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Sample records for filament structure molecular

  1. Structural Modeling and Molecular Dynamics Simulation of the Actin Filament

    SciTech Connect

    Splettstoesser, Thomas; Holmes, Kenneth; Noe, Frank; Smith, Jeremy C

    2011-01-01

    Actin is a major structural protein of the eukaryotic cytoskeleton and enables cell motility. Here, we present a model of the actin filament (F-actin) that not only incorporates the global structure of the recently published model by Oda et al. but also conserves internal stereochemistry. A comparison is made using molecular dynamics simulation of the model with other recent F-actin models. A number of structural determents such as the protomer propeller angle, the number of hydrogen bonds, and the structural variation among the protomers are analyzed. The MD comparison is found to reflect the evolution in quality of actin models over the last 6 years. In addition, simulations of the model are carried out in states with both ADP or ATP bound and local hydrogen-bonding differences characterized.

  2. Towards a molecular description of intermediate filament structure and assembly

    SciTech Connect

    Parry, David A.D.; Strelkov, Sergei V.; Burkhard, Peter; Aebi, Ueli; Herrmann, Harald . E-mail: h.herrmann@dkfz.de

    2007-06-10

    Intermediate filaments (IFs) represent one of the prominent cytoskeletal elements of metazoan cells. Their constituent proteins are coded by a multigene family, whose members are expressed in complex patterns that are controlled by developmental programs of differentiation. Hence, IF proteins found in epidermis differ significantly from those in muscle or neuronal tissues. Due to their fibrous nature, which stems from a fairly conserved central {alpha}-helical coiled-coil rod domain, IF proteins have long resisted crystallization and thus determination of their atomic structure. Since they represent the primary structural elements that determine the shape of the nucleus and the cell more generally, a major challenge is to arrive at a more rational understanding of how their nanomechanical properties effect the stability and plasticity of cells and tissues. Here, we review recent structural results of the coiled-coil dimer, assembly intermediates and growing filaments that have been obtained by a hybrid methods approach involving a rigorous combination of X-ray crystallography, small angle X-ray scattering, cryo-electron tomography, computational analysis and molecular modeling.

  3. Invertebrate muscles: thin and thick filament structure; molecular basis of contraction and its regulation, catch and asynchronous muscle

    PubMed Central

    Hooper, Scott L.; Hobbs, Kevin H.; Thuma, Jeffrey B.

    2008-01-01

    This is the second in a series of canonical reviews on invertebrate muscle. We cover here thin and thick filament structure, the molecular basis of force generation and its regulation, and two special properties of some invertebrate muscle, catch and asynchronous muscle. Invertebrate thin filaments resemble vertebrate thin filaments, although helix structure and tropomyosin arrangement show small differences. Invertebrate thick filaments, alternatively, are very different from vertebrate striated thick filaments and show great variation within invertebrates. Part of this diversity stems from variation in paramyosin content, which is greatly increased in very large diameter invertebrate thick filaments. Other of it arises from relatively small changes in filament backbone structure, which results in filaments with grossly similar myosin head placements (rotating crowns of heads every 14.5 nm) but large changes in detail (distances between heads in azimuthal registration varying from three to thousands of crowns). The lever arm basis of force generation is common to both vetebrates and invertebrates, and in some invertebrates this process is understood on the near atomic level. Invertebrate actomyosin is both thin (tropomyosin:troponin) and thick (primarily via direct Ca++ binding to myosin) filament regulated, and most invertebrate muscles are dually regulated. These mechanisms are well understood on the molecular level, but the behavioral utility of dual regulation is less so. The phosphorylation state of the thick filament associated giant protein, twitchin, has been recently shown to be the molecular basis of catch. The molecular basis of the stretch activation underlying asynchronous muscle activity, however, remains unresolved. PMID:18616971

  4. Probing the Physical Structures of Dense Filaments

    NASA Astrophysics Data System (ADS)

    Li, Di

    2015-08-01

    Filament is a common feature in cosmological structures of various scales, ranging from dark matter cosmic web, galaxy clusters, inter-galactic gas flows, to Galactic ISM clouds. Even within cold dense molecular cores, filaments have been detected. Theories and simulations with (or without) different combination of physical principles, including gravity, thermal balance, turbulence, and magnetic field, can reproduce intriguing images of filaments. The ubiquity of filaments and the similarity in simulated ones make physical parameters, beyond dust column density, a necessity for understanding filament evolution. I report three projects attempting to measure physical parameters of filaments. We derive the volume density of a dense Taurus filament based on several cyanoacetylene transitions observed by GBT and ART. We measure the gas temperature of the OMC 2-3 filament based on combined GBT+VLA ammonia images. We also measured the sub-millimeter polarization vectors along OMC3. These filaments were found to be likely a cylinder-type structure, without dynamic heating, and likely accreting mass along the magnetic field lines.

  5. Filament wound structure and method

    DOEpatents

    Dritt, William S.; Gerth, Howard L.; Knight, Jr., Charles E.; Pardue, Robert M.

    1977-01-01

    The present invention relates to a filament wound spherical structure comprising a plurality of filament band sets disposed about the surface of a mandrel with each band of each set formed of a continuous filament circumferentially wound about the mandrel a selected number of circuits and with each circuit of filament being wound parallel to and contiguous with an immediate previously wound circuit. Each filament band in each band set is wound at the same helix angle from the axis of revolution of the mandrel and all of the bands of each set are uniformly distributed about the mandrel circumference. The pole-to-equator wall thickness taper associated with each band set, as several contiguous band sets are wound about the mandrel starting at the poles, is accumulative as the band sets are nested to provide a complete filament wound sphere of essentially uniform thickness.

  6. Kiloparsec-Scale Simulations of Star Formation in Disk Galaxies III. Structure and Dynamics of Filaments and Clumps in Giant Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Butler, Michael J.; Tan, Jonathan C.; Van Loo, Sven

    2015-05-01

    We present hydrodynamic simulations of self-gravitating dense gas in a galactic disk, exploring scales ranging from 1 kpc down to ˜0.1 pc. Our primary goal is to understand how dense filaments form in giant molecular clouds (GMCs). These structures, often observed as infrared dark clouds (IRDCs) in the Galactic plane, are thought to be the precursors to massive stars and star clusters, so their formation may be the rate-limiting step controlling global star formation rates in galactic systems as described by the Kennicutt-Schmidt relation. Our study follows on from Van Loo et al., which carried out simulations to 0.5 pc resolution and examined global aspects of the formation of dense gas clumps and the resulting star formation rate. Here, using our higher resolution, we examine the detailed structural, kinematic, and dynamical properties of dense filaments and clumps, including mass surface density (Σ) probability distribution functions, filament mass per unit length and its dispersion, lateral Σ profiles, filament fragmentation, filament velocity gradients and infall, and degree of filament and clump virialization. Where possible, these properties are compared to observations of IRDCs. By many metrics, especially too large mass fractions of high {Σ }\\gt 1 g c{{m}-2} material, too high mass per unit length dispersion due to dense clump formation, too high velocity gradients, and too high velocity dispersion for a given mass per unit length, the simulated filaments differ from observed IRDCs. We thus conclude that IRDCs do not form from global fast collapse of GMCs. Rather, we expect that IRDC formation and collapse are slowed significantly by the influence of dynamically important magnetic fields, which may thus play a crucial role in regulating galactic star formation rates.

  7. Filaments in the Lupus molecular clouds

    NASA Astrophysics Data System (ADS)

    Benedettini, M.; Schisano, E.; Pezzuto, S.; Elia, D.; André, P.; Könyves, V.; Schneider, N.; Tremblin, P.; Arzoumanian, D.; di Giorgio, A. M.; Di Francesco, J.; Hill, T.; Molinari, S.; Motte, F.; Nguyen-Luong, Q.; Palmeirim, P.; Rivera-Ingraham, A.; Roy, A.; Rygl, K. L. J.; Spinoglio, L.; Ward-Thompson, D.; White, G. J.

    2015-10-01

    We have studied the filaments extracted from the column density maps of the nearby Lupus 1, 3, and 4 molecular clouds, derived from photometric maps observed with the Herschel satellite. Filaments in the Lupus clouds have quite low column densities, with a median value of ˜1.5 × 1021 cm-2 and most have masses per unit length lower than the maximum critical value for radial gravitational collapse. Indeed, no evidence of filament contraction has been seen in the gas kinematics. We find that some filaments, that on average are thermally subcritical, contain dense cores that may eventually form stars. This is an indication that in the low column density regime, the critical condition for the formation of stars may be reached only locally and this condition is not a global property of the filament. Finally, in Lupus we find multiple observational evidences of the key role that the magnetic field plays in forming filaments, and determining their confinement and dynamical evolution.

  8. 13CO filaments in the Taurus molecular cloud

    NASA Astrophysics Data System (ADS)

    Panopoulou, G. V.; Tassis, K.; Goldsmith, P. F.; Heyer, M. H.

    2014-11-01

    We have carried out a search for filamentary structures in the Taurus molecular cloud using 13CO line emission data from the Five Colleges Radio Astronomy Observatory survey of ˜100 deg2. We have used the topological analysis tool, Discrete Persistent Structures Extractor (DISPERSE), and post-processed its results to include a more strict definition of filaments that requires an aspect ratio of at least 3:1 and cross-section intensity profiles peaked on the spine of the filament. In the velocity-integrated intensity map only 10 of the hundreds of filamentary structures identified by DISPERSE comply with our criteria. Unlike Herschel analyses, which find a characteristic width for filaments of ˜0.1 pc, we find a much broader distribution of profile widths in our structures, with a peak at 0.4 pc. Furthermore, even if the identified filaments are cylindrical objects, their complicated velocity structure and velocity dispersions imply that they are probably gravitationally unbound. Analysis of velocity channel maps reveals the existence of hundreds of `velocity-coherent' filaments. The distribution of their widths is peaked at lower values (0.2 pc) while the fluctuation of their peak intensities is indicative of stochastic origin. These filaments are suppressed in the integrated intensity map due to the blending of diffuse emission from different velocities. Conversely, integration over velocities can cause filamentary structures to appear. Such apparent filaments can also be traced, using the same methodology, in simple simulated maps consisting of randomly placed cores. They have profile shapes similar to observed filaments and contain most of the simulated cores.

  9. CARMA LARGE AREA STAR FORMATION SURVEY: OBSERVATIONAL ANALYSIS OF FILAMENTS IN THE SERPENS SOUTH MOLECULAR CLOUD

    SciTech Connect

    Fernández-López, M.; Looney, L.; Lee, K.; Segura-Cox, D.; Arce, H. G.; Plunkett, A.; Mundy, L. G.; Storm, S.; Teuben, P. J.; Pound, M.; Isella, A.; Kauffmann, J.; Tobin, J. J.; Rosolowsky, E.; Kwon, W.; Ostriker, E.; Tassis, K.; Shirley, Y. L.

    2014-08-01

    We present the N{sub 2}H{sup +} (J = 1 → 0) map of the Serpens South molecular cloud obtained as part of the CARMA Large Area Star Formation Survey. The observations cover 250 arcmin{sup 2} and fully sample structures from 3000 AU to 3 pc with a velocity resolution of 0.16 km s{sup –1}, and they can be used to constrain the origin and evolution of molecular cloud filaments. The spatial distribution of the N{sub 2}H{sup +} emission is characterized by long filaments that resemble those observed in the dust continuum emission by Herschel. However, the gas filaments are typically narrower such that, in some cases, two or three quasi-parallel N{sub 2}H{sup +} filaments comprise a single observed dust continuum filament. The difference between the dust and gas filament widths casts doubt on Herschel ability to resolve the Serpens South filaments. Some molecular filaments show velocity gradients along their major axis, and two are characterized by a steep velocity gradient in the direction perpendicular to the filament axis. The observed velocity gradient along one of these filaments was previously postulated as evidence for mass infall toward the central cluster, but these kind of gradients can be interpreted as projection of large-scale turbulence.

  10. Structure of Flexible Filamentous Plant Viruses

    SciTech Connect

    Kendall, Amy; McDonald, Michele; Bian, Wen; Bowles, Timothy; Baumgarten, Sarah C.; Shi, Jian; Stewart, Phoebe L.; Bullitt, Esther; Gore, David; Irving, Thomas C.; Havens, Wendy M.; Ghabrial, Said A.; Wall, Joseph S.; Stubbs, Gerald

    2008-10-23

    Flexible filamentous viruses make up a large fraction of the known plant viruses, but in comparison with those of other viruses, very little is known about their structures. We have used fiber diffraction, cryo-electron microscopy, and scanning transmission electron microscopy to determine the symmetry of a potyvirus, soybean mosaic virus; to confirm the symmetry of a potexvirus, potato virus X; and to determine the low-resolution structures of both viruses. We conclude that these viruses and, by implication, most or all flexible filamentous plant viruses share a common coat protein fold and helical symmetry, with slightly less than 9 subunits per helical turn.

  11. The intermediate-sized filaments in rat kangaroo PtK2 cells. II. Structure and composition of isolated filaments.

    PubMed

    Franke, W W; Schmid, E; Osborn, M; Weber, K

    1978-08-01

    When cultured cells of the rat kangaroo cell line PtK2 grown on plastic or glass surfaces are lysed and extracted with combinations of low and high salt buffers and the non-ionic detergent Triton X-100 cytoskeletal preparations are obtained that show an enrichment of 6 to 11 nm thick filaments. The arrays of these filaments have been examined by various light and electron microscopic techniques, including ultrathin sectioning, whole mount transmission electron microscopy, negative staining, and indirect immunofluorescence microscopy. In addition, 6 to 11 nm filaments isolated from these cells with similar extraction procedures and with centrifugation techniques have been examined by electron microscopy. The arrays of these isolated intermediate-sized filaments, their ultrastructure and their specific decoration by certain antibodies present in normal rabbit sera as well as by guinea pig antibodies against purified bovine prekeratin is demonstrated. When preparations enriched in these intermediate-sized filaments are examined by SDS-polyacrylamide gel electrophoresis a corresponding enrichment of three polypeptide bands with apparent molecular weights of about 45 000, 52 000 and 58 000 (the latter component sometimes appears split into two bands) is observed, besides some residual actin and a few high molecular weight bands. The morphology of the isolated filaments, their immunological reaction with antibodies decorating prekeratin-containing structures, and the sizes of their constitutive polypeptides suggest that these filaments are closely related to prekeratin-containing filaments observed in a variety of epithelial cells.

  12. Structure and mechanical properties of liquid crystalline filaments

    SciTech Connect

    Eremin, Alexey; Nemes, Alexandru; Stannarius, Ralf; Schulz, Mario; Nadasi, Hajnalka; Weissflog, Wolfgang

    2005-03-01

    The formation of stable freely suspended filaments is an interesting peculiarity of some liquid crystal phases. So far, little is known about their structure and stability. Similarly to free-standing smectic films, an internal molecular structure of the mesophase stabilizes these macroscopically well-ordered objects with length to diameter ratios of 10{sup 3} and above. In this paper, we report observations of smectic liquid crystal fibers formed by bent-shaped molecules in different mesophases. Our study, employing several experimental techniques, focuses on mechanical and structural aspects of fiber formation such as internal structure, stability, and mechanical and optical properties.

  13. ALMA observations of cold molecular gas filaments trailing rising radio bubbles in PKS 0745-191

    NASA Astrophysics Data System (ADS)

    Russell, H. R.; McNamara, B. R.; Fabian, A. C.; Nulsen, P. E. J.; Edge, A. C.; Combes, F.; Murray, N. W.; Parrish, I. J.; Salomé, P.; Sanders, J. S.; Baum, S. A.; Donahue, M.; Main, R. A.; O'Connell, R. W.; O'Dea, C. P.; Oonk, J. B. R.; Tremblay, G.; Vantyghem, A. N.; Voit, G. M.

    2016-05-01

    We present ALMA observations of the CO(1-0) and CO(3-2) line emission tracing filaments of cold molecular gas in the central galaxy of the cluster PKS 0745-191. The total molecular gas mass of 4.6± 0.3× 109 M_{⊙}, assuming a Galactic XCO factor, is divided roughly equally between three filaments each extending radially 3-5 kpc from the galaxy centre. The emission peak is located in the SE filament ˜ 1 arcsec (2 kpc) from the nucleus. The velocities of the molecular clouds in the filaments are low, lying within ± 100 { km s^{-1}} of the galaxy's systemic velocity. Their full width at half-maximum (FWHM) are less than 150 { km s^{-1},} which is significantly below the stellar velocity dispersion. Although the molecular mass of each filament is comparable to a rich spiral galaxy, such low velocities show that the filaments are transient and the clouds would disperse on < 107 yr time-scales unless supported, likely by the indirect effect of magnetic fields. The velocity structure is inconsistent with a merger origin or gravitational free-fall of cooling gas in this massive central galaxy. If the molecular clouds originated in gas cooling even a few kpc from their current locations their velocities would exceed those observed. Instead, the projection of the N and SE filaments underneath X-ray cavities suggests they formed in the updraft behind bubbles buoyantly rising through the cluster atmosphere. Direct uplift of the dense gas by the radio bubbles appears to require an implausibly high coupling efficiency. The filaments are coincident with low temperature X-ray gas, bright optical line emission and dust lanes indicating that the molecular gas could have formed from lifted warmer gas that cooled in situ.

  14. Coiled-coil intermediate filament stutter instability and molecular unfolding.

    PubMed

    Arslan, Melis; Qin, Zhao; Buehler, Markus J

    2011-05-01

    Intermediate filaments (IFs) are the key components of cytoskeleton in eukaryotic cells and are critical for cell mechanics. The building block of IFs is a coiled-coil alpha-helical dimer, consisting of several domains that include linkers and other structural discontinuities. One of the discontinuities in the dimer's coiled-coil region is the so-called 'stutter' region. The stutter is a region where a variation of the amino acid sequence pattern from other parts of the alpha-helical domains of the protein is found. It was suggested in earlier works that due to this sequence variation, the perfect coiled-coil arrangement ceases to exist. Here, we show using explicit water molecular dynamics and well-tempered metadynamics that for the coil2 domain of vimentin IFs the stutter is more stable in a non-alpha-helical, unfolded state. This causes a local structural disturbance in the alpha helix, which has a global effect on the nanomechanics of the structure. Our analysis suggests that the stutter features an enhanced tendency to unfolding even under the absence of external forces, implying a much greater structural instability than previously assumed. As a result it features a smaller local bending stiffness than other segments and presents a seed for the initiation of molecular bending and unfolding at large deformation. PMID:21516532

  15. Filamentous structures in skeletal muscle: anchors for the subsarcolemmal space.

    PubMed

    Khairani, Astrid Feinisa; Tajika, Yuki; Takahashi, Maiko; Ueno, Hitoshi; Murakami, Tohru; Soenggono, Arifin; Yorifuji, Hiroshi

    2015-03-01

    In skeletal muscle fibers, intermediate filaments and actin filaments provide structural support to the myofibrils and the sarcolemma. For many years, it was poorly understood from ultrastructural observations that how these filamentous structures were kept anchored. The present study was conducted to determine the architecture of filamentous anchoring structures in the subsarcolemmal space and the intermyofibrils. The diaphragms (Dp) of adult wild type and mdx mice (mdx is a model for Duchenne muscular dystrophy) were subjected to tension applied perpendicular to the long axis of the muscle fibers, with or without treatment with 1% Triton X-100 or 0.03% saponin. These experiments were conducted to confirm the presence and integrity of the filamentous anchoring structures. Transmission electron microscopy revealed that these structures provide firm transverse connections between the sarcolemma and peripheral myofibrils. Most of the filamentous structures appeared to be inserted into subsarcolemmal densities, forming anchoring connections between the sarcolemma and peripheral myofibrils. In some cases, actin filaments were found to run longitudinally in the subsarcolemmal space to connect to the sarcolemma or in some cases to connect to the intermyofibrils as elongated thin filaments. These filamentous anchoring structures were less common in the mdx Dp. Our data suggest that the transverse and longitudinal filamentous structures form an anchoring system in the subsarcolemmal space and the intermyofibrils.

  16. Intermediate filaments: not just for structure anymore.

    PubMed

    Liem, Ronald K H

    2013-04-22

    A recent paper has identified the tumor suppressor APC as a linker protein between intermediate filaments and microtubules. In the absence of APC, intermediate filaments collapse and the cells are no longer polarized and fail to migrate.

  17. Molecular phylogeny of metazoan intermediate filament proteins.

    PubMed

    Erber, A; Riemer, D; Bovenschulte, M; Weber, K

    1998-12-01

    We have cloned cytoplasmic intermediate filament (IF) proteins from a large number of invertebrate phyla using cDNA probes, the monoclonal antibody IFA, peptide sequence information, and various RT-PCR procedures. Novel IF protein sequences reported here include the urochordata and nine protostomic phyla, i.e., Annelida, Brachiopoda, Chaetognatha, Echiura, Nematomorpha, Nemertea, Platyhelminthes, Phoronida, and Sipuncula. Taken together with the wealth of data on IF proteins of vertebrates and the results on IF proteins of Cephalochordata, Mollusca, Annelida, and Nematoda, two IF prototypes emerge. The L-type, which includes 35 sequences from 11 protostomic phyla, shares with the nuclear lamins the long version of the coil 1b subdomain and, in most cases, a homology segment of some 120 residues in the carboxyterminal tail domain. The S-type, which includes all four subfamilies (types I to IV) of vertebrate IF proteins, lacks 42 residues in the coil 1b subdomain and the carboxyterminal lamin homology segment. Since IF proteins from all three phyla of the chordates have the 42-residue deletion, this deletion arose in a progenitor prior to the divergence of the chordates into the urochordate, cephalochordate, and vertebrate lineages, possibly already at the origin of the deuterostomic branch. Four phyla recently placed into the protostomia on grounds of their 18S rDNA sequences (Brachiopoda, Nemertea, Phoronida, and Platyhelminthes) show IF proteins of the L-type and fit by sequence identity criteria into the lophotrochozoic branch of the protostomia.

  18. Molecular basis of antigenic polymorphism of EspA filaments: development of a peptide display technology.

    PubMed

    Crepin, Valérie F; Shaw, Robert; Knutton, Stuart; Frankel, Gad

    2005-07-01

    Like many Gram-negative pathogens, enteropathogenic (EPEC) and enterohaemorrhagic Escherichia coli (EHEC) use a macromolecular type III secretion system (TTSS) to inject effector proteins into eukaryotic host cells. The membrane-associated needle complex (NC) of the TTSS, which shows broad similarity to the flagellar basal body, is conserved amongst bacterial pathogens. However, the extracellular part of the TTSS of EPEC and EHEC is unique, in that it has a hollow, approximately 12 nm in diameter, filamentous extension to the NC. EspA filaments are homo-polymers made of the translocator protein EspA. The three-dimensional structure of EspA filaments is comparable to that of flagella; the helical symmetry and packing of the subunits forming both filamentous structures are very similar. Like flagella, EspA filaments show antigenic polymorphism as EspA from different EPEC and EHEC clones show no immunological cross-reactivity. In this study, we determined the molecular basis of the antigenic polymorphism of EspA filaments and identified a surface-exposed hypervariable domain that contains the immunodominant EspA epitope. By exchanging the hypervariable domains of EspA(EPEC) and EspA(EHEC) we swapped the antigenic specificity of the EspA filaments. As for the flagellin D3 domain, which is known to tolerate insertions of natural and artificial amino acid sequences, we have inserted short peptides into the surface-exposed, hypervariable domain of EspA. We demonstrated that the inserted peptides are presented on the surface of the recombinant EspA filaments forming a new immunodominant epitope. Accordingly, EspA filaments have a potential to be developed into a novel epitope display system. PMID:15921692

  19. Structure and kinematics of the Bootes filament

    NASA Astrophysics Data System (ADS)

    Nasonova, O.; Karachentsev, I.; Karachentseva, V.

    2016-10-01

    Bootes filament of galaxies is a dispersed chain of groups residing on sky between the Local Void and the Virgo cluster. We consider a sample of 361 galaxies inside the sky area of RA = 13h0...18h.5 and Dec = .5°... + 10° with radial velocities VLG < 2000 km/s to clarify its structure and kinematics. In this region, 161 galaxies have individual distance estimates. We use these data to draw the Hubble relation for galaxy groups, pairs as well as the field galaxies, and to examine the galaxy distribution on peculiar velocities. Our analysis exposes the known Virgo-centric infall at RA < 14h and some signs of outflow from the Local Void at RA > 17h. According to the galaxy grouping criterion, this complex contains the members of 13 groups, 11 pairs and 140 field galaxies. The most prominent group is dominated by NGC 5846. The Bootes filament contains the total stellar mass of 2.7 ×1012 M⊙ and the total virial mass of 9.07×1013 M⊙, having the average density of dark matter to be Ωm = 0.09, i.e. a factor three lower than the global cosmic value.

  20. Colliding filaments and a massive dense core in the Cygnus OB 7 molecular cloud

    SciTech Connect

    Dobashi, Kazuhito; Shimoikura, Tomomi; Akisato, Ko; Ohashi, Kenjiro; Nakagomi, Keisuke; Matsumoto, Tomoaki; Saito, Hiro

    2014-12-10

    We report the results of molecular line observations carried out toward a massive dense core in the Cyg OB 7 molecular cloud. The core has an extraordinarily large mass (∼1.1 × 10{sup 4} M {sub ☉}) and size (∼2 × 5 pc{sup 2}), but there is no massive young star forming therein. We observed this core in various molecular lines such as C{sup 18}O(J = 1-0) using the 45 m telescope at Nobeyama Radio Observatory. We find that the core has an elongated morphology consisting of several filaments and core-like structures. The filaments are massive (10{sup 2}-10{sup 3} M {sub ☉}), and they are apparently colliding with one another. Some candidates for young stellar objects are distributed around their intersection, suggesting that the collisions of the filaments may have influenced their formation. To understand the formation and evolution of such colliding filaments, we performed numerical simulations using the adaptive mesh refinement technique, adopting the observed core parameters (the mass and size) as the initial conditions. The results indicate that the filaments are formed as seen in other earlier simulations for small cores in the literature, but we could not reproduce the collisions of the filaments simply by assuming a large initial mass and size. We find that collisions of the filaments occur only when there is a large velocity gradient in the initial core, in a sense compressing it. We suggest that the observed core was actually compressed by an external effect, e.g., shocks from nearby supernova remnants, including HB 21 which has been suggested to be interacting with the Cyg OB 7 molecular cloud.

  1. Properties of interstellar filaments derived from Herschel, Planck, and molecular line observations

    NASA Astrophysics Data System (ADS)

    Arzoumanian, Doris

    2015-08-01

    The highly filamentary structure of the interstellar medium (ISM) is now impressively revealed by Herschel and Planck images. Previous observations have shown that clouds are filamentary, however, only recently the mapping capabilities of Herscheland Planck have discovered their ubiquity in the ISM. In particular, Herschel images, with their high spatial and intensity dynamic ranges, show that dense filaments are associated with the main sites of star formation, demonstrating their key role in the star formation process.The analysis of the column density profiles of filaments indicates that they all share a common central width of 0.1pc, while they span a wide range in length, column density, mass per unit length. The results derived from observations tracing cold dust and gas emission, in total and polarised intensity, suggest that filaments can be divided into two families: On the one hand, low column density, unbound, and quiescent filaments mostly aligned with the magnetic field orientation, and on the other hand, dense, self-gravitating filaments, which fragment into star forming cores.I will present the properties of the filamentary structures derived from Herschel, Planck, and molecular line observations, and I will discuss the observational constraints on the formation and evolution of interstellar filaments.

  2. The structures, mass motions and footpoints of solar filaments

    NASA Astrophysics Data System (ADS)

    Venkataramanasastry, Aparna

    This thesis focuses on identifying the mechanism by which solar filaments acquire mass. Some of the speculations for how a filament gets its mass are 1) injection of mass from the chromosphere into the filament structure, and 2) condensation of mass from the corona into the region of the filament channel. Mass motion at the footpoints of the filaments is studied to detect mass entering and leaving the filament body. The magnetic properties of the footpoints of the filaments are also studied. Recommendations are drawn by comparing observational properties obtained in this study with the features used in some of the previously developed models. The datasets used for this study are high-resolution image sets of centerline and Doppler wings of Halpha, obtained using the Dutch Open Telescope (DOT). The data were obtained on Oct 30, 2010. The data set contains three filaments in an active region in the northern hemisphere of the Sun. The images in each wavelength are aligned and made into movies to find the footpoints of the filaments through which the mass goes into and comes out of the filaments from and to the chromosphere, respectively. The magnetic properties of the footpoints are studied by overlaying the magnetogram images with the DOT images by using full-disk Halpha images for matching the features in the two. Of the three filaments, one of the filaments is observed to be stable throughout the duration of the observations; another filament erupts after about two hours of the beginning of observations; and the third filament is in its early stages of formation. The ends of the stable filament are clearly observed whereas the ends of the erupting filament and the forming filament are observed clearly intermittently during the duration of the observations. The animations of the region near the ends of filament 1 reveal definite injection and draining of mass via the footpoints into and out of the filament. The mass motion into and out of the filaments are observed

  3. Structural analysis of vimentin and keratin intermediate filaments by cryo-electron tomography

    SciTech Connect

    Norlen, Lars . E-mail: lars.norlen@ki.se; Masich, Sergej; Goldie, Kenneth N.; Hoenger, Andreas

    2007-06-10

    Intermediate filaments are a large and structurally diverse group of cellular filaments that are classified into five different groups. They are referred to as intermediate filaments (IFs) because they are intermediate in diameter between the two other cytoskeletal filament systems that is filamentous actin and microtubules. The basic building block of IFs is a predominantly {alpha}-helical rod with variable length globular N- and C-terminal domains. On the ultra-structural level there are two major differences between IFs and microtubules or actin filaments: IFs are non-polar, and they do not exhibit large globular domains. IF molecules associate via a coiled-coil interaction into dimers and higher oligomers. Structural investigations into the molecular building plan of IFs have been performed with a variety of biophysical and imaging methods such as negative staining and metal-shadowing electron microscopy (EM), mass determination by scanning transmission EM, X-ray crystallography on fragments of the IF stalk and low-angle X-ray scattering. The actual packing of IF dimers into a long filament varies between the different families. Typically the dimers form so called protofibrils that further assemble into a filament. Here we introduce new cryo-imaging methods for structural investigations of IFs in vitro and in vivo, i.e., cryo-electron microscopy and cryo-electron tomography, as well as associated techniques such as the preparation and handling of vitrified sections of cellular specimens.

  4. The myosin filament XIV backbone structure.

    PubMed Central

    Ashton, F T; Weisel, J; Pepe, F A

    1992-01-01

    The substructure of the thick filaments of chemically skinned chicken pectoralis muscle was investigated by electron microscopy. Images of transverse sections of the myosin filaments were determined to have threefold symmetry by cross-correlation analysis, which gives an unbiased determination of the rotational symmetry of the images. Resolution, using the phase residual test (Frank et al. 1981. Science [Wash. DC]. 214:1353-1355), was found to be between 3.2 and 3.6 nm. Three arrangements of nine subfilaments in the backbone were found in all regions of the filament at ionic strengths of 20 and 200 mM. In the average images of two of these, there were three dense central subfilaments and three pairs of subfilaments on the surface of the thick filament. In the average image of the third arrangement, all of the protein mass of the nine subfilaments was on the surface of the filament with three of them showing less variation in position than the others. A fourth arrangement appearing to be transitional between two of these was seen often at 200 mM ionic strength and only rarely at 20 mM. On average, the myosin subfilaments were parallel to the long axis of the filament. The different arrangements of subfilaments appear to be randomly distributed among the filaments in a transverse section of the A-band. Relative rotational orientations with respect to the hexagonal filament lattice, using the three densest subfilaments as reference showed a major clustering (32%) of filaments within one 10 degrees spread, a lesser clustering (15%) at 90 degrees to the first, and the remainder scattered thinly over the rest of the 120 degrees range. There was no obvious pattern of distribution of the two predominant orientations that could define a superlattice in the filament lattice. Images FIGURE 2 FIGURE 6 FIGURE 8 PMID:1617136

  5. The effect of ambipolar diffusion on low-density molecular ISM filaments

    NASA Astrophysics Data System (ADS)

    Ntormousi, Evangelia; Hennebelle, Patrick; André, Philippe; Masson, Jacques

    2016-05-01

    Context. The filamentary structure of the molecular interstellar medium and the potential link of this morphology to star formation have been brought into focus recently by high resolution observational surveys. An especially puzzling matter is that local interstellar filaments appear to have the same thickness, independent of their column density. This requires a theoretical understanding of their formation process and the physics that governs their evolution. Aims: In this work we explore a scenario in which filaments are dissipative structures of the large-scale interstellar turbulence cascade and ion-neutral friction (also called ambipolar diffusion) is affecting their sizes by preventing small-scale compressions. Methods: We employ high-resolution (5123 and 10243), 3D magnetohydrodynamic (MHD) simulations, performed with the grid code RAMSES, to investigate non-ideal MHD turbulence as a filament formation mechanism. We focus the analysis on the mass and thickness distributions of the resulting filamentary structures. Results: Simulations of both driven and decaying MHD turbulence show that the morphologies of the density and the magnetic field are different when ambipolar diffusion is included in the models. In particular, the densest structures are broader and more massive as an effect of ion-neutral friction and the power spectra of both the velocity and the density steepen at a smaller wavenumber. Conclusions: The comparison between ideal and non-ideal MHD simulations shows that ambipolar diffusion causes a shift of the filament thickness distribution towards higher values. However, none of the distributions exhibit the pronounced peak found in the observed local filaments. Limitations in dynamical range and the absence of self-gravity in these numerical experiments do not allow us to conclude at this time whether this is due to the different filament selection or due to the physics inherent of the filament formation.

  6. Ubiquitination and filamentous structure of cytidine triphosphate synthase

    PubMed Central

    Pai, Li-Mei; Wang, Pei-Yu; Lin, Wei-Cheng; Chakraborty, Archan; Yeh, Chau-Ting; Lin, Yu-Hung

    2016-01-01

    ABSTRACT Living organisms respond to nutrient availability by regulating the activity of metabolic enzymes. Therefore, the reversible post-translational modification of an enzyme is a common regulatory mechanism for energy conservation. Recently, cytidine-5′-triphosphate (CTP) synthase was discovered to form a filamentous structure that is evolutionarily conserved from flies to humans. Interestingly, induction of the formation of CTP synthase filament is responsive to starvation or glutamine depletion. However, the biological roles of this structure remain elusive. We have recently shown that ubiquitination regulates CTP synthase activity by promoting filament formation in Drosophila ovaries during endocycles. Intriguingly, although the ubiquitination process was required for filament formation induced by glutamine depletion, CTP synthase ubiquitination was found to be inversely correlated with filament formation in Drosophila and human cell lines. In this article, we discuss the putative dual roles of ubiquitination, as well as its physiological implications, in the regulation of CTP synthase structure. PMID:27116391

  7. A BRIGHT MOLECULAR CORE IN A CRAB NEBULA FILAMENT

    SciTech Connect

    Loh, E. D.; Baldwin, J. A.; Ferland, G. J. E-mail: baldwin@pa.msu.ed

    2010-06-10

    In a sub-arcsec near-infrared survey of the Crab Nebula using the new Spartan Infrared Camera, we have found several knots with high surface brightness in the H{sub 2} 2.12 {mu}m line and a very large H{sub 2} 2.12 {mu}m to Br{gamma} ratio. The brightest of these knots has an intensity ratio I(H{sub 2} 2.12 {mu}m)/I(Br{gamma}) = 18 {+-} 9, which we show sets a lower limit on the ratio of masses in the molecular and recombination (i.e., ionized) zones M{sub mol}/M{sub rec} {>=} 0.9, and a total molecular mass within this single knot M{sub mol} {>=} 5 x 10{sup -5} M{sub sun}. We argue that the knot discussed here probably is able to emit so strongly in the 2.12 {mu}m line because its physical conditions are better tuned for such emission than is the case in other filaments. It is unclear whether this knot has an unusually large M{sub mol}/M{sub rec} ratio, or if many other Crab filaments also have similar amounts of molecular gas which is not emitting because the physical conditions are not so well tuned.

  8. Myosin filament 3D structure in mammalian cardiac muscle☆

    PubMed Central

    AL-Khayat, Hind A.; Morris, Edward P.; Kensler, Robert W.; Squire, John M.

    2008-01-01

    A number of cardiac myopathies (e.g. familial hypertrophic cardiomyopathy and dilated cardiomyopathy) are linked to mutations in cardiac muscle myosin filament proteins, including myosin and myosin binding protein C (MyBP-C). To understand the myopathies it is necessary to know the normal 3D structure of these filaments. We have carried out 3D single particle analysis of electron micrograph images of negatively stained isolated myosin filaments from rabbit cardiac muscle. Single filament images were aligned and divided into segments about 2 × 430 Å long, each of which was treated as an independent ‘particle’. The resulting 40 Å resolution 3D reconstruction showed both axial and azimuthal (no radial) myosin head perturbations within the 430 Å repeat, with successive crown rotations of approximately 60°, 60° and 0°, rather than the regular 40° for an unperturbed helix. However, it is shown that the projecting density peaks appear to start at low radius from origins closer to those expected for an unperturbed helical filament, and that the azimuthal perturbation especially increases with radius. The head arrangements in rabbit cardiac myosin filaments are very similar to those in fish skeletal muscle myosin filaments, suggesting a possible general structural theme for myosin filaments in all vertebrate striated muscles (skeletal and cardiac). PMID:18472277

  9. Computational and theoretical modeling of intermediate filament networks: Structure, mechanics and disease

    NASA Astrophysics Data System (ADS)

    Qin, Zhao; Buehler, Markus J.

    2012-08-01

    Intermediate filaments, in addition to microtubules and actin microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that in most cells, intermediate filament proteins play key roles to reinforce cells subjected to large-deformation, and that they participate in signal transduction, and it was proposed that their nanomechanical properties are critical to perform those functions. However, it is still poorly understood how the nanoscopic structure, as well as the combination of chemical composition, molecular structure and interfacial properties of these protein molecules contribute to the biomechanical properties of filaments and filament networks. Here we review recent progress in computational and theoretical studies of the intermediate filaments network at various levels in the protein's structure. A multiple scale method is discussed, used to couple molecular modeling with atomistic detail to larger-scale material properties of the networked material. It is shown that a finer-trains-coarser methodology as discussed here provides a useful tool in understanding the biomechanical property and disease mechanism of intermediate filaments, coupling experiment and simulation. It further allows us to improve the understanding of associated disease mechanisms and lays the foundation for engineering the mechanical properties of biomaterials.

  10. Dynamics of solar filaments. IV - Structure and mass flow of an active region filament

    NASA Technical Reports Server (NTRS)

    Schmieder, B.; Malherbe, J. M.; Simon, G.; Poland, A. I.

    1985-01-01

    An active region filament near the center of the solar disk was observed on September 29-30, 1980, with the Multichannel Subtractive Double Pass Spectrograph of the Meudon solar tower and the UV Spectrograph and Polarimeter aboard the SMM satellite. H-alpha and C IV measurements are presently used to study brightness and material velocity in the 10,000 and 100,000 K temperature ranges, and photospheric magnetograms are used to investigate the underlying magnetic field. Attention is given to the constraints imposed on possible filament structures by observations, as well as the expected MHD relationships.

  11. Structural design criteria for filament-wound composite shells

    NASA Technical Reports Server (NTRS)

    Hahn, H. T.; Jensen, D. W.; Claus, S. J.; Pai, S. P.; Hipp, P. A.

    1994-01-01

    Advanced composite cylinders, manufactured by filament winding, provide a cost effective solution to many present structural applications; however, the compressive performance of filament-wound cylinders is lower than comparable shells fabricated from unidirectional tape. The objective of this study was to determine the cause of this reduction in thin filament-wound cylinders by relating the manufacturing procedures to the quality of the cylinder and to its compressive performance. The experiments on cylinder buckling were complemented by eigenvalue buckling analysis using a detailed geometric model in a finite element analysis. The applicability of classical buckling analyses was also investigated as a design tool.

  12. Structural changes accompanying phosphorylation of tarantula muscle myosin filaments

    PubMed Central

    1987-01-01

    Electron microscopy has been used to study the structural changes that occur in the myosin filaments of tarantula striated muscle when they are phosphorylated. Myosin filaments in muscle homogenates maintained in relaxing conditions (ATP, EGTA) are found to have nonphosphorylated regulatory light chains as shown by urea/glycerol gel electrophoresis and [32P]phosphate autoradiography. Negative staining reveals an ordered, helical arrangement of crossbridges in these filaments, in which the heads from axially neighboring myosin molecules appear to interact with each other. When the free Ca2+ concentration in a homogenate is raised to 10(-4) M, or when a Ca2+-insensitive myosin light chain kinase is added at low Ca2+ (10(-8) M), the regulatory light chains of myosin become rapidly phosphorylated. Phosphorylation is accompanied by potentiation of the actin activation of the myosin Mg- ATPase activity and by loss of order of the helical crossbridge arrangement characteristic of the relaxed filament. We suggest that in the relaxed state, when the regulatory light chains are not phosphorylated, the myosin heads are held down on the filament backbone by head-head interactions or by interactions of the heads with the filament backbone. Phosphorylation of the light chains may alter these interactions so that the crossbridges become more loosely associated with the filament backbone giving rise to the observed changes and facilitating crossbridge interaction with actin. PMID:2958483

  13. GRAVITATIONAL INFALL ONTO MOLECULAR FILAMENTS. II. EXTERNALLY PRESSURIZED CYLINDERS

    SciTech Connect

    Heitsch, Fabian

    2013-10-10

    Two aspects of the evolution of externally pressurized, hydrostatic filaments are discussed. (1) The free-fall accretion of gas onto such a filament will lead to filament parameters (specifically, FWHM-column-density relations) inconsistent with the observations of Arzoumanian et al., except for two cases: for low-mass, isothermal filaments, agreement is found as in the analysis by Fischera and Martin. Magnetized cases, for which the field scales weakly with the density as B∝n {sup 1/2}, also reproduce observed parameters. (2) Realistically, the filaments will be embedded not only in gas of non-zero pressure, but also of non-zero density. Thus, the appearance of sheet-embedded filaments is explored. Generating a grid of filament models and comparing the resulting column density ratios and profile shapes with observations suggests that the three-dimensional filament profiles are intrinsically flatter than isothermal, beyond projection and evolution effects.

  14. Method for preparing metallated filament-wound structures

    DOEpatents

    Peterson, George R.

    1979-01-01

    Metallated graphite filament-wound structures are prepared by coating a continuous multi-filament carbon yarn with a metal carbide, impregnating the carbide coated yarn with a polymerizable carbon precursor, winding the resulting filament about a mandrel, partially curing the impregnation in air, subjecting the wound composite to heat and pressure to cure the carbon precursor, and thereafter heating the composite in a sizing die at a pressure loading of at least 1000 psi for graphitizing the carbonaceous material in the composite. The carbide in the composite coalesces into rod-like shapes which are disposed in an end-to-end relationship parallel with the filaments to provide resistance to erosion in abrasive laden atmospheres.

  15. Cluster-formation in the Rosette molecular cloud at the junctions of filaments

    NASA Astrophysics Data System (ADS)

    Schneider, N.; Csengeri, T.; Hennemann, M.; Motte, F.; Didelon, P.; Federrath, C.; Bontemps, S.; Di Francesco, J.; Arzoumanian, D.; Minier, V.; André, Ph.; Hill, T.; Zavagno, A.; Nguyen-Luong, Q.; Attard, M.; Bernard, J.-Ph.; Elia, D.; Fallscheer, C.; Griffin, M.; Kirk, J.; Klessen, R.; Könyves, V.; Martin, P.; Men'shchikov, A.; Palmeirim, P.; Peretto, N.; Pestalozzi, M.; Russeil, D.; Sadavoy, S.; Sousbie, T.; Testi, L.; Tremblin, P.; Ward-Thompson, D.; White, G.

    2012-04-01

    Aims: For many years feedback processes generated by OB-stars in molecular clouds, including expanding ionization fronts, stellar winds, or UV-radiation, have been proposed to trigger subsequent star formation. However, hydrodynamic models including radiation and gravity show that UV-illumination has little or no impact on the global dynamical evolution of the cloud. Instead, gravitational collapse of filaments and/or merging of filamentary structures can lead to building up dense high-mass star-forming clumps. However, the overall density structure of the cloud has a large influence on this process, and requires a better understanding. Methods: The Rosette molecular cloud, irradiated by the NGC 2244 cluster, is a template region for triggered star-formation, and we investigated its spatial and density structure by applying a curvelet analysis, a filament-tracing algorithm (DisPerSE), and probability density functions (PDFs) on Herschel column density maps, obtained within the HOBYS key program. Results: The analysis reveals not only the filamentary structure of the cloud but also that all known infrared clusters except one lie at junctions of filaments, as predicted by turbulence simulations. The PDFs of sub-regions in the cloud show systematic differences. The two UV-exposed regions have a double-peaked PDF we interprete as caused by shock compression, while the PDFs of the center and other cloud parts are more complex, partly with a power-law tail. A deviation of the log-normal PDF form occurs at AV ≈ 9m for the center, and around 4m for the other regions. Only the part of the cloud farthest from the Rosette nebula shows a log-normal PDF. Conclusions: The deviations of the PDF from the log-normal shape typically associated with low- and high-mass star-forming regions at AV ≈ 3-4m and 8-10m, respectively, are found here within the very same cloud. This shows that there is no fundamental difference in the density structure of low- and high-mass star

  16. Demonstration of mechanical connections between integrins, cytoskeletal filaments, and nucleoplasm that stabilize nuclear structure

    NASA Technical Reports Server (NTRS)

    Maniotis, A. J.; Chen, C. S.; Ingber, D. E.

    1997-01-01

    We report here that living cells and nuclei are hard-wired such that a mechanical tug on cell surface receptors can immediately change the organization of molecular assemblies in the cytoplasm and nucleus. When integrins were pulled by micromanipulating bound microbeads or micropipettes, cytoskeletal filaments reoriented, nuclei distorted, and nucleoli redistributed along the axis of the applied tension field. These effects were specific for integrins, independent of cortical membrane distortion, and were mediated by direct linkages between the cytoskeleton and nucleus. Actin microfilaments mediated force transfer to the nucleus at low strain; however, tearing of the actin gel resulted with greater distortion. In contrast, intermediate filaments effectively mediated force transfer to the nucleus under both conditions. These filament systems also acted as molecular guy wires to mechanically stiffen the nucleus and anchor it in place, whereas microtubules acted to hold open the intermediate filament lattice and to stabilize the nucleus against lateral compression. Molecular connections between integrins, cytoskeletal filaments, and nuclear scaffolds may therefore provide a discrete path for mechanical signal transfer through cells as well as a mechanism for producing integrated changes in cell and nuclear structure in response to changes in extracellular matrix adhesivity or mechanics.

  17. Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly.

    PubMed

    Bray, David J; Walsh, Tiffany R; Noro, Massimo G; Notman, Rebecca

    2015-01-01

    Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general. PMID:26181054

  18. Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly

    PubMed Central

    Bray, David J.; Walsh, Tiffany R.; Noro, Massimo G.; Notman, Rebecca

    2015-01-01

    Keratins are cytoskeletal proteins that hierarchically arrange into filaments, starting with the dimer sub-unit. They are integral to the structural support of cells, in skin, hair and nails. In skin, keratin is thought to play a critical role in conferring the barrier properties and elasticity of skin. In general, the keratin dimer is broadly described by a tri-domain structure: a head, a central rod and a tail. As yet, no atomistic-scale picture of the entire dimer structure exists; this information is pivotal for establishing molecular-level connections between structure and function in intermediate filament proteins. The roles of the head and tail domains in facilitating keratin filament assembly and function remain as open questions. To address these, we report results of molecular dynamics simulations of the entire epithelial human K1/K10 keratin dimer. Our findings comprise: (1) the first three-dimensional structural models of the complete dimer unit, comprising of the head, rod and tail domains; (2) new insights into the chirality of the rod-domain twist gained from analysis of the full domain structure; (3) evidence for tri-subdomain partitioning in the head and tail domains; and, (4) identification of the residue characteristics that mediate non-covalent contact between the chains in the dimer. Our findings are immediately applicable to other epithelial keratins, such as K8/K18 and K5/K14, and to intermediate filament proteins in general. PMID:26181054

  19. Structural Dynamics of Filament-Wound Booster Rockets

    NASA Technical Reports Server (NTRS)

    Bugg, F. M.

    1987-01-01

    Report summarizes program of measurements and calculations of vibrations in filament-wound composite models of Space Shuttle solid-rocket boosters. Vibrational behavior predicted by finite-element computer model of structural dynamics correlates well with data from tests on full- and quarter-scale models. Computer model developed with NASTRAN general-purpose structural-analysis computer code.

  20. TWO MASS DISTRIBUTIONS IN THE L 1641 MOLECULAR CLOUDS: THE HERSCHEL CONNECTION OF DENSE CORES AND FILAMENTS IN ORION A

    SciTech Connect

    Polychroni, D.; Schisano, E.; Elia, D.; Molinari, S.; Turrini, D.; Rygl, K. L. J.; Benedettini, M.; Busquet, G.; Di Giorgio, A. M.; Pestalozzi, M.; Pezzuto, S.; Roy, A.; André, Ph.; Hennemann, M.; Hill, T.; Könyves, V.; Di Francesco, J.; Arzoumanian, D.; Bontemps, S. [Université de Bordeaux, Laboratoire d' Astrophysique de Bordeaux, CNRS and others

    2013-11-10

    We present Herschel survey maps of the L 1641 molecular clouds in Orion A. We extracted both the filaments and dense cores in the region. We identified which of the dense sources are proto- or pre-stellar, and studied their association with the identified filaments. We find that although most (71%) of the pre-stellar sources are located on filaments there, is still a significant fraction of sources not associated with such structures. We find that these two populations (on and off the identified filaments) have distinctly different mass distributions. The mass distribution of the sources on the filaments is found to peak at 4 M {sub ☉} and drives the shape of the core mass function (CMF) at higher masses, which we fit with a power law of the form dN/dlogM∝M {sup –1.4±0.4}. The mass distribution of the sources off the filaments, on the other hand, peaks at 0.8 M {sub ☉} and leads to a flattening of the CMF at masses lower than ∼4 M {sub ☉}. We postulate that this difference between the mass distributions is due to the higher proportion of gas that is available in the filaments, rather than in the diffuse cloud.

  1. Self-Structured Conductive Filament Nanoheater for Chalcogenide Phase Transition.

    PubMed

    You, Byoung Kuk; Byun, Myunghwan; Kim, Seungjun; Lee, Keon Jae

    2015-06-23

    Ge2Sb2Te5-based phase-change memories (PCMs), which undergo fast and reversible switching between amorphous and crystalline structural transformation, are being utilized for nonvolatile data storage. However, a critical obstacle is the high programming current of the PCM cell, resulting from the limited pattern size of the optical lithography-based heater. Here, we suggest a facile and scalable strategy of utilizing self-structured conductive filament (CF) nanoheaters for Joule heating of chalcogenide materials. This CF nanoheater can replace the lithographical-patterned conventional resistor-type heater. The sub-10 nm contact area between the CF and the phase-change material achieves significant reduction of the reset current. In particular, the PCM cell with a single Ni filament nanoheater can be operated at an ultralow writing current of 20 μA. Finally, phase-transition behaviors through filament-type nanoheaters were directly observed by using transmission electron microscopy. PMID:26039415

  2. Exact Length Distribution of Filamentous Structures Assembled from a Finite Pool of Subunits.

    PubMed

    Harbage, David; Kondev, Jané

    2016-07-01

    Self-assembling filamentous structures made of protein subunits are ubiquitous in cell biology. These structures are often highly dynamic, with subunits in a continuous state of flux, binding to and falling off of filaments. In spite of this constant turnover of their molecular parts, many cellular structures seem to maintain a well-defined size over time, which is often required for their proper functioning. One widely discussed mechanism of size regulation involves the cell maintaining a finite pool of protein subunits available for assembly. This finite pool mechanism can control the length of a single filament by having assembly proceed until the pool of free subunits is depleted to the point when assembly and disassembly are balanced. Still, this leaves open the question of whether the same mechanism can provide size control for multiple filamentous structures that are assembled from a common pool of protein subunits, as is often the case in cells. We address this question by solving the steady-state master equation governing the stochastic assembly and disassembly of multifilament structures made from a shared finite pool of subunits. We find that, while the total number of subunits within a multifilament structure is well-defined, individual filaments within the structure have a wide, power-law distribution of lengths. We also compute the phase diagram for two multifilament structures competing for the same pool of subunits and identify conditions for coexistence when both have a well-defined size. These predictions can be tested in cell experiments in which the size of the subunit pool or the number of filament nucleators is tuned.

  3. Two-level hierarchical fragmentation in the northern filament of the Orion Molecular Cloud 1

    NASA Astrophysics Data System (ADS)

    Teixeira, P. S.; Takahashi, S.; Zapata, L. A.; Ho, P. T. P.

    2016-03-01

    Context. The filamentary structure of molecular clouds may set important constraints on the mass distribution of stars forming within them. It is therefore important to understand which physical mechanism dominates filamentary cloud fragmentation and core formation. Aims: Orion A is the nearest giant molecular cloud, and its so-called ∫-shaped filament is a very active star-forming region that is a good target for such a study. We have recently reported on the collapse and fragmentation properties of the northernmost part of this structure, located ~2.4 pc north of Orion KL - Orion Molecular Cloud (OMC) 3. As part of our project to study the ∫-shaped filament, we analyze the fragmentation properties of the northern OMC 1 filament (located ≲0.3 pc north of Orion KL). This filament is a dense structure previously identified by JCMT/SCUBA submillimeter continuum and VLA NH3 observations and was shown to have fragmented into clumps. Our aim is to search for cores and young protostars embedded within OMC 1n and to study how the filament is fragmenting to form them. Methods: We observed OMC 1North (hereafter OMC 1n) with the Submillimeter Array (SMA) at 1.3 mm and report on our analysis of the continuum data. Results: We discovered 24 new compact sources, ranging in mass from 0.1 to 2.3, in size from 400 to 1300 au, and in density from 2.6 × 107 to 2.8 × 106 cm-3. The masses of these sources are similar to those of the SMA protostars in OMC 3, but their typical sizes and densities are lower by a factor of ten. Only 8% of the new sources have infrared counterparts, but there are five associated CO molecular outflows. These sources are thus likely in the Class 0 evolutionary phase but it cannot be excluded that some of the sources might still be pre-stellar cores. The spatial analysis of the protostars shows that they are divided into small groups that coincide with previously identified JCMT/SCUBA 850 μm and VLA NH3 clumps, which are separated by a quasi

  4. On filament structure and propagation within a commercial plasma globe

    SciTech Connect

    Burin, M. J.; Simmons, G. G.; Ceja, H. G.; Zweben, S. J.; Nagy, A.; Brunkhorst, C.

    2015-05-15

    The filamentary discharge seen within commercial plasma globes is commonly enjoyed yet not well understood. Here, we investigate the discharge properties of a plasma globe using a variable high voltage amplifier. We find that increasing voltage magnitude increases the number of filaments while leaving their individual structure basically unchanged, a result typical of dielectric barrier discharges. The frequency of the voltage also affects filament population but more significantly changes filament structure, with more diffuse filaments seen at lower frequencies. Voltage polarity is observed to be important, especially at lower frequencies, where for negative-gradient voltages the discharge is more diffuse, not filamentary. At late stages of the discharge circular structures appear and expand on the glass boundaries. We find no trend of discharge speed with respect to voltage variables, though this may be due to manufacturer sample-to-sample variation. Each voltage cycle the discharge expands outward at ∼10–15 km/s, a speed significantly higher than the estimated electron drift yet considerably lower than that observed for most streamers. We discuss the physics of these observations and their relation to similar discharges that can be found within nature and industry.

  5. Structural and Mechanical Properties of Intermediate Filaments under Extreme Conditions and Disease

    NASA Astrophysics Data System (ADS)

    Qin, Zhao

    Intermediate filaments are one of the three major components of the cytoskeleton in eukaryotic cells. It was discovered during the recent decades that intermediate filament proteins play key roles to reinforce cells subjected to large-deformation as well as participate in signal transduction. However, it is still poorly understood how the nanoscopic structure, as well as the biochemical properties of these protein molecules contribute to their biomechanical functions. In this research we investigate the material function of intermediate filaments under various extreme mechanical conditions as well as disease states. We use a full atomistic model and study its response to mechanical stresses. Learning from the mechanical response obtained from atomistic simulations, we build mesoscopic models following the finer-trains-coarser principles. By using this multiple-scale model, we present a detailed analysis of the mechanical properties and associated deformation mechanisms of intermediate filament network. We reveal the mechanism of a transition from alpha-helices to beta-sheets with subsequent intermolecular sliding under mechanical force, which has been inferred previously from experimental results. This nanoscale mechanism results in a characteristic nonlinear force-extension curve, which leads to a delocalization of mechanical energy and prevents catastrophic fracture. This explains how intermediate filament can withstand extreme mechanical deformation of > 1 00% strain despite the presence of structural defects. We combine computational and experimental techniques to investigate the molecular mechanism of Hutchinson-Gilford progeria syndrome, a premature aging disease. We find that the mutated lamin tail .domain is more compact and stable than the normal one. This altered structure and stability may enhance the association of intermediate filaments with the nuclear membrane, providing a molecular mechanism of the disease. We study the nuclear membrane association

  6. Multidimensional Simulations of Filament Channel Structure and Evolution

    NASA Astrophysics Data System (ADS)

    Karpen, J. T.

    2007-10-01

    Over the past decade, the NRL Solar Theory group has made steady progress toward formulating a comprehensive model of filament-channel structure and evolution, combining the results of our sheared 3D arcade model for the magnetic field with our thermal nonequilibrium model for the cool, dense material suspended in the corona. We have also discovered that, when a sheared arcade is embedded within the global dipolar field, the resulting stressed filament channel can erupt through the mechanism of magnetic breakout. Our progress has been largely enabled by the development and implementation of state-of-the-art 1D hydrodynamic and 3D magnetohydrodynamic (MHD) codes to simulate the field-aligned plasma thermodynamics and large-scale magnetic-field evolution, respectively. Significant questions remain, however, which could be answered with the advanced observations anticipated from Solar-B. In this review, we summarize what we have learned from our simulations about the magnetic and plasma structure, evolution, and eruption of filament channels, and suggest key observational objectives for Solar-B that will test our filament-channel and CME-initiation models and augment our understanding of the underlying physical processes.

  7. Actin filament nucleation and elongation factors--structure-function relationships.

    PubMed

    Dominguez, Roberto

    2009-01-01

    The spontaneous and unregulated polymerization of actin filaments is inhibited in cells by actin monomer-binding proteins such as profilin and Tbeta4. Eukaryotic cells and certain pathogens use filament nucleators to stabilize actin polymerization nuclei, whose formation is rate-limiting. Known filament nucleators include the Arp2/3 complex and its large family of nucleation promoting factors (NPFs), formins, Spire, Cobl, VopL/VopF, TARP and Lmod. These molecules control the time and location for polymerization, and additionally influence the structures of the actin networks that they generate. Filament nucleators are generally unrelated, but with the exception of formins they all use the WASP-Homology 2 domain (WH2 or W), a small and versatile actin-binding motif, for interaction with actin. A common architecture, found in Spire, Cobl and VopL/VopF, consists of tandem W domains that bind three to four actin subunits to form a nucleus. Structural considerations suggest that NPFs-Arp2/3 complex can also be viewed as a specialized form of tandem W-based nucleator. Formins are unique in that they use the formin-homology 2 (FH2) domain for interaction with actin and promote not only nucleation, but also processive barbed end elongation. In contrast, the elongation function among W-based nucleators has been "outsourced" to a dedicated family of proteins, Eva/VASP, which are related to WASP-family NPFs.

  8. In vivo formation steps of the hard alpha-keratin intermediate filament along a hair follicle: evidence for structural polymorphism.

    PubMed

    Rafik, Mériem Er; Briki, Fatma; Burghammer, Manfred; Doucet, Jean

    2006-04-01

    Several aspects of the intermediate filaments' molecular architecture remain mysterious despite decades of study. The growth process and the final architecture may depend on the physical, chemical, and biochemical environment. Aiming at clarifying this issue, we have revisited the structure of the human hair follicle by means of X-ray microdiffraction. We conclude that the histology-based growth zones along the follicle are correlated to the fine architecture of the filaments deduced from X-ray microdiffraction. Our analysis reveals the existence of two major polymorph intermediate filament architectures. Just above the bulb, the filaments are characterized by a diameter of 100 Angstroms and a low-density core. The following zone upwards is characterized by the lateral aggregation of the filaments into a compact network of filaments, by a contraction of their diameter (to 75 Angstroms) and by the setting up of a long-range longitudinal ordering. In the upper zone, the small structural change associated with the tissue hardening likely concerns the terminal domains. The architecture of the intermediate filament in the upper zones could be specific to hard alpha-keratin whilst the other architecture found in the lower zone could be representative for intermediate filaments in a different environment.

  9. A Molecular Perspective of Inter-filament Bonding in Fused Deposition Modeling 3-D Printing

    NASA Astrophysics Data System (ADS)

    Duranty, Edward; Spradlin, Brandon; Dadmun, Mark

    2015-03-01

    Fused deposition 3D printing is an important tool for low-cost and rapid prototyping of objects with complex geometries. 3D printed materials are composed of many filaments deposited on a heated substrate, requiring the bonding of neighboring filaments during the deposition process. Filament deposition often creates voids between filaments, which requires necking between them to create a robust sample. Therefore the amount of interfacial contact and interdiffusion between filaments become important parameters that control the macroscopic physical properties of the printed prototype. Our research focuses on quantifying the interfacial adhesion between ABS filaments and its impact on structural properties. The time evolution of the temperature profile near the heated substrate demonstrates that the deposited filaments are repeatedly heated above the Tg of ABS allowing interpenetration of the polymer chains between adjacent filaments. Results of DMA experiments on samples of different geometries have been correlated to microphotography that monitors the degree of necking between filaments and the thermal history. Results indicate that interfacial contact area between filaments and increased thermal energy are crucial to their mechanical properties.

  10. Flexible filamentous virus structure from fiber diffraction

    SciTech Connect

    Stubbs, Gerald; Kendall, Amy; McDonald, Michele; Bian, Wen; Bowles, Timothy; Baumgarten, Sarah; McCullough, Ian; Shi, Jian; Stewart, Phoebe; Bullitt, Esther; Gore, David; Ghabrial, Said

    2008-10-24

    Fiber diffraction data have been obtained from Narcissus mosaic virus, a potexvirus from the family Flexiviridae, and soybean mosaic virus (SMV), a potyvirus from the family Potyviridae. Analysis of the data in conjunction with cryo-electron microscopy data allowed us to determine the symmetry of the viruses and to make reconstructions of SMV at 19 {angstrom} resolution and of another potexvirus, papaya mosaic virus, at 18 {angstrom} resolution. These data include the first well-ordered data ever obtained for the potyviruses and the best-ordered data from the potexviruses, and offer the promise of eventual high resolution structure determinations.

  11. An Early Cretaceous heterodontosaurid dinosaur with filamentous integumentary structures.

    PubMed

    Zheng, Xiao-Ting; You, Hai-Lu; Xu, Xing; Dong, Zhi-Ming

    2009-03-19

    Ornithischia is one of the two major groups of dinosaurs, with heterodontosauridae as one of its major clades. Heterodontosauridae is characterized by small, gracile bodies and a problematic phylogenetic position. Recent phylogenetic work indicates that it represents the most basal group of all well-known ornithischians. Previous heterodontosaurid records are mainly from the Early Jurassic period (205-190 million years ago) of Africa. Here we report a new heterodontosaurid, Tianyulong confuciusi gen. et sp. nov., from the Early Cretaceous period (144-99 million years ago) of western Liaoning Province, China. Tianyulong extends the geographical distribution of heterodontosaurids to Asia and confirms the clade's previously questionable temporal range extension into the Early Cretaceous period. More surprisingly, Tianyulong bears long, singular and unbranched filamentous integumentary (outer skin) structures. This represents the first confirmed report, to our knowledge, of filamentous integumentary structures in an ornithischian dinosaur. PMID:19295609

  12. An Early Cretaceous heterodontosaurid dinosaur with filamentous integumentary structures.

    PubMed

    Zheng, Xiao-Ting; You, Hai-Lu; Xu, Xing; Dong, Zhi-Ming

    2009-03-19

    Ornithischia is one of the two major groups of dinosaurs, with heterodontosauridae as one of its major clades. Heterodontosauridae is characterized by small, gracile bodies and a problematic phylogenetic position. Recent phylogenetic work indicates that it represents the most basal group of all well-known ornithischians. Previous heterodontosaurid records are mainly from the Early Jurassic period (205-190 million years ago) of Africa. Here we report a new heterodontosaurid, Tianyulong confuciusi gen. et sp. nov., from the Early Cretaceous period (144-99 million years ago) of western Liaoning Province, China. Tianyulong extends the geographical distribution of heterodontosaurids to Asia and confirms the clade's previously questionable temporal range extension into the Early Cretaceous period. More surprisingly, Tianyulong bears long, singular and unbranched filamentous integumentary (outer skin) structures. This represents the first confirmed report, to our knowledge, of filamentous integumentary structures in an ornithischian dinosaur.

  13. Elasticity of a semiflexible filament with a discontinuous tension due to a cross-link or a molecular motor

    NASA Astrophysics Data System (ADS)

    Razbin, Mohammadhosein; Benetatos, Panayotis; Zippelius, Annette

    2016-05-01

    We analyze the stretching elasticity of a wormlike chain with a tension discontinuity resulting from a Hookean spring connecting its backbone to a fixed point. The elasticity of isolated semiflexible filaments has been the subject in a significant body of literature, primarily because of its relevance to the mechanics of biological matter. In real systems, however, these filaments are usually part of supramolecular structures involving cross-linkers or molecular motors, which cause tension discontinuities. Our model is intended as a minimal structural element incorporating such a discontinuity. We obtain analytical results in the weakly bending limit of the filament, concerning its force-extension relation and the response of the two parts in which the filament is divided by the spring. For a small tension discontinuity, the linear response of the filament extension to this discontinuity strongly depends on the external tension. For large external tension f , the spring force contributes a subdominant correction ˜1 /f3 /2 to the well-known ˜1 /√{f } -dependence of the end-to-end extension.

  14. Dynamics of CO(2) laser pulse filamentation in air influenced by spectrally selective molecular absorption.

    PubMed

    Geints, Yuri E; Zemlyanov, Alexander A

    2014-09-01

    The theoretical aspects of self-focusing and filamentation of high-power pulsed CO(2) laser radiation with carrier wavelength 10.6 μm in air are considered. The spectrally selective molecular absorption of realistic atmospheric air is included in the theoretical model. In the conditions of strong pulse self-phase modulation and pulse spectral broadening, the supercontinual radiation spectrum is substantially influenced by the selective atmospheric absorption that destabilizes the filamentation process and results in considerable shortening of the filamentation length. PMID:25321358

  15. Structural basis of thymosin-β4/profilin exchange leading to actin filament polymerization

    PubMed Central

    Xue, Bo; Leyrat, Cedric; Grimes, Jonathan M.; Robinson, Robert C.

    2014-01-01

    Thymosin-β4 (Tβ4) and profilin are the two major sequestering proteins that maintain the pool of monomeric actin (G-actin) within cells of higher eukaryotes. Tβ4 prevents G-actin from joining a filament, whereas profilin:actin only supports barbed-end elongation. Here, we report two Tβ4:actin structures. The first structure shows that Tβ4 has two helices that bind at the barbed and pointed faces of G-actin, preventing the incorporation of the bound G-actin into a filament. The second structure displays a more open nucleotide binding cleft on G-actin, which is typical of profilin:actin structures, with a concomitant disruption of the Tβ4 C-terminal helix interaction. These structures, combined with biochemical assays and molecular dynamics simulations, show that the exchange of bound actin between Tβ4 and profilin involves both steric and allosteric components. The sensitivity of profilin to the conformational state of actin indicates a similar allosteric mechanism for the dissociation of profilin during filament elongation. PMID:25313062

  16. Giant molecular filaments in the Milky Way. II. The fourth Galactic quadrant

    NASA Astrophysics Data System (ADS)

    Abreu-Vicente, J.; Ragan, S.; Kainulainen, J.; Henning, Th.; Beuther, H.; Johnston, K.

    2016-05-01

    Context. Filamentary structures are common morphological features of the cold, molecular interstellar medium (ISM). Recent studies have discovered massive, hundred-parsec-scale filaments that may be connected to the large-scale, Galactic spiral arm structure. Addressing the nature of these giant molecular filaments (GMFs) requires a census of their occurrence and properties. Aims: We perform a systematic search of GMFs in the fourth Galactic quadrant and determine their basic physical properties. Methods: We identify GMFs based on their dust extinction signatures in the near- and mid-infrared and the velocity structure probed by 13CO line emission. We use the 13CO line emission and ATLASGAL dust emission data to estimate the total and dense gas masses of the GMFs. We combine our sample with an earlier sample from literature and study the Galactic environment of the GMFs. Results: We identify nine GMFs in the fourth Galactic quadrant: six in the Centaurus spiral arm and three in inter-arm regions. Combining this sample with an earlier study using the same identification criteria in the first Galactic quadrant results in 16 GMFs, nine of which are located within spiral arms. The GMFs have sizes of 80-160 pc and 13CO-derived masses between 5-90 × 104M⊙. Their dense gas mass fractions are between 1.5-37%, which is higher in the GMFs connected to spiral arms. We also compare the different GMF-identification methods and find that emission and extinction-based techniques overlap only partially, thereby highlighting the need to use both to achieve a complete census. Table A.2 is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/590/A131

  17. Functional complexity of intermediate filament cytoskeletons: from structure to assembly to gene ablation.

    PubMed

    Herrmann, Harald; Hesse, Michael; Reichenzeller, Michaela; Aebi, Ueli; Magin, Thomas M

    2003-01-01

    The cell biology of intermediate filament (IF) proteins and their filaments is complicated by the fact that the members of the gene family, which in humans amount to at least 65, are differentially expressed in very complex patterns during embryonic development. Thus, different tissues and cells express entirely different sets and amounts of IF proteins, the only exception being the nuclear B-type lamins, which are found in every cell. Moreover, in the course of evolution the individual members of this family have, within one species, diverged so much from each other with regard to sequence and thus molecular properties that it is hard to envision a unifying kind of function for them. The known epidermolytic diseases, caused by single point mutations in keratins, have been used as an argument for a role of IFs in mechanical "stress resistance," something one would not have easily ascribed to the beaded chain filaments, a special type of IF in the eye lens, or to nuclear lamins. Therefore, the power of plastic dish cell biology may be limited in revealing functional clues for these structural elements, and it may therefore be of interest to go to the extreme ends of the life sciences, i.e., from the molecular properties of individual molecules including their structure at the atomic level to targeted inactivation of their genes in living animals, mouse, and worm to define their role more precisely in metazoan cell physiology. PMID:12641211

  18. Fullerenol Nanoparticles with Structural Activity Induce Variable Intracellular Actin Filament Morphologies.

    PubMed

    Jin, Junjiang; Dong, Ying; Wang, Ying; Xia, Lin; Gu, Weihong; Bai, Xue; Chang, Yanan; Zhang, Mingyi; Chen, Kui; Li, Juan; Zhao, Lina; Xing, Gengmei

    2016-06-01

    Fullerenol nanoparticles are promising for various biological applications; many studies have shown that they induce variable and diverse biological effects including side effects. Separation and purification of two fractions of fullerenols has demonstrated that they have varied chemical structures on the surfaces of their carbon cages. Actin is an important structural protein that is able to transform functional structures under varied physiological conditions. We assessed the abilities of the two fractions of fullerenols to attach to actin and induce variable morphological features in actin filament structures. Specifically the fullerenol fraction with a surface electric charge of -1.913 ± 0.008q (x10(-6) C) has percentages of C-OH and C=O on the carbon cage of 16.14 ± 0.60 and 17.55 ± 0.69. These features allow it to form intermolecular hydrogen bonds with actin at a stoichiometric ratio of four fullerenols per actin subunit. Molecular simulations revealed these specific binding sites and binding modes in atomic details in the interaction between the active fullerenol and actin filament. Conversely, these interactions were not possible for the other fraction of fullerenol with that percentages of C-OH and C=O on the carbon cage were 15.59 ± 0.01 and 1.94 ± 0.11. Neither sample induced appreciable cytotoxicity or acute cell death. After entering cells, active fullerenol binding to actin induces variable morphological features and may transform ATP-actin to ADP-actin. These changes facilitate the binding of ADF/cofilin, allowing cofilin to sever actin filaments to form cofilin/actin/fullerenol rods. Our findings suggest that fullerenol with structural activity binding disturbs actin filament structure, which may inhibit locomotion of cell or induce chronic side effects in to cells. PMID:27319217

  19. Inroads into the Structure and Function of Intermediate Filament Networks

    PubMed Central

    Goldman, Robert D.; Cleland, Megan M.; Murthy, Prasanna; Mahammad, Saleemulla; Kuczmarski, Edward R.

    2011-01-01

    Although intermediate filaments are one of three major cytoskeletal systems of vertebrate cells, they remain the least understood with respect to their structure and function. This is due in part to the fact that they are encoded by a large gene family which is developmentally regulated in a cell and tissue type specific fashion. This article is in honor of Ueli Aebi. It highlights the studies on IF that have been carried out by our laboratory for more than 40 years. Many of our advances in understanding IF are based on conversations with Ueli which have taken place during adventurous and sometimes dangerous hiking and biking trips throughout the world. PMID:22120848

  20. The Structure and Assembly Mechanism of a Novel Three-Stranded Tubulin Filament that Centers Phage DNA

    PubMed Central

    Zehr, Elena A.; Kraemer, James A.; Erb, Marcella L.; Coker, Joanna K.C.; Montabana, Elizabeth A.; Pogliano, Joe; Agard, David A.

    2014-01-01

    SUMMARY Tubulins are a universally conserved protein superfamily that carry out diverse biological roles by assembling filaments with very different architectures. The underlying basis of this structural diversity is poorly understood. Here, we determine a 7.1 Å cryo-EM reconstruction of the bacteriophage-encoded PhuZ filament and provide molecular-level insight into its cooperative assembly mechanism. The PhuZ family of tubulins is required to actively center the phage within infected host cells, facilitating efficient phage replication. Our reconstruction and derived model reveal the first example of a three-stranded tubulin filament. We show that the elongated C-terminal tail simultaneously stabilizes both longitudinal and lateral interactions, which in turn define filament architecture. Identified interaction surfaces are conserved within the PhuZ family, and their mutagenesis compromises polymerization in vitro and in vivo. Combining kinetic modeling of PhuZ filament assembly and structural data we suggest a common filament structure and assembly mechanism for the PhuZ family of tubulins. PMID:24631461

  1. Förster resonance energy transfer structural kinetic studies of cardiac thin filament deactivation.

    PubMed

    Xing, Jun; Jayasundar, Jayant J; Ouyang, Yexin; Dong, Wen-Ji

    2009-06-12

    Cardiac thin filament deactivation is initiated by Ca2+ dissociation from troponin C (cTnC), followed by multiple structural changes of thin filament proteins. These structural transitions are the molecular basis underlying the thin filament regulation of cardiac relaxation, but the detailed mechanism remains elusive. In this study Förster resonance energy transfer (FRET) was used to investigate the dynamics and kinetics of the Ca2+-induced conformational changes of the cardiac thin filaments, specifically the closing of the cTnC N-domain, the cTnC-cTnI (troponin I) interaction, and the cTnI-actin interaction. The cTnC N-domain conformational change was examined by monitoring FRET between a donor (AEDANS) attached to one cysteine residue and an acceptor (DDPM) attached the other cysteine of the mutant cTnC(L13C/N51C). The cTnC-cTnI interaction was investigated by monitoring the distance changes from residue 89 of cTnC to residues 151 and 167 of cTnI, respectively. The cTnI-actin interaction was investigated by monitoring the distance changes from residues 151 and 167 of cTnI to residue 374 of actin. FRET Ca2+ titrations and stopped-flow kinetic measurements show that different thin filament structural transitions have different Ca2+ sensitivities and Ca2+ dissociation-induced kinetics. The observed structural transitions involving the regulatory region and the mobile domain of cTnI occurred at fast kinetic rates, whereas the kinetics of the structural transitions involving the cTnI inhibitory region was slow. Our results suggest that the thin filament deactivation upon Ca2+ dissociation is a two-step process. One step involves rapid binding of the mobile domain of cTnI to actin, which is kinetically coupled with the conformational change of the N-domain of cTnC and the dissociation of the regulatory region of cTnI from cTnC. The other step involves switching the inhibitory region of cTnI from interacting with cTnC to interacting with actin. The latter processes

  2. Förster Resonance Energy Transfer Structural Kinetic Studies of Cardiac Thin Filament Deactivation*

    PubMed Central

    Xing, Jun; Jayasundar, Jayant J.; Ouyang, Yexin; Dong, Wen-Ji

    2009-01-01

    Cardiac thin filament deactivation is initiated by Ca2+ dissociation from troponin C (cTnC), followed by multiple structural changes of thin filament proteins. These structural transitions are the molecular basis underlying the thin filament regulation of cardiac relaxation, but the detailed mechanism remains elusive. In this study Förster resonance energy transfer (FRET) was used to investigate the dynamics and kinetics of the Ca2+-induced conformational changes of the cardiac thin filaments, specifically the closing of the cTnC N-domain, the cTnC-cTnI (troponin I) interaction, and the cTnI-actin interaction. The cTnC N-domain conformational change was examined by monitoring FRET between a donor (AEDANS) attached to one cysteine residue and an acceptor (DDPM) attached the other cysteine of the mutant cTnC(L13C/N51C). The cTnC-cTnI interaction was investigated by monitoring the distance changes from residue 89 of cTnC to residues 151 and 167 of cTnI, respectively. The cTnI-actin interaction was investigated by monitoring the distance changes from residues 151 and 167 of cTnI to residue 374 of actin. FRET Ca2+ titrations and stopped-flow kinetic measurements show that different thin filament structural transitions have different Ca2+ sensitivities and Ca2+ dissociation-induced kinetics. The observed structural transitions involving the regulatory region and the mobile domain of cTnI occurred at fast kinetic rates, whereas the kinetics of the structural transitions involving the cTnI inhibitory region was slow. Our results suggest that the thin filament deactivation upon Ca2+ dissociation is a two-step process. One step involves rapid binding of the mobile domain of cTnI to actin, which is kinetically coupled with the conformational change of the N-domain of cTnC and the dissociation of the regulatory region of cTnI from cTnC. The other step involves switching the inhibitory region of cTnI from interacting with cTnC to interacting with actin. The latter processes

  3. Intermediate filament structure: the bottom-up approach.

    PubMed

    Chernyatina, Anastasia A; Guzenko, Dmytro; Strelkov, Sergei V

    2015-02-01

    Intermediate filaments (IFs) result from a key cytoskeletal protein class in metazoan cells, but currently there is no consensus as to their three-dimensional architecture. IF proteins form elongated dimers based on the coiled-coil structure within their central 'rod' domain. Here we focus on the atomic structure of this elementary dimer, elucidated using X-ray crystallography on multiple fragments and electron paramagnetic resonance experiments on spin-labelled vimentin samples. In line with conserved sequence features, the rod of all IF proteins is composed of three coiled-coil segments containing heptad and hendecad repeats and interconnected by linkers. In addition, the next assembly intermediate beyond the dimer, the tetramer, could be modelled. The impact of these structural results towards understanding the assembly mechanism is discussed.

  4. Negative Stains Containing Trehalose: Application to Tubular and Filamentous Structures

    NASA Astrophysics Data System (ADS)

    Harris, J. Robin; Gerber, Max; Gebauer, Wolfgang; Wernicke, Wolfgang; Markl, Jürgen

    1996-02-01

    Several examples are presented that show the successful application of uranyl acetate and ammonium molybdate negative staining in the presence of trehalose for TEM studies of filamentous and tubular structures. The principal benefit to be gained from the inclusion of trehalose stems from the considerably reduced flattening of the large tubular structures and the greater orientational freedom of single molecules due to an increased depth of the negative stain in the presence of trehalose. Trehalose is likely to provide considerable protection to protein molecules and their assemblies during the drying of negatively stained specimens. Some reduction in the excessive density imparted by uranyl acetate around large assemblies is also achieved. Nevertheless, in the presence of 1% (w/v) trehalose, it is desirable to increase the concentration of negative stain to 5% (w/v) for ammonium molybdate and to 4% for uranyl acetate to produce satisfactory image contrast. In general, the ammonium molybdate-trehalose negative stain is more satisfactory than the uranyl acetate-trehalose combination, because of the greater electron beam sensitivity of the uranyl negative stain. Reassembled taxol-stabilized pig brain microtubules, together with collagen fibrils, sperm tails, helical filaments, and reassociated hemocyanin (KLH2), all from the giant keyhole limpet Megathura crenulata, have been studied by negative staining in the presence of trehalose. In all cases satisfactory TEM imaging conditions were readily obtained on the specimens, as long as regions of excessively deep stain were avoided.

  5. Filamentary structures in dense plasma focus: Current filaments or vortex filaments?

    SciTech Connect

    Soto, Leopoldo Pavez, Cristian; Moreno, José; Castillo, Fermin; Veloso, Felipe; Auluck, S. K. H.

    2014-07-15

    Recent observations of an azimuthally distributed array of sub-millimeter size sources of fusion protons and correlation between extreme ultraviolet (XUV) images of filaments with neutron yield in PF-1000 plasma focus have re-kindled interest in their significance. These filaments have been described variously in literature as current filaments and vortex filaments, with very little experimental evidence in support of either nomenclature. This paper provides, for the first time, experimental observations of filaments on a table-top plasma focus device using three techniques: framing photography of visible self-luminosity from the plasma, schlieren photography, and interferometry. Quantitative evaluation of density profile of filaments from interferometry reveals that their radius closely agrees with the collision-less ion skin depth. This is a signature of relaxed state of a Hall fluid, which has significant mass flow with equipartition between kinetic and magnetic energy, supporting the “vortex filament” description. This interpretation is consistent with empirical evidence of an efficient energy concentration mechanism inferred from nuclear reaction yields.

  6. Molecular mechanism of Ena/VASP-mediated actin-filament elongation.

    PubMed

    Breitsprecher, Dennis; Kiesewetter, Antje K; Linkner, Joern; Vinzenz, Marlene; Stradal, Theresia E B; Small, John Victor; Curth, Ute; Dickinson, Richard B; Faix, Jan

    2011-02-01

    Ena/VASP proteins are implicated in a variety of fundamental cellular processes including axon guidance and cell migration. In vitro, they enhance elongation of actin filaments, but at rates differing in nearly an order of magnitude according to species, raising questions about the molecular determinants of rate control. Chimeras from fast and slow elongating VASP proteins were generated and their ability to promote actin polymerization and to bind G-actin was assessed. By in vitro TIRF microscopy as well as thermodynamic and kinetic analyses, we show that the velocity of VASP-mediated filament elongation depends on G-actin recruitment by the WASP homology 2 motif. Comparison of the experimentally observed elongation rates with a quantitative mathematical model moreover revealed that Ena/VASP-mediated filament elongation displays a saturation dependence on the actin monomer concentration, implying that Ena/VASP proteins, independent of species, are fully saturated with actin in vivo and generally act as potent filament elongators. Moreover, our data showed that spontaneous addition of monomers does not occur during processive VASP-mediated filament elongation on surfaces, suggesting that most filament formation in cells is actively controlled.

  7. Hub-Filament Systems and Spiral Structures from Cloud to Core Scales

    NASA Astrophysics Data System (ADS)

    Galvan-Madrid, Roberto; Liu, Hauyu Baobab; Immer, Katharina; Juarez, Carmen; Palau, Aina

    2015-08-01

    We present evidence, from several separate observational studies, that molecular clouds and the clumps and cores within are (sometimes) arranged in a hub-filament morphology with spiral-like features. This arrangementoccurs at multiple scales: from the < 0.05 pc scales of low-mass star-forming cores, to the ~0.5 pc scales of clumps in massive star formation regions, to Giant Molecular Clouds. These structures have appeared in data of well known sources because of the increased sensitivy of new instruments like ALMA or the CSO SHARC-II, or after a detailed combination of single-dish and interferometer data. Reports of such structures may become more common in the near future. Presumably, these structures appear in systems that are dense enough to be prone to gravitational instabilities, and that have a non-negligible angularmomentum.

  8. Molecular dynamics simulation of a myosin subfragment-1 docking with an actin filament.

    PubMed

    Masuda, Tadashi

    2013-09-01

    Myosins are typical molecular motor proteins, which convert the chemical energy of ATP into mechanical work. The fundamental mechanism of this energy conversion is still unknown. To explain the experimental results observed in molecular motors, Masuda has proposed a theory called the "Driven by Detachment (DbD)" mechanism for the working principle of myosins. Based on this theory, the energy used during the power stroke of the myosins originates from the attractive force between a detached myosin head and an actin filament, and does not directly arise from the energy of ATP. According to this theory, every step in the myosin working process may be reproduced by molecular dynamics (MD) simulations, except for the ATP hydrolysis step. Therefore, MD simulations were conducted to reproduce the docking process of a myosin subfragment-1 (S1) against an actin filament. A myosin S1 directed toward the barbed end of an actin filament was placed at three different positions by shifting it away from the filament axis. After 30 ns of MD simulations, in three cases out of ten trials on average, the myosin made a close contact with two actin monomers by changing the positions and the orientation of both the myosin and the actin as predicted in previous studies. Once the docking was achieved, the distance between the myosin and the actin showed smaller fluctuations, indicating that the docking is stable over time. If the docking was not achieved, the myosin moved randomly around the initial position or moved away from the actin filament. MD simulations thus successfully reproduced the docking of a myosin S1 with an actin filament. By extending the similar MD simulations to the other steps of the myosin working process, the validity of the DbD theory may be computationally demonstrated.

  9. Structural transition of the inhibitory region of troponin I within the regulated cardiac thin filament.

    PubMed

    Dong, Wen-Ji; An, Jianli; Xing, Jun; Cheung, Herbert C

    2006-12-15

    +) sensitivity and accelerated the structural transition rate of the inhibitory region of cTnI on thin filaments. These results support the idea of a feedback mechanism by strong cross-bridge interaction with actin and provide insights on the molecular basis for the fine tuning of cardiac function by beta-adrenergic stimulation.

  10. Structural transition of the inhibitory region of troponin I within the regulated cardiac thin filament

    PubMed Central

    Dong, Wen-Ji; An, Jianli; Xing, Jun; Cheung, Herbert C.

    2007-01-01

    accelerated the structural transition rate of the inhibitory region of cTnI on thin filaments. These results support the idea of a feedback mechanism by strong cross-bridge interaction with actin and provide insights on the molecular basis for the fine tuning of cardiac function by β-adrenergic stimulation. PMID:16962989

  11. Theoretical analysis of fluorescence signals in filamentation of femtosecond laser pulses in nitrogen molecular gas

    SciTech Connect

    Arevalo, E.; Becker, A.

    2005-10-15

    We study numerically and analytically the role of the combined effect of self-focusing, geometrical focusing, and the plasma defocusing in the formation of the fluorescence signal during the filamentation of a Ti:sapphire laser pulse in nitrogen molecular gas. Results of numerical simulations are used to estimate the number of excited ions in the focal volume, which is proportional to the fluorescence signal. We find good agreement between the theoretical results and the experimental data, showing that such data can be used to get further insight into the effective focal volume during filamentation of femtosecond laser pulses in transparent media.

  12. Intermediate filament: structure, function, and applications in cytology.

    PubMed

    Dey, Pranab; Togra, Jyoti; Mitra, Suvradeep

    2014-07-01

    Intermediate filament (IF) constitutes an important cytoskeletal component in nearly all the vertebrate cells. IFs are present both in the cytoplasm and in the nucleus. They play an important role in providing mechanical strength of the cell and tissue, growth and regeneration, cell survival and apoptosis, and finally cell migration. IFs are also expressed differentially in different body tissues. Therefore, judicious use of IF may provide the diagnosis and confirmation of different malignancies. This is particularly helpful in the diagnosis of metastatic malignant tumor from an unknown primary. Expression of IFs particularly cytokeratin and vimentin is also related to prognosis of tumors. In this review, we have discussed the basic structure, dynamics, distribution of IF in cells, and its role in diagnosis of cytology. Possible prognostic roles of IF are also discussed.

  13. Plasticity in PYD assembly revealed by cryo-EM structure of the PYD filament of AIM2

    PubMed Central

    Lu, Alvin; Li, Yang; Yin, Qian; Ruan, Jianbin; Yu, Xiong; Egelman, Edward; Wu, Hao

    2015-01-01

    Absent in melanoma 2 (AIM2) is an essential cytosolic double-stranded DNA receptor that assembles with the adaptor, apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC), and caspase-1 to form the AIM2 inflammasome, which leads to proteolytic maturation of cytokines and pyroptotic cell death. AIM2 contains an N-terminal Pyrin domain (PYD) that interacts with ASC through PYD/PYD interactions and nucleates ASCPYD filament formation. To elucidate the molecular basis of AIM2-induced ASCPYD polymerization, we generated AIM2PYD filaments fused to green fluorescent protein (GFP) and determined its cryo-electron microscopic (cryo-EM) structure. The map showed distinct definition of helices, allowing fitting of the crystal structure. Surprisingly, the GFP-AIM2PYD filament is a 1-start helix with helical parameters distinct from those of the 3-start ASCPYD filament. However, despite the apparent symmetry difference, helical net and detailed interface analyses reveal minimal changes in subunit packing. GFP-AIM2PYD nucleated ASCPYD filament formation in comparable efficiency as untagged AIM2PYD, suggesting assembly plasticity in both AIM2PYD and ASCPYD. The DNA-binding domain of AIM2 is able to form AIM2/DNA filaments, within which the AIM2PYD is brought into proximity to template ASCPYD filament assembly. Because ASC is able to interact with many PYD-containing receptors for the formation of inflammasomes, the observed structural plasticity may be critically important for this versatility in the PYD/PYD interactions. PMID:26583071

  14. Inclusion of polyaniline filaments in zeolite molecular sieves

    SciTech Connect

    Enzel, P.; Bein, T. )

    1989-08-24

    Polyaniline has been synthesized in the channels of mordenite (one-dimensional) and zeolite Y (three-dimensional). Aniline was diffused from hexane solution into dehydrated zeolite pores containing different concentrations of framework hydroxyl groups. Addition of (NH{sub 4}){sub 2}S{sub 2}O{sub 8} to an aqueous suspension of the loaded zeolites afforded intrazeolite polyaniline chains, as demonstrated by FTIR, electronic absorption data, and recovery of the included polymer. Stoichiometric, kinetic, XPS, and microscopic data and the absence of bulk conductivity of the polymer/zeolite powders lead to the conclusion that the polymer is formed inside the host channel system. While the polyaniline chains in mordenite channels appear to be more highly oxidized than in Y zeolite, both systems show spectroscopic features typical of emeraldine base and emeraldine salt polymers. The polyaniline/zeolite hybrids represent a new class of materials containing synthetic conductors encapsulated in crystalline inorganic hosts with channel systems of molecular dimensions.

  15. Ultrasonic analysis of Kevlar-epoxy filament wound structures

    SciTech Connect

    Brosey, W.D.

    1985-07-16

    Composite structures are often desirable for their strength and weight characteristics. Since composites are not as well characterized mechanically as metallic or ceramic structures, much work has been performed at the Oak Ridge Y-12 Plant to obtain that characterization and to develop methods of determining the mechanical properties of a composite nondestructively. Most of the work to date has been performed on nonenclosed structures. One notable exception has been the holographic evaluation of spherical Kevlar-epoxy composite pressure vessels. Several promising nondestructive evaluation techniques have been used to locate flaws and predict the integrity of the composite. Several of these include thermography, Moire interferometry, ultrasonic stress wave factor, ultrasonic C-scan image enhancement, radiography, and nuclear magnetic resonance. As a first step in this transfer and development of NDE techniques, known defects were placed within spherical Kevlar-epoxy, filament-wound test specimens to determine the extent to which they could be detected. These defects included Teflon shim-simulated delaminations, macrosphere-simulated voids, dry-band sets, variable tension, Kevlar 29 fiber instead of the higher strength Kevlar 40 fiber, and an alternate high-void-content winding pattern. Ultrasonic waveform analysis was performed in both the time and frequency domains to determine the detectability and locatability of structural flaws within the composite. Preparation has been made at Virginia Polytechnic Institute and State University and at the University of Delaware, to examine the specimens using various NDE techniques. This work is a compilation of interim project reports in partial fulfillment of the contracts between Virginia Polytechnic Institute and State University, the University of Delaware, and Y-12 Plant.

  16. Ultrasonic analysis of Kevlar-epoxy filament wound structures

    NASA Astrophysics Data System (ADS)

    Brosey, W. D.

    1985-07-01

    Composite structures are often desirable for their strength and weight characteristics. Since composites are not as well characterized mechanically as metallic or ceramic structures, much work has been performed at the Oak Ridge Y-12 Plant to obtain that characterization and to develop methods of determining the mechanical properties of a composite nondestructively. Most of the work to date has been performed on nonenclosed structures. One notable exception has been the holographic evaluation of spherical Kevlar-epoxy composite pressure vessels. Several promising nondestructive evaluation techniques have been used to locate flaws and predict the integrity of the composite. Several of these include thermography, Moire interferometry, ultrasonic stress wave factor, ultrasonic C-scan image enhancement, radiography, and nuclear magnetic resonance. As a first step in this transfer and development of NDE techniques, known defects were placed within spherical Kevlar-epoxy, filament-wound test specimens to determine the extent to which they could be detected. These defects included Teflon shim-simulated delaminations, macrosphere-simulated voids, dry-band sets, variable tension, Kevlar 29 fiber instead of the higher strength Kevlar 40 fiber, and an alternate high-void-content winding pattern. Ultrasonic waveform analysis was performed in both the time and frequency domains to determine the detectability and locatability of structural flaws within the composite. Preparation has been made at Virginia Polytechnic Institute and State University and at the University of Delaware, to examine the specimens using various NDE techniques. This work is a compilation of interim project reports in partial fulfillment of the contracts between Virginia Polytechnic Institute and State University, the University of Delaware, and Y-12 Plant.

  17. Zebrafish cardiac muscle thick filaments: isolation technique and three-dimensional structure.

    PubMed

    González-Solá, Maryví; Al-Khayat, Hind A; Behra, Martine; Kensler, Robert W

    2014-04-15

    To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes.

  18. Zebrafish Cardiac Muscle Thick Filaments: Isolation Technique and Three-Dimensional Structure

    PubMed Central

    González-Solá, Maryví; AL-Khayat, Hind A.; Behra, Martine; Kensler, Robert W.

    2014-01-01

    To understand how mutations in thick filament proteins such as cardiac myosin binding protein-C or titin, cause familial hypertrophic cardiomyopathies, it is important to determine the structure of the cardiac thick filament. Techniques for the genetic manipulation of the zebrafish are well established and it has become a major model for the study of the cardiovascular system. Our goal is to develop zebrafish as an alternative system to the mammalian heart model for the study of the structure of the cardiac thick filaments and the proteins that form it. We have successfully isolated thick filaments from zebrafish cardiac muscle, using a procedure similar to those for mammalian heart, and analyzed their structure by negative-staining and electron microscopy. The isolated filaments appear well ordered with the characteristic 42.9 nm quasi-helical repeat of the myosin heads expected from x-ray diffraction. We have performed single particle image analysis on the collected electron microscopy images for the C-zone region of these filaments and obtained a three-dimensional reconstruction at 3.5 nm resolution. This reconstruction reveals structure similar to the mammalian thick filament, and demonstrates that zebrafish may provide a useful model for the study of the changes in the cardiac thick filament associated with disease processes. PMID:24739166

  19. Shocks, Superbubbles, and Filaments: Investigations into Large Scale Gas Motions in Giant Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Pon, Andrew Richard

    2013-12-01

    Giant molecular clouds (GMCs), out of which stars form, are complex, dynamic systems, which both influence and are shaped by the process of star formation. In this dissertation, I examine three different facets of the dynamical motions within GMCs. Collapse modes in different dimensional objects. Molecular clouds contain lower dimensional substructures, such as filaments and sheets. The collapse properties of finite filaments and sheets differ from those of spherical objects as well as infinite sheets and filaments. I examine the importance of local collapse modes of small central perturbations, relative to global collapse modes, in different dimensional objects to elucidate whether strong perturbations are required for molecular clouds to fragment to form stars. I also calculate the dependence of the global collapse timescale upon the aspect ratio of sheets and filaments. I find that lower dimensional objects are more readily fragmented, and that for a constant density, lower dimensional objects and clouds with larger aspect ratios collapse more slowly. An edge-driven collapse mode also exists in sheets and filaments and is most important in elongated filaments. The failure to consider the geometry of a gas cloud is shown to lead to an overestimation of the star formation rate by up to an order of magnitude. Molecular tracers of turbulent energy dissipation. Molecular clouds contain supersonic turbulence that simulations predict will decay rapidly via shocks. I use shock models to predict which species emit the majority of the turbulent energy dissipated in shocks and find that carbon monoxide, CO, is primarily responsible for radiating away this energy. By combining these shock models with estimates for the turbulent energy dissipation rate of molecular clouds, I predict the expected shock spectra of CO from molecular clouds. I compare the results of these shock models to predictions for the emission from the unshocked gas in GMCs and show that mid

  20. Molecular biology of demosponge axial filaments and their roles in biosilicification.

    PubMed

    Weaver, James C; Morse, Daniel E

    2003-11-01

    For hundreds of years, the skeletal elements of marine and freshwater sponges have intrigued investigators with a diverse array of remarkably complex morphologies. Early studies of demosponge monaxonal megascleres revealed the presence of a central organic axial filament running their entire length. Until recently, however, the precise function of these axial filaments was largely unknown. The spicules from the temperate Eastern Pacific demosponge, Tethya aurantia, comprise approximately 75% of the dry weight of this species, facilitating the large-scale isolation and purification of the biosilica-associated proteins. Silicateins, the most abundant proteins comprising the axial filaments of these spicules, prove to be members of a well-known superfamily of proteolytic and hydrolytic enzymes and can be easily collected after silica demineralization with hydrofluoric acid. Consistent with these findings, the intact filaments are more than simple, passive templates; in vitro, they actively catalyze and spatially direct the hydrolysis and polycondensation of silicon alkoxides to yield silica at neutral pH and low temperature. Catalytic activity also is exhibited by the monomeric subunits obtained by disaggregation of the protein filaments and those produced from recombinant DNA templates cloned in bacteria. These proteins also can be used to direct the polymerization of organosilicon polymers (silicones) from the corresponding organically functionalized silicon alkoxides. Based on these observations, the silicateins are currently being used as models for the design of biomimetic agents with unique catalytic and structure-directing properties. The presence of axial filaments in a diversity of spicule types and the evolutionary implications of these findings are also discussed.

  1. Frealix: Model-based refinement of helical filament structures from electron micrographs

    PubMed Central

    Rohou, Alexis; Grigorieff, Nikolaus

    2014-01-01

    The structures of many helical protein filaments can be derived from electron micrographs of their suspensions in thin films of vitrified aqueous solutions. The most successful and generally-applicable approach treats short segments of these filaments as independent “single particles”, yielding near-atomic resolution for rigid and well-ordered filaments. The single-particle approach can also accommodate filament deformations, yielding sub-nanometer resolution for more flexible filaments. However, in the case of thin and flexible filaments, such as some amyloid-β (Aβ) fibrils, the single-particle approach may fail because helical segments can be curved or otherwise distorted and their alignment can be inaccurate due to low contrast in the micrographs. We developed new software called Frealix that allows the use of arbitrarily short filament segments during alignment to approximate even high curvatures. All segments in a filament are aligned simultaneously with constraints that ensure that they connect to each other in space to form a continuous helical structure. In this paper, we describe the algorithm and benchmark it against datasets of Aβ(1–40) fibrils and tobacco mosaic virus (TMV), both analyzed in earlier work. In the case of TMV, our algorithm achieves similar results to single-particle analysis. In the case of Aβ(1–40) fibrils, we match the previously-obtained resolution but we are also able to obtain reliable alignments and ~8-Å reconstructions from curved filaments. Our algorithm also offers a detailed characterization of filament deformations in three dimensions and enables a critical evaluation of the worm-like chain model for biological filaments. PMID:24657230

  2. Purified thick filaments from the nematode Caenorhabditis elegans: evidence for multiple proteins associated with core structures

    PubMed Central

    1988-01-01

    The thick filaments of the nematode, Caenorhabditis elegans, arising predominantly from the body-wall muscles, contain two myosin isoforms and paramyosin as their major proteins. The two myosins are located in distinct regions of the surfaces, while paramyosin is located within the backbones of the filaments. Tubular structures constitute the cores of the polar regions, and electron-dense material is present in the cores of the central regions (Epstein, H.F., D.M. Miller, I. Ortiz, and G.C. Berliner. 1985. J. Cell Biol. 100:904-915). Biochemical, genetic, and immunological experiments indicate that the two myosins and paramyosin are not necessary core components (Epstein, H.F., I. Ortiz, and L.A. Traeger Mackinnon. 1986. J. Cell Biol. 103:985-993). The existence of the core structures suggests, therefore, that additional proteins may be associated with thick filaments in C. elegans. To biochemically detect minor associated proteins, a new procedure for the isolation of thick filaments of high purity and structural preservation has been developed. The final step, glycerol gradient centrifugation, yielded fractions that are contaminated by, at most, 1-2% with actin, tropomyosin, or ribosome-associated proteins on the basis of Coomassie Blue staining and electron microscopy. Silver staining and radioautography of gel electrophoretograms of unlabeled and 35S-labeled proteins, respectively, revealed at least 10 additional bands that cosedimented with thick filaments in glycerol gradients. Core structures prepared from wild-type thick filaments contained at least six of these thick filament-associated protein bands. The six proteins also cosedimented with thick filaments purified by gradient centrifugation from CB190 mutants lacking myosin heavy chain B and from CB1214 mutants lacking paramyosin. For these reasons, we propose that the six associated proteins are potential candidates for putative components of core structures in the thick filaments of body-wall muscles of

  3. Discovery of a pre-existing molecular filament associated with supernova remnant G127.1+0.5

    SciTech Connect

    Zhou, Xin; Yang, Ji; Fang, Min; Su, Yang

    2014-08-20

    We performed millimeter observations in CO lines toward the supernova remnant (SNR) G127.1+0.5. We found a molecular filament at 4-13 km s{sup –1} consisting of two distinct parts: a straight part coming out of the remnant region and a curved part in the remnant region. The curved part is coincides well with the bright SNR shell detected in 1420 MHz radio continuum and mid-infrared observations in the northeastern region. In addition, redshifted line wing broadening is found only in the curved part of the molecular filament, which indicates a physical interaction. These provide strong evidences, for the first time, to confirm the association between an SNR and a pre-existing long molecular filament. Multi-band observations in the northeastern remnant shell could be explained by the interaction between the remnant shock and the dense molecular filament. RADEX radiative transfer modeling of the quiet and shocked components yield physical conditions consistent with the passage of a non-dissociative J-type shock. We argue that the curved part of the filament is fully engulfed by the remnant's forward shock. A spatial correlation between aggregated young stellar objects (YSOs) and the adjacent molecular filament close to the SNR is also found, which could be related to the progenitor's activity.

  4. The missing link: Tracing molecular gas in the outer filament of Centaurus A

    NASA Astrophysics Data System (ADS)

    Morganti, Raffaella; Oosterloo, Tom; Oonk, J. B. Raymond; Santoro, Francesco; Tadhunter, Clive

    2016-08-01

    We report the detection, using observations of the CO(2-1) line performed with the Atacama Pathfinder EXperiment (APEX), of molecular gas in the region of the outer filament of Centaurus A, a complex region known to show various signatures of an interaction between the radio jet, an H i cloud, and ionised gas filaments. We detect CO(2-1) at all observed locations, which were selected to represent regions with very different physical conditions. The H2 masses of the detections range between 0.2 × 106 and 1.1 × 106M⊙, for conservative choices of the CO to H2 conversion factor. Surprisingly, the stronger detections are not coincident with the H i cloud, but instead are in the region of the ionised filaments. We also find variations in the widths of the CO(2-1) lines throughout the region, with broader lines in the region of the ionised gas, i.e. where the jet-cloud interaction is strongest, and with narrow profiles in the H i cloud. This may indicate that the molecular gas in the region of the ionised gas has the momentum of the jet-cloud interaction encoded in it, in the same way as the ionised gas does. These molecular clouds may therefore be the result of very efficient cooling of the down-stream gas photo- or shock-ionised by the interaction. On the other hand, the molecular clouds with narrower profiles, which are closer to or inside the H i cloud, could be pre-existing cold H2 cores which manage to survive the effects of the passing jet.

  5. Structure determination of helical filaments by solid-state NMR spectroscopy

    PubMed Central

    Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

    2016-01-01

    The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVSCARD filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers. PMID:26733681

  6. Structure determination of helical filaments by solid-state NMR spectroscopy.

    PubMed

    He, Lichun; Bardiaux, Benjamin; Ahmed, Mumdooh; Spehr, Johannes; König, Renate; Lünsdorf, Heinrich; Rand, Ulfert; Lührs, Thorsten; Ritter, Christiane

    2016-01-19

    The controlled formation of filamentous protein complexes plays a crucial role in many biological systems and represents an emerging paradigm in signal transduction. The mitochondrial antiviral signaling protein (MAVS) is a central signal transduction hub in innate immunity that is activated by a receptor-induced conversion into helical superstructures (filaments) assembled from its globular caspase activation and recruitment domain. Solid-state NMR (ssNMR) spectroscopy has become one of the most powerful techniques for atomic resolution structures of protein fibrils. However, for helical filaments, the determination of the correct symmetry parameters has remained a significant hurdle for any structural technique and could thus far not be precisely derived from ssNMR data. Here, we solved the atomic resolution structure of helical MAVS(CARD) filaments exclusively from ssNMR data. We present a generally applicable approach that systematically explores the helical symmetry space by efficient modeling of the helical structure restrained by interprotomer ssNMR distance restraints. Together with classical automated NMR structure calculation, this allowed us to faithfully determine the symmetry that defines the entire assembly. To validate our structure, we probed the protomer arrangement by solvent paramagnetic resonance enhancement, analysis of chemical shift differences relative to the solution NMR structure of the monomer, and mutagenesis. We provide detailed information on the atomic contacts that determine filament stability and describe mechanistic details on the formation of signaling-competent MAVS filaments from inactive monomers.

  7. The Small Heat Shock Protein Hsp27 Affects Assembly Dynamics and Structure of Keratin Intermediate Filament Networks

    PubMed Central

    Kayser, Jona; Haslbeck, Martin; Dempfle, Lisa; Krause, Maike; Grashoff, Carsten; Buchner, Johannes; Herrmann, Harald; Bausch, Andreas R.

    2013-01-01

    The mechanical properties of living cells are essential for many processes. They are defined by the cytoskeleton, a composite network of protein fibers. Thus, the precise control of its architecture is of paramount importance. Our knowledge about the molecular and physical mechanisms defining the network structure remains scarce, especially for the intermediate filament cytoskeleton. Here, we investigate the effect of small heat shock proteins on the keratin 8/18 intermediate filament cytoskeleton using a well-controlled model system of reconstituted keratin networks. We demonstrate that Hsp27 severely alters the structure of such networks by changing their assembly dynamics. Furthermore, the C-terminal tail domain of keratin 8 is shown to be essential for this effect. Combining results from fluorescence and electron microscopy with data from analytical ultracentrifugation reveals the crucial role of kinetic trapping in keratin network formation. PMID:24138853

  8. Desmin: molecular interactions and putative functions of the muscle intermediate filament protein.

    PubMed

    Costa, M L; Escaleira, R; Cataldo, A; Oliveira, F; Mermelstein, C S

    2004-12-01

    Desmin is the intermediate filament (IF) protein occurring exclusively in muscle and endothelial cells. There are other IF proteins in muscle such as nestin, peripherin, and vimentin, besides the ubiquitous lamins, but they are not unique to muscle. Desmin was purified in 1977, the desmin gene was characterized in 1989, and knock-out animals were generated in 1996. Several isoforms have been described. Desmin IFs are present throughout smooth, cardiac and skeletal muscle cells, but can be more concentrated in some particular structures, such as dense bodies, around the nuclei, around the Z-line or in costameres. Desmin is up-regulated in muscle-derived cellular adaptations, including conductive fibers in the heart, electric organs, some myopathies, and experimental treatments with drugs that induce muscle degeneration, like phorbol esters. Many molecules have been reported to associate with desmin, such as other IF proteins (including members of the membrane dystroglycan complex), nebulin, the actin and tubulin binding protein plectin, the molecular motor dynein, the gene regulatory protein MyoD, DNA, the chaperone alphaB-crystallin, and proteases such as calpain and caspase. Desmin has an important medical role, since it is used as a marker of tumors' origin. More recently, several myopathies have been described, with accumulation of desmin deposits. Yet, after almost 30 years since its identification, the function of desmin is still unclear. Suggested functions include myofibrillogenesis, mechanical support for the muscle, mitochondrial localization, gene expression regulation, and intracellular signaling. This review focuses on the biochemical interactions of desmin, with a discussion of its putative functions.

  9. THE FORMATION AND MAGNETIC STRUCTURES OF ACTIVE-REGION FILAMENTS OBSERVED BY NVST, SDO, AND HINODE

    SciTech Connect

    Yan, X. L.; Xue, Z. K.; Wang, J. C.; Xiang, Y. Y.; Kong, D. F.; Yang, L. H.; Pan, G. M.

    2015-08-15

    To better understand the properties of solar active-region filaments, we present a detailed study on the formation and magnetic structures of two active-region filaments in active region NOAA 11884 during a period of four days. It is found that the shearing motion of the opposite magnetic polarities and the rotation of the small sunspots with negative polarity play an important role in the formation of two active-region filaments. During the formation of these two active-region filaments, one foot of the filaments was rooted in a small sunspot with negative polarity. The small sunspot rotated not only around another small sunspot with negative polarity, but also around the center of its umbra. By analyzing the nonlinear force-free field extrapolation using the vector magnetic fields in the photosphere, twisted structures were found in the two active-region filaments prior to their eruptions. These results imply that the magnetic fields were dragged by the shearing motion between opposite magnetic polarities and became more horizontal. The sunspot rotation twisted the horizontal magnetic fields and finally formed the twisted active-region filaments.

  10. Molecular transformation, gene cloning, and gene expression systems for filamentous fungi

    USGS Publications Warehouse

    Gold, Scott E.; Duick, John W.; Redman, Regina S.; Rodriguez, Rusty J.

    2001-01-01

    This chapter discusses the molecular transformation, gene cloning, and gene expression systems for filamentous fungi. Molecular transformation involves the movement of discrete amounts of DNA into cells, the expression of genes on the transported DNA, and the sustainable replication of the transforming DNA. The ability to transform fungi is dependent on the stable replication and expression of genes located on the transforming DNA. Three phenomena observed in bacteria, that is, competence, plasmids, and restriction enzymes to facilitate cloning, were responsible for the development of molecular transformation in fungi. Initial transformation success with filamentous fungi, involving the complementation of auxotrophic mutants by exposure to sheared genomic DNA or RNA from wt isolates, occurred with low transformation efficiencies. In addition, it was difficult to retrieve complementing DNA fragments and isolate genes of interest. This prompted the development of transformation vectors and methods to increase efficiencies. The physiological studies performed with fungi indicated that the cell wall could be removed to generate protoplasts. It was evident that protoplasts could be transformed with significantly greater efficiencies than walled cells.

  11. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments.

    PubMed

    Calvaresi, Matteo; Eckhart, Leopold; Alibardi, Lorenzo

    2016-06-01

    The hard corneous material of avian and reptilian scales, claws, beak and feathers is mainly derived from the presence of proteins formerly known as beta-keratins but now termed Corneous beta-proteins of sauropsids to distinguish them from keratins, which are members of the intermediate filament protein family. The modeling of the conserved 34 amino acid residues long central beta-sheet region of Corneous beta-proteins using an ab initio protein folding and structure prediction algorithm indicates that this region is formed by four antiparallel beta-sheets. Molecular dynamic simulations and Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) analysis showed that the disposition of polar and apolar amino acids within the beta-region gives rise to an amphipathic core whose stability is further increased, especially in an aqueous environment, by the association into a dimer due to apolar interactions and specific amino-acid interactions. The dimers in turn polymerize into a 3nm thick linear beta-filament due to van der Waals and hydrogen-bond interactions. It is suggested that once this nuclear core of anti-parallel sheets evolved in the genome of a reptilian ancestor of the extant reptiles and birds about 300 millions years ago, new properties emerged in the corneous material forming scales, claws, beaks and feathers in these amniotes based on the tendency of these unique corneous proteins to form stable filaments different from keratin intermediate filaments or sterical structures formed by other corneous proteins so far known.

  12. Slender Vortex Filament with Slowly Varying Core Structure

    NASA Technical Reports Server (NTRS)

    Ting, Lu; Tung, Chee

    2000-01-01

    We give a brief review of the asymptotic theory of slender vortex filaments with emphases on the choices of scalings characterizing the physical problems and the corresponding assumptions and/or restrictions introduced in the formation of the asymptotic theory of Callegari and Ting (1978) and its extension by Klein and Ting (1992). In particular, the slender filaments considered are assumed to be forming loops or tori. Because of this restriction, the theory is not applicable to the trailing vortex system of a rotorcraft. We describe the multiple length scales characterizing the vortex system, formulate the expansion scheme, derive the governing equations and then identify the assumptions or restrictions inherent in the multi-scale analysis and needed for the validity of the asymptotic theory of the trailing vortex system.

  13. Thin Filament Structure and the Steric Blocking Model.

    PubMed

    Lehman, William

    2016-04-01

    By interacting with the troponin-tropomyosin complex on myofibrillar thin filaments, Ca2+ and myosin govern the regulatory switching processes influencing contractile activity of mammalian cardiac and skeletal muscles. A possible explanation of the roles played by Ca2+ and myosin emerged in the early 1970s when a compelling "steric model" began to gain traction as a likely mechanism accounting for muscle regulation. In its most simple form, the model holds that, under the control of Ca2+ binding to troponin and myosin binding to actin, tropomyosin strands running along thin filaments either block myosin-binding sites on actin when muscles are relaxed or move away from them when muscles are activated. Evidence for the steric model was initially based on interpretation of subtle changes observed in X-ray fiber diffraction patterns of intact skeletal muscle preparations. Over the past 25 years, electron microscopy coupled with three-dimensional reconstruction directly resolved thin filament organization under many experimental conditions and at increasingly higher resolution. At low-Ca2+, tropomyosin was shown to occupy a "blocked-state" position on the filament, and switched-on in a two-step process, involving first a movement of tropomyosin away from the majority of the myosin-binding site as Ca2+ binds to troponin and then a further movement to fully expose the site when small numbers of myosin heads bind to actin. In this contribution, basic information on Ca2+-regulation of muscle contraction is provided. A description is then given relating the voyage of discovery taken to arrive at the present understanding of the steric regulatory model. PMID:27065174

  14. The identification of filaments on far-infrared and submillimiter images: Morphology, physical conditions and relation with star formation of filamentary structure

    SciTech Connect

    Schisano, E.; Carey, S.; Paladini, R.; Rygl, K. L. J.; Molinari, S.; Elia, D.; Pestalozzi, M.; Busquet, G.; Billot, N.; Noriega-Crespo, A.; Moore, T. J. T.; Plume, R.; Glover, S. C. O.; Vázquez-Semadeni, E.

    2014-08-10

    Observations of molecular clouds reveal a complex structure, with gas and dust often arranged in filamentary, rather than spherical geometries. The association of pre- and proto-stellar cores with the filaments suggests a direct link with the process of star formation. Any study of the properties of such filaments requires representative samples from different environments for an unbiased detection method. We developed such an approach using the Hessian matrix of a surface-brightness distribution to identify filaments and determine their physical and morphological properties. After testing the method on simulated, but realistic, filaments, we apply the algorithms to column-density maps computed from Herschel observations of the Galactic plane obtained by the Hi-GAL project. We identified ∼500 filaments, in the longitude range of l = 216.°5 to l = 225.°5, with lengths from ∼1 pc up to ∼30 pc and widths between 0.1 pc and 2.5 pc. Average column densities are between 10{sup 20} cm{sup –2} and 10{sup 22} cm{sup –2}. Filaments include the majority of dense material with N{sub H{sub 2}} > 6 × 10{sup 21} cm{sup –2}. We find that the pre- and proto-stellar compact sources already identified in the same region are mostly associated with filaments. However, surface densities in excess of the expected critical values for high-mass star formation are only found on the filaments, indicating that these structures are necessary to channel material into the clumps. Furthermore, we analyze the gravitational stability of filaments and discuss their relationship with star formation.

  15. Filament-Level Modeling of Aramid-Based High-Performance Structural Materials

    NASA Astrophysics Data System (ADS)

    Grujicic, M.; Bell, W. C.; Glomski, P. S.; Pandurangan, B.; Yen, C.-F.; Cheeseman, B. A.

    2011-11-01

    Molecular statics and molecular dynamics are employed to study the effects of various microstructural and topological defects (e.g., chain ends, axial chain misalignment, inorganic solvent impurities, and sheet stacking faults) on the strength, ductility, and stiffness of p-phenylene terephthalamide (PPTA) fibers/filaments. These fibers can be considered as prototypes for advanced high strength/high-stiffness fibers like Kevlar®, Twaron®, New Star®, etc. While modeling these fibers, it was taken into account that they are essentially crystalline materials consisting of stacks of sheets, with each sheet containing an array of nearly parallel hydrogen-bonded molecules/chains. The inter-sheet bonding, on the other hand, was considered as mainly being of van der Waals or p-electron character. The effects of various deviations of the PPTA fiber structure from that of the perfectly crystalline structure (i.e., microstructural/topological defects) on the material's mechanical properties are then considered. The results obtained show that while the presence of these defects decreases all the mechanical properties of PPTA fibers, specific properties display an increased level of sensitivity to the presence of certain defects. For example, longitudinal tensile properties are found to be most sensitive to the presence of chain ends, in-sheet transverse properties to the presence of chain misalignments, while cross-sheet transverse properties are found to be most affected by the presence of sheet stacking faults.

  16. Understanding molecular structure from molecular mechanics.

    PubMed

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  17. Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament

    PubMed Central

    Lee, Mina; Lipfert, Jan; Sanchez, Humberto; Wyman, Claire; Dekker, Nynke H.

    2013-01-01

    Human RAD51 is a key protein in the repair of DNA by homologous recombination. Its assembly onto DNA, which induces changes in DNA structure, results in the formation of a nucleoprotein filament that forms the basis of strand exchange. Here, we determine the structural and mechanical properties of RAD51-dsDNA filaments. Our measurements use two recently developed magnetic tweezers assays, freely orbiting magnetic tweezers and magnetic torque tweezers, designed to measure the twist and torque of individual molecules. By directly monitoring changes in DNA twist on RAD51 binding, we determine the unwinding angle per RAD51 monomer to be 45°, in quantitative agreement with that of its bacterial homolog, RecA. Measurements of the torque that is built up when RAD51-dsDNA filaments are twisted show that under conditions that suppress ATP hydrolysis the torsional persistence length of the RAD51-dsDNA filament exceeds that of its RecA counterpart by a factor of three. Examination of the filament’s torsional stiffness for different combinations of divalent ions and nucleotide cofactors reveals that the Ca2+ ion, apart from suppressing ATPase activity, plays a key role in increasing the torsional stiffness of the filament. These quantitative measurements of RAD51-imposed DNA distortions and accumulated mechanical stress suggest a finely tuned interplay between chemical and mechanical interactions within the RAD51 nucleoprotein filament. PMID:23703213

  18. Swirling around filaments: are large-scale structure vortices spinning up dark haloes?

    NASA Astrophysics Data System (ADS)

    Laigle, C.; Pichon, C.; Codis, S.; Dubois, Y.; Le Borgne, D.; Pogosyan, D.; Devriendt, J.; Peirani, S.; Prunet, S.; Rouberol, S.; Slyz, A.; Sousbie, T.

    2015-01-01

    The kinematic analysis of dark matter and hydrodynamical simulations suggests that the vorticity in large-scale structure is mostly confined to, and predominantly aligned with, their filaments, with an excess of probability of 20 per cent to have the angle between vorticity and filaments direction lower than 60° relative to random orientations. The cross-sections of these filaments are typically partitioned into four quadrants with opposite vorticity sign, arising from multiple flows, originating from neighbouring walls. The spins of haloes embedded within these filaments are consistently aligned with this vorticity for any halo mass, with a stronger alignment for the most massive structures up to an excess of probability of 165 per cent. The global geometry of the flow within the cosmic web is therefore qualitatively consistent with a spin acquisition for smaller haloes induced by this large-scale coherence, as argued in Codis et al. In effect, secondary anisotropic infall (originating from the vortex-rich filament within which these lower-mass haloes form) dominates the angular momentum budget of these haloes. The transition mass from alignment to orthogonality is related to the size of a given multi-flow region with a given polarity. This transition may be reconciled with the standard tidal torque theory if the latter is augmented so as to account for the larger scale anisotropic environment of walls and filaments.

  19. Monitoring the integrity of filament-wound structures using built-in sensor networks

    NASA Astrophysics Data System (ADS)

    Lin, Mark; Kumar, Amrita; Qing, Xinlin; Beard, Shawn J.; Russell, Samuel S.; Walker, James L.; Delay, Thomas K.

    2003-08-01

    Monitoring the integrity of filament wound composite structures such as solid rocket motors and liquid fuel bottles is important in order to prevent catastrophic failures and to prolong the service life of these structures. To ensure the safety and reliability of rocket components, they require frequent inspection for structural damages that might have occurred during manufacturing, transportation, and storage. The timely and accurate detection, characterization and monitoring of structural cracking, delamination, debonding and other types of damage is a major concern in the operational environment. Utilization of a sensor network system integrated with the structure itself can greatly reduce this inspection burden through fast in-situ data collection and processing. Acellent Technologies, Inc. is currently developing integrated structural monitoring tools for continuous monitoring of composite and metal structures on aircraft and spacecraft. Acellent's integrated structural monitoring system consists of a flexible sensor/actuator network layer called the SMART Layer, supporting diagnostic hardware, and data processing/analysis software. Recently, Acellent has been working with NASA Marshall Space Flight Center to develop ways of embedding the SMART Layer inside filament wound composite bottles. SMART Layers were designed and manufactured for the filament wound bottles and embedded in them during the filament winding process. Acellent has been working on developing a complete structural health monitoring system for the filament wound bottles including data processing tools to interpret the changes in sensor signal caused by changes in the structural condition or material property. A prototype of a filament wound composite bottle with an embedded sensor network has been fabricated and preliminary data analysis tools have been developed.

  20. Cryo-electron microscopy structure of human peroxiredoxin-3 filament reveals the assembly of a putative chaperone.

    PubMed

    Radjainia, Mazdak; Venugopal, Hariprasad; Desfosses, Ambroise; Phillips, Amy J; Yewdall, N Amy; Hampton, Mark B; Gerrard, Juliet A; Mitra, Alok K

    2015-05-01

    Peroxiredoxins (Prxs) are a ubiquitous class of thiol-dependent peroxidases that play an important role in the protection and response of cells to oxidative stress. The catalytic unit of typical 2-Cys Prxs are homodimers, which can self-associate to form complex assemblies that are hypothesized to have signaling and chaperone activity. Mitochondrial Prx3 forms dodecameric toroids, which can further stack to form filaments, the so-called high-molecular-weight (HMW) form that has putative holdase activity. We used single-particle analysis and helical processing of electron cryomicroscopy images of human Prx3 filaments induced by low pH to generate a ∼7-Å resolution 3D structure of the HMW form, the first such structure for a 2-Cys Prx. The pseudo-atomic model reveals interactions that promote the stacking of the toroids and shows that unlike previously reported data, the structure can accommodate a partially folded C terminus. The HMW filament lumen displays hydrophobic patches, which we hypothesize bestow holdase activity.

  1. FilFinder: Filamentary structure in molecular clouds

    NASA Astrophysics Data System (ADS)

    Koch, Eric W.; Rosolowsky, Erik W.

    2016-08-01

    FilFinder extracts and analyzes filamentary structure in molecular clouds. In particular, it is capable of uniformly extracting structure over a large dynamical range in intensity. It returns the main filament properties: local amplitude and background, width, length, orientation and curvature. FilFinder offers additional tools to, for example, create a filament-only image based on the properties of the radial fits. The resulting mask and skeletons may be saved in FITS format, and property tables may be saved as a CSV, FITS or LaTeX table.

  2. The dynamics of filamentous structures in the apical band, oral crescent, fission line and the postoral meridional filament in Tetrahymena thermophila revealed by monoclonal antibody 12G9.

    PubMed

    Jerka-Dziadosz, M; Strzyewska-Jówko, I; Wojsa-Lugowska, U; Krawczyńska, W; Krzywicka, A

    2001-05-01

    The ciliate Tetrahymena thermophila possesses a multitude of cytoskeletal structures whose differentiation is related to the basal bodies - the main mediators of the cortical pattern. This investigation deals with immunolocalization using light and electron microscopy of filaments labeled by the monoclonal antibody 12G9, which in other ciliates identifies filaments involved in transmission of cellular polarities and marks cell meridians with the highest morphogenetic potential. In Tetrahymena interphase cells, mAb 12G9 localizes to the sites of basal bodies and to the striated ciliary rootlets, to the apical band of filaments and to the fine fibrillar oral crescent. We followed the sequence of development of these structures during divisional morphogenesis. The labeling of the maternal oral crescent disappears in pre-metaphase cells and reappears during anaphase, concomitantly with differentiation of the new structure in the posterior daughter cell. In the posterior daughter cell, the new apical band originates as small clusters of filaments located at the base of the anterior basal bodies of the apical basal body couplets during early anaphase. The differentiation of the band is completed in the final stages of cytokinesis and in the young post-dividing cell. The maternal band is reorganized earlier, simultaneously with the oral structure. The mAb 12G9 identifies two transient structures present only in dividing cells. One is a medial structure demarcating the two daughter cells during metaphase and anaphase, and defining the new anterior border of the posterior daughter cell. The other is a post-oral meridional filament marking the stomatogenic meridian in postmetaphase cells. Comparative analysis of immunolocalization of transient filaments labeled with mAb12G9 in Tetrahymena and other ciliates indicates that this antibody identifies a protein bound to filamentous structures, which might play a role in relying polarities of cortical domains and could be a part

  3. The structural basis of actin filament branching by the Arp2/3 complex

    PubMed Central

    Rouiller, Isabelle; Xu, Xiao-Ping; Amann, Kurt J.; Egile, Coumaran; Nickell, Stephan; Nicastro, Daniela; Li, Rong; Pollard, Thomas D.; Volkmann, Niels; Hanein, Dorit

    2008-01-01

    The actin-related protein 2/3 (Arp2/3) complex mediates the formation of branched actin filaments at the leading edge of motile cells and in the comet tails moving certain intracellular pathogens. Crystal structures of the Arp2/3 complex are available, but the architecture of the junction formed by the Arp2/3 complex at the base of the branch was not known. In this study, we use electron tomography to reconstruct the branch junction with sufficient resolution to show how the Arp2/3 complex interacts with the mother filament. Our analysis reveals conformational changes in both the mother filament and Arp2/3 complex upon branch formation. The Arp2 and Arp3 subunits reorganize into a dimer, providing a short-pitch template for elongation of the daughter filament. Two subunits of the mother filament undergo conformational changes that increase stability of the branch. These data provide a rationale for why branch formation requires cooperative interactions among the Arp2/3 complex, nucleation-promoting factors, an actin monomer, and the mother filament. PMID:18316411

  4. The structural basis of actin filament branching by the Arp2/3 complex.

    PubMed

    Rouiller, Isabelle; Xu, Xiao-Ping; Amann, Kurt J; Egile, Coumaran; Nickell, Stephan; Nicastro, Daniela; Li, Rong; Pollard, Thomas D; Volkmann, Niels; Hanein, Dorit

    2008-03-10

    The actin-related protein 2/3 (Arp2/3) complex mediates the formation of branched actin filaments at the leading edge of motile cells and in the comet tails moving certain intracellular pathogens. Crystal structures of the Arp2/3 complex are available, but the architecture of the junction formed by the Arp2/3 complex at the base of the branch was not known. In this study, we use electron tomography to reconstruct the branch junction with sufficient resolution to show how the Arp2/3 complex interacts with the mother filament. Our analysis reveals conformational changes in both the mother filament and Arp2/3 complex upon branch formation. The Arp2 and Arp3 subunits reorganize into a dimer, providing a short-pitch template for elongation of the daughter filament. Two subunits of the mother filament undergo conformational changes that increase stability of the branch. These data provide a rationale for why branch formation requires cooperative interactions among the Arp2/3 complex, nucleation-promoting factors, an actin monomer, and the mother filament.

  5. Self-propelled worm-like filaments: spontaneous spiral formation, structure, and dynamics.

    PubMed

    Isele-Holder, Rolf E; Elgeti, Jens; Gompper, Gerhard

    2015-09-28

    Worm-like filaments that are propelled homogeneously along their tangent vector are studied by Brownian dynamics simulations. Systems in two dimensions are investigated, corresponding to filaments adsorbed to interfaces or surfaces. A large parameter space covering weak and strong propulsion, as well as flexible and stiff filaments is explored. For strongly propelled and flexible filaments, the free-swimming filaments spontaneously form stable spirals. The propulsion force has a strong impact on dynamic properties, such as the rotational and translational mean square displacement and the rate of conformational sampling. In particular, when the active self-propulsion dominates thermal diffusion, but is too weak for spiral formation, the rotational diffusion coefficient has an activity-induced contribution given by v(c)/ξ(P), where v(c) is the contour velocity and ξ(P) the persistence length. In contrast, structural properties are hardly affected by the activity of the system, as long as no spirals form. The model mimics common features of biological systems, such as microtubules and actin filaments on motility assays or slender bacteria, and artificially designed microswimmers. PMID:26256415

  6. Nanoscopic structural rearrangements of the Cu-filament in conductive-bridge memories.

    PubMed

    Celano, U; Giammaria, G; Goux, L; Belmonte, A; Jurczak, M; Vandervorst, W

    2016-07-21

    The electrochemical reactions triggering resistive switching in conductive-bridge resistive random access memory (CBRAM) are spatially confined in few tens of nm(3). The formation and dissolution of nanoscopic Cu-filaments rely on the displacement of ions in such confined volume, and it is driven by the electric field induced ion migration and nanoscaled redox reactions. The stochastic nature of these fundamental processes leads to a large variability of the device performance. In this work, a combination of two- and three-dimensional scanning probe microscopy (SPM) techniques are used to study the conductive filament (CF) formation, rupture and its nanoscopic structural rearrangements. The high spatial confinement of our approach enables to locally induce RS in a confined area and image it in 3D. A conical shape of the CF is consistently observed, indicating that the ion migration is the rate limiting step in the filament formation when using high quality dielectrics as switching layers. The sub-10 nm electrical contact size of the AFM tip is used to study the filament's dissolution and detect the hopping conduction of Cu during the CF rupture. We consistently observe a tunnel gap formation associated with the tip-induced filament reset. Finally, aiming to match the fundamental understanding with the integrated device operations, we apply scalpel SPM to failed memory cells and directly observe the appearance of filament multiplicity as a major source of failures and variability in CBRAM. PMID:27441315

  7. Carbon doping in molecular beam epitaxy of GaAs from a heated graphite filament

    NASA Technical Reports Server (NTRS)

    Malik, R. J.; Nottenberg, R. N.; Schubert, E. F.; Walker, J. F.; Ryan, R. W.

    1988-01-01

    Carbon doping of GaAs grown by molecular beam epitaxy has been obtained for the first time by use of a heated graphite filament. Controlled carbon acceptor concentrations over the range of 10 to the 17th-10 to the 20th/cu cm were achieved by resistively heating a graphite filament with a direct current power supply. Capacitance-voltage, p/n junction and secondary-ion mass spectrometry measurements indicate that there is negligible diffusion of carbon during growth and with postgrowth rapid thermal annealing. Carbon was used for p-type doping in the base of Npn AlGaAs/GaAs heterojunction bipolar transistors. Current gains greater than 100 and near-ideal emitter heterojunctions were obtained in transistors with a carbon base doping of 1 x 10 to the 19th/cu cm. These preliminary results indicate that carbon doping from a solid graphite source may be an attractive substitute for beryllium, which is known to have a relatively high diffusion coefficient in GaAs.

  8. Structural analysis and modeling reveals new mechanisms governing ESCRT-III spiral filament assembly.

    PubMed

    Shen, Qing-Tao; Schuh, Amber L; Zheng, Yuqing; Quinney, Kyle; Wang, Lei; Hanna, Michael; Mitchell, Julie C; Otegui, Marisa S; Ahlquist, Paul; Cui, Qiang; Audhya, Anjon

    2014-09-15

    The scission of biological membranes is facilitated by a variety of protein complexes that bind and manipulate lipid bilayers. ESCRT-III (endosomal sorting complex required for transport III) filaments mediate membrane scission during the ostensibly disparate processes of multivesicular endosome biogenesis, cytokinesis, and retroviral budding. However, mechanisms by which ESCRT-III subunits assemble into a polymer remain unknown. Using cryogenic electron microscopy (cryo-EM), we found that the full-length ESCRT-III subunit Vps32/CHMP4B spontaneously forms single-stranded spiral filaments. The resolution afforded by two-dimensional cryo-EM combined with molecular dynamics simulations revealed that individual Vps32/CHMP4B monomers within a filament are flexible and able to accommodate a range of bending angles. In contrast, the interface between monomers is stable and refractory to changes in conformation. We additionally found that the carboxyl terminus of Vps32/CHMP4B plays a key role in restricting the lateral association of filaments. Our findings highlight new mechanisms by which ESCRT-III filaments assemble to generate a unique polymer capable of membrane remodeling in multiple cellular contexts. PMID:25202029

  9. Dark Ribbons Propagating and Sweeping Across Extreme Ultraviolet Structures After Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Xiao, Junmin; Zhang, Jun; Li, Ting; Yang, Shuhong

    2015-05-01

    With observations from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory, we first report that dark ribbons (DRs) moved apart from the filament channel and swept across EUV structures after filament eruptions on 2013 June 23 and 2012 February 10 and 24, respectively. In the first event, the DR with a length of 168 Mm appeared at 100 Mm to the northwest of the filament channel, where the filament erupted 15 hr previously. The DR moved toward the northwest with the different sections having different velocities, ranging from 0.3 to 1.6 km s‑1. When the DR’s middle part swept across a strong EUV structure, the motion of this part was blocked, appearing to deflect the DR. With the DR propagation, the connection of the surrounding EUV structures gradually changed. After one day passed, the DR eventually disappeared. In the other two events, the dynamic evolution of the DRs was similar to that in the first event. Based on the observations, we speculate that the reconnection during the filament eruption changes the configuration of the surrounding magnetic fields systematically. During the reconnection process, magnetic fields are deflecting and the former arbitrarily distributed magnetic fields are rearranged along specific directions. The deflection of magnetic fields results in an instantaneous void region where the magnetic strength is smaller and the plasma density is lower. Consequently, the void region is observed as a DR and propagates outward with the reconnection developing.

  10. Dark Ribbons Propagating and Sweeping Across Extreme Ultraviolet Structures After Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Xiao, Junmin; Zhang, Jun; Li, Ting; Yang, Shuhong

    2015-05-01

    With observations from the Atmospheric Imaging Assembly on board the Solar Dynamics Observatory, we first report that dark ribbons (DRs) moved apart from the filament channel and swept across EUV structures after filament eruptions on 2013 June 23 and 2012 February 10 and 24, respectively. In the first event, the DR with a length of 168 Mm appeared at 100 Mm to the northwest of the filament channel, where the filament erupted 15 hr previously. The DR moved toward the northwest with the different sections having different velocities, ranging from 0.3 to 1.6 km s-1. When the DR’s middle part swept across a strong EUV structure, the motion of this part was blocked, appearing to deflect the DR. With the DR propagation, the connection of the surrounding EUV structures gradually changed. After one day passed, the DR eventually disappeared. In the other two events, the dynamic evolution of the DRs was similar to that in the first event. Based on the observations, we speculate that the reconnection during the filament eruption changes the configuration of the surrounding magnetic fields systematically. During the reconnection process, magnetic fields are deflecting and the former arbitrarily distributed magnetic fields are rearranged along specific directions. The deflection of magnetic fields results in an instantaneous void region where the magnetic strength is smaller and the plasma density is lower. Consequently, the void region is observed as a DR and propagates outward with the reconnection developing.

  11. Myosin filament sliding through the Z-disc relates striated muscle fibre structure to function.

    PubMed

    Rode, Christian; Siebert, Tobias; Tomalka, Andre; Blickhan, Reinhard

    2016-03-16

    Striated muscle contraction requires intricate interactions of microstructures. The classic textbook assumption that myosin filaments are compressed at the meshed Z-disc during striated muscle fibre contraction conflicts with experimental evidence. For example, myosin filaments are too stiff to be compressed sufficiently by the muscular force, and, unlike compressed springs, the muscle fibres do not restore their resting length after contractions to short lengths. Further, the dependence of a fibre's maximum contraction velocity on sarcomere length is unexplained to date. In this paper, we present a structurally consistent model of sarcomere contraction that reconciles these findings with the well-accepted sliding filament and crossbridge theories. The few required model parameters are taken from the literature or obtained from reasoning based on structural arguments. In our model, the transition from hexagonal to tetragonal actin filament arrangement near the Z-disc together with a thoughtful titin arrangement enables myosin filament sliding through the Z-disc. This sliding leads to swivelled crossbridges in the adjacent half-sarcomere that dampen contraction. With no fitting of parameters required, the model predicts straightforwardly the fibre's entire force-length behaviour and the dependence of the maximum contraction velocity on sarcomere length. Our model enables a structurally and functionally consistent view of the contractile machinery of the striated fibre with possible implications for muscle diseases and evolution.

  12. Monitoring intermediate filament assembly by small-angle x-ray scattering reveals the molecular architecture of assembly intermediates

    PubMed Central

    Sokolova, Anna V.; Kreplak, Laurent; Wedig, Tatjana; Mücke, Norbert; Svergun, Dmitri I.; Herrmann, Harald; Aebi, Ueli; Strelkov, Sergei V.

    2006-01-01

    Intermediate filaments (IFs), along with microtubules, microfilaments, and associated cross-bridging proteins, constitute the cytoskeleton of metazoan cells. While crystallographic data on the dimer representing the elementary IF “building block” have recently become available, little structural detail is known about both the mature IF architecture and its assembly pathway. Here, we have applied solution small-angle x-ray scattering to investigate the in vitro assembly of a 53-kDa human IF protein vimentin at pH 8.4 by systematically varying the ionic strength conditions, and complemented these experiments by electron microscopy and analytical ultracentrifugation. While a vimentin solution in 5 mM Tris·HCl (pH 8.4) contains predominantly tetramers, addition of 20 mM NaCl induces further lateral assembly evidenced by the shift of the sedimentation coeficient and yields a distinct octameric intermediate. Four octamers eventually associate into unit-length filaments (ULFs) that anneal longitudinally. Based on the small-angle x-ray scattering experiments supplemented by crystallographic data and additional structural constraints, 3D molecular models of the vimentin tetramer, octamer, and ULF were constructed. Within each of the three oligomers, the adjacent dimers are aligned exclusively in an approximately half-staggered antiparallel A11 mode with a distance of 3.2–3.4 nm between their axes. The ULF appears to be a dynamic and a relatively loosely packed structure with a roughly even mass distribution over its cross-section. PMID:17050693

  13. The structure of the archeabacterial flagellar filament of the extreme halophile Halobacterium salinarum R1M1 and its relation to eubacterial flagellar filaments and type IV pili.

    PubMed

    Cohen-Krausz, Sara; Trachtenberg, Shlomo

    2002-08-16

    Although the phenomenology and mechanics of swimming are very similar in eubacteria and archaeabacteria (e.g. reversible rotation, helical polymorphism of the filament and formation of bundles), the dynamic flagellar filaments seem completely unrelated in terms of morphogenesis, structure and amino acid composition. Archeabacterial flagellar filaments share important features with type IV pili, which are components of retractable linear motors involved in twitching motility and cell adhesion. The archeabacterial filament is unique in: (1) having a relatively smooth surface and a small diameter of approximately 100A as compared to approximately 240A of eubacterial filaments and approximately 50A of type IV pili; (2) being glycosylated and sulfated in a pattern similar to the S-layer; (3) being synthesized as pre-flagellin with a signal-peptide cleavable by membrane peptidases upon transport; and (4) having an N terminus highly hydrophobic and homologous with that of the olygomerization domain of pilin. The synthesis of archeabacterial flagellin monomers as pre-flagellin and their post-translational, extracellular glycosylation suggest a different mode of monomer transport and polymerization at the cell-proximal end of the filament, similar to pili rather than to eubacterial flagellar filaments. The polymerization mode and small diameter may indicate the absence of a central channel in the filament. Using low-electron-dose images of cryo-negative-stained filaments, we determined the unique symmetry of the flagellar filament of the extreme halophile Halobacterium salinarum strain R1M1 and calculated a three-dimensional density map to a resolution of 19A. The map is based on layer-lines of order n=0, +10, -7, +3, -4, +6, and -1. The cross-section of the density map has a triskelion shape and is dominated by seven outer densities clustered into three groups, which are connected by lower-density arms to a dense central core surrounded by a lower-density shell. There is

  14. Four-wave mixing in molecular gases under filamentation of the collimated femtosecond beam

    NASA Astrophysics Data System (ADS)

    Panov, N.; Kurilova, M.; Uryupina, D.; Volkov, M.; Mazhorova, A.; Volkov, R.; Kosareva, O.; Savel'ev, A.

    2014-12-01

    The four-wave mixing process during a single-color femtosecond filamentation in the molecular gas is observed experimentally. The role of the seed is represented by the self-shifted to infrared region Raman bullet and the new blue-shifted component burns up as a result of the interaction between the Raman bullet and the reservoir radiation. The blue-shifted component propagates along the beam axis. The theoretical analysis of the four-wave mixing process synchronism shows that the on-axis forward propagation of the blue-shifted component occurs when the plasma concentration is higher than a certain threshold (3.3  ×  1016 cm-3 at the fundamental wavelength of 800 nm).

  15. Structural characterization of a capping protein interaction motif defines a family of actin filament regulators

    PubMed Central

    Hernandez-Valladares, Maria; Kim, Taekyung; Kannan, Balakrishnan; Tung, Alvin; Aguda, Adeleke H; Larsson, Mårten; Cooper, John A; Robinson, Robert C

    2011-01-01

    Capping protein (CP) regulates actin dynamics by binding the barbed ends of actin filaments. Removal of CP may be one means to harness actin polymerization for processes such as cell movement and endocytosis. Here we structurally and biochemically investigated a CP interaction (CPI) motif present in the otherwise unrelated proteins CARMIL and CD2AP. The CPI motif wraps around the stalk of the mushroom-shaped CP at a site distant from the actin-binding interface, which lies on the top of the mushroom cap. We propose that the CPI motif may act as an allosteric modulator, restricting CP to a low-affinity, filament-binding conformation. Structure-based sequence alignments extend the CPI motif–containing family to include CIN85, CKIP-1, CapZIP and a relatively uncharacterized protein, WASHCAP (FAM21). Peptides comprising these CPI motifs are able to inhibit CP and to uncap CP-bound actin filaments. PMID:20357771

  16. Specific Transformation of Assembly with Actin Filaments and Molecular Motors in a Cell-Sized Self-Emerged Liposome

    NASA Astrophysics Data System (ADS)

    Takiguchi, Kingo; Negishi, Makiko; Tanaka-Takiguchi, Yohko; Hayashi, Masahito; Yoshikawa, Kenichi

    2014-12-01

    Eukaryotes, by the same combination of cytoskeleton and molecular motor, for example actin filament and myosin, can generate a variety of movements. For this diversity, the organization of biological machineries caused by the confinement and/or crowding effects of internal living cells, may play very important roles.

  17. Myosin light chain phosphorylation enhances contraction of heart muscle via structural changes in both thick and thin filaments.

    PubMed

    Kampourakis, Thomas; Sun, Yin-Biao; Irving, Malcolm

    2016-05-24

    Contraction of heart muscle is triggered by calcium binding to the actin-containing thin filaments but modulated by structural changes in the myosin-containing thick filaments. We used phosphorylation of the myosin regulatory light chain (cRLC) by the cardiac isoform of its specific kinase to elucidate mechanisms of thick filament-mediated contractile regulation in demembranated trabeculae from the rat right ventricle. cRLC phosphorylation enhanced active force and its calcium sensitivity and altered thick filament structure as reported by bifunctional rhodamine probes on the cRLC: the myosin head domains became more perpendicular to the filament axis. The effects of cRLC phosphorylation on thick filament structure and its calcium sensitivity were mimicked by increasing sarcomere length or by deleting the N terminus of the cRLC. Changes in thick filament structure were highly cooperative with respect to either calcium concentration or extent of cRLC phosphorylation. Probes on unphosphorylated myosin heads reported similar structural changes when neighboring heads were phosphorylated, directly demonstrating signaling between myosin heads. Moreover probes on troponin showed that calcium sensitization by cRLC phosphorylation is mediated by the thin filament, revealing a signaling pathway between thick and thin filaments that is still present when active force is blocked by Blebbistatin. These results show that coordinated and cooperative structural changes in the thick and thin filaments are fundamental to the physiological regulation of contractility in the heart. This integrated dual-filament concept of contractile regulation may aid understanding of functional effects of mutations in the protein components of both filaments associated with heart disease.

  18. Myosin light chain phosphorylation enhances contraction of heart muscle via structural changes in both thick and thin filaments

    PubMed Central

    Kampourakis, Thomas; Sun, Yin-Biao; Irving, Malcolm

    2016-01-01

    Contraction of heart muscle is triggered by calcium binding to the actin-containing thin filaments but modulated by structural changes in the myosin-containing thick filaments. We used phosphorylation of the myosin regulatory light chain (cRLC) by the cardiac isoform of its specific kinase to elucidate mechanisms of thick filament-mediated contractile regulation in demembranated trabeculae from the rat right ventricle. cRLC phosphorylation enhanced active force and its calcium sensitivity and altered thick filament structure as reported by bifunctional rhodamine probes on the cRLC: the myosin head domains became more perpendicular to the filament axis. The effects of cRLC phosphorylation on thick filament structure and its calcium sensitivity were mimicked by increasing sarcomere length or by deleting the N terminus of the cRLC. Changes in thick filament structure were highly cooperative with respect to either calcium concentration or extent of cRLC phosphorylation. Probes on unphosphorylated myosin heads reported similar structural changes when neighboring heads were phosphorylated, directly demonstrating signaling between myosin heads. Moreover probes on troponin showed that calcium sensitization by cRLC phosphorylation is mediated by the thin filament, revealing a signaling pathway between thick and thin filaments that is still present when active force is blocked by Blebbistatin. These results show that coordinated and cooperative structural changes in the thick and thin filaments are fundamental to the physiological regulation of contractility in the heart. This integrated dual-filament concept of contractile regulation may aid understanding of functional effects of mutations in the protein components of both filaments associated with heart disease. PMID:27162358

  19. Structural and functional evaluation of branched myofibers lacking intermediate filaments.

    PubMed

    Goodall, Mariah H; Ward, Christopher W; Pratt, Stephen J P; Bloch, Robert J; Lovering, Richard M

    2012-07-15

    Intermediate filaments (IFs), composed of desmin and keratins, link myofibrils to each other and to the sarcolemma in skeletal muscle. Fast-twitch muscle of mice lacking the IF proteins, desmin and keratin 19 (K19), showed reduced specific force and increased susceptibility to injury in earlier studies. Here we tested the hypothesis that the number of malformed myofibers in mice lacking desmin (Des(-/-)), keratin 19 (K19(-/-)), or both IF proteins (double knockout, DKO) is increased and is coincident with altered excitation-contraction (EC) coupling Ca(2+) kinetics, as reported for mdx mice. We quantified the number of branched myofibers, characterized their organization with confocal and electron microscopy (EM), and compared the Ca(2+) kinetics of EC coupling in flexor digitorum brevis myofibers from adult Des(-/-), K19(-/-), or DKO mice and compared them to age-matched wild type (WT) and mdx myofibers. Consistent with our previous findings, 9.9% of mdx myofibers had visible malformations. Des(-/-) myofibers had more malformations (4.7%) than K19(-/-) (0.9%) or DKO (1.3%) myofibers. Confocal and EM imaging revealed no obvious changes in sarcomere misalignment at the branch points, and the neuromuscular junctions in the mutant mice, while more variably located, were limited to one per myofiber. Global, electrically evoked Ca(2+) signals showed a decrease in the rate of Ca(2+) uptake (decay rate) into the sarcoplasmic reticulum after Ca(2+) release, with the most profound effect in branched DKO myofibers (44% increase in uptake relative to WT). Although branched DKO myofibers showed significantly faster rates of Ca(2+) clearance, the milder branching phenotype observed in DKO muscle suggests that the absence of K19 corrects the defect created by the absence of desmin alone. Thus, there are complex roles for desmin-based and K19-based IFs in skeletal muscle, with the null and DKO mutations having different effects on Ca(2+) reuptake and myofiber branching.

  20. The Filament Sensor for Near Real-Time Detection of Cytoskeletal Fiber Structures

    PubMed Central

    Eltzner, Benjamin; Wollnik, Carina; Gottschlich, Carsten; Huckemann, Stephan; Rehfeldt, Florian

    2015-01-01

    A reliable extraction of filament data from microscopic images is of high interest in the analysis of acto-myosin structures as early morphological markers in mechanically guided differentiation of human mesenchymal stem cells and the understanding of the underlying fiber arrangement processes. In this paper, we propose the filament sensor (FS), a fast and robust processing sequence which detects and records location, orientation, length, and width for each single filament of an image, and thus allows for the above described analysis. The extraction of these features has previously not been possible with existing methods. We evaluate the performance of the proposed FS in terms of accuracy and speed in comparison to three existing methods with respect to their limited output. Further, we provide a benchmark dataset of real cell images along with filaments manually marked by a human expert as well as simulated benchmark images. The FS clearly outperforms existing methods in terms of computational runtime and filament extraction accuracy. The implementation of the FS and the benchmark database are available as open source. PMID:25996921

  1. The filament sensor for near real-time detection of cytoskeletal fiber structures.

    PubMed

    Eltzner, Benjamin; Wollnik, Carina; Gottschlich, Carsten; Huckemann, Stephan; Rehfeldt, Florian

    2015-01-01

    A reliable extraction of filament data from microscopic images is of high interest in the analysis of acto-myosin structures as early morphological markers in mechanically guided differentiation of human mesenchymal stem cells and the understanding of the underlying fiber arrangement processes. In this paper, we propose the filament sensor (FS), a fast and robust processing sequence which detects and records location, orientation, length, and width for each single filament of an image, and thus allows for the above described analysis. The extraction of these features has previously not been possible with existing methods. We evaluate the performance of the proposed FS in terms of accuracy and speed in comparison to three existing methods with respect to their limited output. Further, we provide a benchmark dataset of real cell images along with filaments manually marked by a human expert as well as simulated benchmark images. The FS clearly outperforms existing methods in terms of computational runtime and filament extraction accuracy. The implementation of the FS and the benchmark database are available as open source. PMID:25996921

  2. Structural basis for the prion-like MAVS filaments in antiviral innate immunity

    PubMed Central

    Xu, Hui; He, Xiaojing; Zheng, Hui; Huang, Lily J; Hou, Fajian; Yu, Zhiheng; de la Cruz, Michael Jason; Borkowski, Brian; Zhang, Xuewu; Chen, Zhijian J; Jiang, Qiu-Xing

    2014-01-01

    Mitochondrial antiviral signaling (MAVS) protein is required for innate immune responses against RNA viruses. In virus-infected cells MAVS forms prion-like aggregates to activate antiviral signaling cascades, but the underlying structural mechanism is unknown. Here we report cryo-electron microscopic structures of the helical filaments formed by both the N-terminal caspase activation and recruitment domain (CARD) of MAVS and a truncated MAVS lacking part of the proline-rich region and the C-terminal transmembrane domain. Both structures are left-handed three-stranded helical filaments, revealing specific interfaces between individual CARD subunits that are dictated by electrostatic interactions between neighboring strands and hydrophobic interactions within each strand. Point mutations at multiple locations of these two interfaces impaired filament formation and antiviral signaling. Super-resolution imaging of virus-infected cells revealed rod-shaped MAVS clusters on mitochondria. These results elucidate the structural mechanism of MAVS polymerization, and explain how an α-helical domain uses distinct chemical interactions to form self-perpetuating filaments. DOI: http://dx.doi.org/10.7554/eLife.01489.001 PMID:24569476

  3. Solid-state NMR studies of the dynamics and structure of mouse keratin intermediate filaments

    SciTech Connect

    Mack, J.W.; Torchia, D.A.; Steinert, P.M.

    1988-07-26

    The molecular dynamics and structural organization of mouse epidermal keratin intermediate filaments (IF) have been studied via solid-state nuclear magnetic resonance (NMR) experiments performed on IF labeled both in vivo and in vitro with isotopically enriched amino acids. As a probe of the organization of the peripheral glycine-rich end domains of the IF, carbon-13 NMR experiments have been performed on subfilamentous forms (prekeratin) and on IF reassembled in vitro that had been labeled with either (1-/sup 13/C)glycine or (2-/sup 13/C)glycine, as more than 90% of the glycines of the keratins are located in the end domains. Measurements of carbon relaxation times, nuclear Overhauser enhancements, and signal intensities show that the motions of the peptide backbone in the end domains are effectively isotropic. These results indicate that the end domains of IF are remarkably flexible and have little or no structural order. To probe the structural organization of the coiled-coil rod domains of the IF, separate samples of native keratin IF, raised in primary tissue culture, were labeled with L-(1-/sup 13/C)leucine, L-(/sup 2/H/sub 10/)leucine, or L-(2,3,3-/sup 2/H/sub 3/)leucine, as greater than 90% of the leucyl residues of the keratin IF types studied are located in the coiled coils which form the central core of IF. Deuterium NMR experiments performed on IF labeled with deuteriated leucines indeed reveal a marked degree of peptide backbone rigidity within the coiled coils, confirming the initial conclusions of the carbon-13 data. These data, demonstrating relative peptide backbone rigidity yet side-chain flexibility, are interpreted to mean that the coiled coils of these keratin IF are not tightly packed together but rather form a somewhat looser structure which permits a significant degree of side-chain mobility.

  4. Probing the flexibility of tropomyosin and its binding to filamentous actin using molecular dynamics simulations.

    PubMed

    Zheng, Wenjun; Barua, Bipasha; Hitchcock-DeGregori, Sarah E

    2013-10-15

    Tropomyosin (Tm) is a coiled-coil protein that binds to filamentous actin (F-actin) and regulates its interactions with actin-binding proteins like myosin by moving between three positions on F-actin (the blocked, closed, and open positions). To elucidate the molecular details of Tm flexibility in relation to its binding to F-actin, we conducted extensive molecular dynamics simulations for both Tm alone and Tm-F-actin complex in the presence of explicit solvent (total simulation time >400 ns). Based on the simulations, we systematically analyzed the local flexibility of the Tm coiled coil using multiple parameters. We found a good correlation between the regions with high local flexibility and a number of destabilizing regions in Tm, including six clusters of core alanines. Despite the stabilization by F-actin binding, the distribution of local flexibility in Tm is largely unchanged in the absence and presence of F-actin. Our simulations showed variable fluctuations of individual Tm periods from the closed position toward the open position. In addition, we performed Tm-F-actin binding calculations based on the simulation trajectories, which support the importance of Tm flexibility to Tm-F-actin binding. We identified key residues of Tm involved in its dynamic interactions with F-actin, many of which have been found in recent mutational studies to be functionally important, and the rest of which will make promising targets for future mutational experiments.

  5. Nanoscopic structural rearrangements of the Cu-filament in conductive-bridge memories

    NASA Astrophysics Data System (ADS)

    Celano, U.; Giammaria, G.; Goux, L.; Belmonte, A.; Jurczak, M.; Vandervorst, W.

    2016-07-01

    The electrochemical reactions triggering resistive switching in conductive-bridge resistive random access memory (CBRAM) are spatially confined in few tens of nm3. The formation and dissolution of nanoscopic Cu-filaments rely on the displacement of ions in such confined volume, and it is driven by the electric field induced ion migration and nanoscaled redox reactions. The stochastic nature of these fundamental processes leads to a large variability of the device performance. In this work, a combination of two- and three-dimensional scanning probe microscopy (SPM) techniques are used to study the conductive filament (CF) formation, rupture and its nanoscopic structural rearrangements. The high spatial confinement of our approach enables to locally induce RS in a confined area and image it in 3D. A conical shape of the CF is consistently observed, indicating that the ion migration is the rate limiting step in the filament formation when using high quality dielectrics as switching layers. The sub-10 nm electrical contact size of the AFM tip is used to study the filament's dissolution and detect the hopping conduction of Cu during the CF rupture. We consistently observe a tunnel gap formation associated with the tip-induced filament reset. Finally, aiming to match the fundamental understanding with the integrated device operations, we apply scalpel SPM to failed memory cells and directly observe the appearance of filament multiplicity as a major source of failures and variability in CBRAM.The electrochemical reactions triggering resistive switching in conductive-bridge resistive random access memory (CBRAM) are spatially confined in few tens of nm3. The formation and dissolution of nanoscopic Cu-filaments rely on the displacement of ions in such confined volume, and it is driven by the electric field induced ion migration and nanoscaled redox reactions. The stochastic nature of these fundamental processes leads to a large variability of the device performance. In this

  6. Fine-scale structures and material flows of quiescent filaments observed by the New Vacuum Solar Telescope

    NASA Astrophysics Data System (ADS)

    Yan, Xiao-Li; Xue, Zhi-Ke; Xiang, Yong-Yuan; Yang, Li-Heng

    2015-10-01

    Study of the small-scale structures and material flows associated with solar quiescent filaments is very important for understanding the formation and equilibrium of solar filaments. Using high resolution Hα data observed by the New Vacuum Solar Telescope, we present the structures of barbs and material flows along the threads across the spine in two quiescent filaments on 2013 September 29 and on 2012 November 2, respectively. During the evolution of the filament barb, several parallel tube-shaped structures formed and the width of the structures ranged from about 2.3 Mm to 3.3 Mm. The parallel tube-shaped structures merged together accompanied by material flows from the spine to the barb. Moreover, the boundary between the barb and surrounding atmosphere was very neat. The counter-streaming flows were not found to appear alternately in the adjacent threads of the filament. However, the large-scale patchy counter-streaming flows were detected in the filament. The flows in one patch of the filament have the same direction but flows in the adjacent patch have opposite direction. The patches of two opposite flows with a size of about 10″ were alternately exhibited along the spine of the filament. The velocity of these material flows ranged from 5.6 km s-1 to 15.0 km s-1. The material flows along the threads of the filament did not change their direction for about two hours and fourteen minutes during the evolution of the filament. Our results confirm that the large-scale counter-streaming flows with a certain width along the threads of solar filaments exist and are coaligned well with the threads.

  7. [Localization of minor proteins and structural changes in the myosin filaments of vertebrate striated muscle].

    PubMed

    Lednev, V V; Srebnitskaia, L K; Kornev, A N; Khromov, A S; Malinchik, S B

    1981-01-01

    The origin of meridional reflections in the X-ray diffraction patterns of vertebrate skeletal muscles in resting and rigor states was studied. The main results may be summarized as follows. 1. Most of the meridional reflections localized in groups at the positions of successive orders of the repeat period of about 430 A are contributed mainly by the C-protein component of thick filaments. 2. The meridional reflections at about 143 and 72 A in the X-ray diffraction pattern of the resting muscle are contributed mainly by the cross-bridge axial repeat period, while in the X-ray diffraction patterns of the rigorized muscle the reflections at approximately the same positions are contributed mainly by C-protein. The change in the positions of these particular reflections accompanying the transition of the muscle from rest to rigor and from rest to contraction cannot be considered as an indication of a change in the axial repeat period of the cross-bridges, as it was earlier suggested by some authors. 3. The transition of the muscle from resting to rigor state is accompanied by substantial changes in the positions of the meridional reflections contributed my minor proteins, which is indicative of the structural transition in the thick filaments. The observed changes may be interpreted as the result of the thick filaments elongation by about 1.5% or, alternatively, as a consequence of the redistribution of electron density of the meridional reflections 215 and 143 A during a single twitch of the muscle (Huxley et al., Nature, 1980 284, 140) may be interpreted as a natural consequence of the structural change in the thick filaments. It is concluded therefore that on stimulation of the vertebrate skeletal muscle the thickness filaments undergo a reversible structural change which may reflect the existence of myosin-linked regulation in that type of muscle.

  8. Formation of dense structures induced by filament collisions. Correlation of density, kinematics, and magnetic field in the Pipe nebula

    NASA Astrophysics Data System (ADS)

    Frau, P.; Girart, J. M.; Alves, F. O.; Franco, G. A. P.; Onishi, T.; Román-Zúñiga, C. G.

    2015-02-01

    Context. The Pipe nebula is a molecular cloud that lacks star formation feedback and has a relatively simple morphology and velocity structure. This makes it an ideal target for testing cloud evolution through collisions. Aims: We aim at drawing a comprehensive picture of this relatively simple cloud to better understand the formation and evolution of molecular clouds on large scales. Methods: We use archival data to compare the optical polarization properties, the visual extinction, and the 13CO velocities and linewidths of the entire cloud in order to identify trends among the observables. Results: The Pipe nebula can be roughly divided into two filaments with different orientations and gas velocity ranges: E-W at 2-4 km s-1 and N-S at 6-7 km s-1. The two filaments overlap at the bowl, where the gas shows a velocity gradient spanning from 2 to 7 km s-1. Compared to the rest of the Pipe nebula, the bowl gas appears to be denser and exhibits larger linewidths. In addition, the polarization data at the bowl shows lower angular dispersion and higher polarization degree. Cores in the bowl tend to cluster in space and to follow the 13CO velocity gradient. In the stem, cores tend to cluster in regions with properties similar to those of the bowl. Conclusions: The velocity pattern points to a collision between the filaments in the bowl region. The magnetic field seems to be compressed and strengthened in the shocked region. The proportional increase in density and magnetic field strength by a factor similar to the Alfvénic Mach number suggests a continuous shock at low Alfvénic Mach number under the flux-freezing condition. Shocked regions seem to enhance the formation and clustering of dense cores. A movie associated to Fig. 2 is available at http://www.aanda.org

  9. SnoRNAs from the filamentous fungus Neurospora crassa: structural, functional and evolutionary insights

    PubMed Central

    2009-01-01

    Background SnoRNAs represent an excellent model for studying the structural and functional evolution of small non-coding RNAs involved in the post-transcriptional modification machinery for rRNAs and snRNAs in eukaryotic cells. Identification of snoRNAs from Neurospora crassa, an important model organism playing key roles in the development of modern genetics, biochemistry and molecular biology will provide insights into the evolution of snoRNA genes in the fungus kingdom. Results Fifty five box C/D snoRNAs were identified and predicted to guide 71 2'-O-methylated sites including four sites on snRNAs and three sites on tRNAs. Additionally, twenty box H/ACA snoRNAs, which potentially guide 17 pseudouridylations on rRNAs, were also identified. Although not exhaustive, the study provides the first comprehensive list of two major families of snoRNAs from the filamentous fungus N. crassa. The independently transcribed strategy dominates in the expression of box H/ACA snoRNA genes, whereas most of the box C/D snoRNA genes are intron-encoded. This shows that different genomic organizations and expression modes have been adopted by the two major classes of snoRNA genes in N. crassa . Remarkably, five gene clusters represent an outstanding organization of box C/D snoRNA genes, which are well conserved among yeasts and multicellular fungi, implying their functional importance for the fungus cells. Interestingly, alternative splicing events were found in the expression of two polycistronic snoRNA gene hosts that resemble the UHG-like genes in mammals. Phylogenetic analysis further revealed that the extensive separation and recombination of two functional elements of snoRNA genes has occurred during fungus evolution. Conclusion This is the first genome-wide analysis of the filamentous fungus N. crassa snoRNAs that aids in understanding the differences between unicellular fungi and multicellular fungi. As compared with two yeasts, a more complex pattern of methylation guided by

  10. Chaperonin filaments: The archaeal cytoskeleton?

    PubMed Central

    Trent, Jonathan D.; Kagawa, Hiromi K.; Yaoi, Takuro; Olle, Eric; Zaluzec, Nestor J.

    1997-01-01

    Chaperonins are high molecular mass double-ring structures composed of 60-kDa protein subunits. In the hyperthermophilic archaeon Sulfolobus shibatae the two chaperonin proteins represent ≈4% of its total protein and have a combined intracellular concentration of >30 mg/ml. At concentrations ≥ 0.5 mg/ml purified chaperonins form filaments in the presence of Mg2+ and nucleotides. Filament formation requires nucleotide binding (not hydrolysis), and occurs at physiological temperatures in biologically relevant buffers, including a buffer made from cell extracts. These observations suggest that chaperonin filaments may exist in vivo and the estimated 4600 chaperonins per cell suggest that such filaments could form an extensive cytostructure. We observed filamentous structures in unfixed, uranyl-acetate-stained S. shibatae cells, which resemble the chaperonin filaments in size and appearance. ImmunoGold (Janssen) labeling using chaperonin antibodies indicated that many chaperonins are associated with insoluble cellular structures and these structures appear to be filamentous in some areas, although they could not be uranyl-acetate-stained. The existence of chaperonin filaments in vivo suggests a mechanism whereby their protein-folding activities can be regulated. More generally, the filaments themselves may play a cytoskeletal role in Archaea. PMID:9144246

  11. [Congenital myopathies - skeletal muscle diseases related to disorder of actin filament structure and functions].

    PubMed

    Robaszkiewicz, Katarzyna; Moraczewska, Joanna

    2011-01-01

    Congenital myopathies are clinically and genetically heterogeneous disorders characterized by muscle structural abnormalities, muscle weakness and deformities. The clinical spectrum of the disease ranges from severe cases with early death to adult-onset cases with slow progression. In the skeletal muscle fibers, the specific structural changes are rod-shaped structures present in the sarcoplasm (nemaline myopathy – NM) or nuclei (intranuclear rod myopathy – IRM), cap-like structures peripherally located within muscle fibers (cap disease – CD), accumulations of actin filaments (actin myopathy – AM), changes in the fiber type proportion and size (congenital fiber type disproportion – CFTD), irregularity of Z-lines and abnormal localization of myofiber nuclei. Mutations in several genes encoding muscle proteins have been linked to congenital myopathy. These genes include a-skeletal actin (ACTA1), tropomyosin (TPM2 and TPM3), troponin (TNNT1) and nebulin (NEB). In vitro and in vivo studies show that mutations identified within these genes have varying impacts on thin filament protein structure, which affect polymerization and stabilization of actin filament, actin cellular localization and regulation of actin-myosin activity. Many lines of evidence suggest that mutated proteins have "toxic" effects. Unfortunately, there is no existing simple correlation between the degree of protein disruption, muscle pathologies and disease severity. PMID:21677359

  12. Structure of the Acidianus Filamentous Virus 3 and Comparative Genomics of Related Archaeal Lipothrixviruses▿

    PubMed Central

    Vestergaard, Gisle; Aramayo, Ricardo; Basta, Tamara; Häring, Monika; Peng, Xu; Brügger, Kim; Chen, Lanming; Rachel, Reinhard; Boisset, Nicolas; Garrett, Roger A.; Prangishvili, David

    2008-01-01

    Four novel filamentous viruses with double-stranded DNA genomes, namely, Acidianus filamentous virus 3 (AFV3), AFV6, AFV7, and AFV8, have been characterized from the hyperthermophilic archaeal genus Acidianus, and they are assigned to the Betalipothrixvirus genus of the family Lipothrixviridae. The structures of the approximately 2-μm-long virions are similar, and one of them, AFV3, was studied in detail. It consists of a cylindrical envelope containing globular subunits arranged in a helical formation that is unique for any known double-stranded DNA virus. The envelope is 3.1 nm thick and encases an inner core with two parallel rows of protein subunits arranged like a zipper. Each end of the virion is tapered and carries three short filaments. Two major structural proteins were identified as being common to all betalipothrixviruses. The viral genomes were sequenced and analyzed, and they reveal a high level of conservation in both gene content and gene order over large regions, with this similarity extending partly to the earlier described betalipothrixvirus Sulfolobus islandicus filamentous virus. A few predicted gene products of each virus, in addition to the structural proteins, could be assigned specific functions, including a putative helicase involved in Holliday junction branch migration, a nuclease, a protein phosphatase, transcriptional regulators, and glycosyltransferases. The AFV7 genome appears to have undergone intergenomic recombination with a large section of an AFV2-like viral genome, apparently resulting in phenotypic changes, as revealed by the presence of AFV2-like termini in the AFV7 virions. Shared features of the genomes include (i) large inverted terminal repeats exhibiting conserved, regularly spaced direct repeats; (ii) a highly conserved operon encoding the two major structural proteins; (iii) multiple overlapping open reading frames, which may be indicative of gene recoding; (iv) putative 12-bp genetic elements; and (v) partial gene

  13. A rapid PCR-based approach for molecular identification of filamentous fungi.

    PubMed

    Chen, Yuanyuan; Prior, Bernard A; Shi, Guiyang; Wang, Zhengxiang

    2011-08-01

    In this study, a novel rapid and efficient DNA extraction method based on alkaline lysis, which can deal with a large number of filamentous fungal isolates in the same batch, was established. The filamentous fungal genomic DNA required only 20 min to prepare and can be directly used as a template for PCR amplification. The amplified internal transcribed spacer regions were easy to identify by analysis. The extracted DNA also can be used to amplify other protein-coding genes for fungal identification. This method can be used for rapid systematic identification of filamentous fungal isolates.

  14. Structural changes in the trichocyte intermediate filaments accompanying the transition from the reduced to the oxidized form.

    PubMed

    Fraser, R D Bruce; Parry, David A D

    2007-07-01

    Earlier studies established that substantial changes take place in the three-dimensional structure of the newly assembled trichocyte keratin intermediate filament (IF) during the oxidation process (Wang, H., Parry, D.A.D., Jones, L.N., Idler, W.W., Marekov, L.N., Steinert, P.M. 2000. In vitro assembly and structure of trichocyte keratin intermediate filaments: A novel role for stabilization by disulfide bonding. J. Cell Biol. 151, 1459-1468). The present contribution describes a re-examination of previous data in which more accurate values for the axial dispositions of the molecules have been obtained to yield the most detailed picture yet available of the structural changes that occur in vivo. In particular, it is shown that in the newly assembled (reduced) IF the crosslinking data are consistent with the detailed (8+0) model suggested earlier (Fraser, R.D.B., Parry, D.A.D. 2005. The three-dimensional structure of trichocyte (hard alpha-) keratin intermediate filaments: Features of the molecular packing deduced from the sites of induced crosslinks. J. Struct. Biol. 151, 171-181), in which eight four-chain protofilaments are arranged on an annular ring. For oxidized IF, however, the existing X-ray data require a periodic imperfection in the surface lattice which is substantial in the case of an (8+0) model and hence difficult to explain. In contrast, an alternative (7+1) model (Fraser, R.D.B., MacRae, T.P., Parry, D.A.D., Suzuki, E. 1986. Intermediate filaments in alpha-keratin. Proc. Natl. Acad. Sci. USA 83, 1179-1183) requires only a minor imperfection, and it is suggested that this is associated with the central protofilament. This suggestion is shown to be compatible with both the crosslinking data and a model for the axial distribution of electron density derived from the meridional X-ray pattern. In addition, evidence from an X-ray diffraction study of the follicle (Er Rafik, M., Briki, F., Burghammer, M., Doucet, J. 2006. In vivo formation of the hard alpha

  15. Extracellular matrix of adipogenically differentiated mesenchymal stem cells reveals a network of collagen filaments, mostly interwoven by hexagonal structural units.

    PubMed

    Ullah, Mujib; Sittinger, Michael; Ringe, Jochen

    2013-01-01

    Extracellular matrix (ECM) is the non-cellular component of tissues, which not only provides biological shelter but also takes part in the cellular decisions for diverse functions. Every tissue has an ECM with unique composition and topology that governs the process of determination, differentiation, proliferation, migration and regeneration of cells. Little is known about the structural organization of matrix especially of MSC-derived adipogenic ECM. Here, we particularly focus on the composition and architecture of the fat ECM to understand the cellular behavior on functional bases. Thus, mesenchymal stem cells (MSC) were adipogenically differentiated, then, were transferred to adipogenic propagation medium, whereas they started the release of lipid droplets leaving bare network of ECM. Microarray analysis was performed, to indentify the molecular machinery of matrix. Adipogenesis was verified by Oil Red O staining of lipid droplets and by qPCR of adipogenic marker genes PPARG and FABP4. Antibody staining demonstrated the presence of collagen type I, II and IV filaments, while alkaline phosphatase activity verified the ossified nature of these filaments. In the adipogenic matrix, the hexagonal structures were abundant followed by octagonal structures, whereas they interwoven in a crisscross manner. Regarding molecular machinery of adipogenic ECM, the bioinformatics analysis revealed the upregulated expression of COL4A1, ITGA7, ITGA7, SDC2, ICAM3, ADAMTS9, TIMP4, GPC1, GPC4 and downregulated expression of COL14A1, ADAMTS5, TIMP2, TIMP3, BGN, LAMA3, ITGA2, ITGA4, ITGB1, ITGB8, CLDN11. Moreover, genes associated with integrins, glycoproteins, laminins, fibronectins, cadherins, selectins and linked signaling pathways were found. Knowledge of the interactive-language between cells and matrix could be beneficial for the artificial designing of biomaterials and bioscaffolds. PMID:23851162

  16. Density filament and helical field line structures in three dimensional Weibel-mediated collisionless shocks

    NASA Astrophysics Data System (ADS)

    Moritaka, Toseo; Sakawa, Youichi; Kuramitsu, Yasuhiro; Morita, Taichi; Yamaura, Yuta; Ishikawa, Taishi; Takabe, Hideaki

    2016-03-01

    Collisionless shocks mediated by Weibel instability are attracting attention for their relevance to experimental demonstrations of astrophysical shocks in high-intensity laser facilities. The three dimensional structure of Weibel-mediated shocks is investigated through a fully kinetic particle-in-cell simulation. The structures obtained are characterized by the following features: (i) helical magnetic field lines elongated in the direction upstream of the shock region, (ii) high and low density filaments inside the helical field lines. These structures originate from the interaction between counter-streaming plasma flow and magnetic vortexes caused by Weibel instability, and potentially affect the shock formation mechanism.

  17. The Structure of HIV-1 Rev Filaments Suggests a Bilateral Model for Rev-RRE Assembly.

    PubMed

    DiMattia, Michael A; Watts, Norman R; Cheng, Naiqian; Huang, Rick; Heymann, J Bernard; Grimes, Jonathan M; Wingfield, Paul T; Stuart, David I; Steven, Alasdair C

    2016-07-01

    HIV-1 Rev protein mediates the nuclear export of viral RNA genomes. To do so, Rev oligomerizes cooperatively onto an RNA motif, the Rev response element (RRE), forming a complex that engages with the host nuclear export machinery. To better understand Rev oligomerization, we determined four crystal structures of Rev N-terminal domain dimers, which show that they can pivot about their dyad axis, giving crossing angles of 90° to 140°. In parallel, we performed cryoelectron microscopy of helical Rev filaments. Filaments vary from 11 to 15 nm in width, reflecting variations in dimer crossing angle. These structures contain additional density, indicating that C-terminal domains become partially ordered in the context of filaments. This conformational variability may be exploited in the assembly of RRE/Rev complexes. Our data also revealed a third interface between Revs, which offers an explanation for how the arrangement of Rev subunits adapts to the "A"-shaped architecture of the RRE in export-active complexes. PMID:27265851

  18. Freely Suspended Smectic Filaments and the Structure of the B7 Phase of MHOBOW

    NASA Technical Reports Server (NTRS)

    Clark, N.; Link, D. R.; Maclennan, J. E.

    2000-01-01

    Our recent discovery of the spontaneous formation of chiral domains in fluid smectic phases of achiral bow-shaped molecules opens up a wide variety of possibilities for new liquid crystal phases and phenomena. The basic, spontaneously chiral layer structure of the highest temperature fluid smectic phases, the B2 and B7, are shown. One of the most intriguing aspects of this structure is the plethora of possible phases coming from different stacking sequences of the polar ordering and tilt directions. The four possibilities of next-nearest neighbor alternation are shown. In the original material studied, NOBOW, the ground states found are antiferroelectric, either the racemic SmC(sub S)P(sub A) or the chiral SmC(sub A)P(sub A). We are currently studying MHOBOW, synthesized by D. Walba which, by virtue of its methyl hexyloxy tail has a tendency to form anticlinic layer interfaces, in the hope of finding a phase with a ferroelectric ground state, either SmC(sub A)P(sub S) or SmC(sub S)P(sub A), which can be obtained in NOBOW only by applying a field. Preliminary observations of MHO-BOW have made its study, from the point of view of understanding novel LC structures, extremely high priority. The following truly remarkable characteristics have been revealed: (i) The smectic phase grows out of the isotropic in the form of helical ribbons. The resulting planar aligned textures of focal conics with layers normal to glass plates exhibit bizarre modulations, including stripes and checker-boards. These have also been seen in other materials suggesting that this is a new phase (tentatively called B7), which is a fluid smectic with some kind of in-layer structure. (ii) It is virtually impossible to make freely suspended films of MHOBOW. Rather it makes the freely suspended filaments which preliminary x-ray scattering experiments reveal to have the nested cylinder layer structure indicated; (iii) The powder x-ray diffraction exhibits four resolution-limited smectic layering peaks

  19. Predicting Structural Behavior of Filament Wound Composite Pressure Vessel Using Three Dimensional Shell Analysis

    NASA Astrophysics Data System (ADS)

    Madhavi, M.; Venkat, R.

    2014-01-01

    Fiber reinforced polymer composite materials with their higher specific strength, moduli and tailorability characteristics will result in reduction of weight of the structure. The composite pressure vessels with integrated end domes develop hoop stresses that are twice longitudinal stresses and when isotropic materials like metals are used for development of the hardware and the material is not fully utilized in the longitudinal/meridional direction resulting in over weight components. The determination of a proper winding angles and thickness is very important to decrease manufacturing difficulties and to increase structural efficiency. In the present study a methodology is developed to understand structural characteristics of filament wound pressure vessels with integrated end domes. Progressive ply wise failure analysis of composite pressure vessel with geodesic end domes is carried out to determine matrix crack failure, burst pressure values at various positions of the shell. A three dimensional finite element analysis is computed to predict the deformations and stresses in the composite pressure vessel. The proposed method could save the time to design filament wound structures, to check whether the ply design is safe for the given input conditions and also can be adapted to non-geodesic structures. The results can be utilized to understand structural characteristics of filament wound pressure vessels with integrated end domes. This approach can be adopted for various applications like solid rocket motor casings, automobile fuel storage tanks and chemical storage tanks. Based on the predictions a composite pressure vessel is designed and developed. Hydraulic test is performed on the composite pressure vessel till the burst pressure.

  20. Fabrication of low cost composite tooling for filament winding large structures

    NASA Astrophysics Data System (ADS)

    Miller, Timothy S.; Fortin, Christopher J.

    A TQM/concurrent engineering approach has been used to create a low cost filament-winding mandrel for large launch-vehicle structure fabrication. The process involves the fabrication of a low cost/low temperature master model, followed by the building of the mandrel and its backup structure within the master. Mandrels fabricated by these means are able to maintain full vacuum integrity and dimensional stability throughout high-temperature cure cycles; the reduced thermal mass of the mandrel results in part-cure cycles that are shorter than those associated with conventional mandrel materials.

  1. Cytoskeleton Molecular Motors: Structures and Their Functions in Neuron

    PubMed Central

    Xiao, Qingpin; Hu, Xiaohui; Wei, Zhiyi; Tam, Kin Yip

    2016-01-01

    Cells make use of molecular motors to transport small molecules, macromolecules and cellular organelles to target region to execute biological functions, which is utmost important for polarized cells, such as neurons. In particular, cytoskeleton motors play fundamental roles in neuron polarization, extension, shape and neurotransmission. Cytoskeleton motors comprise of myosin, kinesin and cytoplasmic dynein. F-actin filaments act as myosin track, while kinesin and cytoplasmic dynein move on microtubules. Cytoskeleton motors work together to build a highly polarized and regulated system in neuronal cells via different molecular mechanisms and functional regulations. This review discusses the structures and working mechanisms of the cytoskeleton motors in neurons. PMID:27570482

  2. Effect of high-power laser divergence on the plasma structural parameters during multiple filamentation in air

    NASA Astrophysics Data System (ADS)

    Geints, Yu. E.; Zemlyanov, A. A.

    2016-06-01

    Multiple filamentation of an infrared high-power laser pulse in air is considered. Based on the numerical solution to the unidirectional pulse propagation equation, the effect of radiation external focusing on the spatial structure of the plasma area produced in the filamentation region is studied. We show that the number of generated plasma channels in the beam wake and the density of their spatial distribution over the filamentation region depend on the initial divergence of laser radiation. We found that in a specific range of beam focusing the number of produced plasma channels could be minimized due to the formation of a consolidated thick plasma bunch at the beam axis.

  3. Structural and Functional Studies of H. seropedicae RecA Protein – Insights into the Polymerization of RecA Protein as Nucleoprotein Filament

    PubMed Central

    Galvão, Carolina W.; Saab, Sérgio C.; Iulek, Jorge; Etto, Rafael M.; Steffens, Maria B. R.; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L.; Cox, Michael M.

    2016-01-01

    The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament. PMID:27447485

  4. Structural and Functional Studies of H. seropedicae RecA Protein - Insights into the Polymerization of RecA Protein as Nucleoprotein Filament.

    PubMed

    Leite, Wellington C; Galvão, Carolina W; Saab, Sérgio C; Iulek, Jorge; Etto, Rafael M; Steffens, Maria B R; Chitteni-Pattu, Sindhu; Stanage, Tyler; Keck, James L; Cox, Michael M

    2016-01-01

    The bacterial RecA protein plays a role in the complex system of DNA damage repair. Here, we report the functional and structural characterization of the Herbaspirillum seropedicae RecA protein (HsRecA). HsRecA protein is more efficient at displacing SSB protein from ssDNA than Escherichia coli RecA protein. HsRecA also promotes DNA strand exchange more efficiently. The three dimensional structure of HsRecA-ADP/ATP complex has been solved to 1.7 Å resolution. HsRecA protein contains a small N-terminal domain, a central core ATPase domain and a large C-terminal domain, that are similar to homologous bacterial RecA proteins. Comparative structural analysis showed that the N-terminal polymerization motif of archaeal and eukaryotic RecA family proteins are also present in bacterial RecAs. Reconstruction of electrostatic potential from the hexameric structure of HsRecA-ADP/ATP revealed a high positive charge along the inner side, where ssDNA is bound inside the filament. The properties of this surface may explain the greater capacity of HsRecA protein to bind ssDNA, forming a contiguous nucleoprotein filament, displace SSB and promote DNA exchange relative to EcRecA. Our functional and structural analyses provide insight into the molecular mechanisms of polymerization of bacterial RecA as a helical nucleoprotein filament. PMID:27447485

  5. Streptococcus salivarius Fimbriae Are Composed of a Glycoprotein Containing a Repeated Motif Assembled into a Filamentous Nondissociable Structure

    PubMed Central

    Lévesque, Céline; Vadeboncoeur, Christian; Chandad, Fatiha; Frenette, Michel

    2001-01-01

    Streptococcus salivarius, a gram-positive bacterium found in the human oral cavity, expresses flexible peritrichous fimbriae. In this paper, we report purification and partial characterization of S. salivarius fimbriae. Fimbriae were extracted by shearing the cell surface of hyperfimbriated mutant A37 (a spontaneous mutant of S. salivarius ATCC 25975) with glass beads. Preliminary experiments showed that S. salivarius fimbriae did not dissociate when they were incubated at 100°C in the presence of sodium dodecyl sulfate. This characteristic was used to separate them from other cell surface components by successive gel filtration chromatography procedures. Fimbriae with molecular masses ranging from 20 × 106 to 40 × 106 Da were purified. Examination of purified fimbriae by electron microscopy revealed the presence of filamentous structures up to 1 μm long and 3 to 4 nm in diameter. Biochemical studies of purified fimbriae and an amino acid sequence analysis of a fimbrial internal peptide revealed that S. salivarius fimbriae were composed of a glycoprotein assembled into a filamentous structure resistant to dissociation. The internal amino acid sequence was composed of a repeated motif of two amino acids alternating with two modified residues: A/X/T-E-Q-M/φ, where X represents a modified amino acid residue and φ represents a blank cycle. Immunolocalization experiments also revealed that the fimbriae were associated with a wheat germ agglutinin-reactive carbohydrate. Immunolabeling experiments with antifimbria polyclonal antibodies showed that antigenically related fimbria-like structures were expressed in two other human oral streptococcal species, Streptococcus mitis and Streptococcus constellatus. PMID:11292790

  6. Intermediate Filaments as Organizers of Cellular Space: How They Affect Mitochondrial Structure and Function

    PubMed Central

    Schwarz, Nicole; Leube, Rudolf E.

    2016-01-01

    Intermediate filaments together with actin filaments and microtubules form the cytoskeleton, which is a complex and highly dynamic 3D network. Intermediate filaments are the major mechanical stress protectors but also affect cell growth, differentiation, signal transduction, and migration. Using intermediate filament-mitochondrial crosstalk as a prominent example, this review emphasizes the importance of intermediate filaments as crucial organizers of cytoplasmic space to support these functions. We summarize observations in different mammalian cell types which demonstrate how intermediate filaments influence mitochondrial morphology, subcellular localization, and function through direct and indirect interactions and how perturbations of these interactions may lead to human diseases. PMID:27399781

  7. Morphological and molecular identification of filamentous Aspergillus flavus and Aspergillus parasiticus isolated from compound feeds in South Africa.

    PubMed

    Iheanacho, Henry E; Njobeh, Patrick B; Dutton, Francis M; Steenkamp, Paul A; Steenkamp, Lucia; Mthombeni, Julian Q; Daru, Barnabas H; Makun, Anthony H

    2014-12-01

    Isolation of filamentous species of two Aspergillum genera from compound feeds produced in South Africa, and subsequent extraction of their individual DNA in this study, presents a simple but rapid molecular procedure for high through-put analysis of the individual morphological forms. DNA was successfully isolated from the Aspergillus spp. from agar cultures by use of a commercial kit. Agarose gel electrophoresis fractionation of the fungi DNA, showed distinct bands. The DNA extracted by this procedure appears to be relatively pure with a ratio absorbance at 260 and 280 nm. However, the overall morphological and molecular data indicated that 67.5 and 51.1% of feed samples were found to be contaminated with Aspergillus flavus and Aspergillus parasiticus, respectively, with poultry feed having the highest contamination mean level of 5.7 × 105 CFU/g when compared to cattle (mean: 4.0 × 106 CFU/g), pig (mean: 2.7 × 104 CFU/g) and horse (1.0 × 102 CFU) feed. This technique presents a readily achievable, easy to use method in the extraction of filamentous fungal DNA and it's identification. Hence serves as an important tool towards molecular study of these organisms for routine analysis check in monitoring and improving compound feed quality against fungal contamination.

  8. Searching for filaments and large-scale structure around DAFT/FADA clusters

    NASA Astrophysics Data System (ADS)

    Durret, F.; Márquez, I.; Acebrón, A.; Adami, C.; Cabrera-Lavers, A.; Capelato, H.; Martinet, N.; Sarron, F.; Ulmer, M. P.

    2016-04-01

    Context. Clusters of galaxies are located at the intersection of cosmic filaments and are still accreting galaxies and groups along these preferential directions. However, because of their relatively low contrast on the sky, filaments are difficult to detect (unless a large amount of spectroscopic data are available), and unambiguous detections have been limited until now to relatively low redshifts (z< ~ 0.3). Aims: This project is aimed at searching for extensions and filaments around clusters, traced by galaxies selected to be at the cluster redshift based on the red sequence. In the 0.4 filaments. Methods: We have searched for extensions and filaments around the thirty clusters of the DAFT/FADA survey for which we had deep wide field photometric data. For each cluster, based on a colour-magnitude diagram, we selected galaxies that were likely to belong to the red sequence, and hence to be at the cluster redshift, and built density maps. By computing the background for each of these maps and drawing 3σ contours, we estimated the elongations of the structures detected in this way. Whenever possible, we identified the other structures detected on the density maps with clusters listed in NED. Results: We find clear elongations in twelve clusters out of thirty, with sizes that can reach up to 7.6 Mpc. Eleven other clusters have neighbouring structures, but the zones linking them are not detected in the density maps at a 3σ level. Three clusters show no extended structure and no neighbours, and four clusters are of too low contrast to be clearly visible on our density maps. Conclusions: The simple method we have applied appears to work well to show the existence of filaments and/or extensions around a number of clusters in the redshift range 0.4

  9. Direct observation of anodic dissolution and filament growth behavior in polyethylene-oxide-based atomic switch structures

    NASA Astrophysics Data System (ADS)

    Krishnan, Karthik; Tsuruoka, Tohru; Aono, Masakazu

    2016-06-01

    We directly observed anodic dissolution and subsequent filament growth behavior in a planar atomic switch structure with Ag salt incorporated polyethylene oxide (Ag-PEO) film using in situ optical microscopy and ex situ scanning electron microscopy. The high ionic conductivities of Ag-PEO films enable the investigation of filament formation under voltage bias, even in micrometer-scaled devices. It was found that the filament formation changes from unidirectional growth to dendritic growth, depending on its distance from the grounded electrode. Based on this understanding of filament growth dynamics in planar devices, highly stable resistive switching was achieved in an Ag/Ag-PEO/Pt stacked device with an Ag-PEO film thickness of 100 nm. The device showed repeated switching operations for more than 102 sweep cycles, with a high ON/OFF resistance ratio of 105.

  10. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair

    PubMed Central

    Zhang, Yuchen; Alsop, Richard J.; Soomro, Asfia; Yang, Fei-Chi

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3–90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

  11. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

    PubMed

    Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers. PMID:26557428

  12. Effect of shampoo, conditioner and permanent waving on the molecular structure of human hair.

    PubMed

    Zhang, Yuchen; Alsop, Richard J; Soomro, Asfia; Yang, Fei-Chi; Rheinstädter, Maikel C

    2015-01-01

    The hair is a filamentous biomaterial consisting of the cuticle, the cortex and the medulla, all held together by the cell membrane complex. The cortex mostly consists of helical keratin proteins that spiral together to form coiled-coil dimers, intermediate filaments, micro-fibrils and macro-fibrils. We used X-ray diffraction to study hair structure on the molecular level, at length scales between ∼3-90 Å, in hopes of developing a diagnostic method for diseases affecting hair structure allowing for fast and noninvasive screening. However, such an approach can only be successful if common hair treatments do not affect molecular hair structure. We found that a single use of shampoo and conditioner has no effect on packing of keratin molecules, structure of the intermediate filaments or internal lipid composition of the membrane complex. Permanent waving treatments are known to break and reform disulfide linkages in the hair. Single application of a perming product was found to deeply penetrate the hair and reduce the number of keratin coiled-coils and change the structure of the intermediate filaments. Signals related to the coiled-coil structure of the α-keratin molecules at 5 and 9.5 Å were found to be decreased while a signal associated with the organization of the intermediate filaments at 47 Å was significantly elevated in permed hair. Both these observations are related to breaking of the bonds between two coiled-coil keratin dimers.

  13. Structure, Dynamics, and Assembly of Filamentous Bacteriophages by Nuclear Magnetic Resonance Spectroscopy

    NASA Astrophysics Data System (ADS)

    Opella, Stanley J.; Zeri, Ana Carolina; Park, Sang Ho

    2008-05-01

    Filamentous bacteriophages serve as model systems for the development and implementation of spectroscopic methods suitable for biological supramolecular assemblies. Not only are their coat proteins small and readily prepared in the laboratory, but they also have two primary roles as membrane proteins and as the principal structural element of the virus particles. As a bacterial system, they are readily labeled with stable isotopes, and this has opened possibilities for the many nuclear magnetic resonance (NMR) studies described in this review. In particular, solid-state NMR of aligned samples has been used to determine the three-dimensional structures of both the membrane-bound forms of coat proteins in phospholipid bilayers and structural forms in virus particles, which has led to an analysis of the assembly mechanism for virus particles as they are extruded through the cell membrane.

  14. Structural and functional changes in myocardial thin filaments in experimental hypothyrosis.

    PubMed

    Sukoyan, G V; Berberashvili, T M; Asatiani, K Dzh

    2007-05-01

    Fluorescence resonance energy transfer study revealed decreased intermonomer mobility of Ca-actin and Mg-actin filaments of myocardial myofibrils in myocardial dystrophy caused by diffuse endocrine disorders, e. g. hypothyrosis. Cis374 axial distance in Ca-actin filament protomer increased in hypothyrosis. Intracellular pH has no effect on inter-monomer mobility of Ca-actin filament.

  15. Structural changes in intermediate filament networks alter the activity of insulin-degrading enzyme

    PubMed Central

    Chou, Ying-Hao; Kuo, Wen-Liang; Rosner, Marsha Rich; Tang, Wei-Jen; Goldman, Robert D.

    2009-01-01

    The intermediate filament (IF) protein nestin coassembles with vimentin and promotes the disassembly of these copolymers when vimentin is hyperphosphorylated during mitosis. The aim of this study is to determine the function of these nonfilamentous particles by identifying their interacting partners. In this study, we report that these disassembled vimentin/nestin complexes interact with insulin degrading enzyme (IDE). Both vimentin and nestin interact with IDE in vitro, but vimentin binds IDE with a higher affinity than nestin. Although the interaction between vimentin and IDE is enhanced by vimentin phosphorylation at Ser-55, the interaction between nestin and IDE is phosphorylation independent. Further analyses show that phosphorylated vimentin plays the dominant role in targeting IDE to the vimentin/nestin particles in vivo, while the requirement for nestin is related to its ability to promote vimentin IF disassembly. The binding of IDE to either nestin or phosphorylated vimentin regulates IDE activity differently, depending on the substrate. The insulin degradation activity of IDE is suppressed ∼50% by either nestin or phosphorylated vimentin, while the cleavage of bradykinin-mimetic peptide by IDE is increased 2- to 3-fold. Taken together, our data demonstrate that the nestin-mediated disassembly of vimentin IFs generates a structure capable of sequestering and modulating the activity of IDE.—Chou, Y.-H., Kuo, W.-L., Rich Rosner, M., Tang, W.-J., Goldman, R. D. Structural changes in intermediate filament networks alter the activity of insulin-degrading enzyme. PMID:19584300

  16. The primary structure of component 8c-1, a subunit protein of intermediate filaments in wool keratin. Relationships with proteins from other intermediate filaments.

    PubMed Central

    Dowling, L M; Crewther, W G; Inglis, A S

    1986-01-01

    Component 8c-1, one of four highly homologous component-8 subunit proteins present in the microfibrils of wool, was isolated as its S-carboxymethyl derivative and its amino acid sequence was determined. Large peptides were isolated after cleaving the protein chemically or enzymically and the sequence of each was determined with an automatic Sequenator. The peptides were ordered by sequence overlaps and, in some instances, by homology with known sequences from other component-8 subunits. The C-terminal residues were identified by three procedures. Full details of the various procedures used have been deposited as Supplementary Publication SUP 50133 (4 pp.) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1986) 233, 5. The result showed that the protein comprises 412 residues and has an Mr, including the N-terminal acetyl group, of 48,300. The sequence of residues 98-200 of component 8c-1 was found to correspond to the partial or complete sequences of four homologous type I helical segments previously isolated from helical fragments recovered from chymotryptic digests of microfibrillar proteins of wool [Crewther & Dowling (1971) Appl. Polym. Symp. 18, 1-20; Crewther, Gough, Inglis & McKern (1978) Text. Res. J. 48, 160-162; Gough, Inglis & Crewther (1978) Biochem. J. 173, 385]. Considered in relation to amino acid sequences of other intermediate-filament proteins, the sequence is in accord with the view that keratin filament proteins are of two types [Hanukoglu & Fuchs (1983) Cell (Cambridge, Mass.) 33, 915-924]. Filament proteins from non-keratinous tissues, such as desmin, vimentin, neurofilament proteins and the glial fibrillary acidic protein, which form monocomponent filaments, constitute a third type. It is suggested that as a whole the proteins from intermediate filaments be classed as filamentins, the three types at present identified forming

  17. The structure of FtsZ filaments in vivo suggests a force-generating role in cell division

    PubMed Central

    Li, Zhuo; Trimble, Michael J; Brun, Yves V; Jensen, Grant J

    2007-01-01

    In prokaryotes, FtsZ (the filamentous temperature sensitive protein Z) is a nearly ubiquitous GTPase that localizes in a ring at the leading edge of constricting plasma membranes during cell division. Here we report electron cryotomographic reconstructions of dividing Caulobacter crescentus cells wherein individual arc-like filaments were resolved just underneath the inner membrane at constriction sites. The filaments' position, orientation, time of appearance, and resistance to A22 all suggested that they were FtsZ. Predictable changes in the number, length, and distribution of filaments in cells where the expression levels and stability of FtsZ were altered supported that conclusion. In contrast to the thick, closed-ring-like structure suggested by fluorescence light microscopy, throughout the constriction process the Z-ring was seen here to consist of just a few short (∼100 nm) filaments spaced erratically near the division site. Additional densities connecting filaments to the cell wall, occasional straight segments, and abrupt kinks were also seen. An ‘iterative pinching' model is proposed wherein FtsZ itself generates the force that constricts the membrane in a GTP-hydrolysis-driven cycle of polymerization, membrane attachment, conformational change, depolymerization, and nucleotide exchange. PMID:17948052

  18. Identification of a Gene Essential for Sheathed Structure Formation in Sphaerotilus natans, a Filamentous Sheathed Bacterium

    PubMed Central

    Suzuki, Toshihiko; Kanagawa, Takahiro; Kamagata, Yoichi

    2002-01-01

    Sphaerotilus natans, a filamentous bacterium that causes bulking in activated sludge processes, can assume two distinct morphologies, depending on the substrate concentration for growth; in substrate-rich media it grows as single rod-shaped cells, whereas in substrate-limited media it grows as filaments. To identify genes responsible for sheath formation, we carried out transposon Tn5 mutagenesis. Of the approximately 20,000 mutants obtained, 7 did not form sheathed structures. Sequencing of the Tn5-flanking regions showed that five of the seven Tn5 insertions converged at the same open reading frame, designated sthA. The deduced amino acids encoded by sthA were found to be homologous to glycosyltransferase, which is known to be involved in linking sugars to lipid carriers during bacterial exopolysaccharide biosynthesis. Disruption of the gene of the wild-type strain by inserting a kanamycin resistance gene cassette also resulted in sheathless growth under either type of nutrient condition. These findings indicate that sthA is a crucial component responsible for sheath formation. PMID:11772646

  19. Structural basis for activation, assembly and membrane binding of ESCRT-III Snf7 filaments

    PubMed Central

    Tang, Shaogeng; Henne, W Mike; Borbat, Peter P; Buchkovich, Nicholas J; Freed, Jack H; Mao, Yuxin; Fromme, J Christopher; Emr, Scott D

    2015-01-01

    The endosomal sorting complexes required for transport (ESCRTs) constitute hetero-oligomeric machines that catalyze multiple topologically similar membrane-remodeling processes. Although ESCRT-III subunits polymerize into spirals, how individual ESCRT-III subunits are activated and assembled together into a membrane-deforming filament remains unknown. Here, we determine X-ray crystal structures of the most abundant ESCRT-III subunit Snf7 in its active conformation. Using pulsed dipolar electron spin resonance spectroscopy (PDS), we show that Snf7 activation requires a prominent conformational rearrangement to expose protein-membrane and protein-protein interfaces. This promotes the assembly of Snf7 arrays with ~30 Å periodicity into a membrane-sculpting filament. Using a combination of biochemical and genetic approaches, both in vitro and in vivo, we demonstrate that mutations on these protein interfaces halt Snf7 assembly and block ESCRT function. The architecture of the activated and membrane-bound Snf7 polymer provides crucial insights into the spatially unique ESCRT-III-mediated membrane remodeling. DOI: http://dx.doi.org/10.7554/eLife.12548.001 PMID:26670543

  20. Filament winding

    NASA Astrophysics Data System (ADS)

    Shibley, A. M.

    The major aspects of filament winding are discussed, emphasizing basic reinforcement and matrix materials, winding procedures, process controls, and cured composite properties. Fiberglass (E-glass and S-glass strengths are 500,000 and 665,000 psi respectively) and polyester resins are the principal reinforcement constituent materials. Graphite and aramid reinforcements are being used more frequently, primarily for the more critical pressure vessels. Matrix systems are most commonly based on epoxy as it has superior mechanical properties, fatigue behavior, and heat resistance as compard with polyesters. A fiberglass overwrap of PVC pipe is an anticipated development in on-site winding and combination winding, and the compression molding of filament wound lay-ups will be investigated. The fabrication of weight-sensitive structural components may be achieved by using such moldings.

  1. Visualizing the Nonhomogeneous Structure of RAD51 Filaments Using Nanofluidic Channels.

    PubMed

    Fornander, Louise H; Frykholm, Karolin; Fritzsche, Joachim; Araya, Joshua; Nevin, Philip; Werner, Erik; Çakır, Ali; Persson, Fredrik; Garcin, Edwige B; Beuning, Penny J; Mehlig, Bernhard; Modesti, Mauro; Westerlund, Fredrik

    2016-08-23

    RAD51 is the key component of the homologous recombination pathway in eukaryotic cells and performs its task by forming filaments on DNA. In this study we investigate the physical properties of RAD51 filaments formed on DNA using nanofluidic channels and fluorescence microscopy. Contrary to the bacterial ortholog RecA, RAD51 forms inhomogeneous filaments on long DNA in vitro, consisting of several protein patches. We demonstrate that a permanent "kink" in the filament is formed where two patches meet if the stretch of naked DNA between the patches is short. The kinks are readily seen in the present microscopy approach but would be hard to identify using conventional single DNA molecule techniques where the DNA is more stretched. We also demonstrate that protein patches separated by longer stretches of bare DNA roll up on each other and this is visualized as transiently overlapping filaments. RAD51 filaments can be formed at several different conditions, varying the cation (Mg(2+) or Ca(2+)), the DNA substrate (single-stranded or double-stranded), and the RAD51 concentration during filament nucleation, and we compare the properties of the different filaments formed. The results provide important information regarding the physical properties of RAD51 filaments but also demonstrate that nanofluidic channels are perfectly suited to study protein-DNA complexes. PMID:27479732

  2. Temperature-induced structural changes in the myosin thick filament of skinned rabbit psoas muscle.

    PubMed

    Malinchik, S; Xu, S; Yu, L C

    1997-11-01

    By using synchrotron radiation and an imaging plate for recording diffraction patterns, we have obtained high-resolution x-ray patterns from relaxed rabbit psoas muscle at temperatures ranging from 1 degree C to 30 degrees C. This allowed us to obtain intensity profiles of the first six myosin layer lines and apply a model-building approach for structural analysis. At temperatures 20 degrees C and higher, the layer lines are sharp with clearly defined maxima. Modeling based on the data obtained at 20 degrees C reveals that the average center of the cross-bridges is at 135 A from the center of the thick filament and both of the myosin heads appear to wrap around the backbone. At 10 degrees C and lower, the layer lines become very weak and diffuse scattering increases considerably. At 4 degrees C, the peak of the first layer line shifts toward the meridian from 0.0047 to 0.0038 A(-1) and decreases in intensity approximately by a factor of four compared to that at 20 degrees C, although the intensities of higher-order layer lines remain approximately 10-15% of the first layer line. Our modeling suggests that as the temperature is lowered from 20 degrees C to 4 degrees C the center of cross-bridges extends radially away from the center of the filament (135 A to 175 A). Furthermore, the fraction of helically ordered cross-bridges decreases at least by a factor of two, while the isotropic disorder (the temperature factor) remains approximately unchanged. Our results on the order/disordering effects of temperature are in general agreement with earlier results of Wray [Wray, J. 1987. Structure of relaxed myosin filaments in relation to nucleotide state in vertebrate skeletal muscle. J. Muscle Res. Cell Motil. 8:62a (Abstr.)] and Lowy et al. (Lowy, J., D. Popp, and A. A. Stewart. 1991. X-ray studies of order-disorder transitions in the myosin heads of skinned rabbit psoas muscles. Biophys. J. 60:812-824). and support Poulsen and Lowy's hypothesis of coexistence of ordered

  3. The structure and poloidal dynamics of blob filaments in TJ-K

    NASA Astrophysics Data System (ADS)

    Garland, S.; Fuchert, G.; Ramisch, M.; Hirth, T.

    2016-04-01

    Relatively dense, field-aligned, filament-like structures (blobs) have been observed to propagate radially and poloidally through the scrape-off layer (SOL) in magnetically confined fusion plasmas, and contribute significantly to SOL transport. A detailed understanding of blob structure and dynamics, and their dependence on magnetic field geometry, is important in magnetic confinement physics for the prediction of heat loads on reactor wall facing components, as well as for understanding plasma confinement and neutral particle recycling. Experimentally deduced centre of mass poloidal blob velocity components, obtained using the conditional averaging technique, have been compared to an analytical blob model which has been simplified to express blob velocity in terms of the magnetic field curvature vector. Background flows are not incorporated into the analytical model, and must be added in to obtain good agreement with the experimental data. In addition, the 3D structure of blobs in TJ-K has been investigated using the conditional average of density fluctuations in two toroidally separated poloidal planes. Blobs are observed to be aligned to a flux tube near to the last closed flux surface, in the blob birth region. However at positions further along the blob trajectory, the structures do not deform according to the magnetic shear, rather they remain rigid, and retain their original form.

  4. Cell adhesion in zebrafish myogenesis: distribution of intermediate filaments, microfilaments, intracellular adhesion structures and extracellular matrix.

    PubMed

    Costa, Manoel L; Escaleira, Roberta C; Jazenko, Fernanda; Mermelstein, Claudia S

    2008-10-01

    To overcome the limitations of in vitro studies, we have been studying myogenesis in situ in zebrafish embryos, at a sub-cellular level. While in previous works we focused on myofibrillogenesis and some aspects of adhesion structures, here we describe in more detail cell adhesion structures and interactions among cytoskeletal components, membrane and extracellular matrix during zebrafish muscle development. We studied the intermediate filaments, and we describe the full range of desmin distribution in zebrafish development, from perinuclear to striated, until its deposition around the intersomite septa of older somites. This adhesion structure, positive for desmin and actin, has not been previously observed in myogenesis in vitro. We also show that actin is initially located in the intersomite septum region whereas it is confined to the myofibrils later on. While actin localization changes during development, the adhesion complex proteins vinculin, paxillin, talin, dystrophin, laminin and fibronectin always appear exclusively at the intersomite septa, and appear to be co-distributed, even though the extracellular proteins accumulates before the intracellular ones. Contrary to the adhesion proteins, that are continuously distributed, desmin and sarcomeric actin form triangular aggregates among the septa and the cytoskeleton. We studied the cytoskeletal linker plectin as well, and we show that it has a distribution similar to desmin and not to actin. We conclude that the in situ adhesion structures differ from their in vitro counterparts, and that the actual zebrafish embryo myogenesis is quite different than that which occurs in in vitro systems.

  5. Interactive Modelling of Molecular Structures

    NASA Astrophysics Data System (ADS)

    Rustad, J. R.; Kreylos, O.; Hamann, B.

    2004-12-01

    The "Nanotech Construction Kit" (NCK) [1] is a new project aimed at improving the understanding of molecular structures at a nanometer-scale level by visualization and interactive manipulation. Our very first prototype is a virtual-reality program allowing the construction of silica and carbon structures from scratch by assembling them one atom at a time. In silica crystals or glasses, the basic building block is an SiO4 unit, with the four oxygen atoms arranged around the central silicon atom in the shape of a regular tetrahedron. Two silicate units can connect to each other by their silicon atoms covalently bonding to one shared oxygen atom. Geometrically, this means that two tetrahedra can link at their vertices. Our program is based on geometric representations and uses simple force fields to simulate the interaction of building blocks, such as forming/breaking of bonds and repulsion. Together with stereoscopic visualization and direct manipulation of building blocks using wands or data gloves, this enables users to create realistic and complex molecular models in short amounts of time. The NCK can either be used as a standalone tool, to analyze or experiment with molecular structures, or it can be used in combination with "traditional" molecular dynamics (MD) simulations. In a first step, the NCK can create initial configurations for subsequent MD simulation. In a more evolved setup, the NCK can serve as a visual front-end for an ongoing MD simulation, visualizing changes in simulation state in real time. Additionally, the NCK can be used to change simulation state on-the-fly, to experiment with different simulation conditions, or force certain events, e.g., the forming of a bond, and observe the simulation's reaction. [1] http://graphics.cs.ucdavis.edu/~okreylos/ResDev/NanoTech

  6. An acidic protein aligns magnetosomes along a filamentous structure in magnetotactic bacteria.

    PubMed

    Scheffel, André; Gruska, Manuela; Faivre, Damien; Linaroudis, Alexandros; Plitzko, Jürgen M; Schüler, Dirk

    2006-03-01

    Magnetotactic bacteria are widespread aquatic microorganisms that use unique intracellular organelles to navigate along the Earth's magnetic field. These organelles, called magnetosomes, consist of membrane-enclosed magnetite crystals that are thought to help to direct bacterial swimming towards growth-favouring microoxic zones at the bottom of natural waters. Questions in the study of magnetosome formation include understanding the factors governing the size and redox-controlled synthesis of the nano-sized magnetosomes and their assembly into a regular chain in order to achieve the maximum possible magnetic moment, against the physical tendency of magnetosome agglomeration. A deeper understanding of these mechanisms is expected from studying the genes present in the identified chromosomal 'magnetosome island', for which the connection with magnetosome synthesis has become evident. Here we use gene deletion in Magnetospirillum gryphiswaldense to show that magnetosome alignment is coupled to the presence of the mamJ gene product. MamJ is an acidic protein associated with a novel filamentous structure, as revealed by fluorescence microscopy and cryo-electron tomography. We suggest a mechanism in which MamJ interacts with the magnetosome surface as well as with a cytoskeleton-like structure. According to our hypothesis, magnetosome architecture represents one of the highest structural levels achieved in prokaryotic cells.

  7. Using Data Mining and Computational Approaches to Study Intermediate Filament Structure and Function.

    PubMed

    Parry, David A D

    2016-01-01

    Experimental and theoretical research aimed at determining the structure and function of the family of intermediate filament proteins has made significant advances over the past 20 years. Much of this has either contributed to or relied on the amino acid sequence databases that are now available online, and the data mining approaches that have been developed to analyze these sequences. As the quality of sequence data is generally high, it follows that it is the design of the computational and graphical methodologies that are of especial importance to researchers who aspire to gain a greater understanding of those sequence features that specify both function and structural hierarchy. However, these techniques are necessarily subject to limitations and it is important that these be recognized. In addition, no single method is likely to be successful in solving a particular problem, and a coordinated approach using a suite of methods is generally required. A final step in the process involves the interpretation of the results obtained and the construction of a working model or hypothesis that suggests further experimentation. While such methods allow meaningful progress to be made it is still important that the data are interpreted correctly and conservatively. New data mining methods are continually being developed, and it can be expected that even greater understanding of the relationship between structure and function will be gleaned from sequence data in the coming years.

  8. A comparative study of current and magnetic structures of Weibel and filamentation instabilities

    NASA Astrophysics Data System (ADS)

    Huynh, Cong Tuan; Ryu, Chang-Mo

    2014-09-01

    A comparative study of the Weibel instability (WI) driven by anisotropic temperature and the Filamentation instability (FI) by counterstreaming plasmas are made by using a 2D Particle-in-cell code. Under the comparable initial conditions, the linear growth rates of the WI and the FI are almost the same as the theory predicts, but in the nonlinear phase, the maximum and nonlinearly saturated magnetic fields generated by the WI are always smaller than those generated by the FI. It is noted that in the initial linear growth phase, the WI and the FI both have center-filled currents, but in the nonlinear phase, the WI and the FI develop different types of current structures such that the WI maintains a center-filled current structure, whereas the FI develops a hollow current structure. Significant particle acceleration around the drift velocity is observed for the FI, whereas it is almost absent in the WI, which indicates that the enhanced velocity of the electron by particle acceleration is related to the hollow current production in the FI.

  9. On the Structure and Evolution of a Polar Crown Prominence/Filament System

    NASA Astrophysics Data System (ADS)

    Panesar, N. K.; Innes, D. E.; Schmit, D. J.; Tiwari, S. K.

    2014-08-01

    Polar crown prominences, that partially circle the Sun's poles between 60° and 70° latitude, are made of chromospheric plasma. We aim to diagnose the 3D dynamics of a polar crown prominence using high-cadence EUV images from the Solar Dynamics Observatory (SDO)/AIA at 304, 171, and 193 Å and the Ahead spacecraft of the Solar Terrestrial Relations Observatory (STEREO-A)/EUVI at 195 Å. Using time series across specific structures, we compare flows across the disk in 195 Å with the prominence dynamics seen on the limb. The densest prominence material forms vertical columns that are separated by many tens of Mm and connected by dynamic bridges of plasma that are clearly visible in 304/171 Å two-colour images. We also observe intermittent but repetitious flows with velocity 15 km s-1 in the prominence that appear to be associated with EUV bright points on the solar disk. The boundary between the prominence and the overlying cavity appears as a sharp edge. We discuss the structure of the coronal cavity seen both above and around the prominence. SDO/HMI and GONG magnetograms are used to infer the underlying magnetic topology. The evolution and structure of the prominence with respect to the magnetic field seems to agree with the filament-linkage model.

  10. Shared antigenicity between the polar filaments of myxosporeans and other Cnidaria.

    PubMed

    Ringuette, Maurice J; Koehler, Anne; Desser, Sherwin S

    2011-02-01

    Nematocysts containing coiled polar filaments are a distinguishing feature of members of the phylum Cnidaria. As a first step to characterizing the molecular structure of polar filaments, a polyclonal antiserum was raised in rabbits against a cyanogen bromide-resistant protein extract of mature cysts containing spores of Myxobolus pendula. The antiserum reacted only with proteins associated with extruded polar filaments. Western blot and whole-mount immunohistochemical analyses indicated a conservation of polar filament epitopes between M. pendula and 2 related cnidarians, i.e., the anthozoan, Nematostella vectensis, and the hydrozoan, Hydra vulgaris. This conservation of polar filament epitopes lends further support to a shared affinity between Myxozoa and cnidarians.

  11. An electrostatic spatial resonance model for coaxial helical structures with applications to the filamentous bacteriophages.

    PubMed Central

    Marzec, C J; Day, L A

    1994-01-01

    A model is presented that treats the symmetry matching problem in structures made of two interacting coaxial helices of point charges. The charges are sources of a potential field that mediates a non-specific attractive interaction between the helices. The problem is represented in Fourier space, which affords the most generality. It is found that coaxial helices with optimally mated symmetries can lock into spatial resonance configurations that maximize their interaction. The resonances are represented as vectors in a discrete three-dimensional space. Two algebraic relations are given for the four symmetry parameters of two helices in resonance. One-start inner helices interacting with coaxial one-start or NR-start outer helices are considered. Applications are made to the filamentous bacteriophages Ff, Pf1, Xf, and Pf3. The interaction given by the linearized Poisson-Boltzmann equation is calculated in this formalism to allow comparison of the electrostatic free energy of interaction of different resonance structures. Experimental nucleotide/subunit ratios are accounted for, and models for the DNA-protein interfaces are presented, with particular emphasis on Pf1. PMID:7696463

  12. Cores, Filaments, and Bundles: Hierarchical core formation in the B213 filament in Taurus

    NASA Astrophysics Data System (ADS)

    Hacar, Alvaro; Tafalla, Mario; Kauffmann, Jens; Kovacs, Attila

    2013-07-01

    Characterizing the dense core formation in filaments is a critical step for our understanding of the star formation process within molecular clouds. Using different molecular tracers to study the gas kinematics at different scales and density regimes, we have investigated the dense core formation in the B213/L1495 filament in Taurus, one of the most prominent structures identified in nearby clouds (see Hacar et al 2013, A&A, 554, A55). Our analysis of its internal kinematics demonstrates that this filament is actually a bundle of 35 velocity-coherent filaments, typically with lengths of ˜ 0.5 pc and oscillatory-like and sonic velocity field, each of them exhibiting linear masses close to the expected mass for a filament in hydrostatic equilibrium. Among them, only a small fraction of these filaments (˜1/4) are "fertile" and efficiently fragment forming all the cores identified within this region, while most of them (˜3/4) do not form cores and remain "sterile". Our observations then suggest that core formation in Taurus occurs in two steps. First, 0.5 pc-long velocity-coherent filaments condense out of the cloud gas, probably as a result of the turbulent cascade. After that, the dense cores condense quasi-statically in only those "fertile" filaments that have accumulated enough mass to became gravitational unstable, inheriting their kinematic properties. The formation of these velocity-coherent filaments appears therefore as a critical step on the star formation process being the first subsonic structures formed out of the turbulent regime that dominates the cloud dynamics at large scales.

  13. Three new structures of left-handed RADA helical filaments: structural flexibility of N-terminal domain is critical for recombinase activity.

    PubMed

    Chang, Yu-Wei; Ko, Tzu-Ping; Lee, Chien-Der; Chang, Yuan-Chih; Lin, Kuei-Ann; Chang, Chia-Seng; Wang, Andrew H-J; Wang, Ting-Fang

    2009-01-01

    RecA family proteins, including bacterial RecA, archaeal RadA, and eukaryotic Dmc1 and Rad51, mediate homologous recombination, a reaction essential for maintaining genome integrity. In the presence of ATP, these proteins bind a single-strand DNA to form a right-handed nucleoprotein filament, which catalyzes pairing and strand exchange with a homologous double-stranded DNA (dsDNA), by as-yet unknown mechanisms. We recently reported a structure of RadA left-handed helical filament, and here present three new structures of RadA left-handed helical filaments. Comparative structural analysis between different RadA/Rad51 helical filaments reveals that the N-terminal domain (NTD) of RadA/Rad51, implicated in dsDNA binding, is highly flexible. We identify a hinge region between NTD and polymerization motif as responsible for rigid body movement of NTD. Mutant analysis further confirms that structural flexibility of NTD is essential for RadA's recombinase activity. These results support our previous hypothesis that ATP-dependent axial rotation of RadA nucleoprotein helical filament promotes homologous recombination.

  14. Structural characterization of filaments formed by human Xrcc4–Cernunnos/XLF complex involved in nonhomologous DNA end-joining

    PubMed Central

    Ropars, Virginie; Drevet, Pascal; Legrand, Pierre; Baconnais, Sonia; Amram, Jeremy; Faure, Guilhem; Márquez, José A.; Piétrement, Olivier; Guerois, Raphaël; Callebaut, Isabelle; Le Cam, Eric; Revy, Patrick; de Villartay, Jean-Pierre; Charbonnier, Jean-Baptiste

    2011-01-01

    Cernunnos/XLF is a core protein of the nonhomologous DNA end-joining (NHEJ) pathway that processes the majority of DNA double-strand breaks in mammals. Cernunnos stimulates the final ligation step catalyzed by the complex between DNA ligase IV and Xrcc4 (X4). Here we present the crystal structure of the X41–157-Cernunnos1–224 complex at 5.5-Å resolution and identify the relative positions of the two factors and their binding sites. The X-ray structure reveals a filament arrangement for X41–157 and Cernunnos1–224 homodimers mediated by repeated interactions through their N-terminal head domains. A filament arrangement of the X4–Cernunnos complex was confirmed by transmission electron microscopy analyses both with truncated and full-length proteins. We further modeled the interface and used structure-based site-directed mutagenesis and calorimetry to characterize the roles of various residues at the X4–Cernunnos interface. We identified four X4 residues (Glu55, Asp58, Met61, and Phe106) essential for the interaction with Cernunnos. These findings provide new insights into the molecular bases for stimulatory and bridging roles of Cernunnos in the final DNA ligation step. PMID:21768349

  15. Solution structure of the single-stranded DNA binding protein of the filamentous Pseudomonas phage Pf3: similarity to other proteins binding to single-stranded nucleic acids.

    PubMed Central

    Folmer, R H; Nilges, M; Konings, R N; Hilbers, C W

    1995-01-01

    The three-dimensional structure of the homodimeric single-stranded DNA binding protein encoded by the filamentous Pseudomonas bacteriophage Pf3 has been determined using heteronuclear multidimensional NMR techniques and restrained molecular dynamics. NMR experiments and structure calculations have been performed on a mutant protein (Phe36 --> His) that was successfully designed to reduce the tendency of the protein to aggregate. The protein monomer is composed of a five-stranded antiparallel beta-sheet from which two beta-hairpins and a large loop protrude. The structure is compared with the single-stranded DNA binding protein encoded by the filamentous Escherichia coli phage Ff, a protein with a similar biological function and DNA binding properties, yet quite different amino acid sequence, and with the major cold shock protein of Escherichia coli, a single-stranded DNA binding protein with an entirely different sequence, biological function and binding characteristics. The amino acid sequence of the latter is highly homologous to the nucleic acid binding domain (i.e. the cold shock domain) of proteins belonging to the Y-box family. Despite their differences in amino acid sequence and function, the folds of the three proteins are remarkably similar, suggesting that this is a preferred folding pattern shared by many single-stranded DNA binding proteins. Images PMID:7556054

  16. Paired helical filaments (PHFs) are a family of single filament structures with a common helical turn period: negatively stained PHF imaged by TEM and measured before and after sonication, deglycosylation, and dephosphorylation.

    PubMed

    Ruben, George C; Wang, Jian-Zhi; Iqbal, Khalid; Grundke-Iqbal, Inge

    2005-07-01

    Isolated paired helical filaments (PHFs) were visualized on glutaraldehyde vapor-treated thin approximately 10-nm thick indirect carbon films using high-resolution transmission electron microscopy (TEM) and the negative stain, phosphotungstate acid (PTA) at near neutral pH of 6.8. PHF preparations were prepared with and without 1 minute of sonication. These same PHF were also deglycosylated with endoglycosidase F/N-glycosidase F for 1 hour or the PHF were dephosphorylated with PP-2A for 1 hour. The negatively stained PHF filaments were quantitatively studied by measuring their wide regions (W) their thin regions (T) and their helical turn period (L) and these separate parameters were averaged for each filament. In the unsonicated PHF preparation there were PHF, cylindrical filaments with periodic thin regions (CF-PT), cylindrical filaments (CF), as well as 2.0-nm tau polymer-like filaments. The CF-PT were characterized by W, T, and L measurements and the CF were characterized by diameter measurements. The paired helical filament model proposed by Kidd (1963, Nature 197:192-193) of two approximately 10 nm filaments twisting around each other every approximately 80 nm with a thin region of 10 nm and a wide region of 25 nm does not correspond to the PHF structures found. None of the PHF we observed were composed of a pair of filaments and all of the PHF appear to be a single filament. The wide regions ranged from 12.5-27 nm and the thin regions ranged from 4.5-12.3 nm. The helical turn periods ranged from 76-85 nm and were generally about 80 nm. Only the helical turn period of approximately 80 nm was a common property of the whole family of PHF structures. The CF-PT appear to be a PHF precursor filament. Deglycosylation of the PHF and CF-PT reduced their sizes by 0.5-0.6 nm and 0.7-1.0 nm, respectively, and the right-hand helicity of the PHF was lost after deglycosylation. Dephosphorylation with PP-2A reduced the PHF wide regions by 6.0 nm and the thin regions by 2

  17. Role of lattice structure and low temperature resistivity in fast-electron-beam filamentation in carbon

    NASA Astrophysics Data System (ADS)

    Dance, R. J.; Butler, N. M. H.; Gray, R. J.; MacLellan, D. A.; Rusby, D. R.; Scott, G. G.; Zielbauer, B.; Bagnoud, V.; Xu, H.; Robinson, A. P. L.; Desjarlais, M. P.; Neely, D.; McKenna, P.

    2016-01-01

    The influence of low temperature (eV to tens-of-eV) electrical resistivity on the onset of the filamentation instability in fast-electron transport is investigated in targets comprising of layers of ordered (diamond) and disordered (vitreous) carbon. It is shown experimentally and numerically that the thickness of the disordered carbon layer influences the degree of filamentation of the fast-electron beam. Strong filamentation is produced if the thickness is of the order of 60 μm or greater, for an electron distribution driven by a sub-picosecond, mid-1020 Wcm-2 laser pulse. It is shown that the position of the vitreous carbon layer relative to the fast-electron source (where the beam current density and background temperature are highest) does not have a strong effect because the resistive filamentation growth rate is high in disordered carbon over a wide range of temperatures up to the Spitzer regime.

  18. An electron microscopic and optical diffraction analysis of the structure of Limulus telson muscle thick filaments

    PubMed Central

    1982-01-01

    Long, thick filaments (greater than 4.0 micrometer) rapidly and gently isolated from fresh, unstimulated Limulus muscle by an improved procedure have been examined by electron microscopy and optical diffraction. Images of negatively stained filaments appear highly periodic with a well-preserved myosin cross-bridge array. Optical diffraction patterns of the electron micrographs show a wealth of detail and are consistent with a myosin helical repeat of 43.8 nm, similar to that observed by x-ray diffraction. Analysis of the optical diffraction patterns, in conjunction with the appearance in electron micrographs of the filaments, supports a model for the filament in which the myosin cross-bridges are arranged on a four-stranded helix, with 12 cross-bridges per turn or each helix, thus giving an axial repeat every third level of cross-bridges (43.8 nm). PMID:7199531

  19. Structural and energetic basis of infection by the filamentous bacteriophage IKe.

    PubMed

    Jakob, Roman P; Geitner, Anne-Juliane; Weininger, Ulrich; Balbach, Jochen; Dobbek, Holger; Schmid, Franz X

    2012-06-01

    Filamentous phage use the two N-terminal domains of their gene-3-proteins to initiate infection of Escherichia coli. One domain interacts with a pilus, and then the other domain binds to TolA at the cell surface. In phage fd, these two domains are tightly associated with each other, which renders the phage robust but non-infectious, because the TolA binding site is inaccessible. Activation for infection requires partial unfolding, domain disassembly and prolyl isomerization. Phage IKe infects E. coli less efficiently than phage fd. Unlike in phage fd, the pilus- and TolA-binding domains of phage IKe are independent of each other in stability and folding. The site for TolA binding is thus always accessible, but the affinity is very low. The structures of the two domains, analysed by X-ray crystallography and by NMR spectroscopy, revealed a unique fold for the N-pilus-binding domain and a conserved fold for the TolA-binding domain. The absence of an activation mechanism as in phage fd and the low affinity for TolA probably explain the low infectivity of phage IKe. They also explain why, in a previous co-evolution experiment with a mixture of phage fd and phage IKe, all hybrid phage adopted the superior infection mechanism of phage fd.

  20. The Rapid Formation of a Filament Caused by Magnetic Reconnection between Two Sets of Dark Threadlike Structures

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Jiang, Yunchun; Yang, Jiayan; Yu, Shunping; Xu, Zhe

    2016-01-01

    Taking advantage of the high spatiotemporal resolution observations from the Atmospheric Imaging Assembly (AIA) and the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we present rare observations of the rapid formation of a filament caused by magnetic reconnection between two sets of dark threadlike structures. The two sets of dark threadlike structures belong to distinct flux systems with their adjacent ends anchored in an opposite-polarity magnetic field region, where the calculated photospheric velocity field shows that converging flows dominate there. Due to the converging flows, opposite-polarity magnetic flux converged and then canceled, leading to the formation of extreme ultraviolet (EUV) brightening that spread in opposite directions along the spine of the dark threadlike structures. Meanwhile, very weak remote brightening in the other terminals of the dark threadlike structures, as well as EUV loops, which rooted in the opposite-polarity magnetic field region, appeared. In addition, all of the AIA Fe line observations reveal that a flux rope was formed and underwent a rolling motion during the fadeaway of the EUV brightening. Soon after, as the EUV brightening disappeared, a filament that is very likely composed of two sets of intertwined dark threadlike structures was formed. Via differential emission measure (EM) analysis, it is found that both the EM and temperature of the plasma around the flux-canceling site increased during the brightening, implying that there, magnetic reconnection may occur to heat the plasma. These observations provide evidence that the filament is formed by magnetic reconnection associated with flux convergence and cancellation, and the magnetic structure of the filament is most likely a flux rope.

  1. THE RAPID FORMATION OF A FILAMENT CAUSED BY MAGNETIC RECONNECTION BETWEEN TWO SETS OF DARK THREADLIKE STRUCTURES

    SciTech Connect

    Yang, Bo; Jiang, Yunchun; Yang, Jiayan; Yu, Shunping; Xu, Zhe E-mail: yjy@ynao.ac.cn

    2016-01-01

    Taking advantage of the high spatiotemporal resolution observations from the Atmospheric Imaging Assembly (AIA) and the Helioseismic and Magnetic Imager on board the Solar Dynamics Observatory, we present rare observations of the rapid formation of a filament caused by magnetic reconnection between two sets of dark threadlike structures. The two sets of dark threadlike structures belong to distinct flux systems with their adjacent ends anchored in an opposite-polarity magnetic field region, where the calculated photospheric velocity field shows that converging flows dominate there. Due to the converging flows, opposite-polarity magnetic flux converged and then canceled, leading to the formation of extreme ultraviolet (EUV) brightening that spread in opposite directions along the spine of the dark threadlike structures. Meanwhile, very weak remote brightening in the other terminals of the dark threadlike structures, as well as EUV loops, which rooted in the opposite-polarity magnetic field region, appeared. In addition, all of the AIA Fe line observations reveal that a flux rope was formed and underwent a rolling motion during the fadeaway of the EUV brightening. Soon after, as the EUV brightening disappeared, a filament that is very likely composed of two sets of intertwined dark threadlike structures was formed. Via differential emission measure (EM) analysis, it is found that both the EM and temperature of the plasma around the flux-canceling site increased during the brightening, implying that there, magnetic reconnection may occur to heat the plasma. These observations provide evidence that the filament is formed by magnetic reconnection associated with flux convergence and cancellation, and the magnetic structure of the filament is most likely a flux rope.

  2. The Molecular Architecture for the Intermediate Filaments of Hard α -Keratin Based on the Superlattice Data Obtained from a Study of Mammals Using Synchrotron Fibre Diffraction

    DOE PAGES

    James, Veronica

    2011-01-01

    High- and low-angle X-ray diffraction studies of hard α -keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard α -keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, includingmore » multiple-time exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard α -keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid α -keratin structure.« less

  3. The Molecular Architecture for the Intermediate Filaments of Hard α-Keratin Based on the Superlattice Data Obtained from a Study of Mammals Using Synchrotron Fibre Diffraction

    PubMed Central

    James, Veronica

    2011-01-01

    High- and low-angle X-ray diffraction studies of hard α-keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard α-keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-time exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard α-keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid α-keratin structure. PMID:22028970

  4. The Molecular Architecture for the Intermediate Filaments of Hard [alpha]-Keratin Based on the Superlattice Data Obtained from a Study ofMammals Using Synchrotron Fibre Diffraction

    SciTech Connect

    James, Veronica

    2014-09-24

    High- and low-angle X-ray diffraction studies of hard {alpha}-keratin have been studied, and various models have been proposed over the last 70 years. Most of these studies have been confined to one or two forms of alpha keratin. This high- and low-angle synchrotron fibre diffraction study extends the study to cover all available data for all known forms of hard {alpha}-keratin including hairs, fingernails, hooves, horn, and quills from mammals, marsupials, and a monotreme, and it confirms that the model proposed is universally acceptable for all mammals. A complete Bragg analysis of the meridional diffraction patterns, including multiple-time exposures to verify any weak reflections, verified the existence of a superlattice consisting of two infinite lattices and three finite lattices. An analysis of the equatorial patterns establishes the radii of the oligomeric levels of dimers, tetramers, and intermediate filaments (IFs) together with the centre to centre distance for the IFs, thus confirming the proposed helices within helices molecular architecture for hard {alpha}-keratin. The results verify that the structure proposed by Feughelman and James meets the criteria for a valid {alpha}-keratin structure.

  5. Structural basis for stabilization of the hypervariable D3 domain of Salmonella flagellin upon filament formation.

    PubMed

    Muskotál, Adél; Seregélyes, Csaba; Sebestyén, Anett; Vonderviszt, Ferenc

    2010-11-01

    The hypervariable D3 domain of Salmonella flagellin, composed of residues 190-283, is situated at the outer surface of flagellar filaments. A flagellin mutant deprived of the complete D3 domain (ΔD3_FliC) exhibited a significantly decreased thermal stability (T(m) 41.9 °C) as compared to intact flagellin (T(m) 47.3 °C). However, the stability of filaments formed from ΔD3_FliC subunits was virtually identical with that of native flagellar filaments. While D3 comprises the most stable part of monomeric flagellin playing an important role in the stabilization of the other two (D1 and D2) domains, the situation is reversed in the polymeric state. Upon filament formation, ordering of the disordered terminal regions of flagellin in the core part of the filament results in the stabilization of the radially arranged D1 and D2 domains, and there is a substantial increase of stability even in the distant outermost D3 domain, which is connected to D2 via a pair of short antiparallel β-strands. Our experiments revealed that crosslinking the ends of the isolated D3 domain through a disulfide bridge gives rise to a stabilization effect reminiscent of that observed upon polymerization. It appears that the short interdomain linker between domains D2 and D3 serves as a stabilization center that facilitates propagation of the conformational signal from the filament core to the outer part of filament. Because D3 is a largely independent part of flagellin, its replacement by heterologous proteins or domains might offer a promising approach for creation of various fusion proteins possessing polymerization ability.

  6. Band Spectra and Molecular Structure

    NASA Astrophysics Data System (ADS)

    Kronig, R. De L.

    2011-06-01

    Introduction; Part I. The Energy Levels of Diatomic Molecules and their Classification by Means of Quantum Numbers: 1. General foundations; 2. Wave mechanics of diatomic molecules; 3. Electronic levels; 4. Vibrational levels; 5. Rotational levels; 6. Stark and Zeeman effect; 7. Energy levels of polyatomic molecules; Part II. Fine Structure and Wave Mechanical Properties of the Energy Levels of Diatomic Molecules: 8. The perturbation function; 9. Rotational distortion of spin multiplets; 10. Fine structure; 11. Perturbations and predissociation; 12. Even and odd levels; 13. Symmetrical and antisymmetrical levels; Part III. Selection Rules and Intensities in Diatomic Molecules: 14. General foundations; 15. Electronic bands; 16. Vibrational bands; 17. Rotational bands; 18. Band spectra and nuclear structure; 19. Transitions in the Stark and Zeeman effect; Part IV. Macroscopic Properties of Molecular Gases: 20. Scattering; 21. Dispersion; 22. Kerr and Faraday effect; 23. Dielectric constants; 24. Magnetic susceptibilities; 25. Specific heats; Part V. Molecule Formation and Chemical Binding: 26. Heteropolar molecules; 27. Homopolar molecules. Chemical forces between two H-atoms and two He-atoms; 28. The general theory of homopolar compounds; Bibliography; Subject index.

  7. FRET Study of the Structural and Kinetic Effects of PKC Phosphomimetic Cardiac Troponin T Mutants on Thin Filament Regulation

    PubMed Central

    Schlecht, William; Zhou, Zhiqun; Li, King-Lun; Rieck, Daniel; Ouyang, Yexin; Dong, Wen-Ji

    2014-01-01

    FRET was used to investigate the structural and kinetic effects that PKC phosphorylations exert on Ca2+ and myosin subfragment-1 dependent conformational transitions of the cardiac thin filament. PKC phosphorylations of cTnT were mimicked by glutamate substitution. Ca2+ and S1-induced distance changes between the central linker of cTnC and the switch region of cTnI (cTnI-Sr) were monitored in reconstituted thin filaments using steady state and time resolved FRET, while kinetics of structural transitions were determined using stopped flow. Thin filament Ca2+ sensitivity was found to be significantly blunted by the presence of the cTnT(T204E) mutant, whereas pseudo-phosphorylation at additional sites increased the Ca2+-sensitivty. The rate of Ca2+-dissociation induced structural changes was decreased in the C-terminal end of cTnI-Sr in the presence of pseudo-phosphorylations while remaining unchanged at the N-terminal end of this region. Additionally, the distance between cTnI-Sr and cTnC was decreased significantly for the triple and quadruple phosphomimetic mutants cTnT(T195E/S199E/T204E) and cTnT(T195E/S199E/T204E/T285E), which correlated with the Ca2+-sensitivity increase seen in these same mutants. We conclude that significant changes in thin filament Ca2+-sensitivity, structure and kinetics are brought about through PKC phosphorylation of cTnT. These changes can either decrease or increase Ca2+-sensitivity and likely play an important role in cardiac regulation. PMID:24708997

  8. Morphological, molecular, and mycotoxigenic identification of dominant filamentous fungi from moldy civil cheese.

    PubMed

    Cakmakci, Songul; Cetin, Bulent; Gurses, Mustafa; Dagdemir, Elif; Hayaloglu, Ali Adnan

    2012-11-01

    Moldy Civil is a mold-ripened variety of cheese produced mainly in eastern Turkey. This cheese is produced with Civil cheese and whey curd cheese (Lor). Civil cheese has had a geographical presence since 2009 and is manufactured with skim milk. In the production of Moldy Civil cheese, Civil cheese or a mixture of Civil and Lor cheese is pressed into goat skins or plastic bags and ripened for 3 months or longer. During the ripening period, natural contaminating molds grow on the surface of and inside the cheese. In this study, 186 mold strains were isolated from 41 samples of Moldy Civil cheese, and 165 of these strains were identified as Penicillium roqueforti. Identification and mycotoxicologic analyses were conducted using morphotypic and molecular methods. PCR amplicons of the ITS1-5.8S-ITS4 region were subjected to sequence analysis. This research is the first using molecular methods on Moldy Civil cheese. Mycotoxicologic analyses were conducted using thin-layer chromatography, and random amplified polymorphic DNA genotypes were determined using the ari1 primer. Of 165 isolates, only 28 produced no penicillic acid, P. roqueforti toxin, or roquefortine.

  9. USING CORONAL CELLS TO INFER THE MAGNETIC FIELD STRUCTURE AND CHIRALITY OF FILAMENT CHANNELS

    SciTech Connect

    Sheeley, N. R. Jr.; Warren, H. P.; Martin, S. F.; Panasenco, O.

    2013-08-01

    Coronal cells are visible at temperatures of {approx}1.2 MK in Fe XII coronal images obtained from the Solar Dynamics Observatory and Solar Terrestrial Relations Observatory spacecraft. We show that near a filament channel, the plumelike tails of these cells bend horizontally in opposite directions on the two sides of the channel like fibrils in the chromosphere. Because the cells are rooted in magnetic flux concentrations of majority polarity, these observations can be used with photospheric magnetograms to infer the direction of the horizontal field in filament channels and the chirality of the associated magnetic field. This method is similar to the procedure for inferring the direction of the magnetic field and the chirality of the fibril pattern in filament channels from H{alpha} observations. However, the coronal cell observations are easier to use and provide clear inferences of the horizontal field direction for heights up to {approx}50 Mm into the corona.

  10. How is kinematic structure connected to the core scale from filament scale?; Mopra mapping observations with multi-lines of dense cores in Lupus I

    NASA Astrophysics Data System (ADS)

    Kiyokane, Kazuhiro; Saito, Masao; Tachihara, Kengo; Saigo, Kazuya; van Kempen, Tim; Cortes, Paulo; Hill, Tracey; Knee, Lewis; Kurono, Yasutaka; Takahashi, Satoko; Aya, Higuchi; Nyman, Lars-Ake

    2014-06-01

    Recently, high sensitivity mappings of nearby molecular clouds in far-infrared and submillimeter wavelengths with Hershel and AzTEC/ASTE show ubiquitous existence of the filamentary structures with 0.1-pc uniform width. It is important to investigate dense core formation from large scale structure via fragmentation. We have conducted MOPRA multi-line mapping observations covered on 0.02 - 0.2 pc scales of 8 dense cores in a filamentary cloud of nearby Lupus I at 140 pc. A class 0/I protostellar core IRAS 15398-3359 is included as a sample, which has an adjacent prestellar core with the separation of 0.13pc in the west. The maps of N2H+, HNC, HC3N show well associated with each core. The velocity field of C18O shows 1.4 km/s/pc from north to south over the region containing two dense cores, which is consistent with past observation of NANTEN. In contrast to C18O results, the velocity field of HC3N shows different structures, which suggest counter rotation of two dense cores; 1.2 km/s/pc from north-west to south-east around a protostellar core and 0.8 km/s/pc from east to west around a presteller core. The filament will be fragmentized and collapsed to dense cores when the line density is over 2Cs/G (where Cs is sound speed and G is gravitational constant). If that velocity gradient was caused by such situation, it should be red-blue-red-blue across two dense cores but the observed kinematics is not consistent with this scenario, which requires that the filament structure would be extremely curved with a skew angle. Although we cannot reject the collapsing interruption, those results suggest the spin-up rotating picture separated from large-scale structure.

  11. RUI: Structure and Behavior of RF-Driven Plasma Filaments in High-Pressure Gases

    SciTech Connect

    Burin, Michael J.

    2014-11-18

    The filamentary discharge seen within commercial plasma globes is commonly enjoyed, yet not well understood. We investigate filament properties in a plasma globe using a variable high voltage amplifier. Results from the 3-year grant period and their physics are discussed.

  12. Safety evaluation design of filament wound structures - Cases of pressure vessels and pipes

    NASA Astrophysics Data System (ADS)

    Kawahara, Masanori; Mori, Takao; Hirase, Yosihiro; Katoh, Akihiko; Ishihara, Toshio

    Procedures are presented for the safety-related evaluation of filament-wound composite products, such as pressure vessels and pipes. In order to increase the fatigue strength of pressure vessel metallic liners subject to cyclic internal pressures, by controlling residual stresses, the 'autofrettage' overpressuring treatment has been devised.

  13. Atomic structure of the vimentin central α-helical domain and its implications for intermediate filament assembly.

    PubMed

    Chernyatina, Anastasia A; Nicolet, Stefan; Aebi, Ueli; Herrmann, Harald; Strelkov, Sergei V

    2012-08-21

    Together with actin filaments and microtubules, intermediate filaments (IFs) are the basic cytoskeletal components of metazoan cells. Over 80 human diseases have been linked to mutations in various IF proteins to date. However, the filament structure is far from being resolved at the atomic level, which hampers rational understanding of IF pathologies. The elementary building block of all IF proteins is a dimer consisting of an α-helical coiled-coil (CC) "rod" domain flanked by the flexible head and tail domains. Here we present three crystal structures of overlapping human vimentin fragments that comprise the first half of its rod domain. Given the previously solved fragments, a nearly complete atomic structure of the vimentin rod has become available. It consists of three α-helical segments (coils 1A, 1B, and 2) interconnected by linkers (L1 and L12). Most of the CC structure has a left-handed twist with heptad repeats, but both coil 1B and coil 2 also exhibit untwisted, parallel stretches with hendecad repeats. In the crystal structure, linker L1 was found to be α-helical without being involved in the CC formation. The available data allow us to construct an atomic model of the antiparallel tetramer representing the second level of vimentin assembly. Although the presence of the nonhelical head domains is essential for proper tetramer stabilization, the precise alignment of the dimers forming the tetramer appears to depend on the complementarity of their surface charge distribution patterns, while the structural plasticity of linker L1 and coil 1A plays a role in the subsequent IF assembly process.

  14. Titin strain contributes to the Frank-Starling law of the heart by structural rearrangements of both thin- and thick-filament proteins.

    PubMed

    Ait-Mou, Younss; Hsu, Karen; Farman, Gerrie P; Kumar, Mohit; Greaser, Marion L; Irving, Thomas C; de Tombe, Pieter P

    2016-02-23

    The Frank-Starling mechanism of the heart is due, in part, to modulation of myofilament Ca(2+) sensitivity by sarcomere length (SL) [length-dependent activation (LDA)]. The molecular mechanism(s) that underlie LDA are unknown. Recent evidence has implicated the giant protein titin in this cellular process, possibly by positioning the myosin head closer to actin. To clarify the role of titin strain in LDA, we isolated myocardium from either WT or homozygous mutant (HM) rats that express a giant splice isoform of titin, and subjected the muscles to stretch from 2.0 to 2.4 μm of SL. Upon stretch, HM compared with WT muscles displayed reduced passive force, twitch force, and myofilament LDA. Time-resolved small-angle X-ray diffraction measurements of WT twitching muscles during diastole revealed stretch-induced increases in the intensity of myosin (M2 and M6) and troponin (Tn3) reflections, as well as a reduction in cross-bridge radial spacing. Independent fluorescent probe analyses in relaxed permeabilized myocytes corroborated these findings. X-ray electron density reconstruction revealed increased mass/ordering in both thick and thin filaments. The SL-dependent changes in structure observed in WT myocardium were absent in HM myocardium. Overall, our results reveal a correlation between titin strain and the Frank-Starling mechanism. The molecular basis underlying this phenomenon appears not to involve interfilament spacing or movement of myosin toward actin but, rather, sarcomere stretch-induced simultaneous structural rearrangements within both thin and thick filaments that correlate with titin strain and myofilament LDA.

  15. Titin strain contributes to the Frank–Starling law of the heart by structural rearrangements of both thin- and thick-filament proteins

    PubMed Central

    Ait-Mou, Younss; Hsu, Karen; Farman, Gerrie P.; Kumar, Mohit; Greaser, Marion L.; Irving, Thomas C.; de Tombe, Pieter P.

    2016-01-01

    The Frank–Starling mechanism of the heart is due, in part, to modulation of myofilament Ca2+ sensitivity by sarcomere length (SL) [length-dependent activation (LDA)]. The molecular mechanism(s) that underlie LDA are unknown. Recent evidence has implicated the giant protein titin in this cellular process, possibly by positioning the myosin head closer to actin. To clarify the role of titin strain in LDA, we isolated myocardium from either WT or homozygous mutant (HM) rats that express a giant splice isoform of titin, and subjected the muscles to stretch from 2.0 to 2.4 μm of SL. Upon stretch, HM compared with WT muscles displayed reduced passive force, twitch force, and myofilament LDA. Time-resolved small-angle X-ray diffraction measurements of WT twitching muscles during diastole revealed stretch-induced increases in the intensity of myosin (M2 and M6) and troponin (Tn3) reflections, as well as a reduction in cross-bridge radial spacing. Independent fluorescent probe analyses in relaxed permeabilized myocytes corroborated these findings. X-ray electron density reconstruction revealed increased mass/ordering in both thick and thin filaments. The SL-dependent changes in structure observed in WT myocardium were absent in HM myocardium. Overall, our results reveal a correlation between titin strain and the Frank–Starling mechanism. The molecular basis underlying this phenomenon appears not to involve interfilament spacing or movement of myosin toward actin but, rather, sarcomere stretch-induced simultaneous structural rearrangements within both thin and thick filaments that correlate with titin strain and myofilament LDA. PMID:26858417

  16. Structure of myosin filaments from relaxed Lethocerus flight muscle by cryo-EM at 6 Å resolution

    PubMed Central

    Hu, Zhongjun; Taylor, Dianne W.; Reedy, Michael K.; Edwards, Robert J.; Taylor, Kenneth A.

    2016-01-01

    We describe a cryo–electron microscopy three-dimensional image reconstruction of relaxed myosin II–containing thick filaments from the flight muscle of the giant water bug Lethocerus indicus. The relaxed thick filament structure is a key element of muscle physiology because it facilitates the reextension process following contraction. Conversely, the myosin heads must disrupt their relaxed arrangement to drive contraction. Previous models predicted that Lethocerus myosin was unique in having an intermolecular head-head interaction, as opposed to the intramolecular head-head interaction observed in all other species. In contrast to the predicted model, we find an intramolecular head-head interaction, which is similar to that of other thick filaments but oriented in a distinctly different way. The arrangement of myosin’s long α-helical coiled-coil rod domain has been hypothesized as either curved layers or helical subfilaments. Our reconstruction is the first report having sufficient resolution to track the rod α helices in their native environment at resolutions ~5.5 Å, and it shows that the layer arrangement is correct for Lethocerus. Threading separate paths through the forest of myosin coiled coils are four nonmyosin peptides. We suggest that the unusual position of the heads and the rod arrangement separated by nonmyosin peptides are adaptations for mechanical signal transduction whereby applied tension disrupts the myosin heads as a component of stretch activation. PMID:27704041

  17. Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8

    PubMed Central

    Nagayoshi, Yuko; Kumagae, Kenta; Mori, Kazuki; Tashiro, Kosuke; Nakamura, Ayano; Fujino, Yasuhiro; Hiromasa, Yasuaki; Iwamoto, Takeo; Kuhara, Satoru; Ohshima, Toshihisa; Doi, Katsumi

    2016-01-01

    A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell. PMID:26941711

  18. Physiological Properties and Genome Structure of the Hyperthermophilic Filamentous Phage φOH3 Which Infects Thermus thermophilus HB8.

    PubMed

    Nagayoshi, Yuko; Kumagae, Kenta; Mori, Kazuki; Tashiro, Kosuke; Nakamura, Ayano; Fujino, Yasuhiro; Hiromasa, Yasuaki; Iwamoto, Takeo; Kuhara, Satoru; Ohshima, Toshihisa; Doi, Katsumi

    2016-01-01

    A filamentous bacteriophage, φOH3, was isolated from hot spring sediment in Obama hot spring in Japan with the hyperthermophilic bacterium Thermus thermophilus HB8 as its host. Phage φOH3, which was classified into the Inoviridae family, consists of a flexible filamentous particle 830 nm long and 8 nm wide. φOH3 was stable at temperatures ranging from 70 to 90°C and at pHs ranging from 6 to 9. A one-step growth curve of the phage showed a 60-min latent period beginning immediately postinfection, followed by intracellular virus particle production during the subsequent 40 min. The released virion number of φOH3 was 109. During the latent period, both single stranded DNA (ssDNA) and the replicative form (RF) of phage DNA were multiplied from min 40 onward. During the release period, the copy numbers of both ssDNA and RF DNA increased sharply. The size of the φOH3 genome is 5688 bp, and eight putative open reading frames (ORFs) were annotated. These ORFs were encoded on the plus strand of RF DNA and showed no significant homology with any known phage genes, except ORF 5, which showed 60% identity with the gene VIII product of the Thermus filamentous phage PH75. All the ORFs were similar to predicted genes annotated in the Thermus aquaticus Y51MC23 and Meiothermus timidus DSM 17022 genomes at the amino acid sequence level. This is the first report of the whole genome structure and DNA multiplication of a filamentous T. thermophilus phage within its host cell. PMID:26941711

  19. Rheology of Vimentin Intermediate Filament Networks

    NASA Astrophysics Data System (ADS)

    Wu, Huayin

    2012-02-01

    A cell's ability to function is highly dependent on its structure and material properties - its capacity to withstand and respond to forces in its environment. The cytoskeleton, which largely determines the cellular mechanical properties, is comprised of biopolymer networks, including filamentous actin, microtubules, and intermediate filaments (IF). Intermediate filaments are much less studied than actin and microtubules. They are much more varied and specialized as well, and have been suggested as being an important platform in mechanotransduction processes in cells. It is thought that they can withstand very high strains and exhibit strain stiffening behavior. We are characterizing vimentin, a type III IF that is found in all vertebrate cells, using rheological techniques. Vimentin elasticity increases upon addition of multivalent cations, which act like molecular crosslinkers. By varying the concentration of cations, we can extract valuable information about how the networks assemble and function.

  20. Spectro-polarimetric observation of the fine structure of a quiescent filament

    NASA Astrophysics Data System (ADS)

    Zong, W. G.; Tang, Y. H.; Fang, C.; Mein, P.; Mein, N.; Xu, A. A.

    2003-12-01

    This paper presents the spectro-polarimetric measurements of a big quiescent filament observed by the MSDP mode of the THEMIS on August 24, 2000. The Hα , CaII 8542 and NaI D2 line profiles of a segment of the filament were obtained. By use of the Hα images with high spatial resolution, the two barb endpoints were identified. The parameters at the barbs' endpoints, including intensity, velocity and longitudinal magnetic field were measured. Using the data with high spatial resolution (0.16'' per pixel), we have found the following results. 1) There was mass motion at the barb endpoints in the chromosphere, the values and the directions of the mass motion at the barb endpoints change in several minutes. 2) The two barb endpoints are located between the majority polarities and the minority polarities.

  1. Structural CNT Composites. Part I; Developing a Carbon Nanotube Filament Winder

    NASA Technical Reports Server (NTRS)

    Sauti, Godfrey; Kim, Jae-Woo; Wincheski, Russell A.; Antczak, Andrew; Campero, Jamie C.; Luong, Hoa H.; Shanahan, Michelle H.; Stelter, Christopher J.; Siochi, Emilie J.

    2015-01-01

    Carbon nanotube (CNT) based materials promise advances in the production of high strength and multifunctional components for aerospace and other applications. Specifically, in tension dominated applications, the latest CNT based filaments are yielding composite properties comparable to or exceeding composites from more established fibers such as Kevlar and carbon fiber. However, for the properties of these materials to be fully realized at the component level, suitable manufacturing processes have to be developed. These materials handle differently from conventional fibers, with different wetting characteristics and behavior under load. The limited availability of bulk forms also requires that the equipment be scaled down accordingly to tailor the process development approach to material availability. Here, the development of hardware and software for filament winding of carbon nanotube based tapes and yarns is described. This hardware features precision guidance of the CNT material and control of the winding tension over a wide range in an open architecture that allows for effective process control and troubleshooting during winding. Use of the filament winder to develop CNT based Composite Overwrapped Pressure Vessels (COPVs) shall also be discussed.

  2. G359.97-0.038: A Hard X-Ray Filament Associated with a Supernova Shell-Molecular Cloud Interaction

    NASA Astrophysics Data System (ADS)

    Nynka, Melania; Hailey, Charles J.; Zhang, Shuo; Morris, Mark M.; Zhao, Jun-Hui; Goss, Miller; Bauer, Franz E.; Boggs, Stephen E.; Craig, William W.; Christensen, Finn E.; Gotthelf, Eric V.; Harrison, Fiona A.; Mori, Kaya; Perez, Kerstin M.; Stern, Daniel; Zhang, William W.

    2015-02-01

    We present the first high-energy X-ray (>10 keV) observations of the non-thermal filament G359.97-0.038 using the Nuclear Spectroscopic Telescope Array (NuSTAR). This filament is one of approximately 20 X-ray filaments of unknown origin located in the central 20 pc region in the Galactic Center near Sgr A*. Its NuSTAR and Chandra broadband spectrum is characterized by a single power law with Γ = 1.3 ± 0.3 that extends from 2 to 50 keV, with an unabsorbed luminosity of 1.3 × 1033 erg s-1 (d/8 kpc)2 in the 2-8 keV band. Despite possessing a cometary X-ray morphology that is typical of a pulsar wind nebula (PWN) in high-resolution Chandra imaging, our spatially resolved Chandra spectral analysis found no significant spectral softening along the filament as would be expected from particle synchrotron cooling. Coincident radio emission is detected using the Very Large Array at 5.5 and 8.3 GHz. We examine and subsequently discard a PWN or magnetic flux tube as the origin of G359.97-0.038. We use broadband spectral characteristics and a morphological analysis to show that G359.97-0.038 is likely an interaction site between the shell of Sgr A East and an adjacent molecular cloud. This is supported by CS molecular line spectroscopy and the presence of an OH maser.

  3. G359.97-0.038: A HARD X-RAY FILAMENT ASSOCIATED WITH A SUPERNOVA SHELL-MOLECULAR CLOUD INTERACTION

    SciTech Connect

    Nynka, Melania; Hailey, Charles J.; Zhang, Shuo; Gotthelf, Eric V.; Mori, Kaya; Perez, Kerstin M.; Morris, Mark M.; Zhao, Jun-Hui; Goss, Miller; Bauer, Franz E.; Boggs, Stephen E.; Craig, William W.; Christensen, Finn E.; Harrison, Fiona A.; Stern, Daniel; Zhang, William W.

    2015-02-20

    We present the first high-energy X-ray (>10 keV) observations of the non-thermal filament G359.97-0.038 using the Nuclear Spectroscopic Telescope Array (NuSTAR). This filament is one of approximately 20 X-ray filaments of unknown origin located in the central 20 pc region in the Galactic Center near Sgr A*. Its NuSTAR and Chandra broadband spectrum is characterized by a single power law with Γ = 1.3 ± 0.3 that extends from 2 to 50 keV, with an unabsorbed luminosity of 1.3 × 10{sup 33} erg s{sup –1} (d/8 kpc){sup 2} in the 2-8 keV band. Despite possessing a cometary X-ray morphology that is typical of a pulsar wind nebula (PWN) in high-resolution Chandra imaging, our spatially resolved Chandra spectral analysis found no significant spectral softening along the filament as would be expected from particle synchrotron cooling. Coincident radio emission is detected using the Very Large Array at 5.5 and 8.3 GHz. We examine and subsequently discard a PWN or magnetic flux tube as the origin of G359.97-0.038. We use broadband spectral characteristics and a morphological analysis to show that G359.97-0.038 is likely an interaction site between the shell of Sgr A East and an adjacent molecular cloud. This is supported by CS molecular line spectroscopy and the presence of an OH maser.

  4. Insights into the mechanism of Rad51 recombinase from the structure and properties of a filament interface mutant

    SciTech Connect

    Chen, Jianhong; Villanueva, Nicolas; Rould, Mark A.; Morrical, Scott W.

    2010-09-03

    Rad51 protein promotes homologous recombination in eukaryotes. Recombination activities are activated by Rad51 filament assembly on ssDNA. Previous studies of yeast Rad51 showed that His352 occupies an important position at the filament interface, where it could relay signals between subunits and active sites. To investigate, we characterized yeast Rad51 H352A and H352Y mutants, and solved the structure of H352Y. H352A forms catalytically competent but salt-labile complexes on ssDNA. In contrast, H352Y forms salt-resistant complexes on ssDNA, but is defective in nucleotide exchange, RPA displacement and strand exchange with full-length DNA substrates. The 2.5 {angstrom} crystal structure of H352Y reveals a right-handed helical filament in a high-pitch (130 {angstrom}) conformation with P61 symmetry. The catalytic core and dimer interface regions of H352Y closely resemble those of DNA-bound Escherichia coli RecA protein. The H352Y mutation stabilizes Phe187 from the adjacent subunit in a position that interferes with the {gamma}-phosphate-binding site of the Walker A motif/P-loop, potentially explaining the limited catalysis observed. Comparison of Rad51 H352Y, RecA-DNA and related structures reveals that the presence of bound DNA correlates with the isomerization of a conserved cis peptide near Walker B to the trans configuration, which appears to prime the catalytic glutamate residue for ATP hydrolysis.

  5. Solid friction between soft filaments.

    PubMed

    Ward, Andrew; Hilitski, Feodor; Schwenger, Walter; Welch, David; Lau, A W C; Vitelli, Vincenzo; Mahadevan, L; Dogic, Zvonimir

    2015-06-01

    Any macroscopic deformation of a filamentous bundle is necessarily accompanied by local sliding and/or stretching of the constituent filaments. Yet the nature of the sliding friction between two aligned filaments interacting through multiple contacts remains largely unexplored. Here, by directly measuring the sliding forces between two bundled F-actin filaments, we show that these frictional forces are unexpectedly large, scale logarithmically with sliding velocity as in solid-like friction, and exhibit complex dependence on the filaments' overlap length. We also show that a reduction of the frictional force by orders of magnitude, associated with a transition from solid-like friction to Stokes's drag, can be induced by coating F-actin with polymeric brushes. Furthermore, we observe similar transitions in filamentous microtubules and bacterial flagella. Our findings demonstrate how altering a filament's elasticity, structure and interactions can be used to engineer interfilament friction and thus tune the properties of fibrous composite materials.

  6. Spatial structure of scrape-off-layer filaments near the midplane and X-point regions of Alcator C-Mod

    SciTech Connect

    Terry, J L; Zweben, S J; Umansky, M V; Cziegler, I; Grulke, O; LaBombard, B; Stotler, D P

    2008-05-22

    Movies of edge turbulence at both the outboard midplane and the region outboard of the typical lower X-point location in C-Mod have been obtained using Gas-Puff-Imaging together with fast-framing cameras. Intermittent turbulent structures, typically referred to as blobs or filaments, are observed in both locations. Near the midplane the filaments are roughly circular in cross-section, while in the X-point region they are highly elongated. Filament velocities in this region are {approx}3x faster than the radial velocities at the midplane, in a direction roughly normal to the local flux surfaces. The observations are consistent with the picture that the filaments arise in outboard region and, as a consequence of the rapid parallel diffusion of the potential perturbations, map along field lines. A simulation using the 3D BOUT turbulence code has been made, with the result that reproduces many of the spatial features observed in the experiment.

  7. Filament theory based WORM memory devices using aluminum/poly(9-vinylcarbazole)/aluminum structures.

    PubMed

    Suresh, Aswin; Krishnakumar, Govind; Namboothiry, Manoj A G

    2014-07-14

    Spin coated poly(N-vinylcarbazole) (PVK) sandwiched between thermally evaporated aluminum (Al) electrodes on a glass substrate showed unipolar Write Once Read Many times (WORM) characteristics. The pristine devices were in the low resistance ON state exhibiting ohmic behavior and at a voltage near -2 V, they switched abruptly to the high resistance OFF state showing space charge limited current (SCLC). We suggest that the rupturing of metallic filaments due to Joule heating may explain the effect. The WORM devices exhibited an ON/OFF ratio of 10(8), a retention of 1000 s and an endurance of ∼10(6) cycles in both ON and OFF states. PMID:24888392

  8. Effect of Tropomyosin on Formin-Bound Actin Filaments

    PubMed Central

    Ujfalusi, Zoltán; Vig, Andrea; Hild, Gábor; Nyitrai, Miklós

    2009-01-01

    Abstract Formins are conservative proteins with important roles in the regulation of the microfilament system in eukaryotic cells. Previous studies showed that the binding of formins to actin made the structure of actin filaments more flexible. Here, the effects of tropomyosin on formin-induced changes in actin filaments were investigated using fluorescence spectroscopic methods. The temperature dependence of the Förster-type resonance energy transfer showed that the formin-induced increase of flexibility of actin filaments was diminished by the binding of tropomyosin to actin. Fluorescence anisotropy decay measurements also revealed that the structure of flexible formin-bound actin filaments was stabilized by the binding of tropomyosin. The stabilizing effect reached its maximum when all binding sites on actin were occupied by tropomyosin. The effect of tropomyosin on actin filaments was independent of ionic strength, but became stronger as the magnesium concentration increased. Based on these observations, we propose that in cells there is a molecular mechanism in which tropomyosin binding to actin plays an important role in forming mechanically stable actin filaments, even in the case of formin-induced rapid filament assembly. PMID:18931257

  9. Molecular and Supermolecular Structure of Commercial Pyrodextrins.

    PubMed

    Le Thanh-Blicharz, Joanna; Błaszczak, Wioletta; Szwengiel, Artur; Paukszta, Dominik; Lewandowicz, Grażyna

    2016-09-01

    Size exclusion chromatography with triple detection as well as infrared spectroscopy studies of commercially available pyrodextrins proved that these molecules are characterized not only by significantly lower molecular mass, in comparison to that of native starch, but also by increased branching. Therefore, pyrodextrins adopt a very compact structure in solution and show Newtonian behavior under shear in spite of their molecular masses of tens of thousands Daltons. The results also indicate that 50% reduction of digestibility of pyrodextrins is, to a minor extent, caused by formation of low-molecular color compounds containing carbonyl functional groups. The main reason is, as postulated in the literature, transglycosidation that leads to decreased occurrence of α-1,4-glycoside bonds in the molecular structure. In the process of dextrinization starch also undergoes changes in supermolecular structure, which, however, have no influence on digestibility. Likewise, the effect of formation of low-molecular colorful compounds containing carbonyl groups is not crucial.

  10. Molecular and Supermolecular Structure of Commercial Pyrodextrins.

    PubMed

    Le Thanh-Blicharz, Joanna; Błaszczak, Wioletta; Szwengiel, Artur; Paukszta, Dominik; Lewandowicz, Grażyna

    2016-09-01

    Size exclusion chromatography with triple detection as well as infrared spectroscopy studies of commercially available pyrodextrins proved that these molecules are characterized not only by significantly lower molecular mass, in comparison to that of native starch, but also by increased branching. Therefore, pyrodextrins adopt a very compact structure in solution and show Newtonian behavior under shear in spite of their molecular masses of tens of thousands Daltons. The results also indicate that 50% reduction of digestibility of pyrodextrins is, to a minor extent, caused by formation of low-molecular color compounds containing carbonyl functional groups. The main reason is, as postulated in the literature, transglycosidation that leads to decreased occurrence of α-1,4-glycoside bonds in the molecular structure. In the process of dextrinization starch also undergoes changes in supermolecular structure, which, however, have no influence on digestibility. Likewise, the effect of formation of low-molecular colorful compounds containing carbonyl groups is not crucial. PMID:27447364

  11. Activation of protonated peptides and molecular ions of small molecules using heated filaments in Fourier-transform ion cyclotron resonance mass spectrometry

    NASA Astrophysics Data System (ADS)

    Wong, Richard L.; Robinson, Errol W.; Williams, Evan R.

    2004-05-01

    A new apparatus that uses heated filaments to dissociate ions in Fourier-transform ion cyclotron resonance mass spectrometry is described. With this apparatus, molecular ions of both acetophenone and n-butylbenzene can be dissociated very rapidly. A plot of the natural log of the dissociation rate constant versus inverse radiant temperature yields a straight line from which an Arrhenius activation energy is obtained. From this value, the threshold dissociation energy can be estimated. For acetophenone, we find a value that is within the range of previously measured values. However, for n-butylbenzene, the calculated threshold dissociation energy value is too high. We attribute this result, and the appearance of a higher energy dissociation product, to the absorption of visible photons produced at the high filament temperatures used, a factor not currently included in our modeling. In contrast to the small ions, larger peptide ions do not undergo significant dissociation with the current apparatus. The "effective" internal temperature of the larger ions can be measured by using the heated filaments in combination with blackbody infrared radiative dissociation. The "effective" temperature of the peptide ions is increased substantially less than that for the smaller ions.

  12. Hyperpurification of paired helical filaments reveals elevations in hydroxyproline content and a core structure related peptide fragment.

    PubMed

    Vogelsang, G D; Zemlan, F P; Dean, G E

    1989-01-01

    We have subjected conventionally-purified Alzheimer's paired helical filaments (PHF) to electrophoresis in a Tris/borate/SDS buffer and obtained the separation of PHF core protein(s) (PHFi) from solubilized PHF-associated proteins (PHFs). Electron microscopy revealed intact PHF structures before and after this separation, but no evidence of any other structures in the PHFi fraction. The percent mass of hydroxyproline and glycine increased in the PHFi fraction after 4.5 hr of electrophoresis to account for 5.8% and 13.6% of the total mass, respectively. ELISA data confirmed that our PHFi and PHFs fractions were reactive with several putative PHF-specific antibodies. These data suggest that inappropriate hydroxylation of proline residues occurs in precursor PHF protein(s), resulting in the polymerization and subsequent insolubility of PHF in brain regions affected with Alzheimer's disease. Neurofibrillary tangles (NFT), one of the primary neuropathological features of Alzheimer's disease, are comprised of cytosolic bundles of uniform proteins which microscopically appear to be paired helical filaments (PHF). PHF are thought to be responsible for the cellular necrosis associated with the clinical symptoms of Alzheimer's disease (Dayan, 1970; Hirano and Zimmerman, 1962). Optical reconstruction of PHF has recently indicated that the true structure is more accurately described as a twisted ribbon of 30 A in the axial direction (Wischik et al., 1988). Immunological studies have suggested that tubulin (Grundke-Iqbal et al., 1979), microtubule associated proteins (Grundke-Iqbal et al., 1986; Kosik et al., 1986; Wood et al., 1986; Ksiezak-Reding et al., 1987), intermediate filaments (Yen et al., 1983), neurofilaments (Anderton et al., 1982), and ubiquitin (Mori et al., 1987; Perry et al., 1987), form part of the PHF core protein. To date, however, no study has been able to definitively show that any one of these purported PHF components is contained in the PHF core structure

  13. Analysis on the Filament Structure Evolution in Reset Transition of Cu/HfO2/Pt RRAM Device.

    PubMed

    Zhang, Meiyun; Long, Shibing; Li, Yang; Liu, Qi; Lv, Hangbing; Miranda, Enrique; Suñé, Jordi; Liu, Ming

    2016-12-01

    The resistive switching (RS) process of resistive random access memory (RRAM) is dynamically correlated with the evolution process of conductive path or conductive filament (CF) during its breakdown (rupture) and recovery (reformation). In this study, a statistical evaluation method is developed to analyze the filament structure evolution process in the reset operation of Cu/HfO2/Pt RRAM device. This method is based on a specific functional relationship between the Weibull slopes of reset parameters' distributions and the CF resistance (R on). The CF of the Cu/HfO2/Pt device is demonstrated to be ruptured abruptly, and the CF structure of the device has completely degraded in the reset point. Since no intermediate states are generated in the abrupt reset process, it is quite favorable for the reliable and stable one-bit operation in RRAM device. Finally, on the basis of the cell-based analytical thermal dissolution model, a Monte Carlo (MC) simulation is implemented to further verify the experimental results. This work provides inspiration for RRAM reliability and performance design to put RRAM into practical application.

  14. Analysis on the Filament Structure Evolution in Reset Transition of Cu/HfO2/Pt RRAM Device

    NASA Astrophysics Data System (ADS)

    Zhang, Meiyun; Long, Shibing; Li, Yang; Liu, Qi; Lv, Hangbing; Miranda, Enrique; Suñé, Jordi; Liu, Ming

    2016-05-01

    The resistive switching (RS) process of resistive random access memory (RRAM) is dynamically correlated with the evolution process of conductive path or conductive filament (CF) during its breakdown (rupture) and recovery (reformation). In this study, a statistical evaluation method is developed to analyze the filament structure evolution process in the reset operation of Cu/HfO2/Pt RRAM device. This method is based on a specific functional relationship between the Weibull slopes of reset parameters' distributions and the CF resistance ( R on). The CF of the Cu/HfO2/Pt device is demonstrated to be ruptured abruptly, and the CF structure of the device has completely degraded in the reset point. Since no intermediate states are generated in the abrupt reset process, it is quite favorable for the reliable and stable one-bit operation in RRAM device. Finally, on the basis of the cell-based analytical thermal dissolution model, a Monte Carlo (MC) simulation is implemented to further verify the experimental results. This work provides inspiration for RRAM reliability and performance design to put RRAM into practical application.

  15. Analysis on the Filament Structure Evolution in Reset Transition of Cu/HfO2/Pt RRAM Device.

    PubMed

    Zhang, Meiyun; Long, Shibing; Li, Yang; Liu, Qi; Lv, Hangbing; Miranda, Enrique; Suñé, Jordi; Liu, Ming

    2016-12-01

    The resistive switching (RS) process of resistive random access memory (RRAM) is dynamically correlated with the evolution process of conductive path or conductive filament (CF) during its breakdown (rupture) and recovery (reformation). In this study, a statistical evaluation method is developed to analyze the filament structure evolution process in the reset operation of Cu/HfO2/Pt RRAM device. This method is based on a specific functional relationship between the Weibull slopes of reset parameters' distributions and the CF resistance (R on). The CF of the Cu/HfO2/Pt device is demonstrated to be ruptured abruptly, and the CF structure of the device has completely degraded in the reset point. Since no intermediate states are generated in the abrupt reset process, it is quite favorable for the reliable and stable one-bit operation in RRAM device. Finally, on the basis of the cell-based analytical thermal dissolution model, a Monte Carlo (MC) simulation is implemented to further verify the experimental results. This work provides inspiration for RRAM reliability and performance design to put RRAM into practical application. PMID:27389343

  16. The Molecular Structure of Penicillin

    NASA Astrophysics Data System (ADS)

    Bentley, Ronald

    2004-10-01

    The chemical structure of penicillin was determined between 1942 and 1945 under conditions of secrecy established by the U.S. and U.K. governments. The evidence was not published in the open literature but as a monograph. This complex volume does not present a structure proof that can be readily comprehended by a student. In this article, a basic structural proof for the penicillin molecule is provided, emphasizing the chemical work. The stereochemistry of penicillin is also described, and various rearrangements are considered on the basis of the accepted β-lactam structure.

  17. Structure of Importin-α from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal.

    PubMed

    Bernardes, Natalia E; Takeda, Agnes A S; Dreyer, Thiago R; Freitas, Fernanda Z; Bertolini, Maria Célia; Fontes, Marcos R M

    2015-01-01

    Neurospora crassa is a filamentous fungus that has been extensively studied as a model organism for eukaryotic biology, providing fundamental insights into cellular processes such as cell signaling, growth and differentiation. To advance in the study of this multicellular organism, an understanding of the specific mechanisms for protein transport into the cell nucleus is essential. Importin-α (Imp-α) is the receptor for cargo proteins that contain specific nuclear localization signals (NLSs) that play a key role in the classical nuclear import pathway. Structures of Imp-α from different organisms (yeast, rice, mouse, and human) have been determined, revealing that this receptor possesses a conserved structural scaffold. However, recent studies have demonstrated that the Impα mechanism of action may vary significantly for different organisms or for different isoforms from the same organism. Therefore, structural, functional, and biophysical characterization of different Impα proteins is necessary to understand the selectivity of nuclear transport. Here, we determined the first crystal structure of an Impα from a filamentous fungus which is also the highest resolution Impα structure already solved to date (1.75 Å). In addition, we performed calorimetric analysis to determine the affinity and thermodynamic parameters of the interaction between Imp-α and the classical SV40 NLS peptide. The comparison of these data with previous studies on Impα proteins led us to demonstrate that N. crassa Imp-α possess specific features that are distinct from mammalian Imp-α but exhibit important similarities to rice Imp-α, particularly at the minor NLS binding site.

  18. Structure of Importin-α from a Filamentous Fungus in Complex with a Classical Nuclear Localization Signal

    PubMed Central

    Dreyer, Thiago R.; Freitas, Fernanda Z.; Bertolini, Maria Célia; Fontes, Marcos R. M.

    2015-01-01

    Neurospora crassa is a filamentous fungus that has been extensively studied as a model organism for eukaryotic biology, providing fundamental insights into cellular processes such as cell signaling, growth and differentiation. To advance in the study of this multicellular organism, an understanding of the specific mechanisms for protein transport into the cell nucleus is essential. Importin-α (Imp-α) is the receptor for cargo proteins that contain specific nuclear localization signals (NLSs) that play a key role in the classical nuclear import pathway. Structures of Imp-α from different organisms (yeast, rice, mouse, and human) have been determined, revealing that this receptor possesses a conserved structural scaffold. However, recent studies have demonstrated that the Impα mechanism of action may vary significantly for different organisms or for different isoforms from the same organism. Therefore, structural, functional, and biophysical characterization of different Impα proteins is necessary to understand the selectivity of nuclear transport. Here, we determined the first crystal structure of an Impα from a filamentous fungus which is also the highest resolution Impα structure already solved to date (1.75 Å). In addition, we performed calorimetric analysis to determine the affinity and thermodynamic parameters of the interaction between Imp-α and the classical SV40 NLS peptide. The comparison of these data with previous studies on Impα proteins led us to demonstrate that N. crassa Imp-α possess specific features that are distinct from mammalian Imp-α but exhibit important similarities to rice Imp-α, particularly at the minor NLS binding site. PMID:26091498

  19. The Molecular Structure of Penicillin

    ERIC Educational Resources Information Center

    Bentley, Ronald

    2004-01-01

    Overviews of the observations that constitute a structure proof for penicillin, specifically aimed at the general student population, are presented. Melting points and boiling points were criteria of purity and a crucial tool was microanalysis leading to empirical formulas.

  20. Structural Analysis of Helios Filament-Wound Tanks Subjected to Internal Pressure and Cooling

    NASA Technical Reports Server (NTRS)

    Ko, William L

    2005-01-01

    A finite-element stress analysis is performed on Helios filament-wound hydrogen tanks to examine the stress field and effect of end dome geometry on the stress field. Each tank is composed of a central circular cylindrical section with either geodesic or hemispherical end domes, which have metallic polar bosses. The tanks are subjected to combined and separate internal pressure and temperature loading conditions, and the stress contributions of each loading component are examined. The tank-wall-polar-boss interfacial meridional tensile stress in the hemispherical dome is found to be approximately 27 percent lower than that in the geodesic dome. The effects of both material anisotropy and the aluminum lining on the intensities of tensile meridional stress at the tank-wall-polar-boss bonding interface are examined.

  1. Three-dimensional structure of the Z-ring as a random network of FtsZ filaments.

    PubMed

    Piro, Oreste; Carmon, Gideon; Feingold, Mario; Fishov, Itzhak

    2013-12-01

    The spatial organization of the Z-ring, the central element of the bacterial division machinery, is not yet fully understood. Using optical tweezers and subpixel image analysis, we have recently shown that the radial width of the Z-ring in unconstricted Escherichia coli is about 100 nm. The relatively large width is consistent with the observations of others. Moreover, simulation of the experimental FtsZ distribution using the theoretical three-dimensional (3D) point spread function was strongly in favour of a toroidal rather than a thin cylindrical model of the Z-ring. Here, we show that the low density of FtsZ filaments in the ring coincides within experimental uncertainty with the critical density of a 3D random network of cylindrical sticks. This suggests that the Z-ring may consist of a percolating network of FtsZ filaments. Several factors that are expected to affect the polymerization state and the extent of self-interaction of FtsZ within the Z-ring, as well as the functional implications of its sparse toroidal structure, are discussed in terms of percolation theory.

  2. STRUCTURED MOLECULAR GAS REVEALS GALACTIC SPIRAL ARMS

    SciTech Connect

    Sawada, Tsuyoshi; Hasegawa, Tetsuo; Koda, Jin

    2012-11-01

    We explore the development of structures in molecular gas in the Milky Way by applying the analysis of the brightness distribution function and the brightness distribution index (BDI) in the archival data from the Boston University-Five College Radio Astronomy Observatory {sup 13}CO J = 1-0 Galactic Ring Survey. The BDI measures the fractional contribution of spatially confined bright molecular emission over faint emission extended over large areas. This relative quantity is largely independent of the amount of molecular gas and of any conventional, pre-conceived structures, such as cores, clumps, or giant molecular clouds. The structured molecular gas traced by higher BDI is located continuously along the spiral arms in the Milky Way in the longitude-velocity diagram. This clearly indicates that molecular gas changes its structure as it flows through the spiral arms. Although the high-BDI gas generally coincides with H II regions, there is also some high-BDI gas with no/little signature of ongoing star formation. These results support a possible evolutionary sequence in which unstructured, diffuse gas transforms itself into a structured state on encountering the spiral arms, followed by star formation and an eventual return to the unstructured state after the spiral arm passage.

  3. Filaments in the twist-grain-boundary smectic-A phase

    NASA Astrophysics Data System (ADS)

    Lejček, Lubor; Novotná, Vladimíra; Glogarová, Milada

    2015-09-01

    A model of filaments of the twist-grain-boundary smectic-A phase (TGBA) arising from the homeotropic smectic-A phase and nucleating on the sample surface is proposed. The model is based on the concept of finite blocks of parallel smectic layers forming a helical structure. The blocks are surrounded by dislocation loops. The model describes the filament structure near the sample surface and the observed inclination of the filament axis with respect to the easy direction of the molecular anchoring on the surface. The model is based on the observations of filament textures of the TGBA phase in a chiral liquid crystalline compound, but can be applied for forming of TGBA filaments in any compound. The compression modulus of the compound has been estimated using such parameters as anchoring energy, estimated from the field necessary to transform the structure into the homeotropic smectic-A .

  4. Filaments in the twist-grain-boundary smectic-A phase.

    PubMed

    Lejček, Lubor; Novotná, Vladimíra; Glogarová, Milada

    2015-09-01

    A model of filaments of the twist-grain-boundary smectic-A phase (TGBA) arising from the homeotropic smectic-A phase and nucleating on the sample surface is proposed. The model is based on the concept of finite blocks of parallel smectic layers forming a helical structure. The blocks are surrounded by dislocation loops. The model describes the filament structure near the sample surface and the observed inclination of the filament axis with respect to the easy direction of the molecular anchoring on the surface. The model is based on the observations of filament textures of the TGBA phase in a chiral liquid crystalline compound, but can be applied for forming of TGBA filaments in any compound. The compression modulus of the compound has been estimated using such parameters as anchoring energy, estimated from the field necessary to transform the structure into the homeotropic smectic-A.

  5. Structural changes of the regulatory proteins bound to the thin filaments in skeletal muscle contraction by X-ray fiber diffraction

    SciTech Connect

    Sugimoto, Yasunobu Takezawa, Yasunori; Matsuo, Tatsuhito; Ueno, Yutaka; Minakata, Shiho; Tanaka, Hidehiro; Wakabayashi, Katsuzo

    2008-04-25

    In order to clarify the structural changes related to the regulation mechanism in skeletal muscle contraction, the intensity changes of thin filament-based reflections were investigated by X-ray fiber diffraction. The time course and extent of intensity changes of the first to third order troponin (TN)-associated meridional reflections with a basic repeat of 38.4 nm were different for each of these reflections. The intensity of the first and second thin filament layer lines changed in a reciprocal manner both during initial activation and during the force generation process. The axial spacings of the TN-meridional reflections decreased by {approx}0.1% upon activation relative to the relaxing state and increased by {approx}0.24% in the force generation state, in line with that of the 2.7-nm reflection. Ca{sup 2+}-binding to TN triggered the shortening and a change in the helical symmetry of the thin filaments. Modeling of the structural changes using the intensities of the thin filament-based reflections suggested that the conformation of the globular core domain of TN altered upon activation, undergoing additional conformational changes at the tension plateau. The tail domain of TN moved together with tropomyosin during contraction. The results indicate that the structural changes of regulatory proteins bound to the actin filaments occur in two steps, the first in response to the Ca{sup 2+}-binding and the second induced by actomyosin interaction.

  6. CO-dark gas and molecular filaments in Milky Way-type galaxies - II. The temperature distribution of the gas

    NASA Astrophysics Data System (ADS)

    Glover, Simon C. O.; Smith, Rowan J.

    2016-11-01

    We investigate the temperature distribution of CO-dark molecular hydrogen (H2) in a series of disc galaxies simulated using the AREPO moving-mesh code. In conditions similar to those in the Milky Way, we find that H2 has a flat temperature distribution ranging from 10 to 100 K. At T < 30 K, the gas is almost fully molecular and has a high CO content, whereas at T > 30 K, the H2 fraction spans a broader range and the CO content is small, allowing us to classify gas in these two regimes as CO-bright and CO-dark, respectively. The mean sound speed in the CO-dark H2 is cs, dark = 0.64 km s-1, significantly lower than the value in the cold atomic gas (cs, CNM = 1.15 km s-1), implying that the CO-dark molecular phase is more susceptible to turbulent compression and gravitational collapse than its atomic counterpart. We further show that the temperature of the CO-dark H2 is highly sensitive to the strength of the interstellar radiation field, but that conditions in the CO-bright H2 remain largely unchanged. Finally, we examine the usefulness of the [C II] and [O I] fine-structure lines as tracers of the CO-dark gas. We show that in Milky Way-like conditions, diffuse [C II] emission from this gas should be detectable. However, it is a problematic tracer of this gas, as there is only a weak correlation between the brightness of the emission and the H2 surface density. The situation is even worse for the [O I] line, which shows no correlation with the H2 surface density.

  7. A ROBUST MEASURE OF COSMIC STRUCTURE BEYOND THE POWER SPECTRUM: COSMIC FILAMENTS AND THE TEMPERATURE OF DARK MATTER

    SciTech Connect

    Obreschkow, D.; Power, C.; Bruderer, M.; Bonvin, C.

    2013-01-10

    We discover that the mass of dark matter particles m {sub DM} is imprinted in phase correlations of the cosmic density field more significantly than in the two-point correlation. In particular, phase correlations trace m {sub DM} out to scales about five times larger than the two-point correlation. This result relies on a new estimator l(r) of pure phase information in Fourier space, which can be interpreted as a parameter-free and scale-invariant tracer of filament-like structure. Based on simulated density fields, we show how m {sub DM} can, in principle, be measured using l(r), given a suitably reconstructed density field.

  8. Self-Assembled DNA Structures for Molecular Force Measurement: A Magnetically Actuated Approach

    NASA Astrophysics Data System (ADS)

    Armstrong, M.; Lauback, S.; Miller, C.; Peace, C.; Castro, C.; Sooryakumar, R.

    2015-03-01

    Understanding molecular forces is important to comprehend many of the underlying properties of molecular machines and biological processes. The relevant forces in these cases often lie in the picoNewton range, and thus experiments on individual biomolecules must integrate techniques capable of measuring such forces. A mechanical system to measure molecular forces associated with interacting DNA strands is being developed by using self-assembled DNA nanostructures and super-paramagnetic beads. The DNA nanostructure consists of single-stranded DNA molecules which can be folded into a precise compact geometry using hundreds of short oligonucleotides, i.e., staples, via programmed molecular self-assembly. These nanostructures can be polymerized into micron-scale filaments. By functionalizing the filament ends with bispecific conjugate staples, the structure can be attached to a surface as well as labeled with magnetic beads in order to apply a force on the system. External magnetic fields provide the means to maneuver and manipulate the magnetically labeled DNA structures. Preliminary findings associated with the DNA constructs and their manipulation lay the groundwork to establish real-time control of DNA nanodevices with micromanipulation.

  9. Collagen-like glycoprotein BclS is involved in the formation of filamentous structures of the Lysinibacillus sphaericus exosporium.

    PubMed

    Zhao, Ni; Ge, Yong; Shi, Tingyu; Hu, Xiaomin; Yuan, Zhiming

    2014-11-01

    Lysinibacillus sphaericus produces mosquitocidal binary toxins (Bin toxins) deposited within a balloon-like exosporium during sporulation. Unlike Bacillus cereus group strains, the exosporium of L. sphaericus is usually devoid of the hair-like nap, an external filamentous structure formed by a collagen-like protein, BclA. In this study, a new collagen-like exosporium protein encoded by Bsph_0411 (BclS) from L. sphaericus C3-41 was characterized. Thin-section electron microscopy revealed that deletion of bclS resulted in the loss of the filamentous structures that attach to the exosporium basal layer and spread through the interspace of spores. In vivo visualization of BclS-green fluorescent protein (GFP)/mCherry fusion proteins revealed a dynamic pattern of fluorescence that encased the spore from the mother cell-distal (MCD) pole of the forespore, and the BclS-GFP fusions were found to be located in the interspace of the spore, as confirmed by three-dimensional (3D) superresolution fluorescence microscopy. Further studies demonstrated that the bclS mutant spores were more sensitive to wet-heat treatment and germinated at a lower rate than wild-type spores and that these phenotypes were significantly restored in the bclS-complemented strain. These results suggested novel roles of collagen-like protein in exosporium assembly and spore germination, providing a hint for a further understanding of the genetic basis of the high level of persistence of Bin toxins in nature. PMID:25149519

  10. Structures in Molecular Clouds: Modeling

    SciTech Connect

    Kane, J O; Mizuta, A; Pound, M W; Remington, B A; Ryutov, D D

    2006-04-20

    We attempt to predict the observed morphology, column density and velocity gradient of Pillar II of the Eagle Nebula, using Rayleigh Taylor (RT) models in which growth is seeded by an initial perturbation in density or in shape of the illuminated surface, and cometary models in which structure is arises from a initially spherical cloud with a dense core. Attempting to mitigate suppression of RT growth by recombination, we use a large cylindrical model volume containing the illuminating source and the self-consistently evolving ablated outflow and the photon flux field, and use initial clouds with finite lateral extent. An RT model shows no growth, while a cometary model appears to be more successful at reproducing observations.

  11. [Oligoglycine surface structures: molecular dynamics simulation].

    PubMed

    Gus'kova, O A; Khalatur, P G; Khokhlov, A R; Chinarev, A A; Tsygankova, S V; Bovin, N V

    2010-01-01

    The full-atomic molecular dynamics (MD) simulation of adsorption mode for diantennary oligoglycines [H-Gly4-NH(CH2)5]2 onto graphite and mica surface is described. The resulting structure of adsorption layers is analyzed. The peptide second structure motives have been studied by both STRIDE (structural identification) and DSSP (dictionary of secondary structure of proteins) methods. The obtained results confirm the possibility of polyglycine II (PGII) structure formation in diantennary oligoglycine (DAOG) monolayers deposited onto graphite surface, which was earlier estimated based on atomic-force microscopy measurements.

  12. On the emergence of molecular structure

    SciTech Connect

    Matyus, Edit; Reiher, Markus; Hutter, Juerg; Mueller-Herold, Ulrich

    2011-05-15

    The structure of (a{sup {+-}},a{sup {+-}},b{sup {+-}})-type Coulombic systems is characterized by the effective ground-state density of the a-type particles, computed via nonrelativistic quantum mechanics without introduction of the Born-Oppenheimer approximation. A structural transition is observed when varying the relative mass of the a- and b-type particles, e.g., between atomic H{sup -} and molecular H{sub 2}{sup +}. The particle-density profile indicates a molecular-type behavior for the positronium ion, Ps{sup -}.

  13. Subhalo Accretion through Filaments

    NASA Astrophysics Data System (ADS)

    González, Roberto E.; Padilla, Nelson D.

    2016-09-01

    We track subhalo orbits of galaxy- and group-sized halos in cosmological simulations. We identify filamentary structures around halos and use these to define a sample of subhalos accreted from filaments, as well as a control sample of subhalos accreted from other directions. We use these samples to study differences in satellite orbits produced by filamentary accretion. Our results depend on host halo mass. We find that for low masses, subhalos accreted from filaments show ∼10% shorter lifetimes compared to the control sample, show a tendency toward more radial orbits, reach halo central regions earlier, and are more likely to merge with the host. For higher-mass halos this lifetime difference dissipates and even reverses for cluster-sized halos. This behavior appears to be connected to the fact that more massive hosts are connected to stronger filaments with higher velocity coherence and density, with slightly more radial subhalo orbits. Because subhalos tend to follow the coherent flow of the filament, it is possible that such thick filaments are enough to shield the subhalo from the effect of dynamical friction at least during their first infall. We also identify subhalo pairs/clumps that merge with one another after accretion. They survive as a clump for only a very short time, which is even shorter for higher subhalo masses, suggesting that the Magellanic Clouds and other Local group satellite associations may have entered the Milky Way virial radius very recently and probably are in their first infall.

  14. Mutations of tau protein in frontotemporal dementia promote aggregation of paired helical filaments by enhancing local beta-structure.

    PubMed

    von Bergen, M; Barghorn, S; Li, L; Marx, A; Biernat, J; Mandelkow, E M; Mandelkow, E

    2001-12-21

    The microtubule-associated protein tau is a natively unfolded protein in solution, yet it is able to polymerize into the ordered paired helical filaments (PHF) of Alzheimer's disease. In the splice isoforms lacking exon 10, this process is facilitated by the formation of beta-structure around the hexapeptide motif PHF6 ((306)VQIVYK(311)) encoded by exon 11. We have investigated the structural requirements for PHF polymerization in the context of adult tau isoforms containing four repeats (including exon 10). In addition to the PHF6 motif there exists a related PHF6* motif ((275)VQIINK(280)) in the repeat encoded by the alternatively spliced exon 10. We show that this PHF6* motif also promotes aggregation by the formation of beta-structure and that there is a cross-talk between the two hexapeptide motifs during PHF aggregation. We also show that two of the tau mutations found in hereditary frontotemporal dementias, DeltaK280 and P301L, have a much stronger tendency for PHF aggregation which correlates with their high propensity for beta-structure around the hexapeptide motifs.

  15. Comparison of Prestellar Core Elongations and Large-scale Molecular Cloud Structures in the Lupus I Region

    NASA Astrophysics Data System (ADS)

    Poidevin, Frédérick; Ade, Peter A. R.; Angile, Francesco E.; Benton, Steven J.; Chapin, Edward L.; Devlin, Mark J.; Fissel, Laura M.; Fukui, Yasuo; Gandilo, Natalie N.; Gundersen, Joshua O.; Hargrave, Peter C.; Klein, Jeffrey; Korotkov, Andrei L.; Matthews, Tristan G.; Moncelsi, Lorenzo; Mroczkowski, Tony K.; Netterfield, Calvin B.; Novak, Giles; Nutter, David; Olmi, Luca; Pascale, Enzo; Savini, Giorgio; Scott, Douglas; Shariff, Jamil A.; Diego Soler, Juan; Tachihara, Kengo; Thomas, Nicholas E.; Truch, Matthew D. P.; Tucker, Carole E.; Tucker, Gregory S.; Ward-Thompson, Derek

    2014-08-01

    Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on sub-parsec to 100 parsec scales, leading to the formation of starless cores, are not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 μm maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large-scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of the morphology of the cores is observed with respect to the mean orientation of the large-scale filament in Lupus I, nor relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 μm with the Balloon-borne Large Aperture Telescope for Polarimetry during its 2010 campaign. Here again we do not find any correlation between the core morphology distribution and the average orientation of the magnetic fields on parsec scales. Our main conclusion is that the local filament dynamics—including secondary filaments that often run orthogonally to the primary filament—and possibly small-scale variations in the local magnetic field direction, could be the dominant factors for explaining the final orientation of each core.

  16. Comparison of prestellar core elongations and large-scale molecular cloud structures in the Lupus I region

    SciTech Connect

    Poidevin, Frédérick; Ade, Peter A. R.; Hargrave, Peter C.; Nutter, David; Angile, Francesco E.; Devlin, Mark J.; Klein, Jeffrey; Benton, Steven J.; Netterfield, Calvin B.; Chapin, Edward L.; Fissel, Laura M.; Gandilo, Natalie N.; Fukui, Yasuo; Gundersen, Joshua O.; Korotkov, Andrei L.; Matthews, Tristan G.; Novak, Giles; Moncelsi, Lorenzo; Mroczkowski, Tony K.; Olmi, Luca; and others

    2014-08-10

    Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on sub-parsec to 100 parsec scales, leading to the formation of starless cores, are not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 μm maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large-scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of the morphology of the cores is observed with respect to the mean orientation of the large-scale filament in Lupus I, nor relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 μm with the Balloon-borne Large Aperture Telescope for Polarimetry during its 2010 campaign. Here again we do not find any correlation between the core morphology distribution and the average orientation of the magnetic fields on parsec scales. Our main conclusion is that the local filament dynamics—including secondary filaments that often run orthogonally to the primary filament—and possibly small-scale variations in the local magnetic field direction, could be the dominant factors for explaining the final orientation of each core.

  17. Crystal Structure of C-Terminal Coiled-Coil Domain of SYCP1 Reveals Non-Canonical Anti-Parallel Dimeric Structure of Transverse Filament at the Synaptonemal Complex.

    PubMed

    Seo, Eun Kyung; Choi, Jae Young; Jeong, Jae-Hee; Kim, Yeon-Gil; Park, Hyun Ho

    2016-01-01

    The synaptonemal complex protein 1 (SYCP1) is the main structural element of transverse filaments (TFs) of the synaptonemal complex (SC), which is a meiosis-specific complex structure formed at the synapse of homologue chromosomes to hold them together. The N-terminal domain of SYCP1 is known to be located within the central elements (CEs), whereas the C-terminal domain is located toward lateral elements (LEs). SYCP1 is a well-known meiosis marker that is also known to be a prognostic marker in the early stage of several cancers including breast, gliomas, and ovarian cancers. The structure of SC, especially the TF structure formed mainly by SYCP1, remains unclear without any structural information. To elucidate a molecular basis of SC formation and function, we first solved the crystal structure of C-terminal coiled-coil domain of SYCP1. The coiled-coil domain of SYCP1 forms asymmetric, anti-parallel dimers in solution. PMID:27548613

  18. Crystal Structure of C-Terminal Coiled-Coil Domain of SYCP1 Reveals Non-Canonical Anti-Parallel Dimeric Structure of Transverse Filament at the Synaptonemal Complex

    PubMed Central

    Jeong, Jae-Hee; Kim, Yeon-Gil; Park, Hyun Ho

    2016-01-01

    The synaptonemal complex protein 1 (SYCP1) is the main structural element of transverse filaments (TFs) of the synaptonemal complex (SC), which is a meiosis-specific complex structure formed at the synapse of homologue chromosomes to hold them together. The N-terminal domain of SYCP1 is known to be located within the central elements (CEs), whereas the C-terminal domain is located toward lateral elements (LEs). SYCP1 is a well-known meiosis marker that is also known to be a prognostic marker in the early stage of several cancers including breast, gliomas, and ovarian cancers. The structure of SC, especially the TF structure formed mainly by SYCP1, remains unclear without any structural information. To elucidate a molecular basis of SC formation and function, we first solved the crystal structure of C-terminal coiled-coil domain of SYCP1. The coiled-coil domain of SYCP1 forms asymmetric, anti-parallel dimers in solution. PMID:27548613

  19. Molecular Structure of Human-Liver Glycogen

    PubMed Central

    Deng, Bin; Sullivan, Mitchell A.; Chen, Cheng; Li, Jialun; Powell, Prudence O.; Hu, Zhenxia; Gilbert, Robert G.

    2016-01-01

    Glycogen is a highly branched glucose polymer which is involved in maintaining blood-sugar homeostasis. Liver glycogen contains large composite α particles made up of linked β particles. Previous studies have shown that the binding which links β particles into α particles is impaired in diabetic mice. The present study reports the first molecular structural characterization of human-liver glycogen from non-diabetic patients, using transmission electron microscopy for morphology and size-exclusion chromatography for the molecular size distribution; the latter is also studied as a function of time during acid hydrolysis in vitro, which is sensitive to certain structural features, particularly glycosidic vs. proteinaceous linkages. The results are compared with those seen in mice and pigs. The molecular structural change during acid hydrolysis is similar in each case, and indicates that the linkage of β into α particles is not glycosidic. This result, and the similar morphology in each case, together imply that human liver glycogen has similar molecular structure to those of mice and pigs. This knowledge will be useful for future diabetes drug targets. PMID:26934359

  20. Molecular Association and Structure of Hydrogen Peroxide.

    ERIC Educational Resources Information Center

    Giguere, Paul A.

    1983-01-01

    The statement is sometimes made in textbooks that liquid hydrogen peroxide is more strongly associated than water, evidenced by its higher boiling point and greater heat of vaporization. Discusses these and an additional factor (the nearly double molecular mass of the peroxide), focusing on hydrogen bonds and structure of the molecule. (JN)

  1. How We Teach Molecular Structure to Freshmen.

    ERIC Educational Resources Information Center

    Hurst, Michael O.

    2002-01-01

    Currently molecular structure is taught in general chemistry using three theories, this being based more on historical development rather than logical pedagogy. Electronegativity is taught with a confusing mixture of definitions that do not correspond to modern practice. Valence bond theory and VSEPR are used together in a way that often confuses…

  2. Students' Understanding of Molecular Structure Representations

    ERIC Educational Resources Information Center

    Ferk, Vesna; Vrtacnik, Margareta; Blejec, Andrej; Gril, Alenka

    2003-01-01

    The purpose of the investigation was to determine the meanings attached by students to the different kinds of molecular structure representations used in chemistry teaching. The students (n = 124) were from primary (aged 13-14 years) and secondary (aged 17-18 years) schools and a university (aged 21-25 years). A computerised "Chemical…

  3. Site-specific cation release drives actin filament severing by vertebrate cofilin

    PubMed Central

    Kang, Hyeran; Bradley, Michael J.; Cao, Wenxiang; Zhou, Kaifeng; Grintsevich, Elena E.; Michelot, Alphée; Sindelar, Charles V.; Hochstrasser, Mark; De La Cruz, Enrique M.

    2014-01-01

    Actin polymerization powers the directed motility of eukaryotic cells. Sustained motility requires rapid filament turnover and subunit recycling. The essential regulatory protein cofilin accelerates network remodeling by severing actin filaments and increasing the concentration of ends available for elongation and subunit exchange. Although cofilin effects on actin filament assembly dynamics have been extensively studied, the molecular mechanism of cofilin-induced filament severing is not understood. Here we demonstrate that actin filament severing by vertebrate cofilin is driven by the linked dissociation of a single cation that controls filament structure and mechanical properties. Vertebrate cofilin only weakly severs Saccharomyces cerevisiae actin filaments lacking this “stiffness cation” unless a stiffness cation-binding site is engineered into the actin molecule. Moreover, vertebrate cofilin rescues the viability of a S. cerevisiae cofilin deletion mutant only when the stiffness cation site is simultaneously introduced into actin, demonstrating that filament severing is the essential function of cofilin in cells. This work reveals that site-specific interactions with cations serve a key regulatory function in actin filament fragmentation and dynamics. PMID:25468977

  4. Periodic colour-centre structure formed under filamentation of mid-IR femtosecond laser radiation in a LiF crystal

    NASA Astrophysics Data System (ADS)

    Kuznetsov, A. V.; Kompanets, V. O.; Dormidonov, A. E.; Chekalin, S. V.; Shlenov, S. A.; Kandidov, V. P.

    2016-04-01

    A colour-centre structure formed in a LiF crystal under filamentation of a femtosecond mid-IR laser pulse with a power slightly exceeding the critical power for self-focusing has been experimentally and theoretically investigated. Strictly periodic oscillations have been detected for the first time for the density of the colour centres induced in an isotropic LiF crystal under filamentation of a laser beam with a wavelength tuned in the range from 2600 to 3350 nm. The structure period is found to be about 30 μm. With an increase in the laser radiation wavelength, the period of the oscillations decreases and their amplitude increases. The maximum colour centre density, observed under filamentation of a 3100-nm beam, is related to the increased contribution of the direct generation of colour centres as a result of the absorption of an integer number of photons by the exciton band. It is numerically shown that the formation of a periodic colour-centre structure in LiF is due to the periodic change in the light field amplitude in the light bullet (1.5 optical periods long) formed under filamentation.

  5. Molecular and structural analysis of viscoelastic properties

    NASA Astrophysics Data System (ADS)

    Yapp, Rebecca D.; Kalyanam, Sureshkumar; Insana, Michael F.

    2007-03-01

    Elasticity imaging is emerging as an important tool for breast cancer detection and monitoring of treatment. Viscoelastic image contrast in breast lesions is generated by disease specific processes that modify the molecular structure of connective tissues. We showed previously that gelatin hydrogels exhibit mechanical behavior similar to native collagen found in breast tissue and therefore are suitable as phantoms for elasticity imaging. This paper summarizes our study of the viscoelastic properties of hydrogels designed to discover molecular-scale sources of elasticity image contrast.

  6. Challenges in determining causation in structure-function studies using molecular biological techniques.

    PubMed

    de los Reyes, Francis L

    2010-09-01

    The use of molecular biological techniques for determining the levels and types of different microbial populations in bioreactors has led to the emergence of the microbial community 'structure-function' paradigm that is often used in research. Typically, lab- or full-scale systems are monitored for the relevant parameters, and these parameters are related to the changes in microbial populations. Research in activated sludge phenomena, such as filamentous bulking, filamentous foaming, nitrogen removal, and phosphorus removal, are replete with many examples of this 'structure-function' paradigm, most commonly those that involve 16S rRNA gene-based analysis of the microbial populations. In many cases, such studies assume a causal microbial population (e.g., a species that causes bulking or foaming), or conclude in identifying a causal population. However, assigning cause to specific organisms and populations is problematic in a complex environment such as wastewater bioreactors. The Koch-Henle postulates, the gold standard in evaluating causation of disease, have limitations when applied to systems with mixed microbial communities with complex interactions, particularly if pure cultures are not available. Molecular techniques that allow specific identification and quantification of organisms have been used by researchers to overcome the limitations of culture-based techniques, and at the same time, raised new questions on the applicability of causation postulates in environmental systems. In this paper, various causation criteria improving on the Koch-Henle postulates are presented. Complicating issues in assigning cause in wastewater bioreactors are identified. Approaches for determining cause-effect relationships are illustrated using 16S rDNA-based investigations of filaments that cause bulking and foaming in activated sludge. The hope is that a causation framework that accounts for the assumptions in molecular studies, as applied to wastewater treatment research

  7. The velocity characteristics of dusty filaments in the JCMT GBS clouds

    NASA Astrophysics Data System (ADS)

    Buckle, J. V.; Salji, C.; Richer, J. S.

    2013-07-01

    Large scale, high resolution spectral and continuum imaging maps have revealed, to an unprecedented extent, the characteristics of filamentary structure in star-forming molecular clouds, and their close association with star-forming cores. The filaments are associated with the formation of dense molecular cores where star formation occurs, and recent models highlight the important relationship between filaments and star-forming clusters. Velocity-coherent filaments have been proposed as the parent structures of star forming cores in Taurus. In Serpens, accretion flows along filaments have been proposed as the continuous source of mass for the star forming cluster. An evolutionary scenario for filaments based on velocity dispersion and column density measurements has recently been proposed, which we test with large scale molecular line and dust continuum maps. The JCMT Gould Belt Survey with SCUBA-2 and HARP provides dust continuum observations at 850 and 450 micron, and 12CO/13CO/C18O J=3-2 spectral line mapping of several nearby molecular clouds, covering large angular scales at high resolution. Velocities and linewidths of optically thin species, such as C18O which traces the warm, dense gas associated with star formation, are critical for an estimate of the virial stability of filamentary structures. The data and analyses that we present provide robust statistics over a large range of starless and protostellar evolutionary states. We present the velocity characteristics of dusty filaments in Orion, probing the physics at the boundary of filamentary structure and star formation. Using C18O, we investigate the internal structure of filaments, based on fragmentation and velocity coherence in the molecular line data. Through velocity dispersion measurements, we determine whether the filamentary structures are bound, and compare results between clouds of different star formation characteristics.

  8. Assignment of the sup 1 H NMR spectrum and secondary structure elucidation of the single-stranded DNA binding protein encoded by the filamentous bacteriophage IKe

    SciTech Connect

    van Duynhoven, J.P.M.; Folkers, P.J.M.; Prinse, C.W.J.M.; Harmsen, B.J.M.; Konings, R.N.H.; Hilbers, C.W. )

    1992-02-04

    By means of 2D NMR techniques, all backbone resonances in the {sup 1}H NMR spectrum of the single-stranded DNA binding protein encoded by gene V of the filamentous phage IKe have been assigned sequence specifically. In addition, a major part of the side chain resonances could be assigned as well. Analysis of NOESY data permitted the elucidation of the secondary structure of IKe gene V protein. The major part of the secondary structure is present as an antiparallel {beta}-sheet, i.e., as two {beta}-loops which partly combine into a triple-stranded {beta}-sheet structure, one {beta}-loop and one triple-stranded {beta}-sheet structure. It is shown that a high degree of homology exists with the single-stranded DNA binding protein encoded by gene V of the distantly related filamentous phase M13.

  9. Role of Intermediate Filaments in Vesicular Traffic.

    PubMed

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  10. Role of Intermediate Filaments in Vesicular Traffic

    PubMed Central

    Margiotta, Azzurra; Bucci, Cecilia

    2016-01-01

    Intermediate filaments are an important component of the cellular cytoskeleton. The first established role attributed to intermediate filaments was the mechanical support to cells. However, it is now clear that intermediate filaments have many different roles affecting a variety of other biological functions, such as the organization of microtubules and microfilaments, the regulation of nuclear structure and activity, the control of cell cycle and the regulation of signal transduction pathways. Furthermore, a number of intermediate filament proteins have been involved in the acquisition of tumorigenic properties. Over the last years, a strong involvement of intermediate filament proteins in the regulation of several aspects of intracellular trafficking has strongly emerged. Here, we review the functions of intermediate filaments proteins focusing mainly on the recent knowledge gained from the discovery that intermediate filaments associate with key proteins of the vesicular membrane transport machinery. In particular, we analyze the current understanding of the contribution of intermediate filaments to the endocytic pathway. PMID:27120621

  11. 2004 Reversible Associations in Structure & Molecular Biology

    SciTech Connect

    Edward Eisenstein Nancy Ryan Gray

    2005-03-23

    The Gordon Research Conference (GRC) on 2004 Gordon Research Conference on Reversible Associations in Structure & Molecular Biology was held at Four Points Sheraton, CA, 1/25-30/2004. The Conference was well attended with 82 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students.

  12. Silylated carbodiimides in molecular and extended structures

    NASA Astrophysics Data System (ADS)

    Kroll, Peter; Riedel, Ralf; Hoffmann, Roald

    1999-08-01

    This work studies the ternary Si-C-N phases SiC2N4 and Si2CN4,exploiting an analogy between the NCN and O groups. Starting from the molecular model of N,N'-bis(trimethylsilyl)-carbodiimide and proceeding to extended models, we calculate that the energy hypersurface associated with the Si-N=C bond angle φN is very shallow, for both molecular and extended structures. We propose a crystal structure for the low-temperature modification α-SiC2N4 in space group P4322 (95), which is 40 meV (~4 kJ/mol) lower in energy than an ideal cubic arrangement in space group Pn3¯m.A second structure, β-SiC2N4 [space group P4¯n2 (118)], is slightly higher in energy than α-SiC2N4,but still more stable than the cubic structure, and may be the high-temperature structure of SiC2N4.Both variants of SiC2N4 show a small bulk modulus of about 8 GPa (~0.13 Mbar),suggesting a high compressibility of these nonoxide covalently bonded materials. For Si2CN4 we refined the crystal structure of the compound within the experimentally determined space group Aba2 (41). We also found a second candidate nearly equal in energy, with space group Cmc21,differing only in the connection pattern of the SiN2 layered sheets. Both ternary compounds appear to be thermodynamically unstable with respect to decomposition into Si3N4,C, and molecular N2.

  13. Bridged filaments of histone-like nucleoid structuring protein pause RNA polymerase and aid termination in bacteria

    PubMed Central

    Kotlajich, Matthew V; Hron, Daniel R; Boudreau, Beth A; Sun, Zhiqiang; Lyubchenko, Yuri L; Landick, Robert

    2015-01-01

    Bacterial H-NS forms nucleoprotein filaments that spread on DNA and bridge distant DNA sites. H-NS filaments co-localize with sites of Rho-dependent termination in Escherichia coli, but their direct effects on transcriptional pausing and termination are untested. In this study, we report that bridged H-NS filaments strongly increase pausing by E. coli RNA polymerase at a subset of pause sites with high potential for backtracking. Bridged but not linear H-NS filaments promoted Rho-dependent termination by increasing pause dwell times and the kinetic window for Rho action. By observing single H-NS filaments and elongating RNA polymerase molecules using atomic force microscopy, we established that bridged filaments surround paused complexes. Our results favor a model in which H-NS-constrained changes in DNA supercoiling driven by transcription promote pausing at backtracking-susceptible sites. Our findings provide a mechanistic rationale for H-NS stimulation of Rho-dependent termination in horizontally transferred genes and during pervasive antisense and noncoding transcription in bacteria. DOI: http://dx.doi.org/10.7554/eLife.04970.001 PMID:25594903

  14. Intermediate Filaments: A Historical Perspective

    PubMed Central

    Oshima, Robert G.

    2007-01-01

    Intracellular protein filaments intermediate in size between actin microfilaments and microtubules are composed of a surprising variety of tissue specific proteins commonly interconnected with other filamentous systems for mechanical stability and decorated by a variety of proteins that provide specialized functions. The sequence conservation of the coiled-coil, alpha-helical structure responsible for polymerization into individual 10 nm filaments defines the classification of intermediate filament proteins into a large gene family. Individual filaments further assemble into bundles and branched cytoskeletons visible in the light microscope. However, it is the diversity of the variable terminal domains that likely contributes most to different functions. The search for the functions of intermediate filament proteins has led to discoveries of roles in diseases of the skin, heart, muscle, liver, brain, adipose tissues and even premature aging. The diversity of uses of intermediate filaments as structural elements and scaffolds for organizing the distribution of decorating molecules contrasts with other cytoskeletal elements. This review is an attempt to provide some recollection of how such a diverse field emerged and changed over about 30 years. PMID:17493611

  15. Unwinding motion of a twisted active region filament

    SciTech Connect

    Yan, X. L.; Xue, Z. K.; Kong, D. F.; Liu, J. H.; Xu, C. L.

    2014-12-10

    To better understand the structures of active region filaments and the eruption process, we study an active region filament eruption in active region NOAA 11082 in detail on 2010 June 22. Before the filament eruption, the opposite unidirectional material flows appeared in succession along the spine of the filament. The rising of the filament triggered two B-class flares at the upper part of the filament. As the bright material was injected into the filament from the sites of the flares, the filament exhibited a rapid uplift accompanying the counterclockwise rotation of the filament body. From the expansion of the filament, we can see that the filament consisted of twisted magnetic field lines. The total twist of the filament is at least 5π obtained by using a time slice method. According to the morphology change during the filament eruption, it is found that the active region filament was a twisted flux rope and its unwinding motion was like a solar tornado. We also find that there was a continuous magnetic helicity injection before and during the filament eruption. It is confirmed that magnetic helicity can be transferred from the photosphere to the filament. Using the extrapolated potential fields, the average decay index of the background magnetic fields over the filament is 0.91. Consequently, these findings imply that the mechanism of solar filament eruption could be due to the kink instability and magnetic helicity accumulation.

  16. Metabolic regulation via enzyme filamentation

    PubMed Central

    Aughey, Gabriel N.; Liu, Ji-Long

    2016-01-01

    Abstract Determining the mechanisms of enzymatic regulation is central to the study of cellular metabolism. Regulation of enzyme activity via polymerization-mediated strategies has been shown to be widespread, and plays a vital role in mediating cellular homeostasis. In this review, we begin with an overview of the filamentation of CTP synthase, which forms filamentous structures termed cytoophidia. We then highlight other important examples of the phenomenon. Moreover, we discuss recent data relating to the regulation of enzyme activity by compartmentalization into cytoophidia. Finally, we hypothesize potential roles for enzyme filament formation in the regulation of metabolism, development and disease. PMID:27098510

  17. Determination of the persistence length of actin filaments on microcontact printed myosin patterns

    NASA Astrophysics Data System (ADS)

    Hajne, Joanna; Hanson, Kristi L.; van Zalinge, Harm; Nicolau, Dan V.; Nicolau, Dan V.

    2015-03-01

    Protein molecular motors, which convert chemical energy into kinetic energy, are prime candidates for use in nanodevice in which active transport is required. To be able to design these devices it is essential that the properties of the cytoskeletal filaments propelled by the molecular motors are well established. Here we used micro-contact printed BSA to limit the amount of HMM that can adsorb creating a tightly confined pathway for the filaments to travel. Both the image and statistical analysis of the movement of the filaments through these structures have been used to new insights into the motility behaviour of actomyosin on topographically homogenous, but motor-heterogeneous planar systems. It will be shown that it is possible to determine the persistence length of the filaments and that it is related to the amount of locally adsorbed HMM. This provides a basis that can be used to optimize the design of future nanodevices incorporating the actomyosin system for the active transport.

  18. Triggering filamentation using turbulence

    NASA Astrophysics Data System (ADS)

    Eeltink, D.; Berti, N.; Marchiando, N.; Hermelin, S.; Gateau, J.; Brunetti, M.; Wolf, J. P.; Kasparian, J.

    2016-09-01

    We study the triggering of single filaments due to turbulence in the beam path for a laser of power below the filamenting threshold. Turbulence can act as a switch between the beam not filamenting and producing single filaments. This positive effect of turbulence on the filament probability, combined with our observation of off-axis filaments, suggests the underlying mechanism is modulation instability caused by transverse perturbations. We hereby experimentally explore the interaction of modulation instability and turbulence, commonly associated with multiple filaments, in the single-filament regime.

  19. Real-time assembly and disassembly of human RAD51 filaments on individual DNA molecules

    PubMed Central

    van der Heijden, Thijn; Seidel, Ralf; Modesti, Mauro; Kanaar, Roland; Wyman, Claire; Dekker, Cees

    2007-01-01

    The human DNA repair protein RAD51 is the crucial component of helical nucleoprotein filaments that drive homologous recombination. The molecular mechanistic details of how this structure facilitates the requisite DNA strand rearrangements are not known but must involve dynamic interactions between RAD51 and DNA. Here, we report the real-time kinetics of human RAD51 filament assembly and disassembly on individual molecules of both single- and double-stranded DNA, as measured using magnetic tweezers. The relative rates of nucleation and filament extension are such that the observed filament formation consists of multiple nucleation events that are in competition with each other. For varying concentration of RAD51, a Hill coefficient of 4.3 ± 0.5 is obtained for both nucleation and filament extension, indicating binding to dsDNA with a binding unit consisting of multiple (≥4) RAD51 monomers. We report Monte Carlo simulations that fit the (dis)assembly data very well. The results show that, surprisingly, human RAD51 does not form long continuous filaments on DNA. Instead each nucleoprotein filament consists of a string of many small filament patches that are only a few tens of monomers long. The high flexibility and dynamic nature of this arrangement is likely to facilitate strand exchange. PMID:17709342

  20. Structural features of sugars that trigger or support conidial germination in the filamentous fungus Aspergillus niger.

    PubMed

    Hayer, Kimran; Stratford, Malcolm; Archer, David B

    2013-11-01

    The asexual spores (conidia) of Aspergillus niger germinate to produce hyphae under appropriate conditions. Germination is initiated by conidial swelling and mobilization of internal carbon and energy stores, followed by polarization and emergence of a hyphal germ tube. The effects of different pyranose sugars, all analogues of d-glucose, on the germination of A. niger conidia were explored, and we define germination as the transition from a dormant conidium into a germling. Within germination, we distinguish two distinct stages, the initial swelling of the conidium and subsequent polarized growth. The stage of conidial swelling requires a germination trigger, which we define as a compound that is sensed by the conidium and which leads to catabolism of d-trehalose and isotropic growth. Sugars that triggered germination and outgrowth included d-glucose, d-mannose, and d-xylose. Sugars that triggered germination but did not support subsequent outgrowth included d-tagatose, d-lyxose, and 2-deoxy-d-glucose. Nontriggering sugars included d-galactose, l-glucose, and d-arabinose. Certain nontriggering sugars, including d-galactose, supported outgrowth if added in the presence of a complementary triggering sugar. This division of functions indicates that sugars are involved in two separate events in germination, triggering and subsequent outgrowth, and the structural features of sugars that support each, both, or none of these events are discussed. We also present data on the uptake of sugars during the germination process and discuss possible mechanisms of triggering in the absence of apparent sugar uptake during the initial swelling of conidia.

  1. Bacillus subtilis Bactofilins Are Essential for Flagellar Hook- and Filament Assembly and Dynamically Localize into Structures of Less than 100 nm Diameter underneath the Cell Membrane.

    PubMed

    El Andari, Jihad; Altegoer, Florian; Bange, Gert; Graumann, Peter L

    2015-01-01

    Bactofilins are a widely conserved protein family implicated in cell shape maintenance and in bacterial motility. We show that the bactofilins BacE and BacF from Bacillus subtilis are essential for motility. The proteins are required for the establishment of flagellar hook- and filament structures, but apparently not for the formation of basal bodies. Functional YFP fusions to BacE and to BacF localize as discrete assemblies at the B. subtilis cell membrane, and have a diameter of 60 to 70 nm. BacF assemblies are relatively static, and partially colocalize with flagellar basal bodies, while BacE assemblies are fewer per cell than those of BacF and are highly mobile. Tracking of BacE foci showed that the assemblies arrest at a single point for a few hundred milliseconds, showing that a putative interaction with flagellar structures would be transient and fast. When overexpressed or expressed in a heterologous cell system, bactofilins can form filamentous structures, and also form multimers as purified proteins. Our data reveal a propensity for bactofilins to form filaments, however, in B. subtilis cells, bactofilins assemble into defined size assemblies that show a dynamic localization pattern and play a role in flagellar assembly. PMID:26517549

  2. Bacillus subtilis Bactofilins Are Essential for Flagellar Hook- and Filament Assembly and Dynamically Localize into Structures of Less than 100 nm Diameter underneath the Cell Membrane

    PubMed Central

    El Andari, Jihad; Altegoer, Florian; Bange, Gert; Graumann, Peter L.

    2015-01-01

    Bactofilins are a widely conserved protein family implicated in cell shape maintenance and in bacterial motility. We show that the bactofilins BacE and BacF from Bacillus subtilis are essential for motility. The proteins are required for the establishment of flagellar hook- and filament structures, but apparently not for the formation of basal bodies. Functional YFP fusions to BacE and to BacF localize as discrete assemblies at the B. subtilis cell membrane, and have a diameter of 60 to 70 nm. BacF assemblies are relatively static, and partially colocalize with flagellar basal bodies, while BacE assemblies are fewer per cell than those of BacF and are highly mobile. Tracking of BacE foci showed that the assemblies arrest at a single point for a few hundred milliseconds, showing that a putative interaction with flagellar structures would be transient and fast. When overexpressed or expressed in a heterologous cell system, bactofilins can form filamentous structures, and also form multimers as purified proteins. Our data reveal a propensity for bactofilins to form filaments, however, in B. subtilis cells, bactofilins assemble into defined size assemblies that show a dynamic localization pattern and play a role in flagellar assembly. PMID:26517549

  3. PARTIAL SLINGSHOT RECONNECTION BETWEEN TWO FILAMENTS

    SciTech Connect

    Jiang, Yunchun; Hong, Junchao; Yang, Jiayan; Bi, Yi; Zheng, Ruisheng; Yang, Bo; Li, Haidong; Yang, Dan

    2013-02-10

    We present a rare observation of an interaction between two filaments around AR 11358 and AR 11361 on 2011 December 3 that is strongly suggestive of the occurrence of slingshot reconnection. A small elbow-shaped active-region filament (F12) underwent a failed eruption that brought it into contact with a nearby larger, thicker filament (F34). Accompanied by the appearance of complicated internal structures below the erupting F12, its two legs separated away from each other and then connected into F34. This process led the filaments to change their connectivity to form two newly linked filaments, and one of them showed a clear inverse {gamma}-shape. However, the alteration in the filament connectivity was imperfect since F34 is discernible after the eruption. These observations can be interpreted as a partial slingshot reconnection between two filaments that had unequal axial magnetic flux.

  4. Role of (p)ppGpp in biofilm formation and expression of filamentous structures in Bordetella pertussis.

    PubMed

    Sugisaki, Kentaro; Hanawa, Tomoko; Yonezawa, Hideo; Osaki, Takako; Fukutomi, Toshiyuki; Kawakami, Hayato; Yamamoto, Tomoko; Kamiya, Shigeru

    2013-07-01

    Bordetella pertussis, the causative agent of whooping cough, is highly adapted to cause human infection. The production of virulence factors, such as adhesins and toxins, is just part of an array of mechanisms by which B. pertussis causes infection. The stringent response is a global bacterial response to nutritional limitation that is mediated by the accumulation of cellular ppGpp and pppGpp [termed together as (p)ppGpp]. Here, we demonstrate that production of (p)ppGpp was controlled by RelA and SpoT proteins in B. pertussis, and that mutation-induced loss of both proteins together caused deficiencies in (p)ppGpp production. The (p)ppGpp-deficient mutants also exhibited defects in growth regulation, decreases in viability under nutritionally limited conditions, increases in susceptibility to oxidative stress and defects in biofilm formation. Analysis of the secreted proteins and the respective transcripts showed that lack of (p)ppGpp led to decreased expression of fim3 and bsp22, which encode a fimbrial subunit and the self-polymerizing type III secretion system tip protein, respectively. Moreover, electron microscopic analysis also indicated that (p)ppGpp regulated the formation of filamentous structures. Most virulence genes - including fim3 and bsp22 - were expressed in the Bvg(+) phase during which the BvgAS two-component system was activated. Although fim3 and bsp22 were downregulated in a (p)ppGpp-deficient mutant, normal expression of fhaB, cyaA and ptxA persisted. Lack of coherence between virulence gene expression and (p)ppGpp production indicated that (p)ppGpp did not modulate the Bvg phase. Taken together, our data indicate that (p)ppGpp may govern an as-yet-unrecognized system that influences B. pertussis pathogenicity.

  5. Assembly of Superparamagnetic Filaments in External Field.

    PubMed

    Wei, Jiachen; Song, Fan; Dobnikar, Jure

    2016-09-13

    We present a theoretical and simulation study of anchored magneto-elastic filaments in external magnetic field. The filaments are composed of a mixture of superparamagnetic and nonmagnetic colloidal beads interlinked with elastic springs. We explore the steady-state structures of filaments with various composition and bending rigidity subject to external magnetic field parallel to the surface. The interplay of elastic and induced magnetic interactions results in a rich phase behavior with morphologies reminiscent of macromolecular folding: bent filaments, loops, sheets, helicoids, and other collapsed structures. Our results provide new insights into the design of hierarchically assembled supramolecular structures with controlled response to external stimuli. PMID:27536958

  6. Colocalization properties of elementary Ca(2+) release signals with structures specific to the contractile filaments and the tubular system of intact mouse skeletal muscle fibers.

    PubMed

    Georgiev, Tihomir; Zapiec, Bolek; Förderer, Moritz; Fink, Rainer H A; Vogel, Martin

    2015-12-01

    Ca(2+) regulates several important intracellular processes. We combined second harmonic generation (SHG) and two photon excited fluorescence microscopy (2PFM) to simultaneously record the SHG signal of the myosin filaments and localized elementary Ca(2+) release signals (LCSs). We found LCSs associated with Y-shaped structures of the myosin filament pattern (YMs), so called verniers, in intact mouse skeletal muscle fibers under hypertonic treatment. Ion channels crucial for the Ca(2+) regulation are located in the tubular system, a system that is important for Ca(2+) regulation and excitation-contraction coupling. We investigated the tubular system of intact, living mouse skeletal muscle fibers using 2PFM and the fluorescent Ca(2+) indicator Fluo-4 dissolved in the external solution or the membrane dye di-8-ANEPPS. We simultaneously measured the SHG signal from the myosin filaments of the skeletal muscle fibers. We found that at least a subset of the YMs observed in SHG images are closely juxtaposed with Y-shaped structures of the transverse tubules (YTs). The distances of corresponding YMs and YTs yield values between 1.3 μm and 4.1 μm including pixel uncertainty with a mean distance of 2.52±0.10 μm (S.E.M., n=41). Additionally, we observed that some of the linear-shaped areas in the tubular system are colocalized with linear-shaped areas in the SHG images.

  7. A novel protocol for molecularly imprinted polymer filaments online coupled to GC-MS for the determination of androgenic steroids in urine.

    PubMed

    Zhong, Qisheng; Hu, Yufei; Li, Gongke

    2013-12-01

    An online system that can perform dynamic microextraction, on-coating derivatization and desorption, and subsequent GC-MS analysis with a large-volume injection was developed. A derivatization cell as the conjunction of the online system was developed for the online extraction and derivatization. To evaluate the feasibility of the online system, methyltestosterone molecularly imprinted polymer filaments (MIPFs) were prepared for the selective online extraction of five androgenic steroids, namely, methyltestosterone, testosterone, epitestosterone, nandrolone, and metandienone. Under the optimized conditions, the detection limits of testosterone and epitestosterone were 0.09 and 0.12 μg/L, respectively, which were under the minimum required performance limits between 2 and 10 μg/L from the World Anti-Doping Agency. The detection limits of the other three androgenic steroids were varied from 0.04 to 0.18 μg/L. Finally, the MIPFs-GC-MS method was applied for the determination of androgenic steroids in urine, and satisfactory recovery (78.0-96.9%) and reproducibility (3.2-8.9%) were obtained. The proposed online coupling system offers an attractive alternative for hyphenation to GC instruments and could also be extended to other adsorptive materials. PMID:24151099

  8. Neurofilament architecture combines structural principles of intermediate filaments with carboxy-terminal extensions increasing in size between triplet proteins.

    PubMed Central

    Geisler, N; Kaufmann, E; Fischer, S; Plessmann, U; Weber, K

    1983-01-01

    Mammalian neurofilament triplet proteins (68 K, 160 K and 200 K) have been correlated by a biochemical, immunological and protein chemical study. The 160 K and 200 K triplet proteins are intermediate filament proteins in their own right, since they reveal the alpha-helical coiled-coil rod domain analyzed in detail for the 68 K protein. Triplet proteins display two distinct arrays. Their amino-terminal region built analogously to non-neuronal intermediate filament proteins should allow a co-polymerization process via the interaction of coiled-coil domains. The extra mass of all triplet proteins is allocated to carboxy-terminally located extensions of increasing size and unique amino acid sequences. These may provide highly charged scaffolds suitable for interactions with other neuronal components. Such a domain of 68 K reveals, in sequence analysis, 47 glutamic acids within 106 residues. The epitope recognized by a monoclonal antibody reacting probably with all intermediate filament proteins has been mapped. It is located within the last 20 residues of the rods, where six distinct intermediate filament proteins point to a consensus sequence. Images Fig. 1. PMID:10872323

  9. Genetic engineering of filamentous fungi.

    PubMed

    Timberlake, W E; Marshall, M A

    1989-06-16

    Filamentous fungi are important in medicine, industry, agriculture, and basic biological research. For example, some fungal species are pathogenic to humans, whereas others produce beta-lactam antibiotics (penicillin and cephalosporin). Industrial strains produce large amounts of enzymes, such as glucoamylase and proteases, and low molecular weight compounds, such as citric acid. The largest and most economically important group of plant pathogens are fungi. Several fungal species have biological properties and genetic systems that make them ideally suited for basic biological research. Recently developed techniques for genetic engineering of filamentous fungi make it possible to alter their detrimental and beneficial activities in novel ways.

  10. Observations of an active region filament

    NASA Astrophysics Data System (ADS)

    Zong, W. G.; Tang, Y. H.; Fang, C.; Xu, A. A.

    An active region filament was well observed on September 4, 2002 with THEMIS at the Teide observatory and SOHO/MDI. The full Stokes parameters of the filament were obtained in Hα and FeI 6302 Å lines. Using the data, we have studied the fine structure of the filament and obtained the parameters at the barb endpoints, including intensity, velocity and longitudinal magnetic field. Our results indicate: (a) the Doppler velocities are quiet different at barb endpoints; (b) the longitudinal magnetic fields at the barb endpoints are very weak; (c) there is a strong magnetic field structure under the filament spine.

  11. A universal filament width? The effect of ambipolar diffusion on the size distribution of dense filaments.

    NASA Astrophysics Data System (ADS)

    Ntormousi, Evangelia; Hennebelle, Patrick; André, Philippe

    2015-08-01

    The filamentary structure of molecular clouds and its potential link to star formation have been brought into focus by Herschel's high resolution observations of the local Interstellar Medium. An especially puzzling result from the same surveys is that local interstellar filaments have a preferred thickness of 0.1 pc, independent of their column density. What can be the origin of this apparently universal property?Filamentary structure is characteristic of MHD turbulence, appearing as a result of shear, magnetic tension and shocks. If the observed filaments are indeed the dissipative structures of interstellar turbulence, then ambipolar diffusion is the best candidate for setting a characteristic thickness by damping MHD waves. We test this hyporthesis with high-resolution, 3D MHD simulations performed with the AMR code RAMSES. To avoid confusion with grid effects, our simulations reach a physical resolution of 200 AU, resolving the observed 0.1 pc with about 100 cells.These simulations of both driven and decaying MHD turbulence show that the fluid assumes a different morphology when ambipolar diffusion is included in the models: ion-neutral friction acts on a characteristic scale to cut off the cascade, broadening the dense structures and flattening their mass spectra with respect to the corresponding ideal MHD situation. Altough the peak in the thickness distribution of filaments is not as dramatic in this series of simulations as in the observations, the comparison between ideal and non-ideal MHD points to ion-neutral friction as a very good candidate for setting a characteristic scale for interstellar filaments.

  12. Structure and Dynamics of Cellulose Molecular Solutions

    NASA Astrophysics Data System (ADS)

    Wang, Howard; Zhang, Xin; Tyagi, Madhusudan; Mao, Yimin; Briber, Robert

    Molecular dissolution of microcrystalline cellulose has been achieved through mixing with ionic liquid 1-Ethyl-3-methylimidazolium acetate (EMIMAc), and organic solvent dimethylformamide (DMF). The mechanism of cellulose dissolution in tertiary mixtures has been investigated by combining quasielastic and small angle neutron scattering (QENS and SANS). As SANS data show that cellulose chains take Gaussian-like conformations in homogenous solutions, which exhibit characteristics of having an upper critical solution temperature, the dynamic signals predominantly from EMIMAc molecules indicate strong association with cellulose in the dissolution state. The mean square displacement quantities support the observation of the stoichiometric 3:1 EMIMAc to cellulose unit molar ratio, which is a necessary criterion for the molecular dissolution of cellulose. Analyses of dynamics structure factors reveal the temperature dependence of a slow and a fast process for EMIMAc's bound to cellulose and in DMF, respectively, as well as a very fast process due possibly to the rotational motion of methyl groups, which persisted to near the absolute zero.

  13. [Morphogenesis in a community of filamentous cyanobacteria].

    PubMed

    Sumina, E L; Sumin, D L

    2013-01-01

    Reversible differentiation was experimentally discovered in a community of modern filamentous cyanobacteria Oscillatoria terebriformis. Splitting of the initially uniform community into differentiated parts (strands, multiradiate aggregates, networks, etc.) occurs only for the duration of a function facilitating the activity of this community as an integral unit. The structures are formed as a result of regrouping of the filaments, without their specialization. A morphologically regulatory system (polygonal network) was found to develop under the impact of extreme factors. The levels of structural organization of filamentous cyanobacteria and multicellular eukaryotes were compared (individual cells in a filament--cell organelles; filaments--individual cells; community--organism), and the similarities and differences in morphogenesis of these groups were analyzed using the data on the embryonic regulation in multicellular eukaryotes. Spatial information in morphogenesis was shown to result not from direct realization of an inherited program but is created by the elements of integral organisms (cells and filaments) in the course of development.

  14. Computing stoichiometric molecular composition from crystal structures

    PubMed Central

    Gražulis, Saulius; Merkys, Andrius; Vaitkus, Antanas; Okulič-Kazarinas, Mykolas

    2015-01-01

    Crystallographic investigations deliver high-accuracy information about positions of atoms in crystal unit cells. For chemists, however, the structure of a molecule is most often of interest. The structure must thus be reconstructed from crystallographic files using symmetry information and chemical properties of atoms. Most existing algorithms faithfully reconstruct separate molecules but not the overall stoichiometry of the complex present in a crystal. Here, an algorithm that can reconstruct stoichiometrically correct multimolecular ensembles is described. This algorithm uses only the crystal symmetry information for determining molecule numbers and their stoichiometric ratios. The algorithm can be used by chemists and crystallographers as a standalone implementation for investigating above-molecular ensembles or as a function implemented in graphical crystal analysis software. The greatest envisaged benefit of the algorithm, however, is for the users of large crystallographic and chemical databases, since it will permit database maintainers to generate stoichiometrically correct chemical representations of crystal structures automatically and to match them against chemical databases, enabling multidisciplinary searches across multiple databases. PMID:26089747

  15. Molecular composition, structure, and sensitivity of explosives

    SciTech Connect

    Storm, C.B.; Travis, J.R.

    1992-01-01

    High explosives, blasting agents, propellants, and pyrotechnics are all metastable relative to reaction products and are termed energetic materials. They are thermodynamically unstable but the kinetics of decomposition at ambient conditions are sufficiently slow that they can be handled safely under controlled conditions. The ease with which an energetic material can be caused to undergo a violent reaction or detonation is called its sensitivity. Sensitivity tests for energetic materials are aimed at defining the response of the material to a specific situation, usually prompt shock initiation or a delayed reaction in an accident. The observed response is always due to a combination of the physical state and the molecular structure of the material. Modeling of any initiation process must consider both factors. The physical state of the material determines how and where the energy is deposited in the material. The molecular structure determines the mechanism of decomposition of the material and the rate of energy release. Slower inherent reaction chemistry leads to longer reaction zones in detonation and inherently safer materials. Slower chemistry also requires hot spots involved in initiation to be hotter and to survive for longer periods of time. High thermal conductivity also leads to quenching of small hot spots and makes a material more difficult to initiate. Early endothermic decomposition chemistry also delays initiation by delaying heat release to support hot spot growth. The growth to violent reaction or detonation also depends on the nature of the early reaction products. If chemical intermediates are produced that drive further accelerating autocatalytic decomposition the initiation will grow rapidly to a violent reaction.

  16. A Network of Three Types of Filaments Organizes Synaptic Vesicles for Storage, Mobilization, and Docking

    PubMed Central

    Chen, Xiaobing; Reese, Thomas S.

    2016-01-01

    Synaptic transmission between neurons requires precise management of synaptic vesicles. While individual molecular components of the presynaptic terminal are well known, exactly how the molecules are organized into a molecular machine serving the storage and mobilization of synaptic vesicles to the active zone remains unclear. Here we report three filament types associated with synaptic vesicles in glutamatergic synapses revealed by electron microscope tomography in unstimulated, dissociated rat hippocampal neurons. One filament type, likely corresponding to the SNAREpin complex, extends from the active zone membrane and surrounds docked vesicles. A second filament type contacts all vesicles throughout the active zone and pairs vesicles together. On the third filament type, vesicles attach to side branches extending from the long filament core and form vesicle clusters that are distributed throughout the vesicle cloud and along the active zone membrane. Detailed analysis of presynaptic structure reveals how each of the three filament types interacts with synaptic vesicles, providing a means to traffic reserved and recycled vesicles from the cloud of vesicles into the docking position at the active zone. SIGNIFICANCE STATEMENT The formation and release of synaptic vesicles has been extensively investigated. Explanations of the release of synaptic vesicles generally begin with the movement of vesicles from the cloud into the synaptic active zone. However, the presynaptic terminal is filled with filamentous material that would appear to limit vesicular diffusion. Here, we provide a systematic description of three filament types connecting synaptic vesicles. A picture emerges illustrating how the cooperative attachment and release of these three filament types facilitate the movement of vesicles to the active zone to become docked in preparation for release. PMID:26985032

  17. Wide-field SCUBA-2 observations of NGC 2264: submillimetre clumps and filaments

    NASA Astrophysics Data System (ADS)

    Buckle, J. V.; Richer, J. S.

    2015-10-01

    We present wide-field observations of the NGC 2264 molecular cloud in the dust continuum at 850 and 450 μm using SCUBA-2 on the James Clerk Maxwell Telescope. Using 12CO 3 → 2 molecular line data, we determine that emission from CO contaminates the 850 μm emission at levels ˜30 per cent in localized regions associated with high-velocity molecular outflows. Much higher contamination levels of 60 per cent are seen in shocked regions near the massive star S Mon. If not removed, the levels of CO contamination would contribute an extra 13 per cent to the dust mass in NGC 2264. We use the FELLWALKER routine to decompose the dust into clumpy structures, and a Hessian-based routine to decompose the dust into filamentary structures. The filaments can be described as a hub-filament structure, with lower column density filaments radiating from the NGC 2264 C protocluster hub. Above mean filament column densities of 2.4 × 1022 cm-2, star formation proceeds with the formation of two or more protostars. Below these column densities, filaments are starless, or contain only a single protostar.

  18. Plant sex chromosomes: molecular structure and function.

    PubMed

    Jamilena, M; Mariotti, B; Manzano, S

    2008-01-01

    Recent molecular and genomic studies carried out in a number of model dioecious plant species, including Asparagus officinalis, Carica papaya, Silene latifolia, Rumex acetosa and Marchantia polymorpha, have shed light on the molecular structure of both homomorphic and heteromorphic sex chromosomes, and also on the gene functions they have maintained since their evolution from a pair of autosomes. The molecular structure of sex chromosomes in species from different plant families represents the evolutionary pathway followed by sex chromosomes during their evolution. The degree of Y chromosome degeneration that accompanies the suppression of recombination between the Xs and Ys differs among species. The primitive Ys of A. officinalis and C. papaya have only diverged from their homomorphic Xs in a short male-specific and non-recombining region (MSY), while the heteromorphic Ys of S. latifolia, R. acetosa and M. polymorpha have diverged from their respective Xs. As in the Y chromosomes of mammals and Drosophila, the accumulation of repetitive DNA, including both transposable elements and satellite DNA, has played an important role in the divergence and size enlargement of plant Ys, and consequently in reducing gene density. Nevertheless, the degeneration process in plants does not appear to have reached the Y-linked genes. Although a low gene density has been found in the sequenced Y chromosome of M. polymorpha, most of its genes are essential and are expressed in the vegetative and reproductive organs in both male and females. Similarly, most of the Y-linked genes that have been isolated and characterized up to now in S. latifolia are housekeeping genes that have X-linked homologues, and are therefore expressed in both males and females. Only one of them seems to be degenerate with respect to its homologous region in the X. Sequence analysis of larger regions in the homomorphic X and Y chromosomes of papaya and asparagus, and also in the heteromorphic sex chromosomes

  19. Self-Organization of Treadmilling Filaments

    NASA Astrophysics Data System (ADS)

    Doubrovinski, K.; Kruse, K.

    2007-11-01

    The cytoskeleton is an active network of polar filaments. The activity can lead to the polymerization of filaments at one end and depolymerization at the other. This phenomenon is called treadmilling and is essential for many cellular processes, in particular, the crawling of cells on a substrate. We develop a microscopic theoretical framework for describing systems of treadmilling filaments. We show that such systems can self-organize into structures observed in cell fragments, in particular, asters and moving spots.

  20. Structural transitions in tau k18 on micelle binding suggest a hierarchy in the efficacy of individual microtubule-binding repeats in filament nucleation.

    PubMed

    Barré, Patrick; Eliezer, David

    2013-08-01

    The protein tau is found in an aggregated filamentous state in the intraneuronal paired helical filament deposits characteristic of Alzheimer's disease and other related dementias and mutations in tau protein and mRNA cause frontotemproal dementia. Tau isoforms include a microtubule-binding domain containing either three or four imperfect tandem microtubule binding repeats that also form the core of tau filaments and contain hexapaptide motifs that are critical for tau aggregation. The tau microtubule-binding domain can also engage in direct interactions with detergents, fatty acids, or membranes, which can greatly facilitate tau aggregation and may also mediate some tau functions. Here, we show that the alternatively spliced second microtubule-binding repeat exhibits significantly different structural characteristics compared with the other three repeats in the context of the intact repeat domain. Most notably, the PHF6* hexapeptide motif located at the N-terminus of repeat 2 has a lower propensity to form strand-like structure than the corresponding PHF6 motif in repeat 3, and unlike PHF6 converts to partially helical structure in the micelle-bound state. Interestingly, the behavior of the Module-B motif, located at the beginning of repeat 4, resembles that of PHF6* rather than PHF6. Our observations, combined with previous results showing that PHF6* and Module-B are both less effective than PHF6 in nucleating tau aggregation, suggest a hierarchy in the efficacy of these motifs in nucleating tau aggregation that originates in differences in their intrinsic propensities for extended strand-like structure and the resistance of these propensities to changes in tau's environment.

  1. Molecular structure input on the web.

    PubMed

    Ertl, Peter

    2010-02-02

    A molecule editor, that is program for input and editing of molecules, is an indispensable part of every cheminformatics or molecular processing system. This review focuses on a special type of molecule editors, namely those that are used for molecule structure input on the web. Scientific computing is now moving more and more in the direction of web services and cloud computing, with servers scattered all around the Internet. Thus a web browser has become the universal scientific user interface, and a tool to edit molecules directly within the web browser is essential.The review covers a history of web-based structure input, starting with simple text entry boxes and early molecule editors based on clickable maps, before moving to the current situation dominated by Java applets. One typical example - the popular JME Molecule Editor - will be described in more detail. Modern Ajax server-side molecule editors are also presented. And finally, the possible future direction of web-based molecule editing, based on technologies like JavaScript and Flash, is discussed.

  2. Isolation and structural elucidation of two secondary metabolites from the filamentous fungus Penicillium ochrochloron with antimicrobial activity.

    PubMed

    Rančić, Ana; Soković, Marina; Karioti, Anastasia; Vukojević, Jelena; Skaltsa, Helen

    2006-07-01

    In this investigation, the extracts of filamentous fungi exhibited inhibitory effect on the growth of Gram positive and Gram negative bacteria, as well as against the yeast Candida albicans. Penicillium ochrochloron has been proven as the most active fungus against all tested microorganisms. Further bio-guided chemical analysis of P. ochrochloron afforded two components with antimicrobial activity identified as (-) 2, 3, 4-trihydroxybutanamide and (-) erythritol.

  3. Relating a Prominence Observed from the Solar Optical Telescope on the Hinode Satellite to Known 3-D Structures of Filaments

    NASA Astrophysics Data System (ADS)

    Martin, S. F.; Panasenco, O.; Agah, Y.; Engvold, O.; Lin, Y.

    2009-12-01

    We address only a first step in relating limb and disk observations by illustrating and comparing the spines and barbs of three different quiescent prominences and filaments observed in Hα by three different telescopes. Although the appearance of the three quiescent prominences is quite different, we show that each consists of a spine, barbs extending from the spine, and arcs at the base of some of the curtains of barb threads.

  4. Patterns and intrinsic fluctuations in semi-dilute motor-filament systems.

    SciTech Connect

    Swaminathan, S.; Ziebert, F.; Aranson, I. S.; Karpeev, D.; Northwestern Univ.; UMR CNRS Gulliver

    2010-04-01

    We perform Brownian dynamics simulations of molecular motor-induced ordering and structure formations in semi-dilute cytoskeletal filament solutions. In contrast to the previously studied dilute case where binary filament interactions prevail, the semi-dilute regime is characterized by multiple motor-mediated interactions. Moreover, the forces and torques exerted by motors on filaments are intrinsically fluctuating quantities. We incorporate the influences of thermal and motor fluctuations into our model as additive and multiplicative noises, respectively. Numerical simulations reveal that filament bundles and vortices emerge from a disordered initial state. Subsequent analysis of motor noise effects reveals: (i) Pattern formation is very robust against fluctuations in motor force; (ii) bundle formation is associated with a significant reduction of the motor fluctuation contributions; (iii) the time scale of vortex formation and coalescence decreases with increases in motor noise amplitude.

  5. Hydrodynamic instabilities provide a generic route to spontaneous biomimetic oscillations in chemomechanically active filaments

    PubMed Central

    Laskar, Abhrajit; Singh, Rajeev; Ghose, Somdeb; Jayaraman, Gayathri; Kumar, P. B. Sunil; Adhikari, R.

    2013-01-01

    Non-equilibrium processes which convert chemical energy into mechanical motion enable the motility of organisms. Bundles of inextensible filaments driven by energy transduction of molecular motors form essential components of micron-scale motility engines like cilia and flagella. The mimicry of cilia-like motion in recent experiments on synthetic active filaments supports the idea that generic physical mechanisms may be sufficient to generate such motion. Here we show, theoretically, that the competition between the destabilising effect of hydrodynamic interactions induced by force-free and torque-free chemomechanically active flows, and the stabilising effect of nonlinear elasticity, provides a generic route to spontaneous oscillations in active filaments. These oscillations, reminiscent of prokaryotic and eukaryotic flagellar motion, are obtained without having to invoke structural complexity or biochemical regulation. This minimality implies that biomimetic oscillations, previously observed only in complex bundles of active filaments, can be replicated in simple chains of generic chemomechanically active beads. PMID:23752497

  6. Hydrodynamic instabilities provide a generic route to spontaneous biomimetic oscillations in chemomechanically active filaments

    NASA Astrophysics Data System (ADS)

    Laskar, Abhrajit; Singh, Rajeev; Ghose, Somdeb; Jayaraman, Gayathri; Kumar, P. B. Sunil; Adhikari, R.

    2013-06-01

    Non-equilibrium processes which convert chemical energy into mechanical motion enable the motility of organisms. Bundles of inextensible filaments driven by energy transduction of molecular motors form essential components of micron-scale motility engines like cilia and flagella. The mimicry of cilia-like motion in recent experiments on synthetic active filaments supports the idea that generic physical mechanisms may be sufficient to generate such motion. Here we show, theoretically, that the competition between the destabilising effect of hydrodynamic interactions induced by force-free and torque-free chemomechanically active flows, and the stabilising effect of nonlinear elasticity, provides a generic route to spontaneous oscillations in active filaments. These oscillations, reminiscent of prokaryotic and eukaryotic flagellar motion, are obtained without having to invoke structural complexity or biochemical regulation. This minimality implies that biomimetic oscillations, previously observed only in complex bundles of active filaments, can be replicated in simple chains of generic chemomechanically active beads.

  7. Amino acid sequence homologies in the hard keratins of birds and reptiles, and their implications for molecular structure and physical properties.

    PubMed

    Fraser, R D Bruce; Parry, David A D

    2014-12-01

    Avian and reptilian epidermal appendages such as feathers, claws and scales exhibit a filament-matrix texture. Previous studies have established that both components reside within the same single-chain molecule. In the present study the homology in a wide range of aligned sequences is used to gain insights into the structure and function of the molecular segments associated with the filament and with the matrix. The notion that all molecules contain a β-rich 34-residue segment associated with the framework of the filament is reinforced by the present study. In addition, the residues involved in the polymerization of the molecules to form filaments are identified. In the Archosaurs (birds, crocodiles and turtles), and the Squamates (snakes and lizards) segments rich in glycine and tyrosine can be identified in the C-terminal domain. In Rhynocephalians (tuataras) and Squamates a similar segment is inserted at a specific point in the N-terminal domain. In some Archosaurian appendages (both avian and reptilian) segments rich in charged residues and cysteine are found in the N-terminal domain. The likely effect of these segments will be to soften the tissue without compromising its insolubility. The structure and role of the various molecular segments identified in this study and the way in which they might manifest themselves in terms of the physical properties of the particular epidermal appendage in which they appear are also discussed.

  8. Monolayer Filaments versus Multilayer Stacking of Bent-Core Molecules.

    PubMed

    Matraszek, Joanna; Topnani, Neha; Vaupotič, Natasa; Takezoe, Hideo; Mieczkowski, Jozef; Pociecha, Damian; Gorecka, Ewa

    2016-03-01

    Bent-core materials exhibiting lamellar crystals (B4 phase), when dissolved in organic solvents, formed gels with helical ribbons made of molecular monolayers and bilayers, whereas strongly deformed stacks of 5-6 layers were found in the bulk samples. The width and pitch of the helical filaments were governed by molecular length; they both increased with terminal-chain elongation. It was also found that bulk samples were optically active, in contrast to the corresponding gels, which lacked optical activity. The optical activity of samples originated from the internal structure of the crystal layers rather than from the helicity of the filaments. A theoretical model predicts a strong increase in optical activity as the number of layers in the stack increases and its saturation for few layers, thus explaining the smaller optical activity for gels than for bulk samples. A strong increase and redshift in fluorescence was detected in gels as compared to the sol state. PMID:26833945

  9. Femtosecond Laser Filamentation for Atmospheric Sensing

    PubMed Central

    Xu, Huai Liang; Chin, See Leang

    2011-01-01

    Powerful femtosecond laser pulses propagating in transparent materials result in the formation of self-guided structures called filaments. Such filamentation in air can be controlled to occur at a distance as far as a few kilometers, making it ideally suited for remote sensing of pollutants in the atmosphere. On the one hand, the high intensity inside the filaments can induce the fragmentation of all matters in the path of filaments, resulting in the emission of characteristic fluorescence spectra (fingerprints) from the excited fragments, which can be used for the identification of various substances including chemical and biological species. On the other hand, along with the femtosecond laser filamentation, white-light supercontinuum emission in the infrared to UV range is generated, which can be used as an ideal light source for absorption Lidar. In this paper, we present an overview of recent progress concerning remote sensing of the atmosphere using femtosecond laser filamentation. PMID:22346566

  10. Femtosecond laser filamentation for atmospheric sensing.

    PubMed

    Xu, Huai Liang; Chin, See Leang

    2011-01-01

    Powerful femtosecond laser pulses propagating in transparent materials result in the formation of self-guided structures called filaments. Such filamentation in air can be controlled to occur at a distance as far as a few kilometers, making it ideally suited for remote sensing of pollutants in the atmosphere. On the one hand, the high intensity inside the filaments can induce the fragmentation of all matters in the path of filaments, resulting in the emission of characteristic fluorescence spectra (fingerprints) from the excited fragments, which can be used for the identification of various substances including chemical and biological species. On the other hand, along with the femtosecond laser filamentation, white-light supercontinuum emission in the infrared to UV range is generated, which can be used as an ideal light source for absorption Lidar. In this paper, we present an overview of recent progress concerning remote sensing of the atmosphere using femtosecond laser filamentation. PMID:22346566

  11. Scrape-off Layer Current Model for Filament Structure Observed during Edge Localized Modes (ELMs) in the DIII-D Tokamak

    SciTech Connect

    Takahashi, Hironori; Fredrickson, E. D.; Schaffer, M. J.

    2008-04-15

    The plasma in tokamaks often exhibits a relaxation oscillation called the edge localized mode (ELM), which is generally attributed to MHD instability driven by strong gradients at the plasma boundary. It is shown here that field-aligned currents flowing just outside the boundary may also play a role in the ELM process. The poloidal perturbation magnetic field during ELMs in the DIII–D tokamak calculated from measured currents can reproduce prominent observed features, including a narrow magnetic structure at the outboard midplane similar to filaments observed earlier in DIII–D and NSTX.

  12. Dependence of reactive metal layer on resistive switching in a bi-layer structure Ta/HfOx filament type resistive random access memory

    NASA Astrophysics Data System (ADS)

    Lee, Daeseok; Woo, Jiyong; Park, Sangsu; Cha, Euijun; Lee, Sangheon; Hwang, Hyunsang

    2014-02-01

    The dependence of reactive metal layer on resistive switching characteristics is investigated in a bi-layer structural Ta/HfOx filament type resistive random access memory (ReRAM). By increasing the oxygen absorption rate of the reactive metal layer, formation of an induced resistive switching region that led to significant changes in the resistive switching characteristics of the ReRAM was observed. Electrical and physical analyses showed that the induced TaOx-resistive switching region can result in self-compliance behavior, uniform resistive switching, and a gradual set process, which can be utilized for low power and analog operations.

  13. Quantitative nanoscale imaging of orientational order in biological filaments by polarized superresolution microscopy

    PubMed Central

    Valades Cruz, Cesar Augusto; Shaban, Haitham Ahmed; Kress, Alla; Bertaux, Nicolas; Monneret, Serge; Mavrakis, Manos; Savatier, Julien; Brasselet, Sophie

    2016-01-01

    Essential cellular functions as diverse as genome maintenance and tissue morphogenesis rely on the dynamic organization of filamentous assemblies. For example, the precise structural organization of DNA filaments has profound consequences on all DNA-mediated processes including gene expression, whereas control over the precise spatial arrangement of cytoskeletal protein filaments is key for mechanical force generation driving animal tissue morphogenesis. Polarized fluorescence is currently used to extract structural organization of fluorescently labeled biological filaments by determining the orientation of fluorescent labels, however with a strong drawback: polarized fluorescence imaging is indeed spatially limited by optical diffraction, and is thus unable to discriminate between the intrinsic orientational mobility of the fluorophore labels and the real structural disorder of the labeled biomolecules. Here, we demonstrate that quantitative single-molecule polarized detection in biological filament assemblies allows not only to correct for the rotational flexibility of the label but also to image orientational order of filaments at the nanoscale using superresolution capabilities. The method is based on polarized direct stochastic optical reconstruction microscopy, using dedicated optical scheme and image analysis to determine both molecular localization and orientation with high precision. We apply this method to double-stranded DNA in vitro and microtubules and actin stress fibers in whole cells. PMID:26831082

  14. HST imaging of the dusty filaments and nucleus swirl in NGC4696 at the centre of the Centaurus Cluster

    NASA Astrophysics Data System (ADS)

    Fabian, A. C.; Walker, S. A.; Russell, H. R.; Pinto, C.; Canning, R. E. A.; Salome, P.; Sanders, J. S.; Taylor, G. B.; Zweibel, E. G.; Conselice, C. J.; Combes, F.; Crawford, C. S.; Ferland, G. J.; Gallagher, J. S., III; Hatch, N. A.; Johnstone, R. M.; Reynolds, C. S.

    2016-09-01

    Narrow-band HST imaging has resolved the detailed internal structure of the 10 kpc diameter H α+[N II] emission line nebulosity in NGC4696, the central galaxy in the nearby Centaurus cluster, showing that the dusty, molecular, filaments have a width of about 60 pc. Optical morphology and velocity measurements indicate that the filaments are dragged out by the bubbling action of the radio source as part of the active galactic nucleus feedback cycle. Using the drag force we find that the magnetic field in the filaments is in approximate pressure equipartition with the hot gas. The filamentary nature of the cold gas continues inwards, swirling around and within the Bondi accretion radius of the central black hole, revealing the magnetic nature of the gas flows in massive elliptical galaxies. HST imaging resolves the magnetic, dusty, molecular filaments at the centre of the Centaurus cluster to a swirl around and within the Bondi radius.

  15. Filamentation of plasma in the auroral region by an ion-ion instability - A process for the formation of bidimensional potential structures

    NASA Astrophysics Data System (ADS)

    Mottez, F.; Chanteur, G.; Roux, A.

    1992-07-01

    The nonlinear behavior of electrostatic ion waves generated by an ion beam flowing through a thermal ion and electron background in a strongly magnetized plasma is investigated by means of a 2D, explicit, electrostatic particle code. To follow the nonlinear evolution of these ion waves, a long-lasting simulation is run with a large simulation grid: 128 x 512 lambda(d). Beam ions are shown to generate oblique waves. The nonlinear beatings between these oblique waves produce purely transverse waves, which leads to a strong modulation of the density and of the electric potential in a direction transverse to the magnetic field. The transverse scale of these essentially field-aligned filaments is 10 rho(i), where rho(i) is the ion Larmor radius of beam ions. Within these filaments, relatively stable field-aligned density and potential structures develop. Unlike the potential structures that develop in a two-component plasma with downgoing electrons, these structures move upward.

  16. The Determination of Molecular Structure from Rotational Spectra

    DOE R&D Accomplishments Database

    Laurie, V. W.; Herschbach, D. R.

    1962-07-01

    An analysis is presented concerning the average molecular configuration variations and their effects on molecular structure determinations. It is noted that the isotopic dependence of the zero-point is often primarily governed by the isotopic variation of the average molecular configuration. (J.R.D.)

  17. Filament Eruption Onset

    NASA Technical Reports Server (NTRS)

    Sterling, Alphonse C.; Moore, Ronald L.

    2011-01-01

    We have been investigating filament eruptions in recent years. Use filament eruptions as markers of the coronal field evolution. Data from SoHO, Yohkoh, TRACE, Hinode, and other sources. We and others have observed: (1)Filaments often show slow rise, followed by fast rise, (2) Brightenings, preflares, microflares during slow rise (3) Magnetic evolution in hours prior to eruption onset. We investigated What do Hinode and SDO show for filament eruptions?

  18. Molecular cloning of chicken aggrecan. Structural analyses.

    PubMed Central

    Chandrasekaran, L; Tanzer, M L

    1992-01-01

    The large, aggregating chondroitin sulphate proteoglycan of cartilage, aggrecan, has served as a generic model of proteoglycan structure. Molecular cloning of aggrecans has further defined their amino acid sequences and domain structures. In this study, we have obtained the complete coding sequence of chicken sternal cartilage aggrecan by a combination of cDNA and genomic DNA sequencing. The composite sequence is 6117 bp in length, encoding 1951 amino acids. Comparison of chicken aggrecan protein primary structure with rat, human and bovine aggrecans has disclosed both similarities and differences. The domains which are most highly conserved at 70-80% identity are the N-terminal domains G1 and G2 and the C-terminal domain G3. The chondroitin sulphate domain of chicken aggrecan is smaller than that of rat and human aggrecans and has very distinctive repeat sequences. It has two separate sections, one comprising 12 consecutive Ser-Gly-Glu repeats of 20 amino acids each, adjacent to the other which has 23 discontinuous Ser-Gly-Glu repeats of 10 amino acids each; this latter region, N-terminal to the former one, appears to be unique to chicken aggrecan. The two regions contain a total of 94 potential chondroitin sulphate attachment sites. Genomic comparison shows that, although chicken exons 11-14 are identical in size to the rat and human exons, chicken exon 10 is the smallest of the three species. This is also reflected in the size of its chondroitin sulphate coding region and in the total number of Ser-Gly pairs. The putative keratan sulphate domain shows 31-45% identity with the other species and lacks the repetitive sequences seen in the others. In summary, while the linear arrangement of specific domains of chicken aggrecan is identical to that in the aggrecans of other species, and while there is considerable identity of three separate domains, chicken aggrecan demonstrates unique features, notably in its chondroitin sulphate domain and its keratan sulphate

  19. Structural Studies of Interactions between Cardiac Troponin I and Actin in Regulated Thin Filament using Förster Resonance Energy Transfer

    PubMed Central

    Xing, Jun; Chinnaraj, Mathivanan; Zhang, Zhihong; Cheung, Herbert C.; Dong, Wen-Ji

    2008-01-01

    The Ca2+-induced interaction between cardiac troponin I (cTnI) and actin plays a key role in the regulation of cardiac muscle contraction and relaxation. In this report we investigated changes of this interaction in response to strong crossbridge formation between myosin S1 and actin and PKA phosphorylation of cTnI within reconstituted thin filament. The interaction was monitored by measuring Förster resonance energy transfer (FRET) between the fluorescent donor 5-(iodoacetamidoethyl)aminonaphthalene-1-sulfonic acid (AEDANS) attached to the residues 131, 151, 160 167, 188 and 210 of cTnI and the nonfluorescent acceptor 4-dimethylaminophenylazophenyl-4′-maleimide (DABM) attached to cysteine 374 of actin. The FRET distance measurements showed that bound Ca2+ induced large increases in the distances from actin to the cTnI sites, indicating a Ca2+-triggered separation of actin from cTnI. Strongly bound myosin S1 induced additional increases in these distances in the presence of bound Ca2+. These two-step changes in the observed FRET distances provide a direct link of structural changes at the interface between cTnI and actin to the three-state model of thin filament regulation of muscle contraction and relaxation. When cTnC was inactivated through mutations of key residues within the 12-residue Ca2+-binding loop, strongly bound S1 alone induced increases in the distances in spite of the fact that the filaments no longer bound regulatory Ca2+. These results suggest bound Ca2+ or strongly bound S1 alone can partially activate thin filament, but full activation requires both bound Ca2+ and strongly bound S1. The distributions of the FRET distances revealed different structural dynamics associated with different regions of cTnI in different biochemical states. The second actin-binding region appears more rigid than the inhibitory/regulatory region. In the Mg2+ state, the regulatory region appears more flexible than the inhibitory region, and in the Ca2+ state, the

  20. Intermediate Filaments in Caenorhabditis elegans.

    PubMed

    Zuela, Noam; Gruenbaum, Yosef

    2016-01-01

    More than 70 different genes in humans and 12 different genes in Caenorhabditis elegans encode the superfamily of intermediate filament (IF) proteins. In C. elegans, similar to humans, these proteins are expressed in a cell- and tissue-specific manner, can assemble into heteropolymers and into 5-10nm wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. At least 5 of the 11 cytoplasmic IFs, as well as the nuclear IF, lamin, are essential. In this chapter, we will include a short review of our current knowledge of both cytoplasmic and nuclear IFs in C. elegans and will describe techniques used for their analyses.

  1. Nonequilibrium transport in superconducting filaments

    NASA Technical Reports Server (NTRS)

    Arutyunov, K. YU.; Danilova, N. P.; Nikolaeva, A. A.

    1995-01-01

    The step-like current-voltage characteristics of highly homogeneous single-crystalline tin and indium thin filaments has been measured. The length of the samples L approximately 1 cm was much greater than the nonequilibrium quasiparticle relaxation length Lambda. It was found that the activation of a successive i-th voltage step occurs at current significantly greater than the one derived with the assumption that the phase slip centers are weakly interacting on a scale L much greater than Lambda. The observation of 'subharmonic' fine structure on the voltage-current characteristics of tin filaments confirms the hypothesis of the long-range phase slip centers interaction.

  2. STAR FORMATION IN THE TAURUS FILAMENT L 1495: FROM DENSE CORES TO STARS

    SciTech Connect

    Schmalzl, Markus; Kainulainen, Jouni; Henning, Thomas; Launhardt, Ralf; Quanz, Sascha P.; Alves, Joao; Goodman, Alyssa A.; Pineda, Jaime E.; Roman-Zuniga, Carlos G.

    2010-12-10

    We present a study of dense structures in the L 1495 filament in the Taurus Molecular Cloud and examine its star-forming properties. In particular, we construct a dust extinction map of the filament using deep near-infrared observations, exposing its small-scale structure in unprecedented detail. The filament shows highly fragmented substructures and a high mass-per-length value of M{sub line} = 17 M{sub sun} pc{sup -1}, reflecting star-forming potential in all parts of it. However, a part of the filament, namely B 211, is remarkably devoid of young stellar objects. We argue that in this region the initial filament collapse and fragmentation is still taking place and star formation is yet to occur. In the star-forming part of the filament, we identify 39 cores with masses from 0.4 to 10 M{sub sun} and preferred separations in agreement with the local Jeans length. Most of these cores exceed the Bonnor-Ebert critical mass, and are therefore likely to collapse and form stars. The dense core mass function follows a power law with exponent {Gamma} = 1.2 {+-} 0.2, a form commonly observed in star-forming regions.

  3. A “Mechanistic” Explanation of the Multiple Helical Forms Adopted by Bacterial Flagellar Filaments

    PubMed Central

    Calladine, C.R.; Luisi, B.F.; Pratap, J.V.

    2013-01-01

    The corkscrew-like flagellar filaments emerging from the surface of bacteria such as Salmonella typhimurium propel the cells toward nutrient and away from repellents. This kind of motility depends upon the ability of the flagellar filaments to adopt a range of distinct helical forms. A filament is typically constructed from ~ 30,000 identical flagellin molecules, which self-assemble into a tubular structure containing 11 near-longitudinal protofilaments. A “mechanical” model, in which the flagellin building block has the capacity to switch between two principal interfacial states, predicts that the filament can assemble into a “canonical” family of 12 distinct helical forms, each having unique curvature and twist: these include two “extreme” straight forms having left- and right-handed twists, respectively, and 10 intermediate helical forms. Measured shapes of the filaments correspond well with predictions of the model. This report is concerned with two unanswered questions. First, what properties of the flagellin determine which of the 12 discrete forms is preferred? Second, how does the interfacial “switch” work, at a molecular level? Our proposed solution of these problems is based mainly on a detailed examination of differences between the available electron cryo-microscopy structures of the straight L and R filaments, respectively. PMID:23274110

  4. Molecular structure and motion in zero field magnetic resonance

    SciTech Connect

    Jarvie, T.P.

    1989-10-01

    Zero field magnetic resonance is well suited for the determination of molecular structure and the study of motion in disordered materials. Experiments performed in zero applied magnetic field avoid the anisotropic broadening in high field nuclear magnetic resonance (NMR) experiments. As a result, molecular structure and subtle effects of motion are more readily observed.

  5. Myosin and Tropomyosin Stabilize the Conformation of Formin-nucleated Actin Filaments*

    PubMed Central

    Ujfalusi, Zoltán; Kovács, Mihály; Nagy, Nikolett T.; Barkó, Szilvia; Hild, Gábor; Lukács, András; Nyitrai, Miklós; Bugyi, Beáta

    2012-01-01

    The conformational elasticity of the actin cytoskeleton is essential for its versatile biological functions. Increasing evidence supports that the interplay between the structural and functional properties of actin filaments is finely regulated by actin-binding proteins; however, the underlying mechanisms and biological consequences are not completely understood. Previous studies showed that the binding of formins to the barbed end induces conformational transitions in actin filaments by making them more flexible through long range allosteric interactions. These conformational changes are accompanied by altered functional properties of the filaments. To get insight into the conformational regulation of formin-nucleated actin structures, in the present work we investigated in detail how binding partners of formin-generated actin structures, myosin and tropomyosin, affect the conformation of the formin-nucleated actin filaments using fluorescence spectroscopic approaches. Time-dependent fluorescence anisotropy and temperature-dependent Förster-type resonance energy transfer measurements revealed that heavy meromyosin, similarly to tropomyosin, restores the formin-induced effects and stabilizes the conformation of actin filaments. The stabilizing effect of heavy meromyosin is cooperative. The kinetic analysis revealed that despite the qualitatively similar effects of heavy meromyosin and tropomyosin on the conformational dynamics of actin filaments the mechanisms of the conformational transition are different for the two proteins. Heavy meromyosin stabilizes the formin-nucleated actin filaments in an apparently single step reaction upon binding, whereas the stabilization by tropomyosin occurs after complex formation. These observations support the idea that actin-binding proteins are key elements of the molecular mechanisms that regulate the conformational and functional diversity of actin filaments in living cells. PMID:22753415

  6. X-ray analysis of filaments in galaxy clusters

    NASA Astrophysics Data System (ADS)

    Walker, S. A.; Kosec, P.; Fabian, A. C.; Sanders, J. S.

    2015-11-01

    We perform a detailed X-ray study of the filaments surrounding the brightest cluster galaxies in a sample of nearby galaxy clusters using deep Chandra observations, namely the Perseus, Centaurus and Virgo clusters, and Abell 1795. We compare the X-ray properties and spectra of the filaments in all of these systems, and find that their Chandra X-ray spectra are all broadly consistent with an absorbed two-temperature thermal model, with temperature components at 0.75 and 1.7 keV. We find that it is also possible to model the Chandra ACIS filament spectra with a charge exchange model provided a thermal component is also present, and the abundance of oxygen is suppressed relative to the abundance of Fe. In this model, charge exchange provides the dominant contribution to the spectrum in the 0.5-1.0 keV band. However, when we study the high spectral resolution RGS spectrum of the filamentary plume seen in X-rays in Centaurus, the opposite appears to be the case. The properties of the filaments in our sample of clusters are also compared to the X-ray tails of galaxies in the Coma cluster and Abell 3627. In the Perseus cluster, we search for signs of absorption by a prominent region of molecular gas in the filamentary structure around NGC 1275. We do find a decrement in the X-ray spectrum below 2 keV, indicative of absorption. However, the spectral shape is inconsistent with this decrement being caused by simply adding an additional absorbing component. We find that the spectrum can be well fit (with physically sensible parameters) with a model that includes both absorption by molecular gas and X-ray emission from the filament, which partially counteracts the absorption.

  7. Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching.

    PubMed

    Lee, Lawrence K; Ginsburg, Michael A; Crovace, Claudia; Donohoe, Mhairi; Stock, Daniela

    2010-08-19

    The flagellar motor drives the rotation of flagellar filaments at hundreds of revolutions per second, efficiently propelling bacteria through viscous media. The motor uses the potential energy from an electrochemical gradient of cations across the cytoplasmic membrane to generate torque. A rapid switch from anticlockwise to clockwise rotation determines whether a bacterium runs smoothly forward or tumbles to change its trajectory. A protein called FliG forms a ring in the rotor of the flagellar motor that is involved in the generation of torque through an interaction with the cation-channel-forming stator subunit MotA. FliG has been suggested to adopt distinct conformations that induce switching but these structural changes and the molecular mechanism of switching are unknown. Here we report the molecular structure of the full-length FliG protein, identify conformational changes that are involved in rotational switching and uncover the structural basis for the formation of the FliG torque ring. This allows us to propose a model of the complete ring and switching mechanism in which conformational changes in FliG reverse the electrostatic charges involved in torque generation. PMID:20676082

  8. Structure of the torque ring of the flagellar motor and the molecular basis for rotational switching

    SciTech Connect

    Lee, Lawrence K.; Ginsburg, Michael A.; Crovace, Claudia; Donohoe, Mhairi; Stock, Daniela

    2010-09-13

    The flagellar motor drives the rotation of flagellar filaments at hundreds of revolutions per second, efficiently propelling bacteria through viscous media. The motor uses the potential energy from an electrochemical gradient of cations across the cytoplasmic membrane to generate torque. A rapid switch from anticlockwise to clockwise rotation determines whether a bacterium runs smoothly forward or tumbles to change its trajectory. A protein called FliG forms a ring in the rotor of the flagellar motor that is involved in the generation of torque through an interaction with the cation-channel-forming stator subunit MotA. FliG has been suggested to adopt distinct conformations that induce switching but these structural changes and the molecular mechanism of switching are unknown. Here we report the molecular structure of the full-length FliG protein, identify conformational changes that are involved in rotational switching and uncover the structural basis for the formation of the FliG torque ring. This allows us to propose a model of the complete ring and switching mechanism in which conformational changes in FliG reverse the electrostatic charges involved in torque generation.

  9. Molecular clouds and galactic spiral structure

    NASA Technical Reports Server (NTRS)

    Dame, T. M.

    1984-01-01

    Galactic CO line emission at 115 GHz was surveyed in order to study the distribution of molecular clouds in the inner galaxy. Comparison of this survey with similar H1 data reveals a detailed correlation with the most intense 21 cm features. To each of the classical 21 cm H1 spiral arms of the inner galaxy there corresponds a CO molecular arm which is generally more clearly defined and of higher contrast. A simple model is devised for the galactic distribution of molecular clouds. The modeling results suggest that molecular clouds are essentially transient objects, existing for 15 to 40 million years after their formation in a spiral arm, and are largely confined to spiral features about 300 pc wide.

  10. Side-binding proteins modulate actin filament dynamics.

    PubMed

    Crevenna, Alvaro H; Arciniega, Marcelino; Dupont, Aurélie; Mizuno, Naoko; Kowalska, Kaja; Lange, Oliver F; Wedlich-Söldner, Roland; Lamb, Don C

    2015-01-01

    Actin filament dynamics govern many key physiological processes from cell motility to tissue morphogenesis. A central feature of actin dynamics is the capacity of filaments to polymerize and depolymerize at their ends in response to cellular conditions. It is currently thought that filament kinetics can be described by a single rate constant for each end. In this study, using direct visualization of single actin filament elongation, we show that actin polymerization kinetics at both filament ends are strongly influenced by the binding of proteins to the lateral filament surface. We also show that the pointed-end has a non-elongating state that dominates the observed filament kinetic asymmetry. Estimates of flexibility as well as effects on fragmentation and growth suggest that the observed kinetic diversity arises from structural alteration. Tuning elongation kinetics by exploiting the malleability of the filament structure may be a ubiquitous mechanism to generate a rich variety of cellular actin dynamics. PMID:25706231

  11. Inhibitory region of troponin I: Ca(2+)-dependent structural and environmental changes in the troponin-tropomyosin complex and in reconstituted thin filaments.

    PubMed

    Kobayashi, T; Kobayashi, M; Gryczynski, Z; Lakowicz, J R; Collins, J H

    2000-01-11

    In muscle thin filaments, the inhibitory region (residues 96-117) of troponin I (TnI) is thought to interact with troponin C (TnC) in the presence of Ca(2+) and with actin in the absence of Ca(2+). To better understand these interactions, we prepared mutant TnIs which contained a single Cys-96 or Cys-117 and labeled them with the thiol-specific fluorescent probe N-(iodoacetyl)-N'-(1-sulfo-5-naphthyl)ethylenediamine (IAEDANS). We characterized the microenvironments of the AEDANS labels on TnI in the presence and absence of Ca(2+) by measuring the extent of acrylamide quenching of fluorescence and lifetime-resolved anisotropy. In the troponin-tropomyosin (Tn-Tm) complex, the AEDANS labels on both Cys-96 and Cys-117 were less accessible to solvent and less flexible in the presence of Ca(2+), reflecting closer interactions with TnC under these conditions. In reconstituted thin filaments, the environment of the AEDANS on Cys-96 was not greatly affected by Ca(2+), while the AEDANS on Cys-117 was more accessible but significantly less flexible as it moved away from actin and interacted strongly with TnC in the presence of Ca(2+). We used fluorescence resonance energy transfer (FRET) to measure distances between AEDANS on TnI Cys-96 or Cys-117 and 4-¿[(dimethylamino)phenyl]azo¿phenyl-4'-maleimide (DABmal) on actin Cys-374 in reconstituted thin filaments. In the absence of Ca(2+), the mean distances were 40.2 A for Cys-96 and 35.2 A for Cys-117. In the presence of Ca(2+), Cys-96 moved away from actin Cys-374 by approximately 3.6 A, while Cys-117 moved away by approximately 8 A. This suggests the existence of a flexible "hinge" region near the middle of TnI, allowing amino acid residues in the N-terminal half of TnI to interact with TnC in a Ca(2+)-independent manner, while the C-terminal half of TnI binds to actin in the absence of Ca(2+) or to TnC in the presence of Ca(2+). This is the first report to demonstrate structural movement of the inhibitory region of TnI in the

  12. METHOD OF MAKING TUNGSTEN FILAMENTS

    DOEpatents

    Frazer, J.W.

    1962-12-18

    A method of making tungsten filaments is described in which the tungsten is completely free of isotope impurities in the range of masses 234 to 245 for use in mass spectrometers. The filament comprises a tantalum core generally less than 1 mil in diameter having a coating of potassium-free tantalum-diffused tungsten molecularly bonded thereto. In the preferred process of manufacture a short, thin tantalum filament is first mounted between terminal posts mounted in insulated relation through a backing plate. The tungsten is most conveniently vapor plated onto the tantalum by a tungsten carbonyl vapor decomposition method having a critical step because of the tendency of the tantalum to volatilize at the temperature of operntion of the filament. The preferred recipe comprises volatilizing tantalum by resistance henting until the current drops by about 40%, cutting the voltage back to build up the tungsten, and then gradually building the temperature back up to balance the rate of tungsten deposition with the rate of tantalum volatilization. (AEC)

  13. Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

    PubMed

    Bassen, David M; Hou, Yubo; Bowser, Samuel S; Banavali, Nilesh K

    2016-01-01

    Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure. PMID:27539392

  14. Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

    PubMed Central

    Bassen, David M.; Hou, Yubo; Bowser, Samuel S.; Banavali, Nilesh K.

    2016-01-01

    Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure. PMID:27539392

  15. Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera.

    PubMed

    Bassen, David M; Hou, Yubo; Bowser, Samuel S; Banavali, Nilesh K

    2016-08-19

    Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

  16. Maintenance of electrostatic stabilization in altered tubulin lateral contacts may facilitate formation of helical filaments in foraminifera

    NASA Astrophysics Data System (ADS)

    Bassen, David M.; Hou, Yubo; Bowser, Samuel S.; Banavali, Nilesh K.

    2016-08-01

    Microtubules in foraminiferan protists (forams) can convert into helical filament structures, in which longitudinal intraprotofilament interactions between tubulin heterodimers are thought to be lost, while lateral contacts across protofilaments are still maintained. The coarse geometric features of helical filaments are known through low-resolution negative stain electron microscopy (EM). In this study, geometric restraints derived from these experimental data were used to generate an average atomic-scale helical filament model, which anticipated a modest reorientation in the lateral tubulin heterodimer interface. Restrained molecular dynamics (MD) simulations of the nearest neighbor interactions combined with a Genalized Born implicit solvent model were used to assess the lateral, longitudinal, and seam contacts in 13-3 microtubules and the reoriented lateral contacts in the helical filament model. This electrostatic analysis suggests that the change in the lateral interface in the helical filament does not greatly diminish the lateral electrostatic interaction. After longitudinal dissociation, the 13-3 seam interaction is much weaker than the reoriented lateral interface in the helical filament model, providing a plausible atomic-detail explanation for seam-to-lateral contact transition that enables the transition to a helical filament structure.

  17. THERMAL AND CHEMICAL EVOLUTION OF COLLAPSING FILAMENTS

    SciTech Connect

    Gray, William J.; Scannapieco, Evan

    2013-05-10

    Intergalactic filaments form the foundation of the cosmic web that connect galaxies together, and provide an important reservoir of gas for galaxy growth and accretion. Here we present very high resolution two-dimensional simulations of the thermal and chemical evolution of such filaments, making use of a 32 species chemistry network that tracks the evolution of key molecules formed from hydrogen, oxygen, and carbon. We study the evolution of filaments over a wide range of parameters including the initial density, initial temperature, strength of the dissociating UV background, and metallicity. In low-redshift, Z Almost-Equal-To 0.1 Z{sub Sun} filaments, the evolution is determined completely by the initial cooling time. If this is sufficiently short, the center of the filament always collapses to form a dense, cold core containing a substantial fraction of molecules. In high-redshift, Z = 10{sup -3} Z{sub Sun} filaments, the collapse proceeds much more slowly. This is mostly due to the lower initial temperatures, which lead to a much more modest increase in density before the atomic cooling limit is reached, making subsequent molecular cooling much less efficient. Finally, we study how the gravitational potential from a nearby dwarf galaxy affects the collapse of the filament and compare this to NGC 5253, a nearby starbursting dwarf galaxy thought to be fueled by the accretion of filament gas. In contrast to our fiducial case, a substantial density peak forms at the center of the potential. This peak evolves faster than the rest of the filament due to the increased rate at which chemical species form and cooling occurs. We find that we achieve similar accretion rates as NGC 5253 but our two-dimensional simulations do not recover the formation of the giant molecular clouds that are seen in radio observations.

  18. Thermal and Chemical Evolution of Collapsing Filaments

    SciTech Connect

    Gray, William J.; Scannapieco, Evan

    2013-01-15

    Intergalactic filaments form the foundation of the cosmic web that connect galaxies together, and provide an important reservoir of gas for galaxy growth and accretion. Here we present very high resolution two-dimensional simulations of the thermal and chemical evolution of such filaments, making use of a 32 species chemistry network that tracks the evolution of key molecules formed from hydrogen, oxygen, and carbon. We study the evolution of filaments over a wide range of parameters including the initial density, initial temperature, strength of the dissociating UV background, and metallicity. In low-redshift, Z ≈ 0.1Z filaments, the evolution is determined completely by the initial cooling time. If this is sufficiently short, the center of the filament always collapses to form dense, cold core containing a substantial fraction of molecules. In high-redshift, Z = 10-3Z filaments, the collapse proceeds much more slowly. This is due mostly to the lower initial temperatures, which leads to a much more modest increase in density before the atomic cooling limit is reached, making subsequent molecular cooling much less efficient. Finally, we study how the gravitational potential from a nearby dwarf galaxy affects the collapse of the filament and compare this to NGC 5253, a nearby starbusting dwarf galaxy thought to be fueled by the accretion of filament gas. In contrast to our fiducial case, a substantial density peak forms at the center of the potential. This peak evolves faster than the rest of the filament due to the increased rate at which chemical species form and cooling occur. We find that we achieve similar accretion rates as NGC 5253 but our two-dimensional simulations do not recover the formation of the giant molecular clouds that are seen in radio observations.

  19. Cytoplasmic filaments of Amoeba proteus. I. The role of filaments in consistency changes and movement.

    PubMed

    Pollard, T D; Ito, S

    1970-08-01

    The role of filaments in consistency changes and movement in a motile cytoplasmic extract of Amoeba proteus was investigated by correlating light and electron microscopic observations with viscosity measurements. The extract is prepared by the method of Thompson and Wolpert (1963). At 0 degrees C, this extract is nonmotile and similar in structure to ameba cytoplasm, consisting of groundplasm, vesicles, mitochondria, and a few 160 A filaments. The extract undergoes striking ATP-stimulated streaming when warmed to 22 degrees C. Two phases of movement are distinguished. During the first phase, the apparent viscosity usually increases and numerous 50-70 A filaments appear in samples of the extract prepared for electron microscopy, suggesting that the increase in viscosity in caused, at least in part, by the formation of these thin filaments. During this initial phase of ATP-stimulated movement, these thin filaments are not detectable by phase-contrast or polarization microscopy, but later, in the second phase of movement, 70 A filaments aggregate to form birefringent microscopic fibrils. A preparation of pure groundplasm with no 160 A filaments or membranous organelles exhibits little or no ATP-stimulated movement, but 50-70 A filaments form and aggregate into birefringent fibrils. This observation and the structural relationship of the 70 A and the 160 A filaments in the motile extract suggest that both types of filaments may be required for movement. These two types of filaments, 50-70 A and 160 A, are also present in the cytoplasm of intact amebas. Fixed cells could not be used to study the distribution of these filaments during natural ameboid movement because of difficulties in preserving the normal structure of the ameba during preparation for electron microscopy.

  20. A Statistical Study of Solar Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Schanche, Nicole; Aggarwal, Ashna; Reeves, Kathy; Kempton, Dustin James; Angryk, Rafal

    2016-05-01

    Solar filaments are cool, dark channels of partially-ionized plasma that lie above the chromosphere. Their structure follows the neutral line between local regions of opposite magnetic polarity. Previous research (e.g. Schmieder et al. 2013, McCauley et al. 2015) has shown a positive correlation (70-80%) between the occurrence of filament eruptions and coronal mass ejections (CME’s). In this study, we attempt to use properties of the filament in order to predict whether or not a given filament will erupt. This prediction would help to better predict the occurrence of an oncoming CME. To track the evolution of a filament over time, a spatio-temporal algorithm that groups separate filament instances from the Heliophysics Event Knowledgebase (HEK) into filament tracks was developed. Filament features from the HEK metadata, such as length, chirality, and tilt are then combined with other physical features, such as the overlying decay index for two sets of filaments tracks - those that erupt and those that remain bound. Using statistical methods such as the Kolmogrov-Smirnov test and a Random Forest Classifier, we determine the effectiveness of the combined features in prediction. We conclude that there is significant overlap between the properties of filaments that erupt and those that do not, leading to predictions only ~5-10% above chance. However, the changes in features, such as a change in the filament's length over time, were determined to have the highest predictive power. We discuss the possible physical connections with the change in these features."This project has been supported by funding from the Division of Advanced Cyberinfrastructure within the Directorate for Computer and Information Science and Engineering, the Division of Astronomical Sciences within the Directorate for Mathematical and Physical Sciences, and the Division of Atmospheric and Geospace Sciences within the Directorate for Geosciences, under NSF award #1443061.”

  1. Stability and Reformation of Partially Eruptive Filament

    NASA Astrophysics Data System (ADS)

    Joshi, Navin Chandra; Prasad Choudhary, Debi; Chandra, Ramesh; Srivastava, Abhishek K.; Dwivedi, B. N.; Kayshap, Pradeep; Filippov, Boris; Uddin, Wahab

    We present an observation of the confined partial filament eruption on 4 August 2012 which later exhibits a rapid reformation along the same magnetic channel within ≈2 hours. We used BBSO and GONG Halpha as well as SDO AIA 171 Å observations to study the filament properties and its kinematics. SDO/AIA observations over the disk are used to study at coronal temperature the plasma dynamics associated with the filament. STEREO/SECCHI provides the limb observations of the filament dynamics. On the basis of the filament internal fine structure as evident in the Halpha observations and its position relative to the photospheric magnetic fields, it is found that the filament chirality is sinistral. On the other hand, the activated enveloping flux rope shows right-handed twist in the SDO/AIA 171 Å observations. Therefore, this dynamic event exhibits one-to-one correspondence between the filament chirality (sinistral) and the enveloping flux rope helicity (positive). Filament plasma goes into dynamic motion at ≈11:20 UT from its middle part towards the north-west direction with an average speed of ≈100 km s(-1) . Brightening underneath the eruptive part of the filament shows the most likely signature of low atmospheric reconnection. After traveling a distance of around ≈215 Mm towards north-west, the cool filament plasma stops and returns back at ≈12:00 UT towards its eastern foot point with the speed of ≈60 km s(-1) . We calculated the coronal magnetic field decay index (n) near the flux rope. Using this estimation, we conjecture that the filament lies within the stability domain n <1, which is the cause of its stability and possibility of prompt reformation.

  2. Kinetic theory of protein filament growth: Self-consistent methods and perturbative techniques

    NASA Astrophysics Data System (ADS)

    Michaels, Thomas C. T.; Knowles, Tuomas P. J.

    2015-12-01

    Filamentous protein structures are of high relevance for the normal functioning of the cell, where they provide the structural component for the cytoskeleton, but are also implicated in the pathogenesis of many disease states. The self-assembly of these supra-molecular structures from monomeric proteins has been studied extensively in the past 50 years and much interest has focused on elucidating the microscopic events that drive linear growth phenomena in a biological setting. Master equations have proven to be particularly fruitful in this context, allowing specific assembly mechanisms to be linked directly to experimental observations of filamentous growth. Recently, these approaches have increasingly been applied to aberrant protein polymerization, elucidating potential implications for controlling or combating the formation of pathological filamentous structures. This article reviews recent theoretical advances in the field of filamentous growth phenomena through the use of the master-equation formalism. We use perturbation and self-consistent methods for obtaining analytical solutions to the rate equations describing fibrillar growth and show how the resulting closed-form expressions can be used to shed light on the general physical laws underlying this complex phenomenon. We also present a connection between the underlying ideas of the self-consistent analysis of filamentous growth and the perturbative renormalization group.

  3. Spatial distribution of filament elasticity determines the migratory behaviors of a cell

    PubMed Central

    Harn, Hans I-Chen; Hsu, Chao-Kai; Wang, Yang-Kao; Huang, Yi-Wei; Chiu, Wen-Tai; Lin, Hsi-Hui; Cheng, Chao-Min; Tang, Ming-Jer

    2016-01-01

    ABSTRACT Any cellular response leading to morphological changes is highly tuned to balance the force generated from structural reorganization, provided by actin cytoskeleton. Actin filaments serve as the backbone of intracellular force, and transduce external mechanical signal via focal adhesion complex into the cell. During migration, cells not only undergo molecular changes but also rapid mechanical modulation. Here we focus on determining, the role of spatial distribution of mechanical changes of actin filaments in epithelial, mesenchymal, fibrotic and cancer cells with non-migration, directional migration, and non-directional migration behaviors using the atomic force microscopy. We found 1) non-migratory cells only generated one type of filament elasticity, 2) cells generating spatially distributed two types of filament elasticity showed directional migration, and 3) pathologic cells that autonomously generated two types of filament elasticity without spatial distribution were actively migrating non-directionally. The demonstration of spatial regulation of filament elasticity of different cell types at the nano-scale highlights the coupling of cytoskeletal function with physical characters at the sub-cellular level, and provides new research directions for migration related disease. PMID:26919488

  4. Differential assembly of alpha- and gamma-filagenins into thick filaments in Caenorhabditis elegans

    NASA Technical Reports Server (NTRS)

    Liu, F.; Ortiz, I.; Hutagalung, A.; Bauer, C. C.; Cook, R. G.; Epstein, H. F.

    2000-01-01

    Muscle thick filaments are highly organized supramolecular assemblies of myosin and associated proteins with lengths, diameters and flexural rigidities characteristic of their source. The cores of body wall muscle thick filaments of the nematode Caenorhabditis elegans are tubular structures of paramyosin sub-filaments coupled by filagenins and have been proposed to serve as templates for the assembly of native thick filaments. We have characterized alpha- and gamma-filagenins, two novel proteins of the cores with calculated molecular masses of 30,043 and 19,601 and isoelectric points of 10.52 and 11.49, respectively. Western blot and immunoelectron microscopy using affinity-purified antibodies confirmed that the two proteins are core components. Immunoelectron microscopy of the cores revealed that they assemble with different periodicities. Immunofluorescence microscopy showed that alpha-filagenin is localized in the medial regions of the A-bands of body wall muscle cells whereas gamma-filagenin is localized in the flanking regions, and that alpha-filagenin is expressed in 1.5-twofold embryos while gamma-filagenin becomes detectable only in late vermiform embryos. The expression of both proteins continues throughout later stages of development. C. elegans body wall muscle thick filaments of these developmental stages have distinct lengths. Our results suggest that the differential assembly of alpha- and gamma-filagenins into thick filaments of distinct lengths may be developmentally regulated.

  5. Enigmatic reticulated filaments in subsurface granite.

    PubMed

    Miller, A Z; Hernández-Mariné, M; Jurado, V; Dionísio, A; Barquinha, P; Fortunato, E; Afonso, M J; Chaminé, H I; Saiz-Jimenez, C

    2012-12-01

    In the last few years, geomicrobiologists have focused their researches on the nature and origin of enigmatic reticulated filaments reported in modern and fossil samples from limestone caves and basalt lava tubes. Researchers have posed questions on these filaments concerning their nature, origin, chemistry, morphology, mode of formation and growth. A tentative microbial origin has been elusive since these filaments are found as hollow tubular sheaths and could not be affiliated to any known microorganism. We describe the presence of similar structures in a 16th century granite tunnel in Porto, Northwest Portugal. The reticulated filaments we identify exhibit fine geometry surface ornamentation formed by cross-linked Mn-rich nanofibres, surrounded by a large amount of extracellular polymeric substances. Within these Mn-rich filaments we report for the first time the occurrence of microbial cells. PMID:23760930

  6. Enigmatic reticulated filaments in subsurface granite.

    PubMed

    Miller, A Z; Hernández-Mariné, M; Jurado, V; Dionísio, A; Barquinha, P; Fortunato, E; Afonso, M J; Chaminé, H I; Saiz-Jimenez, C

    2012-12-01

    In the last few years, geomicrobiologists have focused their researches on the nature and origin of enigmatic reticulated filaments reported in modern and fossil samples from limestone caves and basalt lava tubes. Researchers have posed questions on these filaments concerning their nature, origin, chemistry, morphology, mode of formation and growth. A tentative microbial origin has been elusive since these filaments are found as hollow tubular sheaths and could not be affiliated to any known microorganism. We describe the presence of similar structures in a 16th century granite tunnel in Porto, Northwest Portugal. The reticulated filaments we identify exhibit fine geometry surface ornamentation formed by cross-linked Mn-rich nanofibres, surrounded by a large amount of extracellular polymeric substances. Within these Mn-rich filaments we report for the first time the occurrence of microbial cells.

  7. Externally refuelled optical filaments

    NASA Astrophysics Data System (ADS)

    Scheller, Maik; Mills, Matthew S.; Miri, Mohammad-Ali; Cheng, Weibo; Moloney, Jerome V.; Kolesik, Miroslav; Polynkin, Pavel; Christodoulides, Demetrios N.

    2014-04-01

    Plasma channels produced in air through femtosecond laser filamentation hold great promise for a number of applications, including remote sensing, attosecond physics and spectroscopy, channelling microwaves and lightning protection. In such settings, extended filaments are desirable, yet their longitudinal span is limited by dissipative processes. Although various techniques aiming to prolong this process have been explored, the substantial extension of optical filaments remains a challenge. Here, we experimentally demonstrate that the natural range of a plasma column can be enhanced by at least an order of magnitude when the filament is prudently accompanied by an auxiliary beam. In this arrangement, the secondary low-intensity `dressing' beam propagates linearly and acts as a distributed energy reservoir, continuously refuelling the optical filament. Our approach offers an efficient and viable route towards the generation of extended light strings in air without inducing premature wave collapse or an undesirable beam break-up into multiple filaments.

  8. Electron microscopic imaging revealed the flexible filamentous structure of the cell attachment protein P2 of Rice dwarf virus located around the icosahedral 5-fold axes.

    PubMed

    Miyazaki, Naoyuki; Higashiura, Akifumi; Higashiura, Tomoko; Akita, Fusamichi; Hibino, Hiroyuki; Omura, Toshihiro; Nakagawa, Atsushi; Iwasaki, Kenji

    2016-02-01

    The minor outer capsid protein P2 of Rice dwarf virus (RDV), a member of the genus Phytoreovirus in the family Reoviridae, is essential for viral cell entry. Here, we clarified the structure of P2 and the interactions to host insect cells. Negative stain electron microscopy (EM) showed that P2 proteins are monomeric and flexible L-shaped filamentous structures of ∼20 nm in length. Cryo-EM structure revealed the spatial arrangement of P2 in the capsid, which was prescribed by the characteristic virion structure. The P2 proteins were visualized as partial rod-shaped structures of ∼10 nm in length in the cryo-EM map and accommodated in crevasses on the viral surface around icosahedral 5-fold axes with hydrophobic interactions. The remaining disordered region of P2 assumed to be extended to the radial direction towards exterior. Electron tomography clearly showed that RDV particles were away from the cellular membrane at a uniform distance and several spike-like densities, probably corresponding to P2, connecting a viral particle to the host cellular membrane during cell entry. By combining the in vitro and in vivo structural information, we could gain new insights into the detailed mechanism of the cell entry of RDV.

  9. The molecular structure of 1-methyl- trans-cyclooctene

    NASA Astrophysics Data System (ADS)

    Traetteberg, M.; Bakken, P.; Almenningen, A.

    1981-07-01

    The molecular structure of 1 -methyl- trans-cyclooctene has been studied by the gas electron diffraction method. A molecular mechanics calculation has been done for the title compound and for trans-cyclooctene and 1,2-dimethyl- trans-cyclooctene.

  10. The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses

    PubMed Central

    Agirrezabala, Xabier; Méndez-López, Eduardo; Lasso, Gorka; Sánchez-Pina, M Amelia; Aranda, Miguel; Valle, Mikel

    2015-01-01

    Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies – a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses. DOI: http://dx.doi.org/10.7554/eLife.11795.001 PMID:26673077

  11. The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses.

    PubMed

    Agirrezabala, Xabier; Méndez-López, Eduardo; Lasso, Gorka; Sánchez-Pina, M Amelia; Aranda, Miguel; Valle, Mikel

    2015-12-16

    Flexible filamentous viruses include economically important plant pathogens. Their viral particles contain several hundred copies of a helically arrayed coat protein (CP) protecting a (+)ssRNA. We describe here a structure at 3.9 Å resolution, from electron cryomicroscopy, of Pepino mosaic virus (PepMV), a representative of the genus Potexvirus (family Alphaflexiviridae). Our results allow modeling of the CP and its interactions with viral RNA. The overall fold of PepMV CP resembles that of nucleoproteins (NPs) from the genus Phlebovirus (family Bunyaviridae), a group of enveloped (-)ssRNA viruses. The main difference between potexvirus CP and phlebovirus NP is in their C-terminal extensions, which appear to determine the characteristics of the distinct multimeric assemblies - a flexuous, helical rod or a loose ribonucleoprotein. The homology suggests gene transfer between eukaryotic (+) and (-)ssRNA viruses.

  12. Structures of High Density Molecular Fluids

    SciTech Connect

    Baer, B; Cynn, H; Iota, V; Yoo, C-S

    2002-02-01

    The goal of this proposal is to develop an in-situ probe for high density molecular fluids. We will, therefore, use Coherent Anti-Stokes Raman Spectroscopy (CARS) applied to laser heated samples in a diamond-anvil cell (DAC) to investigate molecular fluids at simultaneous conditions of high temperatures (T > 2000K) and high pressures (P > 10 GPa.) Temperatures sufficient to populate vibrational levels above the ground state will allow the vibrational potential to be mapped by CARS. A system capable of heating and probing these samples will be constructed. Furthermore, the techniques that enable a sample to be sufficiently heated and probed while held at static high pressure in a diamond-anvil-cell will be developed. This will be an in-situ investigation of simple molecules under conditions relevant to the study of detonation chemistry and the Jovain planet interiors using state of the art non-linear spectroscopy, diamond-anvil-cells, and laser heating technology.

  13. Colour Chemistry, Part I, Principles, Colour, and Molecular Structure

    ERIC Educational Resources Information Center

    Hallas, G.

    1975-01-01

    Discusses various topics in color chemistry, including the electromagnetic spectrum, the absorption and reflection of light, additive and subtractive color mixing, and the molecular structure of simple colored substances. (MLH)

  14. The global velocity field of the filament in NGC 6334

    NASA Astrophysics Data System (ADS)

    Zernickel, A.; Schilke, P.; Smith, R. J.

    2013-06-01

    Aims: Star formation involves the collapse of gas from the scale of giant molecular clouds down to dense cores. Our aim is to trace the velocities in the filamentary, massive star-forming region NGC 6334 and to explain its dynamics. Methods: The main filament was mapped with the single-dish telescope APEX in HCO+ (J = 3-2) at 267.6 GHz to trace the dense gas. In order to reproduce the position-velocity diagram, we use a 3D radiative transfer code and create a model of a cylinder that undergoes a gravitational collapse toward its center. Results: We find a velocity gradient in the filament from the end toward its center, with the highest masses being found at both ends. Similar velocities have been predicted by recent calculations of the gravitational collapse of a sheet or cylinder of gas, and the observed velocities are consistent with these predictions. The 3D structure is revealed by taking the inclination and curvature of the filament into account. The free-fall collapse timescale of the filamentary molecular cloud is estimated to be ~1 Myr. This publication is based on data acquired with the Atacama Pathfinder Experiment (APEX). APEX is a collaboration between the Max-Planck-Institut für Radioastronomie, the European Southern Observatory, and the Onsala Space Observatory.

  15. Myosin 18A coassembles with nonmuscle myosin 2 to form mixed bipolar filaments.

    PubMed

    Billington, Neil; Beach, Jordan R; Heissler, Sarah M; Remmert, Kirsten; Guzik-Lendrum, Stephanie; Nagy, Attila; Takagi, Yasuharu; Shao, Lin; Li, Dong; Yang, Yi; Zhang, Yingfan; Barzik, Melanie; Betzig, Eric; Hammer, John A; Sellers, James R

    2015-03-30

    Class-18 myosins are most closely related to conventional class-2 nonmuscle myosins (NM2). Surprisingly, the purified head domains of Drosophila, mouse, and human myosin 18A (M18A) lack actin-activated ATPase activity and the ability to translocate actin filaments, suggesting that the functions of M18A in vivo do not depend on intrinsic motor activity. M18A has the longest coiled coil of any myosin outside of the class-2 myosins, suggesting that it might form bipolar filaments similar to conventional myosins. To address this possibility, we expressed and purified full-length mouse M18A using the baculovirus/Sf9 system. M18A did not form large bipolar filaments under any of the conditions tested. Instead, M18A formed an ∼ 65-nm-long bipolar structure with two heads at each end. Importantly, when NM2 was polymerized in the presence of M18A, the two myosins formed mixed bipolar filaments, as evidenced by cosedimentation, electron microscopy, and single-molecule imaging. Moreover, super-resolution imaging of NM2 and M18A using fluorescently tagged proteins and immunostaining of endogenous proteins showed that NM2 and M18A are present together within individual filaments inside living cells. Together, our in vitro and live-cell imaging data argue strongly that M18A coassembles with NM2 into mixed bipolar filaments. M18A could regulate the biophysical properties of these filaments and, by virtue of its extra N- and C-terminal domains, determine the localization and/or molecular interactions of the filaments. Given the numerous, fundamental cellular and developmental roles attributed to NM2, our results have far-reaching biological implications.

  16. Physical properties of cytoplasmic intermediate filaments.

    PubMed

    Block, Johanna; Schroeder, Viktor; Pawelzyk, Paul; Willenbacher, Norbert; Köster, Sarah

    2015-11-01

    Intermediate filaments (IFs) constitute a sophisticated filament system in the cytoplasm of eukaryotes. They form bundles and networks with adapted viscoelastic properties and are strongly interconnected with the other filament types, microfilaments and microtubules. IFs are cell type specific and apart from biochemical functions, they act as mechanical entities to provide stability and resilience to cells and tissues. We review the physical properties of these abundant structural proteins including both in vitro studies and cell experiments. IFs are hierarchical structures and their physical properties seem to a large part be encoded in the very specific architecture of the biopolymers. Thus, we begin our review by presenting the assembly mechanism, followed by the mechanical properties of individual filaments, network and structure formation due to electrostatic interactions, and eventually the mechanics of in vitro and cellular networks. This article is part of a Special Issue entitled: Mechanobiology.

  17. POLARIZATION STRUCTURE OF FILAMENTARY CLOUDS

    SciTech Connect

    Tomisaka, Kohji

    2015-07-01

    Filaments are considered to be basic structures, and molecular clouds consist of filaments. Filaments are often observed as extending in the direction perpendicular to the interstellar magnetic field. The structure of filaments has been studied based on a magnetohydrostatic equilibrium model. Here we simulate the expected polarization pattern for isothermal magnetohydrostatic filaments. The filament exhibits a polarization pattern in which the magnetic field is apparently perpendicular to the filament when observed from the direction perpendicular to the magnetic field. When the line of sight is parallel to the global magnetic field, the observed polarization pattern is dependent on the center-to-surface density ratio for the filament and the concentration of the gas mass toward the central magnetic flux tube. Filaments with low center-to-surface density ratios have an insignificant degree of polarization when observed from the direction parallel to the global magnetic field. However, models with a large center-to-surface density ratio have polarization patterns that indicate that the filament is perpendicularly threaded by the magnetic field. When mass is heavily concentrated at the central magnetic flux tube, which can be realized by the ambipolar diffusion process, the polarization pattern is similar to that expected for a low center-to-surface density contrast.

  18. Adaptive modelling of structured molecular representations for toxicity prediction

    NASA Astrophysics Data System (ADS)

    Bertinetto, Carlo; Duce, Celia; Micheli, Alessio; Solaro, Roberto; Tiné, Maria Rosaria

    2012-12-01

    We investigated the possibility of modelling structure-toxicity relationships by direct treatment of the molecular structure (without using descriptors) through an adaptive model able to retain the appropriate structural information. With respect to traditional descriptor-based approaches, this provides a more general and flexible way to tackle prediction problems that is particularly suitable when little or no background knowledge is available. Our method employs a tree-structured molecular representation, which is processed by a recursive neural network (RNN). To explore the realization of RNN modelling in toxicological problems, we employed a data set containing growth impairment concentrations (IGC50) for Tetrahymena pyriformis.

  19. Instructional Approach to Molecular Electronic Structure Theory

    ERIC Educational Resources Information Center

    Dykstra, Clifford E.; Schaefer, Henry F.

    1977-01-01

    Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

  20. Synthesis and molecular structure of gold triarylcorroles.

    PubMed

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine; Ghosh, Abhik

    2011-12-19

    A number of third-row transition-metal corroles have remained elusive as synthetic targets until now, notably osmium, platinum, and gold corroles. Against this backdrop, we present a simple and general synthesis of β-unsubstituted gold(III) triarylcorroles and the first X-ray crystal structure of such a complex. Comparison with analogous copper and silver corrole structures, supplemented by extensive scalar-relativistic, dispersion-corrected density functional theory calculations, suggests that "inherent saddling" may occur for of all coinage metal corroles. The degree of saddling, however, varies considerably among the three metals, decreasing conspicuously along the series Cu > Ag > Au. The structural differences reflect significant differences in metal-corrole bonding, which are also reflected in the electrochemistry and electronic absorption spectra of the complexes. From Cu to Au, the electronic structure changes from noninnocent metal(II)-corrole(•2-) to relatively innocent metal(III)-corrole(3-). PMID:22111600

  1. Assembly of bipolar microtubule structures by passive cross-linkers and molecular motors

    NASA Astrophysics Data System (ADS)

    Johann, D.; Goswami, D.; Kruse, K.

    2016-06-01

    During cell division, sister chromatids are segregated by the mitotic spindle, a bipolar assembly of interdigitating antiparallel polar filaments called microtubules. The spindle contains the midzone, a stable region of overlapping antiparallel microtubules, that is essential for maintaining bipolarity. Although a lot is known about the molecular players involved, the mechanism underlying midzone formation and maintenance is still poorly understood. We study the interaction of polar filaments that are cross-linked by molecular motors moving directionally and by passive cross-linkers diffusing along microtubules. Using a particle-based stochastic model, we find that the interplay of motors and passive cross-linkers can generate a stable finite overlap between a pair of antiparallel polar filaments. We develop a mean-field theory to study this mechanism in detail and investigate the influence of steric interactions between motors and passive cross-linkers on the overlap dynamics. In the presence of interspecies steric interactions, passive cross-linkers mimic the behavior of molecular motors and stable finite overlaps are generated even for non-cross-linking motors. Finally, we develop a mean-field theory for a bundle of aligned polar filaments and show that they can self-organize into a spindlelike pattern. Our work suggests possible ways as to how cells can generate spindle midzones and control their extensions.

  2. Tungsten Filament Fire

    ERIC Educational Resources Information Center

    Ruiz, Michael J.; Perkins, James

    2016-01-01

    We safely remove the outer glass bulb from an incandescent lamp and burn up the tungsten filament after the glass is removed. This demonstration dramatically illustrates the necessity of a vacuum or inert gas for the environment surrounding the tungsten filament inside the bulb. Our approach has added historical importance since the incandescent…

  3. Tungsten filament fire

    NASA Astrophysics Data System (ADS)

    Ruiz, Michael J.; Perkins, James

    2016-05-01

    We safely remove the outer glass bulb from an incandescent lamp and burn up the tungsten filament after the glass is removed. This demonstration dramatically illustrates the necessity of a vacuum or inert gas for the environment surrounding the tungsten filament inside the bulb. Our approach has added historical importance since the incandescent light bulb is being replaced by compact fluorescent and LED lamps.

  4. COMPLEX FLARE DYNAMICS INITIATED BY A FILAMENT–FILAMENT INTERACTION

    SciTech Connect

    Zhu, Chunming; McAteer, R. T. James; Liu, Rui; Alexander, David; Sun, Xudong

    2015-11-01

    We report on an eruption involving a relatively rare filament–filament interaction on 2013 June 21, observed by SDO and STEREO-B. The two filaments were separated in height with a “double-decker” configuration. The eruption of the lower filament began simultaneously with a descent of the upper filament, resulting in a convergence and direct interaction of the two filaments. The interaction was accompanied by the heating of surrounding plasma and an apparent crossing of a loop-like structure through the upper filament. The subsequent coalescence of the filaments drove a bright front ahead of the erupting structures. The whole process was associated with a C3.0 flare followed immediately by an M2.9 flare. Shrinking loops and descending dark voids were observed during the M2.9 flare at different locations above a C-shaped flare arcade as part of the energy release, giving us unique insight into the flare dynamics.

  5. SMART Observation of Magnetic Helicity in Solar Filaments

    NASA Astrophysics Data System (ADS)

    Hagino, M.; Kitai, R.; Shibata, K.

    2006-08-01

    We examined the magnetic helicity of solar filaments from their structure in the chromosphere and corona. The H-alpha telescope of the Solar Magnetic Activity Research Telescope (SMART) observed 239 intermediate filaments from 2005 July 1 to 2006 May 15. The intermediate filament usually locates between two active regions. Using these images, we identified the filament spine and its barbs, and determined the chromospheric filament helicity from the mean angle between each barbs and a spine. We found that 71% (78 of 110) of intermediate filaments in the northern hemisphere are negative helicity and 67% (87 of 129) of filaments in the southern hemisphere are positive, which agreed with the well-known hemispheric tendency of the magnetic helicity. Additionally, we studied the coronal helicity of intermediate filaments. The coronal filament helicity is defined as the crossing angle of threads formed a filament. The helicity pattern of coronal filaments obtained with EIT/SOHO 171A also shows the helicity hemispheric tendency. Namely, 65% (71 of 110) of coronal filaments in the northern hemisphere exhibit negative helicity and the 65% (84 of 129) of filaments in the southern hemisphere show negative helicity. These data were observed in the same day with the SMART H-alpha data. Moreover, we found 12 filament eruptions in our data. The 7 of 12 filaments show the clear opposite sign of the hemispheric tendency of the magnetic helicity. The helicity seems to be change during temporal evolution. This results suggest that filament instability may be driven by the opposite sign helicity injection from the foot point of the barb.

  6. Role and structural mechanism of WASP-triggered conformational changes in branched actin filament nucleation by Arp2/3 complex.

    PubMed

    Rodnick-Smith, Max; Luan, Qing; Liu, Su-Ling; Nolen, Brad J

    2016-07-01

    The Arp2/3 (Actin-related proteins 2/3) complex is activated by WASP (Wiskott-Aldrich syndrome protein) family proteins to nucleate branched actin filaments that are important for cellular motility. WASP recruits actin monomers to the complex and stimulates movement of Arp2 and Arp3 into a "short-pitch" conformation that mimics the arrangement of actin subunits within filaments. The relative contribution of these functions in Arp2/3 complex activation and the mechanism by which WASP stimulates the conformational change have been unknown. We purified budding yeast Arp2/3 complex held in or near the short-pitch conformation by an engineered covalent cross-link to determine if the WASP-induced conformational change is sufficient for activity. Remarkably, cross-linked Arp2/3 complex bypasses the need for WASP in activation and is more active than WASP-activated Arp2/3 complex. These data indicate that stimulation of the short-pitch conformation is the critical activating function of WASP and that monomer delivery is not a fundamental requirement for nucleation but is a specific requirement for WASP-mediated activation. During activation, WASP limits nucleation rates by releasing slowly from nascent branches. The cross-linked complex is inhibited by WASP's CA region, even though CA potently stimulates cross-linking, suggesting that slow WASP detachment masks the activating potential of the short-pitch conformational switch. We use structure-based mutations and WASP-Arp fusion chimeras to determine how WASP stimulates movement toward the short-pitch conformation. Our data indicate that WASP displaces the autoinhibitory Arp3 C-terminal tail from a hydrophobic groove at Arp3's barbed end to destabilize the inactive state, providing a mechanism by which WASP stimulates the short-pitch conformation and activates Arp2/3 complex. PMID:27325766

  7. Molecular and electronic structure of the peptide subunit of Geobacter sulfurreducens conductive pili from first principles.

    PubMed

    Feliciano, Gustavo T; da Silva, Antonio J R; Reguera, Gemma; Artacho, Emilio

    2012-08-01

    The respiration of metal oxides by the bacterium Geobacter sulfurreducens requires the assembly of a small peptide (the GS pilin) into conductive filaments termed pili. We gained insights into the contribution of the GS pilin to the pilus conductivity by developing a homology model and performing molecular dynamics simulations of the pilin peptide in vacuo and in solution. The results were consistent with a predominantly helical peptide containing the conserved α-helix region required for pilin assembly but carrying a short carboxy-terminal random-coiled segment rather than the large globular head of other bacterial pilins. The electronic structure of the pilin was also explored from first principles and revealed a biphasic charge distribution along the pilin and a low electronic HOMO-LUMO gap, even in a wet environment. The low electronic band gap was the result of strong electrostatic fields generated by the alignment of the peptide bond dipoles in the pilin's α-helix and by charges from ions in solution and amino acids in the protein. The electronic structure also revealed some level of orbital delocalization in regions of the pilin containing aromatic amino acids and in spatial regions of high resonance where the HOMO and LUMO states are, which could provide an optimal environment for the hopping of electrons under thermal fluctuations. Hence, the structural and electronic features of the pilin revealed in these studies support the notion of a pilin peptide environment optimized for electron conduction. PMID:22779741

  8. Molecular cloning, structural analysis, and tissue expression of the TNNT3 gene in Guizhou black goat.

    PubMed

    Chen, Haolin; Zhang, Jinhua; Yu, Bo; Li, Liang; Shang, Yishun

    2015-11-15

    The vertebrate fast skeletal troponin T (TNNT3) protein is an important regulatory and structural component of thin filaments in skeletal muscle, which improves meat quality traits of livestock and poultry. In this study, the troponin T isoforms from adult goat (skeletal muscle mRNA) were identified. We isolated the full-length coding sequence of the goat TNNT3 gene (GenBank: KM042888), analyzed its structure, and investigated its expression in different tissues from different aged goats (10, 30, 90, 180, and 360 days old). Real-time quantitative reverse transcription-polymerase chain reaction analyses revealed that Guizhou black goat TNNT3 was highly expressed in the biceps femoris muscle, abdominal muscle, and longissimus dorsi muscle (P<0.01), and lowly expressed in the cardiac muscle, masseter muscle, and rumen tissue (P>0.05). Western blotting confirmed that the TNNT3 protein was expressed in the muscle tissues listed above, with the highest level found in the longissimus dorsi muscle, and the lowest level in the masseter muscle. In the 10 to 360day study period the TNNT3 protein expression level was the highest when the goats were 30 days old. A peptide, ASPPPAEVPEVHEEVH that may contribute to improved goat meat tenderness was identified. This study provides an insight into the molecular structure of the vertebrate TNNT3 gene.

  9. A polypeptide of 59 kDa is associated with bundles of cytoplasmic filaments in Neurospora crassa.

    PubMed Central

    Rosa, A L; Alvarez, M E; Lawson, D; Maccioni, H J

    1990-01-01

    Complex arrangements of filamentous structures have been isolated from vegetative cells of the fungus Neurospora crassa. They were enriched by differential centrifugation and purified by permeation chromatography. The filamentous structures are made up of units of 8-10 nm diameter and were isolated in bundles of up to six to nine units. The main constituent of these structures is a polypeptide with an apparent molecular mass of 59 kDa (P59Nc), which represents 4-5% of the total N. crassa proteins. The filamentous structures are cold-stable and are not affected by high-ionic-strength solutions or by the presence of 10 mM-EDTA or 1% (w/v) Triton X-100; they were disassembled by raising the pH of the solution or by using Tris-based buffers. The disassembled form assembled into structures sedimentable at 105,000 g after dialysis against the isolation buffer. The sedimentable structures were organized in the form of regular aggregates of 42-45 nm polypeptides and reacted weakly with anti-IFA, a monoclonal antibody which recognizes an epitope common to many of the higher-eukaryote intermediate-filament polypeptides. Immunofluorescence examination of wall-digested hyphae of N. crassa using affinity-purified antibodies prepared against P59Nc showed immunostaining of abundant filamentous and dot-shaped structures distributed in the cytoplasm. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:2141976

  10. UNUSUAL FILAMENTS INSIDE THE UMBRA

    SciTech Connect

    Kleint, L.

    2013-06-10

    We analyze several unusual filamentary structures which appeared in the umbra of one of the sunspots in AR 11302. They do not resemble typical light bridges in morphology or in evolution. We analyze data from SDO/HMI to investigate their temporal evolution, Hinode/SP for photospheric inversions, IBIS for chromospheric imaging, and SDO/AIA for the overlying corona. Photospheric inversions reveal a horizontal, inverse Evershed flow along these structures, which we call umbral filaments. Chromospheric images show brightenings and energy dissipation, while coronal images indicate that bright coronal loops seem to end in these umbral filaments. These rapidly evolving features do not seem to be common, and are possibly related to the high flare-productivity of the active region. Their analysis could help to understand the complex evolution of active regions.

  11. Molecular and cluster structures in 18O

    NASA Astrophysics Data System (ADS)

    von Oertzen, W.; Dorsch, T.; Bohlen, H. G.; Krücken, R.; Faestermann, T.; Hertenberger, R.; Kokalova, Tz.; Mahgoub, M.; Milin, M.; Wheldon, C.; Wirth, H.-F.

    2010-01-01

    We have studied the multi-nucleon transfer reaction 12C ( 7Li ,p) at E lab = 44 MeV, populating states in the oxygen isotope 18O . The experiments were performed at the Tandem accelerator of the Maier-Leibniz Laboratory in Munich using the high-resolution Q3D magnetic spectrograph. States were populated up to an excitation energy of 21.2MeV with an overall energy resolution of 45keV, and 30 new states of 18O have been identified. The structure of the rotational bands observed is discussed in terms of cluster bands with the underlying cluster structures: 14C ⊗ α and 12C ⊗ 2 n ⊗ α . Because of the broken intrinsic reflection symmetry in these structures the corresponding rotational bands appear as parity doublets.

  12. Mechanics of vimentin intermediate filaments

    NASA Technical Reports Server (NTRS)

    Wang, Ning; Stamenovic, Dimitrijie

    2002-01-01

    It is increasingly evident that the cytoskeleton of living cells plays important roles in mechanical and biological functions of the cells. Here we focus on the contribution of intermediate filaments (IFs) to the mechanical behaviors of living cells. Vimentin, a major structural component of IFs in many cell types, is shown to play an important role in vital mechanical and biological functions such as cell contractility, migration, stiffness, stiffening, and proliferation.

  13. Regulation of CTP Synthase Filament Formation During DNA Endoreplication in Drosophila.

    PubMed

    Wang, Pei-Yu; Lin, Wei-Cheng; Tsai, Yi-Cheng; Cheng, Mei-Ling; Lin, Yu-Hung; Tseng, Shu-Heng; Chakraborty, Archan; Pai, Li-Mei

    2015-12-01

    CTP synthase (CTPsyn) plays an essential role in DNA, RNA, and lipid synthesis. Recent studies in bacteria, yeast, and Drosophila all reveal a polymeric CTPsyn structure, which dynamically regulates its enzymatic activity. However, the molecular mechanism underlying the formation of CTPsyn polymers is not completely understood. In this study, we found that reversible ubiquitination regulates the dynamic assembly of the filamentous structures of Drosophila CTPsyn. We further determined that the proto-oncogene Cbl, an E3 ubiquitin ligase, controls CTPsyn filament formation in endocycles. While the E3 ligase activity of Cbl is required for CTPsyn filament formation, Cbl does not affect the protein levels of CTPsyn. It remains unclear whether the regulation of CTPsyn filaments by Cbl is through direct ubiquitination of CTPsyn. In the absence of Cbl or with knockdown of CTPsyn, the progression of the endocycle-associated S phase was impaired. Furthermore, overexpression of wild-type, but not enzymatically inactive CTPsyn, rescued the endocycle defect in Cbl mutant cells. Together, these results suggest that Cbl influences the nucleotide pool balance and controls CTPsyn filament formation in endocycles. This study links Cbl-mediated ubiquitination to the polymerization of a metabolic enzyme and reveals a role for Cbl in endocycles during Drosophila development.

  14. Dynamic Filament Formation by a Divergent Bacterial Actin-Like ParM Protein

    PubMed Central

    Brzoska, Anthony J.; Jensen, Slade O.; Barton, Deborah A.; Davies, Danielle S.; Overall, Robyn L.; Skurray, Ronald A.; Firth, Neville

    2016-01-01

    Actin-like proteins (Alps) are a diverse family of proteins whose genes are abundant in the chromosomes and mobile genetic elements of many bacteria. The low-copy-number staphylococcal multiresistance plasmid pSK41 encodes ParM, an Alp involved in efficient plasmid partitioning. pSK41 ParM has previously been shown to form filaments in vitro that are structurally dissimilar to those formed by other bacterial Alps. The mechanistic implications of these differences are not known. In order to gain insights into the properties and behavior of the pSK41 ParM Alp in vivo, we reconstituted the parMRC system in the ectopic rod-shaped host, E. coli, which is larger and more genetically amenable than the native host, Staphylococcus aureus. Fluorescence microscopy showed a functional fusion protein, ParM-YFP, formed straight filaments in vivo when expressed in isolation. Strikingly, however, in the presence of ParR and parC, ParM-YFP adopted a dramatically different structure, instead forming axial curved filaments. Time-lapse imaging and selective photobleaching experiments revealed that, in the presence of all components of the parMRC system, ParM-YFP filaments were dynamic in nature. Finally, molecular dissection of the parMRC operon revealed that all components of the system are essential for the generation of dynamic filaments. PMID:27310470

  15. Hierarchical composition of the axial filament from spicules of the siliceous sponge Suberites domuncula: from biosilica-synthesizing nanofibrils to structure- and morphology-guiding triangular stems.

    PubMed

    Müller, Werner E G; Mugnaioli, Enrico; Schröder, Heinz C; Schloßmacher, Ute; Giovine, Marco; Kolb, Ute; Wang, Xiaohong

    2013-01-01

    The major structural and enzymatically active protein in spicules from siliceous sponges, e.g., for Suberites domuncula studied here, is silicatein. Silicatein has been established to be the key enzyme that catalyzes the formation of biosilica, a polymer that represents the inorganic scaffold for the spicule. In the present study, it is shown, by application of high-resolution transmission and scanning transmission electron microscopy that, during the initial phase of spicule synthesis, nanofibrils with a diameter of around 10 nm are formed that comprise bundles of between 10 and 20 nanofibrils. In intracellular vacuoles, silicasomes, the nanofibrils form polar structures with a pointed tip and a blunt end. In a time-dependent manner, these nanofibrillar bundles become embedded into a Si-rich matrix, indicative for the formation of biosilica via silicatein molecules that form the nanofibrils. These biosilicified nanofibrillar bundles become extruded from the intracellular space, where they are located in the silicasomes, to the extracellular environment by an evagination process, during which a cellular protrusion forms the axial canal in the growing spicule. The nanofibrillar bundles condense and progressively form the axial filament that becomes localized in the extracellular space. It is concluded that the silicatein-composing nanofibrils act not only as enzymatic silica bio-condensing platforms but also as a structure-giving guidance for the growing spicule.

  16. Time-Resolved High-Spatial-Resolution Measurements of Underwater Laser Ionization and Filamentation

    NASA Astrophysics Data System (ADS)

    Jones, Ted; Helle, Mike; Kaganovich, Dmitri; Ting, Antonio; Penano, Joe; Hafizi, Bahman; Chen, Yu-Hsin

    2014-10-01

    Intense underwater laser propagation, filamentation, and ionization are being investigated at NRL for applications including laser-guided discharges, advanced micromachining, and low-frequency laser acoustic generation. Time-resolved spectroscopy of intense underwater propagation and filamentation reveal strong Stimulated molecular Raman Scattering with ps temporal structure and frequency chirp. In addition, fs-time-resolution perpendicular shadowgraph images of ns underwater laser ionization reveal gas microbubble generation throughout the pump beam path. These microbubbles form in ps timescales with remarkably uniform initial diameters of a few-microns. Simulations using the HELCAP 4D nonlinear laser propagation code accurately predict measured filament fluence profiles and propagation, but also indicate complex, time-dependent and axially non-uniform plasma behavior. Results from recent experiments and simulations will be presented. This work is supported by NRL Base Funds.

  17. Liquid oxygen-compatible filament-winding matrix resin

    NASA Technical Reports Server (NTRS)

    Harrison, E. S.

    1973-01-01

    Polyurethanes derived from hydroxy terminated polyperfluoro propylene oxide prepolymers were evaluated as matrix resins for filament wound composites which would be exposed to liquid (and 100% gaseous) oxygen environments. A number of structural modifications were brought about by variations in prepolymer molecular weight, and alternative curing agents which allowed retention of the oxygen compatibility. Although satisfactory performance was achieved at sub-ambient temperatures, the derived composites suffered considerable property loss at ambient or slightly elevated temperatures. To attain overall effectiveness of the composite system, upgrading of the polymer thermomechanical properties must first be achieved.

  18. Molecular Eigensolution Symmetry Analysis and Fine Structure

    PubMed Central

    Harter, William G.; Mitchell, Justin C.

    2013-01-01

    Spectra of high-symmetry molecules contain fine and superfine level cluster structure related to J-tunneling between hills and valleys on rovibronic energy surfaces (RES). Such graphic visualizations help disentangle multi-level dynamics, selection rules, and state mixing effects including widespread violation of nuclear spin symmetry species. A review of RES analysis compares it to that of potential energy surfaces (PES) used in Born–Oppenheimer approximations. Both take advantage of adiabatic coupling in order to visualize Hamiltonian eigensolutions. RES of symmetric and D2 asymmetric top rank-2-tensor Hamiltonians are compared with Oh spherical top rank-4-tensor fine-structure clusters of 6-fold and 8-fold tunneling multiplets. Then extreme 12-fold and 24-fold multiplets are analyzed by RES plots of higher rank tensor Hamiltonians. Such extreme clustering is rare in fundamental bands but prevalent in hot bands, and analysis of its superfine structure requires more efficient labeling and a more powerful group theory. This is introduced using elementary examples involving two groups of order-6 (C6 and D3~C3v), then applied to families of Oh clusters in SF6 spectra and to extreme clusters. PMID:23344041

  19. Sequential myosin phosphorylation activates tarantula thick filament via a disorder-order transition.

    PubMed

    Espinoza-Fonseca, L Michel; Alamo, Lorenzo; Pinto, Antonio; Thomas, David D; Padrón, Raúl

    2015-08-01

    Phosphorylation of myosin regulatory light chain (RLC) N-terminal extension (NTE) activates myosin in thick filaments. RLC phosphorylation plays a primary regulatory role in smooth muscles and a secondary (modulatory) role in striated muscles, which is regulated by Ca(2+)via TnC/TM on the thin filament. Tarantula striated muscle exhibits both regulatory systems: one switches on/off contraction through thin filament regulation, and another through PKC constitutively Ser35 phosphorylated swaying free heads in the thick filaments that produces quick force on twitches regulated from 0 to 50% and modulation is accomplished recruiting additional force-potentiating free and blocked heads via Ca(2+)4-CaM-MLCK Ser45 phosphorylation. We have used microsecond molecular dynamics (MD) simulations of tarantula RLC NTE to understand the structural basis for phosphorylation-based regulation in tarantula thick filament activation. Trajectory analysis revealed that an inter-domain salt bridge network (R39/E58,E61) facilitates the formation of a stable helix-coil-helix (HCH) motif formed by helices P and A in the unphosphorylated NTE of both myosin heads. Phosphorylation of the blocked head on Ser45 does not induce any substantial structural changes. However, phosphorylation of the free head on Ser35 disrupts this salt bridge network and induces a partial extension of helix P along RLC helix A. While not directly participating in the HCH folding, phosphorylation of Ser35 unlocks a compact structure and allows the NTE to spontaneously undergo coil-helix transitions. The modest structural change induced by the subsequent Ser45 diphosphorylation monophosphorylated Ser35 free head facilitates full helix P extension into a single structurally stable α-helix through a network of intra-domain salt bridges (pS35/R38,R39,R42). We conclude that tarantula thick filament activation is controlled by sequential Ser35-Ser45 phosphorylation via a conserved disorder-to-order transition.

  20. Sequential myosin phosphorylation activates tarantula thick filament via a disorder-order transition.

    PubMed

    Espinoza-Fonseca, L Michel; Alamo, Lorenzo; Pinto, Antonio; Thomas, David D; Padrón, Raúl

    2015-08-01

    Phosphorylation of myosin regulatory light chain (RLC) N-terminal extension (NTE) activates myosin in thick filaments. RLC phosphorylation plays a primary regulatory role in smooth muscles and a secondary (modulatory) role in striated muscles, which is regulated by Ca(2+)via TnC/TM on the thin filament. Tarantula striated muscle exhibits both regulatory systems: one switches on/off contraction through thin filament regulation, and another through PKC constitutively Ser35 phosphorylated swaying free heads in the thick filaments that produces quick force on twitches regulated from 0 to 50% and modulation is accomplished recruiting additional force-potentiating free and blocked heads via Ca(2+)4-CaM-MLCK Ser45 phosphorylation. We have used microsecond molecular dynamics (MD) simulations of tarantula RLC NTE to understand the structural basis for phosphorylation-based regulation in tarantula thick filament activation. Trajectory analysis revealed that an inter-domain salt bridge network (R39/E58,E61) facilitates the formation of a stable helix-coil-helix (HCH) motif formed by helices P and A in the unphosphorylated NTE of both myosin heads. Phosphorylation of the blocked head on Ser45 does not induce any substantial structural changes. However, phosphorylation of the free head on Ser35 disrupts this salt bridge network and induces a partial extension of helix P along RLC helix A. While not directly participating in the HCH folding, phosphorylation of Ser35 unlocks a compact structure and allows the NTE to spontaneously undergo coil-helix transitions. The modest structural change induced by the subsequent Ser45 diphosphorylation monophosphorylated Ser35 free head facilitates full helix P extension into a single structurally stable α-helix through a network of intra-domain salt bridges (pS35/R38,R39,R42). We conclude that tarantula thick filament activation is controlled by sequential Ser35-Ser45 phosphorylation via a conserved disorder-to-order transition. PMID

  1. Sympathetic Solar Filament Eruptions

    NASA Astrophysics Data System (ADS)

    Wang, Rui; Liu, Ying D.; Zimovets, Ivan; Hu, Huidong; Dai, Xinghua; Yang, Zhongwei

    2016-08-01

    The 2015 March 15 coronal mass ejection as one of the two that together drove the largest geomagnetic storm of solar cycle 24 so far was associated with sympathetic filament eruptions. We investigate the relations between the different filaments involved in the eruption. A surge-like small-scale filament motion is confirmed as the trigger that initiated the erupting filament with multi-wavelength observations and using a forced magnetic field extrapolation method. When the erupting filament moved to an open magnetic field region, it experienced an obvious acceleration process and was accompanied by a C-class flare and the rise of another larger filament that eventually failed to erupt. We measure the decay index of the background magnetic field, which presents a critical height of 118 Mm. Combining with a potential field source surface extrapolation method, we analyze the distributions of the large-scale magnetic field, which indicates that the open magnetic field region may provide a favorable condition for F2 rapid acceleration and have some relation with the largest solar storm. The comparison between the successful and failed filament eruptions suggests that the confining magnetic field plays an important role in the preconditions for an eruption.

  2. Ionization probes of molecular structure and chemistry

    SciTech Connect

    Johnson, P.M.

    1993-12-01

    Various photoionization processes provide very sensitive probes for the detection and understanding of the spectra of molecules relevant to combustion processes. The detection of ionization can be selective by using resonant multiphoton ionization or by exploiting the fact that different molecules have different sets of ionization potentials. Therefore, the structure and dynamics of individual molecules can be studied even in a mixed sample. The authors are continuing to develop methods for the selective spectroscopic detection of molecules by ionization, and to use these methods for the study of some molecules of combustion interest.

  3. THE FREE-FALL TIME OF FINITE SHEETS AND FILAMENTS

    SciTech Connect

    Toala, Jesus A.; Vazquez-Semadeni, Enrique; Gomez, Gilberto C.

    2012-01-10

    Molecular clouds often exhibit filamentary or sheet-like shapes. We compute the free-fall time ({tau}{sub ff}) for finite, uniform, self-gravitating circular sheets and filamentary clouds of small but finite thickness, so that their volume density {rho} can still be defined. We find that, for thin sheets, the free-fall time is larger than that of a uniform sphere with the same volume density by a factor proportional to {radical}A, where the aspect ratio A is given by A = R/h, R being the sheet's radius and h is its thickness. For filamentary clouds, the aspect ratio is defined as A=L/R, where L is the filament's half-length and R is its (small) radius, and the modification factor is more complicated, although in the limit of large A it again reduces to nearly {radical}A. We propose that our result for filamentary shapes naturally explains the ubiquitous configuration of clumps fed by filaments observed in the densest structures of molecular clouds. Also, the longer free-fall times for non-spherical geometries in general may contribute toward partially alleviating the 'star formation conundrum', namely, the star formation rate in the Galaxy appears to be proceeding in a timescale much larger than the total molecular mass in the Galaxy divided by its typical free-fall time. If molecular clouds are in general formed by thin sheets and long filaments, then their relevant free-fall time may have been systematically underestimated, possibly by factors of up to one order of magnitude.

  4. Linking numerical simulations of molecular cloud structure with observations.

    NASA Astrophysics Data System (ADS)

    Kainulainen, Jouni

    2015-08-01

    Understanding the physical processes that control the life-cycle of the cold interstellar medium (ISM) is one of the key themes in the astrophysics of galaxies today. This importance derives from the role of the cold ISM as the birthplace of new stars, and consequently, as an indivisible constituent of galaxy evolution. In the current paradigm of turbulence-regulated ISM, star formation is controlled by the internal structure of individual molecular clouds, which in turn is set by a complex interplay of turbulence, gravity, and magnetic fields in the clouds. It is in the very focus of the field to determine how these processes give rise to the observed structure of molecular clouds. In this talk, I will review our current efforts to confront this paradigm with the goal of observationally constraining how different processes regulate molecular cloud structure and star formation. At the heart of these efforts lies the use of numerical simulations of gravo-turbulent media to A) define physically meaningful characteristics that are sensitive to the different cloud-shaping processes, and B) determine if and how such characteristics can be recovered by observations. I will show in my talk how this approach has recently led to new constraints for some fundamental measures of the molecular cloud structure. Such constraints allow us to assess the roles of turbulence and gravity in controlling the ISM structure and star formation. I will also highlight specific recent results, focusing on the nature of filamentary structures within molecular clouds. These results may provide a novel set of observational constraints with which to challenge the turbulence-regulated ISM paradigm. Finally, I will discuss the current challenges and open questions in understanding the link between molecular cloud structure and star formation, and speculate on key directions to aim the near-future studies.

  5. Evolution of the structure of near-surface ultrahigh molecular weight polyethylene nanolayers during orientational drawing

    NASA Astrophysics Data System (ADS)

    Lebedev, D. V.; Ivan'kova, E. M.; Marikhin, V. A.; Myasnikova, L. P.; Radovanova, E. I.; Boiko, Yu. M.; Shtil'man, M. V.

    2014-06-01

    A comparative investigation of the surface structure of ultrahigh molecular weight polyethylene film filaments obtained with different draw ratios from xerogels prepared from 1.5 wt % polymer solutions in decaline and mineral oil has been performed using a SUPRA-55V scanning electron microscope and a nanoluminograph for recording thermoluminescence of ultrathin near-surface layers of solids. It has been found that, with an increase in the draw ratio, the luminescence intensity decreases, and the peaks responsible for the segmental mobility are shifted toward higher temperatures. It has been assumed that this is associated with the improvement of the structure of near-surface layers of the polymer (with a decrease in the number of microcavities and segments of molecules with a high degree of coiling). It has also been revealed that the peaks observed in glow curves of the oriented gel samples from polymer solutions in decaline are shifted more significantly than those of the gel samples from polymer solutions in mineral oil, and the extremely oriented films are characterized by a large discretization of kinetic units of motion.

  6. The Dark Matter filament between Abell 222/223

    NASA Astrophysics Data System (ADS)

    Dietrich, Jörg P.; Werner, Norbert; Clowe, Douglas; Finoguenov, Alexis; Kitching, Tom; Miller, Lance; Simionescu, Aurora

    2016-10-01

    Weak lensing detections and measurements of filaments have been elusive for a long time. The reason is that the low density contrast of filaments generally pushes the weak lensing signal to unobservably low scales. To nevertheless map the dark matter in filaments exquisite data and unusual systems are necessary. SuprimeCam observations of the supercluster system Abell 222/223 provided the required combination of excellent seeing images and a fortuitous alignment of the filament with the line-of-sight. This boosted the lensing signal to a detectable level and led to the first weak lensing mass measurement of a large-scale structure filament. The filament connecting Abell 222 and Abell 223 is now the only one traced by the galaxy distribution, dark matter, and X-ray emission from the hottest phase of the warm-hot intergalactic medium. The combination of these data allows us to put the first constraints on the hot gas fraction in filaments.

  7. A Robust Actin Filaments Image Analysis Framework

    PubMed Central

    Alioscha-Perez, Mitchel; Benadiba, Carine; Goossens, Katty; Kasas, Sandor; Dietler, Giovanni; Willaert, Ronnie; Sahli, Hichem

    2016-01-01

    The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a ‘cartoon’ part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the ‘cartoon’ image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover, it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in osteoblasts

  8. A Robust Actin Filaments Image Analysis Framework.

    PubMed

    Alioscha-Perez, Mitchel; Benadiba, Carine; Goossens, Katty; Kasas, Sandor; Dietler, Giovanni; Willaert, Ronnie; Sahli, Hichem

    2016-08-01

    The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a 'cartoon' part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the 'cartoon' image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover, it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in osteoblasts grown in

  9. Regulation of the filament structure and assembly of Acanthamoeba myosin II by phosphorylation of serines in the heavy-chain nonhelical tailpiece.

    PubMed

    Liu, Xiong; Hong, Myoung-Soon; Shu, Shi; Yu, Shuhua; Korn, Edward D

    2013-01-01

    Acanthamoeba myosin II (AMII) has two heavy chains ending in a 27-residue nonhelical tailpiece and two pairs of light chains. In a companion article, we show that five, and only five, serine residues can be phosphorylated both in vitro and in vivo: Ser639 in surface loop 2 of the motor domain and serines 1489, 1494, 1499, and 1504 in the nonhelical tailpiece of the heavy chains. In that paper, we show that phosphorylation of Ser639 down-regulates the actin-activated MgATPase activity of AMII and that phosphorylation of the serines in the nonhelical tailpiece has no effect on enzymatic activity. Here we show that bipolar tetrameric, hexameric, and octameric minifilaments of AMII with the nonhelical tailpiece serines either phosphorylated or mutated to glutamate have longer bare zones and more tightly clustered heads than minifilaments of unphosphorylated AMII, irrespective of the phosphorylation state of Ser639. Although antiparallel dimers of phosphorylated and unphosphorylated myosins are indistinguishable, phosphorylation inhibits dimerization and filament assembly. Therefore, the different structures of tetramers, hexamers, and octamers of phosphorylated and unphosphorylated AMII must be caused by differences in the longitudinal stagger of phosphorylated and unphosphorylated bipolar dimers and tetramers. Thus, although the actin-activated MgATPase activity of AMII is regulated by phosphorylation of Ser639 in loop 2 of the motor domain, the structure of AMII minifilaments is regulated by phosphorylation of one or more of four serines in the nonhelical tailpiece of the heavy chain. PMID:23248285

  10. Molecular information structures in the brain.

    PubMed

    Conrad, M

    1976-01-01

    This paper presents a theory of memory and memory mediated learning based on the manipulation of macromolecular conformations. The main features of the theory are: 1) the brain contains primary and reference neurons; 2) inputs from the external environment produce particular patterns of primary firing; 3) the firing of a primary neuron sensitizes certain of its dendrites; 4) the sensitized primaries are loaded by the reference neuron active at the time and in such a way that they fire when called by this reference neuron, thus reconstructing the original pattern of primary activity. The reference neurons may also be loaded by primaries, thus making it possible for the reconstruction process to be initiated by some feature of the initial input. Each reference neuron loads and calls at most one primary pattern of activity, thereby preventing superposition of memories. If the primaries are loadable by sequences of impulses, this makes it possible to increase the connectivity among the various types of neurons by using party-line organization. The loading and calling processes themselves are mediated by call molecules. These are allosteric enzymes, located in the dendrites of primary and reference neurons, whose states are set either by an impulse or sequence of impulses and which catalyze events leading to impulse formation whenever this input recurs. The call molecules are capable of duplicating their setting (or conformation) using either intra- or interneuronal potentials, thereby ensuring stability of the memory trace. The theory allows for general powers of memory manipulation (by rememorization), for the construction of time ordered, content ordered, and associative data structures, and for computation with global representations of the environment. It makes a large number of testable predictions, provides a natural interpretation for the structure of the cerebral cortex, and accounts for: resistance to cooling, differential effects of chemical agents on short

  11. Intermediate Filaments in Caenorhabditis elegans.

    PubMed

    Zuela, Noam; Gruenbaum, Yosef

    2016-01-01

    More than 70 different genes in humans and 12 different genes in Caenorhabditis elegans encode the superfamily of intermediate filament (IF) proteins. In C. elegans, similar to humans, these proteins are expressed in a cell- and tissue-specific manner, can assemble into heteropolymers and into 5-10nm wide filaments that account for the principal structural elements at the nuclear periphery, nucleoplasm, and cytoplasm. At least 5 of the 11 cytoplasmic IFs, as well as the nuclear IF, lamin, are essential. In this chapter, we will include a short review of our current knowledge of both cytoplasmic and nuclear IFs in C. elegans and will describe techniques used for their analyses. PMID:26795488

  12. Molecular structure of vapor-deposited amorphous selenium

    NASA Astrophysics Data System (ADS)

    Goldan, A. H.; Li, C.; Pennycook, S. J.; Schneider, J.; Blom, A.; Zhao, W.

    2016-10-01

    The structure of amorphous selenium is clouded with much uncertainty and contradictory results regarding the dominance of polymeric chains versus monomer rings. The analysis of the diffraction radial distribution functions are inconclusive because of the similarities between the crystalline allotropes of selenium in terms of the coordination number, bond length, bond angle, and dihedral angle. Here, we took a much different approach and probed the molecular symmetry of the thermodynamically unstable amorphous state via analysis of structural phase transformations. We verified the structure of the converted metastable and stable crystalline structures using scanning transmission electron microscopy. In addition, given that no experimental technique can tell us the exact three-dimensional atomic arrangements in glassy semiconductors, we performed molecular-dynamic simulations using a well-established empirical three-body interatomic potential. We developed a true vapor-deposited process for the deposition of selenium molecules onto a substrate using empirical molecular vapor compositions and densities. We prepared both vapor-deposited and melt-quenched samples and showed that the simulated radial distribution functions match very well to experiment. The combination of our experimental and molecular-dynamic analyses shows that the structures of vapor- and melt-quenched glassy/amorphous selenium are quite different, based primarily on rings and chains, respectively, reflecting the predominant structure of the parent phase in its thermodynamic equilibrium.

  13. Myosin binding protein-C activates thin filaments and inhibits thick filaments in heart muscle cells.

    PubMed

    Kampourakis, Thomas; Yan, Ziqian; Gautel, Mathias; Sun, Yin-Biao; Irving, Malcolm

    2014-12-30

    Myosin binding protein-C (MyBP-C) is a key regulatory protein in heart muscle, and mutations in the MYBPC3 gene are frequently associated with cardiomyopathy. However, the mechanism of action of MyBP-C remains poorly understood, and both activating and inhibitory effects of MyBP-C on contractility have been reported. To clarify the function of the regulatory N-terminal domains of MyBP-C, we determined their effects on the structure of thick (myosin-containing) and thin (actin-containing) filaments in intact sarcomeres of heart muscle. We used fluorescent probes on troponin C in the thin filaments and on myosin regulatory light chain in the thick filaments to monitor structural changes associated with activation of demembranated trabeculae from rat ventricle by the C1mC2 region of rat MyBP-C. C1mC2 induced larger structural changes in thin filaments than calcium activation, and these were still present when active force was blocked with blebbistatin, showing that C1mC2 directly activates the thin filaments. In contrast, structural changes in thick filaments induced by C1mC2 were smaller than those associated with calcium activation and were abolished or reversed by blebbistatin. Low concentrations of C1mC2 did not affect resting force but increased calcium sensitivity and reduced cooperativity of force and structural changes in both thin and thick filaments. These results show that the N-terminal region of MyBP-C stabilizes the ON state of thin filaments and the OFF state of thick filaments and lead to a novel hypothesis for the physiological role of MyBP-C in the regulation of cardiac contractility.

  14. Structure and stability in TMC-1: Analysis of NH3 molecular line and Herschel continuum data

    NASA Astrophysics Data System (ADS)

    Fehér, O.; Tóth, L. V.; Ward-Thompson, D.; Kirk, J.; Kraus, A.; Pelkonen, V.-M.; Pintér, S.; Zahorecz, S.

    2016-05-01

    Aims: We examined the velocity, density, and temperature structure of Taurus molecular cloud-1 (TMC-1), a filamentary cloud in a nearby quiescent star forming area, to understand its morphology and evolution. Methods: We observed high signal-to-noise (S/N), high velocity resolution NH3(1,1), and (2, 2) emission on an extended map. By fitting multiple hyperfine-split line profiles to the NH3(1, 1) spectra, we derived the velocity distribution of the line components and calculated gas parameters on several positions. Herschel SPIRE far-infrared continuum observations were reduced and used to calculate the physical parameters of the Planck Galactic Cold Clumps (PGCCs) in the region, including the two in TMC-1. The morphology of TMC-1 was investigated with several types of clustering methods in the parameter space consisting of position, velocity, and column density. Results: Our Herschel-based column density map shows a main ridge with two local maxima and a separated peak to the south-west. The H2 column densities and dust colour temperatures are in the range of 0.5-3.3 × 1022 cm-2 and 10.5-12 K, respectively. The NH3 column densities and H2 volume densities are in the range of 2.8-14.2 × 1014 cm-2 and 0.4-2.8 × 104 cm-3. Kinetic temperatures are typically very low with a minimum of 9 K at the maximum NH3 and H2 column density region. The kinetic temperature maximum was found at the protostar IRAS 04381+2540 with a value of 13.7 K. The kinetic temperatures vary similarly to the colour temperatures in spite of the fact that densities are lower than the critical density for coupling between the gas and dust phase. The k-means clustering method separated four sub-filaments in TMC-1 with masses of 32.5, 19.6, 28.9, and 45.9 M⊙ and low turbulent velocity dispersion in the range of 0.13-0.2 km s-1. Conclusions: The main ridge of TMC-1 is composed of four sub-filaments that are close to gravitational equilibrium. We label these TMC-1F1 through F4. The sub-filaments TMC

  15. A Census of Large-scale (≥10 PC), Velocity-coherent, Dense Filaments in the Northern Galactic Plane: Automated Identification Using Minimum Spanning Tree

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Testi, Leonardo; Burkert, Andreas; Walmsley, C. Malcolm; Beuther, Henrik; Henning, Thomas

    2016-09-01

    Large-scale gaseous filaments with lengths up to the order of 100 pc are on the upper end of the filamentary hierarchy of the Galactic interstellar medium (ISM). Their association with respect to the Galactic structure and their role in Galactic star formation are of great interest from both an observational and theoretical point of view. Previous “by-eye” searches, combined together, have started to uncover the Galactic distribution of large filaments, yet inherent bias and small sample size limit conclusive statistical results from being drawn. Here, we present (1) a new, automated method for identifying large-scale velocity-coherent dense filaments, and (2) the first statistics and the Galactic distribution of these filaments. We use a customized minimum spanning tree algorithm to identify filaments by connecting voxels in the position–position–velocity space, using the Bolocam Galactic Plane Survey spectroscopic catalog. In the range of 7\\buildrel{\\circ}\\over{.} 5≤slant l≤slant 194^\\circ , we have identified 54 large-scale filaments and derived mass (∼ {10}3{--}{10}5 {M}ȯ ), length (10–276 pc), linear mass density (54–8625 {M}ȯ pc‑1), aspect ratio, linearity, velocity gradient, temperature, fragmentation, Galactic location, and orientation angle. The filaments concentrate along major spiral arms. They are widely distributed across the Galactic disk, with 50% located within ±20 pc from the Galactic mid-plane and 27% run in the center of spiral arms. An order of 1% of the molecular ISM is confined in large filaments. Massive star formation is more favorable in large filaments compared to elsewhere. This is the first comprehensive catalog of large filaments that can be useful for a quantitative comparison with spiral structures and numerical simulations.

  16. A Census of Large-scale (≥10 PC), Velocity-coherent, Dense Filaments in the Northern Galactic Plane: Automated Identification Using Minimum Spanning Tree

    NASA Astrophysics Data System (ADS)

    Wang, Ke; Testi, Leonardo; Burkert, Andreas; Walmsley, C. Malcolm; Beuther, Henrik; Henning, Thomas

    2016-09-01

    Large-scale gaseous filaments with lengths up to the order of 100 pc are on the upper end of the filamentary hierarchy of the Galactic interstellar medium (ISM). Their association with respect to the Galactic structure and their role in Galactic star formation are of great interest from both an observational and theoretical point of view. Previous “by-eye” searches, combined together, have started to uncover the Galactic distribution of large filaments, yet inherent bias and small sample size limit conclusive statistical results from being drawn. Here, we present (1) a new, automated method for identifying large-scale velocity-coherent dense filaments, and (2) the first statistics and the Galactic distribution of these filaments. We use a customized minimum spanning tree algorithm to identify filaments by connecting voxels in the position-position-velocity space, using the Bolocam Galactic Plane Survey spectroscopic catalog. In the range of 7\\buildrel{\\circ}\\over{.} 5≤slant l≤slant 194^\\circ , we have identified 54 large-scale filaments and derived mass (˜ {10}3{--}{10}5 {M}⊙ ), length (10-276 pc), linear mass density (54-8625 {M}⊙ pc-1), aspect ratio, linearity, velocity gradient, temperature, fragmentation, Galactic location, and orientation angle. The filaments concentrate along major spiral arms. They are widely distributed across the Galactic disk, with 50% located within ±20 pc from the Galactic mid-plane and 27% run in the center of spiral arms. An order of 1% of the molecular ISM is confined in large filaments. Massive star formation is more favorable in large filaments compared to elsewhere. This is the first comprehensive catalog of large filaments that can be useful for a quantitative comparison with spiral structures and numerical simulations.

  17. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments

    PubMed Central

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoît

    2015-01-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  18. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    PubMed

    Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M; Schulten, Klaus; Roux, Benoît

    2015-10-01

    The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels), each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD) of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good agreement with

  19. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  20. Origin and Evolution of Filament-Prominence Systems

    NASA Astrophysics Data System (ADS)

    Martens, Petrus C.; Zwaan, Cornelis

    2001-09-01

    We present a ``head-to-tail'' linkage model for the formation, evolution, and eruption of solar filaments. The magnetic field structure of our model is based on the observation that filaments form exclusively in filament channels with no apparent magnetic connections above the polarity inversion line. The formation of a filament in this configuration is driven by flux convergence and cancellation, which produces looplike filament segments with a half-turn. Filament segments of like chirality may connect and form long quiescent filaments. Such filaments are stabilized through footpoint anchoring until further cancellation at the footpoints causes their eruption. The eruption restores the original filament channel so that filament formation may resume immediately. We then demonstrate that the combined workings of Hale's polarity law, Joy's law, and differential rotation introduce a strong hemispheric preference in the chirality of filaments formed poleward of the sunspot belt, which is in agreement with observations. We analyze the magnetic fine structure of filaments formed through our model and find consistency with the observed hemispheric preference for barb orientation and a simple explanation for barb formation. Finally, we consider the flux tubes retracted below the surface in the process of filament formation. We show that every cancellation event that generates a filament obeying the hemispheric chirality preference injects a flux tube below the surface with a poloidal field opposite that of the ongoing cycle. We suggest that this pattern of submergence of flux represents the specific mechanism for the reversal of the poloidal flux in a Babcock-Leighton-Durney-type model for the solar dynamo.

  1. Importance of Molecular Structure on the Thermophoresis of Binary Mixtures.

    PubMed

    Kumar, Pardeep; Goswami, Debabrata

    2014-12-26

    Using thermal lens spectroscopy, we study the role of molecular structural isomers of butanol on the thermophoresis (or Soret effect) of binary mixtures of methanol in butanol. In this study, we show that the thermal lens signal due to the Soret effect changes its sign for all the different concentrations of binary mixtures of butanol with methanol except for the one containing tertiary-butanol. The magnitude and sign of the Soret coefficients strongly depend on the molecular structure of the isomers of butanol in the binary mixture with methanol. This isomerization dependence is in stark contrast to the expected mass dependence of the Soret effect.

  2. Snake Filament Eruption

    NASA Video Gallery

    A very long solar filament that had been snaking around the Sun erupted on Dec. 6, 2010 with a flourish. NASA's Solar Dynamics Observatory (SDO) caught the action in dramatic detail in extreme ultr...

  3. Co-option of the polarity gene network shapes filament morphology in angiosperms.

    PubMed

    de Almeida, Ana Maria Rocha; Yockteng, Roxana; Schnable, James; Alvarez-Buylla, Elena R; Freeling, Michael; Specht, Chelsea D

    2014-08-29

    The molecular genetic mechanisms underlying abaxial-adaxial polarity in plants have been studied as a property of lateral and flattened organs, such as leaves. In leaves, laminar expansion occurs as a result of balanced abaxial-adaxial gene expression. Over- or under- expression of either abaxializing or adaxializing genes inhibits laminar growth, resulting in a mutant radialized phenotype. Here, we show that co-option of the abaxial-adaxial polarity gene network plays a role in the evolution of stamen filament morphology in angiosperms. RNA-Seq data from species bearing laminar (flattened) or radial (cylindrical) filaments demonstrates that species with laminar filaments exhibit balanced expression of abaxial-adaxial (ab-ad) genes, while overexpression of a YABBY gene is found in species with radial filaments. This result suggests that unbalanced expression of ab-ad genes results in inhibition of laminar outgrowth, leading to a radially symmetric structure as found in many angiosperm filaments. We anticipate that co-option of the polarity gene network is a fundamental mechanism shaping many aspects of plant morphology during angiosperm evolution.

  4. Fragmentation in filamentary molecular clouds

    NASA Astrophysics Data System (ADS)

    Contreras, Yanett; Garay, Guido; Rathborne, Jill M.; Sanhueza, Patricio

    2016-02-01

    Recent surveys of dust continuum emission at sub-mm wavelengths have shown that filamentary molecular clouds are ubiquitous along the Galactic plane. These structures are inhomogeneous, with overdensities that are sometimes associated with infrared emission and active of star formation. To investigate the connection between filaments and star formation, requires an understanding of the processes that lead to the fragmentation of filaments and a determination of the physical properties of the overdensities (clumps). In this paper, we present a multiwavelength study of five filamentary molecular clouds, containing several clumps in different evolutionary stages of star formation. We analyse the fragmentation of the filaments and derive the physical properties of their clumps. We find that the clumps in all filaments have a characteristic spacing consistent with the prediction of the `sausage' instability theory, regardless of the complex morphology of the filaments or their evolutionary stage. We also find that most clumps have sufficient mass and density to form high-mass stars, supporting the idea that high-mass stars and clusters form within filaments.

  5. Scanning tunneling microscopy study of the assembly and structure of filamentous virus M13 bound to graphite

    NASA Astrophysics Data System (ADS)

    Sharma, Prashant

    2012-02-01

    Viruses are an important class of biomaterials used for placing nano particles on inorganic substrates. To accomplish greater control over viral assembly on a substrate it is important to determine the in situ nanoscale structure of the viral protein coat. Scanning tunneling microscopy offers the unique potential for determining the structure and arrangement of the proteins of a virus adsorbed on a conducting substrate. In this work, I develop an experimental technique for isolating and studying M13 viruses that bind to graphite. Using scanning tunneling microscopy in ambient conditions I obtain the correct lateral dimension of the virus and the periodicity of its protein structure when it is bound to graphite. I also analyze the tunneling conductance fluctuations in these measurements and introduce a simple model for tunneling through an assembly of proteins to obtain an accurate estimation of the vertical dimension of a virus bound to a conducting substrate. I discuss broader implications of this scanning tunneling microscopy study for the in situ structure determination of other biomolecules.

  6. From non-random molecular structure to life and mind

    NASA Technical Reports Server (NTRS)

    Fox, S. W.

    1989-01-01

    The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

  7. GRAVITATIONAL COLLAPSE AND FILAMENT FORMATION: COMPARISON WITH THE PIPE NEBULA

    SciTech Connect

    Heitsch, Fabian; Ballesteros-Paredes, Javier; Hartmann, Lee

    2009-10-20

    Recent models of molecular cloud formation and evolution suggest that such clouds are dynamic and generally exhibit gravitational collapse. We present a simple analytic model of global collapse onto a filament and compare this with our numerical simulations of the flow-driven formation of an isolated molecular cloud to illustrate the supersonic motions and infall ram pressures expected in models of gravity-driven cloud evolution. We compare our results with observations of the Pipe Nebula, an especially suitable object for our purposes as its low star formation activity implies insignificant perturbations from stellar feedback. We show that our collapsing cloud model can explain the magnitude of the velocity dispersions seen in the {sup 13}CO filamentary structure by Onishi et al. and the ram pressures required by Lada et al. to confine the lower-mass cores in the Pipe Nebula. We further conjecture that higher-resolution simulations will show small velocity dispersions in the densest core gas, as observed, but which are infall motions and not supporting turbulence. Our results point out the inevitability of ram pressures as boundary conditions for molecular cloud filaments, and the possibility that especially lower-mass cores still can be accreting mass at significant rates, as suggested by observations.

  8. The titin A-band rod domain is dispensable for initial thick filament assembly in zebrafish.

    PubMed

    Myhre, J Layne; Hills, Jordan A; Prill, Kendal; Wohlgemuth, Serene L; Pilgrim, David B

    2014-03-01

    The sarcomeres of skeletal and cardiac muscle are highly structured protein arrays, consisting of thick and thin filaments aligned precisely to one another and to their surrounding matrix. The contractile mechanisms of sarcomeres are generally well understood, but how the patterning of sarcomeres is initiated during early skeletal muscle and cardiac development remains uncertain. Two of the most widely accepted hypotheses for this process include the "molecular ruler" model, in which the massive protein titin defines the length of the sarcomere and provides a scaffold along which the myosin thick filament is assembled, and the "premyofibril" model, which proposes that thick filament formation does not require titin, but that a "premyofibril" consisting of non-muscle myosin, α-actinin and cytoskeletal actin is used as a template. Each model posits a different order of necessity of the various components, but these have been difficult to test in vivo. Zebrafish motility mutants with developmental defects in sarcomere patterning are useful for the elucidation of such mechanisms, and here we report the analysis of the herzschlag mutant, which shows deficits in both cardiac and skeletal muscle. The herzschlag mutant produces a truncated titin protein, lacking the C-terminal rod domain that is proposed to act as a thick filament scaffold, yet muscle patterning is still initiated, with grossly normal thick and thin filament assembly. Only after embryonic muscle contraction begins is breakdown of sarcomeric myosin patterning observed, consistent with the previously noted role of titin in maintaining the contractile integrity of mature sarcomeres. This conflicts with the "molecular ruler" model of early sarcomere patterning and supports a titin-independent model of thick filament organization during sarcomerogenesis. These findings are also consistent with the symptoms of human titin myopathies that exhibit a late onset, such as tibial muscular dystrophy.

  9. The impact of tropomyosins on actin filament assembly is isoform specific.

    PubMed

    Janco, Miro; Bonello, Teresa T; Byun, Alex; Coster, Adelle C F; Lebhar, Helene; Dedova, Irina; Gunning, Peter W; Böcking, Till

    2016-07-01

    Tropomyosin (Tpm) is an α helical coiled-coil dimer that forms a co-polymer along the actin filament. Tpm is involved in the regulation of actin's interaction with binding proteins as well as stabilization of the actin filament and its assembly kinetics. Recent studies show that multiple Tpm isoforms also define the functional properties of distinct actin filament populations within a cell. Subtle structural variations within well conserved Tpm isoforms are the key to their functional specificity. Therefore, we purified and characterized a comprehensive set of 8 Tpm isoforms (Tpm1.1, Tpm1.12, Tpm1.6, Tpm1.7, Tpm1.8, Tpm2.1, Tpm3.1, and Tpm4.2), using well-established actin co-sedimentation and pyrene fluorescence polymerization assays. We observed that the apparent affinity (Kd(app)) to filamentous actin varied in all Tpm isoforms between ∼0.1-5 μM with similar values for both, skeletal and cytoskeletal actin filaments. The data did not indicate any correlation between affinity and size of Tpm molecules, however high molecular weight (HMW) isoforms Tpm1.1, Tpm1.6, Tpm1.7 and Tpm2.1, showed ∼3-fold higher cooperativity compared to low molecular weight (LMW) isoforms Tpm1.12, Tpm1.8, Tpm3.1, and Tpm4.2. The rate of actin filament elongation in the presence of Tpm2.1 increased, while all other isoforms decreased the elongation rate by 27-85 %. Our study shows that the biochemical properties of Tpm isoforms are finely tuned and depend on sequence variations in alternatively spliced regions of Tpm molecules.

  10. The impact of tropomyosins on actin filament assembly is isoform specific.

    PubMed

    Janco, Miro; Bonello, Teresa T; Byun, Alex; Coster, Adelle C F; Lebhar, Helene; Dedova, Irina; Gunning, Peter W; Böcking, Till

    2016-07-01

    Tropomyosin (Tpm) is an α helical coiled-coil dimer that forms a co-polymer along the actin filament. Tpm is involved in the regulation of actin's interaction with binding proteins as well as stabilization of the actin filament and its assembly kinetics. Recent studies show that multiple Tpm isoforms also define the functional properties of distinct actin filament populations within a cell. Subtle structural variations within well conserved Tpm isoforms are the key to their functional specificity. Therefore, we purified and characterized a comprehensive set of 8 Tpm isoforms (Tpm1.1, Tpm1.12, Tpm1.6, Tpm1.7, Tpm1.8, Tpm2.1, Tpm3.1, and Tpm4.2), using well-established actin co-sedimentation and pyrene fluorescence polymerization assays. We observed that the apparent affinity (Kd(app)) to filamentous actin varied in all Tpm isoforms between ∼0.1-5 μM with similar values for both, skeletal and cytoskeletal actin filaments. The data did not indicate any correlation between affinity and size of Tpm molecules, however high molecular weight (HMW) isoforms Tpm1.1, Tpm1.6, Tpm1.7 and Tpm2.1, showed ∼3-fold higher cooperativity compared to low molecular weight (LMW) isoforms Tpm1.12, Tpm1.8, Tpm3.1, and Tpm4.2. The rate of actin filament elongation in the presence of Tpm2.1 increased, while all other isoforms decreased the elongation rate by 27-85 %. Our study shows that the biochemical properties of Tpm isoforms are finely tuned and depend on sequence variations in alternatively spliced regions of Tpm molecules. PMID:27420374

  11. The Cape Ghir filament system in August 2009 (NW Africa)

    NASA Astrophysics Data System (ADS)

    Sangrà, Pablo; Troupin, Charles; Barreiro-González, Beatriz; Desmond Barton, Eric; Orbi, Abdellatif; Arístegui, Javier

    2015-06-01

    In the framework of the Canaries-Iberian marine ecosystem Exchanges (CAIBEX) experiment, an interdisciplinary high-resolution survey was conducted in the NW African region of Cape Ghir (30°38'N) during August 2009. The anatomy of a major filament is investigated on scales down to the submesoscale using in situ and remotely sensed data. The filament may be viewed as a system composed of three intimately connected structures: a small, shallow, and cold filament embedded within a larger, deeper, and cool filament and an intrathermocline anticyclonic eddy (ITE). The cold filament, which stretches 110 km offshore, is a shallow feature 60 m deep and 25 km wide, identified by minimal surface temperatures and rich in chlorophyll a. This structure comprises two asymmetrical submesoscale (˜18 km) fronts with jets flowing in opposite directions. The cold filament is embedded near the equatorward boundary of a much broader region of approximately 120 km width and 150 m depth that forms the cool filament and stretches at least 200 km offshore. This cool region, partly resulting from the influence of cold filament, is limited by two asymmetrical mesoscale (˜50 km) frontal boundaries. At the ITE, located north of the cold filament, we observe evidence of downwelling as indicated by a relatively high concentration of particles extending from the surface to more than 200 m depth. We hypothesize that this ITE may act as a sink of carbon and thus the filament system may serve dual roles of offshore carbon export and carbon sink.

  12. Observations of the Growth of an Active Region Filament

    NASA Astrophysics Data System (ADS)

    Yang, Bo; Jiang, Yunchun; Yang, Jiayan; Bi, Yi; Li, Haidong

    2016-10-01

    We present observations of the growth of an active region filament caused by magnetic interactions among the filament and its adjacent superpenumbral filament (SF) and dark thread-like structures (T). Multistep reconnections are identified during the whole growing process. Magnetic flux convergence and cancellation occurring at the positive footpoint region of the filament is the first step reconnection, which resulted in the filament bifurcating into two sets of intertwined threads. One set anchored in situ, while the other set moved toward and interacted with the SF and part of T. This indicates the second step reconnection, which gave rise to the disappearance of the SF and the formation of a long thread-like structure that connects the far ends of the filament and T. The long thread-like structure further interacted with the T and then separated into two parts, representing the third step reconnection. Finally, another similar long thread-like structure, which intertwined with the fixed filament threads, appeared. H α observations show that this twisted structure is a longer sinistral filament. Based on the observed photospheric vector magnetograms, we performed a non-linear force-free field extrapolation to reconstruct the magnetic fields above the photosphere and found that the coronal magnetic field lines associated with the filament consists of two twisted flux ropes winding around each other. These results suggest that magnetic interactions among filaments and their adjacent SFs and T could lead to the growth of the filaments, and the filament is probably supported in a flux rope.

  13. Connecting molecular structure and exciton diffusion length in rubrene derivatives.

    PubMed

    Mullenbach, Tyler K; McGarry, Kathryn A; Luhman, Wade A; Douglas, Christopher J; Holmes, Russell J

    2013-07-19

    Connecting molecular structure and exciton diffusion length in rubrene derivatives demonstrates how the diffusion length of rubrene can be enhanced through targeted functionalization aiming to enhance self-Förster energy transfer. Functionalization adds steric bulk, forcing the molecules farther apart on average, and leading to increased photoluminescence efficiency. A diffusion length enhancement greater than 50% is realized over unsubstituted rubrene. PMID:23754475

  14. Correlative nanoscale imaging of actin filaments and their complexes

    PubMed Central

    Zhu, Huanqi; Grintsevich, Elena E.; Reisler, Emil

    2014-01-01

    Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP–actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP–actin complexes. PMID:23727693

  15. Correlative nanoscale imaging of actin filaments and their complexes.

    PubMed

    Sharma, Shivani; Zhu, Huanqi; Grintsevich, Elena E; Reisler, Emil; Gimzewski, James K

    2013-07-01

    Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP-actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP-actin complexes.

  16. Positioning and stretching of actin filaments by electric fields

    NASA Astrophysics Data System (ADS)

    Wigge, Christoph; Hinssen, Horst; Reiss, Günter; Herth, Simone

    2010-06-01

    The alignment of biological filaments on surfaces offers a high potential for controllable geometries in lab-on-a-chip-structures and micrototal analysis systems. Actin is a polar filamentous protein with a diameter of 7-8 nm that can be manipulated with strong electric fields. It is demonstrated that with the use of microelectrodes or nanoelectrodes and electric fields of 20 kV/m single actin filaments can be manipulated, stretched, and positioned between gold electrodes.

  17. Role of Active Contraction and Tropomodulins in Regulating Actin Filament Length and Sarcomere Structure in Developing Zebrafish Skeletal Muscle.

    PubMed

    Mazelet, Lise; Parker, Matthew O; Li, Mei; Arner, Anders; Ashworth, Rachel

    2016-01-01

    Whilst it is recognized that contraction plays an important part in maintaining the structure and function of mature skeletal muscle, its role during development remains undefined. In this study the role of movement in skeletal muscle maturation was investigated in intact zebrafish embryos using a combination of genetic and pharmacological approaches. An immotile mutant line (cacnb1 (ts25) ) which lacks functional voltage-gated calcium channels (dihydropyridine receptors) in the muscle and pharmacological immobilization of embryos with a reversible anesthetic (Tricaine), allowed the study of paralysis (in mutants and anesthetized fish) and recovery of movement (reversal of anesthetic treatment). The effect of paralysis in early embryos (aged between 17 and 24 hours post-fertilization, hpf) on skeletal muscle structure at both myofibrillar and myofilament level was determined using both immunostaining with confocal microscopy and small angle X-ray diffraction. The consequences of paralysis and subsequent recovery on the localization of the actin capping proteins Tropomodulin 1 & 4 (Tmod) in fish aged from 17 hpf until 42 hpf was also assessed. The functional consequences of early paralysis were investigated by examining the mechanical properties of the larval muscle. The length-force relationship, active and passive tension, was measured in immotile, recovered and control skeletal muscle at 5 and 7 day post-fertilization (dpf). Recovery of muscle function was also assessed by examining swimming patterns in recovered and control fish. Inhibition of the initial embryonic movements (up to 24 hpf) resulted in an increase in myofibril length and a decrease in width followed by almost complete recovery in both moving and paralyzed fish by 42 hpf. In conclusion, myofibril organization is regulated by a dual mechanism involving movement-dependent and movement-independent processes. The initial contractile event itself drives the localization of Tmod1 to its sarcomeric

  18. Role of Active Contraction and Tropomodulins in Regulating Actin Filament Length and Sarcomere Structure in Developing Zebrafish Skeletal Muscle

    PubMed Central

    Mazelet, Lise; Parker, Matthew O.; Li, Mei; Arner, Anders; Ashworth, Rachel

    2016-01-01

    Whilst it is recognized that contraction plays an important part in maintaining the structure and function of mature skeletal muscle, its role during development remains undefined. In this study the role of movement in skeletal muscle maturation was investigated in intact zebrafish embryos using a combination of genetic and pharmacological approaches. An immotile mutant line (cacnb1ts25) which lacks functional voltage-gated calcium channels (dihydropyridine receptors) in the muscle and pharmacological immobilization of embryos with a reversible anesthetic (Tricaine), allowed the study of paralysis (in mutants and anesthetized fish) and recovery of movement (reversal of anesthetic treatment). The effect of paralysis in early embryos (aged between 17 and 24 hours post-fertilization, hpf) on skeletal muscle structure at both myofibrillar and myofilament level was determined using both immunostaining with confocal microscopy and small angle X-ray diffraction. The consequences of paralysis and subsequent recovery on the localization of the actin capping proteins Tropomodulin 1 & 4 (Tmod) in fish aged from 17 hpf until 42 hpf was also assessed. The functional consequences of early paralysis were investigated by examining the mechanical properties of the larval muscle. The length-force relationship, active and passive tension, was measured in immotile, recovered and control skeletal muscle at 5 and 7 day post-fertilization (dpf). Recovery of muscle function was also assessed by examining swimming patterns in recovered and control fish. Inhibition of the initial embryonic movements (up to 24 hpf) resulted in an increase in myofibril length and a decrease in width followed by almost complete recovery in both moving and paralyzed fish by 42 hpf. In conclusion, myofibril organization is regulated by a dual mechanism involving movement-dependent and movement-independent processes. The initial contractile event itself drives the localization of Tmod1 to its sarcomeric position

  19. Oxidation and nitrosylation of cysteines proximal to the intermediate filament (IF)-binding site of plectin: effects on structure and vimentin binding and involvement in IF collapse.

    PubMed

    Spurny, Radovan; Abdoulrahman, Kamaran; Janda, Lubomir; Rünzler, Dominik; Köhler, Gottfried; Castañón, Maria J; Wiche, Gerhard

    2007-03-16

    As an intermediate filament (IF)-based cytolinker protein, plectin plays a key role in the maintenance of cellular cytoarchitecture and serves at the same time as a scaffolding platform for signaling cascades. Consisting of six structural repeats (R1-6) and harboring binding sites for different IF proteins and proteins involved in signaling, the plectin C-terminal domain is of strategic functional importance. Depending on the species, it contains at least 13 cysteines, 4 of which reside in the R5 domain. To investigate the structural and biological functions of R5 cysteines, we used cysteine-to-serine mutagenesis and spectroscopic, biochemical, and functional analyses. Urea-induced unfolding experiments indicated that wild-type R5 in the oxidized, disulfide bond-mediated conformation was more stable than its cysteine-free mutant derivative. The binding affinity of R5 for vimentin was significantly higher, however, when the protein was in the reduced, more relaxed conformation. Of the four R5 cysteines, one (Cys4) was particularly reactive as reflected by its ability to form disulfide bridges with R5 Cys1 and to serve as a target for nitrosylation in vitro. Using immortalized endothelial cell cultures from mice, we show that endogenous plectin is nitrosylated in vivo, and we found that NO donor-induced IF collapse proceeds dramatically faster in plectin-deficient compared with wild-type cells. Our data suggest an antagonistic role of plectin in nitrosylation (oxidative stress)-mediated alterations of IF cytoarchitecture and a possible role of R5 Cys4 as a regulatory switch. PMID:17224453

  20. High-Yield Production of a Bacterial Xylanase in the Filamentous Fungus Trichoderma reesei Requires a Carrier Polypeptide with an Intact Domain Structure

    PubMed Central

    Paloheimo, Marja; Mäntylä, Arja; Kallio, Jarno; Suominen, Pirkko

    2003-01-01

    A bacterial xylanase gene, Nonomuraea flexuosa xyn11A, was expressed in the filamentous fungus Trichoderma reesei from the strong cellobiohydrolase 1 promoter as fusions to a variety of carrier polypeptides. By using single-copy isogenic transformants, it was shown that production of this xylanase was clearly increased (up to 820 mg/liter) when it was produced as a fusion protein with a carrier polypeptide having an intact domain structure compared to the production (150 to 300 mg/liter) of fusions to the signal sequence alone or to carriers having incomplete domain structures. The carriers tested were the T. reesei mannanase I (Man5A, or MANI) core-hinge and a fragment thereof and the cellulose binding domain of T. reesei cellobiohydrolase II (Cel6A, or CBHII) with and without the hinge region(s) and a fragment thereof. The flexible hinge region was shown to have a positive effect on both the production of Xyn11A and the efficiency of cleavage of the fusion polypeptide. The recombinant Xyn11A produced had properties similar to those of the native xylanase. It constituted 6 to 10% of the total proteins secreted by the transformants. About three times more of the Man5A core-hinge carrier polypeptide than of the recombinant Xyn11A was observed. Even in the best Xyn11A producers, the levels of the fusion mRNAs were only ∼10% of the level of cel7A (cbh1) mRNA in the untransformed host strain. PMID:14660351

  1. Structure of an invertebrate gene encoding cytoplasmic intermediate filament (IF) proteins: implications for the origin and the diversification of IF proteins.

    PubMed Central

    Dodemont, H; Riemer, D; Weber, K

    1990-01-01

    The structure of the single gene encoding the cytoplasmic intermediate filament (IF) proteins in non-neuronal cells of the gastropod Helix aspersa is described. Genomic and cDNA sequences show that the gene is composed of 10 introns and 11 exons, spanning greater than 60 kb of DNA. Alternative RNA processing accounts for two mRNA families which encode two IF proteins differing only in their C-terminal sequence. The intron/exon organization of the Helix rod domain is identical to that of the vertebrate type III IF genes in spite of low overall protein sequence homology and the presence of an additional 42 residues in coil 1b of the invertebrate sequence. Intron position homology extends to the entire coding sequence comprising both the rod and tail domains when the invertebrate IF gene is compared with the nuclear lamin LIII gene of Xenopus laevis presented in the accompanying report of Döring and Stick. In contrast the intron patterns of the tail domains of the invertebrate IF and the lamin genes differ from those of the vertebrate type III genes. The combined data are in line with an evolutionary descent of cytoplasmic IF proteins from a nuclear lamin-like progenitor and suggest a mechanism for this derivation. The unique position of intron 7 in the Helix IF gene indicates that the archetype IF gene arose by the elimination of the nuclear localization sequence due to the recruitment of a novel splice site. The presumptive structural organization of the archetype IF gene allows predictions with respect to the later diversification of metazoan IF genes. Whereas models proposing a direct derivation of neurofilament genes seem unlikely, the earlier speculation of an mRNA transposition mechanism is compatible with current results. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 6. PMID:2249666

  2. Primary structure and carbohydrate binding specificity of a potent anti-HIV lectin isolated from the filamentous cyanobacterium Oscillatoria agardhii.

    PubMed

    Sato, Yuichiro; Okuyama, Satomi; Hori, Kanji

    2007-04-13

    The primary structure of a lectin, designated Oscillatoria agardhii agglutinin (OAA), isolated from the freshwater cyanobacterium O. agardhii NIES-204 was determined by the combination of Edman degradation and electron spray ionization-mass spectrometry. OAA is a polypeptide (Mr 13,925) consisting of two tandem repeats. Interestingly, each repeat sequence of OAA showed a high degree of similarity to those of a myxobacterium, Myxococcus xanthus hemagglutinin, and a marine red alga Eucheuma serra lectin. A systematic binding assay with pyridylaminated oligosaccharides revealed that OAA exclusively binds to high mannose (HM)-type N-glycans but not to other N-glycans, including complex types, hybrid types, and the pentasaccharide core or oligosaccharides from glycolipids. OAA did not interact with any of free mono- and oligomannoses that are constituents of the branched oligomannosides. These results suggest that the core disaccharide, GlcNAc-GlcNAc, is also essential for binding to OAA. The binding activity of OAA to HM type N-glycans was dramatically decreased when alpha1-2 Man was attached to alpha1-3 Man branched from the alpha1-6 Man of the pentasaccharide core. This specificity of OAA for HM-type oligosaccharides is distinct from other HM-binding lectins. Kinetic analysis with an HM heptasaccharide revealed that OAA possesses two carbohydrate binding sites per molecule, with an association constant of 2.41x10(8) m-1. Furthermore, OAA potently inhibits human immunodeficiency virus replication in MT-4 cells (EC50=44.5 nm). Thus, we have found a novel lectin family sharing similar structure and carbohydrate binding specificity among bacteria, cyanobacteria, and marine algae. PMID:17314091

  3. Molecular, Functional, and Structural Imaging of Major Depressive Disorder.

    PubMed

    Zhang, Kai; Zhu, Yunqi; Zhu, Yuankai; Wu, Shuang; Liu, Hao; Zhang, Wei; Xu, Caiyun; Zhang, Hong; Hayashi, Takuya; Tian, Mei

    2016-06-01

    Major depressive disorder (MDD) is a significant cause of morbidity and mortality worldwide, correlating with genetic susceptibility and environmental risk factors. Molecular, functional, and structural imaging approaches have been increasingly used to detect neurobiological changes, analyze neurochemical correlates, and parse pathophysiological mechanisms underlying MDD. We reviewed recent neuroimaging publications on MDD in terms of molecular, functional, and structural alterations as detected mainly by magnetic resonance imaging (MRI) and positron emission tomography. Altered structure and function of brain regions involved in the cognitive control of affective state have been demonstrated. An abnormal default mode network, as revealed by resting-state functional MRI, is likely associated with aberrant metabolic and serotonergic function revealed by radionuclide imaging. Further multi-modal investigations are essential to clarify the characteristics of the cortical network and serotonergic system associated with behavioral and genetic variations in MDD. PMID:27142698

  4. Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments.

    PubMed

    Saladin, Adrien; Amourda, Christopher; Poulain, Pierre; Férey, Nicolas; Baaden, Marc; Zacharias, Martin; Delalande, Olivier; Prévost, Chantal

    2010-10-01

    Homologous recombination is a fundamental process enabling the repair of double-strand breaks with a high degree of fidelity. In prokaryotes, it is carried out by RecA nucleofilaments formed on single-stranded DNA (ssDNA). These filaments incorporate genomic sequences that are homologous to the ssDNA and exchange the homologous strands. Due to the highly dynamic character of this process and its rapid propagation along the filament, the sequence recognition and strand exchange mechanism remains unknown at the structural level. The recently published structure of the RecA/DNA filament active for recombination (Chen et al., Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structure, Nature 2008, 453, 489) provides a starting point for new exploration of the system. Here, we investigate the possible geometries of association of the early encounter complex between RecA/ssDNA filament and double-stranded DNA (dsDNA). Due to the huge size of the system and its dense packing, we use a reduced representation for protein and DNA together with state-of-the-art molecular modeling methods, including systematic docking and virtual reality simulations. The results indicate that it is possible for the double-stranded DNA to access the RecA-bound ssDNA while initially retaining its Watson-Crick pairing. They emphasize the importance of RecA L2 loop mobility for both recognition and strand exchange.

  5. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  6. MOLVIE: an interactive visualization environment for molecular structures.

    PubMed

    Sun, Huandong; Li, Ming; Xu, Ying

    2003-05-01

    A Molecular visualization interactive environment (MOLVIE), is designed to display three-dimensional (3D) structures of molecules and support the structural analysis and research on proteins. The paper presents the features, design considerations and applications of MOLVIE, especially the new functions used to compare the structures of two molecules and view the partial fragment of a molecule. Being developed in JAVA, MOLVIE is platform-independent. Moreover, it may run on a webpage as an applet for remote users. MOLVIE is available at http://www.cs.ucsb.edu/~mli/Bioinf/software/index.html. PMID:12725967

  7. Structural and Kinetic Effects of PAK3 phosphorylation mimic of cTnI(S151E) on the cTnC-cTnI Interaction in the Cardiac Thin Filament

    PubMed Central

    Ouyang, Yexin; Mamidi, Ranganath; Jayasundar, Jayant James; Chandra, Murali; Dong, Wen-Ji

    2010-01-01

    Residue Ser151 of cTnI is known to be phosphorylated by p21-activated kinase 3 (PAK3). It has been found that PAK3-mediated phosphorylation of cTnI induces an increase in myofilament Ca2+ sensitivity, but the detailed mechanism is unknown. We investigated how the structural and kinetic effects mediated by pseudo-phosphorylation of cTnI (S151E) modulates Ca2+-induced activation of cardiac thin filaments. Using steady-state, time-resolved Förster Resonance Energy Transfer (FRET) and stopped-flow kinetic measurements, we monitored Ca2+-induced changes in cTnI-cTnC interactions. Measurements were done using reconstituted thin filaments, which contained the pseudo-phosphorylated cTnI(S151E). We hypothesized that the thin filament regulation is modulated by altered cTnC-cTnI interactions due to charge modification caused by the phosphorylation of Ser151 in cTnI. Our results showed that the pseudo-phosphorylation of cTnI (S151E) sensitizes structural changes to Ca2+ by shortening the intersite distances between cTnC and cTnI. Furthermore, kinetic rates of Ca2+ dissociation-induced structural change in the regulatory region of cTnI were significantly reduced by cTnI (S151E). The aforementioned effects of pseudo-phosphorylation of cTnI were similar to the effects of strong crossbridges on structural changes in cTnI. Our results provide novel information on how cardiac thin filament regulation is modulated by PAK3 phosphorylation of cTnI. PMID:20540949

  8. An invertebrate smooth muscle with striated muscle myosin filaments

    PubMed Central

    Sulbarán, Guidenn; Alamo, Lorenzo; Pinto, Antonio; Márquez, Gustavo; Méndez, Franklin; Padrón, Raúl; Craig, Roger

    2015-01-01

    Muscle tissues are classically divided into two major types, depending on the presence or absence of striations. In striated muscles, the actin filaments are anchored at Z-lines and the myosin and actin filaments are in register, whereas in smooth muscles, the actin filaments are attached to dense bodies and the myosin and actin filaments are out of register. The structure of the filaments in smooth muscles is also different from that in striated muscles. Here we have studied the structure of myosin filaments from the smooth muscles of the human parasite Schistosoma mansoni. We find, surprisingly, that they are indistinguishable from those in an arthropod striated muscle. This structural similarity is supported by sequence comparison between the schistosome myosin II heavy chain and known striated muscle myosins. In contrast, the actin filaments of schistosomes are similar to those of smooth muscles, lacking troponin-dependent regulation. We conclude that schistosome muscles are hybrids, containing striated muscle-like myosin filaments and smooth muscle-like actin filaments in a smooth muscle architecture. This surprising finding has broad significance for understanding how muscles are built and how they evolved, and challenges the paradigm that smooth and striated muscles always have distinctly different components. PMID:26443857

  9. Tropomyosin - master regulator of actin filament function in the cytoskeleton.

    PubMed

    Gunning, Peter W; Hardeman, Edna C; Lappalainen, Pekka; Mulvihill, Daniel P

    2015-08-15

    Tropomyosin (Tpm) isoforms are the master regulators of the functions of individual actin filaments in fungi and metazoans. Tpms are coiled-coil parallel dimers that form a head-to-tail polymer along the length of actin filaments. Yeast only has two Tpm isoforms, whereas mammals have over 40. Each cytoskeletal actin filament contains a homopolymer of Tpm homodimers, resulting in a filament of uniform Tpm composition along its length. Evidence for this 'master regulator' role is based on four core sets of observation. First, spatially and functionally distinct actin filaments contain different Tpm isoforms, and recent data suggest that members of the formin family of actin filament nucleators can specify which Tpm isoform is added to the growing actin filament. Second, Tpms regulate whole-organism physiology in terms of morphogenesis, cell proliferation, vesicle trafficking, biomechanics, glucose metabolism and organ size in an isoform-specific manner. Third, Tpms achieve these functional outputs by regulating the interaction of actin filaments with myosin motors and actin-binding proteins in an isoform-specific manner. Last, the assembly of complex structures, such as stress fibers and podosomes involves the collaboration of multiple types of actin filament specified by their Tpm composition. This allows the cell to specify actin filament function in time and space by simply specifying their Tpm isoform composition.

  10. Tropomyosin - master regulator of actin filament function in the cytoskeleton.

    PubMed

    Gunning, Peter W; Hardeman, Edna C; Lappalainen, Pekka; Mulvihill, Daniel P

    2015-08-15

    Tropomyosin (Tpm) isoforms are the master regulators of the functions of individual actin filaments in fungi and metazoans. Tpms are coiled-coil parallel dimers that form a head-to-tail polymer along the length of actin filaments. Yeast only has two Tpm isoforms, whereas mammals have over 40. Each cytoskeletal actin filament contains a homopolymer of Tpm homodimers, resulting in a filament of uniform Tpm composition along its length. Evidence for this 'master regulator' role is based on four core sets of observation. First, spatially and functionally distinct actin filaments contain different Tpm isoforms, and recent data suggest that members of the formin family of actin filament nucleators can specify which Tpm isoform is added to the growing actin filament. Second, Tpms regulate whole-organism physiology in terms of morphogenesis, cell proliferation, vesicle trafficking, biomechanics, glucose metabolism and organ size in an isoform-specific manner. Third, Tpms achieve these functional outputs by regulating the interaction of actin filaments with myosin motors and actin-binding proteins in an isoform-specific manner. Last, the assembly of complex structures, such as stress fibers and podosomes involves the collaboration of multiple types of actin filament specified by their Tpm composition. This allows the cell to specify actin filament function in time and space by simply specifying their Tpm isoform composition. PMID:26240174

  11. Microtubule-dependent transport and dynamics of vimentin intermediate filaments.

    PubMed

    Hookway, Caroline; Ding, Liya; Davidson, Michael W; Rappoport, Joshua Z; Danuser, Gaudenz; Gelfand, Vladimir I

    2015-05-01

    We studied two aspects of vimentin intermediate filament dynamics-transport of filaments and subunit exchange. We observed transport of long filaments in the periphery of cells using live-cell structured illumination microscopy. We studied filament transport elsewhere in cells using a photoconvertible-vimentin probe and total internal reflection microscopy. We found that filaments were rapidly transported along linear tracks in both anterograde and retrograde directions. Filament transport was microtubule dependent but independent of microtubule polymerization and/or an interaction with the plus end-binding protein APC. We also studied subunit exchange in filaments by long-term imaging after photoconversion. We found that converted vimentin remained in small clusters along the length of filaments rather than redistributing uniformly throughout the network, even in cells that divided after photoconversion. These data show that vimentin filaments do not depolymerize into individual subunits; they recompose by severing and reannealing. Together these results show that vimentin filaments are very dynamic and that their transport is required for network maintenance.

  12. Disruption of the keratin filament network during epithelial cell division.

    PubMed Central

    Lane, E B; Goodman, S L; Trejdosiewicz, L K

    1982-01-01

    The behaviour of keratin filaments during cell division was examined in a wide range of epithelial lines from several species. Almost half of them show keratin disruption as described previously: by immunofluorescence, filaments are replaced during mitosis by a 'speckled' pattern of discrete cytoplasmic dots. In the electron microscope these ' speckles ' are seen as granules around the cell periphery, just below the actin cortical mesh, with no detectable 10 nm filament structure inside them and no keratin filament bundles in the rest of the cytoplasm. A time course of the filament reorganization was constructed from double immunofluorescence data; filaments are disrupted in prophase, and the filament network is intact again by cytokinesis. The phenomenon is restricted to cells rich in keratin filaments, such as keratinocytes; it is unrelated to the co-existence of vimentin in many of these cells, and vimentin is generally maintained as filaments while the keratin is restructured. Some resistance to the effect may be conferred by an extended cycle time. Filament reorganization takes place within minutes, so that a reversible mechanism seems more likely than one involving de novo protein synthesis, at this metabolically quiet stage of the cell cycle. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. Fig. 6. PMID:6202508

  13. Microtubule-dependent transport and dynamics of vimentin intermediate filaments

    PubMed Central

    Hookway, Caroline; Ding, Liya; Davidson, Michael W.; Rappoport, Joshua Z.; Danuser, Gaudenz; Gelfand, Vladimir I.

    2015-01-01

    We studied two aspects of vimentin intermediate filament dynamics—transport of filaments and subunit exchange. We observed transport of long filaments in the periphery of cells using live-cell structured illumination microscopy. We studied filament transport elsewhere in cells using a photoconvertible-vimentin probe and total internal reflection microscopy. We found that filaments were rapidly transported along linear tracks in both anterograde and retrograde directions. Filament transport was microtubule dependent but independent of microtubule polymerization and/or an interaction with the plus end–binding protein APC. We also studied subunit exchange in filaments by long-term imaging after photoconversion. We found that converted vimentin remained in small clusters along the length of filaments rather than redistributing uniformly throughout the network, even in cells that divided after photoconversion. These data show that vimentin filaments do not depolymerize into individual subunits; they recompose by severing and reannealing. Together these results show that vimentin filaments are very dynamic and that their transport is required for network maintenance. PMID:25717187

  14. Develop and demonstrate manufacturing processes for fabricating graphite filament reinforced polymide (Gr/PI) composite structural elements

    NASA Technical Reports Server (NTRS)

    Chase, V. A.; Harrison, E. S.

    1985-01-01

    A study was conducted to assess the merits of using graphite/polyimide, NR-150B2 resin, for structural applications on advanced space launch vehicles. The program was divided into two phases: (1) Fabrication Process Development; and (2) Demonstration Components. The first phase of the program involved the selection of a graphite fiber, quality assurance of the NR-150B2 polyimide resin, and the quality assurance of the graphite/polyimide prepreg. In the second phase of the program, a limited number of components were fabricated before the NR-150B2 resin system was removed from the market by the supplier, Du Pont. The advancement of the NR-150B2 polyimide resin binder was found to vary significantly based on previous time and temperature history during the prepregging operation. Strength retention at 316C (600F) was found to be 50% that of room temperature strength. However, the composite would retain its initial strength after 200 hours exposure at 316C (600F). Basic chemistry studies are required for determining NR-150B2 resin binder quality assurance parameters. Graphite fibers are available that can withstand high temperature cure and postcure cycles.

  15. Evolution of filament barbs.

    NASA Astrophysics Data System (ADS)

    Liu, R.; Xu, Y.; Wang, H.

    We present a selected few cases in which the sense of chirality of filament barbs changed within periods as short as hours. We investigate in detail a quiescent filament on 2003 September 10 and 11. Of its four barbs displaying such changes, only one overlays a small polarity inversion line inside the EUV filament channel (EFC). No magnetic elements with magnitude above the noise level were detected at the endpoints of all barbs. In particular, a pair of barbs first approached toward, and then departed from, each other in Halpha , with the barb endpoints migrating as far as ˜ 10 arcsec. We conclude that the evolution of the barbs was driven by flux emergence and cancellation of small bipolar units at the EFC border.

  16. Significance of settling model structures and parameter subsets in modelling WWTPs under wet-weather flow and filamentous bulking conditions.

    PubMed

    Ramin, Elham; Sin, Gürkan; Mikkelsen, Peter Steen; Plósz, Benedek Gy

    2014-10-15

    Current research focuses on predicting and mitigating the impacts of high hydraulic loadings on centralized wastewater treatment plants (WWTPs) under wet-weather conditions. The maximum permissible inflow to WWTPs depends not only on the settleability of activated sludge in secondary settling tanks (SSTs) but also on the hydraulic behaviour of SSTs. The present study investigates the impacts of ideal and non-ideal flow (dry and wet weather) and settling (good settling and bulking) boundary conditions on the sensitivity of WWTP model outputs to uncertainties intrinsic to the one-dimensional (1-D) SST model structures and parameters. We identify the critical sources of uncertainty in WWTP models through global sensitivity analysis (GSA) using the Benchmark simulation model No. 1 in combination with first- and second-order 1-D SST models. The results obtained illustrate that the contribution of settling parameters to the total variance of the key WWTP process outputs significantly depends on the influent flow and settling conditions. The magnitude of the impact is found to vary, depending on which type of 1-D SST model is used. Therefore, we identify and recommend potential parameter subsets for WWTP model calibration, and propose optimal choice of 1-D SST models under different flow and settling boundary conditions. Additionally, the hydraulic parameters in the second-order SST model are found significant under dynamic wet-weather flow conditions. These results highlight the importance of developing a more mechanistic based flow-dependent hydraulic sub-model in second-order 1-D SST models in the future.

  17. Molecular spectroscopy and molecular structure - Selected communications presented at the 1st International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013)

    NASA Astrophysics Data System (ADS)

    Durig, James R.; Fausto, Rui; Ünsalan, Ozan; Bayarı, Sevgi; Kuş, Nihal; Ildız, Gülce Ö.

    2016-01-01

    The First International Turkish Congress on Molecular Spectroscopy (TURCMOS 2013) took place at the Harbiye Cultural Center & Museum, Istanbul, Turkey, September 15-20, 2013. The main aim of the congress was to encourage the exchange of scientific ideas and collaborations all around the world, introduce new techniques and instruments, and discuss recent developments in the field of molecular spectroscopy. Among the different subjects covered, particular emphasis was given to the relevance of spectroscopy to elucidate details of the molecular structure and the chemical and physical behavior of systems ranging from simple molecules to complex biochemical molecules. Besides experimental spectroscopic approaches, related computational and theoretical methods were also considered. In this volume, selected contributions presented at the congress were put together.

  18. Molecular docking and structure-based drug design strategies.

    PubMed

    Ferreira, Leonardo G; Dos Santos, Ricardo N; Oliva, Glaucius; Andricopulo, Adriano D

    2015-07-22

    Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.

  19. Molecular and structural basis for redox regulation of beta-actin.

    PubMed

    Lassing, Ingrid; Schmitzberger, Florian; Björnstedt, Mikael; Holmgren, Arne; Nordlund, Pär; Schutt, Clarence E; Lindberg, Uno

    2007-07-01

    An essential consequence of growth factor-mediated signal transduction is the generation of intracellular H(2)O(2). It operates as a second messenger in the control of actin microfilament dynamics, causing rapid and dramatic changes in the morphology and motile activity of stimulated cells. Little is understood about the molecular mechanisms causing these changes in the actin system. Here, it is shown that H(2)O(2) acts directly upon several levels of this system, and some of the mechanistic effects are detailed. We describe the impact of oxidation on the polymerizability of non-muscle beta/gamma-actin and compare with that of muscle alpha-actin. Oxidation of beta/gamma-actin can cause a complete loss of polymerizability, crucially, reversible by the thioredoxin system. Further, oxidation of the actin impedes its interaction with profilin and causes depolymerization of filamentous actin. The effects of oxidation are critically dependent on the nucleotide state and the concentration of Ca(2+). We have determined the crystal structure of oxidized beta-actin to a resolution of 2.6 A. The arrangement in the crystal implies an antiparallel homodimer connected by an intermolecular disulfide bond involving cysteine 374. Our data indicate that this dimer forms under non-polymerizing and oxidizing conditions. We identify oxidation of cysteine 272 in the crystallized actin dimer, likely to a cysteine sulfinic acid. In beta/gamma-actin, this is the cysteine residue most reactive towards H(2)O(2) in solution, and we suggest plausible structural determinants for its reactivity. No other oxidative modification was obvious in the structure, highlighting the specificity of the oxidation by H(2)O(2). Possible consequences of the observed effects in a cellular context and their potential relevance are discussed.

  20. Aerogel-supported filament

    DOEpatents

    Wuest, C.R.; Tillotson, T.M.; Johnson, C.V. III

    1995-05-16

    The present invention is a thin filament embedded in a low density aerogel for use in radiation detection instruments and incandescent lamps. The aerogel provides a supportive matrix that is thermally and electrically nonconductive, mechanically strong, highly porous, gas-permeable, and transparent to ionizing radiation over short distances. A low density, open-cell aerogel is cast around a fine filament or wire, which allows the wire to be positioned with little or no tension and keeps the wire in place in the event of breakage. The aerogel support reduces the stresses on the wire caused by vibrational, gravitational, electrical, and mechanical forces. 6 Figs.

  1. Aerogel-supported filament

    DOEpatents

    Wuest, Craig R.; Tillotson, Thomas M.; Johnson, III, Coleman V.

    1995-01-01

    The present invention is a thin filament embedded in a low density aerogel for use in radiation detection instruments and incandescent lamps. The aerogel provides a supportive matrix that is thermally and electrically nonconductive, mechanically strong, highly porous, gas-permeable, and transparent to ionizing radiation over short distances. A low density, open-cell aerogel is cast around a fine filament or wire, which allows the wire to be positioned with little or no tension and keeps the wire in place in the event of breakage. The aerogel support reduces the stresses on the wire caused by vibrational, gravitational, electrical, and mechanical forces.

  2. Semiflexible filamentous composites.

    PubMed

    Huisman, E M; Heussinger, C; Storm, C; Barkema, G T

    2010-09-10

    Inspired by the ubiquity of composite filamentous networks in nature, we investigate models of biopolymer networks that consist of interconnected floppy and stiff filaments. Numerical simulations carried out in three dimensions allow us to explore the microscopic partitioning of stresses and strains between the stiff and floppy fractions cs and cf and reveal a nontrivial relationship between the mechanical behavior and the relative fraction of stiff polymer: when there are few stiff polymers, nonpercolated stiff "inclusions" are protected from large deformations by an encompassing floppy matrix, while at higher fractions of stiff material the stiff network is independently percolated and dominates the mechanical response. PMID:20867610

  3. Improving structure-based function prediction using molecular dynamics

    PubMed Central

    Glazer, Dariya S.; Radmer, Randall J.; Altman, Russ B.

    2009-01-01

    Summary The number of molecules with solved three-dimensional structure but unknown function is increasing rapidly. Particularly problematic are novel folds with little detectable similarity to molecules of known function. Experimental assays can determine the functions of such molecules, but are time-consuming and expensive. Computational approaches can identify potential functional sites; however, these approaches generally rely on single static structures and do not use information about dynamics. In fact, structural dynamics can enhance function prediction: we coupled molecular dynamics simulations with structure-based function prediction algorithms that identify Ca2+ binding sites. When applied to 11 challenging proteins, both methods showed substantial improvement in performance, revealing 22 more sites in one case and 12 more in the other, with a modest increase in apparent false positives. Thus, we show that treating molecules as dynamic entities improves the performance of structure-based function prediction methods. PMID:19604472

  4. A filament supported by different magnetic field configurations

    NASA Astrophysics Data System (ADS)

    Guo, Y.; Schmieder, B.; Démoulin, P.; Wiegelmann, T.; Aulanier, G.; Török, T.; Bommier, V.

    2011-08-01

    A nonlinear force-free magnetic field extrapolation of vector magnetogram data obtained by THEMIS/MTR on 2005 May 27 suggests the simultaneous existence of different magnetic configurations within one active region filament: one part of the filament is supported by field line dips within a flux rope, while the other part is located in dips within an arcade structure. Although the axial field chirality (dextral) and the magnetic helicity (negative) are the same along the whole filament, the chiralities of the filament barbs at different sections are opposite, i.e., right-bearing in the flux rope part and left-bearing in the arcade part. This argues against past suggestions that different barb chiralities imply different signs of helicity of the underlying magnetic field. This new finding about the chirality of filaments will be useful to associate eruptive filaments and magnetic cloud using the helicity parameter in the Space Weather Science.

  5. Dense granule trafficking in Toxoplasma gondii requires a unique class 27 myosin and actin filaments

    PubMed Central

    Heaslip, Aoife T.; Nelson, Shane R.; Warshaw, David M.

    2016-01-01

    The survival of Toxoplasma gondii within its host cell requires protein release from secretory vesicles, called dense granules, to maintain the parasite’s intracellular replicative niche. Despite the importance of DGs, nothing is known about the mechanisms underlying their transport. In higher eukaryotes, secretory vesicles are transported to the plasma membrane by molecular motors moving on their respective cytoskeletal tracks (i.e., microtubules and actin). Because the organization of these cytoskeletal structures differs substantially in T. gondii, the molecular motor dependence of DG trafficking is far from certain. By imaging the motions of green fluorescent protein–tagged DGs in intracellular parasites with high temporal and spatial resolution, we show through a combination of molecular genetics and chemical perturbations that directed DG transport is independent of microtubules and presumably their kinesin/dynein motors. However, directed DG transport is dependent on filamentous actin and a unique class 27 myosin, TgMyoF, which has structural similarity to myosin V, the prototypical cargo transporter. Actomyosin DG transport was unexpected, since filamentous parasite actin has yet to be visualized in vivo due in part to the prevailing model that parasite actin forms short, unstable filaments. Thus our data uncover new critical roles for these essential proteins in the lytic cycle of this devastating pathogen. PMID:27146112

  6. Dense granule trafficking in Toxoplasma gondii requires a unique class 27 myosin and actin filaments.

    PubMed

    Heaslip, Aoife T; Nelson, Shane R; Warshaw, David M

    2016-07-01

    The survival of Toxoplasma gondii within its host cell requires protein release from secretory vesicles, called dense granules, to maintain the parasite's intracellular replicative niche. Despite the importance of DGs, nothing is known about the mechanisms underlying their transport. In higher eukaryotes, secretory vesicles are transported to the plasma membrane by molecular motors moving on their respective cytoskeletal tracks (i.e., microtubules and actin). Because the organization of these cytoskeletal structures differs substantially in T. gondii, the molecular motor dependence of DG trafficking is far from certain. By imaging the motions of green fluorescent protein-tagged DGs in intracellular parasites with high temporal and spatial resolution, we show through a combination of molecular genetics and chemical perturbations that directed DG transport is independent of microtubules and presumably their kinesin/dynein motors. However, directed DG transport is dependent on filamentous actin and a unique class 27 myosin, TgMyoF, which has structural similarity to myosin V, the prototypical cargo transporter. Actomyosin DG transport was unexpected, since filamentous parasite actin has yet to be visualized in vivo due in part to the prevailing model that parasite actin forms short, unstable filaments. Thus our data uncover new critical roles for these essential proteins in the lytic cycle of this devastating pathogen. PMID:27146112

  7. Detection of internal molecular structural motions using anisotropic spectroscopy

    NASA Astrophysics Data System (ADS)

    Singh, Rohit; George, Deepu; Korter, Timothy; Markelz, Andrea

    2012-02-01

    The far infrared spectroscopy of molecular crystals reveals both intra and inter molecular vibrational modes [1,2]. With the significant increase in complexity of structures, one finds increasing overlap in the internal modes. As an overall strategy to measure the correlated structural motions in protein, we use anisotropic and birefringent behavior of molecular crystals to develop a new technique called MOSTS (Modulated Orientation Sensitive THz Spectroscopy). We achieve high sensitivity and mode separation by using single molecular crystal such as sucrose and rapid modulation of the relative alignment of the terahertz polarization and the crystal axes by rotating the sample. By locking into the signal at the rotation frequency we determine the polarization sensitive signal and map out the optically active vibrational resonances. To illustrate the technique we compare our measured spectra with the calculated and find a close agreement. [4pt] [1] D.G. Allis, J.A. Zeitler, P.F.Taday and T.M.Korter, Chem. Phys. Lett., 463, 84 (2008).[0pt] [2] P.U. Jepsen and J.C. Stewart, Chem. Phys. Lett., 442, 275 (2007).

  8. Molecular modeling of nucleic Acid structure: electrostatics and solvation.

    PubMed

    Bergonzo, Christina; Galindo-Murillo, Rodrigo; Cheatham, Thomas E

    2014-01-01

    This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit. PMID:25631536

  9. Modeling Vertical Plasma Flows in Solar Filament Barbs

    NASA Astrophysics Data System (ADS)

    Litvinenko, Y.

    2003-12-01

    Speeds of observed flows in quiescent solar filaments are typically much less than the local Alfvén speed. This is why the flows in filament barbs can be modeled by perturbing a local magnetostatic solution describing the balance between the Lorentz force, gravity, and gas pressure in a barb. Similarly, large-scale filament flows can be treated as adiabatically slow deformations of a force-free magnetic equilibrium that describes the global structure of a filament. This approach reconciles current theoretical models with the puzzling observational result that some of the flows appear to be neither aligned with the magnetic field nor controlled by gravity.

  10. Structure, subunit composition, and molecular weight of RD-114 RNA.

    PubMed Central

    Kung, H J; Bailey, J M; Davidson, N; Nicolson, M O; McAllister, R M

    1975-01-01

    The properties and subunit composition of the RNA extracted from RD-114 virions have been studied. The RNA extracted from the virion has a sedimentation coefficient of 52S in a nondenaturing aqueous electrolyte. The estimated molecular weight by sedimentation in nondenaturing and weakly denaturing media is in the range 5.7 X 10(6) to 7.0 X 10(6). By electron microscopy, under moderately denaturing conditions, the 52S molecule is seen to be an extended single strand with a contour length of about 4.0 mum corresponding to a molecular weight of 5.74 X 10(6). It contains two characteristic secondary structure features: (i) a central Y- or T-shaped structure (the rabbit ears) with a molecular weight of 0.3 X 10(6), (ii) two symmetreically disposed loops on each side of and at equal distance from the center. The 52S molecule consists of two half-size molecules, with molecular weight 2.8 X 10(6), joined together within the central rabbit ears feature. Melting of the rabbit ears with concomitant dissociation of the 52S molecule into subunits, has been caused by either one of two strongly denaturing treatments: incubation in a mixture of CH3HgOH and glyoxal at room temperature, or thermal dissociation in a urea-formamide solvent. When half-size molecules are quenched from denaturing temperatures, a new off-center secondary structure feature termed the branch-like structure is seen. The dissociation behavior of the 52S complex and the molecular weight of the subunits have been confirmed by gel electrophoresis studies. The loop structures melt at fairly low temperatures; the dissociation of the 52S molecule into its two subunits occurs at a higher temperature corresponding to a base composition of about 63% guanosine plus cytosine. Polyadenylic acid mapping by electron microscopy shows that the 52S molecule contains two polyadenylic acid segments, one at each end. It thus appears that 52S RD-114 RNA consists of two 2.8 X 10(6) dalton subunits, each with a characteristic

  11. SOLAR MAGNETIZED 'TORNADOES': RELATION TO FILAMENTS

    SciTech Connect

    Su Yang; Veronig, Astrid; Temmer, Manuela; Wang Tongjiang; Gan Weiqun

    2012-09-10

    Solar magnetized 'tornadoes', a phenomenon discovered in the solar atmosphere, appear as tornado-like structures in the corona but are rooted in the photosphere. Like other solar phenomena, solar tornadoes are a feature of magnetized plasma and therefore differ distinctly from terrestrial tornadoes. Here we report the first analysis of solar 'tornadoes' (two papers which focused on different aspects of solar tornadoes were published in the Astrophysical Journal Letters and Nature, respectively, during the revision of this Letter). A detailed case study of two events indicates that they are rotating vertical magnetic structures probably driven by underlying vortex flows in the photosphere. They usually exist as a group and are related to filaments/prominences, another important solar phenomenon whose formation and eruption are still mysteries. Solar tornadoes may play a distinct role in the supply of mass and twists to filaments. These findings could lead to a new explanation of filament formation and eruption.

  12. Solar Magnetized "Tornadoes:" Relation to Filaments

    NASA Astrophysics Data System (ADS)

    Su, Yang; Wang, Tongjiang; Veronig, Astrid; Temmer, Manuela; Gan, Weiqun

    2012-09-01

    Solar magnetized "tornadoes," a phenomenon discovered in the solar atmosphere, appear as tornado-like structures in the corona but are rooted in the photosphere. Like other solar phenomena, solar tornadoes are a feature of magnetized plasma and therefore differ distinctly from terrestrial tornadoes. Here we report the first analysis of solar "tornadoes" (two papers which focused on different aspects of solar tornadoes were published in the Astrophysical Journal Letters and Nature, respectively, during the revision of this Letter). A detailed case study of two events indicates that they are rotating vertical magnetic structures probably driven by underlying vortex flows in the photosphere. They usually exist as a group and are related to filaments/prominences, another important solar phenomenon whose formation and eruption are still mysteries. Solar tornadoes may play a distinct role in the supply of mass and twists to filaments. These findings could lead to a new explanation of filament formation and eruption.

  13. Effects of amine molecular structure on carbon nanotubes functionalization.

    PubMed

    Jimeno, A; Goyanes, S; Eceiza, A; Kortaberria, G; Mondragon, I; Corcuera, M A

    2009-10-01

    Three amines with different molecular structure, triethylenetetramine (TETA) and two polyetheramines (Jeffamine D-230 and Jeffamine T-403) were employed to functionalize multi-walled carbon nanotubes (MWCNT) previously oxidized by acid treatment. The functionalized MWCNT were characterized by Fourier transform infrared spectroscopy (FT-IR), Raman spectroscopy, UV-vis spectroscopy and the surface modification was investigated by field emission scanning electron microscopy (FE-SEM). Thermogravimetric analysis (TGA) was employed to quantify the amount of amine groups anchored to MWCNTs. The results have shown that the efficiency of amine functionalization is in the order TETA > D-230 > T-403, thus showing that amine chemical structure and molecular weight are important parameters on functionalization of carbon nanotubes. PMID:19908518

  14. Molecular modelling of miraculin: Structural analyses and functional hypotheses.

    PubMed

    Paladino, Antonella; Costantini, Susan; Colonna, Giovanni; Facchiano, Angelo M

    2008-02-29

    Miraculin is a plant protein that displays the peculiar property of modifying taste by swiching sour into a sweet taste. Its monomer is flavourless at all pH as well as at high concentration; the dimer form elicits its taste-modifying activity at acidic pH; a tetrameric form is also reported as active. Two histidine residues, located in exposed regions, are the main responsible of miraculin activity, as demonstrated by mutagenesis studies. Since structural data of miraculin are not available, we have predicted its three-dimensional structure and simulated both its dimer and tetramer forms by comparative modelling and molecular docking techniques. Finally, molecular dynamics simulations at different pH conditions have indicated that at acidic pH the dimer assumes a widely open conformation, in agreement with the hypotheses coming from other studies. PMID:18158914

  15. Interaction and merging of two sinistral filaments

    SciTech Connect

    Jiang, Yunchun; Yang, Jiayan; Liu, Yu; Li, Haidong; Wang, Haimin; Ji, Haisheng; Li, Jianping

    2014-09-20

    In this paper, we report the interaction and subsequent merging of two sinistral filaments (F1 and F2) occurring at the boundary of AR 9720 on 2001 December 6. The two filaments were close and nearly perpendicular to each other. The interaction occurred after F1 was erupted and the eruption was impeded by a more extended filament channel (FC) standing in the way, in which F2 was embedded. The erupted material ran into FC along its axis, causing F1 and F2 to merge into a single structure that subsequently underwent a large-amplitude to-and-fro motion. A significant plasma heating process was observed in the merging process, making the mixed material largely disappear from the Hα passband, but appear in Extreme Ultraviolet Telescope 195 Å images for a while. These observations can serve as strong evidence of merging reconnection between the two colliding magnetic structures. A new sinistral filament was formed along FC after the cooling of the merged and heated material. No coronal mass ejection was observed to be associated with the event; though, the eruption was accompanied by a two-ribbon flare with a separation motion, indicating that the eruption had failed. This event shows that, in addition to overlying magnetic fields, such an interaction is an effective restraint to make a filament eruption fail in this way.

  16. Interaction and Merging of two Sinistral Filaments

    NASA Astrophysics Data System (ADS)

    Jiang, Yunchun; Yang, Jiayan; Wang, Haimin; Ji, Haisheng; Liu, Yu; Li, Haidong; Li, Jianping

    2014-09-01

    In this paper, we report the interaction and subsequent merging of two sinistral filaments (F1 and F2) occurring at the boundary of AR 9720 on 2001 December 6. The two filaments were close and nearly perpendicular to each other. The interaction occurred after F1 was erupted and the eruption was impeded by a more extended filament channel (FC) standing in the way, in which F2 was embedded. The erupted material ran into FC along its axis, causing F1 and F2 to merge into a single structure that subsequently underwent a large-amplitude to-and-fro motion. A significant plasma heating process was observed in the merging process, making the mixed material largely disappear from the Hα passband, but appear in Extreme Ultraviolet Telescope 195 Å images for a while. These observations can serve as strong evidence of merging reconnection between the two colliding magnetic structures. A new sinistral filament was formed along FC after the cooling of the merged and heated material. No coronal mass ejection was observed to be associated with the event; though, the eruption was accompanied by a two-ribbon flare with a separation motion, indicating that the eruption had failed. This event shows that, in addition to overlying magnetic fields, such an interaction is an effective restraint to make a filament eruption fail in this way.

  17. Polarized radio filaments outside the Galactic plane

    NASA Astrophysics Data System (ADS)

    Vidal, Matias; Dickinson, C.; Davies, R. D.; Leahy, J. P.

    2015-09-01

    We used data from the WMAP satellite at 23, 33 and 41 GHz to study the diffuse polarized emission over the entire sky. The emission originates mostly from filamentary structures with well-ordered magnetic fields. Some of these structures have been known for decades in radio continuum maps. Their origin is not clear and there are many filaments that are visible for the first time. We have identified and studied 11 filaments. The polarization fraction of some of them can be as high as 40 per cent, which is a signature of a well-ordered magnetic field. The polarization spectral indices, averaged over 18 regions in the sky is β = -3.06 ± 0.02, consistent with synchrotron radiation. There are significant variations in β over the sky (Δβ ≈ 0.2). We explore the link between the large-scale filaments and the local interstellar medium, using the model of an expanding shell in the solar vicinity. We compared observed polarization angles with the predictions from the model and found good agreement. This strongly suggests that many large-scale filaments and loops are nearby structures. This is important in the context of the Galactic magnetic field as these structures are normally included in global models, neglecting the fact that they might be local. We also studied the level of contamination added by the diffuse filaments to the CMB (cosmic microwave background) polarization power spectra. We conclude that, even though these filaments present low radio brightness, a careful removal will be necessary for future all-sky CMB polarization analysis.

  18. Optimization techniques in molecular structure and function elucidation.

    PubMed

    Sahinidis, Nikolaos V

    2009-12-01

    This paper discusses recent optimization approaches to the protein side-chain prediction problem, protein structural alignment, and molecular structure determination from X-ray diffraction measurements. The machinery employed to solve these problems has included algorithms from linear programming, dynamic programming, combinatorial optimization, and mixed-integer nonlinear programming. Many of these problems are purely continuous in nature. Yet, to this date, they have been approached mostly via combinatorial optimization algorithms that are applied to discrete approximations. The main purpose of the paper is to offer an introduction and motivate further systems approaches to these problems. PMID:20160866

  19. Nanoparticle Probes for Structural and Functional Photoacoustic Molecular Tomography

    PubMed Central

    Chen, Haobin; Yuan, Zhen; Wu, Changfeng

    2015-01-01

    Nowadays, nanoparticle probes have received extensive attention largely due to its potential biomedical applications in structural, functional, and molecular imaging. In addition, photoacoustic tomography (PAT), a method based on the photoacoustic effect, is widely recognized as a robust modality to evaluate the structure and function of biological tissues with high optical contrast and high acoustic resolution. The combination of PAT with nanoparticle probes holds promises for detecting and imaging diseased tissues or monitoring their treatments with high sensitivity. This review will introduce the recent advances in the emerging field of nanoparticle probes and their preclinical applications in PAT, as well as relevant perspectives on future development. PMID:26609534

  20. THE FORMATION OF FILAMENTARY BUNDLES IN TURBULENT MOLECULAR CLOUDS

    SciTech Connect

    Moeckel, Nickolas; Burkert, Andreas E-mail: burkert@usm.uni-muenchen.de

    2015-07-01

    The classical picture of a star-forming filament is a near-equilibrium structure with its collapse dependent on its gravitational criticality. Recent observations have complicated this picture, revealing filaments to be a mess of apparently interacting subfilaments with transsonic internal velocity dispersions and mildly supersonic intra-subfilament dispersions. How structures like this form is unresolved. Here, we study the velocity structure of filamentary regions in a simulation of a turbulent molecular cloud. We present two main findings. First, the observed complex velocity features in filaments arise naturally in self-gravitating hydrodynamic simulations of turbulent clouds without the need for magnetic or other effects. Second, a region that is filamentary only in projection and is in fact made of spatially distinct features can display these same velocity characteristics. The fact that these disjoint structures can masquerade as coherent filaments in both projection and velocity diagnostics highlights the need to continue developing sophisticated filamentary analysis techniques for star formation observations.

  1. Hybrid Molecular Structure of the Giant Protease Tripeptidyl Peptidase II

    PubMed Central

    Chuang, Crystal K.; Rockel, Beate; Seyit, Gönül; Walian, Peter J.; Schönegge, Anne–Marie; Peters, Jürgen; Zwart, Petrus H.; Baumeister, Wolfgang; Jap, Bing K.

    2010-01-01

    Tripeptidyl peptidase II (TPP II) is the largest known eukaryotic protease (6MDa). It is believed to act downstream of the 26S proteasome cleaving tripeptides from the N– termini of longer peptides and it is implicated in numerous cellular processes. Here we report the structure of Drosophila TPP II determined by a hybrid approach: The structure of the dimer was solved by x–ray crystallography and docked into the three– dimensional map of the holocomplex obtained by single-particle cryo-electron microscopy. The resulting structure reveals the compartmentalization of the active sites inside a system of chambers and suggests the existence of a molecular ruler determining the size of the cleavage products. Furthermore, the structure suggests a model for activation of TPP II involving the relocation of a flexible loop and a repositioning of the active–site serine, coupling it to holocomplex assembly and active site sequestration. PMID:20676100

  2. Structure and dynamics of complex liquid water: Molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    S, Indrajith V.; Natesan, Baskaran

    2015-06-01

    We have carried out detailed structure and dynamical studies of complex liquid water using molecular dynamics simulations. Three different model potentials, namely, TIP3P, TIP4P and SPC-E have been used in the simulations, in order to arrive at the best possible potential function that could reproduce the structure of experimental bulk water. All the simulations were performed in the NVE micro canonical ensemble using LAMMPS. The radial distribution functions, gOO, gOH and gHH and the self diffusion coefficient, Ds, were calculated for all three models. We conclude from our results that the structure and dynamical parameters obtained for SPC-E model matched well with the experimental values, suggesting that among the models studied here, the SPC-E model gives the best structure and dynamics of bulk water.

  3. Bending Flexibility of Actin Filaments during Motor-Induced Sliding

    PubMed Central

    Vikhorev, Petr G.; Vikhoreva, Natalia N.; Månsson, Alf

    2008-01-01

    Muscle contraction and other forms of cell motility occur as a result of cyclic interactions between myosin molecules and actin filaments. Force generation is generally attributed to ATP-driven structural changes in myosin, whereas a passive role is ascribed to actin. However, some results challenge this view, predicting structural changes in actin during motor activity, e.g., when the actin filaments slide on a myosin-coated surface in vitro. Here, we analyzed statistical properties of the sliding filament paths, allowing us to detect changes of this type. It is interesting to note that evidence for substantial structural changes that led to increased bending flexibility of the filaments was found in phalloidin-stabilized, but not in phalloidin-free, actin filaments. The results are in accordance with the idea that a high-flexibility structural state of actin is a prerequisite for force production, but not the idea that a low-to-high flexibility transition of the actin filament should be an important component of the force-generating step per se. Finally, our data challenge the general view that phalloidin-stabilized filaments behave as native actin filaments in their interaction with myosin. This has important implications, since phalloidin stabilization is a routine procedure in most studies of actomyosin function. PMID:18835897

  4. Molecular structures of amyloid and prion fibrils: consensus versus controversy.

    PubMed

    Tycko, Robert; Wickner, Reed B

    2013-07-16

    Many peptides and proteins self-assemble into amyloid fibrils. Examples include mammalian and fungal prion proteins, polypeptides associated with human amyloid diseases, and proteins that may have biologically functional amyloid states. To understand the propensity for polypeptides to form amyloid fibrils and to facilitate rational design of amyloid inhibitors and imaging agents, it is necessary to elucidate the molecular structures of these fibrils. Although fibril structures were largely mysterious 15 years ago, a considerable body of reliable structural information about amyloid fibril structures now exists, with essential contributions from solid state nuclear magnetic resonance (NMR) measurements. This Account reviews results from our laboratories and discusses several structural issues that have been controversial. In many cases, the amino acid sequences of amyloid fibrils do not uniquely determine their molecular structures. Self-propagating, molecular-level polymorphism complicates the structure determination problem and can lead to apparent disagreements between results from different laboratories, particularly when different laboratories study different polymorphs. For 40-residue β-amyloid (Aβ₁₋₄₀) fibrils associated with Alzheimer's disease, we have developed detailed structural models from solid state NMR and electron microscopy data for two polymorphs. These polymorphs have similar peptide conformations, identical in-register parallel β-sheet organizations, but different overall symmetry. Other polymorphs have also been partially characterized by solid state NMR and appear to have similar structures. In contrast, cryo-electron microscopy studies that use significantly different fibril growth conditions have identified structures that appear (at low resolution) to be different from those examined by solid state NMR. Based on solid state NMR and electron paramagnetic resonance (EPR) measurements, the in-register parallel β-sheet organization

  5. FtsZ Cytoskeletal Filaments as a Template for Metallic Nanowire Fabrication.

    PubMed

    Ostrov, Nili; Fichman, Galit; Adler-Abramovich, Lihi; Gazit, Ehud

    2015-01-01

    Supramolecular protein assemblies can serve as templates for the fabrication of inorganic nanowires due to their morphological reproducibility and innate proclivity to form well-ordered structures. Amongst the variety of naturally occurring nano-scale assemblies, cytoskeletal fibers from diverse biological sources represent a unique family of scaffolds for biomimetics as they efficiently self-assemble in vitro in a controllable manner to form stable filaments. Here, we harness the bacterial FtsZ filament system as a scaffold for protein-based metal nanowires, and further demonstrate the control of wire alignment with the use of an external magnetic field. Due to the ease at which the bacterial FtsZ is overexpressed and purified, as well as the extensive studies of its ultrastructural properties and physiological significance, FtsZ filaments are an ideal substrate for large-scale production and chemical manipulation. Using a biologically compatible electroless metal deposition technique initiated by adsorption of platinum as a surface catalyst, we demonstrate the coating of assembled FtsZ filaments with iron, nickel, gold, and copper to fabricate continuous nanowires with diameters ranging from 10-50 nm. Organic-inorganic hybrid wires were analyzed using high-resolution field-emission-gun transmission and scanning electron microscopy, and confirmed by energy-dispersive elemental analysis. We also achieved alignment of ferrofluid-coated FtsZ filaments using an external magnetic field. Overall, we provide evidence for the robustness of the FtsZ filament system as a molecular scaffold, and offer an efficient, biocompatible procedure for facile bottom-up assembly of metallic wires on biological templates. We believe that bottom-up fabrication methods as reported herein significantly contribute to the expanding toolkit available for the incorporation of biological materials in nano-scale devices for electronic and electromechanical applications.

  6. FtsZ Cytoskeletal Filaments as a Template for Metallic Nanowire Fabrication.

    PubMed

    Ostrov, Nili; Fichman, Galit; Adler-Abramovich, Lihi; Gazit, Ehud

    2015-01-01

    Supramolecular protein assemblies can serve as templates for the fabrication of inorganic nanowires due to their morphological reproducibility and innate proclivity to form well-ordered structures. Amongst the variety of naturally occurring nano-scale assemblies, cytoskeletal fibers from diverse biological sources represent a unique family of scaffolds for biomimetics as they efficiently self-assemble in vitro in a controllable manner to form stable filaments. Here, we harness the bacterial FtsZ filament system as a scaffold for protein-based metal nanowires, and further demonstrate the control of wire alignment with the use of an external magnetic field. Due to the ease at which the bacterial FtsZ is overexpressed and purified, as well as the extensive studies of its ultrastructural properties and physiological significance, FtsZ filaments are an ideal substrate for large-scale production and chemical manipulation. Using a biologically compatible electroless metal deposition technique initiated by adsorption of platinum as a surface catalyst, we demonstrate the coating of assembled FtsZ filaments with iron, nickel, gold, and copper to fabricate continuous nanowires with diameters ranging from 10-50 nm. Organic-inorganic hybrid wires were analyzed using high-resolution field-emission-gun transmission and scanning electron microscopy, and confirmed by energy-dispersive elemental analysis. We also achieved alignment of ferrofluid-coated FtsZ filaments using an external magnetic field. Overall, we provide evidence for the robustness of the FtsZ filament system as a molecular scaffold, and offer an efficient, biocompatible procedure for facile bottom-up assembly of metallic wires on biological templates. We believe that bottom-up fabrication methods as reported herein significantly contribute to the expanding toolkit available for the incorporation of biological materials in nano-scale devices for electronic and electromechanical applications. PMID:26328401

  7. Structure of kinetochore fibres in crane-fly spermatocytes after irradiation with an ultraviolet microbeam: neither microtubules nor actin filaments remain in the irradiated region.

    PubMed

    Forer, Arthur; Spurck, Tim; Pickett-Heaps, Jeremy D; Wilson, Paula J

    2003-11-01

    We studied chromosome movement after kinetochore microtubules were severed. Severing a kinetochore fibre in living crane-fly spermatocytes with an ultraviolet microbeam creates a kinetochore stub, a birefringent remnant of the spindle fibre connected to the kinetochore and extending only to the edge of the irradiated region. After the irradiation, anaphase chromosomes either move poleward led by their stubs or temporarily stop moving. We examined actin and/or microtubules in irradiated cells by means of confocal fluorescence microscopy or serial-section reconstructions from electron microscopy. For each cell thus examined, chromosome movement had been recorded continuously until the moment of fixation. Kinetochore microtubules were completely severed by the ultraviolet microbeam in cells in which chromosomes continued to move poleward after the irradiation: none were seen in the irradiated regions. Similarly, actin filaments normally present in kinetochore fibres were severed by the ultraviolet microbeam irradiations: the irradiated regions contained no actin filaments and only local spots of non-filamentous actin. There was no difference in irradiated regions when the associated chromosomes continued to move versus when they stopped moving. Thus, one cannot explain motion with severed kinetochore microtubules in terms of either microtubules or actin-filaments bridging the irradiated region. The data seem to negate current models for anaphase chromosome movement and support a model in which poleward chromosome movement results from forces generated within the spindle matrix that propel kinetochore fibres or kinetochore stubs poleward. PMID:14569597

  8. Nonequilibrium structure and dynamics in a microscopic model of thin-film active gels

    NASA Astrophysics Data System (ADS)

    Head, D. A.; Briels, W. J.; Gompper, Gerhard

    2014-03-01

    In the presence of adenosine triphosphate, molecular motors generate active force dipoles that drive suspensions of protein filaments far from thermodynamic equilibrium, leading to exotic dynamics and pattern formation. Microscopic modeling can help to quantify the relationship between individual motors plus filaments to organization and dynamics on molecular and supramolecular length scales. Here, we present results of extensive numerical simulations of active gels where the motors and filaments are confined between two infinite parallel plates. Thermal fluctuations and excluded-volume interactions between filaments are included. A systematic variation of rates for motor motion, attachment, and detachment, including a differential detachment rate from filament ends, reveals a range of nonequilibrium behavior. Strong motor binding produces structured filament aggregates that we refer to as asters, bundles, or layers, whose stability depends on motor speed and differential end detachment. The gross features of the dependence of the observed structures on the motor rate and the filament concentration can be captured by a simple one-filament model. Loosely bound aggregates exhibit superdiffusive mass transport, where filament translocation scales with lag time with nonunique exponents that depend on motor kinetics. An empirical data collapse of filament speed as a function of motor speed and end detachment is found, suggesting a dimensional reduction of the relevant parameter space. We conclude by discussing the perspectives of microscopic modeling in the field of active gels.

  9. A 3D visualization system for molecular structures

    NASA Technical Reports Server (NTRS)

    Green, Terry J.

    1989-01-01

    The properties of molecules derive in part from their structures. Because of the importance of understanding molecular structures various methodologies, ranging from first principles to empirical technique, were developed for computing the structure of molecules. For large molecules such as polymer model compounds, the structural information is difficult to comprehend by examining tabulated data. Therefore, a molecular graphics display system, called MOLDS, was developed to help interpret the data. MOLDS is a menu-driven program developed to run on the LADC SNS computer systems. This program can read a data file generated by the modeling programs or data can be entered using the keyboard. MOLDS has the following capabilities: draws the 3-D representation of a molecule using stick, ball and ball, or space filled model from Cartesian coordinates, draws different perspective views of the molecule; rotates the molecule on the X, Y, Z axis or about some arbitrary line in space, zooms in on a small area of the molecule in order to obtain a better view of a specific region; and makes hard copy representation of molecules on a graphic printer. In addition, MOLDS can be easily updated and readily adapted to run on most computer systems.

  10. Large Molecule Structures by Broadband Fourier Transform Molecular Rotational Spectroscopy

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Seifert, Nathan A.; Spada, Lorenzo; Pate, Brooks

    2016-06-01

    Fourier transform molecular rotational resonance spectroscopy (FT-MRR) using pulsed jet molecular beam sources is a high-resolution spectroscopy technique that can be used for chiral analysis of molecules with multiple chiral centers. The sensitivity of the molecular rotational spectrum pattern to small changes in the three dimensional structure makes it possible to identify diastereomers without prior chemical separation. For larger molecules, there is the additional challenge that different conformations of each diastereomer may be present and these need to be differentiated from the diastereomers in the spectral analysis. Broadband rotational spectra of several larger molecules have been measured using a chirped-pulse FT-MRR spectrometer. Measurements of nootkatone (C15H22O), cedrol (C15H26O), ambroxide (C16H28O) and sclareolide (C16H26O2) are presented. These spectra are measured with high sensitivity (signal-to-noise ratio near 1,000:1) and permit structure determination of the most populated isomers using isotopic analysis of the 13C and 18O isotopologues in natural abundance. The accuracy of quantum chemistry calculations to identify diastereomers and conformers and to predict the dipole moment properties needed for three wave mixing measurements is examined.

  11. A catalytic oligomeric motor that walks along a filament track

    NASA Astrophysics Data System (ADS)

    Huang, Mu-Jie; Kapral, Raymond

    2015-06-01

    Most biological motors in the cell execute chemically powered conformational changes as they walk on biopolymer filaments in order to carry out directed transport functions. Synthetic motors that operate in a similar manner are being studied since they have the potential to perform similar tasks in a variety of applications. In this paper, a synthetic nanomotor that moves along a filament track, without invoking motor conformational changes, is constructed and its properties are studied in detail. The motor is an oligomer comprising three linked beads with specific binding properties. The filament track is a stiff polymer chain, also described by a linear chain of linked coarse-grained molecular groups modeled as beads. Reactions on the filament that are catalyzed by a motor bead and use fuel in the environment, in conjunction within the binding affinities of the motor beads to the filament beads, lead to directed motion. The system operates out of equilibrium due to the state of the filament and supply of fuel. The motor, filament, and surrounding medium are all described at microscopic level that permits a full analysis of the motor motion. A stochastic model that captures the main trends seen in the simulations is also presented. The results of this study point to some of the key features that could be used to construct nanomotors that undergo biased walks powered by chemical reactions on filaments.

  12. A catalytic oligomeric motor that walks along a filament track.

    PubMed

    Huang, Mu-Jie; Kapral, Raymond

    2015-06-28

    Most biological motors in the cell execute chemically powered conformational changes as they walk on biopolymer filaments in order to carry out directed transport functions. Synthetic motors that operate in a similar manner are being studied since they have the potential to perform similar tasks in a variety of applications. In this paper, a synthetic nanomotor that moves along a filament track, without invoking motor conformational changes, is constructed and its properties are studied in detail. The motor is an oligomer comprising three linked beads with specific binding properties. The filament track is a stiff polymer chain, also described by a linear chain of linked coarse-grained molecular groups modeled as beads. Reactions on the filament that are catalyzed by a motor bead and use fuel in the environment, in conjunction within the binding affinities of the motor beads to the filament beads, lead to directed motion. The system operates out of equilibrium due to the state of the filament and supply of fuel. The motor, filament, and surrounding medium are all described at microscopic level that permits a full analysis of the motor motion. A stochastic model that captures the main trends seen in the simulations is also presented. The results of this study point to some of the key features that could be used to construct nanomotors that undergo biased walks powered by chemical reactions on filaments. PMID:26133457

  13. A catalytic oligomeric motor that walks along a filament track

    SciTech Connect

    Huang, Mu-Jie Kapral, Raymond

    2015-06-28

    Most biological motors in the cell execute chemically powered conformational changes as they walk on biopolymer filaments in order to carry out directed transport functions. Synthetic motors that operate in a similar manner are being studied since they have the potential to perform similar tasks in a variety of applications. In this paper, a synthetic nanomotor that moves along a filament track, without invoking motor conformational changes, is constructed and its properties are studied in detail. The motor is an oligomer comprising three linked beads with specific binding properties. The filament track is a stiff polymer chain, also described by a linear chain of linked coarse-grained molecular groups modeled as beads. Reactions on the filament that are catalyzed by a motor bead and use fuel in the environment, in conjunction within the binding affinities of the motor beads to the filament beads, lead to directed motion. The system operates out of equilibrium due to the state of the filament and supply of fuel. The motor, filament, and surrounding medium are all described at microscopic level that permits a full analysis of the motor motion. A stochastic model that captures the main trends seen in the simulations is also presented. The results of this study point to some of the key features that could be used to construct nanomotors that undergo biased walks powered by chemical reactions on filaments.

  14. Hollow cylindrical plasma filament waveguide with discontinuous finite thickness cladding

    SciTech Connect

    Alshershby, Mostafa; Hao Zuoqiang; Lin Jingquan

    2013-01-15

    We have explored here a hollow cylindrical laser plasma multifilament waveguide with discontinuous finite thickness cladding, in which the separation between individual filaments is in the range of several millimeters and the waveguide cladding thickness is in the order of the microwave penetration depth. Such parameters give a closer representation of a realistic laser filament waveguide sustained by a long stable propagation of femtosecond (fs) laser pulses. We report how the waveguide losses depend on structural parameters like normalized plasma filament spacing, filament to filament distance or pitch, normal spatial frequency, and radius of the plasma filament. We found that for typical plasma parameters, the proposed waveguide can support guided modes of microwaves in extremely high frequency even with a cladding consisting of only one ring of plasma filaments. The loss of the microwave radiation is mainly caused by tunneling through the discontinuous finite cladding, i.e., confinement loss, and is weakly dependent on the plasma absorption. In addition, the analysis indicates that the propagation loss is fairly large compared with the loss of a plasma waveguide with a continuous infinite thickness cladding, while they are comparable when using a cladding contains more than one ring. Compared to free space propagation, this waveguide still presents a superior microwave transmission to some distance in the order of the filamentation length; thus, the laser plasma filaments waveguide may be a potential channel for transporting pulsed-modulated microwaves if ensuring a long and stable propagation of fs laser pulses.

  15. SYMPATHETIC FILAMENT ERUPTIONS CONNECTED BY CORONAL DIMMINGS

    SciTech Connect

    Jiang Yunchun; Yang Jiayan; Hong Junchao; Bi Yi; Zheng Ruisheng

    2011-09-10

    We present for the first time detailed observations of three successive, interdependent filament eruptions that occurred one by one within 5 hr from different locations beyond the range of a single active region. The first eruption was observed from an active region and was associated with a coronal mass ejection (CME), during which diffuse and complex coronal dimmings formed, largely extending to the two other filaments located in quiet-Sun regions. Then, both quiescent filaments consecutively underwent the second and third eruptions, while the nearby dimmings were persistent. Comparing the result of a derived coronal magnetic configuration, the magnetic connectivity between the dimmings suggested that they were caused by the joint effect of simple expansion of overlying loop systems forced by the first eruption, as well as by its erupting field interacting or reconnecting with the surrounding magnetic structures. Note that the dimming process in the first eruption indicated a weakening and partial removal of an overlying magnetic field constraint on the two other filaments, and thus one can physically connect these eruptions as sympathetic. It appears that the peculiar magnetic field configuration in our event was largely favorable to the occurrence of sympathetic filament eruptions. Because coronal dimmings are frequent and common phenomena in solar eruptions, especially in CME events, it is very likely that they represent a universal agent that can link consecutive eruptions nearby with sympathetic eruptions.

  16. Heat-induced changes to lipid molecular structure in Vimy flaxseed: Spectral intensity and molecular clustering

    NASA Astrophysics Data System (ADS)

    Yu, Peiqiang; Damiran, Daalkhaijav

    2011-06-01

    Autoclaving was used to manipulate nutrient utilization and availability. The objectives of this study were to characterize any changes of the functional groups mainly associated with lipid structure in flaxseed ( Linum usitatissimum, cv. Vimy), that occurred on a molecular level during the treatment process using infrared Fourier transform molecular spectroscopy. The parameters included lipid CH 3 asymmetric (ca. 2959 cm -1), CH 2 asymmetric (ca. 2928 cm -1), CH 3 symmetric (ca. 2871 cm -1) and CH 2 symmetric (ca. 2954 cm -1) functional groups, lipid carbonyl C dbnd O ester group (ca. 1745 cm -1), lipid unsaturation group (CH attached to C dbnd C) (ca. 3010 cm -1) as well as their ratios. Hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify molecular spectral differences. Flaxseed samples were kept raw for the control or autoclaved in batches at 120 °C for 20, 40 or 60 min for treatments 1, 2 and 3, respectively. Molecular spectral analysis of lipid functional group ratios showed a significant decrease ( P < 0.05) in the CH 2 asymmetric to CH 3 asymmetric stretching band peak intensity ratios for the flaxseed. There were linear and quadratic effects ( P < 0.05) of the treatment time from 0, 20, 40 and 60 min on the ratios of the CH 2 asymmetric to CH 3 asymmetric stretching vibration intensity. Autoclaving had no significant effect ( P > 0.05) on lipid carbonyl C dbnd O ester group and lipid unsaturation group (CH attached to C dbnd C) (with average spectral peak area intensities of 138.3 and 68.8 IR intensity units, respectively). Multivariate molecular spectral analyses, CLA and PCA, were unable to make distinctions between the different treatment original spectra at the CH 3 and CH 2 asymmetric and symmetric region (ca. 2988-2790 cm -1). The results indicated that autoclaving had an impact to the mid-infrared molecular spectrum of flaxseed to identify heat-induced changes in lipid conformation. A future study

  17. Local stability of a gravitating filament: a dispersion relation

    NASA Astrophysics Data System (ADS)

    Freundlich, J.; Jog, C. J.; Combes, F.

    2014-04-01

    Filamentary structures are ubiquitous in astrophysics and are observed at various scales. On a cosmological scale, matter is usually distributed along filaments, and filaments are also typical features of the interstellar medium. Within a cosmic filament, matter can contract and form galaxies, whereas an interstellar gas filament can clump into a series of bead-like structures that can then turn into stars. To investigate the growth of such instabilities, we derive a local dispersion relation for an idealized self-gravitating filament and study some of its properties. Our idealized picture consists of an infinite self-gravitating and rotating cylinder with pressure and density related by a polytropic equation of state. We assume no specific density distribution, treat matter as a fluid, and use hydrodynamics to derive the linearized equations that govern the local perturbations. We obtain a dispersion relation for axisymmetric perturbations and study its properties in the (kR, kz) phase space, where kR and kz are the radial and longitudinal wavenumbers, respectively. While the boundary between the stable and unstable regimes is symmetrical in kR and kz and analogous to the Jeans criterion, the most unstable mode displays an asymmetry that could constrain the shape of the structures that form within the filament. Here the results are applied to a fiducial interstellar filament, but could be extended for other astrophysical systems, such as cosmological filaments and tidal tails. Appendices are available in electronic form at http://www.aanda.org

  18. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  19. Theoretical investigation of the molecular structure of the isoquercitrin molecule

    NASA Astrophysics Data System (ADS)

    Cornard, J. P.; Boudet, A. C.; Merlin, J. C.

    1999-09-01

    Isoquercitrin is a glycosilated flavonoid that has received a great deal of attention because of its numerous biological effects. We present a theoretical study on isoquercitrin using both empirical (Molecular Mechanics (MM), with MMX force field) and quantum chemical (AM1 semiempirical method) techniques. The most stable structures of the molecule obtained by MM calculations have been used as input data for the semiempirical treatment. The position and orientation of the glucose moiety with regard to the remainder of the molecule have been investigated. The flexibility of isoquercitrin principally lies in rotations around the inter-ring bond and the sugar link. In order to know the structural modifications generated by the substitution by a sugar, geometrical parameters of quercetin (aglycon) and isoquercitrin have been compared. The good accordance between theoretical and experimental electronic spectra permits to confirm the reliability of the structural model.

  20. Flexible magnetic filaments as micromechanical sensors.

    PubMed

    Goubault, C; Jop, P; Fermigier, M; Baudry, J; Bertrand, E; Bibette, J

    2003-12-31

    We propose a new micromechanical approach to probe bending rigidity at molecular scale. Long flexible filaments made of magnetic colloids and linkers are shown to adopt under magnetic field a hairpin configuration. Measuring the hairpin curvature as a function of the field intensity and the linker length from diffracted light allows us to deduce the linker bending rigidity kappa. The technique is presented for two types of linkers: a spontaneously adsorbing polymer and a grafted biomolecular.

  1. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes

    NASA Astrophysics Data System (ADS)

    Myasnikov, Alexander G.; Afonina, Zhanna A.; Ménétret, Jean-François; Shirokov, Vladimir A.; Spirin, Alexander S.; Klaholz, Bruno P.

    2014-11-01

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  2. The molecular structure of the left-handed supra-molecular helix of eukaryotic polyribosomes.

    PubMed

    Myasnikov, Alexander G; Afonina, Zhanna A; Ménétret, Jean-François; Shirokov, Vladimir A; Spirin, Alexander S; Klaholz, Bruno P

    2014-11-07

    During protein synthesis, several ribosomes bind to a single messenger RNA (mRNA) forming large macromolecular assemblies called polyribosomes. Here we report the detailed molecular structure of a 100 MDa eukaryotic poly-ribosome complex derived from cryo electron tomography, sub-tomogram averaging and pseudo-atomic modelling by crystal structure fitting. The structure allowed the visualization of the three functional parts of the polysome assembly, the central core region that forms a rather compact left-handed supra-molecular helix, and the more open regions that harbour the initiation and termination sites at either ends. The helical region forms a continuous mRNA channel where the mRNA strand bridges neighbouring exit and entry sites of the ribosomes and prevents mRNA looping between ribosomes. This structure provides unprecedented insights into protein- and RNA-mediated inter-ribosome contacts that involve conserved sites through 40S subunits and long protruding RNA expansion segments, suggesting a role in stabilizing the overall polyribosomal assembly.

  3. Isolation and partial characterization of a cage of filaments that surrounds the mammalian mitotic spindle

    PubMed Central

    1980-01-01

    Mitotic cells have been detergent extracted under conditions that support microtubule assembly. When HeLa cells are lysed in the presence of brain tubulin, mitotic-arrested cells nucleate large asters and true metaphase cells yield spindles that remain enclosed within a roughly spherical cage of filamentous material. Detergent-extracted mitotic Chinese hamster ovary (CHO) cells show a similar, insoluble cage but the mitotic apparatus is only occasionally stabilized. In later stages of mitosis, HeLa cages are observed in elongated and furrowed configurations. In the terminal stages of cell division, two daughter filamentous networks are connected by the intercellular bridge. When observed in the electron microscope the cages include fibers 7-11 nm in diameter. The polypeptide composition of cages isolated from mitotic HeLa cells is complex, but the major polypeptides are a group with mol wt ranging from 43,000-60,000 daltons and a high molecular weight polypeptide. CHO cells contain a subset of these proteins which includes a major 58,000-dalton and a high molecular weight polypeptide. Two different antisera directed against the vimentin-containing intermediate filaments bind to polypeptides in the electrophoretic profiles of isolated HeLa and CHO cages and stain the cages, as visualized by indirect immunofluorescence. These results suggest that the HeLa and CHO cages include intermediate filaments of the vimentin type. The polypeptide composition of HeLa cages suggests that they also contain tonofilaments. The cages apparently form as the cells enter mitosis. We propose that these filamentous cages maintain the structural continuity of the cytoplasm while the cell is in mitosis. PMID:7191425

  4. LINE PROFILES OF CORES WITHIN CLUSTERS. I. THE ANATOMY OF A FILAMENT

    SciTech Connect

    Smith, Rowan J.; Shetty, Rahul; Klessen, Ralf S.; Stutz, Amelia M.

    2012-05-01

    Observations are revealing the ubiquity of filamentary structures in molecular clouds. As cores are often embedded in filaments, it is important to understand how line profiles from such systems differ from those of isolated cores. We perform radiative transfer calculations on a hydrodynamic simulation of a molecular cloud in order to model line emission from collapsing cores embedded in filaments. We model two optically thick lines, CS(2-1) and HCN(1-0), and one optically thin line, N{sub 2}H{sup +}(1-0), from three embedded cores. In the hydrodynamic simulation, gas self-gravity, turbulence, and bulk flows create filamentary regions within which cores form. Though the filaments have large dispersions, the N{sub 2}H{sup +}(1-0) lines indicate subsonic velocities within the cores. We find that the observed optically thick line profiles of CS(2-1) and HCN(1-0) vary drastically with viewing angle. In over 50% of viewing angles, there is no sign of a blue asymmetry, an idealized signature of infall motions in an isolated spherical collapsing core. Profiles that primarily trace the cores, with little contribution from the surrounding filament, are characterized by a systematically higher HCN(1-0) peak intensity. The N{sub 2}H{sup +}(1-0) lines do not follow this trend. We demonstrate that red asymmetric profiles are also feasible in the optically thick lines, due to emission from the filament or one-sided accretion flows onto the core. We conclude that embedded cores may frequently undergo collapse without showing a blue asymmetric profile, and that observational surveys including filamentary regions may underestimate the number of collapsing cores if based solely on profile shapes of optically thick lines.

  5. Line Profiles of Cores within Clusters. I. The Anatomy of a Filament

    NASA Astrophysics Data System (ADS)

    Smith, Rowan J.; Shetty, Rahul; Stutz, Amelia M.; Klessen, Ralf S.

    2012-05-01

    Observations are revealing the ubiquity of filamentary structures in molecular clouds. As cores are often embedded in filaments, it is important to understand how line profiles from such systems differ from those of isolated cores. We perform radiative transfer calculations on a hydrodynamic simulation of a molecular cloud in order to model line emission from collapsing cores embedded in filaments. We model two optically thick lines, CS(2-1) and HCN(1-0), and one optically thin line, N2H+(1-0), from three embedded cores. In the hydrodynamic simulation, gas self-gravity, turbulence, and bulk flows create filamentary regions within which cores form. Though the filaments have large dispersions, the N2H+(1-0) lines indicate subsonic velocities within the cores. We find that the observed optically thick line profiles of CS(2-1) and HCN(1-0) vary drastically with viewing angle. In over 50% of viewing angles, there is no sign of a blue asymmetry, an idealized signature of infall motions in an isolated spherical collapsing core. Profiles that primarily trace the cores, with little contribution from the surrounding filament, are characterized by a systematically higher HCN(1-0) peak intensity. The N2H+(1-0) lines do not follow this trend. We demonstrate that red asymmetric profiles are also feasible in the optically thick lines, due to emission from the filament or one-sided accretion flows onto the core. We conclude that embedded cores may frequently undergo collapse without showing a blue asymmetric profile, and that observational surveys including filamentary regions may underestimate the number of collapsing cores if based solely on profile shapes of optically thick lines.

  6. Structure of a molecular liquid GeI4

    NASA Astrophysics Data System (ADS)

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ˜1 Å-1 in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak’s height is confirmed by a simulation, in which the molecular size is changed.

  7. Structure of a molecular liquid GeI4.

    PubMed

    Fuchizaki, Kazuhiro; Sakagami, Takahiro; Kohara, Shinji; Mizuno, Akitoshi; Asano, Yuta; Hamaya, Nozomu

    2016-11-01

    A molecular liquid GeI4 is a candidate that undergoes a pressure-induced liquid-to-liquid phase transition. This study establishes the reference structure of the low-pressure liquid phase. Synchrotron x-ray diffraction measurements were carried out at several temperatures between the melting and the boiling points under ambient pressure. The molecule has regular tetrahedral symmetry, and the intramolecular Ge-I length of 2.51 Å is almost temperature-independent within the measured range. A reverse Monte Carlo (RMC) analysis is employed to find that the distribution of molecular centers remains self-similar against heating, and thus justifying the length-scaling method adopted in determining the density. The RMC analysis also reveals that the vertex-to-face orientation of the nearest molecules are not straightly aligned, but are inclined at about 20 degrees, thereby making the closest intermolecular I-I distance definitely shorter than the intramolecular one. The prepeak observed at  ∼1 Å(-1) in the structural factor slightly shifts and increases in height with increasing temperature. The origin of the prepeak is clearly identified to be traces of the 111 diffraction peak in the crystalline state. The prepeak, assuming the residual spatial correlation between germanium sites in the densest direction, thus shifts toward lower wavenumbers with thermal expansion. The aspect that a relative reduction in molecular size associated with the volume expansion is responsible for the increase in the prepeak's height is confirmed by a simulation, in which the molecular size is changed. PMID:27605016

  8. Three decades of structure- and property-based molecular design.

    PubMed

    Müller, Klaus

    2014-01-01

    Roche has pioneered structure- and property-based molecular design to drug discovery. While this is an ongoing development, the past three decades feature key events that have revolutionized the way drug discovery is conducted in Big Pharma industry. It has been a great privilege to have been involved in this transformation process, to have been able to collaborate with, direct, guide, or simply encourage outstanding experts in various disciplines to build and further develop what has become a major pillar of modern small-molecule drug discovery. This article is an account of major events that took place since the early decision of Roche to implement computer-assisted molecular modeling 32 years ago and is devoted to the key players involved. It highlights the internal build-up of structural biology, with protein X-ray structure determination at its core, and the early setup of bioinformatics. It describes the strategic shift to large compound libraries and high-throughput screening with the development of novel compound storage and ultra-high-throughput screening facilities, as well as the strategic return to focused screening of small motif-based compound libraries. These developments were accompanied by the rise of miniaturized parallel compound property analytics which resulted in a major paradigm shift in medicinal chemistry from linear to multi-dimensional lead optimization. The rapid growth of huge collections of property data stimulated the development of various novel data mining concepts with 'matched molecular pair' analysis and novel variants thereof playing crucial roles. As compound properties got more prominent in molecular design, exploration of specific structural motifs for property modulation became a research activity complementary to target-oriented medicinal chemistry. The exploration of oxetane is given as an example. For the sake of brevity, this account cannot detail all further developments that have taken place in each individual area of

  9. Multiscale Modelling for investigating single molecule effects on the mechanics of actin filaments

    NASA Astrophysics Data System (ADS)

    A, Deriu Marco; C, Bidone Tamara; Laura, Carbone; Cristina, Bignardi; M, Montevecchi Franco; Umberto, Morbiducci

    2011-12-01

    This work presents a preliminary multiscale computational investigation of the effects of nucleotides and cations on the mechanics of actin filaments (F-actin). At the molecular level, Molecular Dynamics (MD) simulations are employed to characterize the rearrangements of the actin monomers (G-actin) in terms of secondary structures evolution in physiological conditions. At the mesoscale level, a coarse grain (CG) procedure is adopted where each monomer is represented by means of Elastic Network Modeling (ENM) technique. At the macroscale level, actin filaments up to hundreds of nanometers are assumed as isotropic and elastic beams and characterized via Rotation Translation Block (RTB) analysis. F-actin bound to adenosine triphosphate (ATP) shows a persistence length around 5 μm, while actin filaments bound to adenosine diphosphate (ADP) have a persistence length of about 3 μm. With magnesium bound to the high affinity binding site of G-actin, the persistence length of F-actin decreases to about 2 μm only in the ADP-bound form of the filament, while the same ion has no effects, in terms of stiffness variation, on the ATP-bound form of F-actin. The molecular mechanisms behind these changes in flexibility are herein elucidated. Thus, this study allows to analyze how the local binding of cations and nucleotides on G-actin induce molecular rearrangements that transmit to the overall F-actin, characterizing shifts of mechanical properties, that can be related with physiological and pathological cellular phenomena, as cell migration and spreading. Further, this study provides the basis for upcoming investigating of network and cellular remodelling at higher length scales.

  10. Beam wandering of femtosecond laser filament in air.

    PubMed

    Yang, Jing; Zeng, Tao; Lin, Lie; Liu, Weiwei

    2015-10-01

    The spatial wandering of a femtosecond laser filament caused by the filament heating effect in air has been studied. An empirical formula has also been derived from the classical Karman turbulence model, which determines quantitatively the displacement of the beam center as a function of the propagation distance and the effective turbulence structure constant. After fitting the experimental data with this formula, the effective turbulence structure constant has been estimated for a single filament generated in laboratory environment. With this result, one may be able to estimate quantitatively the displacement of a filament over long distance propagation and interpret the practical performance of the experiments assisted by femtosecond laser filamentation, such as remote air lasing, pulse compression, high order harmonic generation (HHG), etc.

  11. Magnetic reconnection between a solar filament and nearby coronal loops

    NASA Astrophysics Data System (ADS)

    Li, Leping; Zhang, Jun; Peter, Hardi; Priest, Eric; Chen, Huadong; Guo, Lijia; Chen, Feng; Mackay, Duncan

    2016-09-01

    Magnetic reconnection is difficult to observe directly but coronal structures on the Sun often betray the magnetic field geometry and its evolution. Here we report the observation of magnetic reconnection between an erupting filament and its nearby coronal loops, resulting in changes in the filament connection. X-type structures form when the erupting filament encounters the loops. The filament becomes straight, and bright current sheets form at the interfaces. Plasmoids appear in these current sheets and propagate bi-directionally. The filament disconnects from the current sheets, which gradually disperse and disappear, then reconnects to the loops. This evolution suggests successive magnetic reconnection events predicted by theory but rarely detected with such clarity in observations. Our results confirm the three-dimensional magnetic reconnection theory and have implications for the evolution of dissipation regions and the release of magnetic energy for reconnection in many magnetized plasma systems.

  12. Beam wandering of femtosecond laser filament in air.

    PubMed

    Yang, Jing; Zeng, Tao; Lin, Lie; Liu, Weiwei

    2015-10-01

    The spatial wandering of a femtosecond laser filament caused by the filament heating effect in air has been studied. An empirical formula has also been derived from the classical Karman turbulence model, which determines quantitatively the displacement of the beam center as a function of the propagation distance and the effective turbulence structure constant. After fitting the experimental data with this formula, the effective turbulence structure constant has been estimated for a single filament generated in laboratory environment. With this result, one may be able to estimate quantitatively the displacement of a filament over long distance propagation and interpret the practical performance of the experiments assisted by femtosecond laser filamentation, such as remote air lasing, pulse compression, high order harmonic generation (HHG), etc. PMID:26480079

  13. The magnetic field and dust filaments in the Polaris Flare

    NASA Astrophysics Data System (ADS)

    Panopoulou, G. V.; Psaradaki, I.; Tassis, K.

    2016-10-01

    In diffuse molecular clouds, possible precursors of star-forming clouds, the effect of the magnetic field is unclear. In this work, we compare the orientations of filamentary structures in the Polaris Flare, as seen through dust emission by Herschel, to the plane-of-the-sky magnetic field orientation (Bpos) as revealed by stellar optical polarimetry with RoboPol. Dust structures in this translucent cloud show a strong preference for alignment with Bpos. Of the field orientations, 70 per cent are consistent with those of the filaments (within 30°). We explore the spatial variation of the relative orientations and find it to be uncorrelated with the dust emission intensity and correlated to the dispersion of polarization angles. Concentrating on the area around the highest column density filament, and on the region with the most uniform field, we infer the Bpos strength to be 24-120 μG. Assuming that the magnetic field can be decomposed into a turbulent and an ordered component, we find a turbulent-to-ordered ratio of 0.2-0.8, implying that the magnetic field is dynamically important, at least in these two areas. We discuss implications for three-dimensional field properties, as well as for the distance estimate of the cloud.

  14. Roles in Modulation of Molecular Structures on Metal Surfaces

    NASA Astrophysics Data System (ADS)

    Gao, H.-J.

    2007-03-01

    We studied the adsorption of organic molecules, their growth behavior, and their physical properties on silver and gold surfaces at the single molecule or sub-molecular scale by using low-temperature scanning tunneling microscopes. Combined with low energy electron diffraction and first-principles density functional theory calculations, the key parameters in modulating molecular structures on metals are analyzed. It is found that the alkyl chains of quinacridone derivatives (QA) determine the orientation of molecular overlayers on an Ag(110) substrate. The interaction of QA and the Ag substrate is primarily due to chemical bonding of oxygen to specific positions at the silver substrate, determining the molecular orientation and preferred adsorption site. However, the intermolecular arrangement can be adjusted via the length of attached alkyl chains. We are thus able to fabricate uniform QA films with very well controlled physical properties. Furthermore, by thermal and chemical control, we are able to self-assemble three dimensional molecular nanostructures, e.g. ordered PTCDA structures exclusively on flat Ag(111) facets, or DMe-DCNQI structures exclusively on stepped Ag(221) facets. It is demonstrated that bonding, the key factor for selectivity, occurs via the end-atoms, while the molecule's mid-region arches away from the substrate. Theoretical results, obtained by high-level theory, are consistent with the experimental observations, which have previously been interpreted in terms of bonding through the mid-region. In collaboration with D.X. Shi, S.X. Du, W. Ji, Z.T. Deng, L. Gao, Institute of Physics, and X. Lin, Chinese Academy of Sciences, China; C. Seidel and H. Fuchs, Universit"at M"unster, Germany; W.A. Hofer, The University of Liverpool, Britain; and S. T. Pantelides, Vanderbilt University, USA. [1] D.X. Shi et al., Phys. Rev. Lett. 96, 226101(2006). [2] S.X. Du et al., Phys. Rev. Lett. 96, 226101(2006). [3] L. Gao et al., Phys. Rev. B 73, 075424(2006).

  15. Global collapse of the DR21 filament

    NASA Astrophysics Data System (ADS)

    Schneider, N.; Csengeri, T.; Bontemps, S.; Motte, F.; Simon, R.; Hennebelle, P.; Federrath, C.; Klessen, R.

    2011-05-01

    The formation of massive stars is a highly complex process in which it is unclear whether the star-forming gas is in global gravitational collapse or an equilibrium state supported by turbulence and/or magnetic fields. By studying the most massive and dense star-forming clump in the Galaxy at a distance of less than 3 kpc, i.e. the filament containing DR21 and DR21(OH), we obtained observational evidence to help us to discriminate between these two views. For that, we used molecular line data from our 13CO 1→0, CS 2→1, and N_2H^+ 1→0 survey of the Cygnus X region (FCRAO) and high-angular resolution observations in isotopomeric lines of CO, CS, HCO^+, N_2H^+, and H_2CO, obtained with the IRAM 30m telescope. The observations reveal a complex velocity field and velocity dispersion in which regions of the highest column-density, i.e. dense cores, have a lower velocity dispersion than the surrounding gas and velocity gradients that are not (only) due to rotation. Infall signatures in optically thick line profiles of HCO^+ and 12CO are observed along and across the whole DR21 filament. By modelling the observed spectra, we obtain a typical infall speed of ˜0.6 km s-1 and mass accretion rates of the order of a few 10-3 M_⊙ yr-1 for the two main clumps constituting the filament. These massive clumps (4900 and 3300 M_⊙ at densities of around 10^5 cm-3 within 1 pc diameter) are both gravitationally contracting (with free-fall times much shorter than sound crossing times and low virial parameter α). The more massive of the clumps, DR21(OH), is connected to a sub-filament, apparently 'falling' onto the clump. This filament runs parallel to the magnetic field. All observed kinematic features in the DR21 filament (velocity field, velocity dispersion, and infall), its filamentary morphology, and the existence of (a) sub-filament(s) can be explained if the DR21 filament was formed by the convergence of flows on large scales and is now in a state of global gravitational

  16. Quantum Theory of Atomic and Molecular Structures and Interactions

    NASA Astrophysics Data System (ADS)

    Makrides, Constantinos

    This dissertation consists of topics in two related areas of research that together provide quantum mechanical descriptions of atomic and molecular interactions and reactions. The first is the ab initio electronic structure calculation that provides the atomic and molecular interaction potential, including the long-range potential. The second is the quantum theory of interactions that uses such potentials to understand scattering, long-range molecules, and reactions. In ab initio electronic structure calculations, we present results of dynamic polarizabilities for a variety of atoms and molecules, and the long-range dispersion coefficients for a number of atom-atom and atom-molecule cases. We also present results of a potential energy surface for the triatomic lithium-ytterbium-lithium system, aimed at understanding the related chemical reactions. In the quantum theory of interactions, we present a multichannel quantum-defect theory (MQDT) for atomic interactions in a magnetic field. This subject, which is complex especially for atoms with hyperfine structure, is essential for the understanding and the realization of control and tuning of atomic interactions by a magnetic field: a key feature that has popularized cold atom physics in its investigations of few-body and many-body quantum systems. Through the example of LiK, we show how MQDT provides a systematic and an efficient understanding of atomic interaction in a magnetic field, especially magnetic Feshbach resonances in nonzero partial waves.

  17. High-Molecular-Weight Paired Helical Filaments from Alzheimer Brain Induces Seeding of Wild-Type Mouse Tau into an Argyrophilic 4R Tau Pathology in Vivo.

    PubMed

    Audouard, Emilie; Houben, Sarah; Masaracchia, Caterina; Yilmaz, Zehra; Suain, Valérie; Authelet, Michèle; De Decker, Robert; Buée, Luc; Boom, Alain; Leroy, Karelle; Ando, Kunie; Brion, Jean-Pierre

    2016-10-01

    In Alzheimer disease, the development of tau pathology follows neuroanatomically connected pathways, suggesting that abnormal tau species might recruit normal tau by passage from cell to cell. Herein, we analyzed the effect of stereotaxic brain injection of human Alzheimer high-molecular-weight paired helical filaments (PHFs) in the dentate gyrus of wild-type and mutant tau THY-Tau22 mice. After 3 months of incubation, wild-type and THY-Tau22 mice developed an atrophy of the dentate gyrus and a tau pathology characterized by Gallyas and tau-positive grain-like inclusions into granule cells that extended in the hippocampal hilus and eventually away into the alveus, and the fimbria. Gallyas-positive neuropil threads and oligodendroglial coiled bodies were also observed. These tau inclusions were composed only of mouse tau, and were immunoreactive with antibodies to 4R tau, phosphotau, misfolded tau, ubiquitin, and p62. Although local hyperphosphorylation of tau was increased in the dentate gyrus in THY-Tau22 mice, the development of neurofibrillary tangles made of mutant human tau was not accelerated in the hippocampus, indicating that wild-type human PHFs were inefficient in seeding tau aggregates made of G272V/P301S mutant human tau. Our results indicate thus that injection of human wild-type Alzheimer PHF seeded aggregation of wild-type murine tau into an argyrophilic 4R tau pathology, and constitutes an interesting model independent of expression of a mutant tau protein.

  18. High-Molecular-Weight Paired Helical Filaments from Alzheimer Brain Induces Seeding of Wild-Type Mouse Tau into an Argyrophilic 4R Tau Pathology in Vivo.

    PubMed

    Audouard, Emilie; Houben, Sarah; Masaracchia, Caterina; Yilmaz, Zehra; Suain, Valérie; Authelet, Michèle; De Decker, Robert; Buée, Luc; Boom, Alain; Leroy, Karelle; Ando, Kunie; Brion, Jean-Pierre

    2016-10-01

    In Alzheimer disease, the development of tau pathology follows neuroanatomically connected pathways, suggesting that abnormal tau species might recruit normal tau by passage from cell to cell. Herein, we analyzed the effect of stereotaxic brain injection of human Alzheimer high-molecular-weight paired helical filaments (PHFs) in the dentate gyrus of wild-type and mutant tau THY-Tau22 mice. After 3 months of incubation, wild-type and THY-Tau22 mice developed an atrophy of the dentate gyrus and a tau pathology characterized by Gallyas and tau-positive grain-like inclusions into granule cells that extended in the hippocampal hilus and eventually away into the alveus, and the fimbria. Gallyas-positive neuropil threads and oligodendroglial coiled bodies were also observed. These tau inclusions were composed only of mouse tau, and were immunoreactive with antibodies to 4R tau, phosphotau, misfolded tau, ubiquitin, and p62. Although local hyperphosphorylation of tau was increased in the dentate gyrus in THY-Tau22 mice, the development of neurofibrillary tangles made of mutant human tau was not accelerated in the hippocampus, indicating that wild-type human PHFs were inefficient in seeding tau aggregates made of G272V/P301S mutant human tau. Our results indicate thus that injection of human wild-type Alzheimer PHF seeded aggregation of wild-type murine tau into an argyrophilic 4R tau pathology, and constitutes an interesting model independent of expression of a mutant tau protein. PMID:27497324

  19. Actin filament organization in the fish keratocyte lamellipodium

    PubMed Central