with the promotion onto vascular cell fate. PMID:24966861

  1. Roughness of the mantle transition zone discontinuities revealed by high-resolution wavefield imaging

    NASA Astrophysics Data System (ADS)

    Wang, Yinzhi; Pavlis, Gary L.

    2016-09-01

    We processed two independent data sets: 2,458,973 three-component seismograms from all EarthScope Transportable Array (USArray) stations and 141,080 pairs of high-quality receiver functions from the EarthScope Automated Receiver Survey using the generalized iterative deconvolution method and shaped the output with a 0.1 Hz Ricker wavelet. We used these data as input to our 3-D plane wave migration method to produce an image volume of P to S scattering surfaces under all of the lower 48 states. Model simulations show that compared to the widely used common conversion point stacking method, our method is capable of resolving not only dipping discontinuities but also subtler details of amplitude and topography variations at scales near the diffraction limit. Maps of attributes derived from these discontinuities reveal several previously unobserved features of the 410 and 660 discontinuities (d410 and d660). Topography with many tens of kilometers is resolved at a range of scales. Additionally, we observed large variations of amplitude on the radial component and in the radial to transverse amplitude ratio that correlate with inferred variations in discontinuity topography. We argue that this combination of observations can be explained by roughness at a range of scales. The structural fabric we imaged is preferentially aligned orthogonal to the Farallon-North American relative motion. Two regions we infer to have exceptional roughness show spatial correlation with locations where tomography models indicate that the subducted slab is passing through the transition zone. We suggest that these rough regions are indicators of vertical mantle flows through the transition zone.

  2. Analysis of neurogenesis during experimental autoimmune encephalomyelitis reveals pitfalls of bioluminescence imaging.

    PubMed

    Ayzenberg, Ilya; Schlevogt, Sibylle; Metzdorf, Judith; Stahlke, Sarah; Pedreitturia, Xiomara; Hunfeld, Anika; Couillard-Despres, Sebastien; Kleiter, Ingo

    2015-01-01

    Bioluminescence imaging is a sensitive approach for longitudinal neuroimaging. Transgenic mice expressing luciferase under the promoter of doublecortin (DCX-luc), a specific marker of neuronal progenitor cells (NPC), allow monitoring of neurogenesis in living mice. Since the extent and time course of neurogenesis during autoimmune brain inflammation are controversial, we investigated neurogenesis in MOG-peptide induced experimental allergic encephalomyelitis (EAE) using DCX-luc reporter mice. We observed a marked, 2- to 4-fold increase of the bioluminescence signal intensity 10 days after EAE induction and a gradual decline 1-2 weeks thereafter. In contrast, immunostaining for DCX revealed no differences between EAE and control mice 2 and 4 weeks after immunization in zones of adult murine neurogenesis such as the dentate gyrus. Ex vivo bioluminescence imaging showed similar luciferase expression in brain homogenates of EAE and control animals. Apart from complete immunization including MOG-peptide also incomplete immunization with complete Freund´s adjuvant and pertussis toxin resulted in a rapid increase of the in vivo bioluminescence signal. Blood-brain barrier (BBB) leakage was demonstrated 10 days after both complete and incomplete immunization and might explain the increased bioluminescence signal in vivo. We conclude, that acute autoimmune inflammation in EAE does not alter neurogenesis, at least at the stage of DCX-expressing NPC. Effects of immunization on the BBB integrity must be considered when luciferase is used as a reporter within the CNS during the active stage of EAE. Models with stable CNS-restricted luciferase expression could serve as technically convenient way to evaluate BBB integrity in a longitudinal manner.

  3. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.

    PubMed

    Boettiger, Alistair N; Bintu, Bogdan; Moffitt, Jeffrey R; Wang, Siyuan; Beliveau, Brian J; Fudenberg, Geoffrey; Imakaev, Maxim; Mirny, Leonid A; Wu, Chao-ting; Zhuang, Xiaowei

    2016-01-21

    Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around individual nucleosomes to segregation of whole chromosomes into distinct territories. At the intermediate scale of kilobases to megabases, which encompasses the sizes of genes, gene clusters and regulatory domains, the three-dimensional (3D) organization of DNA is implicated in multiple gene regulatory mechanisms, but understanding this organization remains a challenge. At this scale, the genome is partitioned into domains of different epigenetic states that are essential for regulating gene expression. Here we investigate the 3D organization of chromatin in different epigenetic states using super-resolution imaging. We classified genomic domains in Drosophila cells into transcriptionally active, inactive or Polycomb-repressed states, and observed distinct chromatin organizations for each state. All three types of chromatin domains exhibit power-law scaling between their physical sizes in 3D and their domain lengths, but each type has a distinct scaling exponent. Polycomb-repressed domains show the densest packing and most intriguing chromatin folding behaviour, in which chromatin packing density increases with domain length. Distinct from the self-similar organization displayed by transcriptionally active and inactive chromatin, the Polycomb-repressed domains are characterized by a high degree of chromatin intermixing within the domain. Moreover, compared to inactive domains, Polycomb-repressed domains spatially exclude neighbouring active chromatin to a much stronger degree. Computational modelling and knockdown experiments suggest that reversible chromatin interactions mediated by Polycomb-group proteins play an important role in these unique packaging properties of the repressed chromatin. Taken together, our super-resolution images reveal distinct chromatin packaging for different epigenetic states at the kilobase-to-megabase scale, a length scale that is directly

  4. Functional magnetic resonance imaging adaptation reveals a noncategorical representation of hue in early visual cortex

    PubMed Central

    Persichetti, Andrew S.; Thompson-Schill, Sharon L.; Butt, Omar H.; Brainard, David H.; Aguirre, Geoffrey K.

    2015-01-01

    Color names divide the fine-grained gamut of color percepts into discrete categories. A categorical transition must occur somewhere between the initial encoding of the continuous spectrum of light by the cones and the verbal report of the name of a color stimulus. Here, we used a functional magnetic resonance imaging (fMRI) adaptation experiment to examine the representation of hue in the early visual cortex. Our stimuli varied in hue between blue and green. We found in the early visual areas (V1, V2/3, and hV4) a smoothly increasing recovery from adaptation with increasing hue distance between adjacent stimuli during both passive viewing (Experiment 1) and active categorization (Experiment 2). We examined the form of the adaptation effect and found no evidence that a categorical representation mediates the release from adaptation for stimuli that cross the blue–green color boundary. Examination of the direct effect of stimulus hue on the fMRI response did, however, reveal an enhanced response to stimuli near the blue–green category border. This was largest in hV4 and when subjects were engaged in active categorization of the stimulus hue. In contrast with a recent report from another laboratory (Bird, Berens, Horner, & Franklin, 2014), we found no evidence for a categorical representation of color in the middle frontal gyrus. A post hoc whole-brain analysis, however, revealed several regions in the frontal cortex with a categorical effect in the adaptation response. Overall, our results support the idea that the representation of color in the early visual cortex is primarily fine grained and does not reflect color categories. PMID:26024465

  5. BOREAS AFM-6 Boundary Layer Height Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from National Oceanic and Atmospheric Adminsitration/Environment Technology Laboratory (NOAA/ETL) operated a 915-MHz wind/Radio Acoustic Sounding System (RASS) profiler system in the Southern Study Area (SSA) near the Old Jack Pine (OJP) site. This data set provides boundary layer height information over the site. The data were collected from 21 May 1994 to 20 Sep 1994 and are stored in tabular ASCII files. The boundary layer height data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  6. BOREAS AFM-06 Mean Wind Profile Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Administration/Environment Technology Laboratory (NOAA/ETL) operated a 915-MHz wind/Radio Acoustic Sounding System (RASS) profiler system in the Southern Study Area (SSA) near the Old Jack Pine (OJP) tower from 21 May 1994 to 20 Sep 1994. The data set provides wind profiles at 38 heights, containing the variables of wind speed; wind direction; and the u-, v-, and w-components of the total wind. The data are stored in tabular ASCII files. The mean wind profile data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  7. BOREAS AFM-06 Mean Temperature Profile Data

    NASA Technical Reports Server (NTRS)

    Wilczak, James; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-6 team from the National Oceanic and Atmospheric Adminsitration/Environment Technology Laboratory (NOAA/ETL) operated a 915-MHz wind/Radio Acoustic Sounding System (RASS) profiler system in the Southern Study Area (SSA) near the Old Jack Pine (OJP) tower from 21 May 1994 to 20 Sep 1994. The data set provides temperature profiles at 15 heights, containing the variables of virtual temperature, vertical velocity, the speed of sound, and w-bar. The data are stored in tabular ASCII files. The mean temperature profile data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  8. Single-Molecule Imaging Reveals the Activation Dynamics of Intracellular Protein Smad3 on Cell Membrane

    NASA Astrophysics Data System (ADS)

    Li, Nan; Yang, Yong; He, Kangmin; Zhang, Fayun; Zhao, Libo; Zhou, Wei; Yuan, Jinghe; Liang, Wei; Fang, Xiaohong

    2016-09-01

    Smad3 is an intracellular protein that plays a key role in propagating transforming growth factor β (TGF-β) signals from cell membrane to nucleus. However whether the transient process of Smad3 activation occurs on cell membrane and how it is regulated remains elusive. Using advanced live-cell single-molecule fluorescence microscopy to image and track fluorescent protein-labeled Smad3, we observed and quantified, for the first time, the dynamics of individual Smad3 molecules docking to and activation on the cell membrane. It was found that Smad3 docked to cell membrane in both unstimulated and stimulated cells, but with different diffusion rates and dissociation kinetics. The change in its membrane docking dynamics can be used to study the activation of Smad3. Our results reveal that Smad3 binds with type I TGF-β receptor (TRI) even in unstimulated cells. Its activation is regulated by TRI phosphorylation but independent of receptor endocytosis. This study offers new information on TGF-β/Smad signaling, as well as a new approach to investigate the activation of intracellular signaling proteins for a better understanding of their functions in signal transduction.

  9. Electrical brain imaging reveals spatio-temporal dynamics of timbre perception in humans.

    PubMed

    Meyer, Martin; Baumann, Simon; Jancke, Lutz

    2006-10-01

    Timbre is a major attribute of sound perception and a key feature for the identification of sound quality. Here, we present event-related brain potentials (ERPs) obtained from sixteen healthy individuals while they discriminated complex instrumental tones (piano, trumpet, and violin) or simple sine wave tones that lack the principal features of timbre. Data analysis yielded enhanced N1 and P2 responses to instrumental tones relative to sine wave tones. Furthermore, we applied an electrical brain imaging approach using low-resolution electromagnetic tomography (LORETA) to estimate the neural sources of N1/P2 responses. Separate significance tests of instrumental vs. sine wave tones for N1 and P2 revealed distinct regions as principally governing timbre perception. In an initial stage (N1), timbre perception recruits left and right (peri-)auditory fields with an activity maximum over the right posterior Sylvian fissure (SF) and the posterior cingulate (PCC) territory. In the subsequent stage (P2), we uncovered enhanced activity in the vicinity of the entire cingulate gyrus. The involvement of extra-auditory areas in timbre perception may imply the presence of a highly associative processing level which might be generally related to musical sensations and integrates widespread medial areas of the human cortex. In summary, our results demonstrate spatio-temporally distinct stages in timbre perception which not only involve bilateral parts of the peri-auditory cortex but also medially situated regions of the human brain associated with emotional and auditory imagery functions.

  10. Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation

    PubMed Central

    Muramoto, Tetsuya; Cannon, Danielle; Gierliński, Marek; Corrigan, Adam; Barton, Geoffrey J.; Chubb, Jonathan R.

    2012-01-01

    Transcription of genes can be discontinuous, occurring in pulses or bursts. It is not clear how properties of transcriptional pulses vary between different genes. We compared the pulsing of five housekeeping and five developmentally induced genes by direct imaging of single gene transcriptional events in individual living Dictyostelium cells. Each gene displayed its own transcriptional signature, differing in probability of firing and pulse duration, frequency, and intensity. In contrast to the prevailing view from both prokaryotes and eukaryotes that transcription displays binary behavior, strongly expressed housekeeping genes altered the magnitude of their transcriptional pulses during development. These nonbinary “tunable” responses may be better suited than stochastic switch behavior for housekeeping functions. Analysis of RNA synthesis kinetics using fluorescence recovery after photobleaching implied modulation of housekeeping-gene pulse strength occurs at the level of transcription initiation rather than elongation. In addition, disparities between single cell and population measures of transcript production suggested differences in RNA stability between gene classes. Analysis of stability using RNAseq revealed no major global differences in stability between developmental and housekeeping transcripts, although strongly induced RNAs showed unusually rapid decay, indicating tight regulation of expression. PMID:22529358

  11. Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation.

    PubMed

    Muramoto, Tetsuya; Cannon, Danielle; Gierlinski, Marek; Corrigan, Adam; Barton, Geoffrey J; Chubb, Jonathan R

    2012-05-08

    Transcription of genes can be discontinuous, occurring in pulses or bursts. It is not clear how properties of transcriptional pulses vary between different genes. We compared the pulsing of five housekeeping and five developmentally induced genes by direct imaging of single gene transcriptional events in individual living Dictyostelium cells. Each gene displayed its own transcriptional signature, differing in probability of firing and pulse duration, frequency, and intensity. In contrast to the prevailing view from both prokaryotes and eukaryotes that transcription displays binary behavior, strongly expressed housekeeping genes altered the magnitude of their transcriptional pulses during development. These nonbinary "tunable" responses may be better suited than stochastic switch behavior for housekeeping functions. Analysis of RNA synthesis kinetics using fluorescence recovery after photobleaching implied modulation of housekeeping-gene pulse strength occurs at the level of transcription initiation rather than elongation. In addition, disparities between single cell and population measures of transcript production suggested differences in RNA stability between gene classes. Analysis of stability using RNAseq revealed no major global differences in stability between developmental and housekeeping transcripts, although strongly induced RNAs showed unusually rapid decay, indicating tight regulation of expression.

  12. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging.

    PubMed

    Yan, Jing; Sharo, Andrew G; Stone, Howard A; Wingreen, Ned S; Bassler, Bonnie L

    2016-09-06

    Biofilms are surface-associated bacterial communities that are crucial in nature and during infection. Despite extensive work to identify biofilm components and to discover how they are regulated, little is known about biofilm structure at the level of individual cells. Here, we use state-of-the-art microscopy techniques to enable live single-cell resolution imaging of a Vibrio cholerae biofilm as it develops from one single founder cell to a mature biofilm of 10,000 cells, and to discover the forces underpinning the architectural evolution. Mutagenesis, matrix labeling, and simulations demonstrate that surface adhesion-mediated compression causes V. cholerae biofilms to transition from a 2D branched morphology to a dense, ordered 3D cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture in V. cholerae biofilms, and this growth pattern is controlled by a single gene, rbmA Competition analyses reveal that the dense growth mode has the advantage of providing the biofilm with superior mechanical properties. Our single-cell technology can broadly link genes to biofilm fine structure and provides a route to assessing cell-to-cell heterogeneity in response to external stimuli.

  13. A single-cell imaging screen reveals multiple effects of secreted small molecules on bacteria

    PubMed Central

    Salje, Jeanne

    2014-01-01

    Bacteria cells exist in close proximity to other cells of both the same and different species. Bacteria secrete a large number of different chemical species, and the local concentrations of these compounds at the surfaces of nearby cells may reach very high levels. It is fascinating to imagine how individual cells might sense and respond to the complex mix of signals at their surface. However, it is difficult to measure exactly what the local environmental composition looks like, or what the effects of individual compounds on nearby cells are. Here, an electron microscopy imaging screen was designed that would detect morphological changes induced by secreted small molecules. This differs from conventional approaches by detecting structural changes in individual cells rather than gene expression or growth rate changes at the population level. For example, one of the changes detected here was an increase in outer membrane vesicle production, which does not necessarily correspond to a change in gene expression. This initial study focussed on Pseudomonas aeruginosa, Escherichia coli, and Burkholderia dolosa, and revealed an intriguing range of effects of secreted small molecules on cells both within and between species. PMID:24910069

  14. Single-Molecule Imaging Reveals the Activation Dynamics of Intracellular Protein Smad3 on Cell Membrane

    PubMed Central

    Li, Nan; Yang, Yong; He, Kangmin; Zhang, Fayun; Zhao, Libo; Zhou, Wei; Yuan, Jinghe; Liang, Wei; Fang, Xiaohong

    2016-01-01

    Smad3 is an intracellular protein that plays a key role in propagating transforming growth factor β (TGF-β) signals from cell membrane to nucleus. However whether the transient process of Smad3 activation occurs on cell membrane and how it is regulated remains elusive. Using advanced live-cell single-molecule fluorescence microscopy to image and track fluorescent protein-labeled Smad3, we observed and quantified, for the first time, the dynamics of individual Smad3 molecules docking to and activation on the cell membrane. It was found that Smad3 docked to cell membrane in both unstimulated and stimulated cells, but with different diffusion rates and dissociation kinetics. The change in its membrane docking dynamics can be used to study the activation of Smad3. Our results reveal that Smad3 binds with type I TGF-β receptor (TRI) even in unstimulated cells. Its activation is regulated by TRI phosphorylation but independent of receptor endocytosis. This study offers new information on TGF-β/Smad signaling, as well as a new approach to investigate the activation of intracellular signaling proteins for a better understanding of their functions in signal transduction. PMID:27641076

  15. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition

    PubMed Central

    Visnapuu, Mari-Liis; Greene, Eric C.

    2009-01-01

    Here we use single-molecule imaging to determine coarse-grained intrinsic energy landscapes for nucleosome deposition on model DNA substrates. Our results reveal distributions that are correlated with recent in silico predictions, reinforcing the hypothesis that DNA contains some intrinsic positioning information. We also show that cis-regulatory sequences in human DNA coincide with peaks in the intrinsic landscape, whereas valleys correspond to non-regulatory regions, and we present evidence arguing that nucleosome deposition in vertebrates is influenced by factors not accounted for by current theory. Finally, we demonstrate that intrinsic landscapes of nucleosomes containing the centromere-specific variant CenH3 are correlated with patterns observed for canonical nucleosomes, arguing that CenH3 does not alter sequence preferences of centromeric nucleosomes. However, the non-histone protein Scm3 alters the intrinsic landscape of CenH3-containing nucleosomes, enabling them to overcome the otherwise exclusionary effects of poly(dA–dT) tracts, which are enriched in centromeric DNA. PMID:19734899

  16. In Vivo Imaging Reveals Composite Coding for Diagonal Motion in the Drosophila Visual System

    PubMed Central

    Zhou, Wei; Chang, Jin

    2016-01-01

    Understanding information coding is important for resolving the functions of visual neural circuits. The motion vision system is a classic model for studying information coding as it contains a concise and complete information-processing circuit. In Drosophila, the axon terminals of motion-detection neurons (T4 and T5) project to the lobula plate, which comprises four regions that respond to the four cardinal directions of motion. The lobula plate thus represents a topographic map on a transverse plane. This enables us to study the coding of diagonal motion by investigating its response pattern. By using in vivo two-photon calcium imaging, we found that the axon terminals of T4 and T5 cells in the lobula plate were activated during diagonal motion. Further experiments showed that the response to diagonal motion is distributed over the following two regions compared to the cardinal directions of motion—a diagonal motion selective response region and a non-selective response region—which overlap with the response regions of the two vector-correlated cardinal directions of motion. Interestingly, the sizes of the non-selective response regions are linearly correlated with the angle of the diagonal motion. These results revealed that the Drosophila visual system employs a composite coding for diagonal motion that includes both independent coding and vector decomposition coding. PMID:27695103

  17. Real-time imaging of glutamate clearance reveals normal striatal uptake in Huntington disease mouse models.

    PubMed

    Parsons, Matthew P; Vanni, Matthieu P; Woodard, Cameron L; Kang, Rujun; Murphy, Timothy H; Raymond, Lynn A

    2016-04-07

    It has become well accepted that Huntington disease (HD) is associated with impaired glutamate uptake, resulting in a prolonged time-course of extracellular glutamate that contributes to excitotoxicity. However, the data supporting this view come largely from work in synaptosomes, which may overrepresent nerve-terminal uptake over astrocytic uptake. Here, we quantify real-time glutamate dynamics in HD mouse models by high-speed imaging of an intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) and electrophysiological recordings of synaptically activated transporter currents in astrocytes. These techniques reveal a disconnect between the results obtained in synaptosomes and those in situ. Exogenous glutamate uptake is impaired in synaptosomes, whereas real-time measures of glutamate clearance in the HD striatum are normal or even accelerated, particularly in the aggressive R6/2 model. Our results highlight the importance of quantifying glutamate dynamics under endogenous release conditions, and suggest that the widely cited uptake impairment in HD does not contribute to pathogenesis.

  18. Real-time imaging of glutamate clearance reveals normal striatal uptake in Huntington disease mouse models

    PubMed Central

    Parsons, Matthew P.; Vanni, Matthieu P.; Woodard, Cameron L.; Kang, Rujun; Murphy, Timothy H.; Raymond, Lynn A.

    2016-01-01

    It has become well accepted that Huntington disease (HD) is associated with impaired glutamate uptake, resulting in a prolonged time-course of extracellular glutamate that contributes to excitotoxicity. However, the data supporting this view come largely from work in synaptosomes, which may overrepresent nerve-terminal uptake over astrocytic uptake. Here, we quantify real-time glutamate dynamics in HD mouse models by high-speed imaging of an intensity-based glutamate-sensing fluorescent reporter (iGluSnFR) and electrophysiological recordings of synaptically activated transporter currents in astrocytes. These techniques reveal a disconnect between the results obtained in synaptosomes and those in situ. Exogenous glutamate uptake is impaired in synaptosomes, whereas real-time measures of glutamate clearance in the HD striatum are normal or even accelerated, particularly in the aggressive R6/2 model. Our results highlight the importance of quantifying glutamate dynamics under endogenous release conditions, and suggest that the widely cited uptake impairment in HD does not contribute to pathogenesis. PMID:27052848

  19. A new engineering approach to reveal correlation of physiological change and spontaneous expression from video images

    NASA Astrophysics Data System (ADS)

    Yang, Fenglei; Hu, Sijung; Ma, Xiaoyun; Hassan, Harnani; Wei, Dongqing

    2015-03-01

    Spontaneous expression is associated with physiological states, i.e., heart rate, respiration, oxygen saturation (SpO2%), and heart rate variability (HRV). There have yet not sufficient efforts to explore correlation of physiological change and spontaneous expression. This study aims to study how spontaneous expression is associated with physiological changes with an approved protocol or through the videos provided from Denver Intensity of Spontaneous Facial Action Database. Not like a posed expression, motion artefact in spontaneous expression is one of evitable challenges to be overcome in the study. To obtain a physiological signs from a region of interest (ROI), a new engineering approach is being developed with an artefact-reduction method consolidated 3D active appearance model (AAM) based track, affine transformation based alignment with opto-physiological mode based imaging photoplethysmography. Also, a statistical association spaces is being used to interpret correlation of spontaneous expressions and physiological states including their probability densities by means of Gaussian Mixture Model. The present work is revealing a new avenue of study associations of spontaneous expressions and physiological states with its prospect of applications on physiological and psychological assessment.

  20. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging

    PubMed Central

    Yan, Jing; Sharo, Andrew G.; Stone, Howard A.; Wingreen, Ned S.; Bassler, Bonnie L.

    2016-01-01

    Biofilms are surface-associated bacterial communities that are crucial in nature and during infection. Despite extensive work to identify biofilm components and to discover how they are regulated, little is known about biofilm structure at the level of individual cells. Here, we use state-of-the-art microscopy techniques to enable live single-cell resolution imaging of a Vibrio cholerae biofilm as it develops from one single founder cell to a mature biofilm of 10,000 cells, and to discover the forces underpinning the architectural evolution. Mutagenesis, matrix labeling, and simulations demonstrate that surface adhesion-mediated compression causes V. cholerae biofilms to transition from a 2D branched morphology to a dense, ordered 3D cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture in V. cholerae biofilms, and this growth pattern is controlled by a single gene, rbmA. Competition analyses reveal that the dense growth mode has the advantage of providing the biofilm with superior mechanical properties. Our single-cell technology can broadly link genes to biofilm fine structure and provides a route to assessing cell-to-cell heterogeneity in response to external stimuli. PMID:27555592

  1. The electromagnetic environment of Magnetic Resonance Imaging systems. Occupational exposure assessment reveals RF harmonics

    NASA Astrophysics Data System (ADS)

    Gourzoulidis, G.; Karabetsos, E.; Skamnakis, N.; Kappas, C.; Theodorou, K.; Tsougos, I.; Maris, T. G.

    2015-09-01

    Magnetic Resonance Imaging (MRI) systems played a crucial role in the postponement of the former occupational electromagnetic fields (EMF) European Directive (2004/40/EC) and in the formation of the latest exposure limits adopted in the new one (2013/35/EU). Moreover, the complex MRI environment will be finally excluded from the implementation of the new occupational limits, leading to an increased demand for Occupational Health and Safety (OHS) surveillance. The gradient function of MRI systems and the application of the RF excitation frequency result in low and high frequency exposures, respectively. This electromagnetic field exposure, in combination with the increased static magnetic field exposure, makes the MRI environment a unique case of combined EMF exposure. The electromagnetic field levels in close proximity of different MRI systems have been assessed at various frequencies. Quality Assurance (QA) & safety issues were also faced. Preliminary results show initial compliance with the forthcoming limits in each different frequency band, but also revealed peculiar RF harmonic components, of no safety concern, to the whole range detected (20-1000MHz). Further work is needed in order to clarify their origin and characteristics.

  2. Computational imaging reveals shape differences between normal and malignant prostates on MRI

    PubMed Central

    Rusu, Mirabela; Purysko, Andrei S.; Verma, Sadhna; Kiechle, Jonathan; Gollamudi, Jay; Ghose, Soumya; Herrmann, Karin; Gulani, Vikas; Paspulati, Raj; Ponsky, Lee; Böhm, Maret; Haynes, Anne-Maree; Moses, Daniel; Shnier, Ron; Delprado, Warick; Thompson, James; Stricker, Phillip; Madabhushi, Anant

    2017-01-01

    We seek to characterize differences in the shape of the prostate and the central gland (combined central and transitional zones) between men with biopsy confirmed prostate cancer and men who were identified as not having prostate cancer either on account of a negative biopsy or had pelvic imaging done for a non-prostate malignancy. T2w MRI from 70 men were acquired at three institutions. The cancer positive group (PCa+) comprised 35 biopsy positive (Bx+) subjects from three institutions (Gleason scores: 6–9, Stage: T1–T3). The negative group (PCa−) combined 24 biopsy negative (Bx−) from two institutions and 11 subjects diagnosed with rectal cancer but with no clinical or MRI indications of prostate cancer (Cl−). The boundaries of the prostate and central gland were delineated on T2w MRI by two expert raters and were used to construct statistical shape atlases for the PCa+, Bx− and Cl− prostates. An atlas comparison was performed via per-voxel statistical tests to localize shape differences (significance assessed at p < 0.05). The atlas comparison revealed central gland hypertrophy in the Bx− subpopulation, resulting in significant volume and posterior side shape differences relative to PCa+ group. Significant differences in the corresponding prostate shapes were noted at the apex when comparing the Cl− and PCa+ prostates. PMID:28145532

  3. Histological Image Feature Mining Reveals Emergent Diagnostic Properties for Renal Cancer.

    PubMed

    Kothari, Sonal; Phan, John H; Young, Andrew N; Wang, May D

    2011-11-01

    Computer-aided histological image classification systems are important for making objective and timely cancer diagnostic decisions. These systems use combinations of image features that quantify a variety of image properties. Because researchers tend to validate their diagnostic systems on specific cancer endpoints, it is difficult to predict which image features will perform well given a new cancer endpoint. In this paper, we define a comprehensive set of common image features (consisting of 12 distinct feature subsets) that quantify a variety of image properties. We use a data-mining approach to determine which feature subsets and image properties emerge as part of an "optimal" diagnostic model when applied to specific cancer endpoints. Our goal is to assess the performance of such comprehensive image feature sets for application to a wide variety of diagnostic problems. We perform this study on 12 endpoints including 6 renal tumor subtype endpoints and 6 renal cancer grade endpoints. Keywords-histology, image mining, computer-aided diagnosis.

  4. Fast calcium and voltage-sensitive dye imaging in enteric neurones reveal calcium peaks associated with single action potential discharge.

    PubMed

    Michel, K; Michaelis, M; Mazzuoli, G; Mueller, K; Vanden Berghe, P; Schemann, M

    2011-12-15

    Slow changes in [Ca(2+)](i) reflect increased neuronal activity. Our study demonstrates that single-trial fast [Ca(2+)](i) imaging (≥200 Hz sampling rate) revealed peaks each of which are associated with single spike discharge recorded by consecutive voltage-sensitive dye (VSD) imaging in enteric neurones and nerve fibres. Fast [Ca(2+)](i) imaging also revealed subthreshold fast excitatory postsynaptic potentials. Nicotine-evoked [Ca(2+)](i) peaks were reduced by -conotoxin and blocked by ruthenium red or tetrodotoxin. Fast [Ca(2+)](i) imaging can be used to directly record single action potentials in enteric neurones. [Ca(2+)](i) peaks required opening of voltage-gated sodium and calcium channels as well as Ca(2+) release from intracellular stores.

  5. Brain tumor classification using AFM in combination with data mining techniques.

    PubMed

    Huml, Marlene; Silye, René; Zauner, Gerald; Hutterer, Stephan; Schilcher, Kurt

    2013-01-01

    Although classification of astrocytic tumors is standardized by the WHO grading system, which is mainly based on microscopy-derived, histomorphological features, there is great interobserver variability. The main causes are thought to be the complexity of morphological details varying from tumor to tumor and from patient to patient, variations in the technical histopathological procedures like staining protocols, and finally the individual experience of the diagnosing pathologist. Thus, to raise astrocytoma grading to a more objective standard, this paper proposes a methodology based on atomic force microscopy (AFM) derived images made from histopathological samples in combination with data mining techniques. By comparing AFM images with corresponding light microscopy images of the same area, the progressive formation of cavities due to cell necrosis was identified as a typical morphological marker for a computer-assisted analysis. Using genetic programming as a tool for feature analysis, a best model was created that achieved 94.74% classification accuracy in distinguishing grade II tumors from grade IV ones. While utilizing modern image analysis techniques, AFM may become an important tool in astrocytic tumor diagnosis. By this way patients suffering from grade II tumors are identified unambiguously, having a less risk for malignant transformation. They would benefit from early adjuvant therapies.

  6. Versatile method for AFM-tip functionalization with biomolecules: fishing a ligand by means of an in situ click reaction

    NASA Astrophysics Data System (ADS)

    Kumar, Rakesh; Ramakrishna, Shivaprakash N.; Naik, Vikrant V.; Chu, Zonglin; Drew, Michael E.; Spencer, Nicholas D.; Yamakoshi, Yoko

    2015-04-01

    A facile and universal method for the functionalization of an AFM tip has been developed for chemical force spectroscopy (CFS) studies of intermolecular interactions of biomolecules. A click reaction between tripod-acetylene and an azide-linker-ligand molecule was successfully carried out on the AFM tip surface and used for the CFS study of ligand-receptor interactions.A facile and universal method for the functionalization of an AFM tip has been developed for chemical force spectroscopy (CFS) studies of intermolecular interactions of biomolecules. A click reaction between tripod-acetylene and an azide-linker-ligand molecule was successfully carried out on the AFM tip surface and used for the CFS study of ligand-receptor interactions. Electronic supplementary information (ESI) available: Experimental details with synthesis and characterization of compounds. Procedures for modifications of Au surfaces and AFM tips. AFM images and full PM-IRRAS spectra of modified surfaces. Detailed procedure for QCM measurement. A table showing ligand-receptor interaction probability. NMR, IR and MS charts. See DOI: 10.1039/c5nr01495f

  7. Characterization of the specific interaction between the DNA aptamer sgc8c and protein tyrosine kinase-7 receptors at the surface of T-cells by biosensing AFM.

    PubMed

    Leitner, Michael; Poturnayova, Alexandra; Lamprecht, Constanze; Weich, Sabine; Snejdarkova, Maja; Karpisova, Ivana; Hianik, Tibor; Ebner, Andreas

    2017-04-01

    We studied the interaction of the specific DNA aptamer sgc8c immobilized at the AFM tip with its corresponding receptor, the protein tyrosine kinase-7 (PTK7) embedded in the membrane of acute lymphoblastic leukemia (ALL) cells (Jurkat T-cells). Performing single molecule force spectroscopy (SMFS) experiments, we showed that the aptamer sgc8c bound with high probability (38.3 ± 7.48%) and high specificity to PTK7, as demonstrated by receptor blocking experiments and through comparison with the binding behavior of a nonspecific aptamer. The determined kinetic off-rate (koff = 5.16 s(-1)) indicates low dissociation of the sgc8c-PTK7 complex. In addition to the pulling force experiments, simultaneous topography and recognition imaging (TREC) experiments using AFM tips functionalized with sgc8c aptamers were realized on the outer regions surface of surface-immobilized Jurkat cells for the first time. This allowed determination of the distribution of PTK7 without any labeling and at near physiological conditions. As a result, we could show a homogeneous distribution of PTK7 molecules on the outer regions of ALL cells with a surface density of 325 ± 12 PTK7 receptors (or small receptor clusters) per μm(2). Graphical Abstract The specific interaction of the DNA aptamer sgc8c and protein tyrosine kinase-7 (PTK7) on acute lymphoblastic leukemia (ALL) cells was characterized. AFM based single molecule force spectroscopy (SMFS) yielded a kinetic off-rate of 5.16 s(-1) of the complex. Simultaneous topography and recognition imaging (TREC) revealed a PTK7 density of 325 ± 12 molecules or clusters per μm(2) in the cell membrane.

  8. Laser lithotripsy with the Ho:YAG laser: fragmentation process revealed by time-resolved imaging

    NASA Astrophysics Data System (ADS)

    Schmidlin, Franz R.; Beghuin, Didier; Delacretaz, Guy P.; Venzi, Giordano; Jichlinski, Patrice; Rink, Klaus; Leisinger, Hans-Juerg; Graber, Peter

    1998-07-01

    Improvements of endoscopic techniques have renewed the interest of urologists in laser lithotripsy in recent years. Laser energy can be easily transmitted through flexible fibers thereby enabling different surgical procedures such as cutting, coagulating and lithotripsy. The Ho:YAG laser offers multiple medical applications in Urology, among them stone fragmentation. However, the present knowledge of its fragmentation mechanism is incomplete. The objective was therefore to analyze the fragmentation process and to discuss the clinical implications related to the underlying fragmentation mechanism. The stone fragmentation process during Ho:YAG laser lithotripsy was observed by time resolved flash video imaging. Possible acoustic transient occurrence was simultaneously monitored with a PVDF-needle hydrophone. Fragmentation was performed on artificial and cystine kidney stones in water. We observed that though the fragmentation process is accompanied with the formation of a cavitation bubble, cavitation has only a minimal effect on stone fragmentation. Fragment ejection is mainly due to direct laser stone heating leading to vaporization of organic stone constituents and interstitial water. The minimal effect of the cavitation bubble is confirmed by acoustic transients measurements, which reveal weak pressure transients. Stone fragmentation with the Holmium laser is the result of vaporization of interstitial (stone) water and organic stone constituents. It is not due to the acoustic effects of a cavitation bubble or plasma formation. The fragmentation process is strongly related with heat production thereby harboring the risk of undesired thermal damage. Therefore, a solid comprehension of the fragmentation process is needed when using the different clinically available laser types of lithotripsy.

  9. Elicitation interval dependent spatiotemporal evolution of cortical spreading depression waves revealed by optical intrinsic signal imaging

    NASA Astrophysics Data System (ADS)

    Chen, Shangbin; Gong, Hui; Zeng, Shaoqun; Luo, Qingming; Li, Pengcheng

    2007-02-01

    This study aimed to investigate the variation of propagation patterns of successive cortical spreading depression (CSD) waves induced by K + or pinprick in rat cortex. In the K + induction group, 18 Sprague-Dawley rats under Î+/--chloralose/urethane anesthesia were used to elicit CSD by 1 M KCl solution in the frontal cortex. Optical intrinsic signal imaging (OISI) at an isosbestic point of hemoglobin (550 nm) was applied to examine regional cerebral blood volume (CBV) changes in the parieto-occipital cortex. In 6 of the 18 rats, OISI was performed in conjunction with DC potential recording of the cortex. The results of this group were reported previously. In the pinprick group, 6 rats were used to induce CSD by pinprick with 8 min interval, and the other 6 rats were pricked with 4 min. CBV changes during CSD appeared as repetitive propagation of wave-like hyperemia at a speed of 3.7+/-0.4 mm/min, which was characterized by a significant negative peak (-14.3+/-3.2%) in the reflectance signal. Except for the first CSD wave, the following waves don't spread fully in the observed cortex all the time and they might abort in the medial area. Independent on the stimulation of pinprick or K+, a short interval of the current CSD to the last CSD no more than 4 min would induce the current CSD be partially propagated. For the first time, the data reveals the time-varying propagation patterns of CSD waves might be affected by the interval between CSD waves. The results suggest that the propagation patterns of a series of CSD waves are time-varying in different regions of rat cortex, and the variation is related to the interval between CSD waves.

  10. Accretion and Preservation of Organic Matter in Carbonaceous Chondrites as Revealed by NanoSIMS Imaging.

    NASA Astrophysics Data System (ADS)

    Remusat, L.; Guan, Y.; Eiler, J.

    2008-12-01

    Carbonaceous chondrites are the most primitive known meteorites. Their parent bodies accreted several discrete components of the early solar system: CAIs, other silicates, oxides, sulfides, ice, organics, and noble gases. Radioactive decay of short live radionucleides quickly heated these parent bodies and drove thermal metamorphism and aqueous alteration of their constituents. Despite this post-acretionary modification, at least some components of the organic matter in the carbaceous chondrites retained distinctive isotopic and molecular properties that may relate to their pre-acretionary origins in the protosolar nebula or in the molecular cloud that gave birth to it [1]. These processes that gave rise to early solar-system organic matter and the extent to which it was modified by parent body processes are still a matter of debate [2]. We have acquired NanoSIMS images of matrices of several CI, CM, CR and CV chondrites to document, in- situ, the distribution of organics and their textural and chemical relationships to co-existing inorganic components. Importantly, we performed these analyses on essentially unmodified fragments of matrix material pressed into indium, rather than on extracts, which have been the focus of most previous work on meteoritic organic matter. Specifically, we simultaneously collected H, D, 12C, 18O, 26CN, 28Si and 32S with a spatial resolution of 200 nm. Inorganic constituents of the imaged domains were determined by SEM imaging and EDS analysis. We identify two textural classes of organic constituents: diffuse organic matter and organic particles ~ 1 micron in diameter. The particles are common and do not exhibit any textural association with any inorganic matrix constituent. This distribution is consistent with previous observations by fluorescence optical microscopy [3]. These organic particles are likely primarily composed of insoluble organic matter (IOM) that grew prior to accretion as pure organic particules and was preserved in

  11. Comparative quantification and statistical analysis of η′ and η precipitates in aluminum alloy AA7075-T651 by TEM and AFM

    SciTech Connect

    Garcia-Garcia, Adrian Luis Dominguez-Lopez, Ivan Lopez-Jimenez, Luis Barceinas-Sanchez, J.D. Oscar

    2014-01-15

    Quantification of nanometric precipitates in metallic alloys has been traditionally performed using transmission electron microscopy, which is nominally a low throughput technique. This work presents a comparative study of quantification of η′ and η precipitates in aluminum alloy AA7075-T651 using transmission electron microscopy (TEM) and non-contact atomic force microscopy (AFM). AFM quantification was compared with 2-D stereological results reported elsewhere. Also, a method was developed, using specialized software, to characterize nanometric size precipitates observed in dark-field TEM micrographs. Statistical analysis of the quantification results from both measurement techniques supports the use of AFM for precipitate characterization. Once the precipitate stoichiometry has been determined by appropriate analytical techniques like TEM, as it is the case for η′ and η in AA7075-T651, the relative ease with which specimens are prepared for AFM analysis could be advantageous in product and process development, and quality control, where a large number of samples are expected for analysis on a regular basis. - Highlights: • Nanometric MgZn{sub 2} precipitates in AA7075-T651 were characterized using AFM and TEM. • Phase-contrast AFM was used to differentiate metal matrix from MgZn{sub 2} precipitates. • TEM and AFM micrographs were analyzed using commercially available software. • AFM image analysis and TEM 2-D stereology render statistically equivalent results.

  12. Manufacturing process of nanofluidics using afm probe

    NASA Astrophysics Data System (ADS)

    Karingula, Varun Kumar

    A new process for fabricating a nano fluidic device that can be used in medical application is developed and demonstrated. Nano channels are fabricated using a nano tip in indentation mode on AFM (Atomic Force Microscopy). The nano channels are integrated between the micro channels and act as a filter to separate biomolecules. Nano channels of 4 to7 m in length, 80nm in width, and at varying depths from 100nm to 850 nm allow the resulting device to separate selected groups of lysosomes and other viruses. Sharply developed vertical micro channels are produced from a deep reaction ion etching followed by deposition of different materials, such as gold and polymers, on the top surface, allowing the study of alternative ways of manufacturing a nanofluidic device. PDMS (Polydimethylsiloxane) bonding is performed to close the top surface of the device. An experimental setup is used to test and validate the device by pouring fluid through the channels. A detailed cost evaluation is conducted to compare the economical merits of the proposed process. It is shown that there is a 47:7% manufacturing time savings and a 60:6% manufacturing cost savings.

  13. Microrheology using a custom-made AFM

    NASA Astrophysics Data System (ADS)

    Kosgodagan Acharige, Sebastien; Benzaquen, Michael; Steinberger, Audrey

    In the past few years, a new method was developed to measure local properties of liquids (X. Xiong et al., Phys. Rev. E 80, 2009). This method consists of gluing a micron-sized glass fiber at the tip of an AFM cantilever and probing the liquid with it. In ENS Lyon, this method was perfected (C. Devailly et al., EPL, 106 5, 2014) with the help of an interferometer developped in the same laboratory (L. Bellon et al., Opt. Commun. 207 49, 2002 and P. Paolino et al., Rev. Sci. Instrum. 84, 2013), which background noise can reach 10-14 m /√{ Hz } . This method allows us to measure a wide range of viscosities (1 mPa . s to 500 mPa . s) of transparent and opaque fluids using a small sample volume ( 5 mL). In this presentation, I will briefly describe the interferometer developped in ENS Lyon, then explain precisely the microrheology measurements and then compare the experimental results to a model developped by M. Benzaquen. This work is supported financially by the ANR project NANOFLUIDYN (Grant Number ANR-13-BS10-0009).

  14. BOREAS AFM-07 SRC Surface Meteorological Data

    NASA Technical Reports Server (NTRS)

    Osborne, Heather; Hall, Forrest G. (Editor); Newcomer, Jeffrey A. (Editor); Young, Kim; Wittrock, Virginia; Shewchuck, Stan; Smith, David E. (Technical Monitor)

    2000-01-01

    The Saskatchewan Research Council (SRC) collected surface meteorological and radiation data from December 1993 until December 1996. The data set comprises Suite A (meteorological and energy balance measurements) and Suite B (diffuse solar and longwave measurements) components. Suite A measurements were taken at each of ten sites, and Suite B measurements were made at five of the Suite A sites. The data cover an approximate area of 500 km (North-South) by 1000 km (East-West) (a large portion of northern Manitoba and northern Saskatchewan). The measurement network was designed to provide researchers with a sufficient record of near-surface meteorological and radiation measurements. The data are provided in tabular ASCII files, and were collected by Aircraft Flux and Meteorology (AFM)-7. The surface meteorological and radiation data are available from the Earth Observing System Data and Information System (EOSDIS) Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC). The data files are available on a CD-ROM (see document number 20010000884).

  15. Spectral imaging reveals microvessel physiology and function from anastomoses to thromboses

    NASA Astrophysics Data System (ADS)

    Wankhede, Mamta; Agarwal, Nikita; Fraga-Silva, Rodrigo A.; Dedeugd, Casey; Raizada, Mohan K.; Oh, S. Paul; Sorg, Brian S.

    2010-01-01

    Abnormal microvascular physiology and function is common in many diseases. Numerous pathologies include hypervascularity, aberrant angiogenesis, or abnormal vascular remodeling among the characteristic features of the disease, and quantitative imaging and measurement of microvessel function can be important to increase understanding of these diseases. Several optical techniques are useful for direct imaging of microvascular function. Spectral imaging is one such technique that can be used to assess microvascular oxygen transport function with high spatial and temporal resolution in microvessel networks through measurements of hemoglobin saturation. We highlight novel observation made with our intravital microscopy spectral imaging system employed with mouse dorsal skin-fold window chambers for imaging hemoglobin saturation in microvessel networks. Specifically, we image acute oxygenation fluctuations in a tumor microvessel network, the development of arteriovenous malformations in a mouse model of hereditary hemorrhagic telangiectasia, and the formation of spontaneous and induced microvascular thromboses and occlusions.

  16. Insights into Brown Adipose Tissue Physiology as Revealed by Imaging Studies

    PubMed Central

    Izzi-Engbeaya, Chioma; Salem, Victoria; Atkar, Rajveer S; Dhillo, Waljit S

    2014-01-01

    There has been resurgence in interest in brown adipose tissue (BAT) following radiological and histological identification of metabolically active BAT in adult humans. Imaging enables BAT to be studied non-invasively and therefore imaging studies have contributed a significant amount to what is known about BAT function in humans. In this review the current knowledge (derived from imaging studies) about the prevalence, function, activity and regulation of BAT in humans (as well as relevant rodent studies), will be summarized. PMID:26167397

  17. 78 FR 55772 - Culturally Significant Object Imported for Exhibition Determinations: “Beauty Revealed: Images of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-11

    ... Qing Dynasty Chinese Painting'' SUMMARY: Notice is hereby given of the following determinations...: Images of Women in Qing Dynasty Chinese Painting,'' imported from abroad for temporary exhibition...

  18. Histological Image Feature Mining Reveals Emergent Diagnostic Properties for Renal Cancer

    PubMed Central

    Kothari, Sonal; Phan, John H.; Young, Andrew N.; Wang, May D.

    2016-01-01

    Computer-aided histological image classification systems are important for making objective and timely cancer diagnostic decisions. These systems use combinations of image features that quantify a variety of image properties. Because researchers tend to validate their diagnostic systems on specific cancer endpoints, it is difficult to predict which image features will perform well given a new cancer endpoint. In this paper, we define a comprehensive set of common image features (consisting of 12 distinct feature subsets) that quantify a variety of image properties. We use a data-mining approach to determine which feature subsets and image properties emerge as part of an “optimal” diagnostic model when applied to specific cancer endpoints. Our goal is to assess the performance of such comprehensive image feature sets for application to a wide variety of diagnostic problems. We perform this study on 12 endpoints including 6 renal tumor subtype endpoints and 6 renal cancer grade endpoints. Keywords-histology, image mining, computer-aided diagnosis PMID:28163980

  19. Fluid ascent and magma storage beneath Gunung Merapi revealed by multi-scale seismic imaging

    NASA Astrophysics Data System (ADS)

    Luehr, Birger-G.; Koulakov, Ivan; Rabbel, Wolfgang; Zschau, Jochen; Ratdomopurbo, Antonius; Brotopuspito, Kirbani Sri; Fauzi, Pak; Sahara, David P.

    2013-07-01

    Magma is fed to a volcano through a complex “plumbing” system that involves not only shallow structures beneath the volcano edifice, but also deep structures and processes within the underlying crust and upper mantle. This paper summarizes seismic experiments carried out over many years at Gunung Merapi in Central Java. These have resolved the 3D seismic velocity structure of the Merapi edifice, and provided a 3D structural image of the lithosphere and subduction zone beneath Central Java. Earthquake locations reveal that with distance from the trench, the dip of the subducting slab steepens from nearly horizontal (0-150 km), through 45° (150-250 km), to 70° (> 250 km). The slab appears as a 30 km thick double layer of seismicity in a depth range of 80 km to 150 km, and it can be identified seismically to a depth of more than 600 km. The active volcanoes of Merapi, Sumbing, and Lawu are located at the edge of a large low velocity body that extends from the upper crust to the upper mantle beneath Central Java. Shear wave signals recorded above this anomaly are strongly attenuated compared to neighboring areas. The anomalous body has a detected volume of > 50,000 km3 and a decrease in P and S velocities relative to adjacent regions of up to 30%. The resulting Vp/Vs ratio of up to 1.9 is unusually high for lower crust. Additionally, the anomaly extends along a 45 degree-slope downward from beneath the volcanic arc and meets the slab at 100 km depth. We interpret this sloping anomaly as a pathway for fluids and partial melts. Increased seismicity is observed at depths of ~ 100 km, possibly as a result of dehydration of the subducting slab with related fluid releases causing partial melting of overlying mantle material. The large velocity reduction and high Vp/Vs ratio in the region are consistent with an increase in temperature, a reduction of shear strength, and the presence of fluids or melts of 13 to 25 vol.%. The detected strong anomaly beneath Central Java

  20. Atomic Force Microscope for Imaging and Spectroscopy

    NASA Technical Reports Server (NTRS)

    Pike, W. T.; Hecht, M. H.; Anderson, M. S.; Akiyama, T.; Gautsch, S.; deRooij, N. F.; Staufer, U.; Niedermann, Ph.; Howald, L.; Mueller, D.

    2000-01-01

    We have developed, built, and tested an atomic force microscope (AFM) for extraterrestrial applications incorporating a micromachined tip array to allow for probe replacement. It is part of a microscopy station originally intended for NASA's 2001 Mars lander to identify the size, distribution, and shape of Martian dust and soil particles. As well as imaging topographically down to nanometer resolution, this instrument can be used to reveal chemical information and perform infrared and Raman spectroscopy at unprecedented resolution.

  1. Quantification of the rat spinal microglial response to peripheral nerve injury as revealed by immunohistochemical image analysis and flow cytometry

    PubMed Central

    Blackbeard, J.; O’Dea, K.P.; Wallace, V.C.J.; Segerdahl, A.; Pheby, T.; Takata, M.; Field, M.J.; Rice, A.S.C.

    2007-01-01

    Microgliosis is implicated in the pathophysiology of several neurological disorders, including neuropathic pain. Consequently, perturbation of microgliosis is a mechanistic and drug development target in neuropathic pain, which highlights the requirement for specific, sensitive and reproducible methods of microgliosis measurement. In this study, we used the spinal microgliosis associated with L5 spinal nerve transection and minocycline-induced attenuation thereof to: (1) evaluate novel software based semi-quantitative image analysis paradigms for the assessment of immunohistochemical images. Microgliosis was revealed by immunoreactivity to OX42. Several image analysis paradigms were assessed and compared to a previously validated subjective categorical rating scale. This comparison revealed that grey scale measurement of the proportion of a defined area of spinal cord occupied by OX42 immunoreactive cells is a robust image analysis paradigm. (2) Develop and validate a flow cytometric approach for quantification of spinal microgliosis. The flow cytometric technique reliably quantified microgliosis in spinal cord cell suspensions, using OX42 and ED9 immunoreactivity to identify microglia. The results suggest that image analysis of immunohistochemical revelation of microgliosis reliably detects the spinal microgliosis in response to peripheral nerve injury and pharmacological attenuation thereof. In addition, flow cytometry provides an alternative approach for quantitative analysis of spinal microgliosis elicited by nerve injury. PMID:17553569

  2. Quantification of the rat spinal microglial response to peripheral nerve injury as revealed by immunohistochemical image analysis and flow cytometry.

    PubMed

    Blackbeard, J; O'Dea, K P; Wallace, V C J; Segerdahl, A; Pheby, T; Takata, M; Field, M J; Rice, A S C

    2007-08-30

    Microgliosis is implicated in the pathophysiology of several neurological disorders, including neuropathic pain. Consequently, perturbation of microgliosis is a mechanistic and drug development target in neuropathic pain, which highlights the requirement for specific, sensitive and reproducible methods of microgliosis measurement. In this study, we used the spinal microgliosis associated with L5 spinal nerve transection and minocycline-induced attenuation thereof to: (1) evaluate novel software based semi-quantitative image analysis paradigms for the assessment of immunohistochemical images. Microgliosis was revealed by immunoreactivity to OX42. Several image analysis paradigms were assessed and compared to a previously validated subjective categorical rating scale. This comparison revealed that grey scale measurement of the proportion of a defined area of spinal cord occupied by OX42 immunoreactive cells is a robust image analysis paradigm. (2) Develop and validate a flow cytometric approach for quantification of spinal microgliosis. The flow cytometric technique reliably quantified microgliosis in spinal cord cell suspensions, using OX42 and ED9 immunoreactivity to identify microglia. The results suggest that image analysis of immunohistochemical revelation of microgliosis reliably detects the spinal microgliosis in response to peripheral nerve injury and pharmacological attenuation thereof. In addition, flow cytometry provides an alternative approach for quantitative analysis of spinal microgliosis elicited by nerve injury.

  3. Two-Photon Intravital Fluorescence Lifetime Imaging of the Kidney Reveals Cell-Type Specific Metabolic Signatures.

    PubMed

    Hato, Takashi; Winfree, Seth; Day, Richard; Sandoval, Ruben M; Molitoris, Bruce A; Yoder, Mervin C; Wiggins, Roger C; Zheng, Yi; Dunn, Kenneth W; Dagher, Pierre C

    2017-03-01

    In the live animal, tissue autofluorescence arises from a number of biologically important metabolites, such as the reduced form of nicotinamide adenine dinucleotide. Because autofluorescence changes with metabolic state, it can be harnessed as a label-free imaging tool with which to study metabolism in vivo Here, we used the combination of intravital two-photon microscopy and frequency-domain fluorescence lifetime imaging microscopy (FLIM) to map cell-specific metabolic signatures in the kidneys of live animals. The FLIM images are analyzed using the phasor approach, which requires no prior knowledge of metabolite species and can provide unbiased metabolic fingerprints for each pixel of the lifetime image. Intravital FLIM revealed the metabolic signatures of S1 and S2 proximal tubules to be distinct and resolvable at the subcellular level. Notably, S1 and distal tubules exhibited similar metabolic profiles despite apparent differences in morphology and autofluorescence emission with traditional two-photon microscopy. Time-lapse imaging revealed dynamic changes in the metabolic profiles of the interstitium, urinary lumen, and glomerulus-areas that are not resolved by traditional intensity-based two-photon microscopy. Finally, using a model of endotoxemia, we present examples of the way in which intravital FLIM can be applied to study kidney diseases and metabolism. In conclusion, intravital FLIM of intrinsic metabolites is a bias-free approach with which to characterize and monitor metabolism in vivo, and offers the unique opportunity to uncover dynamic metabolic changes in living animals with subcellular resolution.

  4. Real-time in vivo imaging of butterfly wing development: revealing the cellular dynamics of the pupal wing tissue.

    PubMed

    Iwata, Masaki; Ohno, Yoshikazu; Otaki, Joji M

    2014-01-01

    Butterfly wings are covered with regularly arranged single-colored scales that are formed at the pupal stage. Understanding pupal wing development is therefore crucial to understand wing color pattern formation. Here, we successfully employed real-time in vivo imaging techniques to observe pupal hindwing development over time in the blue pansy butterfly, Junonia orithya. A transparent sheet of epithelial cells that were not yet regularly arranged was observed immediately after pupation. Bright-field imaging and autofluorescent imaging revealed free-moving hemocytes and tracheal branches of a crinoid-like structure underneath the epithelium. The wing tissue gradually became gray-white, epithelial cells were arranged regularly, and hemocytes disappeared, except in the bordering lacuna, after which scales grew. The dynamics of the epithelial cells and scale growth were also confirmed by fluorescent imaging. Fluorescent in vivo staining further revealed that these cells harbored many mitochondria at the surface of the epithelium. Organizing centers for the border symmetry system were apparent immediately after pupation, exhibiting a relatively dark optical character following treatment with fluorescent dyes, as well as in autofluorescent images. The wing tissue exhibited slow and low-frequency contraction pulses with a cycle of approximately 10 to 20 minutes, mainly occurring at 2 to 3 days postpupation. The pulses gradually became slower and weaker and eventually stopped. The wing tissue area became larger after contraction, which also coincided with an increase in the autofluorescence intensity that might have been caused by scale growth. Examination of the pattern of color development revealed that the black pigment was first deposited in patches in the central areas of an eyespot black ring and a parafocal element. These results of live in vivo imaging that covered wide wing area for a long time can serve as a foundation for studying the cellular dynamics of living

  5. Real-Time In Vivo Imaging of Butterfly Wing Development: Revealing the Cellular Dynamics of the Pupal Wing Tissue

    PubMed Central

    Iwata, Masaki; Ohno, Yoshikazu; Otaki, Joji M.

    2014-01-01

    Butterfly wings are covered with regularly arranged single-colored scales that are formed at the pupal stage. Understanding pupal wing development is therefore crucial to understand wing color pattern formation. Here, we successfully employed real-time in vivo imaging techniques to observe pupal hindwing development over time in the blue pansy butterfly, Junonia orithya. A transparent sheet of epithelial cells that were not yet regularly arranged was observed immediately after pupation. Bright-field imaging and autofluorescent imaging revealed free-moving hemocytes and tracheal branches of a crinoid-like structure underneath the epithelium. The wing tissue gradually became gray-white, epithelial cells were arranged regularly, and hemocytes disappeared, except in the bordering lacuna, after which scales grew. The dynamics of the epithelial cells and scale growth were also confirmed by fluorescent imaging. Fluorescent in vivo staining further revealed that these cells harbored many mitochondria at the surface of the epithelium. Organizing centers for the border symmetry system were apparent immediately after pupation, exhibiting a relatively dark optical character following treatment with fluorescent dyes, as well as in autofluorescent images. The wing tissue exhibited slow and low-frequency contraction pulses with a cycle of approximately 10 to 20 minutes, mainly occurring at 2 to 3 days postpupation. The pulses gradually became slower and weaker and eventually stopped. The wing tissue area became larger after contraction, which also coincided with an increase in the autofluorescence intensity that might have been caused by scale growth. Examination of the pattern of color development revealed that the black pigment was first deposited in patches in the central areas of an eyespot black ring and a parafocal element. These results of live in vivo imaging that covered wide wing area for a long time can serve as a foundation for studying the cellular dynamics of living

  6. Sharp high-aspect-ratio AFM tips fabricated by a combination of deep reactive ion etching and focused ion beam techniques.

    PubMed

    Caballero, David; Villanueva, Guillermo; Plaza, Jose Antonio; Mills, Christopher A; Samitier, Josep; Errachid, Abdelhamid

    2010-01-01

    The shape and dimensions of an atomic force microscope tip are crucial factors to obtain high resolution images at the nanoscale. When measuring samples with narrow trenches, inclined sidewalls near 90 degrees or nanoscaled structures, standard silicon atomic force microscopy (AFM) tips do not provide satisfactory results. We have combined deep reactive ion etching (DRIE) and focused ion beam (FIB) lithography techniques in order to produce probes with sharp rocket-shaped silicon AFM tips for high resolution imaging. The cantilevers were shaped and the bulk micromachining was performed using the same DRIE equipment. To improve the tip aspect ratio we used FIB nanolithography technique. The tips were tested on narrow silicon trenches and over biological samples showing a better resolution when compared with standard AFM tips, which enables nanocharacterization and nanometrology of high-aspect-ratio structures and nanoscaled biological elements to be completed, and provides an alternative to commercial high aspect ratio AFM tips.

  7. BOREAS AFM-12 1-km AVHRR Seasonal Land Cover Classification

    NASA Technical Reports Server (NTRS)

    Steyaert, Lou; Hall, Forrest G.; Newcomer, Jeffrey A. (Editor); Knapp, David E. (Editor); Loveland, Thomas R.; Smith, David E. (Technical Monitor)

    2000-01-01

    The Boreal Ecosystem-Atmosphere Study (BOREAS) Airborne Fluxes and Meteorology (AFM)-12 team's efforts focused on regional scale Surface Vegetation and Atmosphere (SVAT) modeling to improve parameterization of the heterogeneous BOREAS landscape for use in larger scale Global Circulation Models (GCMs). This regional land cover data set was developed as part of a multitemporal one-kilometer Advanced Very High Resolution Radiometer (AVHRR) land cover analysis approach that was used as the basis for regional land cover mapping, fire disturbance-regeneration, and multiresolution land cover scaling studies in the boreal forest ecosystem of central Canada. This land cover classification was derived by using regional field observations from ground and low-level aircraft transits to analyze spectral-temporal clusters that were derived from an unsupervised cluster analysis of monthly Normalized Difference Vegetation Index (NDVI) image composites (April-September 1992). This regional data set was developed for use by BOREAS investigators, especially those involved in simulation modeling, remote sensing algorithm development, and aircraft flux studies. Based on regional field data verification, this multitemporal one-kilometer AVHRR land cover mapping approach was effective in characterizing the biome-level land cover structure, embedded spatially heterogeneous landscape patterns, and other types of key land cover information of interest to BOREAS modelers.The land cover mosaics in this classification include: (1) wet conifer mosaic (low, medium, and high tree stand density), (2) mixed coniferous-deciduous forest (80% coniferous, codominant, and 80% deciduous), (3) recent visible bum, vegetation regeneration, or rock outcrops-bare ground-sparsely vegetated slow regeneration bum (four classes), (4) open water and grassland marshes, and (5) general agricultural land use/ grasslands (three classes). This land cover mapping approach did not detect small subpixel-scale landscape

  8. Intravital live cell triggered imaging system reveals monocyte patrolling and macrophage migration in atherosclerotic arteries

    NASA Astrophysics Data System (ADS)

    McArdle, Sara; Chodaczek, Grzegorz; Ray, Nilanjan; Ley, Klaus

    2015-02-01

    Intravital multiphoton imaging of arteries is technically challenging because the artery expands with every heartbeat, causing severe motion artifacts. To study leukocyte activity in atherosclerosis, we developed the intravital live cell triggered imaging system (ILTIS). This system implements cardiac triggered acquisition as well as frame selection and image registration algorithms to produce stable movies of myeloid cell movement in atherosclerotic arteries in live mice. To minimize tissue damage, no mechanical stabilization is used and the artery is allowed to expand freely. ILTIS performs multicolor high frame-rate two-dimensional imaging and full-thickness three-dimensional imaging of beating arteries in live mice. The external carotid artery and its branches (superior thyroid and ascending pharyngeal arteries) were developed as a surgically accessible and reliable model of atherosclerosis. We use ILTIS to demonstrate Cx3cr1GFP monocytes patrolling the lumen of atherosclerotic arteries. Additionally, we developed a new reporter mouse (Apoe-/-Cx3cr1GFP/+Cd11cYFP) to image GFP+ and GFP+YFP+ macrophages "dancing on the spot" and YFP+ macrophages migrating within intimal plaque. ILTIS will be helpful to answer pertinent open questions in the field, including monocyte recruitment and transmigration, macrophage and dendritic cell activity, and motion of other immune cells.

  9. Confocal Raman spectroscopy and AFM for evaluation of sidewalls in type II superlattice FPAs

    NASA Astrophysics Data System (ADS)

    Rotter, T. J.; Busani, T.; Rathi, P.; Jaeckel, F.; Reyes, P. A.; Malloy, K. J.; Ukhanov, A. A.; Plis, E.; Krishna, S.; Jaime-Vasquez, M.; Baril, N. F.; Benson, J. D.; Tenne, D. A.

    2015-06-01

    We propose to utilize confocal Raman spectroscopy combined with high resolution atomic force microscopy (AFM) for nondestructive characterisation of the sidewalls of etched and passivated small pixel (24 μm×24 μm) focal plane arrays (FPA) fabricated using LW/LWIR InAs/GaSb type-II strained layer superlattice (T2SL) detector material. Special high aspect ratio Si and GaAs AFM probes, with tip length of 13 μm and tip aperture less than 7°, allow characterisation of the sidewall morphology. Confocal microscopy enables imaging of the sidewall profile through optical sectioning. Raman spectra measured on etched T2SL FPA single pixels enable us to quantify the non-uniformity of the mesa delineation process.

  10. Accurate and precise calibration of AFM cantilever spring constants using laser Doppler vibrometry.

    PubMed

    Gates, Richard S; Pratt, Jon R

    2012-09-21

    Accurate cantilever spring constants are important in atomic force microscopy both in control of sensitive imaging and to provide correct nanomechanical property measurements. Conventional atomic force microscope (AFM) spring constant calibration techniques are usually performed in an AFM. They rely on significant handling and often require touching the cantilever probe tip to a surface to calibrate the optical lever sensitivity of the configuration. This can damage the tip. The thermal calibration technique developed for laser Doppler vibrometry (LDV) can be used to calibrate cantilevers without handling or touching the tip to a surface. Both flexural and torsional spring constants can be measured. Using both Euler-Bernoulli modeling and an SI traceable electrostatic force balance technique as a comparison we demonstrate that the LDV thermal technique is capable of providing rapid calibrations with a combination of ease, accuracy and precision beyond anything previously available.

  11. Influence of Fluid Cell Design on the Frequency Response of AFM Microcantilevers in Liquid Media

    PubMed Central

    Motamedi, Ramin; Wood-Adams, Paula M.

    2008-01-01

    A study of the frequency response of AFM microcantilevers in liquid media contained in a commercial fluid cell is presented. Such systems exhibit complicated dynamics which are often not well described by available theories. Their dynamic behavior has a direct effect on the use of the AFM in dynamic mode while imaging in liquid or while extracting the rheological properties of the fluid. We explore the issues related to the design of the cantilever holder/fluid cell and propose an approach for evaluating, minimizing and recognizing the ultimate limitations of commercial cantilever holders. A technique for estimating the frequency response spectrum of the fluid cell itself from experimental data is presented. This spectrum can then be used to evaluate whether or not the fluid cell is suited for the desired purpose. PMID:27873849

  12. High-fidelity AFM scanning stage based on multilayer ceramic capacitors.

    PubMed

    Chen, Jian; Zhang, Lian Sheng; Feng, Zhi Hua

    2016-05-01

    A kind of multilayer ceramic capacitors (MLCCs) has been verified to have good micro-actuating properties, thus making them good candidates for nano-positioning. In this paper, we successfully employed the MLCCs as lateral scanners for a tripod scanning stage. The MLCC-based lateral scanners display hysteresis under 1.5% and a nonlinearity less than 2% even with the simplest open-loop voltage drive. The developed scanning stage was integrated into a commercial AFM to evaluate its imaging performance. Experimental results showed that sample images with high fidelities were obtained. SCANNING 38:184-190, 2016. © 2015 Wiley Periodicals, Inc.

  13. 5D imaging via light sheet microscopy reveals cell dynamics during the eye-antenna disc primordium formation in Drosophila

    NASA Astrophysics Data System (ADS)

    Huang, Yu Shan; Ku, Hui Yu; Tsai, Yun Chi; Chang, Chin Hao; Pao, Sih Hua; Sun, Y. Henry; Chiou, Arthur

    2017-03-01

    5D images of engrailed (en) and eye gone (eyg) gene expressions during the course of the eye-antenna disc primordium (EADP) formation of Drosophila embryos from embryonic stages 13 through 16 were recorded via light sheet microscopy and analyzed to reveal the cell dynamics involved in the development of the EADP. Detailed analysis of the time-lapsed images revealed the process of EADP formation and its invagination trajectory, which involved an inversion of the EADP anterior-posterior axis relative to the body. Furthermore, analysis of the en-expression pattern in the EADP provided strong evidence that the EADP is derived from one of the en-expressing head segments.

  14. 5D imaging via light sheet microscopy reveals cell dynamics during the eye-antenna disc primordium formation in Drosophila

    PubMed Central

    Huang, Yu Shan; Ku, Hui Yu; Tsai, Yun Chi; Chang, Chin Hao; Pao, Sih Hua; Sun, Y. Henry; Chiou, Arthur

    2017-01-01

    5D images of engrailed (en) and eye gone (eyg) gene expressions during the course of the eye-antenna disc primordium (EADP) formation of Drosophila embryos from embryonic stages 13 through 16 were recorded via light sheet microscopy and analyzed to reveal the cell dynamics involved in the development of the EADP. Detailed analysis of the time-lapsed images revealed the process of EADP formation and its invagination trajectory, which involved an inversion of the EADP anterior-posterior axis relative to the body. Furthermore, analysis of the en-expression pattern in the EADP provided strong evidence that the EADP is derived from one of the en-expressing head segments. PMID:28322328

  15. Inducible ablation of melanopsin-expressing retinal ganglion cells reveals their central role in non-image forming visual responses.

    PubMed

    Hatori, Megumi; Le, Hiep; Vollmers, Christopher; Keding, Sheena Racheal; Tanaka, Nobushige; Buch, Thorsten; Waisman, Ari; Schmedt, Christian; Jegla, Timothy; Panda, Satchidananda

    2008-06-11

    Rod/cone photoreceptors of the outer retina and the melanopsin-expressing retinal ganglion cells (mRGCs) of the inner retina mediate non-image forming visual responses including entrainment of the circadian clock to the ambient light, the pupillary light reflex (PLR), and light modulation of activity. Targeted deletion of the melanopsin gene attenuates these adaptive responses with no apparent change in the development and morphology of the mRGCs. Comprehensive identification of mRGCs and knowledge of their specific roles in image-forming and non-image forming photoresponses are currently lacking. We used a Cre-dependent GFP expression strategy in mice to genetically label the mRGCs. This revealed that only a subset of mRGCs express enough immunocytochemically detectable levels of melanopsin. We also used a Cre-inducible diphtheria toxin receptor (iDTR) expression approach to express the DTR in mRGCs. mRGCs develop normally, but can be acutely ablated upon diphtheria toxin administration. The mRGC-ablated mice exhibited normal outer retinal function. However, they completely lacked non-image forming visual responses such as circadian photoentrainment, light modulation of activity, and PLR. These results point to the mRGCs as the site of functional integration of the rod/cone and melanopsin phototransduction pathways and as the primary anatomical site for the divergence of image-forming and non-image forming photoresponses in mammals.

  16. Study of mechanical behavior of AFM silicon tips under mechanical load

    NASA Astrophysics Data System (ADS)

    Kopycinska-Mueller, M.; Gluch, J.; Köhler, B.

    2016-11-01

    In this paper we address critical issues concerning calibration of AFM based methods used for nanoscale mechanical characterization of materials. It has been shown that calibration approaches based on macroscopic models for contact mechanics may yield excellent results in terms of the indentation modulus of the sample, but fail to provide a comprehensive and actual information concerning the tip-sample contact radius or the mechanical properties of the tip. Explanations for the severely reduced indentation modulus of the tip included the inadequacies of the models used for calculations of the tip-sample contact stiffness, discrepancies in the actual and ideal shape of the tip, presence of the amorphous silicon phase within the silicon tip, as well as negligence of the actual size of the stress field created in the tip during elastic interactions. To clarify these issues, we investigated the influence of the mechanical load applied to four AFM silicon tips on their crystalline state by exposing them to systematically increasing loads, evaluating the character of the tip-sample interactions via the load-unload stiffness curves, and assessing the state of the tips from HR-TEM images. The results presented in this paper were obtained in a series of relatively simple and basic atomic force acoustic microscopy (AFAM) experiments. The novel combination of TEM imaging of the AFM tips with the analysis of the load-unload stiffness curves gave us a detailed insight into their mechanical behavior under load conditions. We were able to identify the limits for the elastic interactions, as well as the hallmarks for phase transformation and dislocation formation and movement. The comparison of the physical dimensions of the AFM tips, geometry parameters determined from the values of the contact stiffness, and the information on the crystalline state of the tips allowed us a better understanding of the nanoscale contact.

  17. Anatomy of the Chesapeake Bay impact structure revealed by seismic imaging, Delmarva Peninsula, Virginia, USA

    USGS Publications Warehouse

    Catchings, R.D.; Powars, D.S.; Gohn, G.S.; Horton, J.W.; Goldman, M.R.; Hole, J.A.

    2008-01-01

    A 30-km-long, radial seismic reflection and refraction survey completed across the northern part of the late Eocene Chesapeake Bay impact structure (CBIS) on the Delmarva Peninsula, Virginia, USA, confirms that the CBIS is a complex central-peak crater. We used a tomographic P wave velocity model and low-fold reflection images, constrained by data from two deep boreholes located on the profile, to interpret the structure and composition of the upper 5 km of crust. The seismic images exhibit well-defined structural features, including (with increasing radial distance) a collapsed central uplift, a breccia-filled moat, and a collapsed transient-crater margin (which collectively constitute a ???40-km-wide collapsed transient crater), and a shallowly deformed annular trough. These seismic images are the first to resolve the deep structure of the crater (>1 km) and the boundaries between the central uplift, moat, and annular trough. Several distinct seismic signatures distinguish breccia units from each other and from more coherent crystalline rocks below the central uplift, moat, and annular trough. Within the moat, breccia extends to a minimum depth of 1.5 km or a maximum of 3.5 km, depending upon the interpretation of the deepest layered materials. The images show ???350 to 500 m of postimpact sediments above the impactites. The imaged structure of the CBIS indicates a complex sequence of event during the cratering process that will provide new constraints for numerical modeling. Copyright 2008 by the American Geophysical Union.

  18. Mass spectrometry imaging reveals the sub-organ distribution of carbon nanomaterials

    NASA Astrophysics Data System (ADS)

    Chen, Suming; Xiong, Caiqiao; Liu, Huihui; Wan, Qiongqiong; Hou, Jian; He, Qing; Badu-Tawiah, Abraham; Nie, Zongxiu

    2015-02-01

    Label and label-free methods to image carbon-based nanomaterials exist. However, label-based approaches are limited by the risk of tag detachment over time, and label-free spectroscopic methods have slow imaging speeds, weak photoluminescence signals and strong backgrounds. Here, we present a label-free mass spectrometry imaging method to detect carbon nanotubes, graphene oxide and carbon nanodots in mice. The large molecular weights of nanoparticles are difficult to detect using conventional mass spectrometers, but our method overcomes this problem by using the intrinsic carbon cluster fingerprint signal of the nanomaterials. We mapped and quantified the sub-organ distribution of the nanomaterials in mice. Our results showed that most carbon nanotubes and nanodots were found in the outer parenchyma of the kidney, and all three materials were seen in the red pulp of the spleen. The highest concentrations of nanotubes in the spleen were found within the marginal zone.

  19. Subcellular Imaging of Voltage and Calcium Signals Reveals Neural Processing In Vivo.

    PubMed

    Yang, Helen H; St-Pierre, François; Sun, Xulu; Ding, Xiaozhe; Lin, Michael Z; Clandinin, Thomas R

    2016-06-30

    A mechanistic understanding of neural computation requires determining how information is processed as it passes through neurons and across synapses. However, it has been challenging to measure membrane potential changes in axons and dendrites in vivo. We use in vivo, two-photon imaging of novel genetically encoded voltage indicators, as well as calcium imaging, to measure sensory stimulus-evoked signals in the Drosophila visual system with subcellular resolution. Across synapses, we find major transformations in the kinetics, amplitude, and sign of voltage responses to light. We also describe distinct relationships between voltage and calcium signals in different neuronal compartments, a substrate for local computation. Finally, we demonstrate that ON and OFF selectivity, a key feature of visual processing across species, emerges through the transformation of membrane potential into intracellular calcium concentration. By imaging voltage and calcium signals to map information flow with subcellular resolution, we illuminate where and how critical computations arise.

  20. Jupiter's Upper Atmospheric Winds Revealed in Ultraviolet Images by Hubble Telescope

    NASA Technical Reports Server (NTRS)

    1994-01-01

    These four NASA Hubble Space Telescope images of Jupiter, as seen in visible (violet) and far-ultraviolet (UV) wavelengths, show the remarkable spreading of the clouds of smoke and dust thrown into the atmosphere after the impacts of the fragments of comet P/Shoemaker-Levy 9. These dark regions provide the only information ever obtained on the wind direction and speed in Jupiter's upper atmosphere.

    TOP Three impact sites appear as dark smudges lined up along Jupiter's southern hemisphere (from left to right, sites C, A, and E). This pair of images was obtained on 17 July, several hours after the E impact. These 3 impact sites appear strikingly darker in the far-ultraviolet images to the right. This is because the smoke and dust rising from the fireballs absorbs UV light more strongly than violet light, so that the clouds appear both darker and larger in the UV images. Apparently, the fireball and plume threw large amounts of material completely above the atmosphere. This material diffused back down through the atmosphere with the smaller and lighter particles suspended at high altitudes.

    BOTTOM Hubble's view of the same hemisphere of Jupiter 12-13 days later shows that the smoke and dust have now been spread mainly in the east/west direction by the prevailing winds at the altitude where the dark material is suspended or 'floating' in the atmosphere.

    HST shows that winds in Jupiter's upper atmosphere carry the high altitude smoke and dust in different directions than in the lower atmosphere. For example, the UV image shows a fainter cloud near 45 deg. south latitude, which does not appear in the violet image. The fainter cloud may be due to high altitude material which is drifting with the upper atmospheric winds to the north away from the polar regions. However, in the left-hand impact regions the clouds being observed are lower in the atmosphere where there is apparently no such northerly wind.

    The violet images show the Great Red Spot, on the eastern

  1. Revealing a strongly reddened, faint active galactic nucleus population by stacking deep co-added images

    NASA Astrophysics Data System (ADS)

    Varga, József; Csabai, István.; Dobos, László

    2012-10-01

    More than half of the sources identified by recent radio sky surveys have not been detected by wide-field optical surveys. We present a study, based on our co-added image stacking technique, in which our aim is to detect the optical emission from unresolved, isolated radio sources of the Very Large Array (VLA) Faint Images of the Radio Sky at Twenty-cm (FIRST) survey that have no identified optical counterparts in the Sloan Digital Sky Survey (SDSS) Stripe 82 co-added data set. From the FIRST catalogue, 2116 such radio point sources were selected, and cut-out images, centred on the FIRST coordinates, were generated from the Stripe 82 images. The already co-added cut-outs were stacked once again to obtain images of high signal-to-noise ratio, in the hope that optical emission from the radio sources would become detectable. Multiple stacks were generated, based on the radio luminosity of the point sources. The resulting stacked images show central peaks similar to point sources. The peaks have very red colours with steep optical spectral energy distributions. We have found that the optical spectral index αν falls in the range -2.9 ≤ αν ≤ -2.2 (Sν∝ναν), depending only weakly on the radio flux. The total integration times of the stacks are between 270 and 300 h, and the corresponding 5σ detection limit is estimated to be about mr ≃ 26.6 mag. We argue that the detected light is mainly from the central regions of dust-reddened Type 1 active galactic nuclei. Dust-reddened quasars might represent an early phase of quasar evolution, and thus they can also give us an insight into the formation of massive galaxies. The data used in the paper are available on-line at http://www.vo.elte.hu/doublestacking.

  2. Correlation Effects in Scanning Tunneling Microscopy Images of Molecules Revealed by Quantum Monte Carlo.

    PubMed

    Barborini, Matteo; Sorella, Sandro; Rontani, Massimo; Corni, Stefano

    2016-11-08

    Scanning tunneling microscopy (STM) and spectroscopy probe the local density of states of single molecules electrically insulated from the substrate. The experimental images, although usually interpreted in terms of single-particle molecular orbitals, are associated with quasiparticle wave functions dressed by the whole electron-electron interaction. Here we propose an ab initio approach based on quantum Monte Carlo to calculate the quasiparticle wave functions of molecules. Through the comparison between Monte Carlo wave functions and their uncorrelated Hartree-Fock counterparts we visualize the electronic correlation embedded in the simulated STM images, highlighting the many-body features that might be observed.

  3. Fra Angelico's painting technique revealed by terahertz time-domain imaging (THz-TDI)

    NASA Astrophysics Data System (ADS)

    Koch Dandolo, Corinna Ludovica; Picollo, Marcello; Cucci, Costanza; Jepsen, Peter Uhd

    2016-10-01

    We have investigated with terahertz time-domain imaging (THz-TDI) the well-known Lamentation over the dead Christ panel painting (San Marco Museum, Florence) painted by Fra Giovanni Angelico within 1436 and 1441. The investigation provided a better understanding of the construction and gilding technique used by the eminent artist, as well as the plastering technique used during the nineteenth-century restoration intervention. The evidence obtained from THz-TDI scans was correlated with the available documentation on the preservation history of the art piece. Erosion and damages documented for the wooden support, especially in the lower margin, found confirmation in the THz-TD images.

  4. Retinal damage in chloroquine maculopathy, revealed by high resolution imaging: a case report utilizing adaptive optics scanning laser ophthalmoscopy.

    PubMed

    Bae, Eun Jin; Kim, Kyoung Rae; Tsang, Stephen H; Park, Sung Pyo; Chang, Stanley

    2014-02-01

    A 53-year-old Asian woman was treated with hydroxychloroquine and chloroquine for lupus erythematosus. Within a few years, she noticed circle-shaped shadows in her central vision. Upon examination, the patient's visual acuity was 20 / 25 in both eyes. Humphrey visual field (HVF) testing revealed a central visual defect, and fundoscopy showed a ring-shaped area of parafoveal retinal pigment epithelium depigmentation. Fundus autofluorescence imaging showed a hypofluorescent lesion consistent with bull's eye retinopathy. Adaptive optics scanning laser ophthalmoscope (AO-SLO) revealed patch cone mosaic lesions, in which cones were missing or lost. In addition, the remaining cones consisted of asymmetrical shapes and sizes that varied in brightness. Unlike previous studies employing deformable mirrors for wavefront aberration correction, our AO-SLO approach utilized dual liquid crystal on silicon spatial light modulators. Thus, by using AO-SLO, we were able to create a photographic montage consisting of high quality images. Disrupted cone AO-SLO images were matched with visual field test results and functional deficits were associated with a precise location on the montage, which allowed correlation of histological findings with functional changes determined by HVF. We also investigated whether adaptive optics imaging was more sensitive to anatomical changes compared with spectral-domain optical coherence tomography.

  5. Two-Dimensional Measurement of n+-p Asymmetrical Junctions in Multicrystalline Silicon Solar Cells Using AFM-Based Electrical Techniques with Nanometer Resolution: Preprint

    SciTech Connect

    Jiang, C. S.; Moutinho, H. R.; Li, J. V.; Al-Jassim, M. M.; Heath, J. T.

    2011-07-01

    Lateral inhomogeneities of modern solar cells demand direct electrical imaging with nanometer resolution. We show that atomic force microscopy (AFM)-based electrical techniques provide unique junction characterizations, giving a two-dimensional determination of junction locations. Two AFM-based techniques, scanning capacitance microscopy/spectroscopy (SCM/SCS) and scanning Kelvin probe force microscopy (SKPFM), were significantly improved and applied to the junction characterizations of multicrystalline silicon (mc-Si) cells. The SCS spectra were taken pixel by pixel by precisely controlling the tip positions in the junction area. The spectra reveal distinctive features that depend closely on the position relative to the electrical junction, which allows us to indentify the electrical junction location. In addition, SKPFM directly probes the built-in potential over the junction area modified by the surface band bending, which allows us to deduce the metallurgical junction location by identifying a peak of the electric field. Our results demonstrate resolutions of 10-40 nm, depending on the techniques (SCS or SKPFM). These direct electrical measurements with nanometer resolution and intrinsic two-dimensional capability are well suited for investigating the junction distribution of solar cells with lateral inhomogeneities.

  6. AFM AND XPS Characterization of Zinc-Aluminum Alloy Coatings with Attention to Surface Dross and Flow Lines

    NASA Astrophysics Data System (ADS)

    Harding, Felipe A.; Alarcon, Nelson A.; Toledo, Pedro G.

    Surfaces of various zinc-aluminum alloy (Zn-Al) coated steel samples are studied with attention to foreign surface dross by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS/ESCA). AFM topographic maps of zinc-aluminum alloy surfaces free of dross reveal the perfect nanoscale details of two kinds of dendrites: branched and globular. In all magnifications the dendrites appear smooth and, in general, very clean. XPS analysis of the extreme surface of a Zn-Al sample reveals Al, Zn, Si and O as the main components. The XPS results show no segregation or separation of phases other than those indicated by the ternary Al-Zn-Si diagram. For surfaces of Zn-Al plagued with impurities, high resolution AFM topographic maps reveal three situations: (1) areas with well-defined dendrites, relatively free of dross; (2) areas with small, millimeter-sized black spots known as dross; and (3) areas with large black stains, known as flow lines. Dendrite deformation and dross accumulation increase notably in the neighborhood, apparently clean to the naked eye, of dross or flow lines. XPS results of areas with dross and flow lines indicate unacceptable high concentration of Si and important Si phase separation. These results, in the light of AFM work, reveal that dross and flow lines are a consequence of a high local concentration of Si from high melting point silica and silicate impurities in the Zn-Al alloy source.

  7. Insulated Conducting Cantilevered Nanotips and Two-Chamber Recording System for High Resolution Ion Sensing AFM

    PubMed Central

    Meckes, Brian; Arce, Fernando Teran; Connelly, Laura S.; Lal, Ratnesh

    2014-01-01

    Biological membranes contain ion channels, which are nanoscale pores allowing controlled ionic transport and mediating key biological functions underlying normal/abnormal living. Synthetic membranes with defined pores are being developed to control various processes, including filtration of pollutants, charge transport for energy storage, and separation of fluids and molecules. Although ionic transport (currents) can be measured with single channel resolution, imaging their structure and ionic currents simultaneously is difficult. Atomic force microscopy enables high resolution imaging of nanoscale structures and can be modified to measure ionic currents simultaneously. Moreover, the ionic currents can also be used to image structures. A simple method for fabricating conducting AFM cantilevers to image pore structures at high resolution is reported. Tungsten microwires with nanoscale tips are insulated except at the apex. This allows simultaneous imaging via cantilever deflections in normal AFM force feedback mode as well as measuring localized ionic currents. These novel probes measure ionic currents as small as picoampere while providing nanoscale spatial resolution surface topography and is suitable for measuring ionic currents and conductance of biological ion channels. PMID:24663394

  8. The Architecture of the LkCa 15 Transitional Disk Revealed By High-Contrast Imaging

    NASA Technical Reports Server (NTRS)

    Thalmann, C.; Mulders, G. D.; Hodapp, K.; Janson, M.; Grady, C.A.; Min, M.; de Juan Ovelar, M.; Carson, J.; Brandt, T.; Bonnefoy, M.; McElwain, M. W.; Leisenring, J.; Dominik, C.; Henning, T.; Tamura, M.

    2014-01-01

    We present four new epochs of Ks-band images of the young pre-transitional disk around LkCa 15 and perform extensive forward modeling to derive the physical parameters of the disk. We find indications of strongly anisotropic scattering (Henyey-Greenstein g = 0.67 (+0.18/-0.11)) and a significantly tapered gap edge ("round wall") but see no evidence that the inner disk, whose existence is predicted by the spectral energy distribution, shadows the outer regions of the disk visible in our images.We marginally confirm the existence of an offset between the disk center and the star along the line of nodes; however, the magnitude of this offset (x = 27 (+19/-20) mas) is notably lower than that found in our earlier H-band images. Intriguingly, we also find an offset of y = 69 (+49/-25) mas perpendicular to the line of nodes at high significance. If confirmed by future observations, this would imply a highly elliptical - or otherwise asymmetric - disk gap with an effective eccentricity of e ˜ 0.3. Such asymmetry would most likely be the result of dynamical sculpting by one or more unseen planets in the system. Finally, we find that the bright arc of scattered light we see in direct imaging observations originates from the near side of the disk and appears brighter than the far side because of strong forward scattering.

  9. Cloud top structure of Venus revealed by Subaru/COMICS mid-infrared images

    NASA Astrophysics Data System (ADS)

    Sato, T. M.; Sagawa, H.; Kouyama, T.; Mitsuyama, K.; Satoh, T.; Ohtsuki, S.; Ueno, M.; Kasaba, Y.; Nakamura, M.; Imamura, T.

    2014-04-01

    We have investigated the cloud top structure of Venus by analyzing ground-based images obtained by the Cooled Mid-Infrared Camera and Spectrometer (COMICS), mounted on the 8.2-m Subaru Telescope. In this presentation, we will overview the observational results and discuss their interpretations.

  10. The Architecture of the LkCa 15 Transitional Disk Revealed by High-contrast Imaging

    NASA Technical Reports Server (NTRS)

    Thalmann, C.; Mulders, G. D.; Hodapp, K.; Janson, M.; Grady, C. A.; Min, M.; deJuanOvelar, M.; Carson, J.; Brandt, T.; Bonnefoy, M.; McElwain, M. W.; Leisenring, J.; Dominik, C.; Henning, T.; Tamura, M.

    2014-01-01

    We present four new epochs of Ks-band images of the young pre-transitional disk around LkCa 15, and perform extensive forward modeling to derive the physical parameters of the disk. We find indications of strongly anisotropic scattering (Henyey-Greenstein g = 0.67+0.18 -0.11) and a significantly tapered gap edge ('round wall'), but see no evidence that the inner disk, whose existence is predicted by the spectral energy distribution, shadows the outer regions of the disk visible in our images. We marginally confirm the existence of an offset between the disk center and the star along the line of nodes; however, the magnitude of this offset (x = 27+19 -20 mas) is notably lower than that found in our earlier H-band images (Thalmann et al. 2010). Intriguingly, we also find, at high significance, an offset of y = 69+49 -25 mas perpendicular to the line of nodes. If confirmed by future observations, this would imply a highly elliptical- or otherwise asymmetric-disk gap with an effective eccentricity of e ˜ 0.3. Such asymmetry would most likely be the result of dynamical sculpting by one or more unseen planets in the system. Finally, we find that the bright arc of scattered light we see in direct imaging observations originates from the near side of the disk, and appears brighter than the far side because of strong forward scattering.

  11. White matter microstructure pathology in classic galactosemia revealed by neurite orientation dispersion and density imaging.

    PubMed

    Timmers, Inge; Zhang, Hui; Bastiani, Matteo; Jansma, Bernadette M; Roebroeck, Alard; Rubio-Gozalbo, M Estela

    2015-03-01

    White matter abnormalities have been observed in patients with classic galactosemia, an inborn error of galactose metabolism. However, magnetic resonance imaging (MRI) data collected in the past were generally qualitative in nature. Our objective was to investigate white matter microstructure pathology and examine correlations with outcome and behaviour in this disease, by using multi-shell diffusion weighted imaging. In addition to standard diffusion tensor imaging (DTI), neurite orientation dispersion and density imaging (NODDI) was used to estimate density and orientation dispersion of neurites in a group of eight patients (aged 16-21 years) and eight healthy controls (aged 15-20 years). Extensive white matter abnormalities were found: neurite density index (NDI) was lower in the patient group in bilateral anterior areas, and orientation dispersion index (ODI) was increased mainly in the left hemisphere. These specific regional profiles are in agreement with the cognitive profile observed in galactosemia, showing higher order cognitive impairments, and language and motor impairments, respectively. Less favourable white matter properties correlated positively with age and age at onset of diet, and negatively with behavioural outcome (e.g. visual working memory). To conclude, this study provides evidence of white matter pathology regarding density and dispersion of neurites in these patients. The results are discussed in light of suggested pathophysiological mechanisms.

  12. 3D assembly of upconverting NaYF4 nanocrystals by AFM nanoxerography: creation of anti-counterfeiting microtags

    NASA Astrophysics Data System (ADS)

    Sangeetha, Neralagatta M.; Moutet, Pierre; Lagarde, Delphine; Sallen, Gregory; Urbaszek, Bernhard; Marie, Xavier; Viau, Guillaume; Ressier, Laurence

    2013-09-01

    Formation of 3D close-packed assemblies of upconverting NaYF4 colloidal nanocrystals (NCs) on surfaces, by Atomic Force Microscopy (AFM) nanoxerography is presented. The surface potential of the charge patterns, the NC concentration, the polarizability of the NCs and the polarity of the dispersing solvent are identified as the key parameters controlling the assembly of NaYF4 NCs into micropatterns of the desired 3D architecture. This insight allowed us to fabricate micrometer sized Quick Response (QR) codes encoded in terms of upconversion luminescence intensity or color. Topographically hidden messages could also be readily incorporated within these microtags. This work demonstrates that AFM nanoxerography has enormous potential for generating high-security anti-counterfeiting microtags.Formation of 3D close-packed assemblies of upconverting NaYF4 colloidal nanocrystals (NCs) on surfaces, by Atomic Force Microscopy (AFM) nanoxerography is presented. The surface potential of the charge patterns, the NC concentration, the polarizability of the NCs and the polarity of the dispersing solvent are identified as the key parameters controlling the assembly of NaYF4 NCs into micropatterns of the desired 3D architecture. This insight allowed us to fabricate micrometer sized Quick Response (QR) codes encoded in terms of upconversion luminescence intensity or color. Topographically hidden messages could also be readily incorporated within these microtags. This work demonstrates that AFM nanoxerography has enormous potential for generating high-security anti-counterfeiting microtags. Electronic supplementary information (ESI) available: Detailed experimental procedures for the synthesis of upconverting NaYF4 nanocrystals and their transmission electron microscopy images. KFM and AFM images corresponding to the assembly of positively charged β-NaYF4:Er3+,Yb3+ nanocrystals from water suspensions by AFM nanoxerography. Photoluminescence spectra of β-NaYF4:Er3+,Yb3+ nanocrystals

  13. Interlayer formation of diamond-like carbon coatings on industrial polyethylene: Thickness dependent surface characterization by SEM, AFM and NEXAFS

    NASA Astrophysics Data System (ADS)

    Fischer, Christian B.; Rohrbeck, Magdalena; Wehner, Stefan; Richter, Matthias; Schmeißer, Dieter

    2013-04-01

    The coating of materials with diamond-like carbon (DLC) is a very common way to change and improve their basic characteristics. Although DLC is used on several substrates, the chemical and physical properties throughout the coating process on plastics are yet sparsely investigated. Two types of protective coatings one sp3-enriched (robust, r-type) and one with more sp2-centers (flexible, f-type) have been realized on polyethylene by PECVD deposition. SEM and AFM analysis of coated samples of DLC types revealed diverse surface topographies on different scales and images appeared even differently smoothed by the carbonaceous deposits. Grains of both DLC types are platelet-shaped and nearly double in size for the robust type indicating fundamental differences in the epitaxial DLC growth. NEXAFS spectroscopy showed significant details of carbon centers in chemically different neighborhood displaying a characteristic fingerprint behavior. Comparison of deposition models revealed a mechanism of interlayer formation which is discussed in detail. Interlayer formation is clearly the appropriate explanation of the process for the current carbon deposition between these two unequal materials. An improved understanding of hard DLC and soft polyethylene assembly is given in the presented work.

  14. The Emergence of AFM Applications to Cell Biology: How new technologies are facilitating investigation of human cells in health and disease at the nanoscale.

    PubMed

    Yang, Ruiguo; Xi, Ning; Fung, Carmen Kar Man; Seiffert-Sinha, Kristina; Lai, King Wai Chiu; Sinha, Animesh A

    2011-01-01

    Atomic Force Microscopy (AFM) based nanorobotics has been used for building nano devices in semiconductors for almost a decade. Leveraging the unparallel precision localization capabilities of this technology, high resolution imaging and mechanical property characterization is now increasingly being performed in biological settings. AFM also offers the prospect for handling and manipulating biological materials at nanometer scale. It has unique advantages over other methods, permitting experiments in the liquid phase where physiological conditions can be maintained. Taking advantage of these properties, our group has visualized membrane and cytoskeletal structures of live cells by controlling the interaction force of the AFM tip with cellular components at the nN or sub-nN range. Cell stiffness changes were observed by statistically analyzing the Young's modulus values of human keratinocytes before and after specific antibody treatment. Furthermore, we used the AFM cantilever as a robotic arm for mechanical pushing, pulling and cutting to perform nanoscale manipulations of cell-associated structures. AFM guided nano-dissection, or nanosurgery was enacted on the cell in order to sever intermediate filaments connecting neighboring keratinocytes via sub 100 nm resolution cuts. Finally, we have used a functionalized AFM tip to probe cell surface receptors to obtain binding force measurements. This technique formed the basis for Single Molecule Force Spectroscopy (SMFS). In addition to enhancing our basic understanding of dynamic signaling events in cell biology, these advancements in AFM based biomedical investigations can be expected to facilitate the search for biomarkers related to disease diagnosis progress and treatment.

  15. Therapeutic imaging window of cerebral infarction revealed by multisequence magnetic resonance imaging: An animal and clinical study.

    PubMed

    Lu, Hong; Hu, Hui; He, Zhanping; Han, Xiangjun; Chen, Jing; Tu, Rong

    2012-11-05

    In this study, we established a Wistar rat model of right middle cerebral artery occlusion and observed pathological imaging changes (T2-weighted imaging [T2WI], T2FLAIR, and diffusion-weighted imaging [DWI]) following cerebral infarction. The pathological changes were divided into three phases: early cerebral infarction, middle cerebral infarction, and late cerebral infarction. In the early cerebral infarction phase (less than 2 hours post-infarction), there was evidence of intracellular edema, which improved after reperfusion. This improvement was defined as the ischemic penumbra. In this phase, a high DWI signal and a low apparent diffusion coefficient were observed in the right basal ganglia region. By contrast, there were no abnormal T2WI and T2FLAIR signals. For the middle cerebral infarction phase (2-4 hours post-infarction), a mixed edema was observed. After reperfusion, there was a mild improvement in cell edema, while the angioedema became more serious. A high DWI signal and a low apparent diffusion coefficient signal were observed, and some rats showed high T2WI and T2FLAIR signals. For the late cerebral infarction phase (4-6 hours post-infarction), significant angioedema was visible in the infarction site. After reperfusion, there was a significant increase in angioedema, while there was evidence of hemorrhage and necrosis. A mixed signal was observed on DWI, while a high apparent diffusion coefficient signal, a high T2WI signal, and a high T2FLAIR signal were also observed. All 86 cerebral infarction patients were subjected to T2WI, T2FLAIR, and DWI. MRI results of clinic data similar to the early infarction phase of animal experiments were found in 51 patients, for which 10 patients (10/51) had an onset time greater than 6 hours. A total of 35 patients had MRI results similar to the middle and late infarction phase of animal experiments, of which eight patients (8/35) had an onset time less than 6 hours. These data suggest that defining the

  16. Molecular dynamics study on the mechanism of AFM-based nanoscratching process with water-layer lubrication

    NASA Astrophysics Data System (ADS)

    Ren, Jiaqi; Zhao, Jinsheng; Dong, Zeguang; Liu, Pinkuan

    2015-08-01

    The atomic force microscopy (AFM) based direct nanoscratching has been thoroughly studied but the mechanism of nanoscratching with water-layer lubrication is yet to be well understood. In current study, three-dimensional molecular dynamics (MD) simulations are conducted to evaluate the effects of the water-layer lubrication on the AFM-based nanoscratching process on monocrystalline copper. Comparisons of workpiece deformation, scratching forces, and friction coefficients are made between the water-lubricated and dry scratching under various thickness of water layer, scratching depth and scratching velocity. Simulation results reveal that the water layer has positive impact on the surface quality and significant influence on the scratching forces (normal forces and tangential forces). The friction coefficients of the tip in water-lubricated nanoscratching are significantly bigger than those in the dry process. Our simulation results shed lights on a promising AFM-based nanofabrication method, which can assist to get nanoscale surface morphologies with higher quality than traditional approaches.

  17. Long-Term Spatiotemporal Reconfiguration of Neuronal Activity Revealed by Voltage-Sensitive Dye Imaging in the Cerebellar Granular Layer

    PubMed Central

    Gandolfi, Daniela; Mapelli, Jonathan; D'Angelo, Egidio

    2015-01-01

    Understanding the spatiotemporal organization of long-term synaptic plasticity in neuronal networks demands techniques capable of monitoring changes in synaptic responsiveness over extended multineuronal structures. Among these techniques, voltage-sensitive dye imaging (VSD imaging) is of particular interest due to its good spatial resolution. However, improvements of the technique are needed in order to overcome limits imposed by its low signal-to-noise ratio. Here, we show that VSD imaging can detect long-term potentiation (LTP) and long-term depression (LTD) in acute cerebellar slices. Combined VSD imaging and patch-clamp recordings revealed that the most excited regions were predominantly associated with granule cells (GrCs) generating EPSP-spike complexes, while poorly responding regions were associated with GrCs generating EPSPs only. The correspondence with cellular changes occurring during LTP and LTD was highlighted by a vector representation obtained by combining amplitude with time-to-peak of VSD signals. This showed that LTP occurred in the most excited regions lying in the core of activated areas and increased the number of EPSP-spike complexes, while LTD occurred in the less excited regions lying in the surround. VSD imaging appears to be an efficient tool for investigating how synaptic plasticity contributes to the reorganization of multineuronal activity in neuronal circuits. PMID:26294979

  18. Fast periodic presentation of natural images reveals a robust face-selective electrophysiological response in the human brain.

    PubMed

    Rossion, Bruno; Torfs, Katrien; Jacques, Corentin; Liu-Shuang, Joan

    2015-01-16

    We designed a fast periodic visual stimulation approach to identify an objective signature of face categorization incorporating both visual discrimination (from nonface objects) and generalization (across widely variable face exemplars). Scalp electroencephalographic (EEG) data were recorded in 12 human observers viewing natural images of objects at a rapid frequency of 5.88 images/s for 60 s. Natural images of faces were interleaved every five stimuli, i.e., at 1.18 Hz (5.88/5). Face categorization was indexed by a high signal-to-noise ratio response, specifically at an oddball face stimulation frequency of 1.18 Hz and its harmonics. This face-selective periodic EEG response was highly significant for every participant, even for a single 60-s sequence, and was generally localized over the right occipitotemporal cortex. The periodicity constraint and the large selection of stimuli ensured that this selective response to natural face images was free of low-level visual confounds, as confirmed by the absence of any oddball response for phase-scrambled stimuli. Without any subtraction procedure, time-domain analysis revealed a sequence of differential face-selective EEG components between 120 and 400 ms after oddball face image onset, progressing from medial occipital (P1-faces) to occipitotemporal (N1-faces) and anterior temporal (P2-faces) regions. Overall, this fast periodic visual stimulation approach provides a direct signature of natural face categorization and opens an avenue for efficiently measuring categorization responses of complex visual stimuli in the human brain.

  19. An optimized two-photon method for in vivo lung imaging reveals intimate cell collaborations during infection

    NASA Astrophysics Data System (ADS)

    Fiole, Daniel; Deman, Pierre; Trescos, Yannick; Douady, Julien; Tournier, Jean-Nicolas

    2013-02-01

    Lung tissue motion arising from breathing and heart beating has been described as the largest annoyance of in vivo imaging. Consequently, infected lung tissue has never been imaged in vivo thus far, and little is known concerning the kinetics of the mucosal immune system at the cellular level. We have developed an optimized post-processing strategy to overcome tissue motion, based upon two-photon and second harmonic generation (SHG) microscopy. In contrast to previously published data, we have freed the lung parenchyma from any strain and depression in order to maintain the lungs under optimal physiological parameters. Excitation beams swept the sample throughout normal breathing and heart movements, allowing the collection of many images. Given that tissue motion is unpredictably, it was essential to sort images of interest. This step was enhanced by using SHG signal from collagen as a reference for sampling and realignment phases. A normalized cross-correlation criterion was used between a manually chosen reference image and rigid transformations of all others. Using CX3CR1+/gfp mice this process allowed the collection of high resolution images of pulmonary dendritic cells (DCs) interacting with Bacillus anthracis spores, a Gram-positive bacteria responsible for anthrax disease. We imaged lung tissue for up to one hour, without interrupting normal lung physiology. Interestingly, our data revealed unexpected interactions between DCs and macrophages, two specialized phagocytes. These contacts may participate in a better coordinate immune response. Our results not only demonstrate the phagocytizing task of lung DCs but also infer a cooperative role of alveolar macrophages and DCs.

  20. Effects of light pollution revealed during a nocturnal aerial survey by two hyperspectral imagers

    NASA Astrophysics Data System (ADS)

    Barducci, Alessandro; Marcoionni, Paolo; Pippi, Ivan; Poggesi, Marco

    2003-07-01

    A remote-sensing campaign was performed in September 2001 at nighttime under clear-sky conditions before moonrise to assess the level of light pollution of urban and industrial origin. Two hyperspectral sensors, namely, the Multispectral Infrared and Visible Imaging Spectrometer and the Visible Infrared Scanner-200, which provide spectral coverage from the visible to the thermal infrared, were flown over the Tuscany coast (Italy) on board a Casa 212 airplane. The acquired images were processed to produce radiometrically calibrated data, which were then analyzed and compared with ground-based spectral measurements. Calibrated data acquired at high spectral resolution (~2.5 nm) showed a maximum scene brightness almost of the same order of magnitude as that observed during similar daytime measurements, whereas their average luminosity was 3 orders of magnitude lower. The measurement analysis confirmed that artificial illumination hinders astronomical observations and produces noticeable effects even at great distances from the sources of the illumination.

  1. Effects of light pollution revealed during a nocturnal aerial survey by two hyperspectral imagers.

    PubMed

    Barducci, Alessandro; Marcoionni, Paolo; Pippi, Ivan; Poggesi, Marco

    2003-07-20

    A remote-sensing campaign was performed in September 2001 at nighttime under clear-sky conditions before moonrise to assess the level of light pollution of urban and industrial origin. Two hyperspectral sensors, namely, the Multispectral Infrared and Visible Imaging Spectrometer and the Visible Infrared Scanner-200, which provide spectral coverage from the visible to the thermal infrared, were flown over the Tuscany coast (Italy) on board a Casa 212 airplane. The acquired images were processed to produce radiometrically calibrated data, which were then analyzed and compared with ground-based spectral measurements. Calibrated data acquired at high spectral resolution (approximately 2.5 nm) showed a maximum scene brightness almost of the same order of magnitude as that observed during similar daytime measurements, whereas their average luminosity was 3 orders of magnitude lower. The measurement analysis confirmed that artificial illumination hinders astronomical observations and produces noticeable effects even at great distances from the sources of the illumination.

  2. Imaging of nucleic acids with atomic force microscopy

    PubMed Central

    Lyubchenko, Yuri L.; Shlyakhtenko, Luda S.; Ando, Toshio

    2011-01-01

    Atomic force microscopy (AFM) is a key tool of nanotechnology with great importance in applications to DNA nanotechnology and to the recently emerging field of RNA nanotechnology. Advances in the methodology of AFM now enable reliable and reproducible imaging of DNA of various structures, topologies, and DNA and RNA nanostructures. These advances are reviewed here with emphasis on methods utilizing modification of mica to prepare the surfaces enabling reliable and reproducible imaging of DNA and RNA nanostructures. Since the AFM technology for DNA is more mature, AFM imaging of DNA is introduced in this review to provide experience and background for the improvement of AFM imaging of RNA. Examples of imaging different structures of RNA and DNA are discussed and illustrated. Special attention is given to the potential use of AFM to image the dynamics of nucleic acids at the nanometer scale. As such, we review recent advances with the use of time-lapse AFM. PMID:21310240

  3. Revealing the carbohydrate pattern on a cell surface by super-resolution imaging

    NASA Astrophysics Data System (ADS)

    Chen, Junling; Gao, Jing; Wu, Jiazhen; Zhang, Min; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Tian, Zhiyuan; Wang, Hongda

    2015-02-01

    Carbohydrates are involved in various physiological and pathological activities including cell adhesion, signal transduction and tumor invasion. The distribution of carbohydrates is the molecular basis of their multiple functions, but remains poorly understood. Here, we employed direct stochastic optical reconstruction microscopy (dSTORM) to visualize the pattern of N-acetylglucosamine (N-GlcNAc) on Vero cell membranes at the nanometer level of resolution. We found that N-GlcNAcs exist in irregular clusters on the apical membrane with an average cluster area of about 0.37 μm2. Most of these N-GlcNAc clusters are co-localized with lipid rafts by dual-color dSTORM imaging, suggesting that carbohydrates are closely associated with lipid rafts as the functional domains. Our results demonstrate that super-resolution imaging is capable of characterizing the distribution of carbohydrates on the cellular surface at the molecular level.Carbohydrates are involved in various physiological and pathological activities including cell adhesion, signal transduction and tumor invasion. The distribution of carbohydrates is the molecular basis of their multiple functions, but remains poorly understood. Here, we employed direct stochastic optical reconstruction microscopy (dSTORM) to visualize the pattern of N-acetylglucosamine (N-GlcNAc) on Vero cell membranes at the nanometer level of resolution. We found that N-GlcNAcs exist in irregular clusters on the apical membrane with an average cluster area of about 0.37 μm2. Most of these N-GlcNAc clusters are co-localized with lipid rafts by dual-color dSTORM imaging, suggesting that carbohydrates are closely associated with lipid rafts as the functional domains. Our results demonstrate that super-resolution imaging is capable of characterizing the distribution of carbohydrates on the cellular surface at the molecular level. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr05970k

  4. Two-Photon Autofluorescence Imaging Reveals Cellular Structures Throughout the Retina of the Living Primate Eye

    PubMed Central

    Sharma, Robin; Williams, David R.; Palczewska, Grazyna; Palczewski, Krzysztof; Hunter, Jennifer J.

    2016-01-01

    Purpose Although extrinsic fluorophores can be introduced to label specific cell types in the retina, endogenous fluorophores, such as NAD(P)H, FAD, collagen, and others, are present in all retinal layers. These molecules are a potential source of optical contrast and can enable noninvasive visualization of all cellular layers. We used a two-photon fluorescence adaptive optics scanning light ophthalmoscope (TPF-AOSLO) to explore the native autofluorescence of various cell classes spanning several layers in the unlabeled retina of a living primate eye. Methods Three macaques were imaged on separate occasions using a custom TPF-AOSLO. Two-photon fluorescence was evoked by pulsed light at 730 and 920 nm excitation wavelengths, while fluorescence emission was collected in the visible range from several retinal layers and different locations. Backscattered light was recorded simultaneously in confocal modality and images were postprocessed to remove eye motion. Results All retinal layers yielded two-photon signals and the heterogeneous distribution of fluorophores provided optical contrast. Several structural features were observed, such as autofluorescence from vessel walls, Müller cell processes in the nerve fibers, mosaics of cells in the ganglion cell and other nuclear layers of the inner retina, as well as photoreceptor and RPE layers in the outer retina. Conclusions This in vivo survey of two-photon autofluorescence throughout the primate retina demonstrates a wider variety of structural detail in the living eye than is available through conventional imaging methods, and broadens the use of two-photon imaging of normal and diseased eyes. PMID:26903224

  5. Nonlinear air-coupled emission: The signature to reveal and image microdamage in solid materials

    SciTech Connect

    Solodov, Igor; Busse, Gerd

    2007-12-17

    It is shown that low-frequency elastic vibrations of near-surface planar defects cause high-frequency ultrasonic radiation in surrounding air. The frequency conversion mechanism is concerned with contact nonlinearity of the defect vibrations and provides efficient generation of air-coupled higher-order ultraharmonics, ultrasubharmonics, and combination frequencies. The nonlinear air-coupled ultrasonic emission is applied for location and high-resolution imaging of damage-induced defects in a variety of solid materials.

  6. Analysis of image versus position, scale and direction reveals pattern texture anisotropy

    NASA Astrophysics Data System (ADS)

    Lehoucq, Roland; Weiss, Jerome; Dubrulle, Berengere; Amon, Axelle; Le Bouil, Antoine; Crassous, Jerome; Amitrano, David; Graner, Francois

    2014-12-01

    Pattern heterogeneities and anisotropies often carry significant physical information. We provide a toolbox which: (i) cumulates analysis in terms of position, direction and scale; (ii) is as general as possible; (iii) is simple and fast to understand, implement, execute and exploit. It consists in dividing the image into analysis boxes at a chosen scale; in each box an ellipse (the inertia tensor) is fitted to the signal and thus determines the direction in which the signal is more present. This tensor can be averaged in position and/or be used to study the dependence with scale. This choice is formally linked with Leray transforms and anisotropic wavelet analysis. Such protocol is intutively interpreted and consistent with what the eye detects: relevant scales, local variations in space, priviledged directions. It is fast and parallelizable. Its several variants are adaptable to the user's data and needs. It is useful to statistically characterize anisotropies of 2D or 3D patterns in which individual objects are not easily distinguished, with only minimal pre-processing of the raw image, and more generally applies to data in higher dimensions. It is less sensitive to edge effects, and thus better adapted for a multiscale analysis down to small scale boxes, than pair correlation function or Fourier transform. Easy to understand and implement, it complements more sophisticated methods such as Hough transform or diffusion tensor imaging. We use it on various fracture patterns (sea ice cover, thin sections of granite, granular materials), to pinpoint the maximal anisotropy scales. The results are robust to noise and to user choices. This toolbox could turn also useful for granular materials, hard condensed matter, geophysics, thin films, statistical mechanics, characterisation of networks, fluctuating amorphous systems, inhomogeneous and disordered systems, or medical imaging, among others.

  7. Dynamic views of living cell fine structure revealed by birefringence imaging

    NASA Astrophysics Data System (ADS)

    Oldenbourg, Rudolf

    2001-11-01

    We have been developing and applying a new type of polarized light microscope, the new Pol-Scope, which dramatically enhances the unique capabilities of the traditional polarizing microscope. In living cells, without applying exogenous dyes or florescent labels, we have studied the dynamic organization of filamentous actin in neuronal growth cones and improved the efficiency of spindle imaging for in-vitro fertilization and enucleation procedures.

  8. THE INNER ENVELOPE AND DISK OF L1527 REVEALED: GEMINI L'-BAND-SCATTERED LIGHT IMAGING

    SciTech Connect

    Tobin, John J.; Hartmann, Lee; Loinard, Laurent

    2010-10-10

    We present high-resolution L'-band imaging of the inner scattered light structure of Class 0 protostar L1527 IRS (IRAS 04368+2557) taken with the Gemini North telescope. The central point-source-like feature seen in Spitzer Space Telescope IRAC images is resolved in the Gemini image into a compact bipolar structure with a narrow dark lane in the center. Two scattered light lobes are extended {approx}1.''8 (200 AU) perpendicular to the direction of the outflow and {approx}2.''5 (350 AU) along the outflow axis; the narrow dark lane between the scattered light lobes is {approx}0.''45 (60 AU) thick. The observations are consistent with our initial modeling of a bright inner cavity separated by a dark lane due to extinction along the line of sight of the central protostar by the disk. The bright, compact scattered light might be due to complex inner structure generated by the outflow, as suggested in our first paper, or it may more likely be the upper layers of the disk forming from infalling matter.

  9. Dark field optical imaging reveals vascular changes in an inducible hamster cheek pouch model during carcinogenesis

    PubMed Central

    Hu, Fangyao; Morhard, Robert; Murphy, Helen A.; Zhu, Caigang; Ramanujam, Nimmi

    2016-01-01

    In this study, we propose a low-cost cross-polarized dark field microscopy system for in vivo vascular imaging to detect head and neck cancer. A simple-to-use Gabor-filter-based image processing technique was developed to objectively and automatically quantify several important vascular features, including tortuosity, length, diameter and area fraction, from vascular images. Simulations were performed to evaluate the accuracies of vessel segmentation and feature extraction for our algorithm. Sensitivity and specificity for vessel segmentation of the Gabor masks both remained above 80% at all contrast levels when compared to gold-standard masks. Errors for vascular feature extraction were under 5%. Moreover, vascular contrast and vessel diameter were identified to be the two primary factors which affected the segmentation accuracies. After our algorithm was validated, we monitored the blood vessels in an inducible hamster cheek pouch carcinogen model over 17 weeks and quantified vascular features during carcinogenesis. A significant increase in vascular tortuosity and a significant decrease in vessel length were observed during carcinogenesis. PMID:27699096

  10. Speech processing asymmetry revealed by dichotic listening and functional brain imaging.

    PubMed

    Hugdahl, Kenneth; Westerhausen, René

    2016-12-01

    In this article, we review research in our laboratory from the last 25 to 30 years on the neuronal basis for laterality of speech perception focusing on the upper, posterior parts of the temporal lobes, and its functional and structural connections to other brain regions. We review both behavioral and brain imaging data, with a focus on dichotic listening experiments, and using a variety of imaging modalities. The data have come in most parts from healthy individuals and from studies on normally functioning brain, although we also review a few selected clinical examples. We first review and discuss the structural model for the explanation of the right-ear advantage (REA) and left hemisphere asymmetry for auditory language processing. A common theme across many studies have been our interest in the interaction between bottom-up, stimulus-driven, and top-down, instruction-driven, aspects of hemispheric asymmetry, and how perceptual factors interact with cognitive factors to shape asymmetry of auditory language information processing. In summary, our research have shown laterality for the initial processing of consonant-vowel syllables, first observed as a behavioral REA when subjects are required to report which syllable of a dichotic syllable-pair they perceive. In subsequent work we have corroborated the REA with brain imaging, and have shown that the REA is modulated through both bottom-up manipulations of stimulus properties, like sound intensity, and top-down manipulations of cognitive properties, like attention focus.

  11. A phase 1 study of the bispecific anti-CD30/CD16A antibody construct AFM13 in patients with relapsed or refractory Hodgkin lymphoma

    PubMed Central

    Rothe, Achim; Sasse, Stephanie; Topp, Max S.; Eichenauer, Dennis A.; Hummel, Horst; Reiners, Katrin S.; Dietlein, Markus; Kuhnert, Georg; Kessler, Joerg; Buerkle, Carolin; Ravic, Miroslav; Knackmuss, Stefan; Marschner, Jens-Peter; Pogge von Strandmann, Elke; Borchmann, Peter

    2015-01-01

    AFM13 is a bispecific, tetravalent chimeric antibody construct (TandAb) designed for the treatment of CD30-expressing malignancies. AFM13 recruits natural killer (NK) cells via binding to CD16A as immune effector cells. In this phase 1 dose-escalation study, 28 patients with heavily pretreated relapsed or refractory Hodgkin lymphoma received AFM13 at doses of 0.01 to 7 mg/kg body weight. Primary objectives were safety and tolerability. Secondary objectives included pharmacokinetics, antitumor activity, and pharmacodynamics. Adverse events were generally mild to moderate. The maximum tolerated dose was not reached. Pharmacokinetics assessment revealed a half-life of up to 19 hours. Three of 26 evaluable patients achieved partial remission (11.5%) and 13 patients achieved stable disease (50%), with an overall disease control rate of 61.5%. AFM13 was also active in brentuximab vedotin–refractory patients. In 13 patients who received doses of ≥1.5 mg/kg AFM13, the overall response rate was 23% and the disease control rate was 77%. AFM13 treatment resulted in a significant NK-cell activation and a decrease of soluble CD30 in peripheral blood. In conclusion, AFM13 represents a well-tolerated, safe, and active targeted immunotherapy of Hodgkin lymphoma. A phase 2 study is currently planned to optimize the dosing schedule in order to further improve the therapeutic efficacy. This phase 1 study was registered at www.clinicaltrials.gov as #NCT01221571. PMID:25887777

  12. Enzymatic nanolithography of FRET peptide layer using V8 protease-immobilized AFM probe.

    PubMed

    Nakamura, Chikashi; Miyamoto, Chie; Obataya, Ikuo; Takeda, Seiji; Yabuta, Masayuki; Miyake, Jun

    2007-04-15

    In our study, a method based on Enzymatic nanolithography was successfully performed in a buffered solution using Staphylococcal serine V8 protease and AFM. To estimate the lithographing activity of the protease immobilized on the AFM tip to peptides immobilized on a substrate, we designed fluorescence resonance energy transfer (FRET) peptides as reporter peptides that showed enzymatic action specific to the V8 protease. When the protease digested the reporter peptide a quencher residue was released from the peptide and resulted in the appearance of fluorescence. In the designed 9-mer peptides, TAMRA functioned as a good quencher for FAM. When the fluorescence resonance energy transfer peptides immobilized on a glass substrate were hydrolyzed by V8 protease at the C-terminal of glutamic acid, fluorescence of a reporter dye was observed because of the release of a quencher from the substrate. After contacting and lateral scanning of the protease-immobilized AFM tip to the reporter peptide layer, a fluorescent area was observed by imaging using total internal refection fluorescence microscopy (TIRFM). The increment of fluorescence intensity of the digested peptide indicates the performance of lithography. Lithographing rates increased in inverse relation to scanning rates of the probe. The maximum limit of the scanning rate, i.e., that was too fast to permit cutting of the peptide on the substrate, and the lithographing performance are discussed in this study.

  13. Bacterial adhesion to protein-coated surfaces: An AFM and QCM-D study

    NASA Astrophysics Data System (ADS)

    Strauss, Joshua; Liu, Yatao; Camesano, Terri A.

    2009-09-01

    Bacterial adhesion to biomaterials, mineral surfaces, or other industrial surfaces is strongly controlled by the way bacteria interact with protein layers or organic matter and other biomolecules that coat the materials. Despite this knowledge, many studies of bacterial adhesion are performed under clean conditions, instead of in the presence of proteins or organic molecules. We chose fetal bovine serum (FBS) as a model protein, and prepared FBS films on quartz crystals. The thickness of the FBS layer was characterized using atomic force microscopy (AFM) imaging under liquid and quartz crystal microbalance with dissipation (QCM-D). Next, we characterized how the model biomaterial surface would interact with the nocosomial pathogen Staphylococcus epidermidis. An AFM probe was coated with S. epidermidis cells and used to probe a gold slide that had been coated with FBS or another protein, fibronectin (FN). These experiments show that AFM and QCM-D can be used in complementary ways to study the complex interactions between bacteria, proteins, and surfaces.

  14. AFM-based quantification of conformational changes in DNA caused by reactive oxygen species.

    PubMed

    Berg, Florian; Wilken, Janine; Helm, Christiane A; Block, Stephan

    2015-01-08

    Radical induced modification of DNA plays an important role in many pathological pathways like cancer development, aging, etc. In this work, we quantify radical-induced DNA damage that causes transitions from double to single stranded DNA using atomic force microscopy (AFM). The plasmid pBR322 is attacked by free hydroxyl radicals that are produced by Fenton's reaction; the strength of the radical attack is controlled via the ratio of hydroxyl radical molecules to DNA base pairs. The extent of DNA modification is assessed by AFM tapping mode (TM) imaging of the plasmids (after adsorption onto PAH-functionalized mica) in air. As single stranded DNA chains (height ∼2 Å) are much smaller than intact DNA strands (∼5 Å), their fraction can be quantified based on the height distribution, which allows a simplified data analysis in comparison to similar AFM-based approaches. It is found that the amount of damaged DNA strands increases with increasing strength of radical attack, and decreases if ROS scavengers like sodium acetate are added. Competition curves are calculated for the interaction of hydroxyl radicals with DNA and sodium acetate, which finally allows calculation of relative rate constants for the respective reactions.

  15. A novel dog-bone oscillating AFM probe with thermal actuation and piezoresistive detection.

    PubMed

    Xiong, Zhuang; Mairiaux, Estelle; Walter, Benjamin; Faucher, Marc; Buchaillot, Lionel; Legrand, Bernard

    2014-10-31

    In order to effectively increase the resonance frequency and the quality factor of atomic force microscope (AFM) probes, a novel oscillating probe based on a dog-bone shaped MEMS resonator was conceived, designed, fabricated and evaluated. The novel probe with 400 μm in length, 100 μm in width and 5 μm in thickness was enabled to feature MHz resonance frequencies with integrated thermal actuation and piezoresistive detection. Standard silicon micromachining was employed. Both electrical and optical measurements were carried out in air. The resonance frequency and the quality factor of the novel probe were measured to be 5.4 MHz and 4000 respectively, which are much higher than those (about several hundreds of kHz) of commonly used cantilever probes. The probe was mounted onto a commercial AFM set-up through a dedicated probe-holder and circuit board. Topographic images of patterned resist samples were obtained. It is expected that the resonance frequency and the measurement bandwidth of such probes will be further increased by a proper downscaling, thus leading to a significant increase in the scanning speed capability of AFM instruments.

  16. A Novel Dog-Bone Oscillating AFM Probe with Thermal Actuation and Piezoresistive Detection †

    PubMed Central

    Xiong, Zhuang; Mairiaux, Estelle; Walter, Benjamin; Faucher, Marc; Buchaillot, Lionel; Legrand, Bernard

    2014-01-01

    In order to effectively increase the resonance frequency and the quality factor of atomic force microscope (AFM) probes, a novel oscillating probe based on a dog-bone shaped MEMS resonator was conceived, designed, fabricated and evaluated. The novel probe with 400 μm in length, 100 μm in width and 5 μm in thickness was enabled to feature MHz resonance frequencies with integrated thermal actuation and piezoresistive detection. Standard silicon micromachining was employed. Both electrical and optical measurements were carried out in air. The resonance frequency and the quality factor of the novel probe were measured to be 5.4 MHz and 4000 respectively, which are much higher than those (about several hundreds of kHz) of commonly used cantilever probes. The probe was mounted onto a commercial AFM set-up through a dedicated probe-holder and circuit board. Topographic images of patterned resist samples were obtained. It is expected that the resonance frequency and the measurement bandwidth of such probes will be further increased by a proper downscaling, thus leading to a significant increase in the scanning speed capability of AFM instruments. PMID:25365463

  17. Advantages and limitations of OM, SEM, TEM and AFM in the study of ancient decorated pottery

    NASA Astrophysics Data System (ADS)

    Arenas-Alatorre, J.; Silva-Velazquez, Y.; Alva Medina, A.; Rivera, M.

    2010-03-01

    This paper presents results from the study of two fragments of pre-Hispanic pottery, decorated with red pigment, using Optical Microscopy (OM), Scanning Electron Microscopy (SEM), High Resolution Transmission Electron Microscopy (HRTEM), Atomic Force Microscopy (AFM) and Magnetic Force Microscopy (MFM). Capabilities and limitations of these techniques in the analysis of archaeological material are highlighted with special emphasis on TEM, AFM and MFM due to their contribution in the study of the pigment layer at micro and nano scale. The analyzed samples come from the archaeological sites of El Tajin and Xochicalco, both in Mexico. Results of conventional TEM and HRTEM analysis of the red pigment showed nanometric Fe2O3 particles in both samples but different particle shape and size distributions: specimen from El Tajin presented irregular particles between 50-100 nm while that from Xochicalco exhibited semispherical shapes in the 3-25 nm range. AFM images showed the topography of the pigments, which are related to the texture of their surface and thus to the production process. Finally, MFM showed different contrast regions suggesting the presence of ferromagnetic elements forming clusters and domain orientations on the color layer.

  18. AFM review study on pox viruses and living cells.

    PubMed

    Ohnesorge, F M; Hörber, J K; Häberle, W; Czerny, C P; Smith, D P; Binnig, G

    1997-10-01

    Single living cells were studied in growth medium by atomic force microscopy at a high--down to one image frame per second--imaging rate over time periods of many hours, stably producing hundreds of consecutive scans with a lateral resolution of approximately 30-40 nm. The cell was held by a micropipette mounted onto the scanner-piezo as shown in Häberle, W., J. K. H. Hörber, and G. Binnig. 1991. Force microscopy on living cells. J. Vac. Sci. Technol. B9:1210-0000. To initiate specific processes on the cell surface the cells had been infected with pox viruses as reported earlier and, most likely, the liberation of a progeny virion by the still-living cell was observed, hence confirming and supporting earlier results (Häberle, W., J. K. H. Hörber, F. Ohnesorge, D. P. E. Smith, and G. Binnig. 1992. In situ investigations of single living cells infected by viruses. Ultramicroscopy. 42-44:1161-0000; Hörber, J. K. H., W. Häberle, F. Ohnesorge, G. Binnig, H. G. Liebich, C. P. Czerny, H. Mahnel, and A. Mayr. 1992. Investigation of living cells in the nanometer regime with the atomic force microscope. Scanning Microscopy. 6:919-930). Furthermore, the pox viruses used were characterized separately by AFM in an aqueous environment down to the molecular level. Quasi-ordered structural details were resolved on a scale of a few nm where, however, image distortions and artifacts due to multiple tip effects are probably involved--just as in very high resolution (<15-20 nm) images on the cells. Although in a very preliminary manner, initial studies on the mechanical resonance properties of a single living (noninfected) cell, held by the micropipette, have been performed. In particular, frequency response spectra were recorded that indicate elastic properties and enough stiffness of these cells to make the demonstrated rapid scanning of the imaging tip plausible. Measurements of this kind, especially if they can be proven to be cell-type specific, may perhaps have a large

  19. Autonomous bed-sediment imaging-systems for revealing temporal variability of grain size

    USGS Publications Warehouse

    Buscombe, Daniel; Rubin, David M.; Lacy, Jessica R.; Storlazzi, Curt D.; Hatcher, Gerald; Chezar, Henry; Wyland, Robert; Sherwood, Christopher R.

    2014-01-01

    We describe a remotely operated video microscope system, designed to provide high-resolution images of seabed sediments. Two versions were developed, which differ in how they raise the camera from the seabed. The first used hydraulics and the second used the energy associated with wave orbital motion. Images were analyzed using automated frequency-domain methods, which following a rigorous partially supervised quality control procedure, yielded estimates to within 20% of the true size as determined by on-screen manual measurements of grains. Long-term grain-size variability at a sandy inner shelf site offshore of Santa Cruz, California, USA, was investigated using the hydraulic system. Eighteen months of high frequency (min to h), high-resolution (μm) images were collected, and grain size distributions compiled. The data constitutes the longest known high-frequency record of seabed-grain size at this sample frequency, at any location. Short-term grain-size variability of sand in an energetic surf zone at Praa Sands, Cornwall, UK was investigated using the ‘wave-powered’ system. The data are the first high-frequency record of grain size at a single location of a highly mobile and evolving bed in a natural surf zone. Using this technology, it is now possible to measure bed-sediment-grain size at a time-scale comparable with flow conditions. Results suggest models of sediment transport at sandy, wave-dominated, nearshore locations should allow for substantial changes in grain-size distribution over time-scales as short as a few hours.

  20. Continuous multi-modality brain imaging reveals modified neurovascular seizure response after intervention

    PubMed Central

    Ringuette, Dene; Jeffrey, Melanie A.; Dufour, Suzie; Carlen, Peter L.; Levi, Ofer

    2017-01-01

    We developed a multi-modal brain imaging system to investigate the relationship between blood flow, blood oxygenation/volume, intracellular calcium and electrographic activity during acute seizure-like events (SLEs), both before and after pharmacological intervention. Rising blood volume was highly specific to SLE-onset whereas blood flow was more correlated with all eletrographic activity. Intracellular calcium spiked between SLEs and at SLE-onset with oscillation during SLEs. Modified neurovascular and ionic SLE responses were observed after intervention and the interval between SLEs became shorter and more inconsistent. Comparison of artery and vein pulsatile flow suggest proximal interference and greater vascular leakage prior to intervention. PMID:28270990

  1. Measurement of Fibrin Fiber Strength using AFM

    NASA Astrophysics Data System (ADS)

    Jawerth, Louise; Falvo, Mchael; Canning, Anthony; Matthews, Garrett; Superfine, Richard; Guthold, Martin

    2003-11-01

    Blood clots usually form in the event of injury or damage to blood vessels to prevent the loss of blood. Moreover, as we age, blood clots often form in undesired locations, i.e. in blood vessels around the heart or brain, or in uninjured vessels resulting in heart attacks or strokes. Fibrin fibers, the skeleton of a blood clot, essentially perform the mechanical task of creating a blockage that stems blood flow. Thus, a better understanding of the mechanical properties of these fibers, such as the tensile strength and Young's modulus, will enhance our understanding of blood clots. For quantitative stress and strain measurements, we need to image the deformation of the fiber and measure the applied force simultaneously. For this reason, we are combining fluorescent microscopy with atomic force microscopy. Fibrin fibers were fluorescently labeled with streptavidin-coated quantum dots and deposited on a functionalized glass substrate, imaged and manipulated under buffer. We will describe our progress in obtaining quantitative lateral force measurements under buffer simultaneous with strain measurements from optical microscope images.

  2. High-Content Imaging Reveals Expansion of the Endosomal Compartment during Coxiella burnetii Parasitophorous Vacuole Maturation

    PubMed Central

    Larson, Charles L.; Heinzen, Robert A.

    2017-01-01

    Coxiella burnetii is an obligate intracellular pathogen and the causative agent of human Q fever. Replication of the bacterium within a large parasitophorous vacuole (PV) resembling a host phagolysosome is required for pathogenesis. PV biogenesis is a pathogen driven process that requires engagement of several host cell vesicular trafficking pathways to acquire vacuole components. The goal of this study was to determine if infection by C. burnetii modulates endolysosomal flux to potentially benefit PV formation. HeLa cells, infected with C. burnetii or left uninfected, were incubated with fluorescent transferrin (Tf) for 0–30 min, and the amount of Tf internalized by cells quantitated by high-content imaging. At 3 and 5 days, but not 1 day post-infection, the maximal amounts of fluorescent Tf internalized by infected cells were significantly greater than uninfected cells. The rates of Tf uptake and recycling were the same for infected and uninfected cells; however, residual Tf persisted in EEA.1 positive compartments adjacent to large PV after 30 min of recycling in the absence of labeled Tf. On average, C. burnetii-infected cells contained significantly more CD63-positive endosomes than uninfected cells. In contrast, cells containing large vacuoles generated by Chlamydia trachomatis exhibited increased rates of Tf internalization without increased CD63 expression. Our results suggest that C. burnetii infection expands the endosomal system to increase capacity for endocytic material. Furthermore, this study demonstrates the power of high-content imaging for measurement of cellular responses to infection by intracellular pathogens. PMID:28293541

  3. A Zebrafish Live Imaging Model Reveals Differential Responses of Microglia Toward Glioblastoma Cells In Vivo

    PubMed Central

    Hamilton, Lloyd; Astell, Katy R.; Velikova, Gergana

    2016-01-01

    Abstract Glioblastoma multiforme is the most common and deadliest form of brain cancer. Glioblastomas are infiltrated by a high number of microglia, which promote tumor growth and surrounding tissue invasion. However, it is unclear how microglia and glioma cells physically interact and if there are differences, depending on glioma cell type. Hence, we have developed a novel live imaging assay to study microglia–glioma interactions in vivo in the zebrafish brain. We transplanted well-established human glioblastoma cell lines, U87 and U251, into transgenic zebrafish lines with labelled macrophages/microglia. Our confocal live imaging results show distinct interactions between microglia and U87, as well as U251 glioblastoma cells that differ in number and nature. Importantly these interactions do not appear to be antitumoral as zebrafish microglia do not engulf and phagocytose the human glioblastoma cells. Finally, xenotransplants into the irf8−/− zebrafish mutant that lacks microglia, as well as pharmacological inhibition of the CSF-1 receptor (CSF-1R) on microglia, confirm a prominent role for zebrafish microglia in promoting human glioblastoma cell growth. This new model will be an important tool for drug screening and the development of future immunotherapeutics targeting microglia within glioma. PMID:27779463

  4. Quantitative Analysis of Fundus-Image Sequences Reveals Phase of Spontaneous Venous Pulsations

    PubMed Central

    Moret, Fabrice; Reiff, Charlotte M.; Lagrèze, Wolf A.; Bach, Michael

    2015-01-01

    Purpose Spontaneous venous pulsation correlates negatively with elevated intracranial pressure and papilledema, and it relates to glaucoma. Yet, its etiology remains unclear. A key element to elucidate its underlying mechanism is the time at which collapse occurs with respect to the heart cycle, but previous reports are contradictory. We assessed this question in healthy subjects using quantitative measurements of both vein diameters and artery lateral displacements; the latter being used as the marker of the ocular systole time. Methods We recorded 5-second fundus sequences with a near-infrared scanning laser ophthalmoscope in 12 young healthy subjects. The image sequences were coregistered, cleaned from microsaccades, and filtered via a principal component analysis to remove nonpulsatile dynamic features. Time courses of arterial lateral displacement and of diameter at sites of spontaneous venous pulsation or proximal to the disk were retrieved from those image sequences and compared. Results Four subjects displayed both arterial and venous pulsatile waveforms. On those, we observed venous diameter waveforms differing markedly among the subjects, ranging from a waveform matching the typical intraocular pressure waveform to a close replica of the arterial waveform. Conclusions The heterogeneity in waveforms and arteriovenous phases suggests that the mechanism governing the venous outflow resistance differs among healthy subjects. Translational relevance Further characterizations are necessary to understand the heterogeneous mechanisms governing the venous outflow resistance as this resistance is altered in glaucoma and is instrumental when monitoring intracranial hypertension based on fundus observations. PMID:26396929

  5. The Eye of the Medusa: XRF Imaging Reveals Unknown Traces of Antique Polychromy.

    PubMed

    Alfeld, Matthias; Mulliez, Maud; Martinez, Philippe; Cain, Kevin; Jockey, Philippe; Walter, Philippe

    2017-02-07

    The colorful decoration of statues and buildings in antique times is commonly described by the term antique polychromy. It is well-known among scholars but less so to the general public, and its exact form is the subject of research. In this paper we discuss results obtained from the frieze of the Siphnian Treasury in the Sanctuary of Delphi (Greece). We will present the first application of a mobile instrument for macro-XRF imaging for the in situ investigation of antique polychromy and show that it allows one to identify significant traces not visible to the naked eye and not detectable by XRF spot measurements or any other mobile, noninvasive method. These findings allow for a partial reconstruction of the polychromy. Furthermore, we present a novel approach enabling the correct interpretation of artifacts resulting from changes of the detection geometry in the investigation of complexly shaped samples by XRF imaging. This approach is based on the 3D surface model acquired by photogrammetry and fundamental parameter calculations.

  6. The footprints of visual attention in the Posner cueing paradigm revealed by classification images

    NASA Technical Reports Server (NTRS)

    Eckstein, Miguel P.; Shimozaki, Steven S.; Abbey, Craig K.

    2002-01-01

    In the Posner cueing paradigm, observers' performance in detecting a target is typically better in trials in which the target is present at the cued location than in trials in which the target appears at the uncued location. This effect can be explained in terms of a Bayesian observer where visual attention simply weights the information differently at the cued (attended) and uncued (unattended) locations without a change in the quality of processing at each location. Alternatively, it could also be explained in terms of visual attention changing the shape of the perceptual filter at the cued location. In this study, we use the classification image technique to compare the human perceptual filters at the cued and uncued locations in a contrast discrimination task. We did not find statistically significant differences between the shapes of the inferred perceptual filters across the two locations, nor did the observed differences account for the measured cueing effects in human observers. Instead, we found a difference in the magnitude of the classification images, supporting the idea that visual attention changes the weighting of information at the cued and uncued location, but does not change the quality of processing at each individual location.

  7. MALDI-imaging reveals thymosin beta-4 as an independent prognostic marker for colorectal cancer

    PubMed Central

    Gemoll, Timo; Strohkamp, Sarah; Schillo, Katharina; Thorns, Christoph; Habermann, Jens K.

    2015-01-01

    DNA aneuploidy has been identified as a prognostic factor for epithelial malignancies. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for direct analysis of multiple proteins in tissue sections while maintaining the cellular and molecular integrity. We compared diploid and aneuploid colon cancer tissues against normal mucosa of the colon by means of IMS. DNA image cytometry determined the ploidy status of tissue samples that were subsequently subjected to MALDI-IMS. After obtaining protein profiles through direct analysis of tissue sections, a discovery and independent validation set were used to predict ploidy status by applying proteomic classification algorithms [Supervised Neural Network (SNN) and Receiver Operating Characteristic (ROC)]. Five peaks (m/z 2,395 and 4,977 for diploid vs. aneuploid comparison as well as m/z 3,376, 6,663, and 8,581 for normal mucosa vs. carcinoma comparison) were significant in both SNN and ROC analysis. Among these, m/z 4,977 was identified as thymosin beta 4 (Tβ-4). Tβ-4 was subsequently validated in clinical samples using a tissue microarray to predict overall survival in colon cancer patients. PMID:26556858

  8. Quantitative image analysis reveals distinct structural transitions during aging in Caenorhabditis elegans tissues.

    PubMed

    Johnston, Josiah; Iser, Wendy B; Chow, David K; Goldberg, Ilya G; Wolkow, Catherine A

    2008-07-30

    Aging is associated with functional and structural declines in many body systems, even in the absence of underlying disease. In particular, skeletal muscles experience severe declines during aging, a phenomenon termed sarcopenia. Despite the high incidence and severity of sarcopenia, little is known about contributing factors and development. Many studies focus on functional aspects of aging-related tissue decline, while structural details remain understudied. Traditional approaches for quantifying structural changes have assessed individual markers at discrete intervals. Such approaches are inadequate for the complex changes associated with aging. An alternative is to consider changes in overall morphology rather than in specific markers. We have used this approach to quantitatively track tissue architecture during adulthood and aging in the C. elegans pharynx, the neuromuscular feeding organ. Using pattern recognition to analyze aged-grouped pharynx images, we identified discrete step-wise transitions between distinct morphologies. The morphology state transitions were maintained in mutants with pharynx neurotransmission defects, although the pace of the transitions was altered. Longitudinal measurements of pharynx function identified a predictive relationship between mid-life pharynx morphology and function at later ages. These studies demonstrate for the first time that adult tissues undergo distinct structural transitions reflecting postdevelopmental events. The processes that underlie these architectural changes may contribute to increased disease risk during aging, and may be targets for factors that alter the aging rate. This work further demonstrates that pattern analysis of an image series offers a novel and generally accessible approach for quantifying morphological changes and identifying structural biomarkers.

  9. Geodetic imaging with airborne LiDAR: the Earth's surface revealed.

    PubMed

    Glennie, C L; Carter, W E; Shrestha, R L; Dietrich, W E

    2013-08-01

    The past decade has seen an explosive increase in the number of peer reviewed papers reporting new scientific findings in geomorphology (including fans, channels, floodplains and landscape evolution), geologic mapping, tectonics and faulting, coastal processes, lava flows, hydrology (especially snow and runoff routing), glaciers and geo-archaeology. A common genesis of such findings is often newly available decimeter resolution 'bare Earth' geodetic images, derived from airborne laser swath mapping, a.k.a. airborne LiDAR, observations. In this paper we trace nearly a half century of advances in geodetic science made possible by space age technology, such as the invention of short-pulse-length high-pulse-rate lasers, solid state inertial measurement units, chip-based high speed electronics and the GPS satellite navigation system, that today make it possible to map hundreds of square kilometers of terrain in hours, even in areas covered with dense vegetation or shallow water. To illustrate the impact of the LiDAR observations we present examples of geodetic images that are not only stunning to the eye, but help researchers to develop quantitative models explaining how terrain evolved to its present form, and how it will likely change with time. Airborne LiDAR technology continues to develop quickly, promising ever more scientific discoveries in the years ahead.

  10. Fine functional organization of auditory cortex revealed by Fourier optical imaging.

    PubMed

    Kalatsky, Valery A; Polley, Daniel B; Merzenich, Michael M; Schreiner, Christoph E; Stryker, Michael P

    2005-09-13

    We provide an overall view of the functional tonotopic organization of the auditory cortex in the rat. We apply a recently developed technique for acquiring intrinsic signal optical maps, Fourier imaging, in the rat auditory cortex. These highly detailed maps, derived in a several-minute-long recording procedure, delineate multiple auditory cortical areas and demonstrate their shapes, sizes, and tonotopic order. Beyond the primary auditory cortex, there are at least three distinct areas with fine-scale tonotopic organization, as well as at least one additional high-frequency field. The arrangement of all of these cortical areas is consistent across subjects. The accuracy of these optical maps was confirmed by microelectrode mapping in the same subjects. This imaging method allows fast mapping of the auditory cortex at high spatial resolution comparable to that provided by conventional microelectrode technique. Although spiking activity is largely responsible for the evoked intrinsic signals, certain features of the optical signal cannot be explained by spiking activity only, and should probably be attributed to other mechanisms inducing metabolic activity, such as subthreshold membrane phenomena.

  11. Cellular-resolution population imaging reveals robust sparse coding in the Drosophila Mushroom Body

    PubMed Central

    Honegger, Kyle S.; Campbell, Robert A. A.; Turner, Glenn C.

    2011-01-01

    Sensory stimuli are represented in the brain by the activity of populations of neurons. In most biological systems, studying population coding is challenging since only a tiny proportion of cells can be recorded simultaneously. Here we used 2-photon imaging to record neural activity in the relatively simple Drosophila mushroom body (MB), an area involved in olfactory learning and memory. Using the highly sensitive calcium indicator, GCaMP3, we simultaneously monitored the activity of >100 MB neurons in vivo (about 5% of the total population). The MB is thought to encode odors in sparse patterns of activity, but the code has yet to be explored either on a population level or with a wide variety of stimuli. We therefore imaged responses to odors chosen to evaluate the robustness of sparse representations. Different odors activated distinct patterns of MB neurons, however we found no evidence for spatial organization of neurons by either response probability or odor tuning within the cell body layer. The degree of sparseness was consistent across a wide range of stimuli, from monomolecular odors to artificial blends and even complex natural smells. Sparseness was mainly invariant across concentrations, largely because of the influence of recent odor experience. Finally, in contrast to sensory processing in other systems, no response features distinguished natural stimuli from monomolecular odors. Our results indicate that the fundamental feature of odor processing in the MB is to create sparse stimulus representations in a format that facilitates arbitrary associations between odor and punishment or reward. PMID:21849538

  12. Classification images reveal decision variables and strategies in forced choice tasks.

    PubMed

    Pritchett, Lisa M; Murray, Richard F

    2015-06-09

    Despite decades of research, there is still uncertainty about how people make simple decisions about perceptual stimuli. Most theories assume that perceptual decisions are based on decision variables, which are internal variables that encode task-relevant information. However, decision variables are usually considered to be theoretical constructs that cannot be measured directly, and this often makes it difficult to test theories of perceptual decision making. Here we show how to measure decision variables on individual trials, and we use these measurements to test theories of perceptual decision making more directly than has previously been possible. We measure classification images, which are estimates of templates that observers use to extract information from stimuli. We then calculate the dot product of these classification images with the stimuli to estimate observers' decision variables. Finally, we reconstruct each observer's "decision space," a map that shows the probability of the observer's responses for all values of the decision variables. We use this method to examine decision strategies in two-alternative forced choice (2AFC) tasks, for which there are several competing models. In one experiment, the resulting decision spaces support the difference model, a classic theory of 2AFC decisions. In a second experiment, we find unexpected decision spaces that are not predicted by standard models of 2AFC decisions, and that suggest intrinsic uncertainty or soft thresholding. These experiments give new evidence regarding observers' strategies in 2AFC tasks, and they show how measuring decision variables can answer long-standing questions about perceptual decision making.

  13. Magnetization transfer imaging reveals geniculocalcarine and striate area degeneration in primary glaucoma: a preliminary study

    PubMed Central

    Zhang, Yan; Liang, Wenwen; Wu, Guijun; Zhang, Xuelin

    2016-01-01

    Background Glaucoma is a neurodegenerative disease that affects both the retina and central visual pathway. Magnetization transfer imaging (MTI) is a sensitive magnetic resonance imaging (MRI) technique that can detect degenerative changes in the brain. Purpose To investigate the geniculocalcarine (GCT) and striate areas in primary glaucoma patients using region of interest (ROI) analysis of magnetization transfer ratio (MTR). Material and Methods Twenty patients with primary glaucoma in both eyes were compared with 31 healthy control patients. All of the participants were examined on a 3.0 T scanner using a three-dimensional T1-weighted spoiled gradient recalled acquisition (SPGR) with and without a MT saturation pulse. A two-sample t-test was used to evaluate the MTR difference between the groups. P < 0.05 was used to determine statistical significance. Results The MTR of the glaucoma group was lower than the healthy controls in both the bilateral GCT (t = 3.781, P = 0.001) and striate areas (t = 4.177, P = 0.000). Conclusion The MTR reductions in the bilateral GCT and striate areas suggest that there is GCT demyelination and striate area degeneration in primary glaucoma. These neurodegenerative effects may be induced as a direct effect of retrograde axonal degeneration along with the indirect effect of anterograde trans-synaptic degeneration. PMID:27651931

  14. Fluorescence circadian imaging reveals a PDF-dependent transcriptional regulation of the Drosophila molecular clock

    PubMed Central

    Sabado, Virginie; Vienne, Ludovic; Nunes, José Manuel; Rosbash, Michael; Nagoshi, Emi

    2017-01-01

    Circadian locomotor behaviour is controlled by a pacemaker circuit composed of clock-containing neurons. To interrogate the mechanistic relationship between the molecular clockwork and network communication critical to the operation of the Drosophila circadian pacemaker circuit, we established new fluorescent circadian reporters that permit single-cell recording of transcriptional and post-transcriptional rhythms in brain explants and cultured neurons. Live-imaging experiments combined with pharmacological and genetic manipulations demonstrate that the neuropeptide pigment-dispersing factor (PDF) amplifies the molecular rhythms via time-of-day- and activity-dependent upregulation of transcription from E-box-containing clock gene promoters within key pacemaker neurons. The effect of PDF on clock gene transcription and the known role of PDF in enhancing PER/TIM stability occur via independent pathways downstream of the PDF receptor, the former through a cAMP-independent mechanism and the latter through a cAMP-PKA dependent mechanism. These results confirm and extend the mechanistic understanding of the role of PDF in controlling the synchrony of the pacemaker neurons. More broadly, our results establish the utility of the new live-imaging tools for the study of molecular-neural interactions important for the operation of the circadian pacemaker circuit. PMID:28134281

  15. Brain imaging reveals neuronal circuitry underlying the crow's perception of human faces.

    PubMed

    Marzluff, John M; Miyaoka, Robert; Minoshima, Satoshi; Cross, Donna J

    2012-09-25

    Crows pay close attention to people and can remember specific faces for several years after a single encounter. In mammals, including humans, faces are evaluated by an integrated neural system involving the sensory cortex, limbic system, and striatum. Here we test the hypothesis that birds use a similar system by providing an imaging analysis of an awake, wild animal's brain as it performs an adaptive, complex cognitive task. We show that in vivo imaging of crow brain activity during exposure to familiar human faces previously associated with either capture (threatening) or caretaking (caring) activated several brain regions that allow birds to discriminate, associate, and remember visual stimuli, including the rostral hyperpallium, nidopallium, mesopallium, and lateral striatum. Perception of threatening faces activated circuitry including amygdalar, thalamic, and brainstem regions, known in humans and other vertebrates to be related to emotion, motivation, and conditioned fear learning. In contrast, perception of caring faces activated motivation and striatal regions. In our experiments and in nature, when perceiving a threatening face, crows froze and fixed their gaze (decreased blink rate), which was associated with activation of brain regions known in birds to regulate perception, attention, fear, and escape behavior. These findings indicate that, similar to humans, crows use sophisticated visual sensory systems to recognize faces and modulate behavioral responses by integrating visual information with expectation and emotion. Our approach has wide applicability and potential to improve our understanding of the neural basis for animal behavior.

  16. Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex

    NASA Astrophysics Data System (ADS)

    Ohki, Kenichi; Chung, Sooyoung; Ch'ng, Yeang H.; Kara, Prakash; Reid, R. Clay

    2005-02-01

    Neurons in the cerebral cortex are organized into anatomical columns, with ensembles of cells arranged from the surface to the white matter. Within a column, neurons often share functional properties, such as selectivity for stimulus orientation; columns with distinct properties, such as different preferred orientations, tile the cortical surface in orderly patterns. This functional architecture was discovered with the relatively sparse sampling of microelectrode recordings. Optical imaging of membrane voltage or metabolic activity elucidated the overall geometry of functional maps, but is averaged over many cells (resolution >100µm). Consequently, the purity of functional domains and the precision of the borders between them could not be resolved. Here, we labelled thousands of neurons of the visual cortex with a calcium-sensitive indicator in vivo. We then imaged the activity of neuronal populations at single-cell resolution with two-photon microscopy up to a depth of 400µm. In rat primary visual cortex, neurons had robust orientation selectivity but there was no discernible local structure; neighbouring neurons often responded to different orientations. In area 18 of cat visual cortex, functional maps were organized at a fine scale. Neurons with opposite preferences for stimulus direction were segregated with extraordinary spatial precision in three dimensions, with columnar borders one to two cells wide. These results indicate that cortical maps can be built with single-cell precision.

  17. Geodetic imaging with airborne LiDAR: the Earth's surface revealed

    NASA Astrophysics Data System (ADS)

    Glennie, C. L.; Carter, W. E.; Shrestha, R. L.; Dietrich, W. E.

    2013-08-01

    The past decade has seen an explosive increase in the number of peer reviewed papers reporting new scientific findings in geomorphology (including fans, channels, floodplains and landscape evolution), geologic mapping, tectonics and faulting, coastal processes, lava flows, hydrology (especially snow and runoff routing), glaciers and geo-archaeology. A common genesis of such findings is often newly available decimeter resolution ‘bare Earth’ geodetic images, derived from airborne laser swath mapping, a.k.a. airborne LiDAR, observations. In this paper we trace nearly a half century of advances in geodetic science made possible by space age technology, such as the invention of short-pulse-length high-pulse-rate lasers, solid state inertial measurement units, chip-based high speed electronics and the GPS satellite navigation system, that today make it possible to map hundreds of square kilometers of terrain in hours, even in areas covered with dense vegetation or shallow water. To illustrate the impact of the LiDAR observations we present examples of geodetic images that are not only stunning to the eye, but help researchers to develop quantitative models explaining how terrain evolved to its present form, and how it will likely change with time. Airborne LiDAR technology continues to develop quickly, promising ever more scientific discoveries in the years ahead.

  18. Images from a jointly-arousing collective ritual reveal affective polarization

    PubMed Central

    Bulbulia, Joseph A.; Xygalatas, Dimitris; Schjoedt, Uffe; Fondevila, Sabela; Sibley, Chris G.; Konvalinka, Ivana

    2013-01-01

    Collective rituals are biologically ancient and culturally pervasive, yet few studies have quantified their effects on participants. We assessed two plausible models from qualitative anthropology: ritual empathy predicts affective convergence among all ritual participants irrespective of ritual role; rite-of-passage predicts emotional differences, specifically that ritual initiates will express relatively negative valence when compared with non-initiates. To evaluate model predictions, images of participants in a Spanish fire-walking ritual were extracted from video footage and assessed by nine Spanish raters for arousal and valence. Consistent with rite-of-passage predictions, we found that arousal jointly increased for all participants but that valence differed by ritual role: fire-walkers exhibited increasingly positive arousal and increasingly negative valence when compared with passengers. This result offers the first quantified evidence for rite of passage dynamics within a highly arousing collective ritual. Methodologically, we show that surprisingly simple and non-invasive data structures (rated video images) may be combined with methods from evolutionary ecology (Bayesian Generalized Linear Mixed Effects models) to clarify poorly understood dimensions of the human condition. PMID:24399979

  19. Widespread decadal-scale decrease of glacier speed revealed using repeat optical satellite images

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2012-04-01

    Matching of repeat optical satellite images to derive glacier velocities is an approach that is much used within glaciology. Lately, focus has been put into developing, improving, automating and comparing different image matching methods. This makes it now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have decreased their speeds over the last decades, Pamir by 43 % in average per decade, Caucasus by 8 % in average per decade, Penny Ice Cap by 25 % in average per decade, Alaska Range by 11 % in average per decade and Patagonia by 20 % in average per decade. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area.

  20. Worldwide widespread decadal-scale decrease of glacier speed revealed using repeat optical satellite images

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2011-10-01

    Matching of repeat optical satellite images to derive glacier velocities is an approach that is much used within glaciology. Lately, focus has been put into developing, improving, automating and comparing different image matching methods. This makes it now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have decreased their speeds over the last decades, Pamir by 43 % in average per decade, Caucasus by 8 % in average per decade, Penny Ice Cap by 25 % in average per decade, Alaska Range by 11 % in average per decade and Patagonia by 20 % in average per decade. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area.

  1. Magnetic resonance imaging reveals functional anatomy and biomechanics of a living dragon tree

    PubMed Central

    Hesse, Linnea; Masselter, Tom; Leupold, Jochen; Spengler, Nils; Speck, Thomas; Korvink, Jan Gerrit

    2016-01-01

    Magnetic resonance imaging (MRI) was used to gain in vivo insight into load-induced displacements of inner plant tissues making a non-invasive and non-destructive stress and strain analysis possible. The central aim of this study was the identification of a possible load-adapted orientation of the vascular bundles and their fibre caps as the mechanically relevant tissue in branch-stem-attachments of Dracaena marginata. The complex three-dimensional deformations that occur during mechanical loading can be analysed on the basis of quasi-three-dimensional data representations of the outer surface, the inner tissue arrangement (meristem and vascular system), and the course of single vascular bundles within the branch-stem-attachment region. In addition, deformations of vascular bundles could be quantified manually and by using digital image correlation software. This combination of qualitative and quantitative stress and strain analysis leads to an improved understanding of the functional morphology and biomechanics of D. marginata, a plant that is used as a model organism for optimizing branched technical fibre-reinforced lightweight trusses in order to increase their load bearing capacity. PMID:27604526

  2. Computational imaging reveals mitochondrial morphology as a biomarker of cancer phenotype and drug response

    PubMed Central

    Giedt, Randy J.; Fumene Feruglio, Paolo; Pathania, Divya; Yang, Katherine S.; Kilcoyne, Aoife; Vinegoni, Claudio; Mitchison, Timothy J.; Weissleder, Ralph

    2016-01-01

    Mitochondria, which are essential organelles in resting and replicating cells, can vary in number, mass and shape. Past research has primarily focused on short-term molecular mechanisms underlying fission/fusion. Less is known about longer-term mitochondrial behavior such as the overall makeup of cell populations’ morphological patterns and whether these patterns can be used as biomarkers of drug response in human cells. We developed an image-based analytical technique to phenotype mitochondrial morphology in different cancers, including cancer cell lines and patient-derived cancer cells. We demonstrate that (i) cancer cells of different origins, including patient-derived xenografts, express highly diverse mitochondrial phenotypes; (ii) a given phenotype is characteristic of a cell population and fairly constant over time; (iii) mitochondrial patterns correlate with cell metabolic measurements and (iv) therapeutic interventions can alter mitochondrial phenotypes in drug-sensitive cancers as measured in pre- versus post-treatment fine needle aspirates in mice. These observations shed light on the role of mitochondrial dynamics in the biology and drug response of cancer cells. On the basis of these findings, we propose that image-based mitochondrial phenotyping can provide biomarkers for assessing cancer phenotype and drug response. PMID:27609668

  3. Magnetic resonance imaging reveals functional anatomy and biomechanics of a living dragon tree.

    PubMed

    Hesse, Linnea; Masselter, Tom; Leupold, Jochen; Spengler, Nils; Speck, Thomas; Korvink, Jan Gerrit

    2016-09-08

    Magnetic resonance imaging (MRI) was used to gain in vivo insight into load-induced displacements of inner plant tissues making a non-invasive and non-destructive stress and strain analysis possible. The central aim of this study was the identification of a possible load-adapted orientation of the vascular bundles and their fibre caps as the mechanically relevant tissue in branch-stem-attachments of Dracaena marginata. The complex three-dimensional deformations that occur during mechanical loading can be analysed on the basis of quasi-three-dimensional data representations of the outer surface, the inner tissue arrangement (meristem and vascular system), and the course of single vascular bundles within the branch-stem-attachment region. In addition, deformations of vascular bundles could be quantified manually and by using digital image correlation software. This combination of qualitative and quantitative stress and strain analysis leads to an improved understanding of the functional morphology and biomechanics of D. marginata, a plant that is used as a model organism for optimizing branched technical fibre-reinforced lightweight trusses in order to increase their load bearing capacity.

  4. Optical Imaging of Drug-Induced Metabolism Changes in Murine and Human Pancreatic Cancer Organoids Reveals Heterogeneous Drug Response

    PubMed Central

    Walsh, Alex J.; Castellanos, Jason A.; Nagathihalli, Nagaraj S.; Merchant, Nipun B.; Skala, Melissa C.

    2016-01-01

    Objectives Three-dimensional organoids derived from primary pancreatic ductal adenocarcinomas are an attractive platform for testing potential anticancer drugs on patient-specific tissue. Optical metabolic imaging (OMI) is a novel tool used to assess drug-induced changes in cellular metabolism, and its quantitative end point, the OMI index, is evaluated as a biomarker of drug response in pancreatic cancer organoids. Methods Optical metabolic imaging is used to assess both malignant cell and fibroblast drug response within primary murine and human pancreatic cancer organoids. Results Anticancer drugs induce significant reductions in the OMI index of murine and human pancreatic cancer organoids. Subpopulation analysis of OMI data revealed heterogeneous drug response and elucidated responding and nonresponding cell populations for a 7-day time course. Optical metabolic imaging index significantly correlates with immunofluorescence detection of cell proliferation and cell death. Conclusions Optical metabolic imaging of primary pancreatic ductal adenocarcinoma organoids is highly sensitive to drug-induced metabolic changes, provides a nondestructive method for monitoring dynamic drug response, and presents a novel platform for patient-specific drug testing and drug development. PMID:26495796

  5. History of Mexican Easel Paintings from an Altarpiece Revealed by Non-invasive Terahertz Time-Domain Imaging

    NASA Astrophysics Data System (ADS)

    Gomez-Sepulveda, A. M.; Hernandez-Serrano, A. I.; Radpour, R.; Koch-Dandolo, C. L.; Rojas-Landeros, S. C.; Ascencio-Rojas, L. F.; Zarate, Alvaro; Hernandez, Gerardo; Gonzalez-Tirado, R. C.; Insaurralde-Caballero, M.; Castro-Camus, E.

    2016-12-01

    Four easel paintings attributed to Hermenegildo Bustos (Purísima del Rincón, Guanajuato, Mexico), one of the most renowned painters of the late nineteenth and early twentieth century Mexican art, have been investigated by means of terahertz time-domain imaging (THz-TDI) and standard imaging techniques, such as near-IR reflectography and X-ray radiography. The archival sources and the recent studies on the paintings suggest that the artworks were created in the eighteenth century and underwent several modifications since then until the intervention of Bustos who authored the currently visible depictions. By combining the records of the paintings obtained by imaging with the different methodologies, aspects of the previous depictions and further details on the paintings' history have been revealed, with THz-TDI playing a key role in attributing a chronological evolution of the images. The paintings of Purísima are the first THz-TDI-scanned paintings belonging to the Mexican cultural heritage.

  6. History of Mexican Easel Paintings from an Altarpiece Revealed by Non-invasive Terahertz Time-Domain Imaging

    NASA Astrophysics Data System (ADS)

    Gomez-Sepulveda, A. M.; Hernandez-Serrano, A. I.; Radpour, R.; Koch-Dandolo, C. L.; Rojas-Landeros, S. C.; Ascencio-Rojas, L. F.; Zarate, Alvaro; Hernandez, Gerardo; Gonzalez-Tirado, R. C.; Insaurralde-Caballero, M.; Castro-Camus, E.

    2017-04-01

    Four easel paintings attributed to Hermenegildo Bustos ( Purísima del Rincón, Guanajuato, Mexico), one of the most renowned painters of the late nineteenth and early twentieth century Mexican art, have been investigated by means of terahertz time-domain imaging (THz-TDI) and standard imaging techniques, such as near-IR reflectography and X-ray radiography. The archival sources and the recent studies on the paintings suggest that the artworks were created in the eighteenth century and underwent several modifications since then until the intervention of Bustos who authored the currently visible depictions. By combining the records of the paintings obtained by imaging with the different methodologies, aspects of the previous depictions and further details on the paintings' history have been revealed, with THz-TDI playing a key role in attributing a chronological evolution of the images. The paintings of Purísima are the first THz-TDI-scanned paintings belonging to the Mexican cultural heritage.

  7. Tomographic particle image velocimetry of desert locust wakes: instantaneous volumes combine to reveal hidden vortex elements and rapid wake deformation.

    PubMed

    Bomphrey, Richard J; Henningsson, Per; Michaelis, Dirk; Hollis, David

    2012-12-07

    Aerodynamic structures generated by animals in flight are unstable and complex. Recent progress in quantitative flow visualization has advanced our understanding of animal aerodynamics, but measurements have hitherto been limited to flow velocities at a plane through the wake. We applied an emergent, high-speed, volumetric fluid imaging technique (tomographic particle image velocimetry) to examine segments of the wake of desert locusts, capturing fully three-dimensional instantaneous flow fields. We used those flow fields to characterize the aerodynamic footprint in unprecedented detail and revealed previously unseen wake elements that would have gone undetected by two-dimensional or stereo-imaging technology. Vortex iso-surface topographies show the spatio-temporal signature of aerodynamic force generation manifest in the wake of locusts, and expose the extent to which animal wakes can deform, potentially leading to unreliable calculations of lift and thrust when using conventional diagnostic methods. We discuss implications for experimental design and analysis as volumetric flow imaging becomes more widespread.

  8. Tomographic particle image velocimetry of desert locust wakes: instantaneous volumes combine to reveal hidden vortex elements and rapid wake deformation

    PubMed Central

    Bomphrey, Richard J.; Henningsson, Per; Michaelis, Dirk; Hollis, David

    2012-01-01

    Aerodynamic structures generated by animals in flight are unstable and complex. Recent progress in quantitative flow visualization has advanced our understanding of animal aerodynamics, but measurements have hitherto been limited to flow velocities at a plane through the wake. We applied an emergent, high-speed, volumetric fluid imaging technique (tomographic particle image velocimetry) to examine segments of the wake of desert locusts, capturing fully three-dimensional instantaneous flow fields. We used those flow fields to characterize the aerodynamic footprint in unprecedented detail and revealed previously unseen wake elements that would have gone undetected by two-dimensional or stereo-imaging technology. Vortex iso-surface topographies show the spatio-temporal signature of aerodynamic force generation manifest in the wake of locusts, and expose the extent to which animal wakes can deform, potentially leading to unreliable calculations of lift and thrust when using conventional diagnostic methods. We discuss implications for experimental design and analysis as volumetric flow imaging becomes more widespread. PMID:22977102

  9. Motor dysfunction in the tottering mouse is linked to cerebellar spontaneous low frequency oscillations revealed by flavoprotein autofluorescence optical imaging

    NASA Astrophysics Data System (ADS)

    Chen, Gang; Popa, Laurentiu S.; Wang, Xinming; Gao, Wangcai; Barnes, Justin; Hendrix, Claudia M.; Hess, Ellen J.; Ebner, Timothy J.

    2009-02-01

    Flavoprotein autofluorescence optical imaging is developing into a powerful research tool to study neural activity, particularly in vivo. In this study we used this imaging technique to investigate the neuronal mechanism underlying the episodic movement disorder that is characteristic of the tottering (tg) mouse, a model of episodic ataxia type 2. Both EA2 and the tg mouse are caused by mutations in the gene encoding Cav2.1 (P/Q-type) voltage-gated Ca2+ channels. These mutations result in a reduction in P/Q Ca2+ channel function. Both EA2 patients and tg mice have a characteristic phenotype consisting of transient motor attacks triggered by stress, caffeine or ethanol. The neural events underlying these episodes of dystonia are unknown. Flavoprotein autofluorescence optical imaging revealed spontaneous, transient, low frequency oscillations in the cerebellar cortex of the tg mouse. Lasting from 30 - 120 minutes, the oscillations originate in one area then spread to surrounding regions over 30 - 60 minutes. The oscillations are reduced by removing extracellular Ca2+ and blocking Cav 1.2/1.3 (L-type) Ca2+ channels. The oscillations are not affected by blocking AMPA receptors or by electrical stimulation of the parallel fiber - Purkinje cell circuit, suggesting the oscillations are generated intrinsically in the cerebellar cortex. Conversely, L-type Ca2+ agonists generate oscillations with similar properties. In the awake tg mouse, transcranial flavoprotein imaging revealed low frequency oscillations that are accentuated during caffeine induced attacks of dystonia. The oscillations increase during the attacks of dystonia and are coupled to oscillations in face and hindlimb EMG activity. These transient oscillations and the associated cerebellar dysfunction provide a novel mechanism by which an ion channel disorder results in episodic motor dysfunction.

  10. Microbial Cell Imaging

    SciTech Connect

    Doktycz, Mitchel John; Sullivan, Claretta; Mortensen, Ninell P; Allison, David P

    2011-01-01

    Atomic force microscopy (AFM) is finding increasing application in a variety of fields including microbiology. Until the emergence of AFM, techniques for ivnestigating processes in single microbes were limited. From a biologist's perspective, the fact that AFM can be used to generate high-resolution images in buffers or media is its most appealing feature as live-cell imaging can be pursued. Imaging living cells by AFM allows dynamic biological events to be studied, at the nanoscale, in real time. Few areas of biological research have as much to gain as microbiology from the application of AFM. Whereas the scale of microbes places them near the limit of resolution for light microscopy. AFM is well suited for the study of structures on the order of a micron or less. Although electron microscopy techniques have been the standard for high-resolution imaging of microbes, AFM is quickly gaining favor for several reasons. First, fixatives that impair biological activity are not required. Second, AFM is capable of detecting forces in the pN range, and precise control of the force applied to the cantilever can be maintained. This combination facilitates the evaluation of physical characteristics of microbes. Third, rather than yielding the composite, statistical average of cell populations, as is the case with many biochemical assays, the behavior of single cells can be monitored. Despite the potential of AFM in microbiology, there are several limitations that must be considered. For example, the time required to record an image allows for the study of gross events such as cell division or membrane degradation from an antibiotic but precludes the evaluation of biological reactions and events that happen in just fractions of a second. Additionally, the AFM is a topographical tool and is restricted to imaging surfaces. Therefore, it cannot be used to look inside cells as with opticla and transmission electron microscopes. other practical considerations are the limitation on

  11. Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates

    PubMed Central

    Anné, Jennifer; Edwards, Nicholas P.; Wogelius, Roy A.; Tumarkin-Deratzian, Allison R.; Sellers, William I.; van Veelen, Arjen; Bergmann, Uwe; Sokaras, Dimosthenis; Alonso-Mori, Roberto; Ignatyev, Konstantin; Egerton, Victoria M.; Manning, Phillip L.

    2014-01-01

    Current understanding of bone healing and remodelling strategies in vertebrates has traditionally relied on morphological observations through the histological analysis of thin sections. However, chemical analysis may also be used in such interpretations, as different elements are known to be absorbed and used by bone for different physiological purposes such as growth and healing. These chemical signatures are beyond the detection limit of most laboratory-based analytical techniques (e.g. scanning electron microscopy). However, synchrotron rapid scanning–X-ray fluorescence (SRS–XRF) is an elemental mapping technique that uniquely combines high sensitivity (ppm), excellent sample resolution (20–100 µm) and the ability to scan large specimens (decimetre scale) approximately 3000 times faster than other mapping techniques. Here, we use SRS–XRF combined with microfocus elemental mapping (2–20 µm) to determine the distribution and concentration of trace elements within pathological and normal bone of both extant and extinct archosaurs (Cathartes aura and Allosaurus fragilis). Results reveal discrete chemical inventories within different bone tissue types and preservation modes. Chemical inventories also revealed detail of histological features not observable in thin section, including fine structures within the interface between pathological and normal bone as well as woven texture within pathological tissue. PMID:24806709

  12. Calcium micro-depositions in jugular truncular venous malformations revealed by Synchrotron-based XRF imaging.

    PubMed

    Pascolo, Lorella; Gianoncelli, Alessandra; Rizzardi, Clara; Tisato, Veronica; Salomé, Murielle; Calligaro, Carla; Salvi, Fabrizio; Paterson, David; Zamboni, Paolo

    2014-10-07

    It has been recently demonstrated that the internal jugular vein may exhibit abnormalities classified as truncular venous malformations (TVMs). The investigation of possible morphological and biochemical anomalies at jugular tissue level could help to better understand the link between brain venous drainage and neurodegenerative disorders, recently found associated with jugular TVMs. To this end we performed sequential X-ray Fluorescence (XRF) analyses on jugular tissue samples from two TVM patients and two control subjects, using complementary energies at three different synchrotrons. This investigation, coupled with conventional histological analyses, revealed anomalous micro-formations in the pathological tissues and allowed the determination of their elemental composition. Rapid XRF analyses on large tissue areas at 12.74 keV showed an increased Ca presence in the pathological samples, mainly localized in tunica adventitia microvessels. Investigations at lower energy demonstrated that the high Ca level corresponded to micro-calcifications, also containing P and Mg. We suggest that advanced synchrotron XRF micro-spectroscopy is an important analytical tool in revealing biochemical changes, which cannot be accessed by conventional investigations. Further research on a larger number of samples is needed to understand the pathogenic significance of Ca micro-depositions detected on the intramural vessels of vein walls affected by TVMs.

  13. Synchrotron imaging reveals bone healing and remodelling strategies in extinct and extant vertebrates.

    PubMed

    Anné, Jennifer; Edwards, Nicholas P; Wogelius, Roy A; Tumarkin-Deratzian, Allison R; Sellers, William I; van Veelen, Arjen; Bergmann, Uwe; Sokaras, Dimosthenis; Alonso-Mori, Roberto; Ignatyev, Konstantin; Egerton, Victoria M; Manning, Phillip L

    2014-07-06

    Current understanding of bone healing and remodelling strategies in vertebrates has traditionally relied on morphological observations through the histological analysis of thin sections. However, chemical analysis may also be used in such interpretations, as different elements are known to be absorbed and used by bone for different physiological purposes such as growth and healing. These chemical signatures are beyond the detection limit of most laboratory-based analytical techniques (e.g. scanning electron microscopy). However, synchrotron rapid scanning-X-ray fluorescence (SRS-XRF) is an elemental mapping technique that uniquely combines high sensitivity (ppm), excellent sample resolution (20-100 µm) and the ability to scan large specimens (decimetre scale) approximately 3000 times faster than other mapping techniques. Here, we use SRS-XRF combined with microfocus elemental mapping (2-20 µm) to determine the distribution and concentration of trace elements within pathological and normal bone of both extant and extinct archosaurs (Cathartes aura and Allosaurus fragilis). Results reveal discrete chemical inventories within different bone tissue types and preservation modes. Chemical inventories also revealed detail of histological features not observable in thin section, including fine structures within the interface between pathological and normal bone as well as woven texture within pathological tissue.

  14. Imaging of all dangling bonds and their potential on the Ge/Si105 surface by noncontact atomic force microscopy.

    PubMed

    Eguchi, T; Fujikawa, Y; Akiyama, K; An, T; Ono, M; Hashimoto, T; Morikawa, Y; Terakura, K; Sakurai, T; Lagally, M G; Hasegawa, Y

    2004-12-31

    High-resolution noncontact atomic force microscope (AFM) images were successfully taken on the Ge105-(1 x 2) structure formed on the Si105 substrate and revealed all dangling bonds of the surface regardless of their electronic situation, surpassing scanning tunneling microscopy, whose images strongly deviated from the atomic structure by the electronic states involved. An atomically resolved electrostatic potential profile by a Kelvin-probe method with AFM shows potential variations among the dangling bond states, directly observing a charge transfer between them. These results clearly demonstrate that high-resolution noncontact AFM with a Kelvin-probe method is an ideal tool for analysis of atomic structures and electronic properties of surfaces.

  15. Diffusion tensor imaging reveals thalamus and posterior cingulate cortex abnormalities in internet gaming addicts.

    PubMed

    Dong, Guangheng; DeVito, Elise; Huang, Jie; Du, Xiaoxia

    2012-09-01

    Internet gaming addiction (IGA) is increasingly recognized as a widespread disorder with serious psychological and health consequences. Diminished white matter integrity has been demonstrated in a wide range of other addictive disorders which share clinical characteristics with IGA. Abnormal white matter integrity in addictive populations has been associated with addiction severity, treatment response and cognitive impairments. This study assessed white matter integrity in individuals with internet gaming addiction (IGA) using diffusion tensor imaging (DTI). IGA subjects (N = 16) showed higher fractional anisotropy (FA), indicating greater white matter integrity, in the thalamus and left posterior cingulate cortex (PCC) relative to healthy controls (N = 15). Higher FA in the thalamus was associated with greater severity of internet addiction. Increased regional FA in individuals with internet gaming addiction may be a pre-existing vulnerability factor for IGA, or may arise secondary to IGA, perhaps as a direct result of excessive internet game playing.

  16. Dynamics of supersonic microparticle impact on elastomers revealed by real-time multi-frame imaging.

    PubMed

    Veysset, David; Hsieh, Alex J; Kooi, Steven; Maznev, Alexei A; Masser, Kevin A; Nelson, Keith A

    2016-05-09

    Understanding high-velocity microparticle impact is essential for many fields, from space exploration to medicine and biology. Investigations of microscale impact have hitherto been limited to post-mortem analysis of impacted specimens, which does not provide direct information on the impact dynamics. Here we report real-time multi-frame imaging studies of the impact of 7 μm diameter glass spheres traveling at 700-900 m/s on elastomer polymers. With a poly(urethane urea) (PUU) sample, we observe a hyperelastic impact phenomenon not seen on the macroscale: a microsphere undergoes a full conformal penetration into the specimen followed by a rebound which leaves the specimen unscathed. The results challenge the established interpretation of the behaviour of elastomers under high-velocity impact.

  17. Dynamics of supersonic microparticle impact on elastomers revealed by real–time multi–frame imaging

    PubMed Central

    Veysset, David; Hsieh, Alex J.; Kooi, Steven; Maznev, Alexei A.; Masser, Kevin A.; Nelson, Keith A.

    2016-01-01

    Understanding high–velocity microparticle impact is essential for many fields, from space exploration to medicine and biology. Investigations of microscale impact have hitherto been limited to post–mortem analysis of impacted specimens, which does not provide direct information on the impact dynamics. Here we report real–time multi–frame imaging studies of the impact of 7 μm diameter glass spheres traveling at 700–900 m/s on elastomer polymers. With a poly(urethane urea) (PUU) sample, we observe a hyperelastic impact phenomenon not seen on the macroscale: a microsphere undergoes a full conformal penetration into the specimen followed by a rebound which leaves the specimen unscathed. The results challenge the established interpretation of the behaviour of elastomers under high–velocity impact. PMID:27156501

  18. Live cell imaging reveals the relocation of dsRNA binding proteins upon viral infection.

    PubMed

    Barton, Deborah; Roovers, Elke; Gouil, Quentin; C da Fonseca, Guilherme; Reis, Rodrigo S; Jackson, Craig; Overall, Robyn; Fusaro, Adriana; Waterhouse, Peter

    2017-03-15

    Viral infection triggers a range of plant responses such as the activation of the RNA interference (RNAi) pathway. The double-stranded RNA binding (DRB) proteins, DRB3 and DRB4, are part of this pathway and aid in defending against DNA and RNA viruses, respectively. Using live cell imaging, we show that DRB2, DRB3 and DRB5 relocate from their uniform cytoplasmic distribution to concentrated accumulation in nascent viral replication complexes (VRCs) that develop following cell invasion by viral RNA. Inactivation of the DRB3 gene in Arabidopsis, by T-DNA insertion, rendered these plants less able to repress RNA viral replication. We propose a model for the early stages of virus defense in which DRB2, DRB3 and DRB5 are invasion sensors that relocate to nascent VRCs, where they bind to viral RNA and inhibit virus replication.

  19. Non-contact hemodynamic imaging reveals the jugular venous pulse waveform

    PubMed Central

    Amelard, Robert; Hughson, Richard L.; Greaves, Danielle K.; Pfisterer, Kaylen J.; Leung, Jason; Clausi, David A.; Wong, Alexander

    2017-01-01

    Cardiovascular monitoring is important to prevent diseases from progressing. The jugular venous pulse (JVP) waveform offers important clinical information about cardiac health, but is not routinely examined due to its invasive catheterisation procedure. Here, we demonstrate for the first time that the JVP can be consistently observed in a non-contact manner using a photoplethysmographic imaging system. The observed jugular waveform was strongly negatively correlated to the arterial waveform (r = −0.73 ± 0.17), consistent with ultrasound findings. Pulsatile venous flow was observed over a spatially cohesive region of the neck. Critical inflection points (c, x, v, y waves) of the JVP were observed across all participants. The anatomical locations of the strongest pulsatile venous flow were consistent with major venous pathways identified through ultrasound. PMID:28065933

  20. The complex aerodynamic footprint of desert locusts revealed by large-volume tomographic particle image velocimetry.

    PubMed

    Henningsson, Per; Michaelis, Dirk; Nakata, Toshiyuki; Schanz, Daniel; Geisler, Reinhard; Schröder, Andreas; Bomphrey, Richard J

    2015-07-06

    Particle image velocimetry has been the preferred experimental technique with which to study the aerodynamics of animal flight for over a decade. In that time, hardware has become more accessible and the software has progressed from the acquisition of planes through the flow field to the reconstruction of small volumetric measurements. Until now, it has not been possible to capture large volumes that incorporate the full wavelength of the aerodynamic track left behind during a complete wingbeat cycle. Here, we use a unique apparatus to acquire the first instantaneous wake volume of a flying animal's entire wingbeat. We confirm the presence of wake deformation behind desert locusts and quantify the effect of that deformation on estimates of aerodynamic force and the efficiency of lift generation. We present previously undescribed vortex wake phenomena, including entrainment around the wing-tip vortices of a set of secondary vortices borne of Kelvin-Helmholtz instability in the shear layer behind the flapping wings.

  1. Dynamics of supersonic microparticle impact on elastomers revealed by real–time multi–frame imaging

    NASA Astrophysics Data System (ADS)

    Veysset, David; Hsieh, Alex J.; Kooi, Steven; Maznev, Alexei A.; Masser, Kevin A.; Nelson, Keith A.

    2016-05-01

    Understanding high–velocity microparticle impact is essential for many fields, from space exploration to medicine and biology. Investigations of microscale impact have hitherto been limited to post–mortem analysis of impacted specimens, which does not provide direct information on the impact dynamics. Here we report real–time multi–frame imaging studies of the impact of 7 μm diameter glass spheres traveling at 700–900 m/s on elastomer polymers. With a poly(urethane urea) (PUU) sample, we observe a hyperelastic impact phenomenon not seen on the macroscale: a microsphere undergoes a full conformal penetration into the specimen followed by a rebound which leaves the specimen unscathed. The results challenge the established interpretation of the behaviour of elastomers under high–velocity impact.

  2. Diffusion tensor imaging reveals thalamus and posterior cingulate cortex abnormalities in internet gaming addicts

    PubMed Central

    Dong, Guangheng; DeVito, Elise; Huang, Jie; Du, Xiaoxia

    2013-01-01

    Internet gaming addiction (IGA) is increasingly recognized as a widespread disorder with serious psychological and health consequences. Diminished white matter integrity has been demonstrated in a wide range of other addictive disorders which share clinical characteristics with IGA. Abnormal white matter integrity in addictive populations has been associated with addiction severity, treatment response and cognitive impairments. This study assessed white matter integrity in individuals with internet gaming addiction (IGA) using diffusion tensor imaging (DTI). IGA subjects (N=16) showed higher fractional anisotropy (FA), indicating greater white matter integrity, in the thalamus and left posterior cingulate cortex (PCC) relative to healthy controls (N=15). Higher FA in the thalamus was associated with greater severity of internet addiction. Increased regional FA in individuals with internet gaming addiction may be a pre-existing vulnerability factor for IGA, or may arise secondary to IGA, perhaps as a direct result of excessive internet game playing. PMID:22727905

  3. Confocal imaging reveals three-dimensional fine structure difference between ventral and dorsal nerve roots.

    PubMed

    Wu, Yuxiang; Sui, Tao; Cao, Xiaojian; Lv, Xiaohua; Zeng, Shaoqun; Sun, Peng

    2011-05-01

    Peripheral nerve injury repair is one of the most challenging problems in neurosurgery, partially due to lack of knowledge of three-dimensional (3-D) fine structure and organization of peripheral nerves. In this paper, we explored the structures of nerve fibers in ventral and dorsal nerves with a laser scanning confocal microscopy. Thick tissue staining results suggested that nerve fibers have a different 3-D structure in ventral and dorsal nerves, and reconstruction from serial sectioning images showed that in ventral nerves the nerve fibers travel in a winding form, while in dorsal nerves, the nerve fibers form in a parallel cable pattern. These structural differences could help surgeons to differentiate ventral and dorsal nerves in peripheral nerve injury repair, and also facilitate scientists to get a deeper understanding about nerve fiber organization.

  4. Single-molecule imaging reveals modulation of cell wall synthesis dynamics in live bacterial cells

    PubMed Central

    Lee, Timothy K.; Meng, Kevin; Shi, Handuo; Huang, Kerwyn Casey

    2016-01-01

    The peptidoglycan cell wall is an integral organelle critical for bacterial cell shape and stability. Proper cell wall construction requires the interaction of synthesis enzymes and the cytoskeleton, but it is unclear how the activities of individual proteins are coordinated to preserve the morphology and integrity of the cell wall during growth. To elucidate this coordination, we used single-molecule imaging to follow the behaviours of the two major peptidoglycan synthases in live, elongating Escherichia coli cells and after perturbation. We observed heterogeneous localization dynamics of penicillin-binding protein (PBP) 1A, the synthase predominantly associated with cell wall elongation, with individual PBP1A molecules distributed between mobile and immobile populations. Perturbations to PBP1A activity, either directly through antibiotics or indirectly through PBP1A's interaction with its lipoprotein activator or other synthases, shifted the fraction of mobile molecules. Our results suggest that multiple levels of regulation control the activity of enzymes to coordinate peptidoglycan synthesis. PMID:27774981

  5. Images reveal that atmospheric particles can undergo liquid-liquid phase separations

    NASA Astrophysics Data System (ADS)

    Bertram, A. K.; You, Y.; Renbaum-Wolff, L.; Carreras-Sospedra, M.; Hiranuma, N.; Smith, M.; Zhang, X.; Weber, R.; Shilling, J. E.; Dabdub, D.; Martin, S. T.

    2012-12-01

    A large fraction of submicron atmospheric particles contain both organic material and inorganic salts. As the relative humidity cycles in the atmosphere, these mixed particles can undergo a range of phase transitions, possibly including liquid-liquid phase separation. If liquid-liquid phase separation occurs, the gas-particle partitioning of atmospheric semi-volatile organic compounds, the scattering and absorption of solar radiation, and the uptake of reactive gas species on atmospheric particles may be affected. Here, using optical and fluorescence microscopy, we present images that show the coexistence of two non-crystalline phases in particles generated from samples collected on multiple days in Atlanta, Georgia, and in particles generated in the laboratory using simulated atmospheric conditions. These results show that atmospheric particles can undergo liquid-liquid phase separations.

  6. Revealing Dissociative Electron Attachment Dynamics in Polyatomic Molecules Using Momentum Imaging Experiments and Electron Scattering Calculations

    NASA Astrophysics Data System (ADS)

    Belkacem, Ali; Slaughter, Daniel

    2015-05-01

    Understanding electron-driven chemical reactions is important for improving a variety of technological applications such as materials processing and the important role they play in the radiation damage in bulk matter. Furthermore, dissociative electron attachment often exhibits site-selective bond cleavage, which holds promise for prediction and precise control of electron-driven chemical reactions. Recent dynamical studies of these reactions have demonstrated that an understanding of anion dissociation dynamics beyond simple one-dimensional models is crucial in interpreting the measured fragment angular distributions. We combine ion fragment momentum imaging experiments with electron attachment entrance amplitude calculations to interrogate the non-Born-Oppenheimer dynamics of dissociative electron attachment in polyatomic molecules. We will report recent experimental developments in molecules of technological interest including methanol, methane and uracil. Work supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.

  7. High-speed imaging reveals neurophysiological links to behavior in an animal model of depression.

    PubMed

    Airan, Raag D; Meltzer, Leslie A; Roy, Madhuri; Gong, Yuqing; Chen, Han; Deisseroth, Karl

    2007-08-10

    The hippocampus is one of several brain areas thought to play a central role in affective behaviors, but the underlying local network dynamics are not understood. We used quantitative voltage-sensitive dye imaging to probe hippocampal dynamics with millisecond resolution in brain slices after bidirectional modulation of affective state in rat models of depression. We found that a simple measure of real-time activity-stimulus-evoked percolation of activity through the dentate gyrus relative to the hippocampal output subfield-accounted for induced changes in animal behavior independent of the underlying mechanism of action of the treatments. Our results define a circuit-level neurophysiological endophenotype for affective behavior and suggest an approach to understanding circuit-level substrates underlying psychiatric disease symptoms.

  8. The functional micro-organization of grid cells revealed by cellular-resolution imaging.

    PubMed

    Heys, James G; Rangarajan, Krsna V; Dombeck, Daniel A

    2014-12-03

    Establishing how grid cells are anatomically arranged, on a microscopic scale, in relation to their firing patterns in the environment would facilitate a greater microcircuit-level understanding of the brain's representation of space. However, all previous grid cell recordings used electrode techniques that provide limited descriptions of fine-scale organization. We therefore developed a technique for cellular-resolution functional imaging of medial entorhinal cortex (MEC) neurons in mice navigating a virtual linear track, enabling a new experimental approach to study MEC. Using these methods, we show that grid cells are physically clustered in MEC compared to nongrid cells. Additionally, we demonstrate that grid cells are functionally micro-organized: the similarity between the environment firing locations of grid cell pairs varies as a function of the distance between them according to a "Mexican hat"-shaped profile. This suggests that, on average, nearby grid cells have more similar spatial firing phases than those further apart.

  9. Live imaging reveals the progenitors and cell dynamics of limb regeneration

    PubMed Central

    Alwes, Frederike; Enjolras, Camille; Averof, Michalis

    2016-01-01

    Regeneration is a complex and dynamic process, mobilizing diverse cell types and remodelling tissues over long time periods. Tracking cell fate and behaviour during regeneration in active adult animals is especially challenging. Here, we establish continuous live imaging of leg regeneration at single-cell resolution in the crustacean Parhyale hawaiensis. By live recordings encompassing the first 4-5 days after amputation, we capture the cellular events that contribute to wound closure and morphogenesis of regenerating legs with unprecedented resolution and temporal detail. Using these recordings we are able to track cell lineages, to generate fate maps of the blastema and to identify the progenitors of regenerated epidermis. We find that there are no specialized stem cells for the epidermis. Most epidermal cells in the distal part of the leg stump proliferate, acquire new positional values and contribute to new segments in the regenerating leg. DOI: http://dx.doi.org/10.7554/eLife.19766.001 PMID:27776632

  10. The complex aerodynamic footprint of desert locusts revealed by large-volume tomographic particle image velocimetry

    PubMed Central

    Henningsson, Per; Michaelis, Dirk; Nakata, Toshiyuki; Schanz, Daniel; Geisler, Reinhard; Schröder, Andreas; Bomphrey, Richard J.

    2015-01-01

    Particle image velocimetry has been the preferred experimental technique with which to study the aerodynamics of animal flight for over a decade. In that time, hardware has become more accessible and the software has progressed from the acquisition of planes through the flow field to the reconstruction of small volumetric measurements. Until now, it has not been possible to capture large volumes that incorporate the full wavelength of the aerodynamic track left behind during a complete wingbeat cycle. Here, we use a unique apparatus to acquire the first instantaneous wake volume of a flying animal's entire wingbeat. We confirm the presence of wake deformation behind desert locusts and quantify the effect of that deformation on estimates of aerodynamic force and the efficiency of lift generation. We present previously undescribed vortex wake phenomena, including entrainment around the wing-tip vortices of a set of secondary vortices borne of Kelvin–Helmholtz instability in the shear layer behind the flapping wings. PMID:26040598

  11. Confocal imaging reveals three-dimensional fine structure difference between ventral and dorsal nerve roots

    NASA Astrophysics Data System (ADS)

    Wu, Yuxiang; Sui, Tao; Cao, Xiaojian; Lv, Xiaohua; Zeng, Shaoqun; Sun, Peng

    2011-05-01

    Peripheral nerve injury repair is one of the most challenging problems in neurosurgery, partially due to lack of knowledge of three-dimensional (3-D) fine structure and organization of peripheral nerves. In this paper, we explored the structures of nerve fibers in ventral and dorsal nerves with a laser scanning confocal microscopy. Thick tissue staining results suggested that nerve fibers have a different 3-D structure in ventral and dorsal nerves, and reconstruction from serial sectioning images showed that in ventral nerves the nerve fibers travel in a winding form, while in dorsal nerves, the nerve fibers form in a parallel cable pattern. These structural differences could help surgeons to differentiate ventral and dorsal nerves in peripheral nerve injury repair, and also facilitate scientists to get a deeper understanding about nerve fiber organization.

  12. High-resolution lithosphere viscosity and dynamics revealed by magnetotelluric imaging.

    PubMed

    Liu, Lijun; Hasterok, Derrick

    2016-09-30

    An accurate viscosity structure is critical to truthfully modeling lithosphere dynamics. Here, we report an attempt to infer the effective lithospheric viscosity from a high-resolution magnetotelluric (MT) survey across the western United States. The high sensitivity of MT fields to the presence of electrically conductive fluids makes it a promising proxy for determining mechanical strength variations throughout the lithosphere. We demonstrate how a viscosity structure, approximated from electrical resistivity, results in a geodynamic model that successfully predicts short-wavelength surface topography, lithospheric deformation, and mantle upwelling beneath recent volcanism. We further show that this viscosity is physically consistent with and better constrained than that derived from laboratory-based rheology. We conclude that MT imaging provides a practical observational constraint for quantifying the dynamic evolution of the continental lithosphere.

  13. Non-contact hemodynamic imaging reveals the jugular venous pulse waveform

    NASA Astrophysics Data System (ADS)

    Amelard, Robert; Hughson, Richard L.; Greaves, Danielle K.; Pfisterer, Kaylen J.; Leung, Jason; Clausi, David A.; Wong, Alexander

    2017-01-01

    Cardiovascular monitoring is important to prevent diseases from progressing. The jugular venous pulse (JVP) waveform offers important clinical information about cardiac health, but is not routinely examined due to its invasive catheterisation procedure. Here, we demonstrate for the first time that the JVP can be consistently observed in a non-contact manner using a photoplethysmographic imaging system. The observed jugular waveform was strongly negatively correlated to the arterial waveform (r = ‑0.73 ± 0.17), consistent with ultrasound findings. Pulsatile venous flow was observed over a spatially cohesive region of the neck. Critical inflection points (c, x, v, y waves) of the JVP were observed across all participants. The anatomical locations of the strongest pulsatile venous flow were consistent with major venous pathways identified through ultrasound.

  14. In vivo subcellular resolution optical imaging in the lung reveals early metastatic proliferation and motility

    PubMed Central

    Entenberg, David; Rodriguez-Tirado, Carolina; Kato, Yu; Kitamura, Takanori; Pollard, Jeffrey W; Condeelis, John

    2015-01-01

    To better understand breast cancer metastatic cell seeding, we have employed multiphoton microscopy and a vacuum stabilized window which eliminates the need for complex registration software, video rate microscopy or specialized gating electronics to observe the initial steps of tumor cell seeding within the living, breathing lung. We observe that upon arrival to the lung, tumor cells are found exclusively in capillary vessels, completely fill their volume and display an initial high level of protrusive activity that dramatically reduces over time. Further, we observe a concomitant increase in positional stability during this same period. We employ several techniques accessible to most imaging labs for optimizing signal to noise and resolution which enable us to report the first direct observation, with subcellular resolution, of the arrival, proliferation, and motility of metastatic tumor cells within the lung. PMID:26855844

  15. Image-Based Modeling Reveals Dynamic Redistribution of DNA Damageinto Nuclear Sub-Domains

    SciTech Connect

    Costes Sylvain V., Ponomarev Artem, Chen James L.; Nguyen, David; Cucinotta, Francis A.; Barcellos-Hoff, Mary Helen

    2007-08-03

    Several proteins involved in the response to DNA doublestrand breaks (DSB) f orm microscopically visible nuclear domains, orfoci, after exposure to ionizing radiation. Radiation-induced foci (RIF)are believed to be located where DNA damage occurs. To test thisassumption, we analyzed the spatial distribution of 53BP1, phosphorylatedATM, and gammaH2AX RIF in cells irradiated with high linear energytransfer (LET) radiation and low LET. Since energy is randomly depositedalong high-LET particle paths, RIF along these paths should also berandomly distributed. The probability to induce DSB can be derived fromDNA fragment data measured experimentally by pulsed-field gelelectrophoresis. We used this probability in Monte Carlo simulations topredict DSB locations in synthetic nuclei geometrically described by acomplete set of human chromosomes, taking into account microscope opticsfrom real experiments. As expected, simulations produced DNA-weightedrandom (Poisson) distributions. In contrast, the distributions of RIFobtained as early as 5 min after exposure to high LET (1 GeV/amu Fe) werenon-random. This deviation from the expected DNA-weighted random patterncan be further characterized by "relative DNA image measurements." Thisnovel imaging approach shows that RIF were located preferentially at theinterface between high and low DNA density regions, and were morefrequent than predicted in regions with lower DNA density. The samepreferential nuclear location was also measured for RIF induced by 1 Gyof low-LET radiation. This deviation from random behavior was evidentonly 5 min after irradiation for phosphorylated ATM RIF, while gammaH2AXand 53BP1 RIF showed pronounced deviations up to 30 min after exposure.These data suggest that DNA damage induced foci are restricted to certainregions of the nucleus of human epithelial cells. It is possible that DNAlesions are collected in these nuclear sub-domains for more efficientrepair.

  16. The HDUV Survey: Seven Lyman Continuum Emitter Candidates at z~2 Revealed by HST UV Imaging

    NASA Astrophysics Data System (ADS)

    Naidu, Rohan Potham; Oesch, Pascal; Hubble Deep UV (HDUV) Legacy Survey Team

    2017-01-01

    The fraction of ionizing photons that escape from star-forming galaxies in the early universe is a key unknown in the search for the main drivers of cosmic reionization. Despite significant efforts it has proven difficult to identify galaxies with high ionizing escape fractions (fesc). So far, only a handful of galaxies have been directly detected in their ionizing continuum (λrest<912 Angstrom) in the local universe, and even fewer reliable detections exist at higher redshifts. Here we present seven new Lyman continuum (LyC) emitter candidates at z~2, which we identified in the newly acquired, deep UV imaging of the Hubble Deep UV legacy survey (HDUV) conducted with the Hubble Space Telescope (HST) WFC3/UVIS camera. At the redshift of these sources, the HDUV F275W images partially probe the ionizing continuum. By exploiting the HST multi-wavelength data available in the HDUV/GOODS fields, models of the UV continuum, and detailed Monte-Carlo simulations of the intergalactic medium absorption, we estimate the escape fractions of these galaxies to be larger than 60%. The wealth of surveys and studies in the GOODS fields, especially the near-IR grism spectra from the 3D-HST survey, enable us to discuss the candidates in detail and tentatively test some recently proposed indirect methods to probe LyC leakage--namely, the OIII/OII line ratio and the Hβ-βUV diagram. High-resolution spectroscopic followup of our candidates will help constrain such indirect methods which are our only hope of studying fesc at z~4-9 in the fast-approaching era of the James Webb Space Telescope.

  17. Network asymmetry of motor areas revealed by resting-state functional magnetic resonance imaging.

    PubMed

    Yan, Li-Rong; Wu, Yi-Bo; Hu, De-Wen; Qin, Shang-Zhen; Xu, Guo-Zheng; Zeng, Xiao-Hua; Song, Hua

    2012-02-01

    There are ample functional magnetic resonance imaging (fMRI) studies on functional brain asymmetries, and the asymmetry of cerebral network in the resting state may be crucial to brain function organization. In this paper, a unified schema of voxel-wise functional connectivity and asymmetry analysis was presented and the network asymmetry of motor areas was studied. Twelve healthy male subjects with mean age 29.8 ± 6.4 were studied. Functional network in the resting state was described by using functional connectivity magnetic resonance imaging (fcMRI) analysis. Motor areas were selected as regions of interest (ROIs). Network asymmetry, including intra- and inter-network asymmetries, was formulated and analyzed. The intra-network asymmetry was defined as the difference between the left and right part of a particular functional network. The inter-network asymmetry was defined as the difference between the networks for a specific ROI in the left hemisphere and its homotopic ROI in the right hemisphere. Primary motor area (M1), primary sensory area (S1) and premotor area (PMA) exhibited higher functional correlation with the right parietal-temporal-occipital circuit and the middle frontal gyrus than they did with the left hemisphere. Right S1 and right PMA exhibited higher functional correlation with the ipsilateral precentral and supramarginal areas. There exist the large-scale hierarchical network asymmetries of the motor areas in the resting state. These asymmetries imply the right hemisphere dominance for predictive motor coding based on spatial attention and higher sensory processing load for the motor performance of non-dominant hemisphere.

  18. Patterns of Intersecting Fiber Arrays Revealed in Whole Muscle with Generalized Q-Space Imaging

    PubMed Central

    Taylor, Erik N.; Hoffman, Matthew P.; Aninwene, George E.; Gilbert, Richard J.

    2015-01-01

    The multiscale attributes of mammalian muscle confer significant challenges for structural imaging in vivo. To achieve this, we employed a magnetic resonance method, termed “generalized Q-space imaging”, that considers the effect of spatially distributed diffusion-weighted magnetic field gradients and diffusion sensitivities on the morphology of Q-space. This approach results in a subvoxel scaled probability distribution function whose shape correlates with local fiber orientation. The principal fiber populations identified within these probability distribution functions can then be associated by streamline methods to create multivoxel tractlike constructs that depict the macroscale orientation of myofiber arrays. We performed a simulation of Q-space input parameters, including magnetic field gradient strength and direction, diffusion sensitivity, and diffusional sampling to determine the optimal achievable fiber angle separation in the minimum scan time. We applied this approach to resolve intravoxel crossing myofiber arrays in the setting of the human tongue, an organ with anatomic complexity based on the presence of hierarchical arrays of intersecting myocytes. Using parameters defined by simulation, we imaged at 3T the fanlike configuration of the human genioglossus and the laterally positioned merging fibers of the styloglossus, inferior longitudinalis, chondroglossus, and verticalis. Comparative scans of the excised mouse tongue at 7T demonstrated similar midline and lateral crossing fiber patterns, whereas histological analysis confirmed the presence and distribution of these myofiber arrays at the microscopic scale. Our results demonstrate a magnetic resonance method for acquiring and displaying diffusional data that defines highly ordered myofiber patterns in architecturally complex tissue. Such patterns suggest inherent multiscale fiber organization and provide a basis for structure-function analyses in vivo and in model tissues. PMID:26039175

  19. Fixation based event-related fmri analysis: using eye fixations as events in functional magnetic resonance imaging to reveal cortical processing during the free exploration of visual images.

    PubMed

    Marsman, Jan Bernard C; Renken, Remco; Velichkovsky, Boris M; Hooymans, Johanna M M; Cornelissen, Frans W

    2012-02-01

    Eye movements, comprising predominantly fixations and saccades, are known to reveal information about perception and cognition, and they provide an explicit measure of attention. Nevertheless, fixations have not been considered as events in the analyses of data obtained during functional magnetic resonance imaging (fMRI) experiments. Most likely, this is due to their brevity and statistical properties. Despite these limitations, we used fixations as events to model brain activation in a free viewing experiment with standard fMRI scanning parameters. First, we found that fixations on different objects in different task contexts resulted in distinct cortical patterns of activation. Second, using multivariate pattern analysis, we showed that the BOLD signal revealed meaningful information about the task context of individual fixations and about the object being inspected during these fixations. We conclude that fixation-based event-related (FIBER) fMRI analysis creates new pathways for studying human brain function by enabling researchers to explore natural viewing behavior.

  20. Sub-diffraction nano manipulation using STED AFM.

    PubMed

    Chacko, Jenu Varghese; Canale, Claudio; Harke, Benjamin; Diaspro, Alberto

    2013-01-01

    In the last two decades, nano manipulation has been recognized as a potential tool of scientific interest especially in nanotechnology and nano-robotics. Contemporary optical microscopy (super resolution) techniques have also reached the nanometer scale resolution to visualize this and hence a combination of super resolution aided nano manipulation ineluctably gives a new perspective to the scenario. Here we demonstrate how specificity and rapid determination of structures provided by stimulated emission depletion (STED) microscope can aid another microscopic tool with capability of mechanical manoeuvring, like an atomic force microscope (AFM) to get topological information or to target nano scaled materials. We also give proof of principle on how high-resolution real time visualization can improve nano manipulation capability within a dense sample, and how STED-AFM is an optimal combination for this job. With these evidences, this article points to future precise nano dissections and maybe even to a nano-snooker game with an AFM tip and fluorospheres.

  1. Revealing Amphiphilic Nanodornains of Anti-Biofouling Polymer Coatings

    SciTech Connect

    Amadei, CA; Yang, R; Chiesa, M; Gleason, KK; Santos, S

    2014-04-09

    Undesired bacterial adhesion and biofilm formation on wetted surfaces leads to significant economic and environmental costs in various industries. Amphiphilic coatings with molecular hydrophilic and hydrophobic patches can mitigate such biofouling effectively in an environmentally friendly manner. The coatings are synthesized by copolymerizing (Hydroxyethyl)methacrylate and perfluorodecylacrylate via initiated chemical vapor deposition (iCVD). In previous studies, the size of the patches was estimated to be similar to 1.4-1.75 nm by fitting protein adsorption data to a theoretical model. However, no direct observations of the molecular heterogeneity exist and therefore the origin of the fouling resistance of amphiphilic coatings remains unclear. Here, the amphiphilic nature is investigated by amplitude modulation atomic force microscopy (AM-AFM). High-resolution images obtained by penetrating and oscillating the AFM tip under the naturally present water layer with sub-nanometer amplitudes reveal, for the first time, the existence of amphiphilic nanodomains (1-2 nm(2)). Compositional heterogeneity at the nanoscale is further corroborated by a statistical analysis on the data obtained with dynamic AM-AFM force spectroscopy. Variations in the long range attractive forces, responsible for water affinity, are also identified. These nanoscopic results on the polymers wettability are also confirmed by contact angle measurements (i.e., static and dynamic). The unprecedented ability to visualize the amphiphilic nanodomains as well as sub-nanometer crystalline structures provides strong evidence for the existence of previously postulated nanostructures, and sheds light on the underlying antifouling mechanism of amphiphilic chemistry.

  2. Imaging an optogenetic pH sensor reveals that protons mediate lateral inhibition in the retina

    PubMed Central

    Wang, Tzu-Ming; Holzhausen, Lars C.; Kramer, Richard H.

    2014-01-01

    The reciprocal synapse between photoreceptors and horizontal cells (HCs) underlies lateral inhibition and establishes the antagonistic center-surround receptive fields of retinal neurons, to enhance visual contrast. Despite decades of study, the signal mediating negative feedback from HCs to cones has remained controversial because the small, invaginated synaptic cleft has precluded measurement. Using zebrafish retinas, we show that light elicits a change in synaptic proton concentration with the correct magnitude, kinetics and spatial dependence to account for lateral inhibition. Light, which hyperpolarizes HCs, causes synaptic alkalinization, whereas activating an exogenously expressed ligand-gated Na+ channel, which depolarizes HCs, causes synaptic acidification. While acidification was prevented by blocking a proton pump, re-alkalinization was prevented by blocking proton-permeant ion channels, suggesting that distinct mechanisms underlie proton efflux and influx. These findings reveal that protons mediate lateral inhibition in the retina, raising the possibility that protons are unrecognized retrograde messengers elsewhere in the nervous system. PMID:24441679

  3. Molecular mechanisms of NET formation and degradation revealed by intravital imaging in the liver vasculature

    PubMed Central

    Kolaczkowska, Elzbieta; Jenne, Craig N.; Surewaard, Bas G. J.; Thanabalasuriar, Ajitha; Lee, Woo-Yong; Sanz, Maria-Jesus; Mowen, Kerri; Opdenakker, Ghislain; Kubes, Paul

    2015-01-01

    Neutrophil extracellular traps (NETs) composed of DNA decorated with histones and proteases trap and kill bacteria but also injure host tissue. Here we show that during a bloodstream infection with methicillin-resistant Staphylococcus aureus, the majority of bacteria are sequestered immediately by hepatic Kupffer cells, resulting in transient increases in liver enzymes, focal ischaemic areas and a robust neutrophil infiltration into the liver. The neutrophils release NETs into the liver vasculature, which remain anchored to the vascular wall via von Willebrand factor and reveal significant neutrophil elastase (NE) proteolytic activity. Importantly, DNase although very effective at DNA removal, and somewhat effective at inhibiting NE proteolytic activity, fails to remove the majority of histones from the vessel wall and only partly reduces injury. By contrast, inhibition of NET production as modelled by PAD4-deficiency, or prevention of NET formation and proteolytic activity as modelled in NE−/− mice prevent collateral host tissue damage. PMID:25809117

  4. Live Cell Imaging Reveals Structural Associations between the Actin and Microtubule Cytoskeleton in Arabidopsis [W] [OA

    PubMed Central

    Sampathkumar, Arun; Lindeboom, Jelmer J.; Debolt, Seth; Gutierrez, Ryan; Ehrhardt, David W.; Ketelaar, Tijs; Persson, Staffan

    2011-01-01

    In eukaryotic cells, the actin and microtubule (MT) cytoskeletal networks are dynamic structures that organize intracellular processes and facilitate their rapid reorganization. In plant cells, actin filaments (AFs) and MTs are essential for cell growth and morphogenesis. However, dynamic interactions between these two essential components in live cells have not been explored. Here, we use spinning-disc confocal microscopy to dissect interaction and cooperation between cortical AFs and MTs in Arabidopsis thaliana, utilizing fluorescent reporter constructs for both components. Quantitative analyses revealed altered AF dynamics associated with the positions and orientations of cortical MTs. Reorganization and reassembly of the AF array was dependent on the MTs following drug-induced depolymerization, whereby short AFs initially appeared colocalized with MTs, and displayed motility along MTs. We also observed that light-induced reorganization of MTs occurred in concert with changes in AF behavior. Our results indicate dynamic interaction between the cortical actin and MT cytoskeletons in interphase plant cells. PMID:21693695

  5. Variation in Carbohydrates between Cancer and Normal Cell Membranes Revealed by Super‐Resolution Fluorescence Imaging

    PubMed Central

    Chen, Junling; Liu, Tianzhou; Gao, Jing; Gao, Lan; Zhou, Lulu; Cai, Mingjun; Shi, Yan; Xiong, Wenyong; Jiang, Junguang

    2016-01-01

    Carbohydrate alterations on cell membranes are associated with various cancer processes, including tumorigenesis, malignant transformation, and tumor dissemination. However, variations in the distributions of cancer‐associated carbohydrates are unclear at the molecular level. Herein, direct stochastic optical reconstruction microscopy is used to reveal that seven major types of carbohydrates tended to form obvious clusters on cancer cell membranes compared with normal cell membranes (both cultured and primary cells), and most types of carbohydrates present a similar distributed characteristic on various cancer cells (e.g., HeLa and Os‐Rc‐2 cells). Significantly, sialic acid is found to distribute in larger‐sized clusters with a higher cluster coverage percentage on various cancer cells than normal cells. These findings on the aberrant distributions of cancer‐associated carbohydrates can potentially serve as novel diagnostic and therapeutic targets, as well as making a contribution to clarify how abnormal glycosylations of membrane glycoconjugates participate in tumorigenesis and metastasis. PMID:27981014

  6. Retrieval of the Vacuolar H+-ATPase from Phagosomes Revealed by Live Cell Imaging

    PubMed Central

    Clarke, Margaret; Maddera, Lucinda; Engel, Ulrike; Gerisch, Günther

    2010-01-01

    Background The vacuolar H+-ATPase, or V-ATPase, is a highly-conserved multi-subunit enzyme that transports protons across membranes at the expense of ATP. The resulting proton gradient serves many essential functions, among them energizing transport of small molecules such as neurotransmitters, and acidifying organelles such as endosomes. The enzyme is not present in the plasma membrane from which a phagosome is formed, but is rapidly delivered by fusion with endosomes that already bear the V-ATPase in their membranes. Similarly, the enzyme is thought to be retrieved from phagosome membranes prior to exocytosis of indigestible material, although that process has not been directly visualized. Methodology To monitor trafficking of the V-ATPase in the phagocytic pathway of Dictyostelium discoideum, we fed the cells yeast, large particles that maintain their shape during trafficking. To track pH changes, we conjugated the yeast with fluorescein isothiocyanate. Cells were labeled with VatM-GFP, a fluorescently-tagged transmembrane subunit of the V-ATPase, in parallel with stage-specific endosomal markers or in combination with mRFP-tagged cytoskeletal proteins. Principal Findings We find that the V-ATPase is commonly retrieved from the phagosome membrane by vesiculation shortly before exocytosis. However, if the cells are kept in confined spaces, a bulky phagosome may be exocytosed prematurely. In this event, a large V-ATPase-rich vacuole coated with actin typically separates from the acidic phagosome shortly before exocytosis. This vacuole is propelled by an actin tail and soon acquires the properties of an early endosome, revealing an unexpected mechanism for rapid recycling of the V-ATPase. Any V-ATPase that reaches the plasma membrane is also promptly retrieved. Conclusions/Signficance Thus, live cell microscopy has revealed both a usual route and alternative means of recycling the V-ATPase in the endocytic pathway. PMID:20052281

  7. Adaptive AFM scan speed control for high aspect ratio fast structure tracking

    SciTech Connect

    Ahmad, Ahmad; Schuh, Andreas; Rangelow, Ivo W.

    2014-10-15

    Improved imaging rates in Atomic Force Microscopes (AFM) are of high interest for disciplines such as life sciences and failure analysis of semiconductor wafers, where the sample topology shows high aspect ratios. Also, fast imaging is necessary to cover a large surface under investigation in reasonable times. Since AFMs are composed of mechanical components, they are associated with comparably low resonance frequencies that undermine the effort to increase the acquisition rates. In particular, high and steep structures are difficult to follow, which causes the cantilever to temporarily loose contact to or crash into the sample. Here, we report on a novel approach that does not affect the scanner dynamics, but adapts the lateral scanning speed of the scanner. The controller monitors the control error signal and, only when necessary, decreases the scan speed to allow the z-piezo more time to react to changes in the sample's topography. In this case, the overall imaging rate can be significantly increased, because a general scan speed trade-off decision is not needed and smooth areas are scanned fast. In contrast to methods trying to increase the z-piezo bandwidth, our method is a comparably simple approach that can be easily adapted to standard systems.

  8. Statistical image analysis reveals features affecting fates of Myxococcus xanthus developmental aggregates.

    PubMed

    Xie, Chunyan; Zhang, Haiyang; Shimkets, Lawrence J; Igoshin, Oleg A

    2011-04-05

    Starving Myxococcus xanthus bacteria use their motility systems to self-organize into multicellular fruiting bodies, large mounds in which cells differentiate into metabolically inert spores. Despite the identification of the genetic pathways required for aggregation and the use of microcinematography to observe aggregation dynamics in WT and mutant strains, a mechanistic understanding of aggregation is still incomplete. For example, it is not clear why some of the initial aggregates mature into fruiting bodies, whereas others disperse, merge, or split into two. Here, we develop high-throughput image quantification and statistical analysis methods to gain insight into M. xanthus developmental aggregation dynamics. A quantitative metric of features characterizing each aggregate is used to deduce the properties of the aggregates that are correlated with each fate. The analysis shows that small aggregate size but not neighbor-related parameters correlate with aggregate dispersal. Furthermore, close proximity is necessary but not sufficient for aggregate merging. Finally, splitting occurs for those aggregates that are unusually large and elongated. These observations place severe constraints on the underlying aggregation mechanisms and present strong evidence against the role of long-range morphogenic gradients or biased cell exchange in the dispersal, merging, or splitting of transient aggregates. This approach can be expanded and adapted to study self-organization in other cellular systems.

  9. Automated multidimensional image analysis reveals a role for Abl in embryonic wound repair.

    PubMed

    Zulueta-Coarasa, Teresa; Tamada, Masako; Lee, Eun J; Fernandez-Gonzalez, Rodrigo

    2014-07-01

    The embryonic epidermis displays a remarkable ability to repair wounds rapidly. Embryonic wound repair is driven by the evolutionary conserved redistribution of cytoskeletal and junctional proteins around the wound. Drosophila has emerged as a model to screen for factors implicated in wound closure. However, genetic screens have been limited by the use of manual analysis methods. We introduce MEDUSA, a novel image-analysis tool for the automated quantification of multicellular and molecular dynamics from time-lapse confocal microscopy data. We validate MEDUSA by quantifying wound closure in Drosophila embryos, and we show that the results of our automated analysis are comparable to analysis by manual delineation and tracking of the wounds, while significantly reducing the processing time. We demonstrate that MEDUSA can also be applied to the investigation of cellular behaviors in three and four dimensions. Using MEDUSA, we find that the conserved nonreceptor tyrosine kinase Abelson (Abl) contributes to rapid embryonic wound closure. We demonstrate that Abl plays a role in the organization of filamentous actin and the redistribution of the junctional protein β-catenin at the wound margin during embryonic wound repair. Finally, we discuss different models for the role of Abl in the regulation of actin architecture and adhesion dynamics at the wound margin.

  10. Temporal lobe abnormalities in semantic processing by criminal psychopaths as revealed by functional magnetic resonance imaging.

    PubMed

    Kiehl, Kent A; Smith, Andra M; Mendrek, Adrianna; Forster, Bruce B; Hare, Robert D; Liddle, Peter F

    2004-04-30

    We tested the hypothesis that psychopathy is associated with abnormalities in semantic processing of linguistic information. Functional magnetic resonance imaging (fMRI) was used to elucidate and characterize the neural architecture underlying lexico-semantic processes in criminal psychopathic individuals and in a group of matched control participants. Participants performed a lexical decision task in which blocks of linguistic stimuli alternated with a resting baseline condition. In each lexical decision block, the stimuli were either concrete words and pseudowords or abstract words and pseudowords. Consistent with our hypothesis, psychopathic individuals, relative to controls, showed poorer behavioral performance for processing abstract words. Analysis of the fMRI data for both groups indicated that processing of word stimuli, compared with the resting baseline condition, was associated with neural activation in bilateral fusiform gyrus, anterior cingulate, left middle temporal gyrus, right posterior superior temporal gyrus, and left and right inferior frontal gyrus. Analyses confirmed our prediction that psychopathic individuals would fail to show the appropriate neural differentiation between abstract and concrete stimuli in the right anterior temporal gyrus and surrounding cortex. The results are consistent with other studies of semantic processing in psychopathy and support the theory that psychopathy is associated with right hemisphere abnormalities for processing conceptually abstract material.

  11. Temporal lobe abnormalities in semantic processing by criminal psychopaths as revealed by functional magnetic resonance imaging.

    PubMed

    Kiehl, Kent A; Smith, Andra M; Mendrek, Adrianna; Forster, Bruce B; Hare, Robert D; Liddle, Peter F

    2004-01-15

    We tested the hypothesis that psychopathy is associated with abnormalities in semantic processing of linguistic information. Functional magnetic resonance imaging (fMRI) was used to elucidate and characterize the neural architecture underlying lexico-semantic processes in criminal psychopathic individuals and in a group of matched control participants. Participants performed a lexical decision task in which blocks of linguistic stimuli alternated with a resting baseline condition. In each lexical decision block, the stimuli were either concrete words and pseudowords or abstract words and pseudowords. Consistent with our hypothesis, psychopathic individuals, relative to controls, showed poorer behavioral performance for processing abstract words. Analysis of the fMRI data for both groups indicated that processing of word stimuli, compared with the resting baseline condition, was associated with neural activation in bilateral fusiform gyrus, anterior cingulate, left middle temporal gyrus, right posterior superior temporal gyrus, and left and right inferior frontal gyrus. Analyses confirmed our prediction that psychopathic individuals would fail to show the appropriate neural differentiation between abstract and concrete stimuli in the right anterior temporal gyrus and surrounding cortex. The results are consistent with other studies of semantic processing in psychopathy and support the theory that psychopathy is associated with right hemisphere abnormalities for processing conceptually abstract material.

  12. Gravity wave characteristics in the mesopause region revealed from OH airglow imager observations over Northern Colorado

    NASA Astrophysics Data System (ADS)

    Tang, Yihuan; Dou, Xiankang; Li, Tao; Nakamura, Takuji; Xue, Xianghui; Huang, Can; Manson, Alan; Meek, Chris; Thorsen, Denise; Avery, Susan

    2014-01-01

    Using 5 years of all-sky OH airglow imager data over Yucca Ridge Field Station, CO (40.7°N, 104.9°W), from September 2003 to September 2008, we extract and deduce quasi-monochromatic gravity wave (GW) characteristics in the mesopause region. The intrinsic periods are clustered between approximately 4 and 10 min, and many of them are unstable and evanescent. GW occurrence frequency exhibits a clear semiannual variation with equinoctial minima, which is likely related to the seasonal variation of background wind. The anomalous propagation direction in January 2006, with strong southward before major warming starting in 21 January and weak southward propagation afterward, was most likely affected by stratospheric sudden warming. The momentum fluxes show strongly anticorrelated with the tides, with ~180° out of phase in the zonal component. While in the meridional component, the easterly maximum occurred approximately 2-6 h after maximum easterly tidal wind. However, the anticorrelations are both weakest during the summer. The dissipating and breaking of small-scale and high-frequency GW's components could have a potential impact on the general circulation in the mesopause region.

  13. Noninvasive In Toto Imaging of the Thymus Reveals Heterogeneous Migratory Behavior of Developing T Cells.

    PubMed

    Bajoghli, Baubak; Kuri, Paola; Inoue, Daigo; Aghaallaei, Narges; Hanelt, Marleen; Thumberger, Thomas; Rauzi, Matteo; Wittbrodt, Joachim; Leptin, Maria

    2015-09-01

    The migration of developing T cells (thymocytes) between distinct thymic microenvironments is crucial for their development. Ex vivo studies of thymus tissue explants suggest two distinct migratory behaviors of thymocytes in the thymus. In the cortex, thymocytes exhibit a stochastic migration, whereas medullary thymocytes show confined migratory behavior. Thus far, it has been difficult to follow all thymocytes in an entire thymus and relate their differentiation steps to their migratory dynamics. To understand the spatial organization of the migratory behavior and development of thymocytes in a fully functional thymus, we developed transgenic reporter lines for the chemokine receptors ccr9a and ccr9b, as well as for rag2, and used them for noninvasive live imaging of the entire thymus in medaka (Oryzias latipes). We found that the expression of these two chemokine receptors in the medaka juvenile thymus defined two spatially distinct subpopulations of thymocytes. Landmark events of T cell development including proliferation, somatic recombination, and thymic selection can be mapped to subregions of the thymus. The migratory behavior of thymocytes within each of the subpopulations is equally heterogeneous, and specific migratory behaviors are not associated with particular domains in the thymus. During the period when thymocytes express rag2 their migratory behavior was more homogeneous. Therefore, the migratory behavior of thymocytes is partly correlated with their developmental stage rather than being defined by their spatial localization.

  14. Length-dependent flagellar growth of Vibrio alginolyticus revealed by real time fluorescent imaging

    PubMed Central

    Chen, Meiting; Zhao, Ziyi; Yang, Jin; Peng, Kai; Baker, Matthew AB; Bai, Fan; Lo, Chien-Jung

    2017-01-01

    Bacterial flagella are extracellular filaments that drive swimming in bacteria. During motor assembly, flagellins are transported unfolded through the central channel in the flagellum to the growing tip. Here, we applied in vivo fluorescent imaging to monitor in real time the Vibrio alginolyticus polar flagella growth. The flagellar growth rate is found to be highly length-dependent. Initially, the flagellum grows at a constant rate (50 nm/min) when shorter than 1500 nm. The growth rate decays sharply when the flagellum grows longer, which decreases to ~9 nm/min at 7500 nm. We modeled flagellin transport inside the channel as a one-dimensional diffusive process with an injection force at its base. When the flagellum is short, its growth rate is determined by the loading speed at the base. Only when the flagellum grows longer does diffusion of flagellin become the rate-limiting step, dramatically reducing the growth rate. Our results shed new light on the dynamic building process of this complex extracellular structure. DOI: http://dx.doi.org/10.7554/eLife.22140.001 PMID:28098557

  15. Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging.

    PubMed

    Ritsma, Laila; Ellenbroek, Saskia I J; Zomer, Anoek; Snippert, Hugo J; de Sauvage, Frederic J; Simons, Benjamin D; Clevers, Hans; van Rheenen, Jacco

    2014-03-20

    The rapid turnover of the mammalian intestinal epithelium is supported by stem cells located around the base of the crypt. In addition to the Lgr5 marker, intestinal stem cells have been associated with other markers that are expressed heterogeneously within the crypt base region. Previous quantitative clonal fate analyses have led to the proposal that homeostasis occurs as the consequence of neutral competition between dividing stem cells. However, the short-term behaviour of individual Lgr5(+) cells positioned at different locations within the crypt base compartment has not been resolved. Here we establish the short-term dynamics of intestinal stem cells using the novel approach of continuous intravital imaging of Lgr5- Confetti mice. We find that Lgr5(+) cells in the upper part of the niche (termed 'border cells') can be passively displaced into the transit-amplifying domain, after the division of proximate cells, implying that the determination of stem-cell fate can be uncoupled from division. Through quantitative analysis of individual clonal lineages, we show that stem cells at the crypt base, termed 'central cells', experience a survival advantage over border stem cells. However, through the transfer of stem cells between the border and central regions, all Lgr5(+) cells are endowed with long-term self-renewal potential. These findings establish a novel paradigm for stem-cell maintenance in which a dynamically heterogeneous cell population is able to function long term as a single stem-cell pool.

  16. 3D Mass Spectrometry Imaging Reveals a Very Heterogeneous Drug Distribution in Tumors

    PubMed Central

    Giordano, S.; Morosi, L.; Veglianese, P.; Licandro, S. A.; Frapolli, R.; Zucchetti, M.; Cappelletti, G.; Falciola, L.; Pifferi, V.; Visentin, S.; D’Incalci, M.; Davoli, E.

    2016-01-01

    Mass Spectrometry Imaging (MSI) is a widespread technique used to qualitatively describe in two dimensions the distribution of endogenous or exogenous compounds within tissue sections. Absolute quantification of drugs using MSI is a recent challenge that just in the last years has started to be addressed. Starting from a two dimensional MSI protocol, we developed a three-dimensional pipeline to study drug penetration in tumors and to develop a new drug quantification method by MALDI MSI. Paclitaxel distribution and concentration in different tumors were measured in a 3D model of Malignant Pleural Mesothelioma (MPM), which is known to be a very heterogeneous neoplasm, highly resistant to different drugs. The 3D computational reconstruction allows an accurate description of tumor PTX penetration, adding information about the heterogeneity of tumor drug distribution due to the complex microenvironment. The use of an internal standard, homogenously sprayed on tissue slices, ensures quantitative results that are similar to those obtained using HPLC. The 3D model gives important information about the drug concentration in different tumor sub-volumes and shows that the great part of each tumor is not reached by the drug, suggesting the concept of pseudo-resistance as a further explanation for ineffective therapies and tumors relapse. PMID:27841316

  17. Live imaging and modeling of inner nuclear membrane targeting reveals its molecular requirements in mammalian cells

    PubMed Central

    Boni, Andrea; Politi, Antonio Z.; Strnad, Petr; Xiang, Wanqing; Hossain, M. Julius

    2015-01-01

    Targeting of inner nuclear membrane (INM) proteins is essential for nuclear architecture and function, yet its mechanism remains poorly understood. Here, we established a new reporter that allows real-time imaging of membrane protein transport from the ER to the INM using Lamin B receptor and Lap2β as model INM proteins. These reporters allowed us to characterize the kinetics of INM targeting and establish a mathematical model of this process and enabled us to probe its molecular requirements in an RNA interference screen of 96 candidate genes. Modeling of the phenotypes of genes involved in transport of these INM proteins predicted that it critically depended on the number and permeability of nuclear pores and the availability of nuclear binding sites, but was unaffected by depletion of most transport receptors. These predictions were confirmed with targeted validation experiments on the functional requirements of nucleoporins and nuclear lamins. Collectively, our data support a diffusion retention model of INM protein transport in mammalian cells. PMID:26056140

  18. Cell-specific STORM superresolution imaging reveals nanoscale organization of cannabinoid signaling

    PubMed Central

    Szabó, Szilárd I.; Szabadits, Eszter; Pintér, Balázs; Woodhams, Stephen G.; Henstridge, Christopher M.; Balla, Gyula Y.; Nyilas, Rita; Varga, Csaba; Lee, Sang-Hun; Matolcsi, Máté; Cervenak, Judit; Kacskovics, Imre; Watanabe, Masahiko; Sagheddu, Claudia; Melis, Miriam; Pistis, Marco; Soltesz, Ivan; Katona, István

    2014-01-01

    A major challenge in neuroscience is to determine the nanoscale position and quantity of signaling molecules in a cell-type-, and subcellular compartment-specific manner. We therefore developed a novel approach combining cell-specific physiological and anatomical characterization with superresolution imaging, and studied the molecular and structural parameters shaping the physiological properties of synaptic endocannabinoid signaling in the mouse hippocampus. We found that axon terminals of perisomatically-projecting GABAergic interneurons possess increased CB1 receptor number, active-zone complexity, and receptor/effector ratio compared to dendritically-projecting interneurons, in agreement with higher efficiency of cannabinoid signaling at somatic versus dendritic synapses. Furthermore, chronic Δ9-tetrahydrocannabinol administration, which reduces cannabinoid efficacy on GABA release, evoked dramatic CB1-downregulation in a dose-dependent manner. Full receptor recovery required several weeks after cessation of Δ9-tetrahydrocannabinol treatment. These findings demonstrate that cell-type-specific nanoscale analysis of endogenous protein distribution is possible in brain circuits, and identify novel molecular properties controlling endocannabinoid signaling and cannabis-induced cognitive dysfunction. PMID:25485758

  19. Cell-specific STORM super-resolution imaging reveals nanoscale organization of cannabinoid signaling.

    PubMed

    Dudok, Barna; Barna, László; Ledri, Marco; Szabó, Szilárd I; Szabadits, Eszter; Pintér, Balázs; Woodhams, Stephen G; Henstridge, Christopher M; Balla, Gyula Y; Nyilas, Rita; Varga, Csaba; Lee, Sang-Hun; Matolcsi, Máté; Cervenak, Judit; Kacskovics, Imre; Watanabe, Masahiko; Sagheddu, Claudia; Melis, Miriam; Pistis, Marco; Soltesz, Ivan; Katona, István

    2015-01-01

    A major challenge in neuroscience is to determine the nanoscale position and quantity of signaling molecules in a cell type- and subcellular compartment-specific manner. We developed a new approach to this problem by combining cell-specific physiological and anatomical characterization with super-resolution imaging and studied the molecular and structural parameters shaping the physiological properties of synaptic endocannabinoid signaling in the mouse hippocampus. We found that axon terminals of perisomatically projecting GABAergic interneurons possessed increased CB1 receptor number, active-zone complexity and receptor/effector ratio compared with dendritically projecting interneurons, consistent with higher efficiency of cannabinoid signaling at somatic versus dendritic synapses. Furthermore, chronic Δ(9)-tetrahydrocannabinol administration, which reduces cannabinoid efficacy on GABA release, evoked marked CB1 downregulation in a dose-dependent manner. Full receptor recovery required several weeks after the cessation of Δ(9)-tetrahydrocannabinol treatment. These findings indicate that cell type-specific nanoscale analysis of endogenous protein distribution is possible in brain circuits and identify previously unknown molecular properties controlling endocannabinoid signaling and cannabis-induced cognitive dysfunction.

  20. Live imaging RNAi screen reveals genes essential for meiosis in mammalian oocytes.

    PubMed

    Pfender, Sybille; Kuznetsov, Vitaliy; Pasternak, Michał; Tischer, Thomas; Santhanam, Balaji; Schuh, Melina

    2015-08-13

    During fertilization, an egg and a sperm fuse to form a new embryo. Eggs develop from oocytes in a process called meiosis. Meiosis in human oocytes is highly error-prone, and defective eggs are the leading cause of pregnancy loss and several genetic disorders such as Down's syndrome. Which genes safeguard accurate progression through meiosis is largely unclear. Here we develop high-content phenotypic screening methods for the systematic identification of mammalian meiotic genes. We targeted 774 genes by RNA interference within follicle-enclosed mouse oocytes to block protein expression from an early stage of oocyte development onwards. We then analysed the function of several genes simultaneously by high-resolution imaging of chromosomes and microtubules in live oocytes and scored each oocyte quantitatively for 50 phenotypes, generating a comprehensive resource of meiotic gene function. The screen generated an unprecedented annotated data set of meiotic progression in 2,241 mammalian oocytes, which allowed us to analyse systematically which defects are linked to abnormal chromosome segregation during meiosis, identifying progression into anaphase with misaligned chromosomes as well as defects in spindle organization as risk factors. This study demonstrates how high-content screens can be performed in oocytes, and allows systematic studies of meiosis in mammals.

  1. Alterations of lymph flow after lymphadenectomy in rats revealed by real time fluorescence imaging system.

    PubMed

    Takeno, Y; Fujimoto, E

    2013-03-01

    Secondary lymphedema is one of the sequella of cancer treatment that in inadequately understood. The purpose of the present study is to investigate lymphedema formation and to explore the escape routes for excess interstitial fluid using lymphadenectomy in a rat model. In twelve Wistar rats, lymph nodes in the right inguinal and popliteal fossas were completely removed and lymph vessels carefully ligated. After operation, treated hind limbs were evaluated by indocyanine green lymphography and circumferential measurement. Both evaluations were performed from day 3 to ten weeks. Approximately 2 to 3 weeks after operation, a network-like pattern of the fluorescent signal appeared around the surgical site which then transitioned into a linear pattern in the lower abdomen. Videorecordings identified fluorescent flow moving from the lower abdomen to the ipsilateral axillary lymph node and in some rats, the network-like pattern was also observed to pass transversely over the suprapubic region to the contralateral inguinal lymph nodes. The network-like pattern on the lower abdomen and the linear pattern to the axillary fossa were seen continuously to the end of observation. Circumferential measurements of the treated hind limbs increased initially and then declined over time. This imaging system may be useful to detect early changes in lymphatic flow before swelling occurs and further study is needed.

  2. The functional micro-organization of grid cells revealed by cellular-resolution imaging

    PubMed Central

    Heys, James G.; Rangarajan, Krsna V.; Dombeck, Daniel A.

    2015-01-01

    Summary Establishing how grid cells are anatomically arranged, on a microscopic scale, in relation to their firing patterns in the environment would facilitate a greater micro-circuit level understanding of the brain’s representation of space. However, all previous grid cell recordings used electrode techniques that provide limited descriptions of fine-scale organization. We therefore developed a technique for cellular-resolution functional imaging of medial entorhinal cortex (MEC) neurons in mice navigating a virtual linear track, enabling a new experimental approach to study MEC. Using these methods, we show that grid cells are physically clustered in MEC compared to non-grid cells. Additionally, we demonstrate that grid cells are functionally micro-organized: The similarity between the environment firing locations of grid cell pairs varies as a function of the distance between them according to a “Mexican Hat” shaped profile. This suggests that, on average, nearby grid cells have more similar spatial firing phases than those further apart. PMID:25467986

  3. In vivo imaging reveals a pioneer wave of monocyte recruitment into mouse skin wounds.

    PubMed

    Rodero, Mathieu P; Licata, Fabrice; Poupel, Lucie; Hamon, Pauline; Khosrotehrani, Kiarash; Combadiere, Christophe; Boissonnas, Alexandre

    2014-01-01

    The cells of the mononuclear phagocyte system are essential for the correct healing of adult skin wounds, but their specific functions remain ill-defined. The absence of granulation tissue immediately after skin injury makes it challenging to study the role of mononuclear phagocytes at the initiation of this inflammatory stage. To study their recruitment and migratory behavior within the wound bed, we developed a new model for real-time in vivo imaging of the wound, using transgenic mice that express green and cyan fluorescent proteins and specifically target monocytes. Within hours after the scalp injury, monocytes invaded the wound bed. The complete abrogation of this infiltration in monocyte-deficient CCR2(-/-) mice argues for the involvement of classical monocytes in this process. Monocyte infiltration unexpectedly occurred as early as neutrophil recruitment did and resulted from active release from the bloodstream toward the matrix through microhemorrhages rather than transendothelial migration. Monocytes randomly scouted around the wound bed, progressively slowed down, and stopped. Our approach identified and characterized a rapid and earlier than expected wave of monocyte infiltration and provides a novel framework for investigating the role of these cells during early stages of wound healing.

  4. TIME VARIABILITY IN THE OUTER EDGE OF SATURN'S A-RING REVEALED BY CASSINI IMAGING

    SciTech Connect

    Spitale, J. N.; Porco, C. C.

    2009-11-15

    We examine the outer edge of Saturn's A-ring, whose shape is strongly influenced by the co-orbital satellites Janus and Epimetheus, during the period from day 2005-121 to day 2009-036. Twenty-four Cassini imaging data sets are used, each one giving a picture of the ring during a short interval, allowing us to explore its time variability in detail for the first time. We find that the ring experienced a period of adjustment within {approx}8 months of the 2006 January co-orbital swap, corresponding to the interval during which the two satellites were within about 60 deg. of one another. Outside that adjustment period, the ring is dominated by an m = 7 pattern, as expected near a 7:6 inner Lindblad resonance, but the alignment is opposite in phase to that predicted for isolated test particles, and the amplitude of the radial distortion varies with time. We find that the amplitude variation corresponds to a beat pattern between the perturbations from the two satellites as would be expected if the responses add linearly. However, we also find deviations of limited azimuthal extent from the simple m = 7 pattern. Some of the additional structure may arise from coupling between the two excited modes in the ring, but the origin of these features is still under investigation.

  5. Functional brain imaging in 14 patients with dissociative amnesia reveals right inferolateral prefrontal hypometabolism.

    PubMed

    Brand, Matthias; Eggers, Carsten; Reinhold, Nadine; Fujiwara, Esther; Kessler, Josef; Heiss, Wolf-Dieter; Markowitsch, Hans J

    2009-10-30

    Dissociative amnesia is a condition usually characterized by severely impaired retrograde memory functioning in the absence of structural brain damage. Recent case studies nevertheless found functional brain changes in patients suffering from autobiographical-episodic memory loss in the cause of dissociative amnesia. Functional changes were demonstrated in both resting state and memory retrieval conditions. In addition, some but not all cases also showed other neuropsychological impairments beyond retrograde memory deficits. However, there is no group study available that examined potential functional brain abnormalities and accompanying neuropsychological deteriorations in larger samples of patients with dissociative retrograde amnesia. We report functional imaging and neuropsychological data acquired in 14 patients with dissociative amnesia following stressful or traumatic events. All patients suffered from autobiographical memory loss. In addition, approximately half of the patients had deficits in anterograde memory and executive functioning. Accompanying functional brain changes were measured by [18F]fluorodeoxyglucose positron emission tomography (FDG-PET). Regional glucose utilization of the patients was compared with that of 19 healthy subjects, matched for age and gender. We found significantly decreased glucose utilization in the right inferolateral prefrontal cortex in the patients. Hypometabolism in this brain region, known to be involved in retrieval of autobiographical memories and self-referential processing, may be a functional brain correlate of dissociative amnesia.

  6. Functional magnetic resonance imaging adaptation reveals the cortical networks for processing grasp-relevant object properties.

    PubMed

    Monaco, Simona; Chen, Ying; Medendorp, W P; Crawford, J D; Fiehler, Katja; Henriques, Denise Y P

    2014-06-01

    Grasping behaviors require the selection of grasp-relevant object dimensions, independent of overall object size. Previous neuroimaging studies found that the intraparietal cortex processes object size, but it is unknown whether the graspable dimension (i.e., grasp axis between selected points on the object) or the overall size of objects triggers activation in that region. We used functional magnetic resonance imaging adaptation to investigate human brain areas involved in processing the grasp-relevant dimension of real 3-dimensional objects in grasping and viewing tasks. Trials consisted of 2 sequential stimuli in which the object's grasp-relevant dimension, its global size, or both were novel or repeated. We found that calcarine and extrastriate visual areas adapted to object size regardless of the grasp-relevant dimension during viewing tasks. In contrast, the superior parietal occipital cortex (SPOC) and lateral occipital complex of the left hemisphere adapted to the grasp-relevant dimension regardless of object size and task. Finally, the dorsal premotor cortex adapted to the grasp-relevant dimension in grasping, but not in viewing, tasks, suggesting that motor processing was complete at this stage. Taken together, our results provide a complete cortical circuit for progressive transformation of general object properties into grasp-related responses.

  7. Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging

    NASA Astrophysics Data System (ADS)

    Ritsma, Laila; Ellenbroek, Saskia I. J.; Zomer, Anoek; Snippert, Hugo J.; de Sauvage, Frederic J.; Simons, Benjamin D.; Clevers, Hans; van Rheenen, Jacco

    2014-03-01

    The rapid turnover of the mammalian intestinal epithelium is supported by stem cells located around the base of the crypt. In addition to the Lgr5 marker, intestinal stem cells have been associated with other markers that are expressed heterogeneously within the crypt base region. Previous quantitative clonal fate analyses have led to the proposal that homeostasis occurs as the consequence of neutral competition between dividing stem cells. However, the short-term behaviour of individual Lgr5+ cells positioned at different locations within the crypt base compartment has not been resolved. Here we establish the short-term dynamics of intestinal stem cells using the novel approach of continuous intravital imaging of Lgr5-Confetti mice. We find that Lgr5+ cells in the upper part of the niche (termed `border cells') can be passively displaced into the transit-amplifying domain, after the division of proximate cells, implying that the determination of stem-cell fate can be uncoupled from division. Through quantitative analysis of individual clonal lineages, we show that stem cells at the crypt base, termed `central cells', experience a survival advantage over border stem cells. However, through the transfer of stem cells between the border and central regions, all Lgr5+ cells are endowed with long-term self-renewal potential. These findings establish a novel paradigm for stem-cell maintenance in which a dynamically heterogeneous cell population is able to function long term as a single stem-cell pool.

  8. Revealing praziquantel molecular targets using mass spectrometry imaging: an expeditious approach applied to Schistosoma mansoni.

    PubMed

    Ferreira, Mônica Siqueira; de Oliveira, Rosimeire Nunes; de Oliveira, Diogo Noin; Esteves, Cibele Zanardi; Allegretti, Silmara Marques; Catharino, Rodrigo Ramos

    2015-05-01

    Finding specific molecular targets and the mechanism of action of praziquantel in the treatment of schistosomiasis remains a challenging task. Our efforts were focused on obtaining further information on worm composition before and after exposure to praziquantel in the treatment of schistosomiasis to elucidate the potential sites of action of this drug. Evidence indicates that the lipid bilayer is changed by treatment with praziquantel. Following this rationale, we employed a mass spectrometry imaging-based approach that helped to characterise lipids in specific locations, which are directly involved in the biochemical pathways of the BH strain of Schistosoma mansoni, as well as differentiating the molecular response that each worm sex presents in vivo. Our findings demonstrated significant differences between the chemical markers found in adult worms before and after praziquantel exposure, especially in phospholipids, which were predominantly identified as chemical markers in all samples. Results also indicate that distinct molecular pathways in both male and female worms could be differentially affected by praziquantel treatment. These data shine new light on the mechanism of action of praziquantel, taking a further step towards its full understanding.

  9. Optical imaging in galagos reveals parietal-frontal circuits underlying motor behavior.

    PubMed

    Stepniewska, Iwona; Friedman, Robert M; Gharbawie, Omar A; Cerkevich, Christina M; Roe, Anna W; Kaas, Jon H

    2011-09-13

    The posterior parietal cortex (PPC) of monkeys and prosimian galagos contains a number of subregions where complex, behaviorally meaningful movements, such as reaching, grasping, and body defense, can be evoked by electrical stimulation with long trains of electrical pulses through microelectrodes. Shorter trains of pulses evoke no or simple movements. One possibility for the difference in effectiveness of intracortical microstimulation is that long trains activate much larger regions of the brain. Here, we show that long-train stimulation of PPC does not activate widespread regions of frontal motor and premotor cortex but instead, produces focal, somatotopically appropriate activations of frontal motor and premotor cortex. Shorter stimulation trains activate the same frontal foci but less strongly, showing that longer stimulus trains do not produce less specification. Because the activated sites in frontal cortex correspond to the locations of direct parietal-frontal anatomical connections from the stimulated PPC subregions, the results show the usefulness of optical imaging in conjunction with electrical stimulation in showing functional pathways between nodes in behavior-specific cortical networks. Thus, long-train stimulation is effective in evoking ethologically relevant sequences of movements by activating nodes in a cortical network for a behaviorally relevant period rather than spreading activation in a nonspecific manner.

  10. Structural imaging reveals anatomical alterations in inferotemporal cortex in congenital prosopagnosia.

    PubMed

    Behrmann, Marlene; Avidan, Galia; Gao, Fuqiang; Black, Sandra

    2007-10-01

    Congenital prosopagnosia (CP) refers to the lifelong impairment in face recognition in individuals who have intact low-level visual processing, normal cognitive abilities, and no known neurological disorder. Although the face recognition impairment is profound and debilitating, its neural basis remains elusive. To investigate this, we conducted detailed morphometric and volumetric analyses of the occipitotemporal (OT) cortex in a group of CP individuals and matched control subjects using high-spatial resolution magnetic resonance imaging. Although there were no significant group differences in the depth or deviation from the midline of the OT or collateral sulci, the CP individuals evince a larger anterior and posterior middle temporal gyrus and a significantly smaller anterior fusiform (aF) gyrus. Interestingly, this volumetric reduction in the aF gyrus is correlated with the behavioral decrement in face recognition. These findings implicate a specific cortical structure as the neural basis of CP and, in light of the familial history of CP, target the aF gyrus as a potential site for further, focused genetic investigation.

  11. In situ imaging reveals the biomass of giant protists in the global ocean.

    PubMed

    Biard, Tristan; Stemmann, Lars; Picheral, Marc; Mayot, Nicolas; Vandromme, Pieter; Hauss, Helena; Gorsky, Gabriel; Guidi, Lionel; Kiko, Rainer; Not, Fabrice

    2016-04-28

    Planktonic organisms play crucial roles in oceanic food webs and global biogeochemical cycles. Most of our knowledge about the ecological impact of large zooplankton stems from research on abundant and robust crustaceans, and in particular copepods. A number of the other organisms that comprise planktonic communities are fragile, and therefore hard to sample and quantify, meaning that their abundances and effects on oceanic ecosystems are poorly understood. Here, using data from a worldwide in situ imaging survey of plankton larger than 600 μm, we show that a substantial part of the biomass of this size fraction consists of giant protists belonging to the Rhizaria, a super-group of mostly fragile unicellular marine organisms that includes the taxa Phaeodaria and Radiolaria (for example, orders Collodaria and Acantharia). Globally, we estimate that rhizarians in the top 200 m of world oceans represent a standing stock of 0.089 Pg carbon, equivalent to 5.2% of the total oceanic biota carbon reservoir. In the vast oligotrophic intertropical open oceans, rhizarian biomass is estimated to be equivalent to that of all other mesozooplankton (plankton in the size range 0.2-20 mm). The photosymbiotic association of many rhizarians with microalgae may be an important factor in explaining their distribution. The previously overlooked importance of these giant protists across the widest ecosystem on the planet changes our understanding of marine planktonic ecosystems.

  12. Repeat optical satellite images reveal widespread and long term decrease in land-terminating glacier speeds

    NASA Astrophysics Data System (ADS)

    Heid, T.; Kääb, A.

    2012-04-01

    By matching of repeat optical satellite images it is now possible to investigate glacier dynamics within large regions of the world and also between regions to improve knowledge about glacier dynamics in space and time. In this study we investigate whether the negative glacier mass balance seen over large parts of the world has caused the glaciers to change their speeds. The studied regions are Pamir, Caucasus, Penny Ice Cap, Alaska Range and Patagonia. In addition we derive speed changes for Karakoram, a region assumed to have positive mass balance and that contains many surge-type glaciers. We find that the mapped glaciers in the five regions with negative mass balance have over the last decades decreased their velocity at an average rate per decade of: 43 % in the Pamir, 8 % in the Caucasus, 25 % on Penny Ice Cap, 11 % in the Alaska Range and 20 % in Patagonia. Glaciers in Karakoram have generally increased their speeds, but surging glaciers and glaciers with flow instabilities are most prominent in this area. Therefore the calculated average speed change is not representative for this area.

  13. Augmented laminography, a correlative 3D imaging method for revealing the inner structure of compressed fossils

    PubMed Central

    Zuber, Marcus; Laaß, Michael; Hamann, Elias; Kretschmer, Sophie; Hauschke, Norbert; van de Kamp, Thomas; Baumbach, Tilo; Koenig, Thomas

    2017-01-01

    Non-destructive imaging techniques can be extremely useful tools for the investigation and the assessment of palaeontological objects, as mechanical preparation of rare and valuable fossils is precluded in most cases. However, palaeontologists are often faced with the problem of choosing a method among a wide range of available techniques. In this case study, we employ x-ray computed tomography (CT) and computed laminography (CL) to study the first fossil xiphosuran from the Muschelkalk (Middle Triassic) of the Netherlands. The fossil is embedded in micritic limestone, with the taxonomically important dorsal shield invisible, and only the outline of its ventral part traceable. We demonstrate the complementarity of CT and CL which offers an excellent option to visualize characteristic diagnostic features. We introduce augmented laminography to correlate complementary information of the two methods in Fourier space, allowing to combine their advantages and finally providing increased anatomical information about the fossil. This method of augmented laminography enabled us to identify the xiphosuran as a representative of the genus Limulitella. PMID:28128302

  14. Cellular dynamics during early barley pollen embryogenesis revealed by time-lapse imaging

    PubMed Central

    Daghma, Diaa Eldin S.; Hensel, Goetz; Rutten, Twan; Melzer, Michael; Kumlehn, Jochen

    2014-01-01

    Plants display a remarkable capacity for cellular totipotency. An intriguing and useful example is that immature pollen cultured in vitro can pass through embryogenic development to form haploid or doubled haploid plants. However, a lack of understanding the initial mechanisms of pollen embryogenesis hampers the improvement and more effective and widespread employment of haploid technology in plant research and breeding. To investigate the cellular dynamics during the onset of pollen embryogenesis, we used time-lapse imaging along with transgenic barley expressing nuclear localized Green Fluorescent Protein. The results enabled us to identify nine distinct embryogenic and non-embryogenic types of pollen response to the culture conditions. Cell proliferation in embryogenic pollen normally started via a first symmetric mitosis (54.3% of pollen observed) and only rarely did so via asymmetric pollen mitosis I (4.3% of pollen observed). In the latter case, proliferation generally originated from the vegetative-like cell, albeit the division of the generative-like cell was observed in few types of pollen. Under the culture conditions used, fusion of cell nuclei was the only mechanism of genome duplication observed. PMID:25538715

  15. Gate-tuning of graphene plasmons revealed by infrared nano-imaging.

    PubMed

    Fei, Z; Rodin, A S; Andreev, G O; Bao, W; McLeod, A S; Wagner, M; Zhang, L M; Zhao, Z; Thiemens, M; Dominguez, G; Fogler, M M; Castro Neto, A H; Lau, C N; Keilmann, F; Basov, D N

    2012-07-05

    Surface plasmons are collective oscillations of electrons in metals or semiconductors that enable confinement and control of electromagnetic energy at subwavelength scales. Rapid progress in plasmonics has largely relied on advances in device nano-fabrication, whereas less attention has been paid to the tunable properties of plasmonic media. One such medium--graphene--is amenable to convenient tuning of its electronic and optical properties by varying the applied voltage. Here, using infrared nano-imaging, we show that common graphene/SiO(2)/Si back-gated structures support propagating surface plasmons. The wavelength of graphene plasmons is of the order of 200 nanometres at technologically relevant infrared frequencies, and they can propagate several times this distance. We have succeeded in altering both the amplitude and the wavelength of these plasmons by varying the gate voltage. Using plasmon interferometry, we investigated losses in graphene by exploring real-space profiles of plasmon standing waves formed between the tip of our nano-probe and the edges of the samples. Plasmon dissipation quantified through this analysis is linked to the exotic electrodynamics of graphene. Standard plasmonic figures of merit of our tunable graphene devices surpass those of common metal-based structures.

  16. Augmented laminography, a correlative 3D imaging method for revealing the inner structure of compressed fossils

    NASA Astrophysics Data System (ADS)

    Zuber, Marcus; Laaß, Michael; Hamann, Elias; Kretschmer, Sophie; Hauschke, Norbert; van de Kamp, Thomas; Baumbach, Tilo; Koenig, Thomas

    2017-01-01

    Non-destructive imaging techniques can be extremely useful tools for the investigation and the assessment of palaeontological objects, as mechanical preparation of rare and valuable fossils is precluded in most cases. However, palaeontologists are often faced with the problem of choosing a method among a wide range of available techniques. In this case study, we employ x-ray computed tomography (CT) and computed laminography (CL) to study the first fossil xiphosuran from the Muschelkalk (Middle Triassic) of the Netherlands. The fossil is embedded in micritic limestone, with the taxonomically important dorsal shield invisible, and only the outline of its ventral part traceable. We demonstrate the complementarity of CT and CL which offers an excellent option to visualize characteristic diagnostic features. We introduce augmented laminography to correlate complementary information of the two methods in Fourier space, allowing to combine their advantages and finally providing increased anatomical information about the fossil. This method of augmented laminography enabled us to identify the xiphosuran as a representative of the genus Limulitella.

  17. BOREAS AFM-04 Twin Otter Aircraft Flux Data

    NASA Technical Reports Server (NTRS)

    MacPherson, J. Ian; Hall, Forrest G. (Editor); Knapp, David E. (Editor); Desjardins, Raymond L.; Smith, David E. (Technical Monitor)

    2000-01-01

    The BOREAS AFM-5 team collected and processed data from the numerous radiosonde flights during the project. The goals of the AFM-05 team were to provide large-scale definition of the atmosphere by supplementing the existing AES aerological network, both temporally and spatially. This data set includes basic upper-air parameters collected from the network of upper-air stations during the 1993, 1994, and 1996 field campaigns over the entire study region. The data are contained in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884) or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  18. GPIM AF-M315E Propulsion System

    NASA Technical Reports Server (NTRS)

    Spores, Ronald A.; Masse, Robert; Kimbrel, Scott; McLean, Chris

    2014-01-01

    The NASA Space Technology mission Directorate's (STMD) Green Propellant Infusion Mission (GPIM) Technology Demonstration Mission (TDM) will demonstrate an operational AF-M315E green propellant propulsion system. Aerojet-Rocketdyne is responsible for the development of the propulsion system payload. This paper statuses the propulsion system module development, including thruster design and system design; Initial test results for the 1N engineering model thruster are presented. The culmination of this program will be high-performance, green AF-M315E propulsion system technology at TRL 7+, with components demonstrated to TRL 9, ready for direct infusion to a wide range of applications for the space user community.

  19. Nanoscale imaging and mechanical analysis of Fc receptor-mediated macrophage phagocytosis against cancer cells.

    PubMed

    Li, Mi; Liu, Lianqing; Xi, Ning; Wang, Yuechao; Xiao, Xiubin; Zhang, Weijing

    2014-02-18

    Fc receptor-mediated macrophage phagocytosis against cancer cells is an important mechanism in the immune therapy of cancers. Traditional research about macrophage phagocytosis was based on optical microscopy, which cannot reveal detailed information because of the 200-nm-resolution limit. Quantitatively investigating the macrophage phagocytosis at micro- and nanoscale levels is still scarce. The advent of atomic force microscopy (AFM) offers an excellent analytical instrument for quantitatively investigating the biological processes at single-cell and single-molecule levels under native conditions. In this work, we combined AFM and fluorescence microscopy to visualize and quantify the detailed changes in cell morphology and mechanical properties during the process of Fc receptor-mediated macrophage phagocytosis against cancer cells. Lymphoma cells were discernible by fluorescence staining. Then, the dynamic process of phagocytosis was observed by time-lapse optical microscopy. Next, AFM was applied to investigate the detailed cellular behaviors during macrophage phagocytosis under the guidance of fluorescence recognition. AFM imaging revealed the distinct features in cellular ultramicrostructures for the different steps of macrophage phagocytosis. AFM cell mechanical property measurements indicated that the binding of cancer cells to macrophages could make macrophages become stiffer. The experimental results provide novel insights in understanding the Fc-receptor-mediated macrophage phagocytosis.

  20. The sources of sodium escaping from Io revealed by spectral high definition imaging.

    PubMed

    Mendillo, Michael; Laurent, Sophie; Wilson, Jody; Baumgardner, Jeffrey; Konrad, Janusz; Karl, W Clem

    2007-07-19

    On Jupiter's moon Io, volcanic plumes and evaporating lava flows provide hot gases to form an atmosphere that is subsequently ionized. Some of Io's plasma is captured by the planet's strong magnetic field to form a co-rotating torus at Io's distance; the remaining ions and electrons form Io's ionosphere. The torus and ionosphere are also depleted by three time-variable processes that produce a banana-shaped cloud orbiting with Io, a giant nebula extending out to about 500 Jupiter radii, and a jet close to Io. No spatial constraints exist for the sources of the first two; they have been inferred only from modelling the patterns seen in the trace gas sodium observed far from Io. Here we report observations that reveal a spatially confined stream that ejects sodium only from the wake of the Io-torus interaction, together with a visually distinct, spherically symmetrical outflow region arising from atmospheric sputtering. The spatial extent of the ionospheric wake that feeds the stream is more than twice that observed by the Galileo spacecraft and modelled successfully. This implies considerable variability, and therefore the need for additional modelling of volcanically-driven, episodic states of the great jovian nebula.

  1. Does My Face FIT?: A Face Image Task Reveals Structure and Distortions of Facial Feature Representation

    PubMed Central

    Fuentes, Christina T.; Runa, Catarina; Blanco, Xenxo Alvarez; Orvalho, Verónica; Haggard, Patrick

    2013-01-01

    Despite extensive research on face perception, few studies have investigated individuals’ knowledge about the physical features of their own face. In this study, 50 participants indicated the location of key features of their own face, relative to an anchor point corresponding to the tip of the nose, and the results were compared to the true location of the same individual’s features from a standardised photograph. Horizontal and vertical errors were analysed separately. An overall bias to underestimate vertical distances revealed a distorted face representation, with reduced face height. Factor analyses were used to identify separable subconfigurations of facial features with correlated localisation errors. Independent representations of upper and lower facial features emerged from the data pattern. The major source of variation across individuals was in representation of face shape, with a spectrum from tall/thin to short/wide representation. Visual identification of one’s own face is excellent, and facial features are routinely used for establishing personal identity. However, our results show that spatial knowledge of one’s own face is remarkably poor, suggesting that face representation may not contribute strongly to self-awareness. PMID:24130790

  2. Revealing the cellular localization of STAT1 during the cell cycle by super-resolution imaging

    NASA Astrophysics Data System (ADS)

    Gao, Jing; Wang, Feng; Liu, Yanhou; Cai, Mingjun; Xu, Haijiao; Jiang, Junguang; Wang, Hongda

    2015-03-01

    Signal transducers and activators of transcription (STATs) can transduce cytokine signals and regulate gene expression. The cellular localization and nuclear trafficking of STAT1, a representative of the STAT family with multiple transcriptional functions, is tightly related with transcription process, which usually happens in the interphase of the cell cycle. However, these priority questions regarding STAT1 distribution and localization at the different cell-cycle stages remain unclear. By using direct stochastic optical reconstruction microscopy (dSTORM), we found that the nuclear expression level of STAT1 increased gradually as the cell cycle carried out, especially after EGF stimulation. Furthermore, STAT1 formed clusters in the whole cell during the cell cycle, with the size and the number of clusters also increasing significantly from G1 to G2 phase, suggesting that transcription and other cell-cycle related activities can promote STAT1 to form more and larger clusters for fast response to signals. Our work reveals that the cellular localization and clustering distribution of STAT1 are associated with the cell cycle, and further provides an insight into the mechanism of cell-cycle regulated STAT1 signal transduction.

  3. Heterogeneity of macrophage infiltration and therapeutic response in lung carcinoma revealed by 3D organ imaging

    PubMed Central

    Cuccarese, Michael F.; Dubach, J. Matthew; Pfirschke, Christina; Engblom, Camilla; Garris, Christopher; Miller, Miles A.; Pittet, Mikael J.; Weissleder, Ralph

    2017-01-01

    Involvement of the immune system in tumour progression is at the forefront of cancer research. Analysis of the tumour immune microenvironment has yielded a wealth of information on tumour biology, and alterations in some immune subtypes, such as tumour-associated macrophages (TAM), can be strong prognostic indicators. Here, we use optical tissue clearing and a TAM-targeting injectable fluorescent nanoparticle (NP) to examine three-dimensional TAM composition, tumour-to-tumour heterogeneity, response to colony-stimulating factor 1 receptor (CSF-1R) blockade and nanoparticle-based drug delivery in murine pulmonary carcinoma. The method allows for rapid tumour volume assessment and spatial information on TAM infiltration at the cellular level in entire lungs. This method reveals that TAM density was heterogeneous across tumours in the same animal, overall TAM density is different among separate pulmonary tumour models, nanotherapeutic drug delivery correlated with TAM heterogeneity, and successful response to CSF-1R blockade is characterized by enhanced TAM penetration throughout and within tumours. PMID:28176769

  4. Geophysical imaging reveals brine system beneath an ice-sealed Antarctic lake

    NASA Astrophysics Data System (ADS)

    Dugan, H.; Doran, P. T.; Tulaczyk, S. M.; Mikucki, J.; Arcone, S. A.; Auken, E.; Schamper, C.; Virginia, R. A.

    2014-12-01

    The habitability of polar desert environments on Earth, and other neighboring planets, is dependent on the availability of liquid water. In areas where the surface is frozen, lenses of water present in the subsurface may act as microbial refugia. In the McMurdo Dry Valleys of Antarctica, the presence of highly saline brine in valley lakes raises the potential for the existence of a deep groundwater network. We report on a geophysical study that shows Lake Vida, in Victoria Valley, is nearly frozen, and the remaining brine is confined beneath thick ice. Near surface, bathymetric mapping of grounded lake ice was accomplished from a series of ground penetrating radar surveys. Radar penetration was limited to 20 m. An airborne transient electromagnetic survey (AEM) revealed a low resistivity zone at 30-100 m depth beneath the surface of the lake. Based on previous knowledge of brine chemistry and local geology, this zone is interpreted as brine saturated unconsolidated sediments with a porosity of 23-42%. Brine volume is calculated at 15 to 32 million cubic meters, which is of similar magnitude to the brine volume in nearby saline lakes. The AEM survey provided a means of quantifying the spatial extent of deep subsurface brine in this remote environment, and has provided a new perspective on the potential for subsurface habitats in areas often considered devoid of life.

  5. High spatial and angular resolution diffusion-weighted imaging reveals forniceal damage related to memory impairment☆

    PubMed Central

    Koenig, Katherine A.; Sakaie, Ken E.; Lowe, Mark J.; Lin, Jian; Stone, Lael; Bermel, Robert A.; Beall, Erik B.; Rao, Stephen M.; Trapp, Bruce D.; Phillips, Micheal D.

    2013-01-01

    Introduction Diffusion tensor imaging (DTI) measures in patients with multiple sclerosis (MS), particularly those measures associated with a specific white matter pathway, have consistently shown correlations with function. This study sought to investigate correlations between DTI measures in the fornix and common cognitive deficits in MS patients, including episodic memory, working memory and attention. Materials and Methods Patients with MS and group age- and sex-matched controls underwent high-resolution diffusion scanning (1-mm isotropic voxels) and cognitive testing. Manually drawn forniceal regions of interest were applied to individual maps of tensor-derived measures, and mean values of transverse diffusivity (TD), mean diffusivity (MD), longitudinal diffusivity (LD) and fractional anisotropy (FA) were calculated. Results In 40 patients with MS [mean age±S.D.=42.55±9.1 years; Expanded Disability Status Scale (EDSS)=2.0±1.2; Multiple Sclerosis Functional Composite (MSFC) score=0.38±0.46] and 20 healthy controls (mean age±S.D.=41.35±9.7 years; EDSS=0.0±0; MSFC score=0.74±0.24), we found that FA, MD and TD values in the fornix were significantly different between groups (P<.03), and patient performance on the Brief Visuospatial Memory Test-Revised (BVMT-R) was correlated with DTI measures (P<.03). Discussion These results are consistent with findings of axonal degeneration in MS and support the use of DTI as an indicator of disease progression. PMID:23295147

  6. In vivo imaging of alphaherpesvirus infection reveals synchronized activity dependent on axonal sorting of viral proteins.

    PubMed

    Granstedt, Andrea E; Bosse, Jens B; Thiberge, Stephan Y; Enquist, Lynn W

    2013-09-10

    A clinical hallmark of human alphaherpesvirus infections is peripheral pain or itching. Pseudorabies virus (PRV), a broad host range alphaherpesvirus, causes violent pruritus in many different animals, but the mechanism is unknown. Previous in vitro studies have shown that infected, cultured peripheral nervous system (PNS) neurons exhibited aberrant electrical activity after PRV infection due to the action of viral membrane fusion proteins, yet it is unclear if such activity occurs in infected PNS ganglia in living animals and if it correlates with disease symptoms. Using two-photon microscopy, we imaged autonomic ganglia in living mice infected with PRV strains expressing GCaMP3, a genetically encoded calcium indicator, and used the changes in calcium flux to monitor the activity of many neurons simultaneously with single-cell resolution. Infection with virulent PRV caused these PNS neurons to fire synchronously and cyclically in highly correlated patterns among infected neurons. This activity persisted even when we severed the presynaptic axons, showing that infection-induced firing is independent of input from presynaptic brainstem neurons. This activity was not observed after infections with an attenuated PRV recombinant used for circuit tracing or with PRV mutants lacking either viral glycoprotein B, required for membrane fusion, or viral membrane protein Us9, required for sorting virions and viral glycoproteins into axons. We propose that the viral fusion proteins produced by virulent PRV infection induce electrical coupling in unmyelinated axons in vivo. This action would then give rise to the synchronous and cyclical activity in the ganglia and contribute to the characteristic peripheral neuropathy.

  7. Diffusion tensor imaging of dolphin brains reveals direct auditory pathway to temporal lobe

    PubMed Central

    Berns, Gregory S.; Cook, Peter F.; Foxley, Sean; Jbabdi, Saad; Miller, Karla L.; Marino, Lori

    2015-01-01

    The brains of odontocetes (toothed whales) look grossly different from their terrestrial relatives. Because of their adaptation to the aquatic environment and their reliance on echolocation, the odontocetes' auditory system is both unique and crucial to their survival. Yet, scant data exist about the functional organization of the cetacean auditory system. A predominant hypothesis is that the primary auditory cortex lies in the suprasylvian gyrus along the vertex of the hemispheres, with this position induced by expansion of ‘associative′ regions in lateral and caudal directions. However, the precise location of the auditory cortex and its connections are still unknown. Here, we used a novel diffusion tensor imaging (DTI) sequence in archival post-mortem brains of a common dolphin (Delphinus delphis) and a pantropical dolphin (Stenella attenuata) to map their sensory and motor systems. Using thalamic parcellation based on traditionally defined regions for the primary visual (V1) and auditory cortex (A1), we found distinct regions of the thalamus connected to V1 and A1. But in addition to suprasylvian-A1, we report here, for the first time, the auditory cortex also exists in the temporal lobe, in a region near cetacean-A2 and possibly analogous to the primary auditory cortex in related terrestrial mammals (Artiodactyla). Using probabilistic tract tracing, we found a direct pathway from the inferior colliculus to the medial geniculate nucleus to the temporal lobe near the sylvian fissure. Our results demonstrate the feasibility of post-mortem DTI in archival specimens to answer basic questions in comparative neurobiology in a way that has not previously been possible and shows a link between the cetacean auditory system and those of terrestrial mammals. Given that fresh cetacean specimens are relatively rare, the ability to measure connectivity in archival specimens opens up a plethora of possibilities for investigating neuroanatomy in cetaceans and other species

  8. Functionally independent columns of rat somatosensory barrel cortex revealed with voltage-sensitive dye imaging.

    PubMed

    Petersen, C C; Sakmann, B

    2001-11-01

    Whisker movement is somatotopically represented in rodent neocortex by electrical activity in clearly defined barrels, which can be visualized in living brain slices. The functional architecture of this part of the cortex can thus be mapped in vitro with respect to its physiological input and compared with its anatomical architecture. The spatial extent of excitation was measured at high temporal resolution by imaging optical signals from voltage-sensitive dye evoked by stimulation of individual barrels in layer 4. The optical signals correlated closely with subthreshold EPSPs recorded simultaneously from excitatory neurons in layer 4 and layer 2/3, respectively. Excitation was initially (<2 msec) limited to the stimulated barrel and subsequently (>3 msec) spread in a columnar manner into layer 2/3 and then subsided in both layers after approximately 50 msec. The lateral extent of the response was limited to the cortical column defined structurally by the barrel in layer 4. Two experimental interventions increased the spread of excitation. First, blocking GABA(A) receptor-mediated synaptic inhibition caused excitation to spread laterally throughout wide regions of layer 2/3 and layer 5 but not into neighboring barrels, suggesting that the local excitatory connections within layer 4 are restricted to single barrels and that inhibitory neurons control spread in supragranular and infragranular layers. Second, NMDA receptor-dependent increase of the spread of excitation was induced by pairing repetitive stimulation of a barrel column with coincident stimulation of layer 2/3 in a neighboring column. Such plasticity in the spatial extent of excitation in a barrel column could underlie changes in cortical map structure induced by alterations of sensory experience.

  9. T1ρ Imaging in Premanifest Huntington Disease Reveals Changes Associated with Disease Progression

    PubMed Central

    Wassef, Shafik N.; Wemmie, John; Johnson, Casey P.; Johnson, Hans; Paulsen, Jane S.; Long, Jeffrey D.; Magnotta, Vincent A.

    2016-01-01

    Background Imaging biomarkers sensitive to Huntington’s disease (HD) during the premanifest phase preceding motor diagnosis may accelerate identification and evaluation of potential therapies. For this purpose, quantitative MRI sensitive to tissue microstructure and metabolism may hold great potential. We investigated the potential value of T1ρ relaxation to detect pathological changes in premanifest HD (preHD) relative to other quantitative relaxation parameters. Methods Quantitative MR parametric mapping was used to assess differences between 50 preHD subjects and 26 age- and sex-matched controls. Subjects with preHD were classified into two progression groups based on their CAG-age product (CAP) score; a high and a low/moderate CAP group. Voxel-wise and region-of-interest analyses were used to assess changes in the quantitative relaxation times. Results T1ρ showed a significant increase in the relaxation times in the high-CAP group, as compared to controls, largely in the striatum. The T1ρ changes in the preHD subjects showed a significant relationship with CAP score. No significant changes in T2 or T2* relaxation times were found in the striatum. T2* relaxation changes were found in the globus pallidus, but no significant changes with disease progression were found. Conclusion These data suggest that quantitative T1ρ mapping may provide a useful marker for assessing disease progression in HD. The absence of T2 changes suggests that the T1ρ abnormalities are unlikely owing to altered water content or tissue structure. The established sensitivity of T1ρ to pH and glucose suggests that these factors are altered in HD perhaps owing to abnormal mitochondrial function. PMID:25820773

  10. Combined structural and functional imaging reveals cortical deactivations in grapheme-color synaesthesia

    PubMed Central

    O'Hanlon, Erik; Newell, Fiona N.; Mitchell, Kevin J.

    2013-01-01

    Synaesthesia is a heritable condition in which particular stimuli generate specific and consistent sensory percepts or associations in another modality or processing stream. Functional neuroimaging studies have identified potential correlates of these experiences, including, in some but not all cases, the hyperactivation of visuotemporal areas and of parietal areas thought to be involved in perceptual binding. Structural studies have identified a similarly variable spectrum of differences between synaesthetes and controls. However, it remains unclear the extent to which these neural correlates reflect the synaesthetic experience itself or additional phenotypes associated with the condition. Here, we acquired both structural and functional neuroimaging data comparing thirteen grapheme-color synaesthetes with eleven non-synaesthetes. Using voxel-based morphometry and diffusion tensor imaging, we identify a number of clusters of increased volume of gray matter, of white matter or of increased fractional anisotropy in synaesthetes vs. controls. To assess the possible involvement of these areas in the synaesthetic experience, we used nine areas of increased gray matter volume as regions of interest in an fMRI experiment that characterized the contrast in response to stimuli which induced synaesthesia (i.e., letters) vs. those which did not (non-meaningful symbols). Four of these areas showed sensitivity to this contrast in synaesthetes but not controls. Unexpectedly, in two of them, in left lateral occipital cortex and in postcentral gyrus, the letter stimuli produced a strong negative BOLD signal in synaesthetes. An additional whole-brain fMRI analysis identified 14 areas, three of which were driven mainly by a negative BOLD response to letters in synaesthetes. Our findings suggest that cortical deactivations may be involved in the conscious experience of internally generated synaesthetic percepts. PMID:24198794

  11. Lithospheric geometries revealed through electromagnetic imaging: SAMTEX (Southern Africa MagnetoTelluric Experiment) observations and results

    NASA Astrophysics Data System (ADS)

    Jones, A. G.; Muller, M. R.; Evans, R. L.; Miensopust, M. P.; Khoza, D. T.; Samtex Team

    2011-12-01

    The Southern African Magnetotelluric Experiment (SAMTEX) is imaging the properties and geometries of the lithosphere below southern Africa to depths of 200+ km. Electrical conductivity is highly sensitive to ambient temperature, and to the presence of an interconnected conducting phase, such as a solid phase like graphite or sulphides, a fluid phase like partial melt, or bound water through hydrogen diffusion. Thus, primary geometrical information can be readily obtained from lithospheric-scale MT experiments about the three-dimensional variation in conductivity that can be related to formation and deformation processes. One important piece of information easily obtained from MT data is the depth to the lithosphere-asthenosphere boundary (LAB), due to the sensitivity of conductivity to small fractions (<1%) of partial melt and/or of some hundreds of ppm of bound water. SAMTEX measurements have been made at a total of more than 750 MT sites over an area in excess of a million square kilometres, making it by far the largest-ever regional MT project undertaken. One of the most significant results from SAMTEX is the mapping of the LAB beneath the Archean cratons and bounding mobile belts of Southern Africa, particularly of the previously unknown regions of Namibia and Botswana. The LAB is shallow (150 km) beneath the mobile belts, deep (250 km) in the centres of the cratons, and transitional at the edges. Diamondiferous kimberlites are located primarily where lithosphere is transitional in thickness, or where there is a change in its anisotropy properties, both of which are craton edge effects. The electrical properties of the continental mantle derived from SAMTEX data can be compared with seismic ones derived from data from the South African Seismic Experiment (SASE) of the Kaapvaal Project. Generally there is very good predictive linear agreement between seismic velocity and log(conductivity), indicative of both being influenced by the same bulk property factors

  12. Imaging studies in congenital anophthalmia reveal preservation of brain architecture in 'visual' cortex.

    PubMed

    Bridge, Holly; Cowey, Alan; Ragge, Nicola; Watkins, Kate

    2009-12-01

    The functional specialization of the human brain means that many regions are dedicated to processing a single sensory modality. When a modality is absent, as in congenital total blindness, 'visual' regions can be reliably activated by non-visual stimuli. The connections underlying this functional adaptation, however, remain elusive. In this study, using structural and diffusion-weighted magnetic resonance imaging, we investigated the structural differences in the brains of six bilaterally anophthalmic subjects compared with sighted subjects. Surprisingly, the gross structural differences in the brains were small, even in the occipital lobe where only a small region of the primary visual cortex showed a bilateral reduction in grey matter volume in the anophthalmic subjects compared with controls. Regions of increased cortical thickness were apparent on the banks of the Calcarine sulcus, but not in the fundus. Subcortically, the white matter volume around the optic tract and internal capsule in anophthalmic subjects showed a large decrease, yet the optic radiation volume did not differ significantly. However, the white matter integrity, as measured with fractional anisotropy showed an extensive reduction throughout the brain in the anophthalmic subjects, with the greatest difference in the optic radiations. In apparent contradiction to the latter finding, the connectivity between the lateral geniculate nucleus and primary visual cortex measured with diffusion tractography did not differ between the two populations. However, these findings can be reconciled by a demonstration that at least some of the reduction in fractional anisotropy in the optic radiation is due to an increase in the strength of fibres crossing the radiations. In summary, the major changes in the 'visual' brain in anophthalmic subjects may be subcortical, although the evidence of decreased fractional anisotropy and increased crossing fibres could indicate considerable re-organization.

  13. Conductive area ratio of multiblock copolymer electrolyte membranes evaluated by e-AFM and its impact on fuel cell performance

    NASA Astrophysics Data System (ADS)

    Takimoto, Naohiko; Takamuku, Shogo; Abe, Mitsutaka; Ohira, Akihiro; Lee, Hae-Seung; McGrath, James E.

    The correlation between membrane surface morphology and fuel cell performance was investigated using a series of hydrophilic-hydrophobic multiblock copolymers based on poly(arylene ether sulfone) with different block lengths. The proton conductive regions on the membrane surface were successfully observed by using electrochemical atomic force microscopy (e-AFM). The results revealed a strong dependence of the hydrophilic/hydrophobic microphase-separated structure on the block length. The conductive area ratio (CAR) estimated from the proton conduction image decreased as the block length increased, and it was found to be closely connected with cell resistance that determines fuel cell performance. The well-defined phase-separated structure of multiblock copolymers can improve proton conductivity without any undesirable increments in water uptake or swelling, but in some instances, it affects the interfacial connection with the catalyst layer, resulting in lower fuel cell performance. The results of this study suggest the necessity for further improvement of the membrane morphology by optimizing both the casting conditions and the molecular design of the block sequences.

  14. Live-cell imaging of actin dynamics reveals mechanisms of stereocilia length regulation in the inner ear.

    PubMed

    Drummond, Meghan C; Barzik, Melanie; Bird, Jonathan E; Zhang, Duan-Sun; Lechene, Claude P; Corey, David P; Cunningham, Lisa L; Friedman, Thomas B

    2015-04-21

    The maintenance of sensory hair cell stereocilia is critical for lifelong hearing; however, mechanisms of structural homeostasis remain poorly understood. Conflicting models propose that stereocilia F-actin cores are either continually renewed every 24-48 h via a treadmill or are stable, exceptionally long-lived structures. Here to distinguish between these models, we perform an unbiased survey of stereocilia actin dynamics in more than 500 utricle hair cells. Live-imaging EGFP-β-actin or dendra2-β-actin reveal stable F-actin cores with turnover and elongation restricted to stereocilia tips. Fixed-cell microscopy of wild-type and mutant β-actin demonstrates that incorporation of actin monomers into filaments is required for localization to stereocilia tips. Multi-isotope imaging mass spectrometry and live imaging of single differentiating hair cells capture stereociliogenesis and explain uniform incorporation of (15)N-labelled protein and EGFP-β-actin into nascent stereocilia. Collectively, our analyses support a model in which stereocilia actin cores are stable structures that incorporate new F-actin only at the distal tips.

  15. Simultaneous fNIRS and thermal infrared imaging during cognitive task reveal autonomic correlates of prefrontal cortex activity

    NASA Astrophysics Data System (ADS)

    Pinti, Paola; Cardone, Daniela; Merla, Arcangelo

    2015-12-01

    Functional Near Infrared-Spectroscopy (fNIRS) represents a powerful tool to non-invasively study task-evoked brain activity. fNIRS assessment of cortical activity may suffer for contamination by physiological noises of different origin (e.g. heart beat, respiration, blood pressure, skin blood flow), both task-evoked and spontaneous. Spontaneous changes occur at different time scales and, even if they are not directly elicited by tasks, their amplitude may result task-modulated. In this study, concentration changes of hemoglobin were recorded over the prefrontal cortex while simultaneously recording the facial temperature variations of the participants through functional infrared thermal (fIR) imaging. fIR imaging provides touch-less estimation of the thermal expression of peripheral autonomic. Wavelet analysis revealed task-modulation of the very low frequency (VLF) components of both fNIRS and fIR signals and strong coherence between them. Our results indicate that subjective cognitive and autonomic activities are intimately linked and that the VLF component of the fNIRS signal is affected by the autonomic activity elicited by the cognitive task. Moreover, we showed that task-modulated changes in vascular tone occur both at a superficial and at larger depth in the brain. Combined use of fNIRS and fIR imaging can effectively quantify the impact of VLF autonomic activity on the fNIRS signals.

  16. Limited Ability of Posaconazole To Cure both Acute and Chronic Trypanosoma cruzi Infections Revealed by Highly Sensitive In Vivo Imaging.

    PubMed

    Francisco, Amanda Fortes; Lewis, Michael D; Jayawardhana, Shiromani; Taylor, Martin C; Chatelain, Eric; Kelly, John M

    2015-08-01

    The antifungal drug posaconazole has shown significant activity against Trypanosoma cruzi in vitro and in experimental murine models. Despite this, in a recent clinical trial it displayed limited curative potential. Drug testing is problematic in experimental Chagas disease because of difficulties in demonstrating sterile cure, particularly during the chronic stage of infection when parasite burden is extremely low and tissue distribution is ill defined. To better assess posaconazole efficacy against acute and chronic Chagas disease, we have exploited a highly sensitive bioluminescence imaging system which generates data with greater accuracy than other methods, including PCR-based approaches. Mice inoculated with bioluminescent T. cruzi were assessed by in vivo and ex vivo imaging, with cyclophosphamide-induced immunosuppression used to enhance the detection of relapse. Posaconazole was found to be significantly inferior to benznidazole as a treatment for both acute and chronic T. cruzi infections. Whereas 20 days treatment with benznidazole was 100% successful in achieving sterile cure, posaconazole failed in almost all cases. Treatment of chronic infections with posaconazole did however significantly reduce infection-induced splenomegaly, even in the absence of parasitological cure. The imaging-based screening system also revealed that adipose tissue is a major site of recrudescence in mice treated with posaconazole in the acute, but not the chronic stage of infection. This in vivo screening model for Chagas disease is predictive, reproducible and adaptable to diverse treatment schedules. It should provide greater assurance that drugs are not advanced prematurely into clinical trial.

  17. Simultaneous fNIRS and thermal infrared imaging during cognitive task reveal autonomic correlates of prefrontal cortex activity

    PubMed Central

    Pinti, Paola; Cardone, Daniela; Merla, Arcangelo

    2015-01-01

    Functional Near Infrared-Spectroscopy (fNIRS) represents a powerful tool to non-invasively study task-evoked brain activity. fNIRS assessment of cortical activity may suffer for contamination by physiological noises of different origin (e.g. heart beat, respiration, blood pressure, skin blood flow), both task-evoked and spontaneous. Spontaneous changes occur at different time scales and, even if they are not directly elicited by tasks, their amplitude may result task-modulated. In this study, concentration changes of hemoglobin were recorded over the prefrontal cortex while simultaneously recording the facial temperature variations of the participants through functional infrared thermal (fIR) imaging. fIR imaging provides touch-less estimation of the thermal expression of peripheral autonomic. Wavelet analysis revealed task-modulation of the very low frequency (VLF) components of both fNIRS and fIR signals and strong coherence between them. Our results indicate that subjective cognitive and autonomic activities are intimately linked and that the VLF component of the fNIRS signal is affected by the autonomic activity elicited by the cognitive task. Moreover, we showed that task-modulated changes in vascular tone occur both at a superficial and at larger depth in the brain. Combined use of fNIRS and fIR imaging can effectively quantify the impact of VLF autonomic activity on the fNIRS signals. PMID:26632763

  18. Confocal imaging of whole vertebrate embryos reveals novel insights into molecular and cellular mechanisms of organ development

    NASA Astrophysics Data System (ADS)

    Hadel, Diana M.; Keller, Bradley B.; Sandell, Lisa L.

    2014-03-01

    Confocal microscopy has been an invaluable tool for studying cellular or sub-cellular biological processes. The study of vertebrate embryology is based largely on examination of whole embryos and organs. The application of confocal microscopy to immunostained whole mount embryos, combined with three dimensional (3D) image reconstruction technologies, opens new avenues for synthesizing molecular, cellular and anatomical analysis of vertebrate development. Optical cropping of the region of interest enables visualization of structures that are morphologically complex or obscured, and solid surface rendering of fluorescent signal facilitates understanding of 3D structures. We have applied these technologies to whole mount immunostained mouse embryos to visualize developmental morphogenesis of the mammalian inner ear and heart. Using molecular markers of neuron development and transgenic reporters of neural crest cell lineage we have examined development of inner ear neurons that originate from the otic vesicle, along with the supporting glial cells that derive from the neural crest. The image analysis reveals a previously unrecognized coordinated spatial organization between migratory neural crest cells and neurons of the cochleovestibular nerve. The images also enable visualization of early cochlear spiral nerve morphogenesis relative to the developing cochlea, demonstrating a heretofore unknown association of neural crest cells with extending peripheral neurite projections. We performed similar analysis of embryonic hearts in mouse and chick, documenting the distribution of adhesion molecules during septation of the outflow tract and remodeling of aortic arches. Surface rendering of lumen space defines the morphology in a manner similar to resin injection casting and micro-CT.

  19. Real-time CARS imaging reveals a calpain-dependent pathway for paranodal myelin retraction during high-frequency stimulation.

    PubMed

    Huff, Terry B; Shi, Yunzhou; Sun, Wenjing; Wu, Wei; Shi, Riyi; Cheng, Ji-Xin

    2011-03-03

    High-frequency electrical stimulation is becoming a promising therapy for neurological disorders, however the response of the central nervous system to stimulation remains poorly understood. The current work investigates the response of myelin to electrical stimulation by laser-scanning coherent anti-Stokes Raman scattering (CARS) imaging of myelin in live spinal tissues in real time. Paranodal myelin retraction at the nodes of Ranvier was observed during 200 Hz electrical stimulation. Retraction was seen to begin minutes after the onset of stimulation and continue for up to 10 min after stimulation was ceased, but was found to reverse after a 2 h recovery period. The myelin retraction resulted in exposure of Kv 1.2 potassium channels visualized by immunofluorescence. Accordingly, treating the stimulated tissue with a potassium channel blocker, 4-aminopyridine, led to the appearance of a shoulder peak in the compound action potential curve. Label-free CARS imaging of myelin coupled with multiphoton fluorescence imaging of immuno-labeled proteins at the nodes of Ranvier revealed that high-frequency stimulation induced paranodal myelin retraction via pathologic calcium influx into axons, calpain activation, and cytoskeleton degradation through spectrin break-down.

  20. Wholemount imaging reveals abnormalities of the aqueous outflow pathway and corneal vascularity in Foxc1 and Bmp4 heterozygous mice.

    PubMed

    van der Merwe, Elizabeth L; Kidson, Susan H

    2016-05-01

    Mutations in the FOXC1/Foxc1 gene in humans and mice and Bmp4 in mice are associated with congenital anterior segment dysgenesis (ASD) and the development of the aqueous outflow structures throughout the limbus. The aim of this study was to advance our understanding of anterior segment abnormalities in mouse models of ASD using a 3-D imaging approach. Holistic imaging information combined with quantitative measurements were carried out on PECAM-1 stained individual components of the aqueous outflow vessels and corneal vasculature of Foxc1(+/-) on the C57BL/6Jx129 and ICR backgrounds, Bmp4(+/-) ICR mice, and wildtype mice from each background. In both wildtype and heterozygotes, singular, bifurcated and plexus forms of Schlemm's canal were noted. Of note, missing portions of the canal were seen in the heterozygous groups but not in wildtype animals. In general, we found the number of collector channels to be reduced in both heterozygotes. Lastly, we found a significant increase in the complexity of the corneal arcades and their penetration into the cornea in heterozygotes as compared with wild types. In conclusion, our 3-D imaging studies have revealed a more complex arrangement of both the aqueous vessels and corneal arcades in Foxc1(+/-) and Bmp4(+/-) heterozygotes, and further advance our understanding of how such abnormalities could impact on IOP and the aetiology of glaucoma.

  1. New developments at PTB in 3D-AFM with tapping and torsion AFM mode and vector approach probing strategy

    NASA Astrophysics Data System (ADS)

    Dai, G.; Hässler-Grohne, W.; Hüser, D.; Wolff, H.; Fluegge, J.; Bosse, H.

    2011-06-01

    A new 3D-AFM for true 3D measurements of nano structures has been developed at Physikalisch Technische-Bundesanstalt, the national metrology institute of Germany. In its configuration, two piezo actuators are applied to drive the AFM cantilever near its vertical and torsional resonant frequencies. In such a way, the AFM tip can probe the surface with a vertical and/or a lateral oscillation, offering high 3D probing sensitivity. For enhancing measurement flexibility as well as reducing tip wear, a so called "vector approach probing" (VAP) method has been applied. The sample is measured point by point using this method. At each probing point, the tip is approached towards the surface in its normal direction until the desired tip-sample interaction is detected and then immediately withdrawn from the surface. Preliminary experimental results show promising performance of the developed system. The measurement of a line structure of 800 nm height employing a super sharp AFM tip is performed, showing a repeatability of its 3D profiles of better than 1 nm (p-v). A single crystal critical dimension reference material (SCCDRM) having features with almost vertical sidewall is measured using a flared AFM tip. Results show that the feature has averaged left and right sidewall angles of 88.64° and 88.67deg;, respectively. However, the feature width non-uniformity may reach 10 nm within the measurement range of 1 μm. The standard deviation of the averaged middle CD values of 7 repeated measurements reaches 0.35 nm. In addition, an investigation of long term measurement stability is performed on a PTB photomask. The results shows that the 3D-AFM has a drift rate of about 0.00033 nm per line, which confirms the high measurement stability and the very low tip wear.

  2. Ice-volcano interactions during the 2010 Eyjafjallajökull eruption, as revealed by airborne imaging radar

    NASA Astrophysics Data System (ADS)

    Magnússon, E.; Gudmundsson, M. T.; Roberts, M. J.; Sigurã°Sson, G.; HöSkuldsson, F.; Oddsson, B.

    2012-07-01

    During the eruption of the ice-covered Eyjafjallajökull volcano, a series of images from an airborne Synthetic Aperture Radar (SAR) were obtained by the Icelandic Coast Guard. Cloud obscured the summit from view during the first three days of the eruption, making the weather-independent SAR a valuable monitoring resource. Radar images revealed the development of ice cauldrons in a 200 m thick ice cover within the summit caldera, as well as the formation of cauldrons to the immediate south of the caldera. Additionally, radar images were used to document the subglacial and supraglacial passage of floodwater to the north and south of the eruption site. The eruption breached the ice surface about four hours after its onset at about 01:30 UTC on 14 April 2010. The first SAR images, obtained between 08:55 and 10:42 UTC, show signs of limited supraglacial drainage from the eruption site. Floodwater began to drain from the ice cap almost 5.5 h after the beginning of the eruption, implying storage of meltwater at the eruption site due to initially constricted subglacial drainage from the caldera. Heat transfer rates from magma to ice during early stages of cauldron formation were about 1 MW m-2 in the radial direction and about 4 MW m-2 vertically. Meltwater release was characterized by accumulation and drainage with most of the volcanic material in the ice cauldrons being drained in hyperconcentrated floods. After the third day of the eruption, meltwater generation at the eruption site diminished due to an insulating lag of tephra.

  3. Cantilever's behavior in the AC mode of an AFM

    SciTech Connect

    Nunes, V.B.; Zanette, S.I.; Caride, A.O.; Prioli, R.; Rivas, A.M.F

    2003-03-15

    In this paper, a model with a small number of parameters is used to simulate the motion of a cantilever in the AC mode of an atomic force microscope (AFM). The results elucidate the transition dependence-from noncontact to tapping operating mode-on the height of the contamination layer and on the stiffness of the sample.

  4. Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments.

    PubMed

    Dague, E; Jauvert, E; Laplatine, L; Viallet, B; Thibault, C; Ressier, L

    2011-09-30

    Immobilization of live micro-organisms on solid substrates is an important prerequisite for atomic force microscopy (AFM) bio-experiments. The method employed must immobilize the cells firmly enough to enable them to withstand the lateral friction forces exerted by the tip during scanning but without denaturing the cell interface. In this work, a generic method for the assembly of living cells on specific areas of substrates is proposed. It consists in assembling the living cells within the patterns of microstructured, functionalized poly-dimethylsiloxane (PDMS) stamps using convective/capillary deposition. This versatile approach is validated by applying it to two systems of foremost importance in biotechnology and medicine: Saccharomyces cerevisiae yeasts and Aspergillus fumigatus fungal spores. We show that this method allows multiplexing AFM nanomechanical measurements by force spectroscopy on S. cerevisiae yeasts and high-resolution AFM imaging of germinated Aspergillus conidia in buffer medium. These two examples clearly demonstrate the immense potential of micro-organism assembly on functionalized, microstructured PDMS stamps by convective/capillary deposition for performing rigorous AFM bio-experiments on living cells.

  5. Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments

    NASA Astrophysics Data System (ADS)

    Dague, E.; Jauvert, E.; Laplatine, L.; Viallet, B.; Thibault, C.; Ressier, L.

    2011-09-01

    Immobilization of live micro-organisms on solid substrates is an important prerequisite for atomic force microscopy (AFM) bio-experiments. The method employed must immobilize the cells firmly enough to enable them to withstand the lateral friction forces exerted by the tip during scanning but without denaturing the cell interface. In this work, a generic method for the assembly of living cells on specific areas of substrates is proposed. It consists in assembling the living cells within the patterns of microstructured, functionalized poly-dimethylsiloxane (PDMS) stamps using convective/capillary deposition. This versatile approach is validated by applying it to two systems of foremost importance in biotechnology and medicine: Saccharomyces cerevisiae yeasts and Aspergillus fumigatus fungal spores. We show that this method allows multiplexing AFM nanomechanical measurements by force spectroscopy on S. cerevisiae yeasts and high-resolution AFM imaging of germinated Aspergillus conidia in buffer medium. These two examples clearly demonstrate the immense potential of micro-organism assembly on functionalized, microstructured PDMS stamps by convective/capillary deposition for performing rigorous AFM bio-experiments on living cells.

  6. Adsorption Studies with AFM of Human Plasma Fibrinogen on Silicon Surfaces

    NASA Astrophysics Data System (ADS)

    Gause, Sheena; Kong, Wendy; Rowe

    2007-11-01

    Fibrinogen (FGN) plays an important role in the clotting of blood. Human plasma fibrinogen (HPF) is a protein that readily adsorbs on biomaterial surfaces. The purpose of this experiment was to use the Atomic Force Microscope to study the adsorption of HPF molecules or FGN onto several silicon surfaces with different orientations and resistivities. The size of the FGN molecules found to be somewhat different of Si(111), (100) and (110) were compared to the size of the FGN molecules in solution (45 nm in length, the end dynodes measures to be 6.5 nm in diameter, and the middle dynode measures to be 5 nm in diameter. For this study, the CPR (Thermo-microscope) Atomic Force Microscope (AFM) was used to observe the amount of fibrinogen molecules adsorbed by Si (111) with a resistance of .0281-.0261 φ cm, Si (111) with a resistance of 1 φ cm, Si (100), and Si (110) surfaces. In finding any single fibrinogen molecules, the appropriate image scans and measurements were taken. After collection and analysis of the data, it was found from AFM that the fibrinogen molecules found on Si (110) mostly resembled fibrinogen molecules found in solution. The other images showed that the fibrinogen molecules adsorbed on Silicon substrates is significantly greater (˜10-20 %) than those in solution.

  7. Measuring cell wall elasticity on enteroaggregative Escherichia coli wild type and dispersin mutant by AFM

    SciTech Connect

    Beckmann, Melissa; Venkataraman, Sankar; Doktycz, Mitchel John; Nataro, James P; Sullivan, Claretta J; Morrell-Falvey, Jennifer L; Allison, David P

    2006-07-01

    Enteroaggregative Escherichia coli (EAEC) is pathogenic and produces severe diarrhea in humans. A mutant of EAEC that does not produce dispersin, a cell surface protein, is not pathogenic. It has been proposed that dispersin imparts a positive charge to the bacterial cell surface allowing the bacteria to colonize on the negatively charged intestinal mucosa. However, physical properties of the bacterial cell surface, such as rigidity, may be influenced by the presence of dispersin and may contribute to pathogenicity. Using the system developed in our laboratory for mounting and imaging bacterial cells by atomic force microscopy (AFM), in liquid, on gelatin coated mica surfaces, studies were initiated to measure cell surface elasticity. This was carried out in both wild type EAEC, that produces dispersin, and the mutant that does not produce dispersin. This was accomplished using AFM force-distance (FD) spectroscopy on the wild type and mutant grown in liquid or on solid medium. Images in liquid and in air of both the wild-type and mutant grown in liquid and on solid media are presented. This work represents an initial step in efforts to understand the pathogenic role of the dispersin protein in the wild-type bacteria.

  8. A tetravalent bispecific TandAb (CD19/CD3), AFM11, efficiently recruits T cells for the potent lysis of CD19+ tumor cells

    PubMed Central

    Reusch, Uwe; Duell, Johannes; Ellwanger, Kristina; Herbrecht, Carmen; Knackmuss, Stefan HJ; Fucek, Ivica; Eser, Markus; McAleese, Fionnuala; Molkenthin, Vera; Le Gall, Fabrice; Topp, Max; Little, Melvyn; Zhukovsky, Eugene A

    2015-01-01

    To harness the potent tumor-killing capacity of T cells for the treatment of CD19+ malignancies, we constructed AFM11, a humanized tetravalent bispecific CD19/CD3 tandem diabody (TandAb) consisting solely of Fv domains. The molecule exhibits good manufacturability and stability properties. AFM11 has 2 binding sites for CD3 and 2 for CD19, an antigen that is expressed from early B cell development through differentiation into plasma cells, and is an attractive alternative to CD20 as a target for the development of therapeutic antibodies to treat B cell malignancies. Comparison of the binding and cytotoxicity of AFM11 with those of a tandem scFv bispecific T cell engager (BiTE) molecule targeting the same antigens revealed that AFM11 elicited more potent in vitro B cell lysis. Though possessing high affinity to CD3, the TandAb mediates serial-killing of CD19+ cells with little dependence of potency or efficacy upon effector:target ratio, unlike the BiTE. The advantage of the TandAb over the BiTE was most pronounced at lower effector:target ratios. AFM11 mediated strictly target-dependent T cell activation evidenced by CD25 and CD69 induction, proliferation, and cytokine release, notwithstanding bivalent CD3 engagement. In a NOD/scid xenograft model, AFM11 induced dose-dependent growth inhibition of Raji tumors in vivo, and radiolabeled TandAb exhibited excellent localization to tumor but not to normal tissue. After intravenous administration in mice, half-life ranged from 18.4 to 22.9 h. In a human ex vivo B-cell chronic lymph