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Sample records for regions reveals 12-fold

  1. Timing of isoclinal folds in multiply deformed high metamorphic grade region using FIA succession

    Science.gov (United States)

    Cao, Hui; Cai, Zhihui

    2013-04-01

    Multiply deformed and isoclinally folded interlayered high metamorphic grade gneisses and schists can be very difficult rocks for resolving early formed stratigraphic and structural relationships. When such rocks contain porphyroblasts a new approach is possible because of the way in which porphyroblast growth is affected by crenulation versus reactivation of compositional layering. The asymmetries of the overprinting foliations preserved as inclusion trails that define the FIAs can be used to investigate whether an enigmatic isoclinal fold is an antiform or synform. This approach also reveals when the fold first formed during the tectonic history of the region. Isoclinally folded rocks in the Arkansas River region of Central Colorado contain relics of fold hinges that have been very difficult to ascertain whether they are antiforms or synforms because of younger refolding effects and the locally truncated nature of coarse compositional layering. With the realization that rocks with a schistosity parallel to bedding (S0 parallel S1) have undergone lengthy histories of deformation that predate the obvious first deformation came recognition that large scale regional folds can form early during this process and be preserved throughout orogenesis. This extensive history is lost within the matrix because of reactivational shear on the compositional layering. However, it can be extracted by measuring FIAs. Recent work using this approach has revealed that the trends of axial planes of all map scale folds, when plotted on a rose diagram, strikingly reflect the FIA trends. That is, although it was demonstrated that the largest scale regional folds commonly form early in the total history, other folds can form and be preserved from subsequent destruction in the strain shadows of plutons or through the partitioning of deformation due to heterogeneities at depth.

  2. Macroscopic folded form factors for 12C + 12C inelastic scattering

    International Nuclear Information System (INIS)

    Rickertsen, L.D.; Satchler, G.R.; Stokstad, R.G.; Wieland, R.M.

    1976-01-01

    The angular distributions for the scattering of carbon-12 from carbon-12 at 117.1 MeV are shown as is also the result of coupled-channel calculations for the elastic and inelastic scattering using these folded form factors

  3. One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

    Science.gov (United States)

    Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

    2018-04-12

    The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two

  4. An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior.

    Science.gov (United States)

    Makabe, Koki; Nakamura, Takashi; Dhar, Debanjan; Ikura, Teikichi; Koide, Shohei; Kuwajima, Kunihiro

    2018-04-27

    Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions. Copyright © 2018. Published by Elsevier Ltd.

  5. WW domain folding complexity revealed by infrared spectroscopy.

    Science.gov (United States)

    Davis, Caitlin M; Dyer, R Brian

    2014-09-02

    Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescence spectroscopy, to study the folding of the FBP28 WW domain. Laser-induced temperature jumps coupled with fluorescence or infrared spectroscopy have been used to probe changes in the peptide backbone on the submillisecond time scale. The relaxation dynamics of the β-sheets and β-turn were measured independently by probing the corresponding IR bands assigned in the amide I region. Using these wavelength-dependent measurements, we observe three kinetics phases, with the fastest process corresponding to the relaxation kinetics of the turns. In contrast, fluorescence measurements of the wild-type WW domain and tryptophan mutants exhibit single-exponential kinetics with a lifetime that corresponds to the slowest phase observed by infrared spectroscopy. Mutant sequences provide evidence of an intermediate dry molten globule state. The slowest step in the folding of this WW domain is the tight packing of the side chains in the transition from the dry molten globule intermediate to the native structure. This study demonstrates that using multiple complementary probes enhances the interpretation of protein folding dynamics.

  6. Does Helicobacter pylori exist in vocal fold pathologies and in the interarytenoid region?

    Science.gov (United States)

    Islam, Ahmet; Oguz, Haldun; Yucel, Mihriban; Koca, Gökhan; Gonultas, Mehmet A; Arslan, Necmi; Demirci, Münir

    2013-09-01

    The aim of this study was to investigate the existence of Helicobacter pylori (HP) in patients with benign and malignant vocal fold pathologies. This was a prospective clinical study conducted at a tertiary-care academic medical center. Fifty consecutive patients who had undergone microlaryngoscopy between August 2007 and July 2009 were included in the study. The patients with a reflux symptom index (RSI) above 12 and a reflux finding score (RFS) above 6 were accepted as having laryngopharyngeal reflux. Patients with urea breath test (UBT), HP-IgG, and HP cytotoxin-associated gene A (CagA)-IgG positivity were diagnosed as HP positive. During laryngoscopy, two surgical specimens were obtained, one from the primary vocal fold pathology and one from the interarytenoid region. The interarytenoid biopsy specimen was used for HP culture and PCR. The specimen from the vocal fold pathology was used to investigate the presence of HP. RSI was positive in 23 (46%) patients. The RFS positivity was 56%. The presence of HP was confirmed by UBT in 35 (70%), HP-IgG in 37 (74%), and HP CagA-IgG in 38 (76%) patients. There was no difference between RFS-positive and RFS-negative patients in terms of HP-IgG and UBT. None of the interarytenoid or vocal fold specimens showed the presence of HP. HP was not found in the histological specimens of vocal fold pathologies and the interarytenoid region. The presence of HP in the gastric mucosa does not have an effect on the RFS and RSI.

  7. High Pressure ZZ-Exchange NMR Reveals Key Features of Protein Folding Transition States.

    Science.gov (United States)

    Zhang, Yi; Kitazawa, Soichiro; Peran, Ivan; Stenzoski, Natalie; McCallum, Scott A; Raleigh, Daniel P; Royer, Catherine A

    2016-11-23

    Understanding protein folding mechanisms and their sequence dependence requires the determination of residue-specific apparent kinetic rate constants for the folding and unfolding reactions. Conventional two-dimensional NMR, such as HSQC experiments, can provide residue-specific information for proteins. However, folding is generally too fast for such experiments. ZZ-exchange NMR spectroscopy allows determination of folding and unfolding rates on much faster time scales, yet even this regime is not fast enough for many protein folding reactions. The application of high hydrostatic pressure slows folding by orders of magnitude due to positive activation volumes for the folding reaction. We combined high pressure perturbation with ZZ-exchange spectroscopy on two autonomously folding protein domains derived from the ribosomal protein, L9. We obtained residue-specific apparent rates at 2500 bar for the N-terminal domain of L9 (NTL9), and rates at atmospheric pressure for a mutant of the C-terminal domain (CTL9) from pressure dependent ZZ-exchange measurements. Our results revealed that NTL9 folding is almost perfectly two-state, while small deviations from two-state behavior were observed for CTL9. Both domains exhibited large positive activation volumes for folding. The volumetric properties of these domains reveal that their transition states contain most of the internal solvent excluded voids that are found in the hydrophobic cores of the respective native states. These results demonstrate that by coupling it with high pressure, ZZ-exchange can be extended to investigate a large number of protein conformational transitions.

  8. Crystal structures of the F and pSLT plasmid TraJ N-terminal regions reveal similar homodimeric PAS folds with functional interchangeability

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Jun; Wu, Ruiying; Adkins, Joshua N.; Joachimiak, Andrzej; Glover, Mark

    2014-09-16

    In the F-family of conjugative plasmids, TraJ is an essential transcriptional activator of the tra operon that encodes most of the proteins required for conjugation. Here we report for the first time the X-ray crystal structures of the TraJ N-terminal regions from the prototypic F plasmid (TraJF11-130) and from the Salmonella virulence plasmid pSLT (TraJpSLT 1-128). Both proteins form similar homodimeric Per-ARNT-Sim (PAS) fold structures. Mutational analysis reveals that the observed dimeric interface is critical for TraJF transcriptional activation, indicating that dimerization of TraJ is required for its in vivo function. An artificial ligand (oxidized dithiothreitol) occupies a cavity in the TraJF dimer interface, while a smaller cavity in corresponding region of the TraJpSLT structure lacks a ligand. Gas chromatography/mass spectrometry-electron ionization analysis of dithiothreitol-free TraJF suggests indole may be the natural TraJ ligand; however, disruption of the indole biosynthetic pathway does not affect TraJF function. Heterologous PAS domains from pSLT and R100 TraJ can functionally replace the TraJF PAS domain, suggesting that TraJ allelic specificity is mediated by the region C-terminal to the PAS domain.

  9. Stratigraphy and Folding in the Cenozoic Cover of a Fold-Thrust Belt in the Nallıhan Region (Ankara, Central Turkey)

    Science.gov (United States)

    Karaaǧaç, Serdal; Koral, Hayrettin

    2017-04-01

    This study investigates stratigraphy and structural features in the Cenozoic sedimentary sequence of the fold-thrust belt of the Nallıhan-Ankara region, located to the north of the İzmir-Ankara-Erzincan Suture Zone. Permian-Triassic age marble intercalated with schist-phyllites, the upper Jurassic-lower Cretaceous age limestone and the upper Cretaceous age sandstone-shale alternation compose the basement in the study area. These rocks are unconformably overlain by the Cenozoic age terrestrial sedimentary and volcanic units. The Cenozoic stratigraphy begins with the Paleocene-Eocene age coal-bearing, at times, volcanic intercalated conglomerate-sandstone-mudstone alternation of alluvial-fluvial origins (Aksaklar Formation) and the tuff intercalated with lacustrine limestone, bituminous limestone (Kabalar Formation). These units are conformably overlain by the Eocene age basalt-andesite and pyroclastic rocks (Meyildere volcanics). The Paleocene-Eocene aged units are unconformably overlain by the conglomerate-sandstone-mudstone-marl of a lower-middle Miocene lacustrine environment (Hançili Formation). The terrestrial conglomerate-sandstone alternation (Örencik Formation) is the youngest unit in the Cenozoic stratigraphy, and is assumed to be of Pliocene age based its stratigraphic position on older units. Field study shows existence of both folds and faults in the sedimentary cover. Stereographic projections of bedding measured in the field shows N25W/45NW and N60W/4SE-oriented fold axes in the Paleocene-Eocene age units. There are also N76W/12SE and N88E/8NE-oriented folds. The difference in fold-axis orientations suggests that some folds may have been rotated in blocks bound by faults during the post-Paleocene/Eocene period. Whereas, the lower-middle Miocene units manifest N88W/13SE-oriented fold axes. It is thus proposed that the observed difference in the azimuth of fold axes represent two different folding phases, one with NE-SW and the other with N

  10. Do mesoscale faults in a young fold belt indicate regional or local stress?

    Science.gov (United States)

    Kokado, Akihiro; Yamaji, Atsushi; Sato, Katsushi

    2017-04-01

    The result of paleostress analyses of mesoscale faults is usually thought of as evidence of a regional stress. On the other hand, the recent advancement of the trishear modeling has enabled us to predict the deformation field around fault-propagation folds without the difficulty of assuming paleo mechanical properties of rocks and sediments. We combined the analysis of observed mesoscale faults and the trishear modeling to understand the significance of regional and local stresses for the formation of mesoscale faults. To this end, we conducted the 2D trishear inverse modeling with a curved thrust fault to predict the subsurface structure and strain field of an anticline, which has a more or less horizontal axis and shows a map-scale plane strain perpendicular to the axis, in the active fold belt of Niigata region, central Japan. The anticline is thought to have been formed by fault-propagation folding under WNW-ESE regional compression. Based on the attitudes of strata and the positions of key tephra beds in Lower Pleistocene soft sediments cropping out at the surface, we obtained (1) a fault-propagation fold with the fault tip at a depth of ca. 4 km as the optimal subsurface structure, and (2) the temporal variation of deformation field during the folding. We assumed that mesoscale faults were activated along the direction of maximum shear strain on the faults to test whether the fault-slip data collected at the surface were consistent with the deformation in some stage(s) of folding. The Wallace-Bott hypothesis was used to estimate the consistence of faults with the regional stress. As a result, the folding and the regional stress explained 27 and 33 of 45 observed faults, respectively, with the 11 faults being consistent with the both. Both the folding and regional one were inconsistent with the remaining 17 faults, which could be explained by transfer faulting and/or the gravitational spreading of the growing anticline. The lesson we learnt from this work was

  11. Vocal fold paralysis secondary to phonotrauma.

    Science.gov (United States)

    Klein, Travis A L; Gaziano, Joy E; Ridley, Marion B

    2014-01-01

    A unique case of acute onset vocal fold paralysis secondary to phonotrauma is presented. The cause was forceful vocalization by a drill instructor on a firearm range. Imaging studies revealed extensive intralaryngeal and retropharyngeal hemorrhage. Laryngoscopy showed a complete left vocal fold paralysis. Relative voice rest was recommended, and the patient regained normal vocal fold mobility and function after approximately 12 weeks. Copyright © 2014 The Voice Foundation. All rights reserved.

  12. Evidence for the 3-fold α-cluster symmetry of 12C

    International Nuclear Information System (INIS)

    Rae, W.D.M.; Fry, P.E.; Merchant, A.C.

    1996-01-01

    Recently, resonances have been observed in the reactions 12 C( 12 C, 12 C(O 2 + )) 12 C(3 - ) and 12 C( 12 C, 12 C(3 - )) 12 C(3 - ) at E cm ∼ 33 MeV. Previously resonances in the reaction 12 C( 12 C, 12 C) 12 C(3 - ) have been reported by Fulton et al. Here we present a new model of these resonances. We relate this model to the classical theory of both the asymmetric rotor and the symmetric top. We believe that detailed spin measurements from these data will provide evidence for the 3-fold symmetry of 12 C. (author). Letter-to-the-editor

  13. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Yu, E-mail: yuzhang@xmu.edu.c [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Shao Jun [Shanghai EENT Hospital of Fudan University, Shanghai (China); Krausert, Christopher R. [Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States); Zhang Sai [Key Laboratory of Underwater Acoustic Communication and Marine Information Technology of the Ministry of Education, Xiamen University, Xiamen Fujian 361005 (China); Jiang, Jack J. [Shanghai EENT Hospital of Fudan University, Shanghai (China); Department of Surgery, Division of Otolaryngology - Head and Neck Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI 53792-7375 (United States)

    2011-01-15

    Research highlights: Low-dimensional human glottal area data. Evidence of chaos in human laryngeal activity from high-speed digital imaging. Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic analysis is capable of

  14. High-speed image analysis reveals chaotic vibratory behaviors of pathological vocal folds

    International Nuclear Information System (INIS)

    Zhang Yu; Shao Jun; Krausert, Christopher R.; Zhang Sai; Jiang, Jack J.

    2011-01-01

    Research highlights: → Low-dimensional human glottal area data. → Evidence of chaos in human laryngeal activity from high-speed digital imaging. → Traditional perturbation analysis should be cautiously applied to aperiodic high speed image signals. → Nonlinear dynamic analysis may be helpful for understanding disordered behaviors in pathological laryngeal systems. - Abstract: Laryngeal pathology is usually associated with irregular dynamics of laryngeal activity. High-speed imaging facilitates direct observation and measurement of vocal fold vibrations. However, chaotic dynamic characteristics of aperiodic high-speed image data have not yet been investigated in previous studies. In this paper, we will apply nonlinear dynamic analysis and traditional perturbation methods to quantify high-speed image data from normal subjects and patients with various laryngeal pathologies including vocal fold nodules, polyps, bleeding, and polypoid degeneration. The results reveal the low-dimensional dynamic characteristics of human glottal area data. In comparison to periodic glottal area series from a normal subject, aperiodic glottal area series from pathological subjects show complex reconstructed phase space, fractal dimension, and positive Lyapunov exponents. The estimated positive Lyapunov exponents provide the direct evidence of chaos in pathological human vocal folds from high-speed digital imaging. Furthermore, significant differences between the normal and pathological groups are investigated for nonlinear dynamic and perturbation analyses. Jitter in the pathological group is significantly higher than in the normal group, but shimmer does not show such a difference. This finding suggests that the traditional perturbation analysis should be cautiously applied to high speed image signals. However, the correlation dimension and the maximal Lyapunov exponent reveal a statistically significant difference between normal and pathological groups. Nonlinear dynamic

  15. Electrostatic mechanism of nucleosomal array folding revealed by computer simulation.

    Science.gov (United States)

    Sun, Jian; Zhang, Qing; Schlick, Tamar

    2005-06-07

    Although numerous experiments indicate that the chromatin fiber displays salt-dependent conformations, the associated molecular mechanism remains unclear. Here, we apply an irregular Discrete Surface Charge Optimization (DiSCO) model of the nucleosome with all histone tails incorporated to describe by Monte Carlo simulations salt-dependent rearrangements of a nucleosomal array with 12 nucleosomes. The ensemble of nucleosomal array conformations display salt-dependent condensation in good agreement with hydrodynamic measurements and suggest that the array adopts highly irregular 3D zig-zag conformations at high (physiological) salt concentrations and transitions into the extended "beads-on-a-string" conformation at low salt. Energy analyses indicate that the repulsion among linker DNA leads to this extended form, whereas internucleosome attraction drives the folding at high salt. The balance between these two contributions determines the salt-dependent condensation. Importantly, the internucleosome and linker DNA-nucleosome attractions require histone tails; we find that the H3 tails, in particular, are crucial for stabilizing the moderately folded fiber at physiological monovalent salt.

  16. Interpreting whether isoclinal folds are antiforms or synforms using FIA succession

    Science.gov (United States)

    Cao, H.

    2012-12-01

    Using the asymmetries of the overprinting foliations preserved as inclusion trails that define the FIAs to investigate whether an enigmatic isoclinal fold in the region is an antiform or synform. This approach also reveals when the fold first formed during the tectonic history of the region. Multiply deformed and isoclinally folded interlayered high metamorphic grade gneisses and schists can be very difficult rocks for resolving early formed stratigraphic and structural relationships. When such rocks contain porphyroblasts a new approach is possible because of the way in which porphyroblast growth is affected by crenulation versus reactivation of compositional layering (Bell et al., 2003). Isoclinally folded rocks in the Arkansas River region of South Central Colorado contain relics of fold hinges that have been very difficult to ascertain whether they are antiforms or synforms because of younger refolding effects and the locally truncated nature of coarse compositional layering. With the realization that rocks with a schistosity parallel to bedding (S0 parallel S1) have undergone lengthy histories of deformation that predate the obvious first deformation (e.g. Bell et al., 2003; Sayab, 2006; Yeh, 2007) came recognition that large scale regional folds can form early during this process and be preserved throughout orogenesis (e.g., Ham and Bell, 2004; Bell and Newman, 2006. This extensive history is lost within the matrix because of reactivational shear on the compositional layering (Bell et al., 1998, 2003, 2004, 2005; Ham and Bell, 2004). However, it can be extracted by measuring FIAs. Recent work using this approach has revealed that the trends of axial planes of all map scale folds, when plotted on a rose diagram, strikingly reflect the FIA trends (e.g., Sanislav, 2009; Shah, 2009). That is, although it was demonstrated by Bell et al. (2003) that the largest scale regional folds commonly form early in the total history, other folds can form and be preserved from

  17. The pro region required for folding of carboxypeptidase Y is a partially folded domain with little regular structural core

    DEFF Research Database (Denmark)

    Sørensen, P; Winther, Jakob R.; Kaarsholm, N C

    1993-01-01

    The pro region of carboxypeptidase Y (CPY) from yeast is necessary for the correct folding of the enzyme [Winther, J. R., & Sørensen P. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 9330-9334]. Using fluorescence, circular dichroism, and heteronuclear NMR analyses, it is demonstrated that the isolated...

  18. Biophysical Studies on BEX3, the p75NTR-Associated Cell Death Executor, Reveal a High-Order Oligomer with Partially Folded Regions.

    Directory of Open Access Journals (Sweden)

    Katia M S Cabral

    Full Text Available BEX3 (Brain Expressed X-linked protein 3 is a member of a mammal-specific placental protein family. Several studies have found the BEX proteins to be associated with neurodegeneration, the cell cycle and cancer. BEX3 has been predicted to be intrinsically disordered and also to represent an intracellular hub for cell signaling. The pro-apoptotic activity of BEX3 in association with a number of additional proteins has been widely supported; however, to the best of our knowledge, very limited data are available on the conformation of any of the members of the BEX family. In this study, we structurally characterized BEX3 using biophysical experimental data. Small angle X-ray scattering and atomic force microscopy revealed that BEX3 forms a specific higher-order oligomer that is consistent with a globular molecule. Solution nuclear magnetic resonance, partial proteinase K digestion, circular dichroism spectroscopy, and fluorescence techniques that were performed on the recombinant protein indicated that the structure of BEX3 is composed of approximately 31% α-helix and 20% β-strand, contains partially folded regions near the N- and C-termini, and a core which is proteolysis-resistant around residues 55-120. The self-oligomerization of BEX3 has been previously reported in cell culture and is consistent with our in vitro data.

  19. Biophysical Studies on BEX3, the p75NTR-Associated Cell Death Executor, Reveal a High-Order Oligomer with Partially Folded Regions.

    Science.gov (United States)

    Cabral, Katia M S; Raymundo, Diana P; Silva, Viviane S; Sampaio, Laura A G; Johanson, Laizes; Hill, Luis Fernando; Almeida, Fabio C L; Cordeiro, Yraima; Almeida, Marcius S

    2015-01-01

    BEX3 (Brain Expressed X-linked protein 3) is a member of a mammal-specific placental protein family. Several studies have found the BEX proteins to be associated with neurodegeneration, the cell cycle and cancer. BEX3 has been predicted to be intrinsically disordered and also to represent an intracellular hub for cell signaling. The pro-apoptotic activity of BEX3 in association with a number of additional proteins has been widely supported; however, to the best of our knowledge, very limited data are available on the conformation of any of the members of the BEX family. In this study, we structurally characterized BEX3 using biophysical experimental data. Small angle X-ray scattering and atomic force microscopy revealed that BEX3 forms a specific higher-order oligomer that is consistent with a globular molecule. Solution nuclear magnetic resonance, partial proteinase K digestion, circular dichroism spectroscopy, and fluorescence techniques that were performed on the recombinant protein indicated that the structure of BEX3 is composed of approximately 31% α-helix and 20% β-strand, contains partially folded regions near the N- and C-termini, and a core which is proteolysis-resistant around residues 55-120. The self-oligomerization of BEX3 has been previously reported in cell culture and is consistent with our in vitro data.

  20. Cotranslational protein folding reveals the selective use of ...

    Indian Academy of Sciences (India)

    to fold properly by decelerating the translation rate at these sites. Thus the cotranslational protein folding is believed to be true for many proteins and is an important selection factor for the selective codon usage to optimize proper gene expres- sion and function (Komar 2009). A web server CS and S has been created by ...

  1. Autonomously folding protein fragments reveal differences in the energy landscapes of homologous RNases H.

    Directory of Open Access Journals (Sweden)

    Laura E Rosen

    Full Text Available An important approach to understanding how a protein sequence encodes its energy landscape is to compare proteins with different sequences that fold to the same general native structure. In this work, we compare E. coli and T. thermophilus homologs of the protein RNase H. Using protein fragments, we create equilibrium mimics of two different potential partially-folded intermediates (I(core and I(core+1 hypothesized to be present on the energy landscapes of these two proteins. We observe that both T. thermophilus RNase H (ttRNH fragments are folded and have distinct stabilities, indicating that both regions are capable of autonomous folding and that both intermediates are present as local minima on the ttRNH energy landscape. In contrast, the two E. coli RNase H (ecRNH fragments have very similar stabilities, suggesting that the presence of additional residues in the I(core+1 fragment does not affect the folding or structure as compared to I(core. NMR experiments provide additional evidence that only the I(core intermediate is populated by ecRNH. This is one of the biggest differences that has been observed between the energy landscapes of these two proteins. Additionally, we used a FRET experiment in the background of full-length ttRNH to specifically monitor the formation of the I(core+1 intermediate. We determine that the ttRNH I(core+1 intermediate is likely the intermediate populated prior to the rate-limiting barrier to global folding, in contrast to E. coli RNase H for which I(core is the folding intermediate. This result provides new insight into the nature of the rate-limiting barrier for the folding of RNase H.

  2. Structured pathway across the transition state for peptide folding revealed by molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Lipi Thukral

    2011-09-01

    Full Text Available Small globular proteins and peptides commonly exhibit two-state folding kinetics in which the rate limiting step of folding is the surmounting of a single free energy barrier at the transition state (TS separating the folded and the unfolded states. An intriguing question is whether the polypeptide chain reaches, and leaves, the TS by completely random fluctuations, or whether there is a directed, stepwise process. Here, the folding TS of a 15-residue β-hairpin peptide, Peptide 1, is characterized using independent 2.5 μs-long unbiased atomistic molecular dynamics (MD simulations (a total of 15 μs. The trajectories were started from fully unfolded structures. Multiple (spontaneous folding events to the NMR-derived conformation are observed, allowing both structural and dynamical characterization of the folding TS. A common loop-like topology is observed in all the TS structures with native end-to-end and turn contacts, while the central segments of the strands are not in contact. Non-native sidechain contacts are present in the TS between the only tryptophan (W11 and the turn region (P7-G9. Prior to the TS the turn is found to be already locked by the W11 sidechain, while the ends are apart. Once the ends have also come into contact, the TS is reached. Finally, along the reactive folding paths the cooperative loss of the W11 non-native contacts and the formation of the central inter-strand native contacts lead to the peptide rapidly proceeding from the TS to the native state. The present results indicate a directed stepwise process to folding the peptide.

  3. WW Domain Folding Complexity Revealed by Infrared Spectroscopy

    OpenAIRE

    Davis, Caitlin M.; Dyer, R. Brian

    2014-01-01

    Although the intrinsic tryptophan fluorescence of proteins offers a convenient probe of protein folding, interpretation of the fluorescence spectrum is often difficult because it is sensitive to both global and local changes. Infrared (IR) spectroscopy offers a complementary measure of structural changes involved in protein folding, because it probes changes in the secondary structure of the protein backbone. Here we demonstrate the advantages of using multiple probes, infrared and fluorescen...

  4. The structure of KPN03535 (gi|152972051), a novel putative lipoprotein from Klebsiella pneumoniae, reveals an OB-fold

    International Nuclear Information System (INIS)

    Das, Debanu; Kozbial, Piotr; Han, Gye Won; Carlton, Dennis; Jaroszewski, Lukasz; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Bakolitsa, Constantina; Chen, Connie; Chiu, Hsiu-Ju; Chiu, Michelle; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Ellrott, Kyle; Elsliger, Marc-André; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grzechnik, Anna; Grant, Joanna C.; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Miller, Mitchell D.; Morse, Andrew T.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Oommachen, Silvya; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Wooten, Tiffany; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2009-01-01

    KPN03535 is a protein unique to K. pneumoniae. The crystal structure reveals that KPN03535 represents a novel variant of the OB-fold and is likely to be a DNA-binding lipoprotein. KPN03535 (gi|152972051) is a putative lipoprotein of unknown function that is secreted by Klebsiella pneumoniae MGH 78578. The crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the OB-fold and structurally similar to the bacterial Cpx-pathway protein NlpE, single-stranded DNA-binding (SSB) proteins and toxins. K. pneumoniae MGH 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pathogen that is linked to about 8% of all hospital-acquired infections in the USA. This structure provides the foundation for further investigations into this divergent member of the OB-fold family

  5. RNA folding: structure prediction, folding kinetics and ion electrostatics.

    Science.gov (United States)

    Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

    2015-01-01

    Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

  6. Fracture patterns in the Zagros fold-and-thrust belt, Kurdistan Region of Iraq

    Science.gov (United States)

    Reif, Daniel; Decker, Kurt; Grasemann, Bernhard; Peresson, Herwig

    2012-11-01

    Fracture data have been collected in the Kurdistan Region of Iraq, which is a poorly accessible and unexplored area of the Zagros. Pre to early folding NE-SW striking extensional fractures and NW-SE striking contractive elements represent the older set affecting the exposed multilayer of the area. These latter structures are early syn-folding and followed by folding-related mesostructural assemblages, which include elements striking parallel to the axial trend of major folds (longitudinal fractures). Bedding perpendicular joints and veins, and extensional faults belonging to this second fracture set are located in the outer arc of exposed anticlines, whilst longitudinal reverse faults locate in the inner arcs. Consistently, these elements are associated with syn-folding tangential longitudinal strain. The younger two sets are related to E-W extension and NNE-SSW to N-S shortening, frequently displaying reactivation of the older sets. The last shortening event, which is described along the entire Zagros Belt, probably relates with the onset of N-S compression induced by the northward movement of the Arabian plate relative to the Eurasian Plate. In comparison between the inferred palaeostrain directions and the kinematics of recent GPS measurements, we conclude that the N-S compression and the partitioning into NW-SE trending folds and NW to N trending strike-slip faults likely remained unchanged throughout the Neogene tectonic history of the investigated area.

  7. Asymmetric hindwing foldings in rove beetles.

    Science.gov (United States)

    Saito, Kazuya; Yamamoto, Shuhei; Maruyama, Munetoshi; Okabe, Yoji

    2014-11-18

    Foldable wings of insects are the ultimate deployable structures and have attracted the interest of aerospace engineering scientists as well as entomologists. Rove beetles are known to fold their wings in the most sophisticated ways that have right-left asymmetric patterns. However, the specific folding process and the reason for this asymmetry remain unclear. This study reveals how these asymmetric patterns emerge as a result of the folding process of rove beetles. A high-speed camera was used to reveal the details of the wing-folding movement. The results show that these characteristic asymmetrical patterns emerge as a result of simultaneous folding of overlapped wings. The revealed folding mechanisms can achieve not only highly compact wing storage but also immediate deployment. In addition, the right and left crease patterns are interchangeable, and thus each wing internalizes two crease patterns and can be folded in two different ways. This two-way folding gives freedom of choice for the folding direction to a rove beetle. The use of asymmetric patterns and the capability of two-way folding are unique features not found in artificial structures. These features have great potential to extend the design possibilities for all deployable structures, from space structures to articles of daily use.

  8. Functional results after external vocal fold medialization thyroplasty with the titanium vocal fold medialization implant.

    Science.gov (United States)

    Schneider, Berit; Denk, Doris-Maria; Bigenzahn, Wolfgang

    2003-04-01

    A persistent insufficiency of glottal closure is mostly a consequence of a unilateral vocal fold movement impairment. It can also be caused by vocal fold atrophy or scarring processes with regular bilateral respiratory vocal fold function. Because of consequential voice, breathing, and swallowing impairments, a functional surgical treatment is required. The goal of the study was to outline the functional results after medialization thyroplasty with the titanium vocal fold medialization implant according to Friedrich. In the period of 1999 to 2001, an external vocal fold medialization using the titanium implant was performed on 28 patients (12 women and 16 men). The patients were in the age range of 19 to 84 years. Twenty-two patients had a paralysis of the left-side vocal fold, and six patients, of the right-side vocal fold. Detailed functional examinations were executed on all patients before and after the surgery: perceptive voice sound analysis according to the "roughness, breathiness, and hoarseness" method, judgment of the s/z ratio and voice dysfunction index, voice range profile measurements, videostroboscopy, and pulmonary function tests. In case of dysphagia/aspiration, videofluoroscopy of swallowing was also performed. The respective data were statistically analyzed (paired t test, Wilcoxon-test). All patients reported on improvement of voice, swallowing, and breathing functions postoperatively. Videostroboscopy revealed an almost complete glottal closure after surgery in all of the patients. All voice-related parameters showed a significant improvement. An increase of the laryngeal resistance by the medialization procedure could be excluded by analysis of the pulmonary function test. The results confirm the external medialization of the vocal folds as an adequate method in the therapy of voice, swallowing, and breathing impairment attributable to an insufficient glottal closure. The titanium implant offers, apart from good tissue tolerability, the

  9. CASP10-BCL::Fold efficiently samples topologies of large proteins.

    Science.gov (United States)

    Heinze, Sten; Putnam, Daniel K; Fischer, Axel W; Kohlmann, Tim; Weiner, Brian E; Meiler, Jens

    2015-03-01

    During CASP10 in summer 2012, we tested BCL::Fold for prediction of free modeling (FM) and template-based modeling (TBM) targets. BCL::Fold assembles the tertiary structure of a protein from predicted secondary structure elements (SSEs) omitting more flexible loop regions early on. This approach enables the sampling of conformational space for larger proteins with more complex topologies. In preparation of CASP11, we analyzed the quality of CASP10 models throughout the prediction pipeline to understand BCL::Fold's ability to sample the native topology, identify native-like models by scoring and/or clustering approaches, and our ability to add loop regions and side chains to initial SSE-only models. The standout observation is that BCL::Fold sampled topologies with a GDT_TS score > 33% for 12 of 18 and with a topology score > 0.8 for 11 of 18 test cases de novo. Despite the sampling success of BCL::Fold, significant challenges still exist in clustering and loop generation stages of the pipeline. The clustering approach employed for model selection often failed to identify the most native-like assembly of SSEs for further refinement and submission. It was also observed that for some β-strand proteins model refinement failed as β-strands were not properly aligned to form hydrogen bonds removing otherwise accurate models from the pool. Further, BCL::Fold samples frequently non-natural topologies that require loop regions to pass through the center of the protein. © 2015 Wiley Periodicals, Inc.

  10. Interaction of the Zagros Fold-Thrust Belt and the Arabian-type, deep-seated folds in the Abadan Plain and the Dezful Embayment, SW Iran

    Energy Technology Data Exchange (ETDEWEB)

    Fard, Iraj Abdollahie [National Iranian Oil Co., Exploration Directorate, Tehran (Iran); Braathen, Alvar [Bergen Univ., Centre for Integrated Petroleum Research, Bergen (Norway); Mokhtari, Mohamad [International Institute of Earthquake Engineering and Seismology, Tehran (Iran); Alavi, Seyed Ahmad [Shahid Beheshti Univ., Earth Sciences Faculty, Tehran (Iran)

    2006-07-01

    The Dezful Embayment and Abadan Plain (SW Iran) contain major parts of the remaining Iranian oil reserves. These oil provinces are characterized by two types of structural closure: very gentle N-S- to NE-SW-trending basement-cored anticlines (Arabian-type highs) in the SE; and open to tight, NW-SE-trending thrust-related folds in the NE (Zagros Fold-Thrust Belt; ZFTB). Most deep-seated anticlines are upright and symmetrical in Cretaceous and older units. In some cases they reveal steep faults in their core which, in the light of regional observations, suggest that the basement is involved in the faulting. Untested plays around these anticlines include reefal build-ups, debris flows, truncated sedimentary sections and onlapping clastic units. The ZFTB shows a classic structural style, with overall shortening reflected in thrust displacement declining from the Dezful Embayment towards the frontal zone in the Abadan Plain. The Early Cambrian Hormuz Salt represents the fundamental sole for the fold-thrust belt and locates major fault-propagation folds in the southwestern Dezful Embayment. These folds represent the main petroleum target of the area. Another important unit is the Mid-Miocene Gachsaran Formation. This detachment reveals both in-sequence and out-of-sequence thrusting. Interaction of deep-seated anticlines and fold-thrust structures results in thrust imbrications and formation of duplexes within the Gachsaran Formation when thrusts abut deep-seated anticlines. Above the crest of the anticlines, thrusts are forced up-section into syn-tectonic deposits, whereas the forelimb reveals out-of-the-syncline thrusts. Several petroleum plays are identified in such zones of structural interaction, including anticlines above buttress-related duplexes, out-of-sequence imbricate thrust fans with associated folds above major anticlines, truncation of footwall layers below potentially sealing thrusts, and sub-thrust anticlines. (Author)

  11. A Butterfly in the Making: Revealing the Near-Infrared Structure of Hubble 12

    Science.gov (United States)

    Hora, Joseph L.; Latter, William B.

    1996-01-01

    We present deep narrowband near-IR images and moderate resolution spectra of the young planetary nebula Hubble 12. These data are the first to show clearly the complex structure for this important planetary nebula. Images were obtained at lambda = 2.12, 2.16, and 2.26 micron. The lambda = 2.12 Am image reveals the bipolar nature of the nebula, as well as complex structure near the central star in the equatorial region. The images show an elliptical region of emission, which may indicate a ring or a cylindrical source structure. This structure is possibly related to the mechanism that is producing the bipolar flow. The spectra show the nature of several distinct components. The central object is dominated by recombination lines of H I and He I. The core is not a significant source of molecular hydrogen emission. The east position in the equatorial region is rich in lines of ultraviolet-excited fluorescent H2. A spectrum of part of the central region shows strong [Fe II] emission, which might indicate the presence of shocks.

  12. Mechanical versus kinematical shortening reconstructions of the Zagros High Folded Zone (Kurdistan region of Iraq)

    Science.gov (United States)

    Frehner, Marcel; Reif, Daniel; Grasemann, Bernhard

    2012-06-01

    This paper compares kinematical and mechanical techniques for the palinspastic reconstruction of folded cross sections in collision orogens. The studied area and the reconstructed NE-SW trending, 55.5 km long cross section is located in the High Folded Zone of the Zagros fold-and-thrust belt in the Kurdistan region of Iraq. The present-day geometry of the cross section has been constructed from field as well as remote sensing data. In a first step, the structures and the stratigraphy are simplified and summarized in eight units trying to identify the main geometric and mechanical parameters. In a second step, the shortening is kinematically estimated using the dip domain method to 11%-15%. Then the same cross section is used in a numerical finite element model to perform dynamical unfolding simulations taking various rheological parameters into account. The main factor allowing for an efficient dynamic unfolding is the presence of interfacial slip conditions between the mechanically strong units. Other factors, such as Newtonian versus power law viscous rheology or the presence of a basement, affect the numerical simulations much less strongly. If interfacial slip is accounted for, fold amplitudes are reduced efficiently during the dynamical unfolding simulations, while welded layer interfaces lead to unrealistic shortening estimates. It is suggested that interfacial slip and decoupling of the deformation along detachment horizons is an important mechanical parameter that controlled the folding processes in the Zagros High Folded Zone.

  13. Complex fold and thrust belt structural styles: Examples from the Greater Juha area of the Papuan Fold and Thrust Belt, Papua New Guinea

    Science.gov (United States)

    Mahoney, Luke; Hill, Kevin; McLaren, Sandra; Hanani, Amanda

    2017-07-01

    The remote and inhospitable Papuan Fold Belt in Papua New Guinea is one of the youngest yet least well-documented fold and thrust belts on Earth. Within the frontal Greater Juha area we have carried out >100 km of geological traverses and associated analyses that have added significantly to the contemporary geological and geophysical dataset. Our structural analysis provides evidence of major inversion, detachment and triangle zone faults within the uplifted Eastern Muller Ranges. We have used the dataset to develop a quasi-3D model for the Greater Juha area, with associated cross-sections revealing that the exposed Cenozoic Darai Limestone is well-constrained with very low shortening of 12.6-21.4% yet structures are elevated up to 7 km above regional. We suggest the inversion of pre-existing rift architecture is the primary influence on the evolution of the area and that structures link to the surface via triangle zones and detachment faults within the incompetent Mesozoic passive-margin sedimentary sequence underlying competent Darai Limestone. Arc-normal oriented structures, dominantly oblique dextral, up-to-the-southeast, are pervasive across a range of scales and are here interpreted to relate at depth to weakened pre-existing basement cross-structures. It is proposed that Palaeozoic basement fabric controlled the structural framework of the basin during Early Mesozoic rifting forming regional-scale accommodation zones and related local-scale transfer structures that are now expressed as regional-scale arc-normal lineaments and local-scale arc-normal structures, respectively. Transfer structures, including complexly breached relay ramps, utilise northeast-southwest striking weaknesses associated with the basement fabric, as a mechanism for accommodating displacement along major northwest-southeast striking normal faults. These structures have subsequently been inverted to form arc-normal oriented zones of tear faulting that accommodate laterally variable

  14. A low threshold nanocavity in a two-dimensional 12-fold photonic quasicrystal

    Science.gov (United States)

    Ren, Jie; Sun, XiaoHong; Wang, Shuai

    2018-05-01

    In this article, a low threshold nanocavity is built and investigated in a two-dimensional 12-fold holographic photonic quasicrystal (PQC). The cavity is formed by using the method of multi-beam common-path interference. By finely adjusting the structure parameters of the cavity, the Q factor and the mode volume are optimized, which are two keys to low-threshold on the basis of Purcell effect. Finally, an optimal cavity is obtained with Q value of 6023 and mode volume of 1.24 ×10-12cm3 . On the other hand, by Fourier Transformation of the electric field components in the cavity, the in-plane wave vectors are calculated and fitted to evaluate the cavity performance. The performance analysis of the cavity further proves the effectiveness of the optimization process. This has a guiding significance for the research of low threshold nano-laser.

  15. Transpressional folding and associated cross-fold jointing controlling the geometry of post-orogenic vein-type W-Sn mineralization: examples from Minas da Panasqueira, Portugal

    Science.gov (United States)

    Jacques, Dominique; Vieira, Romeu; Muchez, Philippe; Sintubin, Manuel

    2018-02-01

    The world-class W-Sn Panasqueira deposit consists of an extensive, subhorizontal vein swarm, peripheral to a late-orogenic greisen cupola. The vein swarm consists of hundreds of co-planar quartz veins that are overlapping and connected laterally over large distances. Various segmentation structures, a local zigzag geometry, and the occurrence of straight propagation paths indicate that they exploited a regional joint system. A detailed orientation analysis of the systematic joints reveals a geometrical relationship with the subvertical F2 fold generation, reflecting late-Variscan transpression. The joints are consistently orthogonal to the steeply plunging S0-S2 intersection lineation, both on the regional and the outcrop scale, and are thus defined as cross-fold or ac-joints. The joint system developed during the waning stages of the Variscan orogeny, when already uplifted to an upper-crustal level. Veining reactivated these cross-fold joints under the conditions of hydraulic overpressures and low differential stress. The consistent subperpendicular orientation of the veins relative to the non-cylindrical F2 hinge lines, also when having an inclined attitude, demonstrates that veining did not occur during far-field horizontal compression. Vein orientation is determined by local stress states variable on a meter-scale but with the minimum principal stress consistently subparallel to fold hinge lines. The conspicuous subhorizontal attitude of the Panasqueira vein swarm is thus dictated by the geometry of late-orogenic folds, which developed synchronous with oroclinal buckling of the Ibero-Armorican arc.

  16. Ectasias and varices of the vocal fold: clearing the striking zone.

    Science.gov (United States)

    Hochman, I; Sataloff, R T; Hillman, R E; Zeitels, S M

    1999-01-01

    Vascular malformations such as ectasias and varices (Es and Vs) are frequently encountered in patients who present with recurrent vocal fold hemorrhage and/or other traumatic vocal fold lesions. This study examined Es and Vs with regard to their anatomic presentation, phonomicrosurgical management, and treatment outcome. Forty-two patients (39 of them singers) were treated for a total of 87 Es and Vs: 67 of 87 (77%) were on the superior surface of the vocal fold and 20 of 87 (23%) were on the medial surface of the vocal fold. Eighty-three percent were located in the middle musculomembranous region (the striking zone), where the greatest aerodynamically induced shearing stresses occur during phonation. Treatment was performed with carbon dioxide laser cauterization (13 patients), or a new technique utilizing cold instrument excision by means of epithelial cordotomies (23 patients), while a combined approach was employed in 6 patients. Comparisons of preoperative and postoperative stroboscopy revealed improvement or no significant change in all patients in whom the cold instrument technique was used, and increased epithelial stiffness was noted in 4 of 19 patients in whom the carbon dioxide laser was used. Clearing the striking zone appears to have halted further hemorrhages by removing the the fragile Es and Vs from this injury-prone region of the vocal fold. Interpretations of stroboscopic examinations were directed at providing new insights into the biomechanical forces of vocal fold vibration that probably contribute to the genesis of Es and Vs in the vocal folds.

  17. Characterization of fold defects in AZ91D and AE42 magnesium alloy permanent mold castings

    International Nuclear Information System (INIS)

    Bichler, L.; Ravindran, C.

    2010-01-01

    Casting premium-quality magnesium alloy components for aerospace and automotive applications poses unique challenges. Magnesium alloys are known to freeze rapidly prior to filling a casting cavity, resulting in misruns and cold shuts. In addition, melt oxidation, solute segregation and turbulent metal flow during casting contribute to the formation of fold defects. In this research, formation of fold defects in AZ91D and AE42 magnesium alloys cast via the permanent mold casting process was investigated. Computer simulations of the casting process predicted the development of a turbulent metal flow in a critical casting region with abrupt geometrical transitions. SEM and light optical microscopy examinations revealed the presence of folds in this region for both alloys. However, each alloy exhibited a unique mechanism responsible for fold formation. In the AZ91D alloy, melt oxidation and velocity gradients in the critical casting region prevented fusion of merging metal front streams. In the AE42 alloy, limited solubility of rare-earth intermetallic compounds in the α-Mg phase resulted in segregation of Al 2 RE particles at the leading edge of a metal front and created microstructural inhomogeneity across the fold.

  18. Structures of the first representatives of Pfam family PF06684 (DUF1185) reveal a novel variant of the Bacillus chorismate mutase fold and suggest a role in amino-acid metabolism

    International Nuclear Information System (INIS)

    Bakolitsa, Constantina; Kumar, Abhinav; Jin, Kevin K.; McMullan, Daniel; Krishna, S. Sri; Miller, Mitchell D.; Abdubek, Polat; Acosta, Claire; Astakhova, Tamara; Axelrod, Herbert L.; Burra, Prasad; Carlton, Dennis; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Elias, Ylva; Ellrott, Kyle; Ernst, Dustin; Farr, Carol L.; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Grzechnik, Slawomir K.; Han, Gye Won; Jaroszewski, Lukasz; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Marciano, David; Morse, Andrew T.; Murphy, Kevin D.; Nigoghossian, Edward; Nopakun, Amanda; Okach, Linda; Paulsen, Jessica; Puckett, Christina; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Trout, Christina V.; Bedem, Henry van den; Weekes, Dana; White, Aprilfawn; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-Andre; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    Structures of the first representatives of PF06684 (DUF1185) reveal a Bacillus chorismate mutase-like fold with a potential role in amino-acid synthesis. The crystal structures of BB2672 and SPO0826 were determined to resolutions of 1.7 and 2.1 Å by single-wavelength anomalous dispersion and multiple-wavelength anomalous dispersion, respectively, using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). These proteins are the first structural representatives of the PF06684 (DUF1185) Pfam family. Structural analysis revealed that both structures adopt a variant of the Bacillus chorismate mutase fold (BCM). The biological unit of both proteins is a hexamer and analysis of homologs indicates that the oligomer interface residues are highly conserved. The conformation of the critical regions for oligomerization appears to be dependent on pH or salt concentration, suggesting that this protein might be subject to environmental regulation. Structural similarities to BCM and genome-context analysis suggest a function in amino-acid synthesis

  19. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations.

    Science.gov (United States)

    Atkinson, Holly J; Babbitt, Patricia C

    2009-10-01

    The group of proteins that contain a thioredoxin (Trx) fold is huge and diverse. Assessment of the variation in catalytic machinery of Trx fold proteins is essential in providing a foundation for understanding their functional diversity and predicting the function of the many uncharacterized members of the class. The proteins of the Trx fold class retain common features-including variations on a dithiol CxxC active site motif-that lead to delivery of function. We use protein similarity networks to guide an analysis of how structural and sequence motifs track with catalytic function and taxonomic categories for 4,082 representative sequences spanning the known superfamilies of the Trx fold. Domain structure in the fold class is varied and modular, with 2.8% of sequences containing more than one Trx fold domain. Most member proteins are bacterial. The fold class exhibits many modifications to the CxxC active site motif-only 56.8% of proteins have both cysteines, and no functional groupings have absolute conservation of the expected catalytic motif. Only a small fraction of Trx fold sequences have been functionally characterized. This work provides a global view of the complex distribution of domains and catalytic machinery throughout the fold class, showing that each superfamily contains remnants of the CxxC active site. The unifying context provided by this work can guide the comparison of members of different Trx fold superfamilies to gain insight about their structure-function relationships, illustrated here with the thioredoxins and peroxiredoxins.

  20. Evolution of regional stress state based on faulting and folding near the pit river, Shasta county, California

    Science.gov (United States)

    Austin, Lauren Jean

    We investigate the evolution of the regional stress state near the Pit River, northern California, in order to understand the faulting style in a tectonic transition zone and to inform the hazard analysis of Fault 3432 near the Pit 3 Dam. By analyzing faults and folds preserved in and adjacent to a diatomite mine north of the Pit River, we have determined principal stress directions preserved during the past million years. We find that the stress state has evolved from predominantly normal to strike slip and most recently to reverse, which is consistent with regional structures such as the extensional Hat Creek Fault to the south and the compressional folding of Mushroom Rock to the north. South of the Pit River, we still observe normal and strike slip faults, suggesting that changes in stress state are moving from north to south through time.

  1. Non-cylindrical fold growth in the Zagros fold and thrust belt (Kurdistan, NE-Iraq)

    Science.gov (United States)

    Bartl, Nikolaus; Bretis, Bernhard; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros mountains extends over 1800 km from Kurdistan in N-Iraq to the Strait of Hormuz in Iran and is one of the world most promising regions for the future hydrocarbon exploration. The Zagros Mountains started to form as a result of the collision between the Eurasian and Arabian Plates, whose convergence began in the Late Cretaceous as part of the Alpine-Himalayan orogenic system. Geodetic and seismological data document that both plates are still converging and that the fold and thrust belt of the Zagros is actively growing. Extensive hydrocarbon exploration mainly focuses on the antiforms of this fold and thrust belt and therefore the growth history of the folds is of great importance. This work investigates by means of structural field work and quantitative geomorphological techniques the progressive fold growth of the Permam, Bana Bawi- and Safeen- Anticlines located in the NE of the city of Erbil in the Kurdistan region of Northern Iraq. This part of the Zagros fold and thrust belt belongs to the so-called Simply Folded Belt, which is dominated by gentle to open folding. Faults or fault related folds have only minor importance. The mechanical anisotropy of the formations consisting of a succession of relatively competent (massive dolomite and limestone) and incompetent (claystone and siltstone) sediments essentially controls the deformation pattern with open to gentle parallel folding of the competent layers and flexural flow folding of the incompetent layers. The characteristic wavelength of the fold trains is around 10 km. Due to faster erosion of the softer rock layers in the folded sequence, the more competent lithologies form sharp ridges with steeply sloping sides along the eroded flanks of the anticlines. Using an ASTER digital elevation model in combination with geological field data we quantified 250 drainage basins along the different limbs of the subcylindrical Permam, Bana Bawi- and Safeen- Anticlines. Geomorphological indices of the drainage

  2. An atlas of the thioredoxin fold class reveals the complexity of function-enabling adaptations.

    Directory of Open Access Journals (Sweden)

    Holly J Atkinson

    2009-10-01

    Full Text Available The group of proteins that contain a thioredoxin (Trx fold is huge and diverse. Assessment of the variation in catalytic machinery of Trx fold proteins is essential in providing a foundation for understanding their functional diversity and predicting the function of the many uncharacterized members of the class. The proteins of the Trx fold class retain common features-including variations on a dithiol CxxC active site motif-that lead to delivery of function. We use protein similarity networks to guide an analysis of how structural and sequence motifs track with catalytic function and taxonomic categories for 4,082 representative sequences spanning the known superfamilies of the Trx fold. Domain structure in the fold class is varied and modular, with 2.8% of sequences containing more than one Trx fold domain. Most member proteins are bacterial. The fold class exhibits many modifications to the CxxC active site motif-only 56.8% of proteins have both cysteines, and no functional groupings have absolute conservation of the expected catalytic motif. Only a small fraction of Trx fold sequences have been functionally characterized. This work provides a global view of the complex distribution of domains and catalytic machinery throughout the fold class, showing that each superfamily contains remnants of the CxxC active site. The unifying context provided by this work can guide the comparison of members of different Trx fold superfamilies to gain insight about their structure-function relationships, illustrated here with the thioredoxins and peroxiredoxins.

  3. Crystal structure of CobK reveals strand-swapping between Rossmann-fold domains and molecular basis of the reduced precorrin product trap.

    Science.gov (United States)

    Gu, Shuang; Sushko, Oleksandr; Deery, Evelyne; Warren, Martin J; Pickersgill, Richard W

    2015-11-30

    CobK catalyzes the essential reduction of the precorrin ring in the cobalamin biosynthetic pathway. The crystal structure of CobK reveals that the enzyme, despite not having the signature sequence, comprises two Rossmann fold domains which bind coenzyme and substrate respectively. The two parallel β-sheets have swapped their last β-strands giving a novel sheet topology which is an interesting variation on the Rossmann-fold. The trapped ternary complex with coenzyme and product reveals five conserved basic residues that bind the carboxylates of the tetrapyrrole tightly anchoring the product. A loop, disordered in both the apoenzyme and holoenzyme structures, closes around the product further tightening binding. The structure is consistent with a mechanism involving protonation of C18 and pro-R hydride transfer from NADPH to C19 of precorrin-6A and reveals the interactions responsible for the specificity of CobK. The almost complete burial of the reduced precorrin product suggests a remarkable form of metabolite channeling where the next enzyme in the biosynthetic pathway triggers product release.

  4. Dermofat graft in deep nasolabial fold and facial rhytidectomy.

    Science.gov (United States)

    Hwang, Kun; Han, Jin Yi; Kim, Dae Joong

    2003-01-01

    Fat and dermis or the combined tissues are used commonly in augmentation of the nasolabial fold. Guyuron obtained the dermofat graft from either the suprapubic or the groin region. The thickness of the preauricular skin was measured in seven Korean cadavers, five male and two female. We used the dermofat graft out of the preauricular skin remnant after facial rhytidectomy to augment the deep nasolabial fold in a patient. The average thickness of the epidermis was 56 +/- 12 microm, the dermis was 1820 +/- 265 microm thick, and the subcutaneous tissue was 4783 +/- 137 microm. More dense connective tissues, such as SMAS, are seen in the preauricular skin. The dermofat graft was easily obtained and prepared from the leftover preauricular skin after dissection of the lax skin in face lifting. This technique could be employed effectively and successfully to alleviate a deep nasolabial fold and concomitant facial rhytidectomy in an Asian with a thick preauricular skin.

  5. Cenozoic structural evolution, thermal history, and erosion of the Ukrainian Carpathians fold-thrust belt

    Science.gov (United States)

    Nakapelyukh, Mykhaylo; Bubniak, Ihor; Bubniak, Andriy; Jonckheere, Raymond; Ratschbacher, Lothar

    2018-01-01

    The Carpathians are part of the Alpine-Carpathian-Dinaridic orogen surrounding the Pannonian basin. Their Ukrainian part constitutes an ancient subduction-accretion complex that evolved into a foreland fold-thrust belt with a shortening history that was perpendicular to the orogenic strike. Herein, we constrain the evolution of the Ukrainian part of the Carpathian fold-thrust belt by apatite fission-track dating of sedimentary and volcanic samples and cross-section balancing and restoration. The apatite fission-track ages are uniform in the inner―southwestern part of the fold-thrust belt, implying post-shortening erosion since 12-10 Ma. The ages in the leading and trailing edges record provenance, i.e., sources in the Trans-European suture zone and the Inner Carpathians, respectively, and show that these parts of the fold-thrust were not heated to more than 100 °C. Syn-orogenic strata show sediment recycling: in the interior of the fold-thrust belt―the most thickened and most deeply eroded nappes―the apatite ages were reset, eroded, and redeposited in the syn-orogenic strata closer to the fore- and hinterland; the lag times are only a few million years. Two balanced cross sections, one constructed for this study and based on field and subsurface data, reveal an architecture characterized by nappe stacks separated by high-displacement thrusts; they record 340-390 km shortening. A kinematic forward model highlights the fold-thrust belt evolution from the pre-contractional configuration over the intermediate geometries during folding and thrusting and the post-shortening, erosional-unloading configuration at 12-10 Ma to the present-day geometry. Average shortening rates between 32-20 Ma and 20-12 Ma amounted to 13 and 21 km/Ma, respectively, implying a two-phased deformation of the Ukrainian fold-thrust belt.

  6. Process of tight junction recovery in the injured vocal fold epithelium: Morphological and paracellular permeability analysis.

    Science.gov (United States)

    Suzuki, Ryo; Katsuno, Tatsuya; Kishimoto, Yo; Nakamura, Ryosuke; Mizuta, Masanobu; Suehiro, Atsushi; Yamashita, Masaru; Nakamura, Tatsuo; Tateya, Ichiro; Omori, Koichi

    2018-04-01

    The vocal fold epithelium that includes tight junction (TJ)-based barrier function protects underlying connective tissues from external insults. TJs play an important role to control paracellular permeability of not only solutes but also ions, and preserve the vocal fold homeostasis. However, the distribution of TJs and paracellular diffusion barrier across the entire vocal fold epithelium are still unknown. The aim of this study was to identify the distribution of TJs in the vocal fold epithelium and to characterize the recovery process of TJ-based paracellular diffusion barrier in a rat model of vocal fold injury. Animal experiments with controls. Normal and vocal fold-injured rats were used. Larynges were harvested for immunohistochemical examination of TJ proteins. For functional analysis, a tracer permeability assay was performed using EZ-Link Sulfo-NHS-LC-Biotin. TJ proteins occludin and zonula occludens 1 signals were localized to the junctional regions of the most luminal cell layers of the vocal fold epithelium. The injured region had been recovered with epithelium at 5 days postinjury, but the paracellular diffusion barrier assays revealed that biotinylation reagents diffused into the lamina propria at 5 days postinjury, and were blocked at the epithelium at 14 and 28 days postinjury. It was strongly suggested that TJs in the vocal fold epithelium exist at the junctional regions of the first layer of stratified squamous epithelium. TJ-based paracellular diffusion barrier following vocal fold injury is recovered by 14 days postinjury, and this period corresponds with the time course of structural changes in the regenerating epithelium layer. NA. Laryngoscope, 128:E150-E156, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  7. Vocal Fold Vibratory Changes Following Surgical Intervention.

    Science.gov (United States)

    Chen, Wenli; Woo, Peak; Murry, Thomas

    2016-03-01

    High-speed videoendoscopy (HSV) captures direct cycle-to-cycle visualization of vocal fold movement in real time. This ultrafast recording rate is capable of visualizing the vibratory motion of the vocal folds in severely disordered phonation and provides a direct method for examining vibratory changes after vocal fold surgery. The purpose of this study was to examine the vibratory motion before and after surgical intervention. HSV was captured from two subjects with identifiable midvocal fold benign lesions and six subjects with highly aperiodic vocal fold vibration before and after phonosurgery. Digital kymography (DKG) was used to extract high-speed kymographic vocal fold images sampled at the midmembranous, anterior 1/3, and posterior 1/3 region. Spectral analysis was subsequently applied to the DKG to quantify the cycle-to-cycle movements of the left and the right vocal fold, expressed as a spectrum. Before intervention, the vibratory spectrum consisted of decreased and flat-like spectral peaks with robust power asymmetry. After intervention, increases in spectral power and decreases in power symmetry were noted. Spectral power increases were most remarkable in the midmembranous region of the vocal fold. Surgical modification resulted in improved lateral excursion of the vocal folds, vibratory function, and perceptual measures of Voice Handicap Index-10. These changes in vibratory behavior trended toward normal vocal fold vibration. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  8. Deformation and kinematics of the central Kirthar Fold Belt, Pakistan

    Science.gov (United States)

    Hinsch, Ralph; Hagedorn, Peter; Asmar, Chloé; Nasim, Muhammad; Aamir Rasheed, Muhammad; Kiely, James M.

    2017-04-01

    The Kirthar Fold Belt is part of the lateral mountain belts in Pakistan linking the Himalaya orogeny with the Makran accretionary wedge. This region is deforming very oblique/nearly parallel to the regional plate motion vector. The study area is situated between the prominent Chaman strike-slip fault in the West and the un-deformed foreland (Kirthar Foredeep/Middle Indus Basin) in the East. The Kirthar Fold Belt is subdivided into several crustal blocks/units based on structural orientation and deformation style (e.g. Kallat, Khuzdar, frontal Kirthar). This study uses newly acquired and depth-migrated 2D seismic lines, surface geology observations and Google Earth assessments to construct three balanced cross sections for the frontal part of the fold belt. Further work was done in order to insure the coherency of the built cross-sections by taking a closer look at the regional context inferred from published data, simple analogue modelling, and constructed regional sketch sections. The Khuzdar area and the frontal Kirthar Fold Belt are dominated by folding. Large thrusts with major stratigraphic repetitions are not observed. Furthermore, strike-slip faults in the Khuzdar area are scarce and not observed in the frontal Kirthar Fold Belt. The regional structural elevation rises from the foreland across the Kirthar Fold Belt towards the hinterland (Khuzdar area). These observations indicate that basement-involved deformation is present at depth. The domination of folding indicates a weak decollement below the folds (soft-linked deformation). The fold pattern in the Khuzdar area is complex, whereas the large folds of the central Kirthar Fold Belt trend SSW-NNE to N-S and are best described as large detachment folds that have been slightly uplifted by basement involved transpressive deformation underneath. Towards the foreland, the deformation is apparently more hard-linked and involves fault-propagation folding and a small triangle zone in Cretaceous sediments

  9. Engineering Aromatic-Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins.

    Science.gov (United States)

    Balakrishnan, Swati; Sarma, Siddhartha P

    2017-08-22

    Aromatic interactions are an important force in protein folding as they combine the stability of a hydrophobic interaction with the selectivity of a hydrogen bond. Much of our understanding of aromatic interactions comes from "bioinformatics" based analyses of protein structures and from the contribution of these interactions to stabilizing secondary structure motifs in model peptides. In this study, the structural consequences of aromatic interactions on protein folding have been explored in engineered mutants of the molten globule protein apo-cytochrome b 5 . Structural changes from disorder to order due to aromatic interactions in two variants of the protein, viz., WF-cytb5 and FF-cytb5, result in significant long-range secondary and tertiary structure. The results show that 54 and 52% of the residues in WF-cytb5 and FF-cytb5, respectively, occupy ordered regions versus 26% in apo-cytochrome b 5 . The interactions between the aromatic groups are offset-stacked and edge-to-face for the Trp-Phe and Phe-Phe mutants, respectively. Urea denaturation studies indicate that both mutants have a C m higher than that of apo-cytochrome b 5 and are more stable to chaotropic agents than apo-cytochrome b 5 . The introduction of these aromatic residues also results in "trimer" interactions with existing aromatic groups, reaffirming the selectivity of the aromatic interactions. These studies provide insights into the aromatic interactions that drive disorder-to-order transitions in intrinsically disordered regions of proteins and will aid in de novo protein design beyond small peptide scaffolds.

  10. Regional magnetic anomalies, crustal strength, and the location of the northern Cordilleran fold-and-thrust belt

    Science.gov (United States)

    Saltus, R.W.; Hudson, T.L.

    2007-01-01

    The northern Cordilleran fold-and-thrust belt in Canada and Alaska is at the boundary between the broad continental margin mobile belt and the stable North American craton. The fold-and-thrust belt is marked by several significant changes in geometry: cratonward extensions in the central Yukon Territory and northeastern Alaska are separated by marginward re-entrants. These geometric features of the Cordilleran mobile belt are controlled by relations between lithospheric strength and compressional tectonic forces developed along the continental margin. Regional magnetic anomalies indicate deep thermal and compositional characteristics that contribute to variations in crustal strength. Our detailed analysis of one such anomaly, the North Slope deep magnetic high, helps to explain the geometry of the fold-and-thrust front in northern Alaska. This large magnetic anomaly is inferred to reflect voluminous mafic magmatism in an old (Devonian?) extensional domain. The presence of massive amounts of malic material in the lower crust implies geochemical depletion of the underlying upper mantle, which serves to strengthen the lithosphere against thermal erosion by upper mantle convection. We infer that deep-source magnetic highs are an important indicator of strong lower crust and upper mantle. This stronger lithosphere forms buttresses that play an important role in the structural development of the northern Cordilleran fold-and-thrust belt. ?? 2007 The Geological Society of America.

  11. Evaluation of Dying Vocal Fold Epithelial Cells by Ultrastructural Features and TUNEL Method

    Science.gov (United States)

    Novaleski, Carolyn K.; Mizuta, Masanobu; Rousseau, Bernard

    2016-01-01

    Cell death is a regulated mechanism of eliminating cells to maintain tissue homeostasis. This study described two methodological procedures for evaluating cell death in the epithelium of immobilized, approximated, and vibrated vocal folds from 12 New Zealand white breeder rabbits. The gold standard technique of transmission electron microscopy evaluated high-quality ultrastructural criteria of cell death and a common immunohistochemical marker, terminal deoxynucleotidyl transferase dUTP nick end labeling method, to confirm cell death signaling. Results revealed that ultrastructural characteristics of apoptotic cell death, specifically condensed chromatin and apoptotic bodies, were observed after vocal fold vibration and approximation. Although episodes of necrotic cell death were rare, few enlarged cell nuclei were present after vibration and approximation. The vocal fold expresses an immunohistochemical marker for apoptosis along the apical surface of the epithelium. This study provides a solid foundation for future investigations regarding the role of cell death in vocal fold health and disease. PMID:27537846

  12. A 12-Fold ThSi2 Interpenetrated Network Utilizing a Glycine-Based Pseudopeptidic Ligand

    Directory of Open Access Journals (Sweden)

    Edward Loukopoulos

    2018-01-01

    Full Text Available We report the synthesis and characterization of a 3D Cu(II coordination polymer, [Cu3(L12(H2O8]·8H2O (1, with the use of a glycine-based tripodal pseudopeptidic ligand (H3L1 = N,N′,N″-tris(carboxymethyl-1,3,5-benzenetricarboxamide or trimesoyl-tris-glycine. This compound presents the first example of a 12-fold interpenetrated ThSi2 (ths net. We attempt to justify the unique topology of 1 through a systematic comparison of the synthetic parameters in all reported structures with H3L1 and similar tripodal pseudopeptidic ligands. We additionally explore the catalytic potential of 1 in the A3 coupling reaction for the synthesis of propargylamines. The compound acts as a very good heterogeneous catalyst with yields up to 99% and loadings as low as 3 mol %.

  13. RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry.

    Science.gov (United States)

    Horesh, Yair; Wexler, Ydo; Lebenthal, Ilana; Ziv-Ukelson, Michal; Unger, Ron

    2009-03-04

    Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L free energy (MFE) for the folding of each of the L-sized substrings of S. The consecutive windows folding problem can be naively solved in O(NL3) by applying any of the classical cubic-time RNA folding algorithms to each of the N-L windows of size L. Recently an O(NL2) solution for this problem has been described. Here, we describe and implement an O(NLpsi(L)) engine for the consecutive windows folding problem, where psi(L) is shown to converge to O(1) under the assumption of a standard probabilistic polymer folding model, yielding an O(L) speedup which is experimentally confirmed. Using this tool, we note an intriguing directionality (5'-3' vs. 3'-5') folding bias, i.e. that the minimal free energy (MFE) of folding is higher in the native direction of the DNA than in the reverse direction of various genomic regions in several organisms including regions of the genomes that do not encode proteins or ncRNA. This bias largely emerges from the genomic dinucleotide bias which affects the MFE, however we see some variations in the folding bias in the different genomic regions when normalized to the dinucleotide bias. We also present results from calculating the MFE landscape of a mouse chromosome 1, characterizing the MFE of the long ncRNA molecules that reside in this chromosome. The efficient consecutive windows folding engine described in this paper allows for genome wide scans for ncRNA molecules as well as large-scale statistics. This is implemented here as a software tool, called RNAslider, and applied to the scanning of long chromosomes, leading to the observation of features that are visible only on a large scale.

  14. Synthetic oligorotaxanes exert high forces when folding under mechanical load

    Science.gov (United States)

    Sluysmans, Damien; Hubert, Sandrine; Bruns, Carson J.; Zhu, Zhixue; Stoddart, J. Fraser; Duwez, Anne-Sophie

    2018-01-01

    Folding is a ubiquitous process that nature uses to control the conformations of its molecular machines, allowing them to perform chemical and mechanical tasks. Over the years, chemists have synthesized foldamers that adopt well-defined and stable folded architectures, mimicking the control expressed by natural systems1,2. Mechanically interlocked molecules, such as rotaxanes and catenanes, are prototypical molecular machines that enable the controlled movement and positioning of their component parts3-5. Recently, combining the exquisite complexity of these two classes of molecules, donor-acceptor oligorotaxane foldamers have been synthesized, in which interactions between the mechanically interlocked component parts dictate the single-molecule assembly into a folded secondary structure6-8. Here we report on the mechanochemical properties of these molecules. We use atomic force microscopy-based single-molecule force spectroscopy to mechanically unfold oligorotaxanes, made of oligomeric dumbbells incorporating 1,5-dioxynaphthalene units encircled by cyclobis(paraquat-p-phenylene) rings. Real-time capture of fluctuations between unfolded and folded states reveals that the molecules exert forces of up to 50 pN against a mechanical load of up to 150 pN, and displays transition times of less than 10 μs. While the folding is at least as fast as that observed in proteins, it is remarkably more robust, thanks to the mechanically interlocked structure. Our results show that synthetic oligorotaxanes have the potential to exceed the performance of natural folding proteins.

  15. Silencing ß1,2-xylosyltransferase in transgenic tomato fruits reveals xylose as constitutive component of IgE binding epitopes

    Directory of Open Access Journals (Sweden)

    Kathrin Elisabeth Paulus

    2011-08-01

    Full Text Available Complex plant N-glycans containing β1,2-xylose and core α1,3-fucose are regarded as the major class of the so-called ‘carbohydrate cross-reactive determinants’ reactive with IgE antibodies in sera of many allergic patients, but their clinical relevance is still under debate. Plant glycosyltransferases, β1,2-xylosyltransferase (XylT and core α1,3-fucosyltransferase (FucT are responsible for the transfer of β1,2-linked xylose and core α1,3-linked fucose residues to N-glycans of glycoproteins, respectively. To test the clinical relevance of ß 1,2-xylose containing epitopes, expression of the tomato β1,2-xylosyltransferase was down-regulated by RNA interference (RNAi in transgenic plants. Fruits harvested from these transgenic plants were analysed for accumulation of XylT mRNA, abundance of ß1,2-xylose epitopes and their allergenic potential. Based on qPCR analysis XylT mRNA levels were reduced up to 10-fold in independent transgenic lines as compared to untransformed control, whereas no xylosylated N-glycans could be revealed by MS analysis. Immunoblotting using anti-xylose-specific IgG antibodies revealed a strong reduction of ß1,2-xylose containing epitopes. Incubating protein extracts from untransformed controls and XylT_RNAi plants with sera from tomato allergic patients showed a patient-specific reduction in IgE binding, indicating a reduced allergenic potential of XylT_RNAi tomato fruits, in vitro. To elucidate the clinical relevance of ß1,2-xylose containing complex N-glycans skin prick tests were performed demonstrating a reduced responsiveness of tomato allergic patients, in vivo. This study provides strong evidence for the clinical relevance of ß1,2-xylose containing epitopes in vivo.

  16. RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry

    Directory of Open Access Journals (Sweden)

    Ziv-Ukelson Michal

    2009-03-01

    Full Text Available Abstract Background Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L 3 by applying any of the classical cubic-time RNA folding algorithms to each of the N-L windows of size L. Recently an O(NL2 solution for this problem has been described. Results Here, we describe and implement an O(NLψ(L engine for the consecutive windows folding problem, where ψ(L is shown to converge to O(1 under the assumption of a standard probabilistic polymer folding model, yielding an O(L speedup which is experimentally confirmed. Using this tool, we note an intriguing directionality (5'-3' vs. 3'-5' folding bias, i.e. that the minimal free energy (MFE of folding is higher in the native direction of the DNA than in the reverse direction of various genomic regions in several organisms including regions of the genomes that do not encode proteins or ncRNA. This bias largely emerges from the genomic dinucleotide bias which affects the MFE, however we see some variations in the folding bias in the different genomic regions when normalized to the dinucleotide bias. We also present results from calculating the MFE landscape of a mouse chromosome 1, characterizing the MFE of the long ncRNA molecules that reside in this chromosome. Conclusion The efficient consecutive windows folding engine described in this paper allows for genome wide scans for ncRNA molecules as well as large-scale statistics. This is implemented here as a software tool, called RNAslider, and applied to the scanning of long chromosomes, leading to the observation of features that are visible only on a large scale.

  17. The effect of surface electrical stimulation on vocal fold position.

    Science.gov (United States)

    Humbert, Ianessa A; Poletto, Christopher J; Saxon, Keith G; Kearney, Pamela R; Ludlow, Christy L

    2008-01-01

    Closure of the true and false vocal folds is a normal part of airway protection during swallowing. Individuals with reduced or delayed true vocal fold closure can be at risk for aspiration and may benefit from intervention to ameliorate the problem. Surface electrical stimulation is currently used during therapy for dysphagia, despite limited knowledge of its physiological effects. Prospective single effects study. The immediate physiological effect of surface stimulation on true vocal fold angle was examined at rest in 27 healthy adults using 10 different electrode placements on the submental and neck regions. Fiberoptic nasolaryngoscopic recordings during passive inspiration were used to measure change in true vocal fold angle with stimulation. Vocal fold angles changed only to a small extent during two electrode placements (P vocal fold abduction was 2.4 degrees; while horizontal placements of electrodes in the submental region produced a mean adduction of 2.8 degrees (P = .03). Surface electrical stimulation to the submental and neck regions does not produce immediate true vocal fold adduction adequate for airway protection during swallowing, and one position may produce a slight increase in true vocal fold opening.

  18. Design and simulation of origami structures with smooth folds.

    Science.gov (United States)

    Peraza Hernandez, E A; Hartl, D J; Lagoudas, D C

    2017-04-01

    Origami has enabled new approaches to the fabrication and functionality of multiple structures. Current methods for origami design are restricted to the idealization of folds as creases of zeroth-order geometric continuity. Such an idealization is not proper for origami structures of non-negligible fold thickness or maximum curvature at the folds restricted by material limitations. For such structures, folds are not properly represented as creases but rather as bent regions of higher-order geometric continuity. Such fold regions of arbitrary order of continuity are termed as smooth folds . This paper presents a method for solving the following origami design problem: given a goal shape represented as a polygonal mesh (termed as the goal mesh ), find the geometry of a single planar sheet, its pattern of smooth folds, and the history of folding motion allowing the sheet to approximate the goal mesh. The parametrization of the planar sheet and the constraints that allow for a valid pattern of smooth folds are presented. The method is tested against various goal meshes having diverse geometries. The results show that every determined sheet approximates its corresponding goal mesh in a known folded configuration having fold angles obtained from the geometry of the goal mesh.

  19. Spherical images and inextensible curved folding

    Science.gov (United States)

    Seffen, Keith A.

    2018-02-01

    In their study, Duncan and Duncan [Proc. R. Soc. London A 383, 191 (1982), 10.1098/rspa.1982.0126] calculate the shape of an inextensible surface folded in two about a general curve. They find the analytical relationships between pairs of generators linked across the fold curve, the shape of the original path, and the fold angle variation along it. They present two special cases of generator layouts for which the fold angle is uniform or the folded curve remains planar, for simplifying practical folding in sheet-metal processes. We verify their special cases by a graphical treatment according to a method of Gauss. We replace the fold curve by a piecewise linear path, which connects vertices of intersecting pairs of hinge lines. Inspired by the d-cone analysis by Farmer and Calladine [Int. J. Mech. Sci. 47, 509 (2005), 10.1016/j.ijmecsci.2005.02.013], we construct the spherical images for developable folding of successive vertices: the operating conditions of the special cases in Duncan and Duncan are then revealed straightforwardly by the geometric relationships between the images. Our approach may be used to synthesize folding patterns for novel deployable and shape-changing surfaces without need of complex calculation.

  20. Crystal Structure of Homo Sapiens PTD012 Reveals a Zinc-Containing Hydrolase Fold

    Energy Technology Data Exchange (ETDEWEB)

    Manjasetty,B.; Bussow, K.; Fieber-ErdMan, M.; Roske, Y.; Gobam, J.; Scheich, C.; Gotz, F.; Niesen, F.; Heinemann, U.

    2006-01-01

    The human protein PTD012 is the longer product of an alternatively spliced gene and was described to be localized in the nucleus. The X-ray structure analysis at 1.7 Angstroms resolution of PTD012 through SAD phasing reveals a monomeric protein and a novel fold. The shorter splice form was also studied and appears to be unfolded and non-functional. The structure of PTD012 displays an {alpha}{beta}{beta}{alpha} four-layer topology. A metal ion residing between the central {beta}-sheets is partially coordinated by three histidine residues. X-ray absorption near-edge structure (XANES) analysis identifies the PTD012-bound ion as Zn{sup 2+}. Tetrahedral coordination of the ion is completed by the carboxylate oxygen atom of an acetate molecule taken up from the crystallization buffer. The binding of Zn{sup 2+} to PTD012 is reminiscent of zinc-containing enzymes such as carboxypeptidase, carbonic anhydrase, and {beta}-lactamase. Biochemical assays failed to demonstrate any of these enzyme activities in PTD012. However, PTD012 exhibits ester hydrolase activity on the substrate p-nitrophenyl acetate.

  1. [Clinical analysis of vocal fold firbrous mass].

    Science.gov (United States)

    Chen, Hao; Sun, Jing Wu; Wan, Guang Lun; Hu, Yan Ming

    2018-03-01

    To explore the character of laryngoscopy finding, voice, and therapy of vocal fold fibrous mass. Clinical data, morphology, voice character, surgery and pathology of 15 cases with vocal fold fibrous mass were analyzed. The morbidity of vocal fold fibrous mass might be related to overuse of voice and laryngopharyngeal reflex. Laryngoscopy revealed shuttle line appearance, smoothness and decreased mucosal wave of vocal fold. These patients were invalid for voice training and might be improved by surgery, but recovery is slow. The morbidity of vocal fold fibrous mass might be related to overuse of voice and laryngopharyngeal reflex. Conservative treatment is ineffective for this disease, and surgery might improve. Copyright© by the Editorial Department of Journal of Clinical Otorhinolaryngology Head and Neck Surgery.

  2. Dysphonia and vocal fold telangiectasia in hereditary hemorrhagic telangiectasia.

    Science.gov (United States)

    Chang, Joseph; Yung, Katherine C

    2014-11-01

    This case report is the first documentation of dysphonia and vocal fold telangiectasia as a complication of hereditary hemorrhagic telangiectasia (HHT). Case report of a 40-year-old man with HHT presenting with 2 years of worsening hoarseness. Hoarseness corresponded with a period of anticoagulation. Endoscopy revealed vocal fold scarring, vocal fold telangiectasias, and plica ventricular is suggestive of previous submucosal vocal fold hemorrhage and subsequent counterproductive compensation with ventricular phonation. Hereditary hemorrhagic telangiectasia may present as dysphonia with vocal fold telangiectasias and place patients at risk of vocal fold hemorrhage. © The Author(s) 2014.

  3. Transcriptome Reveals 1400-Fold Upregulation of APOA4-APOC3 and 1100-Fold Downregulation of GIF in the Patients with Polycythemia-Induced Gastric Injury.

    Science.gov (United States)

    Li, Kang; Gesang, Luobu; Dan, Zeng; Gusang, Lamu; Dawa, Ciren; Nie, Yuqiang

    2015-01-01

    High-altitude polycythemia (HAPC) inducing gastric mucosal lesion (GML) is still out of control and molecular mechanisms remain widely unknown. To address the issues, endoscopy and histopathological analyses were performed. Meanwhile, microarray-based transcriptome profiling was conducted in the gastric mucosa from 3 pairs of healthy subjects and HAPC-induced GML patients. HAPC caused morphological changes and pathological damages of the gastric mucosa of GML patients. A total of 10304 differentially expressed genes (DEGs) were identified, including 4941 up-regulated and 5363 down-regulated DEGs in gastric mucosa of GML patients compared with healthy controls (fold change ≥2, Ppolycythemia while polycythemia raises the risk of GML. Therefore, the present findings reveal that HAPC-induced GML inspires the protection responses by up-regulating APOA4 and APOC3, and down-regulating GIF. These results may offer the basic information for the treatment of HAPC-induced gastric lesion in the future.

  4. Structure-guided investigation of lipopolysaccharide O-antigen chain length regulators reveals regions critical for modal length control.

    Science.gov (United States)

    Kalynych, Sergei; Ruan, Xiang; Valvano, Miguel A; Cygler, Miroslaw

    2011-08-01

    The O-antigen component of the lipopolysaccharide (LPS) represents a population of polysaccharide molecules with nonrandom (modal) chain length distribution. The number of the repeat O units in each individual O-antigen polymer depends on the Wzz chain length regulator, an inner membrane protein belonging to the polysaccharide copolymerase (PCP) family. Different Wzz proteins confer vastly different ranges of modal lengths (4 to >100 repeat units), despite having remarkably conserved structural folds. The molecular mechanism responsible for the selective preference for a certain number of O units is unknown. Guided by the three-dimensional structures of PCPs, we constructed a panel of chimeric molecules containing parts of two closely related Wzz proteins from Salmonella enterica and Shigella flexneri which confer different O-antigen chain length distributions. Analysis of the O-antigen length distribution imparted by each chimera revealed the region spanning amino acids 67 to 95 (region 67 to 95), region 200 to 255, and region 269 to 274 as primarily affecting the length distribution. We also showed that there is no synergy between these regions. In particular, region 269 to 274 also influenced chain length distribution mediated by two distantly related PCPs, WzzB and FepE. Furthermore, from the 3 regions uncovered in this study, region 269 to 274 appeared to be critical for the stability of the oligomeric form of Wzz, as determined by cross-linking experiments. Together, our data suggest that chain length determination depends on regions that likely contribute to stabilize a supramolecular complex.

  5. Longitudinal development of cortical thickness, folding, and fiber density networks in the first 2 years of life.

    Science.gov (United States)

    Nie, Jingxin; Li, Gang; Wang, Li; Shi, Feng; Lin, Weili; Gilmore, John H; Shen, Dinggang

    2014-08-01

    Quantitatively characterizing the development of cortical anatomical networks during the early stage of life plays an important role in revealing the relationship between cortical structural connection and high-level functional development. The development of correlation networks of cortical-thickness, cortical folding, and fiber-density is systematically analyzed in this article to study the relationship between different anatomical properties during the first 2 years of life. Specifically, longitudinal MR images of 73 healthy subjects from birth to 2 year old are used. For each subject at each time point, its measures of cortical thickness, cortical folding, and fiber density are projected to its cortical surface that has been partitioned into 78 cortical regions. Then, the correlation matrices for cortical thickness, cortical folding, and fiber density at each time point can be constructed, respectively, by computing the inter-regional Pearson correlation coefficient (of any pair of ROIs) across all 73 subjects. Finally, the presence/absence pattern (i.e., binary pattern) of the connection network is constructed from each inter-regional correlation matrix, and its statistical and anatomical properties are adopted to analyze the longitudinal development of anatomical networks. The results show that the development of anatomical network could be characterized differently by using different anatomical properties (i.e., using cortical thickness, cortical folding, or fiber density). Copyright © 2013 Wiley Periodicals, Inc.

  6. Folded Basinal Compartments of the Southern Mongolian Borderland: A Structural Archive of the Final Consolidation of the Central Asian Orogenic Belt

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    Dickson Cunningham

    2017-01-01

    Full Text Available The Central Asian Orogenic Belt (CAOB records multiple Phanerozoic tectonic events involving consolidation of disparate terranes and cratonic blocks and subsequent reactivation of Eurasia’s continental interior. The final amalgamation of the CAOB terrane collage involved diachronous closure of the Permian-Triassic Solonker suture in northernmost China and the Jurassic Mongol-Okhotsk suture in northeast Mongolia and eastern Siberia. The distribution, style, and kinematics of deformation associated with these two terminal collision events is poorly documented in southern Mongolia and northernmost China because these regions were later tectonically overprinted by widespread Cretaceous basin and range-style crustal extension and Miocene-recent sinistral transpressional mountain building. These younger events structurally compartmentalized the crust into uplifted crystalline basement blocks and intermontane basins. Consequently, widespread Cretaceous and Late Cenozoic clastic sedimentary deposits overlie older Permian-Jurassic sedimentary rocks in most basinal areas and obscure the deformation record associated with Permian-Triassic Solonker and Jurassic Mongol-Okhotsk collisional suturing. In this report, satellite image mapping of basinal compartments that expose folded Permian-Jurassic sedimentary successions that are unconformably overlapped by Cretaceous-Quaternary clastic sediments is presented for remote and poorly studied regions of southern Mongolia and two areas of the Beishan. The largest folds are tens of kilometers in strike length, east-west trending, and reveal north-south Late Jurassic shortening (present coordinates. Late Jurassic fold vergence is dominantly northerly in the southern Gobi Altai within a regional-scale fold-and-thrust belt. Local refolding of older Permian north-south trending folds is also evident in some areas. The folds identified and mapped in this study provide new evidence for the regional distribution and

  7. Folding model analyses of 12C-12C and 16O-16O elastic scattering using the density-dependent LOCV-averaged effective interaction

    Science.gov (United States)

    Rahmat, M.; Modarres, M.

    2018-03-01

    The averaged effective two-body interaction (AEI), which can be generated through the lowest order constrained variational (LOCV) method for symmetric nuclear matter (SNM) with the input [Reid68, Ann. Phys. 50, 411 (1968), 10.1016/0003-4916(68)90126-7] nucleon-nucleon potential, is used as the effective nucleon-nucleon potential in the folding model to describe the heavy-ion (HI) elastic scattering cross sections. The elastic scattering cross sections of 12C-12C and 16O-16O systems are calculated in the above framework. The results are compared with the corresponding calculations coming from the fitting procedures with the input finite range D D M 3 Y 1 -Reid potential and the available experimental data at different incident energies. It is shown that a reasonable description of the elastic 12C-12C and 16O-16O scattering data at the low and medium energies can be obtained by using the above LOCV AEI, without any need to define a parametrized density-dependent function in the effective nucleon-nucleon potential, which is formally considered in the typical D D M 3 Y 1 -Reid interactions.

  8. Visualization of protein folding funnels in lattice models.

    Directory of Open Access Journals (Sweden)

    Antonio B Oliveira

    Full Text Available Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs. In this paper, we introduce a metric to describe the distance between any two conformations, which also allows us to go beyond the one-dimensional representation and visualize the folding funnel in 2D and 3D. In this way it is possible to assess the folding process in detail, e.g., by identifying the connectivity between conformations and establishing the paths to reach the native state, in addition to regions where trapping may occur. Unlike the disconnectivity maps method, which is based on the kinetic connections between states, our methodology is based on structural similarities inferred from the new metric. The method was developed in a 27-mer protein lattice model, folded into a 3×3×3 cube. Five sequences were studied and distinct funnels were generated in an analysis restricted to conformations from the transition-state to the native configuration. Consistent with the expected results from the energy landscape theory, folding routes can be visualized to probe different regions of the phase space, as well as determine the difficulty in folding of the distinct sequences. Changes in the landscape due to mutations were visualized, with the comparison between wild and mutated local minima in a single map, which serves to identify different trapping regions. The extension of this approach to more realistic models and its use in combination with other approaches are discussed.

  9. Vocal fold elasticity of the Rocky Mountain elk (Cervus elaphus nelsoni) – producing high fundamental frequency vocalization with a very long vocal fold

    OpenAIRE

    Riede, Tobias; Titze, Ingo R.

    2008-01-01

    The vocal folds of male Rocky Mountain elk (Cervus elaphus nelsoni) are about 3 cm long. If fundamental frequency were to be predicted by a simple vibrating string formula, as is often done for the human larynx, such long vocal folds would bear enormous stress to produce the species-specific mating call with an average fundamental frequency of 1 kHz. Predictions would be closer to 50 Hz. Vocal fold histology revealed the presence of a large vocal ligament between the vocal fold epithelium and...

  10. Molecular resonances in sub-Coulomb energy region (12C-12C, 12C-24Mg, 12C-9Be systems)

    International Nuclear Information System (INIS)

    Takimoto, Kiyohiko; Shimomura, Susumu; Tanaka, Makoto; Murakami, Tetsuya; Fukada, Mamoru; Sakaguchi, Atsushi

    1982-01-01

    Molecular resonance in sub-Coulomb energy region was studied on 12 C- 12 C, 12 C- 24 Mg and 12 C- 9 Be systems. The excitation functions and the angular distributions were measured on the reactions 12 C( 12 C, 8 Besub(g,s,)) 16 Osub(g,s,), 24 Mg( 12 C, α) 32 S and 9 Be ( 12 C, 8 Besub(g,s,)) 13 Csub(g,s,). Sub-Coulomb resonances were observed in all systems and the contribution of the 12 Csub(2nd)*(0 + , 7.65 MeV) state is proposed. (author)

  11. Quantification of Porcine Vocal Fold Geometry.

    Science.gov (United States)

    Stevens, Kimberly A; Thomson, Scott L; Jetté, Marie E; Thibeault, Susan L

    2016-07-01

    The aim of this study was to quantify porcine vocal fold medial surface geometry and three-dimensional geometric distortion induced by freezing the larynx, especially in the region of the vocal folds. The medial surface geometries of five excised porcine larynges were quantified and reported. Five porcine larynges were imaged in a micro-CT scanner, frozen, and rescanned. Segmentations and three-dimensional reconstructions were used to quantify and characterize geometric features. Comparisons were made with geometry data previously obtained using canine and human vocal folds as well as geometries of selected synthetic vocal fold models. Freezing induced an overall expansion of approximately 5% in the transverse plane and comparable levels of nonuniform distortion in sagittal and coronal planes. The medial surface of the porcine vocal folds was found to compare reasonably well with other geometries, although the compared geometries exhibited a notable discrepancy with one set of published human female vocal fold geometry. Porcine vocal folds are qualitatively geometrically similar to data available for canine and human vocal folds, as well as commonly used models. Freezing of tissue in the larynx causes distortion of around 5%. The data can provide direction in estimating uncertainty due to bulk distortion of tissue caused by freezing, as well as quantitative geometric data that can be directly used in developing vocal fold models. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  12. The Complexity of Folding Self-Folding Origami

    Science.gov (United States)

    Stern, Menachem; Pinson, Matthew B.; Murugan, Arvind

    2017-10-01

    Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of "distractor" folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal's paradox) and other NP-hard satisfiability (SAT) problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out ("folding islands"). Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  13. The role of the mesenchyme in mouse neural fold elevation. II. Patterns of hyaluronate synthesis and distribution in embryos developing in vitro

    International Nuclear Information System (INIS)

    Morris-Wiman, J.; Brinkley, L.L.

    1990-01-01

    Hyaluronate (HA) distribution patterns were examined in the cranial mesenchyme underlying the mesencephalic neural folds of mouse embryos maintained in roller tube culture. Using standard image-processing techniques, the digitized images of Alcian blue-stained or 3H-glucosamine-labeled sections digested with an enzyme specific for HA, were subtracted from adjacent, undigested sections. The resultant difference picture images (DPI) accurately depicted the distribution of stained or labeled HA within the cranial mesenchyme. 3H-glucosamine-labeled HA was distributed uniformly throughout the cranial mesenchyme as 12, 18, and 24 hr of culture. By contrast, the mesenchyme was uniformly stained with Alcian blue at 12 hr, but stain intensity decreased in the central regions of the mesenchyme at 18 and 24 hr. HA distribution patterns were also examined in the cranial mesenchyme of embryos cultured in the presence of diazo-oxo-norleucine (DON), a glutamine analogue that inhibits glycosaminoglycan and glycoprotein synthesis. In DON-treated mesenchyme, Alcian blue staining of HA was decreased from that in controls at 12, 18, and 24 hr. However, incorporation of 3H-glucosamine into HA was increased. The distribution of labeled HA within treated mesenchyme as 12, 18, and 24 hr resembled that in controls at 12 hr. These results indicate that the distribution of HA within the cranial mesenchyme of normal mouse embryos during neural fold elevation and convergence is not determined solely by regional differences in HA synthesis. We propose that HA distribution patterns result from the expansion of the HA-rich extracellular matrix of the central mesenchyme regions. This expansion may play a major role in fold elevation. These results also suggest that DON treatment reversibly inhibits HA synthesis

  14. The Complexity of Folding Self-Folding Origami

    Directory of Open Access Journals (Sweden)

    Menachem Stern

    2017-12-01

    Full Text Available Why is it difficult to refold a previously folded sheet of paper? We show that even crease patterns with only one designed folding motion inevitably contain an exponential number of “distractor” folding branches accessible from a bifurcation at the flat state. Consequently, refolding a sheet requires finding the ground state in a glassy energy landscape with an exponential number of other attractors of higher energy, much like in models of protein folding (Levinthal’s paradox and other NP-hard satisfiability (SAT problems. As in these problems, we find that refolding a sheet requires actuation at multiple carefully chosen creases. We show that seeding successful folding in this way can be understood in terms of subpatterns that fold when cut out (“folding islands”. Besides providing guidelines for the placement of active hinges in origami applications, our results point to fundamental limits on the programmability of energy landscapes in sheets.

  15. Structures of the first representatives of Pfam family PF06938 (DUF1285) reveal a new fold with repeated structural motifs and possible involvement in signal transduction

    International Nuclear Information System (INIS)

    Han, Gye Won; Bakolitsa, Constantina; Miller, Mitchell D.; Kumar, Abhinav; Carlton, Dennis; Najmanovich, Rafael J.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chen, Connie; Chiu, Hsiu-Ju; Clayton, Thomas; Das, Debanu; Deller, Marc C.; Duan, Lian; Ernst, Dustin; Feuerhelm, Julie; Grant, Joanna C.; Grzechnik, Anna; Jaroszewski, Lukasz; Jin, Kevin K.; Johnson, Hope A.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Rife, Christopher L.; Sefcovic, Natasha; Tien, Henry J.; Trame, Christine B.; Bedem, Henry van den; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The crystal structures of SPO0140 and Sbal-2486 revealed a two-domain structure that adopts a novel fold. Analysis of the interdomain cleft suggests a nucleotide-based ligand with a genome context indicating signaling as a possible role for this family. The crystal structures of SPO0140 and Sbal-2486 were determined using the semiautomated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). The structures revealed a conserved core with domain duplication and a superficial similarity of the C-terminal domain to pleckstrin homology-like folds. The conservation of the domain interface indicates a potential binding site that is likely to involve a nucleotide-based ligand, with genome-context and gene-fusion analyses additionally supporting a role for this family in signal transduction, possibly during oxidative stress

  16. Synchrotron radiation circular dichroism spectroscopy study of recombinant T β4 folding

    Science.gov (United States)

    Huang, Yung-Chin; Chu, Hsueh-Liang; Chen, Peng-Jen; Chang, Chia-Ching

    Thymosin beta 4 (T β4) is a 43-amino acid small peptide, has been demonstrated that it can promote cardiac repair, wound repair, tissue protection, and involve in the proliferation of blood cell precursor stem cells of bone marrow. Moreover, T β4 has been identified as a multifunction intrinsically disordered protein, which is lacking the stable tertiary structure. Owing to the small size and disordered character, the T β4 protein degrades rapidly and the storage condition is critical. Therefore, it is not easy to reveal its folding mechanism of native T β4. However, recombinant T β4 protein (rT β4), which fused with a 5-kDa peptide in its amino-terminal, is stable and possesses identical function of T β4. Therefore, rT β4 can be used to study its folding mechanism. By using over-critical folding process, stable folding intermediates of rT β4 can be obtained. Structure analysis of folding intermediates by synchrotron radiation circular dichroism (SRCD) and fluorescence spectroscopies indicate that rT β4 is a random coli major protein and its hydrophobic region becomes compact gradually. Moreover, the rT β4 folding is a two state transition. Thermal denaturation analysis indicates that rT β4 lacks stable tertiary structure. These results indicated that rT β4, similar to T β4, is an intrinsically disordered protein. Research is supported by MOST, Taiwan. MOST 103-2112-M-009-011-MY3. Corresponding author: Chia-Ching Chang; ccchang01@faculty.nctu.edu.tw.

  17. Reinke Edema: Watch For Vocal Fold Cysts.

    Science.gov (United States)

    Tüzüner, Arzu; Demirci, Sule; Yavanoglu, Ahmet; Kurkcuoglu, Melih; Arslan, Necmi

    2015-06-01

    Reinke edema is one of the common cause of dysphonia middle-aged population, and severe thickening of vocal folds require surgical treatment. Smoking plays a major role on etiology. Vocal fold cysts are also benign lesions and vocal trauma blamed for acquired cysts. We would like to present 3 cases with vocal fold cyst related with Reinke edema. First case had a subepidermal epidermoid cyst with Reinke edema, which could be easily observed before surgery during laryngostroboscopy. Second case had a mucous retention cyst into the edematous Reinke tissue, which was detected during surgical intervention, and third case had a epidermoid cyst that occurred 2 months after before microlaryngeal operation regarding Reinke edema reduction. These 3 cases revealed that surgical management of Reinke edema needs a careful dissection and close follow-up after surgery for presence of vocal fold cysts.

  18. A Portrait of Ribosomal DNA Contacts with Hi-C Reveals 5S and 45S rDNA Anchoring Points in the Folded Human Genome.

    Science.gov (United States)

    Yu, Shoukai; Lemos, Bernardo

    2016-12-31

    Ribosomal RNAs (rRNAs) account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, whereas the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. Portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  19. Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

    Science.gov (United States)

    Fazelinia, Hossein; Xu, Ming; Cheng, Hong; Roder, Heinrich

    2014-01-15

    Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two α-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse.

  20. BiP clustering facilitates protein folding in the endoplasmic reticulum.

    Directory of Open Access Journals (Sweden)

    Marc Griesemer

    2014-07-01

    Full Text Available The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum (ER: translocation, protein folding, and ER-associated degradation. To facilitate protein folding, a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level understanding of how multiple BiP molecules bind to nascent and unfolded proteins. Recently, experimental evidence revealed the spatial heterogeneity of BiP within the nuclear and peripheral ER of S. cerevisiae (commonly referred to as 'clusters'. Here, we developed a model to evaluate the potential advantages of accounting for multiple BiP molecules binding to peptides, while proposing that BiP's spatial heterogeneity may enhance protein folding and maturation. Scenarios were simulated to gauge the effectiveness of binding multiple chaperone molecules to peptides. Using two metrics: folding efficiency and chaperone cost, we determined that the single binding site model achieves a higher efficiency than models characterized by multiple binding sites, in the absence of cooperativity. Due to entropic pulling, however, multiple chaperones perform in concert to facilitate the resolubilization and ultimate yield of folded proteins. As a result of cooperativity, multiple binding site models used fewer BiP molecules and maintained a higher folding efficiency than the single binding site model. These insilico investigations reveal that clusters of BiP molecules bound to unfolded proteins may enhance folding efficiency through cooperative action via entropic pulling.

  1. Evaluation of the Grafted Fascia in the Vocal Fold of Dogs: A Histologic Study.

    Science.gov (United States)

    Carvalho, Eduardo G B; Pauna, Henrique F; Machado, Almiro J; Nicola, Ester M D; Altemani, Albina M A M; Crespo, Agrício N

    2017-09-01

    There is no consensus on the ideal graft for medialization surgery of the vocal folds in the literature. One of the most favorable proposals is the use of autologous fascia, which seems limited by the lack of information regarding the integration of grafted tissue. Our study aims to evaluate the degree of fully engrafted fascia integration in the vocal fold lamina propria of dogs. Fourteen adult mongrel dogs that underwent intravenous general anesthesia were selected and kept under spontaneous ventilation. A fascia lata fragment of 4 cm 2 was obtained from the right leg of each dog. The dogs underwent laryngoscopy; a 3 mm incision was made in the vocal process, next to the vestibular process, and the fascia was grafted into the right vocal fold. The left vocal fold was used as a control. The animals were divided into two groups: group A, evaluated after 2 months of the procedure, and group B, evaluated after 6 months of the procedure. Histologic analysis was made semiquantitatively regarding the presence of inflammatory reaction, fibrosis, and neovascularization. Our final studied group comprised 12 dogs. Microscopic examination of the larynx revealed the absence of any detectable inflammation in the incision site. The lamina propria of the grafted vocal fold showed identifiable compact, thick, and eosinophilic collagen bands. The surrounding tissue showed thin collagen bands with some organization, similar to the contralateral vocal fold. The grafted fascia integrates into the vocal fold lamina propria and seems not to cause inflammatory reaction response. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  2. Transiently disordered tails accelerate folding of globular proteins.

    Science.gov (United States)

    Mallik, Saurav; Ray, Tanaya; Kundu, Sudip

    2017-07-01

    Numerous biological proteins exhibit intrinsic disorder at their termini, which are associated with multifarious functional roles. Here, we show the surprising result that an increased percentage of terminal short transiently disordered regions with enhanced flexibility (TstDREF) is associated with accelerated folding rates of globular proteins. Evolutionary conservation of predicted disorder at TstDREFs and drastic alteration of folding rates upon point-mutations suggest critical regulatory role(s) of TstDREFs in shaping the folding kinetics. TstDREFs are associated with long-range intramolecular interactions and the percentage of native secondary structural elements physically contacted by TstDREFs exhibit another surprising positive correlation with folding kinetics. These results allow us to infer probable molecular mechanisms behind the TstDREF-mediated regulation of folding kinetics that challenge protein biochemists to assess by direct experimental testing. © 2017 Federation of European Biochemical Societies.

  3. 15 CFR 923.12 - Uses of regional benefit.

    Science.gov (United States)

    2010-01-01

    ... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Uses of regional benefit. 923.12 Section 923.12 Commerce and Foreign Trade Regulations Relating to Commerce and Foreign Trade (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE OCEAN AND COASTAL RESOURCE...

  4. Radiometric Dating of Folds: A new approach to determine the timing of deformation at shallow-crustal conditions, with examples from the Mexican Fold-Thrust Belt

    Science.gov (United States)

    Fitz Diaz, E.; van der Pluijm, B. A.

    2012-12-01

    We are developing a robust method to obtain absolute ages of folds that were formed at shallow crustal conditions. The method takes advantage of illite neocrystallization in folded, clay-bearing layers and the ability to obtain accurate retention and total gas ages from small size fractions using encapsulated Ar analysis, analogous to prior work on fault gouge dating. We illustrate our approach in folded Cretaceous shale-bentonitic layers that are interbedded with carbonates of the Zimapán and the Tampico-Misantla cretaceous basins in central-eastern Mexico. Basinal carbonates were buried by syntectonic turbidites and inverted during the formation of the Mexican Fold-Thrust in the Late Cretaceous. Results were obtained from four chevron folds that are representative of different stages of deformation, burial/temperature conditions and location within this thin-skinned orogenic wedge: two from the Zimapán Basin (Folds 1 and 2) in the west and two from the Tampico-Misantla Basin (Folds 3 and 4) in the east. Mineralogic compositions and variations in illite-polytypes, crystallite-size (CS) and Ar/Ar ages were obtained from size fractions in limbs and hinges of folded layers. Ar retention ages produce a folding age of ~81 Ma for Fold 1 and ~69 Ma for Fold 2, which are fully consistent with stratigraphic limits from syn-orogenic turbidities and observed overprinting events in the Mexican Fold-Thrust Belt. The total gas age of Fold 3, on the easternmost margin of the Tampico-Misantla Basin is similar to that of Fold 2, indicating that the second event is regional in scale. In addition to presenting a new, reliable method to constrain the timing of local deformation, we interpret folding and associated clay neo-mineralization in terms of the regional burial history, and localization and propagation of deformation within a heterogeneous orogenic wedge involving progressive deformation of two basins separated by a platform block.

  5. Cooperative role of calnexin and TigA in Aspergillus oryzae glycoprotein folding.

    Science.gov (United States)

    Wang, Ning; Seko, Akira; Takeda, Yoichi; Kikuma, Takashi; Ito, Yukishige

    2015-10-01

    Calnexin (CNX), known as a lectin chaperone located in the endoplasmic reticulum (ER), specifically recognizes G1M9GN2-proteins and facilitates their proper folding with the assistance of ERp57 in mammalian cells. However, it has been left unidentified how CNX works in Aspergillus oryzae, which is a filamentous fungus widely exploited in biotechnology. In this study, we found that a protein disulfide isomerase homolog TigA can bind with A. oryzae CNX (AoCNX), which was revealed to specifically recognize monoglucosylated glycans, similarly to CNX derived from other species, and accelerate the folding of G1M9GN2-ribonuclease (RNase) in vitro. For refolding experiments, a homogeneous monoglucosylated high-mannose-type glycoprotein G1M9GN2-RNase was chemoenzymatically synthesized from G1M9GN-oxazoline and GN-RNase. Denatured G1M9GN2-RNase was refolded with highest efficiency in the presence of both soluble form of AoCNX and TigA. TigA contains two thioredoxin domains with CGHC motif, mutation analysis of which revealed that the one in N-terminal regions is involved in binding to AoCNX, while the other in catalyzing protein refolding. The results suggested that in glycoprotein folding process of A. oryzae, TigA plays a similar role as ERp57 in mammalian cells, as a partner protein of AoCNX. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Folding Topology of a Short Coiled-Coil Peptide Structure Templated by an Oligonucleotide Triplex

    DEFF Research Database (Denmark)

    Lou, Chenguang; Christensen, Niels Johan; Martos Maldonado, Manuel Cristo

    2017-01-01

    by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution. The oligonucleotide domain was designed to furnish a stable parallel triplex......, small-angle X-ray scattering (SAXS), and molecular modeling. Stabilizing cooperativity was observed between the trimeric peptide and the oligonucleotide triplex domains, and the overall molecular size (ca. 12nm) in solution was revealed to be independent of concentration. The topological folding...

  7. MARATHON DESPITE UNILATERAL VOCAL FOLD PARALYSIS

    Directory of Open Access Journals (Sweden)

    Matthias Echternach

    2008-06-01

    Full Text Available The principal symptoms of unilateral vocal fold paralysis are hoarseness and difficulty in swallowing. Dyspnea is comparatively rare (Laccourreye et al., 2003. The extent to which unilateral vocal fold paralysis may lead to respiratory problems at all - in contrast to bilateral vocal fold paralysis- has not yet well been determined. On the one hand, inspiration is impaired with unilateral vocal fold paralysis; on the other hand, neither the position of the vocal fold paralysis nor the degree of breathiness correlates with respiratory parameters (Cantarella et al., 2003; 2005. The question of what respiratory stress a patient with a vocal fold paresis can endure has not yet been dealt with.A 43 year-old female patient was suffering from recurrent unspecific respiratory complaints for four months after physical activity. During training for a marathon, she experienced no difficulty in breathing. These unspecific respiratory complaints occurred only after athletic activity and persisted for hours. The patient observed neither an increased coughing nor a stridor. Her voice remained unaltered during the attacks, nor were there any signs of a symptomatic gastroesophageal reflux or infectious disease. A cardio-pulmonary and a radiological examination by means of an X-ray of the thorax also revealed no pathological phenomena. As antiallergic and antiobstructive therapy remained unsuccessful, a laryngological examination was performed in order to exclude a vocal cord dysfunction.Surprisingly enough, the laryngostroboscopy showed, as an initial description, a vocal fold paralysis of the left vocal fold in median position (Figure 1. The anamnestic background for the cause was unclear. The only clue was a thoracotomy on the left side due to a pleuritis in childhood. A subsequent laryngoscopic examination had never been performed. Good mucosa waves and amplitudes were shown bilateral with complete glottal closure. Neither in the acoustic analysis, nor in the

  8. Coarsely resolved topography along protein folding pathways

    Science.gov (United States)

    Fernández, Ariel; Kostov, Konstantin S.; Berry, R. Stephen

    2000-03-01

    The kinetic data from the coarse representation of polypeptide torsional dynamics described in the preceding paper [Fernandez and Berry, J. Chem. Phys. 112, 5212 (2000), preceding paper] is inverted by using detailed balance to obtain a topographic description of the potential-energy surface (PES) along the dominant folding pathway of the bovine pancreatic trypsin inhibitor (BPTI). The topography is represented as a sequence of minima and effective saddle points. The dominant folding pathway displays an overall monotonic decrease in energy with a large number of staircaselike steps, a clear signature of a good structure-seeker. The diversity and availability of alternative folding pathways is analyzed in terms of the Shannon entropy σ(t) associated with the time-dependent probability distribution over the kinetic ensemble of contact patterns. Several stages in the folding process are evident. Initially misfolded states form and dismantle revealing no definite pattern in the topography and exhibiting high Shannon entropy. Passage down a sequence of staircase steps then leads to the formation of a nativelike intermediate, for which σ(t) is much lower and fairly constant. Finally, the structure of the intermediate is refined to produce the native state of BPTI. We also examine how different levels of tolerance to mismatches of side chain contacts influence the folding kinetics, the topography of the dominant folding pathway, and the Shannon entropy. This analysis yields upper and lower bounds of the frustration tolerance required for the expeditious and robust folding of BPTI.

  9. Flips for 3-folds and 4-folds

    CERN Document Server

    Corti, Alessio

    2007-01-01

    This edited collection of chapters, authored by leading experts, provides a complete and essentially self-contained construction of 3-fold and 4-fold klt flips. A large part of the text is a digest of Shokurov's work in the field and a concise, complete and pedagogical proof of the existence of 3-fold flips is presented. The text includes a ten page glossary and is accessible to students and researchers in algebraic geometry.

  10. A new fold-cross metal mesh filter for suppressing side lobe leakage in terahertz region

    Science.gov (United States)

    Lu, Changgui; Qi, Zhengqing; Guo, Wengao; Cui, Yiping

    2018-04-01

    In this paper we propose a new type of fold-cross metal mesh band pass filter, which keeps diffraction side lobe far away from the main transmission peak and shows much better side lobe suppression. Both experimental and theoretical studies are made to analyze the mechanism of side lobe. Compared to the traditional cross filter, the fold-cross filter has a much lower side lobe with almost the same central frequency, bandwidth and highest transmission about 98%. Using the photolithography and electroplating techniques, we experimentally extend the distance between the main peak and diffraction side lobe to larger than 1 THz for the fold-cross filter, which is two times larger than the cross filter while maintaining the main peak transmissions of 89% at 1.25 THz for the two structures. This type of single layer substrate-free fold-cross metal structure shows better design flexibility and structure reliability with the introduction of fold arms for metal mesh band pass filters.

  11. Vascular lesions of the vocal fold.

    Science.gov (United States)

    Gökcan, Kürşat Mustafa; Dursun, Gürsel

    2009-04-01

    The aim of the study was to present symptoms, laryngological findings, clinical course, management modalities, and consequences of vascular lesions of vocal fold. This study examined 162 patients, the majority professional voice users, with vascular lesions regarding their presenting symptoms, laryngological findings, clinical courses and treatment results. The most common complaint was sudden hoarseness with hemorrhagic polyp. Microlaryngoscopic surgery was performed in 108 cases and the main indication of surgery was the presence of vocal fold mass or development of vocal polyp during clinical course. Cold microsurgery was utilized for removal of vocal fold masses and feeding vessels cauterized using low power, pulsed CO(2) laser. Acoustic analysis of patients revealed a significant improvement of jitter, shimmer and harmonics/noise ratio values after treatment. Depending on our clinical findings, we propose treatment algorithm where voice rest and behavioral therapy is the integral part and indications of surgery are individualized for each patient.

  12. In vivo measurement of vocal fold surface resistance.

    Science.gov (United States)

    Mizuta, Masanobu; Kurita, Takashi; Dillon, Neal P; Kimball, Emily E; Garrett, C Gaelyn; Sivasankar, M Preeti; Webster, Robert J; Rousseau, Bernard

    2017-10-01

    A custom-designed probe was developed to measure vocal fold surface resistance in vivo. The purpose of this study was to demonstrate proof of concept of using vocal fold surface resistance as a proxy of functional tissue integrity after acute phonotrauma using an animal model. Prospective animal study. New Zealand White breeder rabbits received 120 minutes of airflow without vocal fold approximation (control) or 120 minutes of raised intensity phonation (experimental). The probe was inserted via laryngoscope and placed on the left vocal fold under endoscopic visualization. Vocal fold surface resistance of the middle one-third of the vocal fold was measured after 0 (baseline), 60, and 120 minutes of phonation. After the phonation procedure, the larynx was harvested and prepared for transmission electron microscopy. In the control group, vocal fold surface resistance values remained stable across time points. In the experimental group, surface resistance (X% ± Y% relative to baseline) was significantly decreased after 120 minutes of raised intensity phonation. This was associated with structural changes using transmission electron microscopy, which revealed damage to the vocal fold epithelium after phonotrauma, including disruption of the epithelium and basement membrane, dilated paracellular spaces, and alterations to epithelial microprojections. In contrast, control vocal fold specimens showed well-preserved stratified squamous epithelia. These data demonstrate the feasibility of measuring vocal fold surface resistance in vivo as a means of evaluating functional vocal fold epithelial barrier integrity. Device prototypes are in development for additional testing, validation, and for clinical applications in laryngology. NA Laryngoscope, 127:E364-E370, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  13. Mapping the kinetic barriers of a Large RNA molecule's folding landscape.

    Directory of Open Access Journals (Sweden)

    Jörg C Schlatterer

    Full Text Available The folding of linear polymers into discrete three-dimensional structures is often required for biological function. The formation of long-lived intermediates is a hallmark of the folding of large RNA molecules due to the ruggedness of their energy landscapes. The precise thermodynamic nature of the barriers (whether enthalpic or entropic that leads to intermediate formation is still poorly characterized in large structured RNA molecules. A classic approach to analyzing kinetic barriers are temperature dependent studies analyzed with Eyring's transition state theory. We applied Eyring's theory to time-resolved hydroxyl radical (•OH footprinting kinetics progress curves collected at eight temperature from 21.5 °C to 51 °C to characterize the thermodynamic nature of folding intermediate formation for the Mg(2+-mediated folding of the Tetrahymena thermophila group I ribozyme. A common kinetic model configuration describes this RNA folding reaction over the entire temperature range studied consisting of primary (fast transitions to misfolded intermediates followed by much slower secondary transitions, consistent with previous studies. Eyring analysis reveals that the primary transitions are moderate in magnitude and primarily enthalpic in nature. In contrast, the secondary transitions are daunting in magnitude and entropic in nature. The entropic character of the secondary transitions is consistent with structural rearrangement of the intermediate species to the final folded form. This segregation of kinetic control reveals distinctly different molecular mechanisms during the two stages of RNA folding and documents the importance of entropic barriers to defining rugged RNA folding landscapes.

  14. Heterochiral Knottin Protein: Folding and Solution Structure.

    Science.gov (United States)

    Mong, Surin K; Cochran, Frank V; Yu, Hongtao; Graziano, Zachary; Lin, Yu-Shan; Cochran, Jennifer R; Pentelute, Bradley L

    2017-10-31

    Homochirality is a general feature of biological macromolecules, and Nature includes few examples of heterochiral proteins. Herein, we report on the design, chemical synthesis, and structural characterization of heterochiral proteins possessing loops of amino acids of chirality opposite to that of the rest of a protein scaffold. Using the protein Ecballium elaterium trypsin inhibitor II, we discover that selective β-alanine substitution favors the efficient folding of our heterochiral constructs. Solution nuclear magnetic resonance spectroscopy of one such heterochiral protein reveals a homogeneous global fold. Additionally, steered molecular dynamics simulation indicate β-alanine reduces the free energy required to fold the protein. We also find these heterochiral proteins to be more resistant to proteolysis than homochiral l-proteins. This work informs the design of heterochiral protein architectures containing stretches of both d- and l-amino acids.

  15. A method for assessing the regional vibratory pattern of vocal folds by analysing the video recording of stroboscopy.

    Science.gov (United States)

    Lee, J S; Kim, E; Sung, M W; Kim, K H; Sung, M Y; Park, K S

    2001-05-01

    Stroboscopy and kymography have been used to examine the motional abnormality of vocal folds and to visualise their regional vibratory pattern. In a previous study (Laryngoscope, 1999), we introduced the conceptual idea of videostrobokymography, in which we applied the concept of kymography on the pre-recorded video images using stroboscopy, and showed its possible clinical application to various disorders in vocal folds. However, a more detailed description about the software and the mathematical formulation used in this system is needed for the reproduction of similar systems. The composition of hardwares, user-interface and detail procedures including mathematical equations in videostrobokymography software is presented in this study. As an initial clinical trial, videostrobokymography was applied to the preoperative and postoperative videostroboscopic images of 15 patients with Reinke's edema. On preoperative examination, videostrobokymograms showed irregular pattern of mucosal wave and, in some patients, a relatively constant glottic gap during phonation. After the operation, the voice quality of all patients was improved in acoustic and aerodynamic assessments, and videostrobokymography showed clearly improved mucosal waves (change in open quotient: mean +/- SD= 0.11 +/- 0.05).

  16. Assessment of thyroplasty for vocal fold paralysis

    DEFF Research Database (Denmark)

    Grøntved, Ågot Møller; Faber, Christian; Jakobsen, John

    2009-01-01

    INTRODUCTION: Thyroplasty with silicone rubber implantation is a surgical procedure for treatment of patients with vocal fold paralysis. The aim of the present study was to evaluate the outcome of the operation and to monitor which of the analyses were the more beneficial. MATERIAL AND METHODS...... because it offers a quantitative measure of the voice capacity and intensity, which are the major problems experienced by patients with vocal fold paralysis. Used together, these tools are highly instrumental in guiding the patient's choice of surgery or no surgery. Udgivelsesdato: 2009-Jan-12...

  17. The structure of the TFIIH p34 subunit reveals a von Willebrand factor A like fold.

    Directory of Open Access Journals (Sweden)

    Dominik R Schmitt

    Full Text Available RNA polymerase II dependent transcription and nucleotide excision repair are mediated by a multifaceted interplay of subunits within the general transcription factor II H (TFIIH. A better understanding of the molecular structure of TFIIH is the key to unravel the mechanism of action of this versatile protein complex within these vital cellular processes. The importance of this complex becomes further evident in the context of severe diseases like xeroderma pigmentosum, Cockayne's syndrome and trichothiodystrophy, that arise from single point mutations in TFIIH subunits. Here we describe the structure of the p34 subunit of the TFIIH complex from the eukaryotic thermophilic fungus Chaetomium thermophilum. The structure revealed that p34 contains a von Willebrand Factor A (vWA like domain, a fold which is generally known to be involved in protein-protein interactions. Within TFIIH p34 strongly interacts with p44, a positive regulator of the helicase XPD. Putative protein-protein interfaces are analyzed and possible binding sites for the p34-p44 interaction suggested.

  18. Structure of the thioredoxin-fold domain of human phosducin-like protein 2

    International Nuclear Information System (INIS)

    Lou, Xiaochu; Bao, Rui; Zhou, Cong-Zhao; Chen, Yuxing

    2009-01-01

    The X-ray crystal structure of the Trx-fold domain of hPDCL2 was solved at 2.70 Å resolution and resembled the Trx-fold domain of rat phosducin. Human phosducin-like protein 2 (hPDCL2) has been identified as belonging to subgroup II of the phosducin (Pdc) family. The members of this family share an N-terminal helix domain and a C-terminal thioredoxin-fold (Trx-fold) domain. The X-ray crystal structure of the Trx-fold domain of hPDCL2 was solved at 2.70 Å resolution and resembled the Trx-fold domain of rat phosducin. Comparative structural analysis revealed the structural basis of their putative functional divergence

  19. High-Pressure NMR and SAXS Reveals How Capping Modulates Folding Cooperativity of the pp32 Leucine-rich Repeat Protein.

    Science.gov (United States)

    Zhang, Yi; Berghaus, Melanie; Klein, Sean; Jenkins, Kelly; Zhang, Siwen; McCallum, Scott A; Morgan, Joel E; Winter, Roland; Barrick, Doug; Royer, Catherine A

    2018-04-27

    Many repeat proteins contain capping motifs, which serve to shield the hydrophobic core from solvent and maintain structural integrity. While the role of capping motifs in enhancing the stability and structural integrity of repeat proteins is well documented, their contribution to folding cooperativity is not. Here we examined the role of capping motifs in defining the folding cooperativity of the leucine-rich repeat protein, pp32, by monitoring the pressure- and urea-induced unfolding of an N-terminal capping motif (N-cap) deletion mutant, pp32-∆N-cap, and a C-terminal capping motif destabilization mutant pp32-Y131F/D146L, using residue-specific NMR and small-angle X-ray scattering. Destabilization of the C-terminal capping motif resulted in higher cooperativity for the unfolding transition compared to wild-type pp32, as these mutations render the stability of the C-terminus similar to that of the rest of the protein. In contrast, deletion of the N-cap led to strong deviation from two-state unfolding. In both urea- and pressure-induced unfolding, residues in repeats 1-3 of pp32-ΔN-cap lost their native structure first, while the C-terminal half was more stable. The residue-specific free energy changes in all regions of pp32-ΔN-cap were larger in urea compared to high pressure, indicating a less cooperative destabilization by pressure. Moreover, in contrast to complete structural disruption of pp32-ΔN-cap at high urea concentration, its pressure unfolded state remained compact. The contrasting effects of the capping motifs on folding cooperativity arise from the differential local stabilities of pp32, whereas the contrasting effects of pressure and urea on the pp32-ΔN-cap variant arise from their distinct mechanisms of action. Copyright © 2018 Elsevier Ltd. All rights reserved.

  20. Incremental fold tests of remagnetized carbonate rocks

    Science.gov (United States)

    Van Der Voo, R.; van der Pluijm, B.

    2017-12-01

    Many unmetamorphosed carbonates all over the world are demonstrably remagnetized, with the age of the secondary magnetizations typically close to that of the nearest orogeny in space and time. This observation did not become compelling until the mid-1980's, when the incremental fold test revealed the Appalachian carbonates to carry a syn-deformational remanence of likely Permian age (Scotese et al., 1982, Phys. Earth Planet. Int., v. 30, p. 385-395; Cederquist et al., 2006, Tectonophysics v. 422, p. 41-54). Since that time scores of Appalachian and Rocky Mountain carbonate rocks have added results to the growing database of paleopoles representing remagnetizations. Late Paleozoic remagnetizations form a cloud of results surrounding the reference poles of the Laurentian APWP. Remagnetizations in other locales and with inferred ages coeval with regional orogenies (e.g., Taconic, Sevier/Laramide, Variscan, Indosinian) are also ubiquitous. To be able to transform this cornucopia into valuable anchor-points on the APWP would be highly desirable. This may indeed become feasible, as will be explained next. Recent studies of faulted and folded carbonate-shale sequences have shown that this deformation enhances the illitization of smectite (Haines & van der Pluijm, 2008, Jour. Struct. Geol., v. 30, p. 525-538; Fitz-Diaz et al., 2014, International Geol. Review, v. 56, p. 734-755). 39Ar-40Ar dating of the authigenic illite (neutralizing any detrital illite contribution by taking the intercept of a mixing line) yields, therefore, the age of the deformation. We know that this date is also the age of the syndeformational remanence; thus we have the age of the corresponding paleopole. Results so far are obtained for the Canadian and U.S. Rocky Mountains and for the Spanish Cantabrian carbonates (Tohver et al., 2008, Earth Planet. Sci. Lett., v. 274, p. 524-530) and make good sense in accord with geological knowledge. Incremental fold tests are the tools used for this

  1. Adapted to roar: functional morphology of tiger and lion vocal folds.

    Directory of Open Access Journals (Sweden)

    Sarah A Klemuk

    Full Text Available Vocal production requires active control of the respiratory system, larynx and vocal tract. Vocal sounds in mammals are produced by flow-induced vocal fold oscillation, which requires vocal fold tissue that can sustain the mechanical stress during phonation. Our understanding of the relationship between morphology and vocal function of vocal folds is very limited. Here we tested the hypothesis that vocal fold morphology and viscoelastic properties allow a prediction of fundamental frequency range of sounds that can be produced, and minimal lung pressure necessary to initiate phonation. We tested the hypothesis in lions and tigers who are well-known for producing low frequency and very loud roaring sounds that expose vocal folds to large stresses. In histological sections, we found that the Panthera vocal fold lamina propria consists of a lateral region with adipocytes embedded in a network of collagen and elastin fibers and hyaluronan. There is also a medial region that contains only fibrous proteins and hyaluronan but no fat cells. Young's moduli range between 10 and 2000 kPa for strains up to 60%. Shear moduli ranged between 0.1 and 2 kPa and differed between layers. Biomechanical and morphological data were used to make predictions of fundamental frequency and subglottal pressure ranges. Such predictions agreed well with measurements from natural phonation and phonation of excised larynges, respectively. We assume that fat shapes Panthera vocal folds into an advantageous geometry for phonation and it protects vocal folds. Its primary function is probably not to increase vocal fold mass as suggested previously. The large square-shaped Panthera vocal fold eases phonation onset and thereby extends the dynamic range of the voice.

  2. Rate constant and reaction coordinate of Trp-cage folding in explicit water

    NARCIS (Netherlands)

    Juraszek, J.; Bolhuis, P.G.

    2008-01-01

    We report rate constant calculations and a reaction coordinate analysis of the rate-limiting folding and unfolding process of the Trp-cage mini-protein in explicit solvent using transition interface sampling. Previous transition path sampling simulations revealed that in this (un)folding process the

  3. Effect of Vocal Fold Medialization on Dysphagia in Patients with Unilateral Vocal Fold Immobility.

    Science.gov (United States)

    Cates, Daniel J; Venkatesan, Naren N; Strong, Brandon; Kuhn, Maggie A; Belafsky, Peter C

    2016-09-01

    The effect of vocal fold medialization (VFM) on vocal improvement in persons with unilateral vocal fold immobility (UVFI) is well established. The effect of VFM on the symptom of dysphagia is uncertain. The purpose of this study is to evaluate dysphagia symptoms in patients with UVFI pre- and post-VFM. Case series with chart review. Academic tertiary care medical center. The charts of 44 persons with UVFI who underwent VFM between June 1, 2013, and December 31, 2014, were abstracted from a prospectively maintained database at the University of California, Davis, Voice and Swallowing Center. Patient demographics, indications, and type of surgical procedure were recorded. Self-reported swallowing impairment was assessed with the validated 10-item Eating Assessment Tool (EAT-10) before and after surgery. A paired samples t test was used to compare pre- and postmedialization EAT-10 scores. Forty-four patients met criteria and underwent either vocal fold injection (73%) or thyroplasty (27%). Etiologies of vocal fold paralysis were iatrogenic (55%), idiopathic (29%), benign or malignant neoplastic (9%), traumatic (5%), or related to the late effects of radiation (2%). EAT-10 (mean ± SD) scores improved from 12.2 ± 11.1 to 7.7 ± 7.2 after medialization (P dysphagia and report significant improvement in swallowing symptoms following VFM. The symptomatic improvement appears to be durable over time. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2016.

  4. Transcriptome reveals the overexpression of a kallikrein gene cluster (KLK1/3/7/8/12) in the Tibetans with high altitude-associated polycythemia.

    Science.gov (United States)

    Li, Kang; Gesang, Luobu; Dan, Zeng; Gusang, Lamu

    2017-02-01

    High altitude-associated polycythemia (HAPC) is a very common disease. However, it the disease is still unmanageable and the related molecular mechanisms remain largely unclear. In the present study, we aimed to explore the molecular mechanisms responsible for the development of HAPC using transcriptome analysis. Transcriptome analysis was conducted in 3 pairs of gastric mucosa tissues from patients with HAPC and healthy residents at a similar altitude. Endoscopy and histopathological analyses were used to examine the injury to gastric tissues. Molecular remodeling was performed for the interaction between different KLK members and cholesterol. HAPC was found to lead to morphological changes and pathological damage to the gastric mucosa of patients. A total of 10,304 differentially expressed genes (DEGs) were identified. Among these genes, 4,941 DEGs were upregulated, while 5,363 DEGs were downregulated in the patients with HAPC (fold change ≥2, P17-fold. All the members had high-score binding cholesterol, particularly for the polymers of KLK7. The kallikrein gene cluster (KLK1/3/7/8/12) is on chromosome 19q13.3-13.4. The elevated levels of KLK1, KLK3, KLK7, KLK8 and KLK12 may be closely associated with the hypertension, inflammation, obesity and other gastric injuries associated with polycythemia. The interaction of KLKs and cholesterol maybe play an important role in the development of hypertension. The findings of the present study revealed that HAPC induces gastric injury by upregulating the kallikrein gene cluster (KLK1/3/7/8/12), which can bind cholesterol and result in kallikrein hypertension. These findings provide some basic information for understanding the molecular mechanisms responsible for HAPC and HAPC-related diseases.

  5. The impact of episodic fault-related folding on Late Holocene degradation terraces along Waipara River, New Zealand

    International Nuclear Information System (INIS)

    Nicol, A.; Campbell, J.K.

    2001-01-01

    The Waipara River flows eastwards through growing folds in the tectonically active foothills of New Zealand's Southern Alps. In the middle Waipara region, flights of degradation terraces are widespread and rise to 55 m above river channels. Ages of terrace surfaces and paleoearthquakes on four faults are constrained by radiocarbon samples and weathering-rind dates from surface cobbles of Torlesse Group sandstone. Terrace ages indicate rapid incision (c. 30-100 mm/yr) of Waipara River and three tributaries during the Late Holocene. Cumulative-incision curves suggest a 15-25 m lowering of regional base level over the last thousand years and an additional 20-25 m of local incision 200-600 yr BP along Waipara River where it crosses Doctors Anticline. Rapid river incision was strongly influenced by rock uplift on the anticline associated with fault rupture during an earthquake 300-400 yr BP. From incision data we infer that the earthquake was preceded and followed by aseismic fold growth. Tectonic uplift during folding was probably, at most, one-third of local river incision; this discrepancy may relate to the short sample period and to locally elevated stream erosive power due in part to a reduction in floodplain width. (author). 41 refs., 12 figs., 2 tabs

  6. Towards the theoretical bases of the folding of the 100-A nucleosome filament

    International Nuclear Information System (INIS)

    Chela Flores, J.

    1994-01-01

    We attempt to model DNA packaging at the various stages of ever increasing DNA folding from the 100-A nucleosome filament to various further stages leading up to the metaphase chromosome. We have assumed that a phase transition has induced chromatin into a condensed mode. The mean-field model allows the simultaneous discussion of chromatin with packaging ration η and DNA replication at various stages of folding. We derive a formula correlating (during the S phase of the cell cycle) the DNA polymerase velocity r f (measured in nucleotides per minute) in a relation of inverse proportionality with the degree of DNA packaging: r f = λη -1/2 , where the dimensional constant λ has been determined. This model suggests that in the heterochromatic regions of chromatin there is reduced activity of DNA polymerases. We discuss the possible relevance of our model to late replicating telomeres in yeast and several higher eukaryotes. (author). 28 refs, 3 tabs

  7. Covering folded shapes

    Directory of Open Access Journals (Sweden)

    Oswin Aichholzer

    2014-05-01

    Full Text Available Can folding a piece of paper flat make it larger? We explore whether a shape S must be scaled to cover a flat-folded copy of itself. We consider both single folds and arbitrary folds (continuous piecewise isometries \\(S\\to\\mathbb{R}^2\\. The underlying problem is motivated by computational origami, and is related to other covering and fixturing problems, such as Lebesgue's universal cover problem and force closure grasps. In addition to considering special shapes (squares, equilateral triangles, polygons and disks, we give upper and lower bounds on scale factors for single folds of convex objects and arbitrary folds of simply connected objects.

  8. Traumatic chorioretinal folds treated with intra-vitreal triamcinolone injection

    Directory of Open Access Journals (Sweden)

    Kook Young Kim

    2013-01-01

    Full Text Available A 34-year-old male visited the hospital due to decreased visual acuity in the left eye following an injury from a car accident. In the left eye, best-corrected visual acuity (BCVA was hand motion and intraocular pressure (IOP was 8 mmHg. Choroidal vasodilation and chorioretinal folds were observed by spectral domain-optical coherence tomography (SD-OCT. Topical and systemic steroid treatments did not improve the chorioretinal folds. Twelve months after the injury, intra-vitreal triamcinolone (4 mg/0.1 ml was injected. Six months after intra-vitreal triamcinolone injection, BCVA in the left eye had improved to 20/100. Fundus examination showed improvement in retinal vascular tortuosity and SD-OCT revealed improvements in choroidal vasodilation and chorioretinal folds. Intra-vitreal triamcinolone injection (IVTI was effective against traumatic chorioretinal folds with no recurrence based on objective observation by fundus photography and SD-OCT.

  9. Trends in Utilization of Vocal Fold Injection Procedures.

    Science.gov (United States)

    Rosow, David E

    2015-11-01

    Office-based vocal fold injections have become increasingly popular over the past 15 years. Examination of trends in procedure coding for vocal fold injections in the United States from 2000 to 2012 was undertaken to see if they reflect this shift. The US Part B Medicare claims database was queried from 2000 through 2012 for multiple Current Procedural Terminology codes. Over the period studied, the number of nonoperative laryngoscopic injections (31513, 31570) and operative medialization laryngoplasties (31588) remained constant. Operative vocal fold injection (31571) demonstrated marked linear growth over the 12-year study period, from 744 procedures in 2000 to 4788 in 2012-an increase >640%. The dramatic increased incidence in the use of code 31571 reflects an increasing share of vocal fold injections being performed in the operating room and not in an office setting, running counter to the prevailing trend toward awake, office-based injection procedures. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2015.

  10. Regeneration of Vocal Fold Mucosa Using Tissue-Engineered Structures with Oral Mucosal Cells

    Science.gov (United States)

    Fukahori, Mioko; Chitose, Shun-ichi; Sato, Kiminori; Sueyoshi, Shintaro; Kurita, Takashi; Umeno, Hirohito; Monden, Yu; Yamakawa, Ryoji

    2016-01-01

    Objectives Scarred vocal folds result in irregular vibrations during phonation due to stiffness of the vocal fold mucosa. To date, a completely satisfactory corrective procedure has yet to be achieved. We hypothesize that a potential treatment option for this disease is to replace scarred vocal folds with organotypic mucosa. The purpose of this study is to regenerate vocal fold mucosa using a tissue-engineered structure with autologous oral mucosal cells. Study Design Animal experiment using eight beagles (including three controls). Methods A 3 mm by 3 mm specimen of canine oral mucosa was surgically excised and divided into epithelial and subepithelial tissues. Epithelial cells and fibroblasts were isolated and cultured separately. The proliferated epithelial cells were co-cultured on oriented collagen gels containing the proliferated fibroblasts for an additional two weeks. The organotypic cultured tissues were transplanted to the mucosa-deficient vocal folds. Two months after transplantation, vocal fold vibrations and morphological characteristics were observed. Results A tissue-engineered vocal fold mucosa, consisting of stratified epithelium and lamina propria, was successfully fabricated to closely resemble the normal layered vocal fold mucosa. Laryngeal stroboscopy revealed regular but slightly small mucosal waves at the transplanted site. Immunohistochemically, stratified epithelium expressed cytokeratin, and the distributed cells in the lamina propria expressed vimentin. Elastic Van Gieson staining revealed a decreased number of elastic fibers in the lamina propria of the transplanted site. Conclusion The fabricated mucosa with autologous oral mucosal cells successfully restored the vocal fold mucosa. This reconstruction technique could offer substantial clinical advantages for treating intractable diseases such as scarring of the vocal folds. PMID:26730600

  11. Effects of Vocal Fold Nodules on Glottal Cycle Measurements Derived from High-Speed Videoendoscopy in Children

    Science.gov (United States)

    2016-01-01

    The goal of this study is to quantify the effects of vocal fold nodules on vibratory motion in children using high-speed videoendoscopy. Differences in vibratory motion were evaluated in 20 children with vocal fold nodules (5–11 years) and 20 age and gender matched typically developing children (5–11 years) during sustained phonation at typical pitch and loudness. Normalized kinematic features of vocal fold displacements from the mid-membranous vocal fold point were extracted from the steady-state high-speed video. A total of 12 kinematic features representing spatial and temporal characteristics of vibratory motion were calculated. Average values and standard deviations (cycle-to-cycle variability) of the following kinematic features were computed: normalized peak displacement, normalized average opening velocity, normalized average closing velocity, normalized peak closing velocity, speed quotient, and open quotient. Group differences between children with and without vocal fold nodules were statistically investigated. While a moderate effect size was observed for the spatial feature of speed quotient, and the temporal feature of normalized average closing velocity in children with nodules compared to vocally normal children, none of the features were statistically significant between the groups after Bonferroni correction. The kinematic analysis of the mid-membranous vocal fold displacement revealed that children with nodules primarily differ from typically developing children in closing phase kinematics of the glottal cycle, whereas the opening phase kinematics are similar. Higher speed quotients and similar opening phase velocities suggest greater relative forces are acting on vocal fold in the closing phase. These findings suggest that future large-scale studies should focus on spatial and temporal features related to the closing phase of the glottal cycle for differentiating the kinematics of children with and without vocal fold nodules. PMID:27124157

  12. The structure of a conserved Piezo channel domain reveals a novel beta sandwich fold

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens; Lee, Jonas; Reid, Michelle; Rees, Douglas C.

    2014-01-01

    Summary Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a novel beta sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in Dehydrated Hereditary Stomatocytosis (DHS) patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. PMID:25242456

  13. Sulfated glycosaminoglycans in human vocal fold lamina propria

    Directory of Open Access Journals (Sweden)

    Sung Woo Park

    Full Text Available Abstract Introduction: The distribution, concentration and function of glycosaminoglycans in the various vocal fold tissues are still unclear. Objective: To evaluate the distribution and concentration of sulfated glycosaminoglycans in different layers of the human vocal fold according to gender and age. Methods: We used 11 vocal folds obtained from cadavers (7 men and 4 women with no laryngeal lesion, less than 12 h after death, and aged between 35 and 98 years. The folds underwent glycosaminoglycans extraction from the cover and ligament, and post-electrophoresis analysis. Data were compared according to the layer, age and gender. Results: The concentration of dermatan sulfate was significantly higher in all layers. No differences were observed in the total concentrations of glycosaminoglycans in layers studied according to gender. It is significantly lower in the cover of individuals aged below 60 years. Conclusion: Dermatan sulfate, chondroitin sulfate, and heparan sulfate were observed in the human vocal folds cover and ligament of both genders, with the concentration of dermatan sulfate being significantly higher in all layers. Glycosaminoglycans concentration on the cover is significantly lower in individuals below 60 years compared with elderly.

  14. Growth of the Zagros Fold-Thrust Belt and Foreland Basin, Northern Iraq, Kurdistan

    Science.gov (United States)

    Koshnaw, Renas; Horton, Brian; Stockli, Daniel; Barber, Douglas; Ghalib, Hafidh; Dara, Rebwar

    2016-04-01

    The Zagros orogenic belt in the Middle Eastern segment of the Alpine-Himalayan system is among the youngest seismically active continental collision zones on Earth. However, due to diachronous and incremental collision, the precise ages and kinematics of shortening and deposition remain poorly understood. The Kurdistan region of the Zagros fold-thrust belt and foreland basin contains well-preserved Neogene wedge-top and foredeep deposits that include clastic nonmarine fill of the Upper Fars, Lower Bakhtiari, and Upper Bakhtiari Formations. These deposits record significant information about orogenic growth, fold-thrust dynamics, and advance of the deformation front. Thermochronologic and geochronologic data from thrust sheets and stratigraphic archives combined with local earthquake data provide a unique opportunity to address the linkages between surface and subsurface geologic relationships. This research seeks to constrain the timing and geometry of exhumation and deformation by addressing two key questions: (1) Did the northwestern Zagros fold-thrust belt evolve from initial thin-skinned shortening to later thick-skinned deformation or vice-versa? (2) Did the fold-thrust belt advance steadily under critical/supercritical wedge conditions involving in-sequence thrusting or propagate intermittently under subcritical conditions with out-of-sequence deformation? From north to south, apatite (U-Th)/He ages from the Main Zagros Thrust, the Mountain Front Flexure (MFF), and additional frontal thrusts suggest rapid exhumation by ~10 Ma, ~5 Ma, and ~8 Ma respectively. Field observations and seismic sections indicate progressive tilting and development of growth strata within the Lower Bakhtiari Formation adjacent to the frontal thrusts and within the Upper Bakhtiari Formation near the MFF. In the Kurdistan region of Iraq, a regional balanced cross section constrained by new thermochronometric results, proprietary seismic reflection profiles, and earthquake hypocenters

  15. Kinematics of tectonic fracture development during regional folding in sandstones of the Kamlial Formation, Khushalgarh, northern Pakistan

    International Nuclear Information System (INIS)

    Sayab, M.

    2005-01-01

    Systematic relationships between the fracture orientation and fold geometry in sedimentary rocks have been used to explain the development of synfolding fractures. Based on field observations at the Khushalgarh syncline, located east of the Kohat Plateau, we proposed that the orientation of fractures was influenced dominantly by two tectonic fracture sets, that is, the NE-SW and NW-SE. The NE-SW fracture set dominantly formed as mode 1 (tensile), where as, the NW-SE fracture set developed as mode 11 (shear) conjugate fractures. The NE-SW trending fractures follow the axis of the syncline, whereas, the NW-SE fracture about crosscuts the fold axis. Most of the NE-SW fractures abut against the NW-SW fracture set. Based on the orientation and crosscutting relationship, their modes in response to stress, we conclude that the NE-SW trending fractures formed early than those of NW-SE fracture set. Though, both the fracture sets are formed during the folding, we suggest that they were not formed at the same time. Their crosscutting relationship suggests that they developed sequentially rather than synchronously. Our interpretations support the laboratory-based models where only one fracture orientation (or set of fractures with one orientation) form in response to single stress. However, as the stress distribution in folded strata changes over time new fractures of distinct orientations can form during or late in the folding history. We conclude that the sandstone units underwent bedding-parallel extension during folding, where bedding is stretched to accommodate extension. Parallel to the fold axis orientation. Bending of the limbs is a likely mechanism for the development of observed NE-SW trending fractures during folding, whereas the NW-SE fractures developed late in the folded history. (author)

  16. Vocal fold submucosal infusion technique in phonomicrosurgery.

    Science.gov (United States)

    Kass, E S; Hillman, R E; Zeitels, S M

    1996-05-01

    Phonomicrosurgery is optimized by maximally preserving the vocal fold's layered microstructure (laminae propriae). The technique of submucosal infusion of saline and epinephrine into the superficial lamina propria (SLP) was examined to delineate how, when, and why it was helpful toward this surgical goal. A retrospective review revealed that the submucosal infusion technique was used to enhance the surgery in 75 of 152 vocal fold procedures that were performed over the last 2 years. The vocal fold epithelium was noted to be adherent to the vocal ligament in 29 of the 75 cases: 19 from previous surgical scarring, 4 from cancer, 3 from sulcus vocalis, 2 from chronic hemorrhage, and 1 from radiotherapy. The submucosal infusion technique was most helpful when the vocal fold epithelium required resection and/or when extensive dissection in the SLP was necessary. The infusion enhanced the surgery by vasoconstriction of the microvasculature in the SLP, which improved visualization during cold-instrument tangential dissection. Improved visualization facilitated maximal preservation of the SLP, which is necessary for optimal pliability of the overlying epithelium. The infusion also improved the placement of incisions at the perimeter of benign, premalignant, and malignant lesions, and thereby helped preserve epithelium uninvolved by the disorder.

  17. Vocal Fold Paralysis

    Science.gov (United States)

    ... here Home » Health Info » Voice, Speech, and Language Vocal Fold Paralysis On this page: What is vocal fold ... Where can I get additional information? What is vocal fold paralysis? Structures involved in speech and voice production ...

  18. Functional analysis of propeptide as an intramolecular chaperone for in vivo folding of subtilisin nattokinase.

    Science.gov (United States)

    Jia, Yan; Liu, Hui; Bao, Wei; Weng, Meizhi; Chen, Wei; Cai, Yongjun; Zheng, Zhongliang; Zou, Guolin

    2010-12-01

    Here, we show that during in vivo folding of the precursor, the propeptide of subtilisin nattokinase functions as an intramolecular chaperone (IMC) that organises the in vivo folding of the subtilisin domain. Two residues belonging to β-strands formed by conserved regions of the IMC are crucial for the folding of the subtilisin domain through direct interactions. An identical protease can fold into different conformations in vivo due to the action of a mutated IMC, resulting in different kinetic parameters. Some interfacial changes involving conserved regions, even those induced by the subtilisin domain, blocked subtilisin folding and altered its conformation. Insight into the interaction between the subtilisin and IMC domains is provided by a three-dimensional structural model. Copyright © 2010 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  19. Expected packing density allows prediction of both amyloidogenic and disordered regions in protein chains

    Energy Technology Data Exchange (ETDEWEB)

    Galzitskaya, Oxana V; Garbuzynskiy, Sergiy O; Lobanov, Michail Yu [Institute of Protein Research, Russian Academy of Sciences, 142290, Pushchino, Moscow Region (Russian Federation)

    2007-07-18

    The determination of factors that influence conformational changes in proteins is very important for the identification of potentially amyloidogenic and disordered regions in polypeptide chains. In our work we introduce a new parameter, mean packing density, to detect both amyloidogenic and disordered regions in a protein sequence. It has been shown that regions with strong expected packing density are responsible for amyloid formation. Our predictions are consistent with known disease-related amyloidogenic regions for 9 of 12 amyloid-forming proteins and peptides in which the positions of amyloidogenic regions have been revealed experimentally. Our findings support the concept that the mechanism of formation of amyloid fibrils is similar for different peptides and proteins. Moreover, we have demonstrated that regions with weak expected packing density are responsible for the appearance of disordered regions. Our method has been tested on datasets of globular proteins and long disordered protein segments, and it shows improved performance over other widely used methods. Thus, we demonstrate that the expected packing density is a useful value for predicting both disordered and amyloidogenic regions of a protein based on sequence alone. Our results are important for understanding the structural characteristics of protein folding and misfolding.

  20. Structure of the first representative of Pfam family PF04016 (DUF364) reveals enolase and Rossmann-like folds that combine to form a unique active site with a possible role in heavy-metal chelation

    International Nuclear Information System (INIS)

    Miller, Mitchell D.; Aravind, L.; Bakolitsa, Constantina; Rife, Christopher L.; Carlton, Dennis; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L.; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kozbial, Piotr; Krishna, S. Sri; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Bedem, Henry van den; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The crystal structure of the first representative of DUF364 family reveals a combination of enolase N-terminal-like and C-terminal Rossmann-like folds. Analysis of the interdomain cleft combined with sequence and genome context conservation among homologs, suggests a unique catalytic site likely involved in the synthesis of a flavin or pterin derivative. The crystal structure of Dhaf4260 from Desulfitobacterium hafniense DCB-2 was determined by single-wavelength anomalous diffraction (SAD) to a resolution of 2.01 Å using the semi-automated high-throughput pipeline of the Joint Center for Structural Genomics (JCSG) as part of the NIGMS Protein Structure Initiative (PSI). This protein structure is the first representative of the PF04016 (DUF364) Pfam family and reveals a novel combination of two well known domains (an enolase N-terminal-like fold followed by a Rossmann-like domain). Structural and bioinformatic analyses reveal partial similarities to Rossmann-like methyltransferases, with residues from the enolase-like fold combining to form a unique active site that is likely to be involved in the condensation or hydrolysis of molecules implicated in the synthesis of flavins, pterins or other siderophores. The genome context of Dhaf4260 and homologs additionally supports a role in heavy-metal chelation

  1. The role of the mesenchyme in cranial neural fold elevation

    International Nuclear Information System (INIS)

    Morris-Wiman, J.A.

    1988-01-01

    It has been previously postulated that the expansion of an hyaluronate-rich extracellular matrix in the fold mesenchyme is responsible for neural fold elevation. In this study we provide evidence that such expansions may play an important role in cranial neural fold elevation by pushing the folds towards the dorsal midline to assist in their elevation. For mesenchymal expansion to result in fold elevation, hyaluronate (HA) and mesenchymal cells must be non-randomly distributed within the mesenchyme. Patterns of mesenchymal cell distribution and cell proliferation were analyzed using the computer-assisted method of smoothed spatial averaging. The distribution of Alcian blue-stained and 3 H-glucosamine-labelled HA was also analyzed during cranial neural fold elevation using established image processing techniques. Analysis of the distribution of 3 H-thymidine-labelled mesenchymal cells indicated that differential mitotic activity was not responsible for decreased mesenchymal cell density. Likewise, analysis of distribution patterns of 3 H-glucosamine-labelled HA indicated that decreased HA concentration was not produced by regional differences in HA synthesis. These results suggest that decreases in mesenchymal cell density and HA concentration that occur during neural fold elevation are produced by mesenchymal expansion

  2. Side chain and backbone contributions of Phe508 to CFTR folding

    Energy Technology Data Exchange (ETDEWEB)

    Thibodeau, Patrick H.; Brautigam, Chad A.; Machius, Mischa; Thomas, Philip J. (U. of Texas-SMED)

    2010-12-07

    Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR), an integral membrane protein, cause cystic fibrosis (CF). The most common CF-causing mutant, deletion of Phe508, fails to properly fold. To elucidate the role Phe508 plays in the folding of CFTR, missense mutations at this position were generated. Only one missense mutation had a pronounced effect on the stability and folding of the isolated domain in vitro. In contrast, many substitutions, including those of charged and bulky residues, disrupted folding of full-length CFTR in cells. Structures of two mutant nucleotide-binding domains (NBDs) reveal only local alterations of the surface near position 508. These results suggest that the peptide backbone plays a role in the proper folding of the domain, whereas the side chain plays a role in defining a surface of NBD1 that potentially interacts with other domains during the maturation of intact CFTR.

  3. Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate.

    Science.gov (United States)

    Krivov, Sergei V

    2018-06-06

    Recent advances in simulation and experiment have led to dramatic increases in the quantity and complexity of produced data, which makes the development of automated analysis tools very important. A powerful approach to analyze dynamics contained in such data sets is to describe/approximate it by diffusion on a free energy landscape - free energy as a function of reaction coordinates (RC). For the description to be quantitatively accurate, RCs should be chosen in an optimal way. Recent theoretical results show that such an optimal RC exists; however, determining it for practical systems is a very difficult unsolved problem. Here we describe a solution to this problem. We describe an adaptive nonparametric approach to accurately determine the optimal RC (the committor) for an equilibrium trajectory of a realistic system. In contrast to alternative approaches, which require a functional form with many parameters to approximate an RC and thus extensive expertise with the system, the suggested approach is nonparametric and can approximate any RC with high accuracy without system specific information. To avoid overfitting for a realistically sampled system, the approach performs RC optimization in an adaptive manner by focusing optimization on less optimized spatiotemporal regions of the RC. The power of the approach is illustrated on a long equilibrium atomistic folding simulation of HP35 protein. We have determined the optimal folding RC - the committor, which was confirmed by passing a stringent committor validation test. It allowed us to determine a first quantitatively accurate protein folding free energy landscape. We have confirmed the recent theoretical results that diffusion on such a free energy profile can be used to compute exactly the equilibrium flux, the mean first passage times, and the mean transition path times between any two points on the profile. We have shown that the mean squared displacement along the optimal RC grows linear with time as for

  4. Fold-recognition and comparative modeling of human α2,3-sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni

    Directory of Open Access Journals (Sweden)

    Balaji Petety V

    2006-04-01

    Full Text Available Abstract Background The 3-D structure of none of the eukaryotic sialyltransferases (SiaTs has been determined so far. Sequence alignment algorithms such as BLAST and PSI-BLAST could not detect a homolog of these enzymes from the protein databank. SiaTs, thus, belong to the hard/medium target category in the CASP experiments. The objective of the current work is to model the 3-D structures of human SiaTs which transfer the sialic acid in α2,3-linkage viz., ST3Gal I, II, III, IV, V, and VI, using fold-recognition and comparative modeling methods. The pair-wise sequence similarity among these six enzymes ranges from 41 to 63%. Results Unlike the sequence similarity servers, fold-recognition servers identified CstII, a α2,3/8 dual-activity SiaT from Campylobacter jejuni as the homolog of all the six ST3Gals; the level of sequence similarity between CstII and ST3Gals is only 15–20% and the similarity is restricted to well-characterized motif regions of ST3Gals. Deriving template-target sequence alignments for the entire ST3Gal sequence was not straightforward: the fold-recognition servers could not find a template for the region preceding the L-motif and that between the L- and S-motifs. Multiple structural templates were identified to model these regions and template identification-modeling-evaluation had to be performed iteratively to choose the most appropriate templates. The modeled structures have acceptable stereochemical properties and are also able to provide qualitative rationalizations for some of the site-directed mutagenesis results reported in literature. Apart from the predicted models, an unexpected but valuable finding from this study is the sequential and structural relatedness of family GT42 and family GT29 SiaTs. Conclusion The modeled 3-D structures can be used for docking and other modeling studies and for the rational identification of residues to be mutated to impart desired properties such as altered stability, substrate

  5. Aspirin Reduces Cardiac Interstitial Fibrosis by Inhibiting Erk1/2-Serpine2 and P-Akt Signalling Pathways.

    Science.gov (United States)

    Li, Xuelian; Wang, GuoYuan; QiLi, MuGe; Liang, HaiHai; Li, TianShi; E, XiaoQiang; Feng, Ying; Zhang, Ying; Liu, Xiao; Qian, Ming; Xu, BoZhi; Shen, ZhiHang; Gitau, Samuel Chege; Zhao, DanDan; Shan, HongLi

    2018-01-01

    Cardiac interstitial fibrosis is an abnormality of various cardiovascular diseases, including myocardial infarction, hypertrophy, and atrial fibrillation, and it can ultimately lead to heart failure. However, there is a lack of practical therapeutic approaches to treat fibrosis and reverse the damage to the heart. The purpose of this study was to investigate the effect of long-term aspirin administration on pressure overload-induced cardiac fibrosis in mice and reveal the underlying mechanisms of aspirin treatment. C57BL/6 mice were subjected to transverse aortic constriction (TAC), and treated with 10 mg·kg-1·day-1 of aspirin for 4 weeks. Masson staining and a collagen content assay were used to detect the effects of aspirin on cardiac fibrosis in vivo and in vitro. Western blot and qRT-PCR were applied to examine the impact of aspirin on extracellular signal-regulated kinases (Erks), p-Akt/β-catenin, SerpinE2, collagen I, and collagen III levels in the mice heart. Aspirin significantly suppressed the expression of α-smooth muscle actin (α-SMA; 1.19±0.19-fold) and collagen I (0.95±0.09-fold) in TAC mice. Aspirin, at doses of 100 and 1000 µM, also significantly suppressed angiotensin II-induced α-SMA and collagen I in cultured CFs. The enhanced phosphorylation of Erk1/2 caused by TAC (p-Erk1, 1.49±0.19-fold; p-Erk2, 1.96±0.68-fold) was suppressed by aspirin (p-Erk1, 1.04±0.15-fold; p-Erk2, 0.87±0.06-fold). SerpinE2 levels were suppressed via the Erk1/2 signalling pathway following treatment with aspirin (1.36±0.12-fold for TAC; 1.06±0.07-fold for aspirin+TAC). The p-Akt and β-catenin levels were also significantly inhibited in vivo and in vitro. Our study reveals a novel mechanism by which aspirin alleviates pressure overload-induced cardiac interstitial fibrosis in TAC mice by suppressing the p-Erk1/2 and p-Akt/β-catenin signalling pathways. © 2018 The Author(s). Published by S. Karger AG, Basel.

  6. On the single-mass model of the vocal folds

    International Nuclear Information System (INIS)

    Howe, M S; McGowan, R S

    2010-01-01

    An analysis is made of the fluid-structure interactions necessary to support self-sustained oscillations of a single-mass mechanical model of the vocal folds subject to a nominally steady subglottal overpressure. The single-mass model of Fant and Flanagan is re-examined and an analytical representation of vortex shedding during 'voiced speech' is proposed that promotes cooperative, periodic excitation of the folds by the glottal flow. Positive feedback that sustains glottal oscillations is shown to occur during glottal contraction, when the flow separates from the 'trailing edge' of the glottis producing a low-pressure 'suction' force that tends to pull the folds together. Details are worked out for flow that can be regarded as locally two-dimensional in the glottal region. Predictions of free-streamline theory are used to model the effects of quasi-static variations in the separation point on the glottal wall. Numerical predictions are presented to illustrate the waveform of the sound radiated towards the mouth from the glottis. The theory is easily modified to include feedback on the glottal flow of standing acoustic waves, both in the vocal tract beyond the glottis and in the subglottal region. (invited paper)

  7. Vocal Fold Vibration Following Surgical Intervention in Three Vocal Pathologies: A Preliminary Study.

    Science.gov (United States)

    Chen, Wenli; Woo, Peak; Murry, Thomas

    2017-09-01

    High-speed videoendoscopy captures the cycle-to-cycle vibratory motion of each individual vocal fold in normal and severely disordered phonation. Therefore, it provides a direct method to examine the specific vibratory changes following vocal fold surgery. The purpose of this study was to examine the vocal fold vibratory pattern changes in the surgically treated pathologic vocal fold and the contralateral vocal fold in three vocal pathologies: vocal polyp (n = 3), paresis or paralysis (n = 3), and scar (n = 3). Digital kymography was used to extract high-speed kymographic vocal fold images at the mid-membranous region of the vocal fold. Spectral analysis was subsequently applied to the digital kymography to quantify the cycle-to-cycle movements of each vocal fold, expressed as a spectrum. Surgical modification resulted in significantly improved spectral power of the treated pathologic vocal fold. Furthermore, the contralateral vocal fold also presented with improved spectral power irrespective of vocal pathology. In comparison with normal vocal fold spectrum, postsurgical vocal fold vibrations continued to demonstrate decreased vibratory amplitude in both vocal folds. Copyright © 2017 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  8. The influence of thyroarytenoid and cricothyroid muscle activation on vocal fold stiffness and eigenfrequencies

    Science.gov (United States)

    Yin, Jun; Zhang, Zhaoyan

    2013-01-01

    The influence of the thyroarytenoid (TA) and cricothyroid (CT) muscle activation on vocal fold stiffness and eigenfrequencies was investigated in a muscularly controlled continuum model of the vocal folds. Unlike the general understanding that vocal fold fundamental frequency was determined by vocal fold tension, this study showed that vocal fold eigenfrequencies were primarily determined by vocal fold stiffness. This study further showed that, with reference to the resting state of zero strain, vocal fold stiffness in both body and cover layers increased with either vocal fold elongation or shortening. As a result, whether vocal fold eigenfrequencies increased or decreased with CT/TA activation depended on how the CT/TA interaction influenced vocal fold deformation. For conditions of strong CT activation and thus an elongated vocal fold, increasing TA contraction reduced the degree of vocal fold elongation and thus reduced vocal fold eigenfrequencies. For conditions of no CT activation and thus a resting or slightly shortened vocal fold, increasing TA contraction increased the degree of vocal fold shortening and thus increased vocal fold eigenfrequencies. In the transition region of a slightly elongated vocal fold, increasing TA contraction first decreased and then increased vocal fold eigenfrequencies. PMID:23654401

  9. Adipose-derived mesenchymal stromal cells prevented rat vocal fold scarring.

    Science.gov (United States)

    Morisaki, Tsuyoshi; Kishimoto, Yo; Tateya, Ichiro; Kawai, Yoshitaka; Suzuki, Ryo; Tsuji, Takuya; Hiwatashi, Nao; Nakamura, Tatsuo; Omori, Koichi; Kitano, Hiroya; Takeuchi, Hiromi; Hirano, Shigeru

    2018-01-01

    This study aimed to reveal the effects of adipose-derived mesenchymal stromal cells (ASCs) on prevention of vocal fold scarring by investigating how the immediate ASCs transplantation into the injured rat vocal fold affect the levels of gene transcription and translation. Prospective animal experiments with controls. ASCs harvested from green fluorescent protein transgenic rat (ASCs group) or saline (sham group) were injected into the thyroarytenoid muscle of Sprague-Dawley rats immediately after stripping the vocal fold. For histological examinations, larynges were extirpated at 3, 14, and 56 days after the injection. Quantitative real-time polymerase chain reaction (PCR) analyses were performed at 3 and 14 days after the injection. Transplanted ASCs were detected only in larynges at day 3. At days 14 and 56, histological examination showed significantly higher amounts of hyaluronic acid and lower deposition of collagen in the ASCs group compared to the sham group. Real-time PCR revealed that the ASCs group showed low expression of procollagen (Col)1a1, Col1a3, matrix metalloproteinase (Mmp)1 and Mmp8 in each time points. The ASCs group showed high expression of fibroblast growth factor (Fgf)2 and Hepatocyte growth factor (Hgf) compared to the sham group at day 14. ASCs increased expressions of Fgf2 and Hgf, and suppressed excessive collagen deposition during vocal fold wound healing. Given the fact that ASCs survived no more than 14 days, ASCs were thought to induce upregulations of growth factors' genes in surrounding cells. These results suggested that ASCs have potential to prevent vocal fold scarring. NA. Laryngoscope, 128:E33-E40, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  10. Vocal-fold vibration of patients with Reinke's edema observed using high-speed digital imaging.

    Science.gov (United States)

    Watanabe, Takeshi; Kaneko, Kenichi; Sakaguchi, Koichi; Takahashi, Haruo

    2016-12-01

    We aimed to assess the vocal-fold vibration of patients with moderate-to-severe Reinke's edema using high-speed digital imaging (HSDI) and videostroboscopy and to confirm HSDI usefulness in examining the vocal folds with Reinke's edema. We examined the vocal folds of seven patients (six severe and one moderate; six females and one male; aged 55-74 years; mean 64.7 years) with Reinke's edema using HSDI and videostroboscopy. The following characteristics were analyzed: glottic closure, mucosal-wave propagation, left-right asymmetry, phase shift, frequency difference, periodicity, and contact of the true vocal fold with the false vocal fold. HSDI revealed complete glottic closure, anterior-posterior phase shift, and obvious contact of at least one side of the edematous true vocal fold with the ipsilateral false vocal fold in all patients. Mucosal-wave propagation increased in six patients and decreased in one. Left-right asymmetry was observed in six patients. Left-right phase shifts and left-right frequency differences were observed in four and two patients, respectively. The vibration was periodic in four patients, quasi-periodic in three, and aperiodic in none. Anterior-posterior frequency differences were not observed for any patient. The vocal-fold vibration always synchronized with strobolights in two patients, while the vibration occasionally and never synchronized in two and three patients, respectively. In one patient whose vibration occasionally synchronized, videostroboscopy could not reveal the slight left-right frequency difference of the vibration. It was often difficult to observe vocal-fold vibration correctly in patients with severe Reinke's edema using videostroboscopy. However, HSDI was useful for examining these patients. Our results suggest that HSDI can be very useful for examining the vocal folds of patients with severe Reinke's edema. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  11. A novel folding blade of wind turbine rotor for effective power control

    International Nuclear Information System (INIS)

    Xie, Wei; Zeng, Pan; Lei, Liping

    2015-01-01

    Highlights: • A novel folding blade for wind turbine power control is proposed. • Wind tunnel experiments were conducted to analyze folding blade validity. • Folding blade is valid to control wind turbine power output. • Compared to pitch control, thrust was reduced by fold control in power regulation. • Optimum fold angles were found for wind turbine start up and aerodynamic brake. - Abstract: A concept of novel folding blade of horizontal axis wind turbine is proposed in current study. The folding blade comprises a stall regulated root blade section and a folding tip blade section with the fold axis inclined relative to blade span. By folding blade, lift force generated on the tip blade section changes and the moment arm also shortens, which leads to variations of power output. The blade folding actuation mechanism with servo motor and worm-gear reducer was designed. Wind turbine rotor control scheme and servo system with double feedback loops for blade fold angle control were proposed. In this study, a small folding blade model was tested in a wind tunnel to analyze its performance. The blade model performance was estimated in terms of rotation torque coefficient and thrust coefficient. Wind tunnel experiments were also conducted for pitch control using the same blade model in order to make a direct comparison. The power control, start up and aerodynamic brake performance of the folding blade were analyzed. According to the wind tunnel experiment results, fold angle magnitude significantly affected blade aerodynamic performance and the thrust characteristic together with the rotation torque characteristic of folding blade were revealed. The experiment results demonstrated that the folding blade was valid to control power output and had advantages in reducing thrust with maximum reduction of 51.1% compared to pitch control. Optimum fold angles of 55° and 90° were also found for start up and aerodynamic brake, respectively

  12. Acute Contained Ruptured Aortic Aneurysm Presenting as Left Vocal Fold Immobility

    OpenAIRE

    Gnagi, Sharon H.; Howard, Brittany E.; Hoxworth, Joseph M.; Lott, David G.

    2015-01-01

    Objective. To recognize intrathoracic abnormalities, including expansion or rupture of aortic aneurysms, as a source of acute onset vocal fold immobility. Methods. A case report and review of the literature. Results. An 85-year-old female with prior history of an aortic aneurysm presented to a tertiary care facility with sudden onset hoarseness. On laryngoscopy, the left vocal fold was immobile in the paramedian position. A CT scan obtained that day revealed a new, large hematoma surrounding ...

  13. Paleomagnetic and structural evidence for oblique slip in a fault-related fold, Grayback monocline, Colorado

    Science.gov (United States)

    Tetreault, J.; Jones, C.H.; Erslev, E.; Larson, S.; Hudson, M.; Holdaway, S.

    2008-01-01

    Significant fold-axis-parallel slip is accommodated in the folded strata of the Grayback monocline, northeastern Front Range, Colorado, without visible large strike-slip displacement on the fold surface. In many cases, oblique-slip deformation is partitioned; fold-axis-normal slip is accommodated within folds, and fold-axis-parallel slip is resolved onto adjacent strike-slip faults. Unlike partitioning strike-parallel slip onto adjacent strike-slip faults, fold-axis-parallel slip has deformed the forelimb of the Grayback monocline. Mean compressive paleostress orientations in the forelimb are deflected 15??-37?? clockwise from the regional paleostress orientation of the northeastern Front Range. Paleomagnetic directions from the Permian Ingleside Formation in the forelimb are rotated 16??-42?? clockwise about a bedding-normal axis relative to the North American Permian reference direction. The paleostress and paleomagnetic rotations increase with the bedding dip angle and decrease along strike toward the fold tip. These measurements allow for 50-120 m of fold-axis-parallel slip within the forelimb, depending on the kinematics of strike-slip shear. This resolved horizontal slip is nearly equal in magnitude to the ???180 m vertical throw across the fold. For 200 m of oblique-slip displacement (120 m of strike slip and 180 m of reverse slip), the true shortening direction across the fold is N90??E, indistinguishable from the regionally inferred direction of N90??E and quite different from the S53??E fold-normal direction. Recognition of this deformational style means that significant amounts of strike slip can be accommodated within folds without axis-parallel surficial faulting. ?? 2008 Geological Society of America.

  14. Quantitative Study of Vibrational Symmetry of Injured Vocal Folds via Digital Kymography in Excised Canine Larynges

    Science.gov (United States)

    Krausert, Christopher R.; Ying, Di; Zhang, Yu; Jiang, Jack J.

    2011-01-01

    Purpose: Digital kymography and vocal fold curve fitting are blended with detailed symmetry analysis of kymograms to provide a comprehensive characterization of the vibratory properties of injured vocal folds. Method: Vocal fold vibration of 12 excised canine larynges was recorded under uninjured, unilaterally injured, and bilaterally injured…

  15. The structure of a conserved piezo channel domain reveals a topologically distinct β sandwich fold.

    Science.gov (United States)

    Kamajaya, Aron; Kaiser, Jens T; Lee, Jonas; Reid, Michelle; Rees, Douglas C

    2014-10-07

    Piezo has recently been identified as a family of eukaryotic mechanosensitive channels composed of subunits containing over 2,000 amino acids, without recognizable sequence similarity to other channels. Here, we present the crystal structure of a large, conserved extramembrane domain located just before the last predicted transmembrane helix of C. elegans PIEZO, which adopts a topologically distinct β sandwich fold. The structure was also determined of a point mutation located on a conserved surface at the position equivalent to the human PIEZO1 mutation found in dehydrated hereditary stomatocytosis patients (M2225R). While the point mutation does not change the overall domain structure, it does alter the surface electrostatic potential that may perturb interactions with a yet-to-be-identified ligand or protein. The lack of structural similarity between this domain and any previously characterized fold, including those of eukaryotic and bacterial channels, highlights the distinctive nature of the Piezo family of eukaryotic mechanosensitive channels. Copyright © 2014 Elsevier Ltd. All rights reserved.

  16. An optical flow-based state-space model of the vocal folds

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas

    2017-01-01

    High-speed movies of the vocal fold vibration are valuable data to reveal vocal fold features for voice pathology diagnosis. This work presents a suitable Bayesian model and a purely theoretical discussion for further development of a framework for continuum biomechanical features estimation. A l...... to capture different deformation patterns between the computed optical flow and the finite element deformation, controlled by the choice of the model tissue parameters........ A linear and Gaussian nonstationary state-space model is proposed and thoroughly discussed. The evolution model is based on a self-sustained three-dimensional finite element model of the vocal folds, and the observation model involves a dense optical flow algorithm. The results show that the method is able...

  17. An optical flow-based state-space model of the vocal folds.

    Science.gov (United States)

    Granados, Alba; Brunskog, Jonas

    2017-06-01

    High-speed movies of the vocal fold vibration are valuable data to reveal vocal fold features for voice pathology diagnosis. This work presents a suitable Bayesian model and a purely theoretical discussion for further development of a framework for continuum biomechanical features estimation. A linear and Gaussian nonstationary state-space model is proposed and thoroughly discussed. The evolution model is based on a self-sustained three-dimensional finite element model of the vocal folds, and the observation model involves a dense optical flow algorithm. The results show that the method is able to capture different deformation patterns between the computed optical flow and the finite element deformation, controlled by the choice of the model tissue parameters.

  18. Origin of 6-fold coordinated aluminum at (010-type pyrophyllite edges

    Directory of Open Access Journals (Sweden)

    M. Okumura

    2017-05-01

    Full Text Available To better understand the aqueous chemical reactivity of clay mineral edges we explored the relationships between hydration and the structure of (010-type edges of pyrophyllite. In particular, we used density functional theory and the quantum theory of atoms in molecules to evaluate the stability of 6-fold coordinated hydrated aluminum at the edge in terms of the electron density distribution. Geometrical optimization revealed an intra-edge hydrogen bond network between aluminol hydroxyls and water ligands completing the aluminum coordination shell. From the electron density isosurfaces one water ligand is not covalently bonded to aluminum. Bader charge analysis revealed that OH2 ligands have small negative charge. In addition, it is also found that the charge of the 6-fold coordinated aluminum is larger than one of the 5-fold aluminum. From these results, the charging of the OH2 ligands is interpreted as charge transfer originated from the formation of the hydrogen bond network and not from Al-OH2 interaction per se. This suggests that the weakly bound water ligand in question, and more generally 6-fold hydrated edge Al coordination, is stabilized primarily by the hydrogen bond network which in turn leads to weak ionic attraction to the aluminum center itself. The finding highlights the importance of cooperative effects between solvent structure and the coordination of metal cations exposed at clay mineral edges.

  19. Uplift rates of marine terraces as a constraint on fault-propagation fold kinematics: Examples from the Hawkswood and Kate anticlines, North Canterbury, New Zealand

    Science.gov (United States)

    Oakley, David O. S.; Fisher, Donald M.; Gardner, Thomas W.; Stewart, Mary Kate

    2018-01-01

    Marine terraces on growing fault-propagation folds provide valuable insight into the relationship between fold kinematics and uplift rates, providing a means to distinguish among otherwise non-unique kinematic model solutions. Here, we investigate this relationship at two locations in North Canterbury, New Zealand: the Kate anticline and Haumuri Bluff, at the northern end of the Hawkswood anticline. At both locations, we calculate uplift rates of previously dated marine terraces, using DGPS surveys to estimate terrace inner edge elevations. We then use Markov chain Monte Carlo methods to fit fault-propagation fold kinematic models to structural geologic data, and we incorporate marine terrace uplift into the models as an additional constraint. At Haumuri Bluff, we find that marine terraces, when restored to originally horizontal surfaces, can help to eliminate certain trishear models that would fit the geologic data alone. At Kate anticline, we compare uplift rates at different structural positions and find that the spatial pattern of uplift rates is more consistent with trishear than with a parallel-fault propagation fold kink-band model. Finally, we use our model results to compute new estimates for fault slip rates ( 1-2 m/ka at Kate anticline and 1-4 m/ka at Haumuri Bluff) and ages of the folds ( 1 Ma), which are consistent with previous estimates for the onset of folding in this region. These results are consistent with previous work on the age of onset of folding in this region, provide revised estimates of fault slip rates necessary to understand the seismic hazard posed by these faults, and demonstrate the value of incorporating marine terraces in inverse fold kinematic models as a means to distinguish among non-unique solutions.

  20. Investigation of hindwing folding in ladybird beetles by artificial elytron transplantation and microcomputed tomography.

    Science.gov (United States)

    Saito, Kazuya; Nomura, Shuhei; Yamamoto, Shuhei; Niiyama, Ryuma; Okabe, Yoji

    2017-05-30

    Ladybird beetles are high-mobility insects and explore broad areas by switching between walking and flying. Their excellent wing transformation systems enabling this lifestyle are expected to provide large potential for engineering applications. However, the mechanism behind the folding of their hindwings remains unclear. The reason is that ladybird beetles close the elytra ahead of wing folding, preventing the observation of detailed processes occurring under the elytra. In the present study, artificial transparent elytra were transplanted on living ladybird beetles, thereby enabling us to observe the detailed wing-folding processes. The result revealed that in addition to the abdominal movements mentioned in previous studies, the edge and ventral surface of the elytra, as well as characteristic shaped veins, play important roles in wing folding. The structures of the wing frames enabling this folding process and detailed 3D shape of the hindwing were investigated using microcomputed tomography. The results showed that the tape spring-like elastic frame plays an important role in the wing transformation mechanism. Compared with other beetles, hindwings in ladybird beetles are characterized by two seemingly incompatible properties: ( i ) the wing rigidity with relatively thick veins and ( ii ) the compactness in stored shapes with complex crease patterns. The detailed wing-folding process revealed in this study is expected to facilitate understanding of the naturally optimized system in this excellent deployable structure.

  1. Prevention of vocal fold scarring by local application of basic fibroblast growth factor in a rat vocal fold injury model.

    Science.gov (United States)

    Suzuki, Ryo; Kawai, Yoshitaka; Tsuji, Takuya; Hiwatashi, Nao; Kishimoto, Yo; Tateya, Ichiro; Nakamura, Tatsuo; Hirano, Shigeru

    2017-02-01

    Vocal fold scarring, which causes severe hoarseness, is intractable. The optimal treatment for vocal fold scarring has not been established; therefore, prevention of scarring is important. The aim of this study was to clarify the effectiveness of basic fibroblast growth factor (bFGF) for prevention of postsurgical vocal fold scarring. Prospective animal experiments with controls. The vocal folds of Sprague-Dawley rats were injured unilaterally or bilaterally after local application of a 10 μL solution of bFGF. Larynges ware harvested for histological and immunohistochemical examination 2 months postoperation and for quantitative real-time polymerase chain reaction (qRT-PCR) analysis 1 week postoperation. Histological examination showed significantly increased hyaluronic acid and decreased deposition of dense collagen in the bFGF-treated group at 100 ng/10 μL compared with the sham-treated group. Immunohistochemical examination showed significantly decreased collagen type III deposition in the bFGF-treated group at 100 ng/10 μL compared with the sham-treated group. qRT-PCR revealed that hyaluronan synthase 2 (Has2), Has3, and hepatocyte growth factor were upregulated in bFGF-treated groups compared with sham-treated group. The current results suggest that local application of bFGF at the time of injury has the potential to prevent vocal fold scarring. Preventive injection of bFGF could be applied at the time of phonomicrosurgery to avoid postoperative scar formation. N/A. Laryngoscope, 2016 127:E67-E74, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

  2. Sequence Ready Characterization of the Pericentromeric Region of 19p12

    Energy Technology Data Exchange (ETDEWEB)

    Evan E. Eichler

    2006-08-31

    Current mapping and sequencing strategies have been inadequate within the proximal portion of 19p12 due, in part, to the presence of a recently expanded ZNF (zinc-finger) gene family and the presence of large (25-50 kb) inverted beta-satellite repeat structures which bracket this tandemly duplicated gene family. The virtual of absence of classically defined “unique” sequence within the region has hampered efforts to identify and characterize a suitable minimal tiling path of clones which can be used as templates required for finished sequencing of the region. The goal of this proposal is to develop and implement a novel sequence-anchor strategy to generate a contiguous BAC map of the most proximal portion of chromosome 19p12 for the purpose of complete sequence characterization. The target region will be an estimated 4.5 Mb of DNA extending from STS marker D19S450 (the beginning of the ZNF gene cluster) to the centromeric (alpha-satellite) junction of 19p11. The approach will entail 1) pre-selection of 19p12 BAC and cosmid clones (NIH approved library) utilizing both 19p12 -unique and 19p12-SPECIFIC repeat probes (Eichler et al., 1998); 2) the generation of a BAC/cosmid end-sequence map across the region with a density of one marker every 8kb; 3) the development of a second-generation of STS (sequence tagged sites) which will be used to identify and verify clonal overlap at the level of the sequence; 4) incorporation of these sequence-anchored overlapping clones into existing cosmid/BAC restriction maps developed at Livermore National Laboratory; and 5) validation of the organization of this region utilizing high-resolution FISH techniques (extended chromatin analysis) on monochromosomal 19 somatic cell hybrids and parental cell lines of source material. The data generated will be used in the selection of the most parsimonious tiling path of BAC clones to be sequenced as part of the JGI effort on chromosome 19 and should serve as a model for the sequence

  3. Identification of a key structural element for protein folding within beta-hairpin turns.

    Science.gov (United States)

    Kim, Jaewon; Brych, Stephen R; Lee, Jihun; Logan, Timothy M; Blaber, Michael

    2003-05-09

    Specific residues in a polypeptide may be key contributors to the stability and foldability of the unique native structure. Identification and prediction of such residues is, therefore, an important area of investigation in solving the protein folding problem. Atypical main-chain conformations can help identify strains within a folded protein, and by inference, positions where unique amino acids may have a naturally high frequency of occurrence due to favorable contributions to stability and folding. Non-Gly residues located near the left-handed alpha-helical region (L-alpha) of the Ramachandran plot are a potential indicator of structural strain. Although many investigators have studied mutations at such positions, no consistent energetic or kinetic contributions to stability or folding have been elucidated. Here we report a study of the effects of Gly, Ala and Asn substitutions found within the L-alpha region at a characteristic position in defined beta-hairpin turns within human acidic fibroblast growth factor, and demonstrate consistent effects upon stability and folding kinetics. The thermodynamic and kinetic data are compared to available data for similar mutations in other proteins, with excellent agreement. The results have identified that Gly at the i+3 position within a subset of beta-hairpin turns is a key contributor towards increasing the rate of folding to the native state of the polypeptide while leaving the rate of unfolding largely unchanged.

  4. Improving breakdown voltage performance of SOI power device with folded drift region

    Science.gov (United States)

    Qi, Li; Hai-Ou, Li; Ping-Jiang, Huang; Gong-Li, Xiao; Nian-Jiong, Yang

    2016-07-01

    A novel silicon-on-insulator (SOI) high breakdown voltage (BV) power device with interlaced dielectric trenches (IDT) and N/P pillars is proposed. In the studied structure, the drift region is folded by IDT embedded in the active layer, which results in an increase of length of ionization integral remarkably. The crowding phenomenon of electric field in the corner of IDT is relieved by the N/P pillars. Both traits improve two key factors of BV, the ionization integral length and electric field magnitude, and thus BV is significantly enhanced. The electric field in the dielectric layer is enhanced and a major portion of bias is borne by the oxide layer due to the accumulation of inverse charges (holes) at the corner of IDT. The average value of the lateral electric field of the proposed device reaches 60 V/μm with a 10 μm drift length, which increases by 200% in comparison to the conventional SOI LDMOS, resulting in a breakdown voltage of 607 V. Project supported by the Guangxi Natural Science Foundation of China (Grant Nos. 2013GXNSFAA019335 and 2015GXNSFAA139300), Guangxi Experiment Center of Information Science of China (Grant No. YB1406), Guangxi Key Laboratory of Wireless Wideband Communication and Signal Processing of China, Key Laboratory of Cognitive Radio and Information Processing (Grant No. GXKL061505), Guangxi Key Laboratory of Automobile Components and Vehicle Technology of China (Grant No. 2014KFMS04), and the National Natural Science Foundation of China (Grant Nos. 61361011, 61274077, and 61464003).

  5. Energetics, kinetics, and pathway of SNARE folding and assembly revealed by optical tweezers.

    Science.gov (United States)

    Zhang, Yongli

    2017-07-01

    Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are universal molecular engines that drive membrane fusion. Particularly, synaptic SNAREs mediate fast calcium-triggered fusion of neurotransmitter-containing vesicles with plasma membranes for synaptic transmission, the basis of all thought and action. During membrane fusion, complementary SNAREs located on two apposed membranes (often called t- and v-SNAREs) join together to assemble into a parallel four-helix bundle, releasing the energy to overcome the energy barrier for fusion. A long-standing hypothesis suggests that SNAREs act like a zipper to draw the two membranes into proximity and thereby force them to fuse. However, a quantitative test of this SNARE zippering hypothesis was hindered by difficulties to determine the energetics and kinetics of SNARE assembly and to identify the relevant folding intermediates. Here, we first review different approaches that have been applied to study SNARE assembly and then focus on high-resolution optical tweezers. We summarize the folding energies, kinetics, and pathways of both wild-type and mutant SNARE complexes derived from this new approach. These results show that synaptic SNAREs assemble in four distinct stages with different functions: slow N-terminal domain association initiates SNARE assembly; a middle domain suspends and controls SNARE assembly; and rapid sequential zippering of the C-terminal domain and the linker domain directly drive membrane fusion. In addition, the kinetics and pathway of the stagewise assembly are shared by other SNARE complexes. These measurements prove the SNARE zippering hypothesis and suggest new mechanisms for SNARE assembly regulated by other proteins. © 2017 The Protein Society.

  6. Fracture zones constrained by neutral surfaces in a fault-related fold: Insights from the Kelasu tectonic zone, Kuqa Depression

    Science.gov (United States)

    Sun, Shuai; Hou, Guiting; Zheng, Chunfang

    2017-11-01

    Stress variation associated with folding is one of the controlling factors in the development of tectonic fractures, however, little attention has been paid to the influence of neutral surfaces during folding on fracture distribution in a fault-related fold. In this study, we take the Cretaceous Bashijiqike Formation in the Kuqa Depression as an example and analyze the distribution of tectonic fractures in fault-related folds by core observation and logging data analysis. Three fracture zones are identified in a fault-related fold: a tensile zone, a transition zone and a compressive zone, which may be constrained by two neutral surfaces of fold. Well correlation reveals that the tensile zone and the transition zone reach the maximum thickness at the fold hinge and get thinner in the fold limbs. A 2D viscoelastic stress field model of a fault-related fold was constructed to further investigate the mechanism of fracturing. Statistical and numerical analysis reveal that the tensile zone and the transition zone become thicker with decreasing interlimb angle. Stress variation associated with folding is the first level of control over the general pattern of fracture distribution while faulting is a secondary control over the development of local fractures in a fault-related fold.

  7. Eight-fold quantum states blossom in a high-temperature superconductor

    CERN Multimedia

    2003-01-01

    "Researchers based at Lawrence Berkeley National Laboratory and the University of California at Berkeley have used a scanning tunneling microscope (STM) to reveal eight-fold patterns of quasiparticle interference in the high-temperature superconductor Bi-2212 (bismuth strontium calcium copper oxide)" (2 pages).

  8. Oral and vocal fold diadochokinesis in dysphonic women.

    Science.gov (United States)

    Louzada, Talita; Beraldinelle, Roberta; Berretin-Felix, Giédre; Brasolotto, Alcione Ghedini

    2011-01-01

    The evaluation of oral and vocal fold diadochokinesis (DDK) in individuals with voice disorders may contribute to the understanding of factors that affect the balanced vocal production. Scientific studies that make use of this assessment tool support the knowledge advance of this area, reflecting the development of more appropriate therapeutic planning. To compare the results of oral and vocal fold DDK in dysphonic women and in women without vocal disorders. For this study, 28 voice recordings of women from 19 to 54 years old, diagnosed with dysphonia and submitted to a voice assessment from speech pathologist and otorhinolaryngologist, were used. The control group included 30 nondysphonic women evaluated in prior research from normal adults. The analysis parameters like number and duration of emissions, as well as the regularity of the repetition of syllables "pa", "ta", "ka" and the vowels "a" and "i," were provided by the Advanced Motor Speech Profile program (MSP) Model-5141, version-2.5.2 (KayPentax). The DDK sequence "pataka" was analyzed quantitatively through the Sound Forge 7.0 program, as well as manually with the audio-visual help of sound waves. Average values of oral and vocal fold DDK dysphonic and nondysphonic women were compared using the "t Student" test and were considered significant when pwomen (CvP=10.42%, 12.79%, 12.05%; JittP=2.05%, 6.05%, 3.63%) compared to the control group (CvP=8.86%; 10.95%, 11.20%; JittP=1.82%, 2.98%, 3.15%). Although the results do not indicate any difficulties in oral and laryngeal motor control in the dysphonic group, the largest instability in vocal fold DDK in the experimental group should be considered, and studies of this ability in individuals with communication disorders must be intensified.

  9. The human vocal fold layers. Their delineation inside vocal fold as a background to create 3D digital and synthetic glottal model

    Czech Academy of Sciences Publication Activity Database

    Klepáček, I.; Jirák, D.; Dušková-Smrčková, Miroslava; Janoušková, Olga; Vampola, T.

    2016-01-01

    Roč. 30, č. 5 (2016), s. 529-537 ISSN 0892-1997 R&D Projects: GA ČR(CZ) GAP101/12/1306 Institutional support: RVO:61389013 Keywords : human vocal fold * vocal ligamentous complex * lamina propria Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.381, year: 2016

  10. Geomorphology of the Southwest Coast of County Cork, Ireland: A Look into the Rocks, Folds, and Glacial Scours

    Science.gov (United States)

    Bowden, S.; Wireman, R.; Sautter, L.; Beutel, E. K.

    2015-12-01

    Bathymetric data were collected off the southwest coast of County Cork, Ireland by the joint INFOMAR project between the Marine Institute of Ireland and the Geologic Survey of Ireland. Data were collected using a Kongsberg EM2040 multibeam sonar on the R/V Celtic Voyager, in August and September 2014, and were post-processed with CARIS HIPS and SIPS 8.1 and 9.0 software to create 2D and 3D bathymetric surfaces. From the computer generated images, some of the lithologic formations were relatively aged and observed. The studied regions range in depth from 20 to 118 m, with shallower areas to the northeast. Several large rock outcrops occur, the larger of which shows a vertical rise of nearly 20 m. These outcrops are oriented in a northeast-southwest direction, and exhibit significant bed folding, regional folding, tilted beds, and cross joints. The folds studied are plunging chevron folds. These folds have a northeast-southwest fold axis orthogonal to the cross joints and are older relative to the jointing systems. The NE-SW joints are older than the NW-SE joints due to their correlation with drainage and erosion patterns. Regional folding is the youngest feature due to its superposition on the chevron folding and jointing systems. The interaction of cross jointing and folding is consistent with the geologic history of the area, and creates a unique bathymetry worthy of further study.

  11. Activation of Erk and JNK MAPK pathways by acute swim stress in rat brain regions

    Directory of Open Access Journals (Sweden)

    Salvadore Christopher

    2004-09-01

    Full Text Available Abstract Background The mitogen-activated protein kinases (MAPKs have been shown to participate in a wide array of cellular functions. A role for some MAPKs (e.g., extracellular signal-regulated kinase, Erk1/2 has been documented in response to certain physiological stimuli, such as ischemia, visceral pain and electroconvulsive shock. We recently demonstrated that restraint stress activates the Erk MAPK pathway, but not c-Jun-N-terminal kinase/stress-activated protein kinase (JNK/SAPK or p38MAPK, in several rat brain regions. In the present study, we investigated the effects of a different stressor, acute forced swim stress, on the phosphorylation (P state of these MAPKs in the hippocampus, neocortex, prefrontal cortex, amygdala and striatum. In addition, effects on the phosphorylation state of the upstream activators of the MAPKs, their respective MAPK kinases (MAPKKs; P-MEK1/2, P-MKK4 and P-MKK3/6, were determined. Finally, because the Erk pathway can activate c-AMP response element (CRE binding (CREB protein, and swim stress has recently been reported to enhance CREB phosphorylation, changes in P-CREB were also examined. Results A single 15 min session of forced swimming increased P-Erk2 levels 2–3-fold in the neocortex, prefrontal cortex and striatum, but not in the hippocampus or amygdala. P-JNK levels (P-JNK1 and/or P-JNK2/3 were increased in all brain regions about 2–5-fold, whereas P-p38MAPK levels remained essentially unchanged. Surprisingly, levels of the phosphorylated MAPKKs, P-MEK1/2 and P-MKK4 (activators of the Erk and JNK pathways, respectively were increased in all five brain regions, and much more dramatically (P-MEK1/2, 4.5 to > 100-fold; P-MKK4, 12 to ~300-fold. Consistent with the lack of forced swim on phosphorylation of p38MAPK, there appeared to be no change in levels of its activator, P-MKK3/6. P-CREB was increased in all but cortical (prefrontal, neocortex areas. Conclusions Swim stress specifically and markedly

  12. 12 CFR 790.2 - Central and regional office organization.

    Science.gov (United States)

    2010-01-01

    ... Central and regional office organization. (a) General organization. NCUA is composed of the Board with a... and conducting research in support of NCUA programs, and for preparing reports on research activities... the analysis and development of legislative proposals and public affairs programs. (12) Office of...

  13. Improving protein fold recognition by extracting fold-specific features from predicted residue-residue contacts.

    Science.gov (United States)

    Zhu, Jianwei; Zhang, Haicang; Li, Shuai Cheng; Wang, Chao; Kong, Lupeng; Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo

    2017-12-01

    Accurate recognition of protein fold types is a key step for template-based prediction of protein structures. The existing approaches to fold recognition mainly exploit the features derived from alignments of query protein against templates. These approaches have been shown to be successful for fold recognition at family level, but usually failed at superfamily/fold levels. To overcome this limitation, one of the key points is to explore more structurally informative features of proteins. Although residue-residue contacts carry abundant structural information, how to thoroughly exploit these information for fold recognition still remains a challenge. In this study, we present an approach (called DeepFR) to improve fold recognition at superfamily/fold levels. The basic idea of our approach is to extract fold-specific features from predicted residue-residue contacts of proteins using deep convolutional neural network (DCNN) technique. Based on these fold-specific features, we calculated similarity between query protein and templates, and then assigned query protein with fold type of the most similar template. DCNN has showed excellent performance in image feature extraction and image recognition; the rational underlying the application of DCNN for fold recognition is that contact likelihood maps are essentially analogy to images, as they both display compositional hierarchy. Experimental results on the LINDAHL dataset suggest that even using the extracted fold-specific features alone, our approach achieved success rate comparable to the state-of-the-art approaches. When further combining these features with traditional alignment-related features, the success rate of our approach increased to 92.3%, 82.5% and 78.8% at family, superfamily and fold levels, respectively, which is about 18% higher than the state-of-the-art approach at fold level, 6% higher at superfamily level and 1% higher at family level. An independent assessment on SCOP_TEST dataset showed consistent

  14. The Port Isabel Fold Belt: Salt enhanced Neogene Gravitational Spreading in the East Breaks, Western Gulf of Mexico

    Science.gov (United States)

    Lebit, Hermann; Clavaud, Marie; Whitehead, Sam; Opdyke, Scott; Luneburg, Catalina

    2017-04-01

    The Port Isabel fold belt is situated at the northwestern corner of the deep water Gulf of Mexico where the regional E-W trending Texas-Louisiana shelf bends into the NNE-SSW trend of the East Mexico Shelf. The fold belt forms an allochthonous wedge that ramps up from West to East with its front occupied by shallow salt complexes (local canopies). It is assumed that the belt predominantly comprises Oligocene siliciclastic sequences which reveal eastward facing folds and thrusts with a NE-SW regional trend. The structural architecture of the fold belt is very well imaged on recently processed 3D seismic volumes. Crystal III is a wide-azimuth survey acquired in 2011 and reprocessed in 2016 leveraging newly developed state-of-the-art technology. 3D deghosting, directional designature and multi-model 3D SRME resulted in broader frequency spectrum. The new image benefits from unique implementation of FWI, combined with classic tomographic updates. Seismically transparent zones indicating over-pressured shales are limited to the core of anticlines or to the footwall of internal thrust. Mobile shales associated with diapirs are absent in the study area. In contrast, salt is mobile and apparently forms the major decollement of the PIFB as indicated by remnant salt preferentially located in triangles along the major thrusts and fault intersections or at the core of anticlines. Shallow salt diapirs seam to root in the fold belt, while lacking evidence for salt feeders being connected to the deep salt underlying the Mesozoic to Paleogene substratum of the fold belt. Towards the WNW the fold belt is transient into a extensional regime, characterized by roll-over structures associated with deep reaching normal faults which form ultra-deep mini basins filled with Neogene deposits. Kinematic restorations confirm the simultaneous evolution of the deep mini basins and the outboard fold belt. This resembles a gravitational spreading system with the extensional tectonics of the deep

  15. Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion.

    Science.gov (United States)

    Cohrs, Randall J; Lee, Katherine S; Beach, Addilynn; Sanford, Bridget; Baird, Nicholas L; Como, Christina; Graybill, Chiharu; Jones, Dallas; Tekeste, Eden; Ballard, Mitchell; Chen, Xiaomi; Yalacki, David; Frietze, Seth; Jones, Kenneth; Lenac Rovis, Tihana; Jonjić, Stipan; Haas, Jürgen; Gilden, Don

    2017-10-15

    The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture. IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture. Copyright © 2017 American Society for Microbiology.

  16. Recognition and Binding of a Helix-Loop-Helix Peptide to Carbonic Anhydrase Occurs via Partly Folded Intermediate Structures

    Science.gov (United States)

    Lignell, Martin; Becker, Hans-Christian

    2010-01-01

    Abstract We have studied the association of a helix-loop-helix peptide scaffold carrying a benzenesulfonamide ligand to carbonic anhydrase using steady-state and time-resolved fluorescence spectroscopy. The helix-loop-helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, interpreted as differently interacting peptide/protein structures. We characterize these peptide/protein complexes as mostly bound but unfolded, bound and partly folded, and strongly bound and folded. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using the amplitudes of these times, we can correlate the lifetime groups with the corresponding fluorescence anisotropy component. The 23-ns rotational correlation time, which appears with the same amplitude as a 17-ns fluorescence lifetime, shows that the dansyl fluorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide/protein complex. A partly folded and partly hydrated interfacial structure is manifested in an 8-ns dansyl fluorescence lifetime and a 1.2-ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure, which allows segmental movement and has a higher degree of solvent exposure of dansyl. Indirect excitation of dansyl on the helix-loop-helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase shows that the helix-loop-helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that binding of the peptide to carbonic anhydrase involves a transition from a disordered to an ordered structure of the

  17. Quantification of Drive-Response Relationships Between Residues During Protein Folding.

    Science.gov (United States)

    Qi, Yifei; Im, Wonpil

    2013-08-13

    Mutual correlation and cooperativity are commonly used to describe residue-residue interactions in protein folding/function. However, these metrics do not provide any information on the causality relationships between residues. Such drive-response relationships are poorly studied in protein folding/function and difficult to measure experimentally due to technical limitations. In this study, using the information theory transfer entropy (TE) that provides a direct measurement of causality between two times series, we have quantified the drive-response relationships between residues in the folding/unfolding processes of four small proteins generated by molecular dynamics simulations. Instead of using a time-averaged single TE value, the time-dependent TE is measured with the Q-scores based on residue-residue contacts and with the statistical significance analysis along the folding/unfolding processes. The TE analysis is able to identify the driving and responding residues that are different from the highly correlated residues revealed by the mutual information analysis. In general, the driving residues have more regular secondary structures, are more buried, and show greater effects on the protein stability as well as folding and unfolding rates. In addition, the dominant driving and responding residues from the TE analysis on the whole trajectory agree with those on a single folding event, demonstrating that the drive-response relationships are preserved in the non-equilibrium process. Our study provides detailed insights into the protein folding process and has potential applications in protein engineering and interpretation of time-dependent residue-based experimental observables for protein function.

  18. Enhanced production of poly glutamic acid by Bacillus sp. SW1-2 ...

    African Journals Online (AJOL)

    مستخدم مقتنع بـ Microsoft Office

    2013-01-30

    Jan 30, 2013 ... Verification experiment was carried out to examine model validation and revealed more than. 95% validity. .... to 5-fold increase. On the other ... coefficients; β12, β13, β14, β23, β24 and β34 are cross product coefficients and ..... Ashiuchi M, Kamei T, Baek D-H, Shin S-Y, Sung M-H, Sod K, Yagi T,. Misono H ...

  19. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

    International Nuclear Information System (INIS)

    Shi, Jade; Schwantes, Christian; Bilsel, Osman

    2017-01-01

    The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

  20. Structural basis of the 9-fold symmetry of centrioles.

    Science.gov (United States)

    Kitagawa, Daiju; Vakonakis, Ioannis; Olieric, Natacha; Hilbert, Manuel; Keller, Debora; Olieric, Vincent; Bortfeld, Miriam; Erat, Michèle C; Flückiger, Isabelle; Gönczy, Pierre; Steinmetz, Michel O

    2011-02-04

    The centriole, and the related basal body, is an ancient organelle characterized by a universal 9-fold radial symmetry and is critical for generating cilia, flagella, and centrosomes. The mechanisms directing centriole formation are incompletely understood and represent a fundamental open question in biology. Here, we demonstrate that the centriolar protein SAS-6 forms rod-shaped homodimers that interact through their N-terminal domains to form oligomers. We establish that such oligomerization is essential for centriole formation in C. elegans and human cells. We further generate a structural model of the related protein Bld12p from C. reinhardtii, in which nine homodimers assemble into a ring from which nine coiled-coil rods radiate outward. Moreover, we demonstrate that recombinant Bld12p self-assembles into structures akin to the central hub of the cartwheel, which serves as a scaffold for centriole formation. Overall, our findings establish a structural basis for the universal 9-fold symmetry of centrioles. Copyright © 2011 Elsevier Inc. All rights reserved.

  1. Separable potential approach in the folding model. Pt. 2

    International Nuclear Information System (INIS)

    Lee, C.L.; Robson, D.

    1982-01-01

    A microscopic folding formalism using a separable potential approach is applied to the elastic scattering of the n-α system. Starting with a separable nucleon-nucleon (NN) potential model, a sum of separable nucleon-nucleus potentials is obtained. A simple structure of the α-particle is assumed and the Tabakin, the Doleschall and the Strobel NN potentials are considered. These phenomenological interactions are of Yukawa or gaussian form with variable parameters for each partial wave. Spin-orbit and tensor forces are included. The resulting potentials developed from our folding calculations give approximately the same ssub(1/2) phase shifts for the n-α elastic scattering. However, in the psub(1/2) and psub(3/2) phase-shift analysis, an effective interaction derived from the NN potential is necessary to reproduce the resonances. One free energy independent parameter is introduced in our approximate G-matrix concept to give a good fit for the phase shifts. Single-nucleon knockout exchange (SNKE) is considered throughout. (orig.)

  2. Medialization thyroplasty in glottis insufficiency due to unilateral vocal fold paralysis and after laser cordectomies - preliminary report.

    Science.gov (United States)

    Rzepakowska, Anna; Osuch-Wójcikiewicz, Ewa; Sielska-Badurek, Ewelina; Niemczyk, Kazimierz

    2017-02-28

    Medialization thyroplasty (type I) is surgical procedure performed on the thyroid cartilage. The major indication for this surgery is significant glottis insufficiency due to unilateral vocal fold paresis. However the proce¬dure is also performed after vocal fold resections during cordectomy. The evaluation of voice results in patients after medialisation throplasty. In Otolaryngology Department of Medical University of Warsaw there were performed so far 8 thyroplasty procedures under local anaesthesia with implantation of medical silicon protesis. 6 patients had unilat¬eral vocal fold paresis and the rest two underwent in the past laser cordectomy due to T1a vocal carcinoma. There were no complications during and post the surgery. The follow up examination in 1st , 3rd, 6th i 12th months postoperatively revealed for all patients significant improvement of glottal closure in laryngeal videostrobos¬copy. The voice quality improved both in perceptual evaluation (GRBAS scale) and acoustic analysis (F0, jitter, shim¬mer, NHR) in both patients groups. However the rate of improvement was much more significant in group with uni¬lateral vocal fold paresis. In all patients the maximum phonation time (MPT) increased. The self-evaluation of voice quality with Voice Handicap Index questionnaire confirmed also individual improvement. The speech rehabilitations is not successful in each patient with glottis insufficiency. The medialisation thyroplasty remains the standard procedure for permanent improvement of voice quality in those cases.

  3. Proximity formulae for folding potentials. [Saxon-Woods form factors, first order corrections

    Energy Technology Data Exchange (ETDEWEB)

    Schechter, H; Canto, L F [Rio de Janeiro Univ. (Brazil). Inst. de Fisica

    1979-03-05

    The proximity formulae of Brink and Stancu are applied to folding potentials. A numerical study is made for the case of single folding potentials with Saxon-Woods form factors. It is found that a proximity formula is accurate to 1-2% at separations of the order of the radius of the Coulomb barrier and that first order corrections due to first curvature are important. The approximations involved are discussed.

  4. Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

    Science.gov (United States)

    Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

    2008-03-01

    It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

  5. The Risk of Vocal Fold Atrophy after Serial Corticosteroid Injections of the Vocal Fold.

    Science.gov (United States)

    Shi, Lucy L; Giraldez-Rodriguez, Laureano A; Johns, Michael M

    2016-11-01

    The aim of this study was to illustrate the risk of vocal fold atrophy in patients who receive serial subepithelial steroid injections for vocal fold scar. This study is a retrospective case report of two patients who underwent a series of weekly subepithelial infusions of 10 mg/mL dexamethasone for benign vocal fold lesion. Shortly after the procedures, both patients developed a weak and breathy voice. The first patient was a 53-year-old man with radiation-induced vocal fold stiffness. Six injections were performed unilaterally, and 1 week later, he developed unilateral vocal fold atrophy with new glottal insufficiency. The second patient was a 67-year-old woman with severe vocal fold inflammation related to laryngitis and calcinosis, Raynaud's phenomenon, esophagean dysmotility, sclerodactyly, and telangiectasia (CREST) syndrome. Five injections were performed bilaterally, and 1 week later, she developed bilateral vocal fold atrophy with a large midline glottal gap during phonation. In both cases, the steroid-induced vocal atrophy resolved spontaneously after 4 months. Serial subepithelial steroid infusions of the vocal folds, although safe in the majority of patients, carry the risk of causing temporary vocal fold atrophy when given at short intervals. Copyright © 2016 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  6. ORIGAMI: DELINEATING HALOS USING PHASE-SPACE FOLDS

    Energy Technology Data Exchange (ETDEWEB)

    Falck, Bridget L.; Neyrinck, Mark C.; Szalay, Alexander S. [Department of Physics and Astronomy, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States)

    2012-08-01

    We present the ORIGAMI method of identifying structures, particularly halos, in cosmological N-body simulations. Structure formation can be thought of as the folding of an initially flat three-dimensional manifold in six-dimensional phase space. ORIGAMI finds the outer folds that delineate these structures. Halo particles are identified as those that have undergone shell-crossing along three orthogonal axes, providing a dynamical definition of halo regions that is independent of density. ORIGAMI also identifies other morphological structures: particles that have undergone shell-crossing along 2, 1, or 0 orthogonal axes correspond to filaments, walls, and voids, respectively. We compare this method to a standard friends-of-friends halo-finding algorithm and find that ORIGAMI halos are somewhat larger, more diffuse, and less spherical, though the global properties of ORIGAMI halos are in good agreement with other modern halo-finding algorithms.

  7. ORIGAMI: DELINEATING HALOS USING PHASE-SPACE FOLDS

    International Nuclear Information System (INIS)

    Falck, Bridget L.; Neyrinck, Mark C.; Szalay, Alexander S.

    2012-01-01

    We present the ORIGAMI method of identifying structures, particularly halos, in cosmological N-body simulations. Structure formation can be thought of as the folding of an initially flat three-dimensional manifold in six-dimensional phase space. ORIGAMI finds the outer folds that delineate these structures. Halo particles are identified as those that have undergone shell-crossing along three orthogonal axes, providing a dynamical definition of halo regions that is independent of density. ORIGAMI also identifies other morphological structures: particles that have undergone shell-crossing along 2, 1, or 0 orthogonal axes correspond to filaments, walls, and voids, respectively. We compare this method to a standard friends-of-friends halo-finding algorithm and find that ORIGAMI halos are somewhat larger, more diffuse, and less spherical, though the global properties of ORIGAMI halos are in good agreement with other modern halo-finding algorithms.

  8. A GWAS follow-up study reveals the association of the IL12RB2 gene with systemic sclerosis in Caucasian populations

    Science.gov (United States)

    Bossini-Castillo, Lara; Martin, Jose-Ezequiel; Broen, Jasper; Gorlova, Olga; Simeón, Carmen P.; Beretta, Lorenzo; Vonk, Madelon C.; Luis Callejas, Jose; Castellví, Ivan; Carreira, Patricia; José García-Hernández, Francisco; Fernández Castro, Mónica; Coenen, Marieke J.H.; Riemekasten, Gabriela; Witte, Torsten; Hunzelmann, Nicolas; Kreuter, Alexander; Distler, Jörg H.W.; Koeleman, Bobby P.; Voskuyl, Alexandre E.; Schuerwegh, Annemie J.; Palm, Øyvind; Hesselstrand, Roger; Nordin, Annika; Airó, Paolo; Lunardi, Claudio; Scorza, Raffaella; Shiels, Paul; van Laar, Jacob M.; Herrick, Ariane; Worthington, Jane; Denton, Christopher; Tan, Filemon K.; Arnett, Frank C.; Agarwal, Sandeep K.; Assassi, Shervin; Fonseca, Carmen; Mayes, Maureen D.; Radstake, Timothy R.D.J.; Martin, Javier

    2012-01-01

    A single-nucleotide polymorphism (SNP) at the IL12RB2 locus showed a suggestive association signal in a previously published genome-wide association study (GWAS) in systemic sclerosis (SSc). Aiming to reveal the possible implication of the IL12RB2 gene in SSc, we conducted a follow-up study of this locus in different Caucasian cohorts. We analyzed 10 GWAS-genotyped SNPs in the IL12RB2 region (2309 SSc patients and 5161 controls). We then selected three SNPs (rs3790567, rs3790566 and rs924080) based on their significance level in the GWAS, for follow-up in an independent European cohort comprising 3344 SSc and 3848 controls. The most-associated SNP (rs3790567) was further tested in an independent cohort comprising 597 SSc patients and 1139 controls from the USA. After conditional logistic regression analysis of the GWAS data, we selected rs3790567 [PMH= 1.92 × 10−5 odds ratio (OR) = 1.19] as the genetic variant with the firmest independent association observed in the analyzed GWAS peak of association. After the first follow-up phase, only the association of rs3790567 was consistent (PMH= 4.84 × 10−3 OR = 1.12). The second follow-up phase confirmed this finding (Pχ2 = 2.82 × 10−4 OR = 1.34). After performing overall pooled-analysis of all the cohorts included in the present study, the association found for the rs3790567 SNP in the IL12RB2 gene region reached GWAS-level significant association (PMH= 2.82 × 10−9 OR = 1.17). Our data clearly support the IL12RB2 genetic association with SSc, and suggest a relevant role of the interleukin 12 signaling pathway in SSc pathogenesis. PMID:22076442

  9. Unusual armadillo fold in the human general vesicular transport factor p115.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available The golgin family gives identity and structure to the Golgi apparatus and is part of a complex protein network at the Golgi membrane. The golgin p115 is targeted by the GTPase Rab1a, contains a large globular head region and a long region of coiled-coil which forms an extended rod-like structure. p115 serves as vesicle tethering factor and plays an important role at different steps of vesicular transport. Here we present the 2.2 A-resolution X-ray structure of the globular head region of p115. The structure exhibits an armadillo fold that is decorated by elongated loops and carries a C-terminal non-canonical repeat. This terminal repeat folds into the armadillo superhelical groove and allows homodimeric association with important implications for p115 mediated multiple protein interactions and tethering.

  10. Sparse genetic tracing reveals regionally specific functional organization of mammalian nociceptors.

    Science.gov (United States)

    Olson, William; Abdus-Saboor, Ishmail; Cui, Lian; Burdge, Justin; Raabe, Tobias; Ma, Minghong; Luo, Wenqin

    2017-10-12

    The human distal limbs have a high spatial acuity for noxious stimuli but a low density of pain-sensing neurites. To elucidate mechanisms underlying regional differences in processing nociception, we sparsely traced non-peptidergic nociceptors across the body using a newly generated Mrgprd CreERT2 mouse line. We found that mouse plantar paw skin is also innervated by a low density of Mrgprd + nociceptors, while individual arbors in different locations are comparable in size. Surprisingly, the central arbors of plantar paw and trunk innervating nociceptors have distinct morphologies in the spinal cord. This regional difference is well correlated with a heightened signal transmission for plantar paw circuits, as revealed by both spinal cord slice recordings and behavior assays. Taken together, our results elucidate a novel somatotopic functional organization of the mammalian pain system and suggest that regional central arbor structure could facilitate the "enlarged representation" of plantar paw regions in the CNS.

  11. Radiology findings in adult patients with vocal fold paralysis

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, S. [Helsinki Medical Imaging Centre, University of Helsinki, Haartmaninkatu, Helsinki (Finland)]. E-mail: s.robinson@dzu.at; Pitkaeranta, A. [Department of Otorhinolaryngology, Haartmaninkatu, Helsinki (Finland)

    2006-10-15

    Aim: To compile imaging findings in patients with vocal fold paralysis. Materials and methods: A retrospective analysis of the medical charts of 100 consecutive patients, admitted to our department with vocal fold paralysis was undertaken. After laryngoscopy, patients were referred for radiological work-up depending on their clinical history and clinical findings. Ultrasound of the neck and/or contrast-enhanced spiral computed tomography (CT) of the neck and mediastinum was performed, extending to include the whole chest if necessary. In one patient, CT of the brain and in two patients, magnetic resonance angiography was undertaken. Analysis of the clinical and radiological data was performed to assess the most frequent causes for vocal fold paralysis. Results: In 66% of patients, the paralysis was related to previous surgery. Thirty-four percent of cases were labelled idiopathic after clinical examination. After imaging and follow-up, only 8% remained unexplained. Nine patients suffered from neoplasms, four from vascular disease, and 12 from infections. One patient developed encephalomyelitis disseminata on follow-up. Conclusion: Thorough radiological work-up helps to reduce the amount of idiopathic cases of vocal fold paralysis and guides appropriate therapy.

  12. Radiology findings in adult patients with vocal fold paralysis

    International Nuclear Information System (INIS)

    Robinson, S.; Pitkaeranta, A.

    2006-01-01

    Aim: To compile imaging findings in patients with vocal fold paralysis. Materials and methods: A retrospective analysis of the medical charts of 100 consecutive patients, admitted to our department with vocal fold paralysis was undertaken. After laryngoscopy, patients were referred for radiological work-up depending on their clinical history and clinical findings. Ultrasound of the neck and/or contrast-enhanced spiral computed tomography (CT) of the neck and mediastinum was performed, extending to include the whole chest if necessary. In one patient, CT of the brain and in two patients, magnetic resonance angiography was undertaken. Analysis of the clinical and radiological data was performed to assess the most frequent causes for vocal fold paralysis. Results: In 66% of patients, the paralysis was related to previous surgery. Thirty-four percent of cases were labelled idiopathic after clinical examination. After imaging and follow-up, only 8% remained unexplained. Nine patients suffered from neoplasms, four from vascular disease, and 12 from infections. One patient developed encephalomyelitis disseminata on follow-up. Conclusion: Thorough radiological work-up helps to reduce the amount of idiopathic cases of vocal fold paralysis and guides appropriate therapy

  13. Axons Pull on the Brain, But Tension Does Not Drive Cortical Folding

    Science.gov (United States)

    Xu, Gang; Knutsen, Andrew K.; Dikranian, Krikor; Kroenke, Christopher D.; Bayly, Philip V.; Taber, Larry A.

    2011-01-01

    During human brain development, the cerebral cortex undergoes substantial folding, leading to its characteristic highly convoluted form. Folding is necessary to accommodate the expansion of the cerbral cortex; abnormal cortical folding is linked to various neurological disorders, including schizophrenia, epilepsy, autism and mental retardation. Although this process requires mechanical forces, the specific force-generating mechanisms that drive folding remain unclear. The two most widely accepted hypotheses are (1) folding is caused by differential growth of the cortex and (2) folding is caused by mechanical tension generated in axons. Direct evidence supporting either theory, however, is lacking. Here we show that axons are indeed under considerable tension in the developing ferret brain, but the patterns of tissue stress are not consistent with a causal role for axonal tension. In particular, microdissection assays reveal that significant tension exists along axons aligned circumferentially in subcortical white matter tracts, as well as those aligned radially inside developing gyri (outward folds). Contrary to previous speculation, however, axonal tension is not directed across developing gyri, suggesting that axon tension does not drive folding. On the other hand, using computational (finite element) models, we show that differential cortical growth accompanied by remodeling of the subplate leads to outward folds and stress fields that are consistent with our microdissection experiments, supporting a mechanism involving differential growth. Local perturbations, such as temporal differences in the initiation of cortical growth, can ensure consistent folding patterns. This study shows that a combination of experimental and computational mechanics can be used to evaluate competing hypotheses of morphogenesis, and illuminate the biomechanics of cortical folding. PMID:20590291

  14. NoFold: RNA structure clustering without folding or alignment.

    Science.gov (United States)

    Middleton, Sarah A; Kim, Junhyong

    2014-11-01

    Structures that recur across multiple different transcripts, called structure motifs, often perform a similar function-for example, recruiting a specific RNA-binding protein that then regulates translation, splicing, or subcellular localization. Identifying common motifs between coregulated transcripts may therefore yield significant insight into their binding partners and mechanism of regulation. However, as most methods for clustering structures are based on folding individual sequences or doing many pairwise alignments, this results in a tradeoff between speed and accuracy that can be problematic for large-scale data sets. Here we describe a novel method for comparing and characterizing RNA secondary structures that does not require folding or pairwise alignment of the input sequences. Our method uses the idea of constructing a distance function between two objects by their respective distances to a collection of empirical examples or models, which in our case consists of 1973 Rfam family covariance models. Using this as a basis for measuring structural similarity, we developed a clustering pipeline called NoFold to automatically identify and annotate structure motifs within large sequence data sets. We demonstrate that NoFold can simultaneously identify multiple structure motifs with an average sensitivity of 0.80 and precision of 0.98 and generally exceeds the performance of existing methods. We also perform a cross-validation analysis of the entire set of Rfam families, achieving an average sensitivity of 0.57. We apply NoFold to identify motifs enriched in dendritically localized transcripts and report 213 enriched motifs, including both known and novel structures. © 2014 Middleton and Kim; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

  15. Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P)*

    Science.gov (United States)

    da Palma, Joel Ramos; Cendron, Laura; Seidah, Nabil Georges; Pasquato, Antonella; Kunz, Stefan

    2016-01-01

    The proprotein convertase subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P) is implicated in lipid homeostasis, the unfolded protein response, and lysosome biogenesis. The protease is further hijacked by highly pathogenic emerging viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P requires removal of an N-terminal prodomain, by a multistep process, generating the mature enzyme. Here, we uncover a modular structure of the human SKI-1/S1P prodomain and define its function in folding and activation. We provide evidence that the N-terminal AB fragment of the prodomain represents an autonomous structural and functional unit that is necessary and sufficient for folding and partial activation. In contrast, the C-terminal BC fragment lacks a defined structure but is crucial for autoprocessing and full catalytic activity. Phylogenetic analysis revealed that the sequence of the AB domain is highly conserved, whereas the BC fragment shows considerable variation and seems even absent in some species. Notably, SKI-1/S1P of arthropods, like the fruit fly Drosophila melanogaster, contains a shorter prodomain comprised of full-length AB and truncated BC regions. Swapping the prodomain fragments between fly and human resulted in a fully mature and active SKI-1/S1P chimera. Our study suggests that primordial SKI-1/S1P likely contained a simpler prodomain consisting of the highly conserved AB fragment that represents an independent folding unit. The BC region appears as a later evolutionary acquisition, possibly allowing more subtle fine-tuning of the maturation process. PMID:26645686

  16. Periodic and stochastic thermal modulation of protein folding kinetics.

    Science.gov (United States)

    Platkov, Max; Gruebele, Martin

    2014-07-21

    Chemical reactions are usually observed either by relaxation of a bulk sample after applying a sudden external perturbation, or by intrinsic fluctuations of a few molecules. Here we show that the two ideas can be combined to measure protein folding kinetics, either by periodic thermal modulation, or by creating artificial thermal noise that greatly exceeds natural thermal fluctuations. We study the folding reaction of the enzyme phosphoglycerate kinase driven by periodic temperature waveforms. As the temperature waveform unfolds and refolds the protein, its fluorescence color changes due to FRET (Förster resonant Energy Transfer) of two donor/acceptor fluorophores labeling the protein. We adapt a simple model of periodically driven kinetics that nicely fits the data at all temperatures and driving frequencies: The phase shifts of the periodic donor and acceptor fluorescence signals as a function of driving frequency reveal reaction rates. We also drive the reaction with stochastic temperature waveforms that produce thermal fluctuations much greater than natural fluctuations in the bulk. Such artificial thermal noise allows the recovery of weak underlying signals due to protein folding kinetics. This opens up the possibility for future detection of a stochastic resonance for protein folding subject to noise with controllable amplitude.

  17. Conformational dynamics of a protein in the folded and the unfolded state

    Energy Technology Data Exchange (ETDEWEB)

    Fitter, Joerg

    2003-08-01

    In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

  18. Glycoprotein folding and quality-control mechanisms in protein-folding diseases

    Directory of Open Access Journals (Sweden)

    Sean P. Ferris

    2014-03-01

    Full Text Available Biosynthesis of proteins – from translation to folding to export – encompasses a complex set of events that are exquisitely regulated and scrutinized to ensure the functional quality of the end products. Cells have evolved to capitalize on multiple post-translational modifications in addition to primary structure to indicate the folding status of nascent polypeptides to the chaperones and other proteins that assist in their folding and export. These modifications can also, in the case of irreversibly misfolded candidates, signal the need for dislocation and degradation. The current Review focuses on the glycoprotein quality-control (GQC system that utilizes protein N-glycosylation and N-glycan trimming to direct nascent glycopolypeptides through the folding, export and dislocation pathways in the endoplasmic reticulum (ER. A diverse set of pathological conditions rooted in defective as well as over-vigilant ER quality-control systems have been identified, underlining its importance in human health and disease. We describe the GQC pathways and highlight disease and animal models that have been instrumental in clarifying our current understanding of these processes.

  19. Phi-value analysis of apo-azurin folding: comparison between experiment and theory.

    Science.gov (United States)

    Zong, Chenghang; Wilson, Corey J; Shen, Tongye; Wolynes, Peter G; Wittung-Stafshede, Pernilla

    2006-05-23

    Pseudomonas aeruginosa azurin is a 128-residue beta-sandwich metalloprotein; in vitro kinetic experiments have shown that it folds in a two-state reaction. Here, we used a variational free energy functional to calculate the characteristics of the transition state ensemble (TSE) for folding of the apo-form of P. aeruginosa azurin and investigate how it responds to thermal and mutational changes. The variational method directly yields predicted chevron plots for wild-type and mutant apo-forms of azurin. In parallel, we performed in vitro kinetic-folding experiments on the same set of azurin variants using chemical perturbation. Like the wild-type protein, all apo-variants fold in apparent two-state reactions both in calculations and in stopped-flow mixing experiments. Comparisons of phi (phi) values determined from the experimental and theoretical chevron parameters reveal an excellent agreement for most positions, indicating a polarized, highly structured TSE for folding of P. aeruginosa apo-azurin. We also demonstrate that careful analysis of side-chain interactions is necessary for appropriate theoretical description of core mutants.

  20. Human brain organoids on a chip reveal the physics of folding

    Science.gov (United States)

    Karzbrun, Eyal; Kshirsagar, Aditya; Cohen, Sidney R.; Hanna, Jacob H.; Reiner, Orly

    2018-05-01

    Human brain wrinkling has been implicated in neurodevelopmental disorders and yet its origins remain unknown. Polymer gel models suggest that wrinkling emerges spontaneously due to compression forces arising during differential swelling, but these ideas have not been tested in a living system. Here, we report the appearance of surface wrinkles during the in vitro development and self-organization of human brain organoids in a microfabricated compartment that supports in situ imaging over a timescale of weeks. We observe the emergence of convolutions at a critical cell density and maximal nuclear strain, which are indicative of a mechanical instability. We identify two opposing forces contributing to differential growth: cytoskeletal contraction at the organoid core and cell-cycle-dependent nuclear expansion at the organoid perimeter. The wrinkling wavelength exhibits linear scaling with tissue thickness, consistent with balanced bending and stretching energies. Lissencephalic (smooth brain) organoids display reduced convolutions, modified scaling and a reduced elastic modulus. Although the mechanism here does not include the neuronal migration seen in vivo, it models the physics of the folding brain remarkably well. Our on-chip approach offers a means for studying the emergent properties of organoid development, with implications for the embryonic human brain.

  1. The occurrence and origin of celestite in the Abolfares region, Iran: Implications for Sr-mineralization in Zagros fold belt (ZFB)

    Science.gov (United States)

    Pourkaseb, Houshang; Zarasvandi, Alireza; Rezaei, Mohsen; Mahdavi, Reyhaneh; Ghanavati, Fatemeh

    2017-10-01

    The major celestite deposits in Zagros Fold belt are associated with coastal marine carbonate and evaporate sediments of Oligo-Miocene Asmari and Lower Miocene Ghachsaran Formations. In the Abolfares region, celestite mineralization is extended in the western limb of Bangestan anticline in the carbonates of Early Miocene (middle part of Asmari Formation), underlying by dolomitic carbonates of Burdigalian. From bottom to top three main types of mineralization can be distinguished in the study area: (1) layer texture resulting from replacement of algal limestone by celestite minerals with some parts showing idiomorphic crystals (geodes) along the walls of the cavities, (2) celestite occurrence as irregular massive shape interconnected small crystals and nodules, and (3) celestite mineralization associated with steeply dipping veins and open space fracture fillings, resulting from late-stage epigenetic processes. Highlightly, the ore-hosting carbonate rocks were deposited in an intertidal - supratidal protected setting with hypersaline conditions, in accordance with other celestite deposits of the Zagros Fold belt. The abundance of diagenetic crystallization rhythmites, carbonate and anhydrite inclusions as confirmed by Laser Raman spectroscopy analysis, high Sr/Ba values (average; 8726.1) and strong negative correlations between SO3 vs CaO (R2 = 0.98), SrO vs CaO (R2 = 0.96) with positive correlations between Ba vs SrO (R2 = 0.54) and SO3 vs SrO (R2 = 0.98) highlight the role of high Sr late-diagenetic brines in replacement of carbonates with celestite minerals. It seems that the inception of compressional folding during or soon after the deposition of the Asmari Formation in the carbonate platform at the margin of NW-trending basin in the foreland of the Zagros orogenic belt lead to the upward refluxing of penetrated high-Sr diagenetic brines and celestite mineralization.

  2. Feasibility of Clinical Endoscopy and Stroboscopy in Children With Bilateral Vocal Fold Lesions.

    Science.gov (United States)

    Zacharias, Stephanie R C; Brehm, Susan Baker; Weinrich, Barbara; Kelchner, Lisa; Tabangin, Meredith; de Alarcon, Alessandro

    2016-11-01

    The purpose of this study was to examine the utility of flexible and rigid endoscopy and stroboscopy for the identification of anatomical and physiological features in children with bilateral vocal fold lesions. The secondary purpose was to describe the age distribution of patients who could tolerate use of the different types of endoscopes. This cross-sectional clinic-based study included 38 children (ages 5 to 12 years) diagnosed with bilateral vocal fold lesions via videoendoscopy. Vocal fold vibratory characteristics (e.g., mucosal wave) were rated by 4 clinicians by consensus. Bilateral vocal fold lesions could be well described anatomically after visualization with both flexible and rigid endoscopes and were most commonly described as symmetrical and broad based. However, the clinicians' confidence in the accuracy of stroboscopy for rating vocal fold vibratory characteristics was limited for both flexible and rigid stroboscopes. Videoendoscopy was adequate for viewing and characterizing anatomical structures of bilateral vocal fold lesions in pediatric patients; however, vibratory characteristics were often not fully visualized with videostroboscopy. In view of the importance of visualizing vocal fold vibration in the differential diagnosis and treatment of vocal fold lesions, other imaging modalities, such as high-speed videoendoscopy, may provide more accurate descriptions of vocal fold vibratory characteristics in this population.

  3. Four residues of propeptide are essential for precursor folding of nattokinase.

    Science.gov (United States)

    Jia, Yan; Cao, Xinhua; Deng, Yu; Bao, Wei; Tang, Changyan; Ding, Hanjing; Zheng, Zhongliang; Zou, Guolin

    2014-11-01

    Subtilisin propeptide functions as an intramolecular chaperone that guides precursor folding. Nattokinase, a member of subtilisin family, is synthesized as a precursor consisting of a signal peptide, a propeptide, and a subtilisin domain, and the mechanism of its folding remains to be understood. In this study, the essential residues of nattokinase propeptide which contribute to precursor folding were determined. Deletion analysis showed that the conserved regions in propeptide were important for precursor folding. Single-site and multi-site mutagenesis studies confirmed the role of Tyr10, Gly13, Gly34, and Gly35. During stage (i) and (ii) of precursor folding, Tyr10 and Gly13 would form the part of interface with subtilisin domain. While Gly34 and Gly35 connected with an α-helix that would stabilize the structure of propeptide. The quadruple Ala mutation, Y10A/G13A/G34A/G35A, resulted in a loss of the chaperone function for the propeptide. This work showed the essential residues of propeptide for precursor folding via secondary structure and kinetic parameter analyses. © The Author 2014. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

  4. Vocal fold immobility from a primary minor salivary gland small-cell carcinoma: case report.

    Science.gov (United States)

    Witt, Robert L; Wilson, Patrick A

    2009-02-01

    Small-cell carcinoma of a minor salivary gland is a rare and to the best of our knowledge previously unreported cause of vocal fold immobility. We describe the case of a 68-year-old woman who presented with hoarseness, dysphagia, and weight loss. Examination revealed left vocal fold immobility. She had no other obvious abnormality of the upper airway, neck, or skin. Computed tomography and magnetic resonance imaging demonstrated a 4-cm submucosal oropharyngeal mass with extension to the parapharyngeal space and involvement of the carotid sheath and the foramen ovale at the skull base; imaging also revealed cervical adenopathy. Fine-needle aspiration biopsy identified the mass as a small-cell carcinoma, a finding that was confirmed by immunohistochemistry. Extensive tumor invasion and multiple comorbidities precluded an aggressive management strategy, and the patient was treated palliatively. She died of her disease shortly after her diagnosis. Vocal fold immobility of unknown etiology mandates imaging from the skull base to the upper mediastinum.

  5. Transcutaneous ultrasound for evaluation of vocal fold movement in patients with thyroid disease

    International Nuclear Information System (INIS)

    Wang, Cheng-Ping; Chen, Tseng-Cheng; Yang, Tsung-Lin; Chen, Chun-Nan; Lin, Chin-Fon; Lou, Pei-Jen; Hu, Ya-Ling; Shieh, Ming-Jium; Hsieh, Fon-Jou

    2012-01-01

    Background: Preoperative evaluation of recurrent laryngeal nerve function is important in the context of thyroid surgery. Transcutaneous ultrasound may be useful to visualize vocal fold movement when evaluating thyroid disease. Methods: A 7–18 MHz linear array transducer was placed transversely on the midline of the thyroid cartilage at the anterior neck of patients with thyroid disease. The gray-scale technique was used, with the scan setting for the thyroid gland. Results: Between August 2008 and March 2010, 705 patients, including 672 patients with normal vocal fold movement and 33 patients with vocal fold paralysis were enrolled. They included 159 male and 546 female patients. Their ages ranged from 10 to 88 years. Vocal fold movement could be seen by ultrasound in 614 (87%) patients, including 589 (88%) patients with normal vocal fold movement and 25 (76%) patients with vocal fold paralysis (p = 0.06). The mean age of patients with visible and invisible vocal fold movement was 46.6 and 57.9 years old, respectively (p = 0.001). Ultrasound was able to see vocal fold movement in 533 (98%) female patients but only in 81 (51%) male patients (p = 0.001). Among the patients with vocal fold paralysis, ultrasound revealed palsied vocal folds in 17 of 18 (94%) female patients but in only 8 of 15 (53%) male patients (p = 0.01). Conclusion: Transcutaneous ultrasound represents an alternative tool to evaluate vocal fold movement for more than 85% of patients with thyroid disease, including more than 90% of female patients and about half of male patients.

  6. Collagen Content Limits Optical Coherence Tomography Image Depth in Porcine Vocal Fold Tissue.

    Science.gov (United States)

    Garcia, Jordan A; Benboujja, Fouzi; Beaudette, Kathy; Rogers, Derek; Maurer, Rie; Boudoux, Caroline; Hartnick, Christopher J

    2016-11-01

    Vocal fold scarring, a condition defined by increased collagen content, is challenging to treat without a method of noninvasively assessing vocal fold structure in vivo. The goal of this study was to observe the effects of vocal fold collagen content on optical coherence tomography imaging to develop a quantifiable marker of disease. Excised specimen study. Massachusetts Eye and Ear Infirmary. Porcine vocal folds were injected with collagenase to remove collagen from the lamina propria. Optical coherence tomography imaging was performed preinjection and at 0, 45, 90, and 180 minutes postinjection. Mean pixel intensity (or image brightness) was extracted from images of collagenase- and control-treated hemilarynges. Texture analysis of the lamina propria at each injection site was performed to extract image contrast. Two-factor repeated measure analysis of variance and t tests were used to determine statistical significance. Picrosirius red staining was performed to confirm collagenase activity. Mean pixel intensity was higher at injection sites of collagenase-treated vocal folds than control vocal folds (P Fold change in image contrast was significantly increased in collagenase-treated vocal folds than control vocal folds (P = .002). Picrosirius red staining in control specimens revealed collagen fibrils most prominent in the subepithelium and above the thyroarytenoid muscle. Specimens treated with collagenase exhibited a loss of these structures. Collagen removal from vocal fold tissue increases image brightness of underlying structures. This inverse relationship may be useful in treating vocal fold scarring in patients. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2016.

  7. Folding of multidomain proteins: biophysical consequences of tethering even in apparently independent folding.

    Science.gov (United States)

    Arviv, Oshrit; Levy, Yaakov

    2012-12-01

    Most eukaryotic and a substantial fraction of prokaryotic proteins are composed of more than one domain. The tethering of these evolutionary, structural, and functional units raises, among others, questions regarding the folding process of conjugated domains. Studying the folding of multidomain proteins in silico enables one to identify and isolate the tethering-induced biophysical determinants that govern crosstalks generated between neighboring domains. For this purpose, we carried out coarse-grained and atomistic molecular dynamics simulations of two two-domain constructs from the immunoglobulin-like β-sandwich fold. Each of these was experimentally shown to behave as the "sum of its parts," that is, the thermodynamic and kinetic folding behavior of the constituent domains of these constructs seems to occur independently, with the folding of each domain uncoupled from the folding of its partner in the two-domain construct. We show that the properties of the individual domains can be significantly affected by conjugation to another domain. The tethering may be accompanied by stabilizing as well as destabilizing factors whose magnitude depends on the size of the interface, the length, and the flexibility of the linker, and the relative stability of the domains. Accordingly, the folding of a multidomain protein should not be viewed as the sum of the folding patterns of each of its parts, but rather, it involves abrogating several effects that lead to this outcome. An imbalance between these effects may result in either stabilization or destabilization owing to the tethering. Copyright © 2012 Wiley Periodicals, Inc.

  8. Oral and vocal fold diadochokinesis in dysphonic women

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    Talita Louzada

    2011-12-01

    Full Text Available The evaluation of oral and vocal fold diadochokinesis (DDK in individuals with voice disorders may contribute to the understanding of factors that affect the balanced vocal production. Scientific studies that make use of this assessment tool support the knowledge advance of this area, reflecting the development of more appropriate therapeutic planning. Objective: To compare the results of oral and vocal fold DDK in dysphonic women and in women without vocal disorders. Material and methods: For this study, 28 voice recordings of women from 19 to 54 years old, diagnosed with dysphonia and submitted to a voice assessment from speech pathologist and otorhinolaryngologist, were used. The control group included 30 nondysphonic women evaluated in prior research from normal adults. The analysis parameters like number and duration of emissions, as well as the regularity of the repetition of syllables "pa", "ta", "ka" and the vowels "a" and "i," were provided by the Advanced Motor Speech Profile program (MSP Model-5141, version-2.5.2 (KayPentax. The DDK sequence "pataka" was analyzed quantitatively through the Sound Forge 7.0 program, as well as manually with the audio-visual help of sound waves. Average values of oral and vocal fold DDK dysphonic and nondysphonic women were compared using the "t Student" test and were considered significant when p<0.05. Results: The findings showed no significant differences between populations; however, the coefficient of variation of period (CvP and jitter of period (JittP average of the "ka," "a" and "i" emissions, respectively, were higher in dysphonic women (CvP=10.42%, 12.79%, 12.05%; JittP=2.05%, 6.05%, 3.63% compared to the control group (CvP=8.86%; 10.95%, 11.20%; JittP=1.82%, 2.98%, 3.15%. Conclusion: Although the results do not indicate any difficulties in oral and laryngeal motor control in the dysphonic group, the largest instability in vocal fold DDK in the experimental group should be considered, and

  9. Regional differences in islet distribution in the human pancreas--preferential beta-cell loss in the head region in patients with type 2 diabetes.

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    Xiaojun Wang

    Full Text Available While regional heterogeneity in islet distribution has been well studied in rodents, less is known about human pancreatic histology. To fill gaps in our understanding, regional differences in the adult human pancreas were quantitatively analyzed including the pathogenesis of type 2 diabetes (T2D. Cadaveric pancreas specimens were collected from the head, body and tail regions of each donor, including subjects with no history of diabetes or pancreatic diseases (n = 23 as well as patients with T2D (n = 12. The study further included individuals from whom islets were isolated (n = 7 to study islet yield and function in a clinical setting of islet transplantation. The whole pancreatic sections were examined using an innovative large-scale image capture and unbiased detailed quantitative analyses of the characteristics of islets from each individual (architecture, size, shape and distribution. Islet distribution/density is similar between the head and body regions, but is >2-fold higher in the tail region. In contrast to rodents, islet cellular composition and architecture were similar throughout the pancreas and there was no difference in glucose-stimulated insulin secretion in islets isolated from different regions of the pancreas. Further studies revealed preferential loss of large islets in the head region in patients with T2D. The present study has demonstrated distinct characteristics of the human pancreas, which should provide a baseline for the future studies integrating existing research in the field and helping to advance bi-directional research between humans and preclinical models.

  10. Multidimensional effects of voice therapy in patients affected by unilateral vocal fold paralysis due to cancer.

    Science.gov (United States)

    Barcelos, Camila Barbosa; Silveira, Paula Angélica Lorenzon; Guedes, Renata Lígia Vieira; Gonçalves, Aline Nogueira; Slobodticov, Luciana Dall'Agnol Siqueira; Angelis, Elisabete Carrara-de

    2017-08-24

    Patients with unilateral vocal fold paralysis may demonstrate different degrees of voice perturbation depending on the position of the paralyzed vocal fold. Understanding the effectiveness of voice therapy in this population may be an important coefficient to define the therapeutic approach. To evaluate the voice therapy effectiveness in the short, medium and long-term in patients with unilateral vocal fold paralysis and determine the risk factors for voice rehabilitation failure. Prospective study with 61 patients affected by unilateral vocal fold paralysis enrolled. Each subject had voice therapy with an experienced speech pathologist twice a week. A multidimensional assessment protocol was used pre-treatment and in three different times after voice treatment initiation: short-term (1-3 months), medium-term (4-6 months) and long-term (12 months); it included videoendoscopy, maximum phonation time, GRBASI scale, acoustic voice analysis and the portuguese version of the voice handicap index. Multiple comparisons for GRBASI scale and VHI revealed statistically significant differences, except between medium and long term (pvocal improvement over time with stabilization results after 6 months (medium term). From the 28 patients with permanent unilateral vocal fold paralysis, 18 (69.2%) reached complete glottal closure following vocal therapy (p=0.001). The logistic regression method indicated that the Jitter entered the final model as a risk factor for partial improvement. For every unit of increased jitter, there was an increase of 0.1% (1.001) of the chance for partial improvement, which means an increase on no full improvement chance during rehabilitation. Vocal rehabilitation improves perceptual and acoustic voice parameters and voice handicap index, besides favor glottal closure in patients with unilateral vocal fold paralysis. The results were also permanent during the period of 1 year. The Jitter value, when elevated, is a risk factor for the voice therapy

  11. The Arterial Folding Point During Flexion of the Hip Joint

    International Nuclear Information System (INIS)

    Park, Sung Il; Won, Je Hwan; Kim, Byung Moon; Kim, Jae Keun; Lee, Do Yun

    2005-01-01

    Purpose: Endovascular stents placed in periarticular vessels may be at a greater risk of neointimal hyperplasia and eventual occlusion than those placed in non-periarticular vessels. The purpose of this study was to investigate the location of maximal conformational change along the iliac and femoral artery, the folding point, during flexion of the hip joint and its location relative to the hip joint and the inguinal ligament. Methods: Seventy patients undergoing femoral artery catheterization were evaluated. The patients were 47 men and 23 women and ranged in age from 26 to 75 years (mean 54 years). The arteries (right:left = 34:36) were measured using a marked catheter for sizing vessels. Fluoroscopic images were obtained in anteroposterior and lateral projections in neutral position, and in the lateral projection in flexed position of the hip joint. The folding point was determined by comparing the lateral projection images in the neutral and flexed positions. The distance from the acetabular roof to the folding point and the distance from the inguinal ligament to the folding point was evaluated. Results: : The folding point was located 42.8 ± 28.6 mm cranial to the acetabular roof and 35.1 ± 30.1 mm cranial to the inguinal ligament. As the patient’s age increased, the folding point was located more cranially (p < 0.001). Conclusions: The folding point during flexion of the hip joint was located 42.8 ± 28.6 mm cranial to the acetabular roof and 35.1 ± 30.1 mm cranial to the inguinal ligament. As the patient's age increased, the folding point was located more cranially. When a stent is inserted over this region, more attention may be needed during follow-up to monitor possible occlusion and stent failure.

  12. Analysis of the free-energy surface of proteins from reversible folding simulations.

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    Lucy R Allen

    2009-07-01

    Full Text Available Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

  13. Active folding of fluvial terraces across a `blind' Himalayan deformation front in the Kashmir Himalaya, northwest India.

    Science.gov (United States)

    Gavillot, Y. G.; Meigs, A.; Rittenour, T. M.; Malik, M. O. A.

    2016-12-01

    In Kashmir, the Himalayan Frontal thrust (HFT) is blind, characterized by a broad fold, the Suruin-Mastargh anticline, and displays no emergent faults cutting either limb. A lack of knowledge of the rate of shortening and structural framework of the Suruin-Mastargh anticline hampers quantifying the earthquake potential for the deformation front. Our study utilized the geomorphic expression of dated deformed terraces on the Ujh River in Kashmir. Six terraces are recognized, and four yield multiple optically stimulated luminescence (OSL) and depth profiles terrigenous cosmogenic nuclides (TCN) ages between 53 ka and 0.4 ka. Vector fold restoration of long terrace profiles indicates a deformation pattern characterized by regional uplift across the anticlinal axis and back-limb, and by fold limb rotation on the forelimb. Differential uplift across the fold trace suggests localized deformation. Dip data and stratigraphic thicknesses suggest that a duplex structure is emplaced at depth along the basal décollement, folding the overlying roof thrust and Siwalik-Murree strata into a detachment-like fold. Localized faulting at the fold axis explains the asymmetrical fold geometry. Folding of the oldest dated terrace, suggests rock uplift rates across the Suruin-Mastargh anticline range between 1.8-2.5 mm/yr. Assuming a 25° dipping ramp for the blind structure on the basis of dip data constraints, the shortening rates across the Suruin-Mastargh anticline range between 3.8-5.4 mm/yr since 53 ka. Geodetic data indicate that an 11-12 mm/yr arc-normal shortening rate characterizes the interseismic strain accumulation across the plate boundary due to India-Tibet convergence. These data combined with rates of other active internal faults in the Kashmir Himalaya indicate that the Riasi fault accounts for the remainder 60% of the convergence not taken up by the Suruin-Mastargh anticline. We attribute a non-emergent thrust at the deformation front to reflect deformation controlled

  14. Early Events, Kinetic Intermediates and the Mechanism of Protein Folding in Cytochrome c

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    David S. Kliger

    2009-04-01

    Full Text Available Kinetic studies of the early events in cytochrome c folding are reviewed with a focus on the evidence for folding intermediates on the submillisecond timescale. Evidence from time-resolved absorption, circular dichroism, magnetic circular dichroism, fluorescence energy and electron transfer, small-angle X-ray scattering and amide hydrogen exchange studies on the t £ 1 ms timescale reveals a picture of cytochrome c folding that starts with the ~ 1-ms conformational diffusion dynamics of the unfolded chains. A fractional population of the unfolded chains collapses on the 1 – 100 ms timescale to a compact intermediate IC containing some native-like secondary structure. Although the existence and nature of IC as a discrete folding intermediate remains controversial, there is extensive high time-resolution kinetic evidence for the rapid formation of IC as a true intermediate, i.e., a metastable state separated from the unfolded state by a discrete free energy barrier. Final folding to the native state takes place on millisecond and longer timescales, depending on the presence of kinetic traps such as heme misligation and proline mis-isomerization. The high folding rates observed in equilibrium molten globule models suggest that IC may be a productive folding intermediate. Whether it is an obligatory step on the pathway to the high free energy barrier associated with millisecond timescale folding to the native state, however, remains to be determined.

  15. The effect of vocal fold augmentation on cough symptoms in the presence of glottic insufficiency.

    Science.gov (United States)

    Litts, Juliana K; Fink, Daniel S; Clary, Matthew S

    2017-10-08

    To determine the effect of injection augmentation of the vocal folds on chronic cough symptoms in patients with glottic insufficiency. Medical records from 146 consecutive patients who underwent vocal fold injection augmentation by a fellowship-trained laryngologist between 2013 and 2015 were reviewed. Twenty-three patients (12 male) met inclusion criteria of a vocal fold augmentation injection, cough symptoms lasting more than 8 weeks, and glottic insufficiency as determined by shortened closed phase on stroboscopy. Exclusion criteria included lack of cough complaints, diagnosis of vocal fold immobility, previous history of vocal fold augmentation, and incomplete data sets. Data collected included age, gender, pre- and 1-month postinjection Cough Severity Index (CSI) scores, location of injection (unilateral or bilateral), and patient statement of percent change in symptoms that was recorded at 1-month postinjection visit. Paired t test indicated a significant decrease in CSI scores from pre- (m = 18.5) to 1-month postinjection (m = 12.1) (P = 0.004). Eighteen patients (78.2%) reported a 50% or greater improvement in cough symptoms at the 1-month postinjection visit. Injection augmentation of the vocal folds in the presence of glottic insufficiency appears to improve cough symptoms, as was reported by CSI in patients who are refractory to other medical and behavioral treatments. 4. Laryngoscope, 2017. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  16. Human Brain Organoids on a Chip Reveal the Physics of Folding.

    Science.gov (United States)

    Karzbrun, Eyal; Kshirsagar, Aditya; Cohen, Sidney R; Hanna, Jacob H; Reiner, Orly

    2018-05-01

    Human brain wrinkling has been implicated in neurodevelopmental disorders and yet its origins remain unknown. Polymer gel models suggest that wrinkling emerges spontaneously due to compression forces arising during differential swelling, but these ideas have not been tested in a living system. Here, we report the appearance of surface wrinkles during the in vitro development and self-organization of human brain organoids in a micro-fabricated compartment that supports in situ imaging over a timescale of weeks. We observe the emergence of convolutions at a critical cell density and maximal nuclear strain, which are indicative of a mechanical instability. We identify two opposing forces contributing to differential growth: cytoskeletal contraction at the organoid core and cell-cycle-dependent nuclear expansion at the organoid perimeter. The wrinkling wavelength exhibits linear scaling with tissue thickness, consistent with balanced bending and stretching energies. Lissencephalic (smooth brain) organoids display reduced convolutions, modified scaling and a reduced elastic modulus. Although the mechanism here does not include the neuronal migration seen in in vivo , it models the physics of the folding brain remarkably well. Our on-chip approach offers a means for studying the emergent properties of organoid development, with implications for the embryonic human brain.

  17. Narrow-band imaging (NBI for improving the assessment of vocal fold leukoplakia and overcoming the umbrella effect.

    Directory of Open Access Journals (Sweden)

    H Klimza

    Full Text Available It is crucial to find a balance between functional and oncological outcome when choosing an adequate method for the management of vocal fold leukoplakia. Therefore, a detailed examination is a milestone in the decision-making process.To examine whether narrow-band imaging (NBI can be helpful in vocal fold assessment in the case of leukoplakia and how to overcome the "umbrella effect"- understood as the submucosal vascular pattern hidden under the plaque.Prospective cohort of 41 consecutive patients. Inclusion criteria: vocal fold leukoplakia, no previous procedures (surgery, radiotherapy, and preoperative endoscopy with an optical filter for NBI. Two groups: "suspicious" and "normal", according to the submucosal microvascular pattern of peripheral regions of the mucosa surrounding the plaque, were distinguished. Patients were qualified for a full-thickness or partial-thickness biopsy, respectively. Criteria defining suspected characters were well-demarcated brownish areas with scattered brown spots corresponding to type IV, Va, Vb, and Vc NI classifications.In 22/41 (53.7% patients with "suspected" microvascular pattern, full-thickness biopsy was performed. Moderate and severe dysplasia was revealed in 15 type IV and 7 type Va NI patients. In 19/41 (46.3% patients with proper NBI vessel pattern treated by partial-thickness biopsy, hyperkeratosis was diagnosed. There was a strong correlation between the NBI pattern and final histology: Chi2 (2 = 41.0 (p = 0.0000.The results demonstrate that NBI endoscopic assessment of the submucosal microvascular pattern of mucosa surrounding the plaque can be an effective method to categorise the risk in vocal fold leukoplakia prior to treatment.

  18. Vocal fold nodules in school age children: attention deficit hyperactivity disorder as a potential risk factor.

    Science.gov (United States)

    D'Alatri, Lucia; Petrelli, Livia; Calò, Lea; Picciotti, Pasqualina Maria; Marchese, Maria Raffaella; Bussu, Francesco

    2015-05-01

    To evaluate the presence of symptoms of inattention and hyperactivity/impulsivity in a population of school age children affected by vocal fold nodules. Parents and teachers of 18 children with vocal fold nodules (10 males, eight females; aged between 6 and 12 years) and 20 matched controls without dysphonia and/or vocal fold diseases (11 males, nine females; aged between 6 and 12 years) completed Attention-Deficit/Hyperactivity Disorder (ADHD) rating scale for parents (SDAG [Scala per i Disturbi di Attenzione/Iperattività per Genitori]) and teachers (SDAI [Scala per i Disturbi di Attenzione/Iperattività per Insegnanti) rating scales containing in two subscales items that specifically evaluate the symptoms of ADHD according to the DSM-IV. All children were subjected to videolaryngoscopy. The group with vocal fold nodules scored significantly higher than the controls; the difference between the two groups was statistically significant for both the subscales of both questionnaires (SDAG and SDAI) (P ADHD was formulated. ADHD is a possible risk factor for the development of vocal fold nodules in childhood. SDAG and SDAI rating scales may supplement the diagnostic assessment of children with vocal fold nodules. Copyright © 2015 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  19. Vocal fold immobility: a longitudinal analysis of etiology over 20 years.

    Science.gov (United States)

    Rosenthal, Laura H Swibel; Benninger, Michael S; Deeb, Robert H

    2007-10-01

    To determine the current etiology of vocal fold immobility, identify changing trends over the last 20 years, and compare results to historical reports. The present study is a retrospective analysis of all patients seen within a tertiary care institution between 1996 and 2005 with vocal fold immobility. The results were combined with a previous study of patients within the same institution from 1985 through 1995. Results were compared to the literature. The medical records of all patients assigned a primary or additional diagnostic code for vocal cord paralysis were obtained from the electronic database. Eight hundred twenty-seven patients were available for analysis (435 from the most recent cohort), which is substantially larger than any reported series to date. Vocal fold immobility was most commonly associated with a surgical procedure (37%). Nonthyroid surgeries (66%), such as anterior cervical approaches to the spine and carotid endarterectomies, have surpassed thyroid surgery (33%) as the most common iatrogenic causes. These data represent a change from historical figures in which extralaryngeal malignancies were considered the major cause of unilateral immobility. Thyroidectomy continues to cause the majority (80%) of iatrogenic bilateral vocal fold immobility and 30% of all bilateral immobility. This 20-year longitudinal assessment revealed that the etiology of unilateral vocal fold immobility has changed such that there has been a shift from extralaryngeal malignancies to nonthyroid surgical procedures as the major cause. Thyroid surgery remains the most common cause of bilateral vocal fold immobility.

  20. Structural Analyses of Avocado sunblotch viroid Reveal Differences in the Folding of Plus and Minus RNA Strands

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    Clémentine Delan-Forino

    2014-01-01

    Full Text Available Viroids are small pathogenic circular single-stranded RNAs, present in two complementary sequences, named plus and minus, in infected plant cells. A high degree of complementarities between different regions of the RNAs allows them to adopt complex structures. Since viroids are naked non-coding RNAs, interactions with host factors appear to be closely related to their structural and catalytic characteristics. Avocado sunblotch viroid (ASBVd, a member of the family Avsunviroidae, replicates via a symmetric RNA-dependant rolling-circle process, involving self-cleavage via hammerhead ribozymes. Consequently, it is assumed that ASBVd plus and minus strands adopt similar structures. Moreover, by computer analyses, a quasi-rod-like secondary structure has been predicted. Nevertheless, secondary and tertiary structures of both polarities of ASBVd remain unsolved. In this study, we analyzed the characteristic of each strand of ASBVd through biophysical analyses. We report that ASBVd transcripts of plus and minus polarities exhibit differences in electrophoretic mobility under native conditions and in thermal denaturation profiles. Subsequently, the secondary structures of plus and minus polarities of ASBVd were probed using the RNA-selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE method. The models obtained show that both polarities fold into different structures. Moreover, our results suggest the existence of a kissing-loop interaction within the minus strand that may play a role in in vivo viroid life cycle.

  1. Mechanism of Folding and Activation of Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P).

    Science.gov (United States)

    da Palma, Joel Ramos; Cendron, Laura; Seidah, Nabil Georges; Pasquato, Antonella; Kunz, Stefan

    2016-01-29

    The proprotein convertase subtilisin kexin isozyme-1 (SKI-1)/site-1 protease (S1P) is implicated in lipid homeostasis, the unfolded protein response, and lysosome biogenesis. The protease is further hijacked by highly pathogenic emerging viruses for the processing of their envelope glycoproteins. Zymogen activation of SKI-1/S1P requires removal of an N-terminal prodomain, by a multistep process, generating the mature enzyme. Here, we uncover a modular structure of the human SKI-1/S1P prodomain and define its function in folding and activation. We provide evidence that the N-terminal AB fragment of the prodomain represents an autonomous structural and functional unit that is necessary and sufficient for folding and partial activation. In contrast, the C-terminal BC fragment lacks a defined structure but is crucial for autoprocessing and full catalytic activity. Phylogenetic analysis revealed that the sequence of the AB domain is highly conserved, whereas the BC fragment shows considerable variation and seems even absent in some species. Notably, SKI-1/S1P of arthropods, like the fruit fly Drosophila melanogaster, contains a shorter prodomain comprised of full-length AB and truncated BC regions. Swapping the prodomain fragments between fly and human resulted in a fully mature and active SKI-1/S1P chimera. Our study suggests that primordial SKI-1/S1P likely contained a simpler prodomain consisting of the highly conserved AB fragment that represents an independent folding unit. The BC region appears as a later evolutionary acquisition, possibly allowing more subtle fine-tuning of the maturation process. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Glass ionomer application for vocal fold augmentation: Histopathological analysis on rabbit vocal fold.

    Science.gov (United States)

    Demirci, Sule; Tuzuner, Arzu; Callıoglu, Elif Ersoy; Yumusak, Nihat; Arslan, Necmi; Baltacı, Bülent

    2016-04-01

    The aim of this study was to investigate the use of glass ionomer cement (GIC) as an injection material for vocal fold augmentation and to evaluate the biocompatibility of the material. Ten adult New Zealand rabbits were used. Under general anesthesia, 0.1-cc GIC was injected to one vocal fold and the augmentation of vocal fold was observed. No injection was applied to the opposite side, which was accepted as the control group. The animals were sacrificed after 3 months and the laryngeal specimens were histopathologically evaluated. The injected and the noninjected control vocal folds were analyzed. The GIC particles were observed in histological sections on the injected side, and no foreign body giant cells, granulomatous inflammation, necrosis, or marked chronic inflammation were detected around the glass ionomer particles. Mild inflammatory reactions were noticed in only two specimens. The noninjected sides of vocal folds were completely normal. The findings of this study suggest that GIC is biocompatible and may be further investigated as an alternative injection material for augmentation of the vocal fold. Further studies are required to examine the viscoelastic properties of GIC and the long-term effects in experimental studies. NA. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

  3. PREFACE Protein folding: lessons learned and new frontiers Protein folding: lessons learned and new frontiers

    Science.gov (United States)

    Pappu, Rohit V.; Nussinov, Ruth

    2009-03-01

    In appropriate physiological milieux proteins spontaneously fold into their functional three-dimensional structures. The amino acid sequences of functional proteins contain all the information necessary to specify the folds. This remarkable observation has spawned research aimed at answering two major questions. (1) Of all the conceivable structures that a protein can adopt, why is the ensemble of native-like structures the most favorable? (2) What are the paths by which proteins manage to robustly and reproducibly fold into their native structures? Anfinsen's thermodynamic hypothesis has guided the pursuit of answers to the first question whereas Levinthal's paradox has influenced the development of models for protein folding dynamics. Decades of work have led to significant advances in the folding problem. Mean-field models have been developed to capture our current, coarse grain understanding of the driving forces for protein folding. These models are being used to predict three-dimensional protein structures from sequence and stability profiles as a function of thermodynamic and chemical perturbations. Impressive strides have also been made in the field of protein design, also known as the inverse folding problem, thereby testing our understanding of the determinants of the fold specificities of different sequences. Early work on protein folding pathways focused on the specific sequence of events that could lead to a simplification of the search process. However, unifying principles proved to be elusive. Proteins that show reversible two-state folding-unfolding transitions turned out to be a gift of natural selection. Focusing on these simple systems helped researchers to uncover general principles regarding the origins of cooperativity in protein folding thermodynamics and kinetics. On the theoretical front, concepts borrowed from polymer physics and the physics of spin glasses led to the development of a framework based on energy landscape theories. These

  4. HEMATOMA OF THE PROXIMAL NAIL FOLD. REPORT OF 41 CASES

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    Chang Patricia

    2011-04-01

    Full Text Available Background: The proximal fold is an important part of the nail apparatus it contributes to the formation of the nail plate and through the cuticle acts as an impermeable barrier protecting it from any cause.Objective: To know the proximal nail fold hematoma caused by the use of pulse oximeter.Material and Methods: A descriptive study was conducted in 41 patients with proximal nail hematoma secondary to the use of oximetry in patients hospitalized in the Intermediate and Intensive Care Unit at the Hospital General de Enfermedades from December 1, 2007 to December 31, 2010.Results: We studied 41 patients with proximal nail fold hematoma secondary to the use of oximeter, 30 (73.1% were males and 11 (26.8% females. The numbers of fingers affected by pulse oximeter were in one digit. 30 (73.1% cases, in two digits 6 (14.6%, in three digits 3 (7.3%, in 4 digits 1 (2.4% and in 5 digits 1 (2.4% case. The most affected proximal nail fold was right index: 24 (58.5%, right middle 11 (26.8%, right ring 6 (14.6%, left index 12 (29.2%, and left middle 6 (14.6% cases.Conclusions: Hematomas of the proximal nail fold may be caused by different traumatisms. The use of pulse oximeter is one of them.

  5. The Cenozoic fold-and-thrust belt of Eastern Sardinia: Evidences from the integration of field data with numerically balanced geological cross section

    Science.gov (United States)

    Arragoni, S.; Maggi, M.; Cianfarra, P.; Salvini, F.

    2016-06-01

    Newly collected structural data in Eastern Sardinia (Italy) integrated with numerical techniques led to the reconstruction of a 2-D admissible and balanced model revealing the presence of a widespread Cenozoic fold-and-thrust belt. The model was achieved with the FORC software, obtaining a 3-D (2-D + time) numerical reconstruction of the continuous evolution of the structure through time. The Mesozoic carbonate units of Eastern Sardinia and their basement present a fold-and-thrust tectonic setting, with a westward direction of tectonic transport (referred to the present-day coordinates). The tectonic style of the upper levels is thin skinned, with flat sectors prevailing over ramps and younger-on-older thrusts. Three regional tectonic units are present, bounded by two regional thrusts. Strike-slip faults overprint the fold-and-thrust belt and developed during the Sardinia-Corsica Block rotation along the strike of the preexisting fault ramps, not affecting the numerical section balancing. This fold-and-thrust belt represents the southward prosecution of the Alpine Corsica collisional chain and the missing link between the Alpine Chain and the Calabria-Peloritani Block. Relative ages relate its evolution to the meso-Alpine event (Eocene-Oligocene times), prior to the opening of the Tyrrhenian Sea (Tortonian). Results fill a gap of information about the geodynamic evolution of the European margin in Central Mediterranean, between Corsica and the Calabria-Peloritani Block, and imply the presence of remnants of this double-verging belt, missing in the Southern Tyrrhenian basin, within the Southern Apennine chain. The used methodology proved effective for constraining balanced cross sections also for areas lacking exposures of the large-scale structures, as the case of Eastern Sardinia.

  6. Glottal aerodynamics in compliant, life-sized vocal fold models

    Science.gov (United States)

    McPhail, Michael; Dowell, Grant; Krane, Michael

    2013-11-01

    This talk presents high-speed PIV measurements in compliant, life-sized models of the vocal folds. A clearer understanding of the fluid-structure interaction of voiced speech, how it produces sound, and how it varies with pathology is required to improve clinical diagnosis and treatment of vocal disorders. Physical models of the vocal folds can answer questions regarding the fundamental physics of speech, as well as the ability of clinical measures to detect the presence and extent of disorder. Flow fields were recorded in the supraglottal region of the models to estimate terms in the equations of fluid motion, and their relative importance. Experiments were conducted over a range of driving pressures with flow rates, given by a ball flowmeter, and subglottal pressures, given by a micro-manometer, reported for each case. Imaging of vocal fold motion, vector fields showing glottal jet behavior, and terms estimated by control volume analysis will be presented. The use of these results for a comparison with clinical measures, and for the estimation of aeroacoustic source strengths will be discussed. Acknowledge support from NIH R01 DC005642.

  7. Folding and Fracturing of Rocks: the background

    Science.gov (United States)

    Ramsay, John G.

    2017-04-01

    This book was generated by structural geology teaching classes at Imperial College. I was appointed lecturer during 1957 and worked together with Dr Gilbert Wilson teaching basic structural geology at B.Sc level. I became convinced that the subject, being essentially based on geometric field observations, required a firm mathematical basis for its future development. In particular it seemed to me to require a very sound understanding of stress and strain. My field experience suggested that a knowledge of two- and three-demensional strain was critical in understanding natural tectonic processes. I found a rich confirmation for this in early publications of deformed fossils, oolitic limestones and spotted slates made by several geologists around the beginning of the 20th century (Sorby, Philips, Haughton, Harker) often using surprisingly sophisticated mathematical methods. These methods were discussed and elaborated in Folding and Fracturing of Rocks in a practical way. The geometric features of folds were related to folding mechanisms and the fold related small scale structures such as cleavage, schistosity and lineation explained in terms of rock strain. My work in the Scottish Highlands had shown just how repeated fold superposition could produce very complex geometric features, while further work in other localities suggested that such geometric complications are common in many orogenic zones. From the development of structural geological studies over the past decades it seems that the readers of this book have found many of the ideas set out are still of practical application. The mapping of these outcrop-scale structures should be emphasised in all field studies because they can be seen as ''fingerprints'' of regional scale tectonic processes. My own understanding of structural geology has been inspired by field work and I am of the opinion that future progress in understanding will be likewise based on careful observation and measurement of the features of

  8. An efficient and low resistant circumferential overlap trisection helical baffle heat exchanger with folded baffles

    International Nuclear Information System (INIS)

    Dong, Cong; Li, Dongshuang; Zheng, Youqu; Li, Guoneng; Suo, Yange; Chen, Yaping

    2016-01-01

    Highlights: • The novel cothHXf with circumferential overlap and folded baffles is first proposed. • The key sections of cylindrical and dumbbell are constructed to analyze local flow field characteristics. • The restricted leakage, easier to install and low resistant characteristics are emphasized. • The enhanced heat transfer mechanism of Dean Vortex secondary flow is analyzed. • A variety of comprehensive efficiency assessments are used. - Abstract: An efficient and low resistant circumferential overlap trisection helical baffle shell-and-tube heat exchanger with folded baffles (cothHXf) is presented. It is a modified trisection helical baffle heat exchanger with folded helical baffles for setting rods-and-spanning sleeves. It not only inherits all the merits of circumferential overlap helical baffle scheme, but also adds many additional advantages, such as supporting the inclined baffles with the least rods, simplifying the manufacturing process of spanning tubes and effectively inhibiting the reverse leakage at triangular areas between adjacent baffles. The improved flow characteristic and heat transfer enhancement mechanism of this heat exchanger were numerically investigated in comparison with conventional segmental baffles shell-and-tube heat exchanger (segHX). The flow fields within triangular area of adjacent baffles and nearby regions were depicted. The impacts of the folded baffles on shell-side helical flow, secondary vortex flow, and leakage pattern were analyzed. The distribution configurations of fields of velocity, pressure, temperature and local heat flow rate were revealed. The results show that the heat transfer performance and comprehensive performance evaluation indexes of the cothHXf are much better than those of the segHX while the pressure drop of the cothHXf is much lower than that of the segHX. The numerical simulation results of vivid distributions of flow and thermal fields of the cothHXf can provide theoretical basis for an

  9. Periodic folding of viscous sheets

    Science.gov (United States)

    Ribe, Neil M.

    2003-09-01

    The periodic folding of a sheet of viscous fluid falling upon a rigid surface is a common fluid mechanical instability that occurs in contexts ranging from food processing to geophysics. Asymptotic thin-layer equations for the combined stretching-bending deformation of a two-dimensional sheet are solved numerically to determine the folding frequency as a function of the sheet’s initial thickness, the pouring speed, the height of fall, and the fluid properties. As the buoyancy increases, the system bifurcates from “forced” folding driven kinematically by fluid extrusion to “free” folding in which viscous resistance to bending is balanced by buoyancy. The systematics of the numerically predicted folding frequency are in good agreement with laboratory experiments.

  10. Innervation status in chronic vocal fold paralysis and implications for laryngeal reinnervation.

    Science.gov (United States)

    Lin, R Jun; Smith, Libby J; Munin, Michael C; Sridharan, Shaum; Rosen, Clark A

    2018-01-22

    Treatment options for symptomatic unilateral vocal fold paralysis (VFP) include vocal fold augmentation, laryngeal framework surgery, and laryngeal reinnervation. Laryngeal reinnervation (LR) has been suggested to provide "tone" to the paralyzed VF. This implies a loss of tone as a result of denervation without reinnervation. We performed laryngeal electromyography (LEMG) in patients with chronic VFP to understand the innervation status associated with a chronically paralyzed vocal fold. Retrospective review of LEMG data in adult patients with chronic VFP from January 2009 to December 2014. LEMG was performed at least 6 months after-onset of VFP. Qualitative LEMG, quantitative LEMG, and adductory synkinesis testing were performed, and the parameters were collected. Twenty-seven vocal folds were studied (23 unilateral VFP and 2 bilateral VFP). Average age was 59 ± 17 years. The median duration from recurrent laryngeal nerve injury to LEMG was 8.5 months (range 6-90 months). The majority of patients, 24 of 27 (89%), had motor unit potentials during phonation tasks on LEMG, and only 3 of 27 (11%) patients were electrically silent. Quantitative LEMG showed 287.8 mean turns per second (normal ≥ 400). Motor unit configuration was normal in 12 of 27 (44%), polyphasic in 12 of 27 (44%), and absent in the electrically silent patients. Adductory synkinesis was found in 6 of 20 (30%) patients. Chronic vocal fold paralysis is infrequently associated with absent motor-unit recruitment, indicating some degree of preserved innervation and/or reinnervation in these patients. LEMG should be part of the routine workup for chronic VFP prior to consideration of LR. 4. Laryngoscope, 2018. © 2018 The American Laryngological, Rhinological and Otological Society, Inc.

  11. Grain size dependent phase stabilities and presence of a monoclinic (Pm) phase in the MPB region of (1-x)Bi(Mg_1_/_2Ti_1_/_2)O_3_-_xPbTiO_3

    International Nuclear Information System (INIS)

    Upadhyay, A.; Singh, A.K.

    2016-01-01

    The results of the room temperature structural studies on (1-x)Bi(Mg_1_/_2Ti_1_/_2)O_3_-_xPbTiO_3 ceramics using Rietveld analysis of the powder X-ray diffraction data in the composition range 0.28≤x≤0.45 are presented. The morphotropic phase boundary region exhibits coexistence of monoclinic (space group Pm) and tetragonal (space group P4mm) phases in the composition range 0.33≤x≤0.40. The structure is nearly single phase monoclinic (space group Pm) in the composition range 0.28≤x≤0.32. The structure for the compositions with x≥0.45 is found to be predominantly tetragonal with space group P4mm. Rietveld refinement of the structure rules out the coexistence of rhombohedral and tetragonal phases in the morphotropic phase boundary region reported by earlier authors. The Rietveld structure analysis for the sample x=0.35 calcined at various temperatures reveals that phase fraction of the coexisting phases in the morphotropic phase boundary region varies with grain size. The structural parameters of the two coexisting phases also change slightly with changing grain size. (author)

  12. Hierarchical domain structure of lead-free piezoelectric (Na{sub 1/2} Bi{sub 1/2})TiO{sub 3}-(K{sub 1/2} Bi{sub 1/2})TiO{sub 3} single crystals

    Energy Technology Data Exchange (ETDEWEB)

    Luo, Chengtao, E-mail: lchentao@vt.edu; Wang, Yaojin; Ge, Wenwei; Li, Jiefang; Viehland, Dwight [Materials Science and Engineering, Virginia Tech, Blacksburg, Virginia 24061 (United States); Delaire, Olivier [Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Li, Xiaobin; Luo, Haosu [Shanghai Institute of Ceramics, Chinese Academy of Sciences, 215 Chengbei Road, Jiading, Shanghai 201800 (China)

    2016-05-07

    We report a unique hierarchical domain structure in single crystals of (Na{sub 1/2}Bi{sub 1/2})TiO{sub 3}-xat. %(K{sub 1/2}Bi{sub 1/2})TiO{sub 3} for x = 5 and 8 by transmission electron microscopy (TEM). A high density of polar nano-domains with a lamellar morphology was found, which were self-assembled into a quadrant-like configuration, which then assembled into conventional ferroelectric macro-domains. Studies by high resolution TEM revealed that the polar lamellar regions contained a coexistence of in-phase and anti-phase oxygen octahedral tilt regions of a few nanometers in size. Domain frustration over multiple length scales may play an important role in the stabilization of the hierarchy, and in reducing the piezoelectric response of this Pb-free piezoelectric solid solution.

  13. Acute exposure to vibration is an apoptosis-inducing stimulus in the vocal fold epithelium.

    Science.gov (United States)

    Novaleski, Carolyn K; Kimball, Emily E; Mizuta, Masanobu; Rousseau, Bernard

    2016-10-01

    Clinical voice disorders pose significant communication-related challenges to patients. The purpose of this study was to quantify the rate of apoptosis and tumor necrosis factor-alpha (TNF-α) signaling in vocal fold epithelial cells in response to increasing time-doses and cycle-doses of vibration. 20 New Zealand white breeder rabbits were randomized to three groups of time-doses of vibration exposure (30, 60, 120min) or a control group (120min of vocal fold adduction and abduction). Estimated cycle-doses of vocal fold vibration were extrapolated based on mean fundamental frequency. Laryngeal tissue specimens were evaluated for apoptosis and gene transcript and protein levels of TNF-α. Results revealed that terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) staining was significantly higher after 120min of vibration compared to the control. Transmission electron microscopy (TEM) revealed no significant effect of time-dose on the mean area of epithelial cell nuclei. Extrapolated cycle-doses of vibration exposure were closely related to experimental time-dose conditions, although no significant correlations were observed with TUNEL staining or mean area of epithelial cell nuclei. TUNEL staining was positively correlated with TNF-α protein expression. Our findings suggest that apoptosis can be induced in the vocal fold epithelium after 120min of modal intensity phonation. In contrast, shorter durations of vibration exposure do not result in apoptosis signaling. However, morphological features of apoptosis are not observed using TEM. Future studies are necessary to examine the contribution of abnormal apoptosis to vocal fold diseases. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. The structure of SSO2064, the first representative of Pfam family PF01796, reveals a novel two-domain zinc-ribbon OB-fold architecture with a potential acyl-CoA-binding role

    International Nuclear Information System (INIS)

    Krishna, S. Sri; Aravind, L.; Bakolitsa, Constantina; Caruthers, Jonathan; Carlton, Dennis; Miller, Mitchell D.; Abdubek, Polat; Astakhova, Tamara; Axelrod, Herbert L; Chiu, Hsiu-Ju; Clayton, Thomas; Deller, Marc C.; Duan, Lian; Feuerhelm, Julie; Grant, Joanna C.; Han, Gye Won; Jaroszewski, Lukasz; Jin, Kevin K.; Klock, Heath E.; Knuth, Mark W.; Kumar, Abhinav; Marciano, David; McMullan, Daniel; Morse, Andrew T.; Nigoghossian, Edward; Okach, Linda; Reyes, Ron; Rife, Christopher L.; Bedem, Henry van den; Weekes, Dana; Xu, Qingping; Hodgson, Keith O.; Wooley, John; Elsliger, Marc-André; Deacon, Ashley M.; Godzik, Adam; Lesley, Scott A.; Wilson, Ian A.

    2010-01-01

    The crystal structure of SSO2064, the first structural representative of Pfam family PF01796 (DUF35), reveals a two-domain architecture comprising an N-terminal zinc-ribbon domain and a C-terminal OB-fold domain. Analysis of the domain architecture, operon organization and bacterial orthologs combined with the structural features of SSO2064 suggests a role involving acyl-CoA binding for this family of proteins. SSO2064 is the first structural representative of PF01796 (DUF35), a large prokaryotic family with a wide phylogenetic distribution. The structure reveals a novel two-domain architecture comprising an N-terminal, rubredoxin-like, zinc ribbon and a C-terminal, oligonucleotide/oligosaccharide-binding (OB) fold domain. Additional N-terminal helical segments may be involved in protein–protein interactions. Domain architectures, genomic context analysis and functional evidence from certain bacterial representatives of this family suggest that these proteins form a novel fatty-acid-binding component that is involved in the biosynthesis of lipids and polyketide antibiotics and that they possibly function as acyl-CoA-binding proteins. This structure has led to a re-evaluation of the DUF35 family, which has now been split into two entries in the latest Pfam release (v.24.0)

  15. Six-state, three-level, six-fold ferromagnetic wire system

    International Nuclear Information System (INIS)

    Blachowicz, T.; Ehrmann, A.

    2013-01-01

    Six stable states at remanence were identified in iron wire samples of 6-fold spatial symmetry using micromagnetic simulations and the finite element method. Onion and domain-wall magnetic states were tailored by sample shape and guided by an applied magnetic field with a fixed in-plane direction. Different directions of externally applied magnetic fields revealed a tendency for stability or nonstability of the considered states. -- Highlights: ► In a ferromagnetic wire sample six stable states at remanence were discovered. ► Presented wires provide new effects not met in classical thin-layered solutions. ► The mechanism of working results from competing demagnetizing and exchange fields. ► For different physical conditions onion and domain-wall states were observed. ► Wire samples of 6-fold symmetry can lead to many-level information storage devices

  16. Six-state, three-level, six-fold ferromagnetic wire system

    Energy Technology Data Exchange (ETDEWEB)

    Blachowicz, T., E-mail: tomasz.blachowicz@polsl.pl [Institute of Physics, Silesian University of Technology, 44-100 Gliwice (Poland); Ehrmann, A. [Faculty of Textile and Clothing Technology, Niederrhein University of Applied Sciences, 41065 Mönchengladbach (Germany)

    2013-04-15

    Six stable states at remanence were identified in iron wire samples of 6-fold spatial symmetry using micromagnetic simulations and the finite element method. Onion and domain-wall magnetic states were tailored by sample shape and guided by an applied magnetic field with a fixed in-plane direction. Different directions of externally applied magnetic fields revealed a tendency for stability or nonstability of the considered states. -- Highlights: ► In a ferromagnetic wire sample six stable states at remanence were discovered. ► Presented wires provide new effects not met in classical thin-layered solutions. ► The mechanism of working results from competing demagnetizing and exchange fields. ► For different physical conditions onion and domain-wall states were observed. ► Wire samples of 6-fold symmetry can lead to many-level information storage devices.

  17. Epithelial Folding Driven by Apical or Basal-Lateral Modulation: Geometric Features, Mechanical Inference, and Boundary Effects.

    Science.gov (United States)

    Wen, Fu-Lai; Wang, Yu-Chiun; Shibata, Tatsuo

    2017-06-20

    During embryonic development, epithelial sheets fold into complex structures required for tissue and organ functions. Although substantial efforts have been devoted to identifying molecular mechanisms underlying epithelial folding, far less is understood about how forces deform individual cells to sculpt the overall sheet morphology. Here we describe a simple and general theoretical model for the autonomous folding of monolayered epithelial sheets. We show that active modulation of intracellular mechanics along the basal-lateral as well as the apical surfaces is capable of inducing fold formation in the absence of buckling instability. Apical modulation sculpts epithelia into shallow and V-shaped folds, whereas basal-lateral modulation generates deep and U-shaped folds. These characteristic tissue shapes remain unchanged when subject to mechanical perturbations from the surroundings, illustrating that the autonomous folding is robust against environmental variabilities. At the cellular scale, how cells change shape depends on their initial aspect ratios and the modulation mechanisms. Such cell deformation characteristics are verified via experimental measurements for a canonical folding process driven by apical modulation, indicating that our theory could be used to infer the underlying folding mechanisms based on experimental data. The mechanical principles revealed in our model could potentially guide future studies on epithelial folding in diverse systems. Copyright © 2017. Published by Elsevier Inc.

  18. Psoriasis is not associated with IL-12p70/IL-12p40 production and IL12B promoter polymorphism

    DEFF Research Database (Denmark)

    Litjens, Nicolle H R; van der Plas, Mariena J A; Ravensbergen, Bep

    2004-01-01

    Psoriasis is a type-1 T cell-mediated, chronic inflammatory disease. Since interleukin (IL)-12p70 promotes the development of type-1 T cells, we investigated whether psoriasis is associated with an increased production of this cyctokine by blood cells. Results revealed that the production of IL-12p....... The frequencies of the various genotypes for the promoter region of the gene encoding IL-12p40 (IL12B) did not differ between psoriasis patients and controls. No association was observed between the various IL12B promoter genotypes and the LPS-stimulated production of IL-12p70 or IL-12p40 by blood cells. Together......, psoriasis is not associated with a promoter polymorphism in the IL12B gene nor with the production of IL-12p70 by LPS-stimulated blood cells....

  19. Quantification of fold growth of frontal antiforms in the Zagros fold and thrust belt (Kurdistan, NE Iraq)

    Science.gov (United States)

    Bretis, Bernhard; Bartl, Nikolaus; Graseman, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros fold and thrust belt is a seismically active orogen, where actual kinematic models based on GPS networks suggest a north-south shortening between Arabian and Eurasian in the order of 1.5-2.5 cm/yr. Most of this deformation is partitioned in south-southwest oriented folding and thrusting with northwest-southeast to north-south trending dextral strike slip faults. The Zagros fold and thrust belt is of great economic interest because it has been estimated that this area contains about 15% of the global recoverable hydrocarbons. Whereas the SE parts of the Zagros have been investigated by detailed geological studies, the NW extent being part of the Republic of Iraq have experienced considerably less attention. In this study we combine field work and remote sensing techniques in order to investigate the interaction of erosion and fold growth in the area NE of Erbil (Kurdistan, Iraq). In particular we focus on the interaction of the transient development of drainage patterns along growing antiforms, which directly reflects the kinematics of progressive fold growth. Detailed geomorphological studies of the Bana Bawi-, Permam- and Safeen fold trains show that these anticlines have not developed from subcylindrical embryonic folds but they have merged from different fold segments that joined laterally during fold amplification. This fold segments with length between 5 and 25 km have been detected by mapping ancient and modern river courses that initially cut the nose of growing folds and eventually got defeated leaving behind a wind gap. Fold segments, propagating in different directions force rivers to join resulting in steep gorges, which dissect the merging fold noses. Along rapidly lateral growing folds (e.g. at the SE end of the Bana Bawi Anticline) we observed "curved wind gaps", a new type of abandoned river course, where form of the wind gap mimics a formed nose of a growing antiform. The inherited curved segments of uplifted curved river courses strongly

  20. Can Natural Proteins Designed with ‘Inverted’ Peptide Sequences Adopt Native-Like Protein Folds?

    Science.gov (United States)

    Sridhar, Settu; Guruprasad, Kunchur

    2014-01-01

    We have carried out a systematic computational analysis on a representative dataset of proteins of known three-dimensional structure, in order to evaluate whether it would possible to ‘swap’ certain short peptide sequences in naturally occurring proteins with their corresponding ‘inverted’ peptides and generate ‘artificial’ proteins that are predicted to retain native-like protein fold. The analysis of 3,967 representative proteins from the Protein Data Bank revealed 102,677 unique identical inverted peptide sequence pairs that vary in sequence length between 5–12 and 18 amino acid residues. Our analysis illustrates with examples that such ‘artificial’ proteins may be generated by identifying peptides with ‘similar structural environment’ and by using comparative protein modeling and validation studies. Our analysis suggests that natural proteins may be tolerant to accommodating such peptides. PMID:25210740

  1. Prediction of the optimal set of contacts to fold the smallest knotted protein

    International Nuclear Information System (INIS)

    Dabrowski-Tumanski, P; Jarmolinska, A I; Sulkowska, J I

    2015-01-01

    Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map. (paper)

  2. Prediction of the optimal set of contacts to fold the smallest knotted protein

    Science.gov (United States)

    Dabrowski-Tumanski, P.; Jarmolinska, A. I.; Sulkowska, J. I.

    2015-09-01

    Knotted protein chains represent a new motif in protein folds. They have been linked to various diseases, and recent extensive analysis of the Protein Data Bank shows that they constitute 1.5% of all deposited protein structures. Despite thorough theoretical and experimental investigations, the role of knots in proteins still remains elusive. Nonetheless, it is believed that knots play an important role in mechanical and thermal stability of proteins. Here, we perform a comprehensive analysis of native, shadow-specific and non-native interactions which describe free energy landscape of the smallest knotted protein (PDB id 2efv). We show that the addition of shadow-specific contacts in the loop region greatly enhances folding kinetics, while the addition of shadow-specific contacts along the C-terminal region (H3 or H4) results in a new folding route with slower kinetics. By means of direct coupling analysis (DCA) we predict non-native contacts which also can accelerate kinetics. Next, we show that the length of the C-terminal knot tail is responsible for the shape of the free energy barrier, while the influence of the elongation of the N-terminus is not significant. Finally, we develop a concept of a minimal contact map sufficient for 2efv protein to fold and analyze properties of this protein using this map.

  3. Contribution for geochronological evolution study of the Pianco-Alto Brigida fold belt system

    International Nuclear Information System (INIS)

    Brito Neves, B.B. de; Basei, M.A.S.; Van Schmus, W.R.

    1990-01-01

    The Proterozoic Painco-Alto Fold Belt is situated in the central portion of the Borborema Province and it probably is just a segment of a longer structural development encompassed between the Patos (N) and Pernambuco (S) lineaments. The geochronological study was carried out along a cross section in the central part of the belt (Paraiba State) where biotite-muscovite quartz schists are the predominating rock types, including intercalations of bi-modal volcanics, marbles and quartzites. These rocks were metamorphosed in the amphibolite facies, and they display a complex history of folding. Zircons of the acid volcanics (meta-rhyolytes where analysed through U/Pb method and they plot in a discordia diagram with superior intercept indicating ages around 1100 Ma. Whole rocks Rb/Sr analyses on the same meta-volcanics are indicating isochrons of 950Ma. These data are being respectively interpreted as ages of sedimentation (and volcanism) and regional metamorphism associated to the main (D sub(2)) phase of folding. One of the main purpose of this paper is to stress the importance of the ages around 950Ma, in the central domain of the Borborema Province, as result of regional folding and metamorphism. Some other occurence of ages in the 1000-900Ma range will be discussed as support for this interpretation from now on adopted. (author)

  4. The Structure of Plasmodium falciparum Blood-Stage 6-Cys Protein Pf41 Reveals an Unexpected Intra-Domain Insertion Required for Pf12 Coordination.

    Directory of Open Access Journals (Sweden)

    Michelle L Parker

    Full Text Available Plasmodium falciparum is an apicomplexan parasite and the etiological agent of severe human malaria. The complex P. falciparum life cycle is supported by a diverse repertoire of surface proteins including the family of 6-Cys s48/45 antigens. Of these, Pf41 is localized to the surface of the blood-stage merozoite through its interaction with the glycophosphatidylinositol-anchored Pf12. Our recent structural characterization of Pf12 revealed two juxtaposed 6-Cys domains (D1 and D2. Pf41, however, contains an additional segment of 120 residues predicted to form a large spacer separating its two 6-Cys domains. To gain insight into the assembly mechanism and overall architecture of the Pf12-Pf41 complex, we first determined the 2.45 Å resolution crystal structure of Pf41 using zinc single-wavelength anomalous dispersion. Structural analysis revealed an unexpected domain organization where the Pf41 6-Cys domains are, in fact, intimately associated and the additional residues instead map predominately to an inserted domain-like region (ID located between two β-strands in D1. Notably, the ID is largely proteolyzed in the final structure suggesting inherent flexibility. To assess the contribution of the ID to complex formation, we engineered a form of Pf41 where the ID was replaced by a short glycine-serine linker and showed by isothermal titration calorimetry that binding to Pf12 was abrogated. Finally, protease protection assays showed that the proteolytic susceptibility of the ID was significantly reduced in the complex, consistent with the Pf41 ID directly engaging Pf12. Collectively, these data establish the architectural organization of Pf41 and define an essential role for the Pf41 ID in promoting assembly of the Pf12-Pf41 heterodimeric complex.

  5. How do horizontal, frictional discontinuities affect reverse fault-propagation folding?

    Science.gov (United States)

    Bonanno, Emanuele; Bonini, Lorenzo; Basili, Roberto; Toscani, Giovanni; Seno, Silvio

    2017-09-01

    The development of new reverse faults and related folds is strongly controlled by the mechanical characteristics of the host rocks. In this study we analyze the impact of a specific kind of anisotropy, i.e. thin mechanical and frictional discontinuities, in affecting the development of reverse faults and of the associated folds using physical scaled models. We perform analog modeling introducing one or two initially horizontal, thin discontinuities above an initially blind fault dipping at 30° in one case, and 45° in another, and then compare the results with those obtained from a fully isotropic model. The experimental results show that the occurrence of thin discontinuities affects both the development and the propagation of new faults and the shape of the associated folds. New faults 1) accelerate or decelerate their propagation depending on the location of the tips with respect to the discontinuities, 2) cross the discontinuities at a characteristic angle (∼90°), and 3) produce folds with different shapes, resulting not only from the dip of the new faults but also from their non-linear propagation history. Our results may have direct impact on future kinematic models, especially those aimed to reconstruct the tectonic history of faults that developed in layered rocks or in regions affected by pre-existing faults.

  6. Cation-induced folding of alginate-bearing bilayer gels: an unusual example of spontaneous folding along the long axis.

    Science.gov (United States)

    Athas, Jasmin C; Nguyen, Catherine P; Kummar, Shailaa; Raghavan, Srinivasa R

    2018-04-04

    The spontaneous folding of flat gel films into tubes is an interesting example of self-assembly. Typically, a rectangular film folds along its short axis when forming a tube; folding along the long axis has been seen only in rare instances when the film is constrained. Here, we report a case where the same free-swelling gel film folds along either its long or short axis depending on the concentration of a solute. Our gels are sandwiches (bilayers) of two layers: a passive layer of cross-linked N,N'-dimethylyacrylamide (DMAA) and an active layer of cross-linked DMAA that also contains chains of the biopolymer alginate. Multivalent cations like Ca2+ and Cu2+ induce these bilayer gels to fold into tubes. The folding occurs instantly when a flat film of the gel is introduced into a solution of these cations. The likely cause for folding is that the active layer stiffens and shrinks (because the alginate chains in it get cross-linked by the cations) whereas the passive layer is unaffected. The resulting mismatch in swelling degree between the two layers creates internal stresses that drive folding. Cations that are incapable of cross-linking alginate, such as Na+ and Mg2+, do not induce gel folding. Moreover, the striking aspect is the direction of folding. When the Ca2+ concentration is high (100 mM or higher), the gels fold along their long axis, whereas when the Ca2+ concentration is low (40 to 80 mM), the gels fold along their short axis. We hypothesize that the folding axis is dictated by the inhomogeneous nature of alginate-cation cross-linking, i.e., that the edges get cross-linked before the faces of the gel. At high Ca2+ concentration, the stiffer edges constrain the folding; in turn, the gel folds such that the longer edges are deformed less, which explains the folding along the long axis. At low Ca2+ concentration, the edges and the faces of the gel are more similar in their degree of cross-linking; therefore, the gel folds along its short axis. An analogy

  7. Morphotectonic aspects of active folding in Zagros Mountains (Fin, SE of Iran)

    Science.gov (United States)

    Roustaei, M.; Abbasi, M.

    2008-05-01

    Active deformation in Iran, structural province of Zagros is a result of the convergence between the Arabian & Eurasian plates. The Zagros Mountains in southern Iran are one of the seismically active region & is introduced as fold-thrust belt trending NW-SE within the Arabian plate. Fin lies in Hormozgan province; the south of Iran. The vastness is surrounded by central Iran in the north, High Zagros in the North West and west, Folded Zagros in the east, Makran in the south east and Persian Gulf in the south. The study area is determined by complex structures, alternation of folding, salt diapers and faulting. The surface geology mainly comprises Neogene; Marls, Conglomerate, Sandstones (Mishan, Aghajari, Bakhtiyari formations), old fans and alluvium as syncline that Shur River cuts its north limb and passes from the middle of core .The older formations( Ghachsaran, Rzak and Guri member) folded into prominent anticlines. The fold axes mostly follow the parallel trends .Folds trending are NW-SE (Tashkend anticline), NE-SW (Khur anticline), E-W (Guniz & Handun anticline) and the trend of axes Baz fold in the main part is E-W. Hormoz salt also outcrops in the cores of many whaleback anticlines. Thus, anticlines may be cored with evaporates, even though no salt is currently exposed at the surface. Reason of selecting this area as an example referred to active seismcity. Release of energy is gradually in every events, this seismic character cusses that there was not earthquake with high magnitude in the area but it can not be a role. Answer to the question concerning relationship between folding of the crust layer and faulting at depth is more difficult. There is 2 terms to describe this relationship; "detachment folds" and" forced folds". In this paper, we try to analysis of different satellite imagery; Aster, spot and digital elevation model with high resolution (10 m) in order to detect geomorphic indicators which can help us to find a relationship between faulting

  8. Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model.

    Science.gov (United States)

    Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

    2016-04-05

    Thrombin-binding aptamer (TBA) with the sequence 5'GGTTGGTGTGGTTGG3' could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

  9. Protein folding: Over half a century lasting quest. Comment on "There and back again: Two views on the protein folding puzzle" by Alexei V. Finkelstein et al.

    Science.gov (United States)

    Krokhotin, Andrey; Dokholyan, Nikolay V.

    2017-07-01

    Most proteins fold into unique three-dimensional (3D) structures that determine their biological functions, such as catalytic activity or macromolecular binding. Misfolded proteins can pose a threat through aberrant interactions with other proteins leading to a number of diseases including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis [1,2]. What does determine 3D structure of proteins? The first clue to this question came more than fifty years ago when Anfinsen demonstrated that unfolded proteins can spontaneously fold to their native 3D structures [3,4]. Anfinsen's experiments lead to the conclusion that proteins fold to unique native structure corresponding to the stable and kinetically accessible free energy minimum, and protein native structure is solely determined by its amino acid sequence. The question of how exactly proteins find their free energy minimum proved to be a difficult problem. One of the puzzles, initially pointed out by Levinthal, was an inconsistency between observed protein folding times and theoretical estimates. A self-avoiding polymer model of a globular protein of 100-residues length on a cubic lattice can sample at least 1047 states. Based on the assumption that conformational sampling occurs at the highest vibrational mode of proteins (∼picoseconds), predicted folding time by searching among all the possible conformations leads to ∼1027 years (much larger than the age of the universe) [5]. In contrast, observed protein folding time range from microseconds to minutes. Due to tremendous theoretical progress in protein folding field that has been achieved in past decades, the source of this inconsistency is currently understood that is thoroughly described in the review by Finkelstein et al. [6].

  10. Deletion mutants of region E1 a of AD12 E1 plasmids: Effect on oncogenic transformation

    NARCIS (Netherlands)

    Bos, J.L.; Jochemsen, A.G.; Bernards, R.A.; Schrier, P.I.; Ormondt, H. van; Eb, A.J. van der

    1983-01-01

    Plasmids containing the El region of Ad12 DNA can transform certain rodent cells into oncogenic cells. To study the role of the Ela subregion in the process of oncogenic transformation, Ad12 region El mutants carrying deletions in the Ela region were constructed. Deletion mutants pR7 and pR8 affect

  11. Altered vocal fold kinematics in synthetic self-oscillating models that employ adipose tissue as a lateral boundary condition.

    Science.gov (United States)

    Saidi, Hiba; Erath, Byron D.

    2015-11-01

    The vocal folds play a major role in human communication by initiating voiced sound production. During voiced speech, the vocal folds are set into sustained vibrations. Synthetic self-oscillating vocal fold models are regularly employed to gain insight into flow-structure interactions governing the phonation process. Commonly, a fixed boundary condition is applied to the lateral, anterior, and posterior sides of the synthetic vocal fold models. However, physiological observations reveal the presence of adipose tissue on the lateral surface between the thyroid cartilage and the vocal folds. The goal of this study is to investigate the influence of including this substrate layer of adipose tissue on the dynamics of phonation. For a more realistic representation of the human vocal folds, synthetic multi-layer vocal fold models have been fabricated and tested while including a soft lateral layer representative of adipose tissue. Phonation parameters have been collected and are compared to those of the standard vocal fold models. Results show that vocal fold kinematics are affected by adding the adipose tissue layer as a new boundary condition.

  12. Structural analysis of Bacillus pumilus phenolic acid decarboxylase, a lipocalin-fold enzyme

    International Nuclear Information System (INIS)

    Matte, Allan; Grosse, Stephan; Bergeron, Hélène; Abokitse, Kofi; Lau, Peter C. K.

    2010-01-01

    The crystal structure of phenolic acid decarboxylase from B. pumilus strain UI-670 has been determined and refined at 1.69 Å resolution. The enzyme is a dimer, with each subunit adopting a β-barrel structure belonging to the lipocalin fold. The decarboxylation of phenolic acids, including ferulic and p-coumaric acids, to their corresponding vinyl derivatives is of importance in the flavouring and polymer industries. Here, the crystal structure of phenolic acid decarboxylase (PAD) from Bacillus pumilus strain UI-670 is reported. The enzyme is a 161-residue polypeptide that forms dimers both in the crystal and in solution. The structure of PAD as determined by X-ray crystallography revealed a β-barrel structure and two α-helices, with a cleft formed at one edge of the barrel. The PAD structure resembles those of the lipocalin-fold proteins, which often bind hydrophobic ligands. Superposition of structurally related proteins bound to their cognate ligands shows that they and PAD bind their ligands in a conserved location within the β-barrel. Analysis of the residue-conservation pattern for PAD-related sequences mapped onto the PAD structure reveals that the conservation mainly includes residues found within the hydrophobic core of the protein, defining a common lipocalin-like fold for this enzyme family. A narrow cleft containing several conserved amino acids was observed as a structural feature and a potential ligand-binding site

  13. Co-Transcriptional Folding and Regulation Mechanisms of Riboswitches

    Directory of Open Access Journals (Sweden)

    Sha Gong

    2017-07-01

    Full Text Available Riboswitches are genetic control elements within non-coding regions of mRNA. These self-regulatory elements have been found to sense a range of small metabolites, ions, and other physical signals to exert regulatory control of transcription, translation, and splicing. To date, more than a dozen riboswitch classes have been characterized that vary widely in size and secondary structure. Extensive experiments and theoretical studies have made great strides in understanding the general structures, genetic mechanisms, and regulatory activities of individual riboswitches. As the ligand-dependent co-transcriptional folding and unfolding dynamics of riboswitches are the key determinant of gene expression, it is important to investigate the thermodynamics and kinetics of riboswitches both in the presence and absence of metabolites under the transcription. This review will provide a brief summary of the studies about the regulation mechanisms of the pbuE, SMK, yitJ, and metF riboswitches based on the ligand-dependent co-transcriptional folding of the riboswitches.

  14. Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

    International Nuclear Information System (INIS)

    Rumbajan, Janette Mareska; Aoki, Shigehisa; Kohashi, Kenichi; Oda, Yoshinao; Hata, Kenichiro; Saji, Tsutomu; Taguchi, Tomoaki; Tajiri, Tatsuro; Soejima, Hidenobu; Joh, Keiichiro; Maeda, Toshiyuki; Souzaki, Ryota; Mitsui, Kazumasa; Higashimoto, Ken; Nakabayashi, Kazuhiko; Yatsuki, Hitomi; Nishioka, Kenichi; Harada, Ryoko

    2013-01-01

    Aberrant methylation at imprinted differentially methylated regions (DMRs) in human 11p15.5 has been reported in many tumors including hepatoblastoma. However, the methylation status of imprinted DMRs in imprinted loci scattered through the human genome has not been analyzed yet in any tumors. The methylation statuses of 33 imprinted DMRs were analyzed in 12 hepatoblastomas and adjacent normal liver tissue by MALDI-TOF MS and pyrosequencing. Uniparental disomy (UPD) and copy number abnormalities were investigated with DNA polymorphisms. Among 33 DMRs analyzed, 18 showed aberrant methylation in at least 1 tumor. There was large deviation in the incidence of aberrant methylation among the DMRs. KvDMR1 and IGF2-DMR0 were the most frequently hypomethylated DMRs. INPP5Fv2-DMR and RB1-DMR were hypermethylated with high frequencies. Hypomethylation was observed at certain DMRs not only in tumors but also in a small number of adjacent histologically normal liver tissue, whereas hypermethylation was observed only in tumor samples. The methylation levels of long interspersed nuclear element-1 (LINE-1) did not show large differences between tumor tissue and normal liver controls. Chromosomal abnormalities were also found in some tumors. 11p15.5 and 20q13.3 loci showed the frequent occurrence of both genetic and epigenetic alterations. Our analyses revealed tumor-specific aberrant hypermethylation at some imprinted DMRs in 12 hepatoblastomas with additional suggestion for the possibility of hypomethylation prior to tumor development. Some loci showed both genetic and epigenetic alterations with high frequencies. These findings will aid in understanding the development of hepatoblastoma

  15. Ansa-RLN reinnervation for unilateral vocal fold paralysis in adolescents and young adults.

    Science.gov (United States)

    Smith, Marshall E; Roy, Nelson; Stoddard, Kelly

    2008-09-01

    To assess the outcomes of management of unilateral vocal fold paralysis by ansa-RLN reinnervation in a series of patients ages 12-21. Clinical outcomes study. Six consecutive adolescents and young adults (ages 12-21 years) seeking treatment for unilateral vocal fold paralysis and glottal incompetence underwent ansa-RLN neurorraphy. Pre- and post-operative voice recordings acquired at least 1 year following surgery were submitted to acoustic and perceptual analysis. Patient-based measures were also taken. Mean perceptual visual analogue scale rating of dysphonia severity (0mm=profoundly abnormal voice, 100mm=completely normal voice) improved from 50mm pre-operatively to 82mm post-operatively. Mean maximum phonation time improved from 6.5s to 13.2s. Pitch and dynamic range were also observed to improve. Global self-ratings of voice function (0-100%) increased from 31.2% to 81.6% of normal. Ansa-RLN reinnervation is an effective treatment option for adolescents and young adults with unilateral vocal fold paralysis. The procedure has the potential to improve vocal function substantially, especially in those with isolated paralysis of the recurrent laryngeal nerve. The procedure alleviates the disadvantages associated with other surgical options for this age group.

  16. Clinical Significance of Contralateral Reactive Lesion in Vocal Fold Polyp and Cyst.

    Science.gov (United States)

    Cho, Jung-Hae; Choi, Yong-Sug; Joo, Young-Hoon; Park, Young-Hak; Sun, Dong-Il

    2018-01-01

    We investigated the clinical significance of contralateral reactive lesions in patients undergoing laryngeal microsurgery for benign vocal fold lesions such as vocal polyps and cysts. This was a retrospective, single institution cohort study. Patient medical records were reviewed for demographic characteristics; acoustic, aerodynamic, and perceptual analyses; and Voice Handicap Index score before and after laryngeal microsurgery. Definitive diagnoses were made via intraoperative microlaryngoscopic evaluations. Clinical parameters were assessed to identify risk factors for contralateral reactive lesions. We evaluated surgical outcome using voice analysis. We enrolled 268 patients (109 men and 159 women) with benign vocal fold lesions. A total of 195 (72.8%) had a contralateral reactive vocal fold lesion. A multivariable analysis revealed that being a never smoker and having a hoarseness duration ≥6 months, vocal polyps, and small primary lesions were independent risk factors for contralateral reactive lesions (P vocal fold lesions are frequently detected in patients with vocal polyp and cyst. The reactive lesions had an adverse effect on voice quality. Simultaneous excision of primary and contralateral reactive lesions may be an alternative treatment for better voice outcome. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  17. SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

    Science.gov (United States)

    Melvin, Iain; Ie, Eugene; Kuang, Rui; Weston, Jason; Stafford, William Noble; Leslie, Christina

    2007-05-22

    Predicting a protein's structural class from its amino acid sequence is a fundamental problem in computational biology. Much recent work has focused on developing new representations for protein sequences, called string kernels, for use with support vector machine (SVM) classifiers. However, while some of these approaches exhibit state-of-the-art performance at the binary protein classification problem, i.e. discriminating between a particular protein class and all other classes, few of these studies have addressed the real problem of multi-class superfamily or fold recognition. Moreover, there are only limited software tools and systems for SVM-based protein classification available to the bioinformatics community. We present a new multi-class SVM-based protein fold and superfamily recognition system and web server called SVM-Fold, which can be found at http://svm-fold.c2b2.columbia.edu. Our system uses an efficient implementation of a state-of-the-art string kernel for sequence profiles, called the profile kernel, where the underlying feature representation is a histogram of inexact matching k-mer frequencies. We also employ a novel machine learning approach to solve the difficult multi-class problem of classifying a sequence of amino acids into one of many known protein structural classes. Binary one-vs-the-rest SVM classifiers that are trained to recognize individual structural classes yield prediction scores that are not comparable, so that standard "one-vs-all" classification fails to perform well. Moreover, SVMs for classes at different levels of the protein structural hierarchy may make useful predictions, but one-vs-all does not try to combine these multiple predictions. To deal with these problems, our method learns relative weights between one-vs-the-rest classifiers and encodes information about the protein structural hierarchy for multi-class prediction. In large-scale benchmark results based on the SCOP database, our code weighting approach

  18. Graph-representation of oxidative folding pathways

    Directory of Open Access Journals (Sweden)

    Kaján László

    2005-01-01

    Full Text Available Abstract Background The process of oxidative folding combines the formation of native disulfide bond with conformational folding resulting in the native three-dimensional fold. Oxidative folding pathways can be described in terms of disulfide intermediate species (DIS which can also be isolated and characterized. Each DIS corresponds to a family of folding states (conformations that the given DIS can adopt in three dimensions. Results The oxidative folding space can be represented as a network of DIS states interconnected by disulfide interchange reactions that can either create/abolish or rearrange disulfide bridges. We propose a simple 3D representation wherein the states having the same number of disulfide bridges are placed on separate planes. In this representation, the shuffling transitions are within the planes, and the redox edges connect adjacent planes. In a number of experimentally studied cases (bovine pancreatic trypsin inhibitor, insulin-like growth factor and epidermal growth factor, the observed intermediates appear as part of contiguous oxidative folding pathways. Conclusions Such networks can be used to visualize folding pathways in terms of the experimentally observed intermediates. A simple visualization template written for the Tulip package http://www.tulip-software.org/ can be obtained from V.A.

  19. Understanding ensemble protein folding at atomic detail

    International Nuclear Information System (INIS)

    Wallin, Stefan; Shakhnovich, Eugene I

    2008-01-01

    Although far from routine, simulating the folding of specific short protein chains on the computer, at a detailed atomic level, is starting to become a reality. This remarkable progress, which has been made over the last decade or so, allows a fundamental aspect of the protein folding process to be addressed, namely its statistical nature. In order to make quantitative comparisons with experimental kinetic data a complete ensemble view of folding must be achieved, with key observables averaged over the large number of microscopically different folding trajectories available to a protein chain. Here we review recent advances in atomic-level protein folding simulations and the new insight provided by them into the protein folding process. An important element in understanding ensemble folding kinetics are methods for analyzing many separate folding trajectories, and we discuss techniques developed to condense the large amount of information contained in an ensemble of trajectories into a manageable picture of the folding process. (topical review)

  20. Vocal fold injection medialization laryngoplasty.

    Science.gov (United States)

    Modi, Vikash K

    2012-01-01

    Unilateral vocal fold paralysis (UVFP) can cause glottic insufficiency that can result in hoarseness, chronic cough, dysphagia, and/or aspiration. In rare circumstances, UVFP can cause airway obstruction necessitating a tracheostomy. The treatment options for UVFP include observation, speech therapy, vocal fold injection medialization laryngoplasty, thyroplasty, and laryngeal reinnervation. In this chapter, the author will discuss the technique of vocal fold injection for medialization of a UVFP. Copyright © 2012 S. Karger AG, Basel.

  1. THE INFLUENCE OF FOLD AND FRACTURE DEVELOPMENT ON RESERVOIR BEHAVIOR OF THE LISBURNE GROUP OF NORTHERN ALASKA

    Energy Technology Data Exchange (ETDEWEB)

    Wesley K. Wallace; Catherine L. Hanks; Michael T. Whalen; Jerry Jensen; Paul K. Atkinson; Joseph S. Brinton

    2000-05-01

    -and-thrust belt. The steep forelimbs of angular asymmetrical folds typically have been cut and displaced by thrust faults, resulting in superposition of a fault-bend fold geometry on the truncated folds. Remnant uncut folds within trains of thrust-truncated folds and the predominance of detachment folds to the north suggest that these folds originated as detachment folds. Fold asymmetry and a more uniformly competent Lisburne Limestone may have favored accommodation of a significant proportion of shortening by thrust faulting, in contrast with the dominance of fold shortening to the north. Two dominant sets of fractures are present in the least deformed Lisburne Limestone: Early extension fractures normal to the regional fold trend and late extension and shear fractures parallel to the regional fold trend. These two major fracture sets remain as deformation increases, but they are more variable in orientation, character, and relative age. Compared to fold limbs, the fold hinges display greater density and extent of fractures, more conjugate and shear fractures, and more evidence of penetrative strain. This suggests that hinges remained fixed during fold growth. Late extension fractures normal to the fold axis are common even where penetrative strain is greatest. Fracture density is greater in fine-grained carbonates than in coarse-grained carbonates over the entire spectrum of deformation.

  2. Faults in Paleozoic basement and their participation in Alpine deformation of Greater Caucasus – evidences from materials of restored (balanced) sections in folded sedimentary cover

    Science.gov (United States)

    Yakovlev, Fedor

    2015-04-01

    Method. As each fold has information about strain, numerous folds (0.1-1 km width) inside of hinterland (stripe about 1000 x 50 km) of Greater Caucasus (GC) allow to restore structure for whole sedimentary cover. Material of 24 detailed sections of 510 km total actual length in three regions was used for restoration of structure. These sections were split on 505 domains as associations of 2-5 folds. Three parameters of morphology were measured in these domains: dip of axial plain, dip of envelope plain, value of shortening as interlimb angle [1, 2, 3]. Because these parameters correlate with ellipsoid (ellipse) of strain for domain, sequence of three kinematic operations allow to restore actual state of domain to pre-folded state (from ellipse to circle): rotation to horizontal position of envelope plain, horizontal simple shear to vertical axial plain and vertical flattening (pure shear). Aggregation of chain of pre-folded domains is forming a pre-folded state of whole section, and it allows to calculate of shortening value. For correct detailing of strain study, 78 "structural cells" were formed by aggregation of 5-10 domains in each cell. Some additional observations and calculations allow to find initial and post-folded thickness of sedimentary cover, depth of cover bottom, virtual position of cover top (amplitude of erosion) for all tectonic cells. The received result for 78 cells allowed to understand the main features of GC structure, to see a distribution of basement top depth, to give behavior pattern of the basement and to find a role of faults in shortening of the basement and of sedimentary cover. Results. Three regions of GC were studied: North-Western Caucasus (NWC) [1], Chiaur tectonic zone in South Ossetia (ChZ) and two zones in South-Eastern Caucasus - Tfan Zone (TZ) and Shakhdag zone (ShZ) [3]. The shortening values for structural cells were found as 49% in average for ShZ (with deviations 37÷62%), 55% for TZ (36÷67%), 57% for ChZ (46÷67%) and

  3. Bilateral vocal fold paralysis and dysphagia secondary to diffuse idiopathic skeletal hyperostosis.

    Science.gov (United States)

    Allensworth, Jordan J; O'Dell, Karla D; Schindler, Joshua S

    2017-01-01

    Diffuse idiopathic skeletal hyperostosis (DISH) is an idiopathic spinal disease common in the elderly and characterized by flowing ossification and osteophyte formation along the spinal column. Cervical hyperostosis is capable of producing dysphagia, stridor, and airway obstruction; however, there are no extant reports of true paralysis of bilateral vocal folds in patients fulfilling the criteria for DISH. We report a case of a 61-year-old man presenting with dysphagia and dyspnea. Flexible laryngoscopy revealed bilateral true vocal fold paralysis. Cervical radiograph showed flowing ossification of the anterior longitudinal ligament with preservation of intervertebral disc height. Tracheotomy and cervical osteophytectomy were performed, after which the patient showed improved swallowing and speaking ability and was decannulated without complication. In the case presented, cervical osteophytectomy dramatically reversed bilateral vocal fold paralysis and dysphagia secondary to hyperostosis, thus negating the need for prolonged tracheostomy and feeding tube dependence. © 2016 Wiley Periodicals, Inc. Head Neck 39: E1-E3, 2017. © 2016 Wiley Periodicals, Inc.

  4. Defining structural and functional dimensions of the extracellular thyrotropin receptor region.

    Science.gov (United States)

    Kleinau, Gunnar; Mueller, Sandra; Jaeschke, Holger; Grzesik, Paul; Neumann, Susanne; Diehl, Anne; Paschke, Ralf; Krause, Gerd

    2011-06-24

    The extracellular region of the thyrotropin receptor (TSHR) can be subdivided into the leucine-rich repeat domain (LRRD) and the hinge region. Both the LRRD and the hinge region interact with thyrotropin (TSH) or autoantibodies. Structural data for the TSHR LRRD were previously determined by crystallization (amino acids Glu(30)-Thr(257), 10 repeats), but the structure of the hinge region is still undefined. Of note, the amino acid sequence (Trp(258)-Tyr(279)) following the crystallized LRRD comprises a pattern typical for leucine-rich repeats with conserved hydrophobic side chains stabilizing the repeat fold. Moreover, functional data for amino acids between the LRRD and the transmembrane domain were fragmentary. We therefore investigated systematically these TSHR regions by mutagenesis to reveal insights into their functional contribution and potential structural features. We found that mutations of conserved hydrophobic residues between Thr(257) and Tyr(279) cause TSHR misfold, which supports a structural fold of this peptide, probably as an additional leucine-rich repeat. Furthermore, we identified several new mutations of hydrophilic amino acids in the entire hinge region leading to partial TSHR inactivation, indicating that these positions are important for intramolecular signal transduction. In summary, we provide new information regarding the structural features and functionalities of extracellular TSHR regions. Based on these insights and in context with previous results, we suggest an extracellular activation mechanism that supports an intramolecular agonistic unit as a central switch for activating effects at the extracellular region toward the serpentine domain.

  5. Structurally and functionally characterized in vitro model of rabbit vocal fold epithelium.

    Science.gov (United States)

    Mizuta, Masanobu; Kurita, Takashi; Kimball, Emily E; Rousseau, Bernard

    2017-06-01

    In this paper, we describe a method for primary culture of a well differentiated electrically tight rabbit vocal fold epithelial cell multilayer and the measurement of transepithelial electrical resistance (TEER) for the evaluation of epithelial barrier function in vitro. Rabbit larynges were harvested and enzymatically treated to isolate vocal fold epithelial cells and to establish primary culture. Vocal fold epithelial cells were co-cultured with mitomycin C-treated feeder cells on collagen-coated plates. After 10-14 days in primary culture, cells were passaged and cultured until they achieved 70-90% confluence on collagen-coated plates. Epithelial cells were then passaged onto collagen-coated cell culture inserts using 4.5cm 2 membrane filters (1.0μm pore size) with 10% fetal bovine serum or 30μg/mL bovine pituitary extract to investigate the effects of growth-promoting additives on TEER. Additional experiments were performed to investigate optimal seeding density (1.1, 2.2, 4.4, or 8.9×10 5 cells/cm 2 ), the effect of co-culture with feeder cells, and the effect of passage number on epithelial barrier function. Characterization of in vitro cultures was performed using hematoxylin and eosin staining and immunostaining for vocal fold epithelial cell markers and tight junctions. Results revealed higher TEER in cells supplemented with fetal bovine serum compared to bovine pituitary extract. TEER was highest in cells passaged at a seeding density of 2.2×10 4 cells/cm 2 , and TEER was higher in cells at passage two than passage three. Ultrastructural experiments revealed a well-differentiated epithelial cell multilayer, expressing the epithelial cell markers CK13, CK14 and the tight junction proteins occludin and ZO-1. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Structural Insights into DD-Fold Assembly and Caspase-9 Activation by the Apaf-1 Apoptosome.

    Science.gov (United States)

    Su, Tsung-Wei; Yang, Chao-Yu; Kao, Wen-Pin; Kuo, Bai-Jiun; Lin, Shan-Meng; Lin, Jung-Yaw; Lo, Yu-Chih; Lin, Su-Chang

    2017-03-07

    Death domain (DD)-fold assemblies play a crucial role in regulating the signaling to cell survival or death. Here we report the crystal structure of the caspase recruitment domain (CARD)-CARD disk of the human apoptosome. The structure surprisingly reveals that three 1:1 Apaf-1:procaspase-9 CARD protomers form a novel helical DD-fold assembly on the heptameric wheel-like platform of the apoptosome. The small-angle X-ray scattering and multi-angle light scattering data also support that three protomers could form an oligomeric complex similar to the crystal structure. Interestingly, the quasi-equivalent environment of CARDs could generate different quaternary CARD assemblies. We also found that the type II interaction is conserved in all DD-fold complexes, whereas the type I interaction is found only in the helical DD-fold assemblies. This study provides crucial insights into the caspase activation mechanism, which is tightly controlled by a sophisticated and highly evolved CARD assembly on the apoptosome, and also enables better understanding of the intricate DD-fold assembly. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. A comparison of RNA folding measures

    Directory of Open Access Journals (Sweden)

    Gardner Paul P

    2005-10-01

    Full Text Available Abstract Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE than random sequences with the same dinucleotide frequency. Moreover, even when the MFE is significant, many ncRNAs appear to not have a unique fold, but rather several alternative folds, at least when folded in silico. Furthermore, we find that the six investigated measures are correlated to varying degrees. Conclusion Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score and the other to see if the sequence has a unique fold (the average base-pair distance, D.

  8. Vibratory function and healing outcomes after small intestinal submucosa biomaterial implantation for chronic vocal fold scar.

    Science.gov (United States)

    Pitman, Michael J; Kurita, Takashi; Powell, Maria E; Kimball, Emily E; Mizuta, Masanobu; Chang, Siyuan; Garrett, C Gaelyn; Rousseau, Bernard

    2018-04-01

    Vocal fold scar is a major cause of dysphonia, and optimal treatments do not currently exist. Small intestinal submucosa (SIS) is a biomaterial developed for the treatment of a variety of pathologies. The purpose of this study was to investigate the effects of SIS implantation on tissue remodeling in scarred vocal folds using routine staining, immunohistochemistry, and high-speed videoendoscopy (HSV). Prospective, blinded group analysis. Thirteen New Zealand White rabbits underwent a vocal fold scarring procedure followed by microflap elevation with or without SIS implantation. Seven months later, they underwent a phonation procedure with HSV and laryngeal harvest. Alcian blue and elastica van Gieson staining and immunohistochemistry for collagen types I and III were used to evaluate histological healing outcomes. Dynamic functional remodeling of the scarred vocal fold in the presence of SIS implants was evaluated using HSV imaging to capture restoration of vibratory amplitude, amplitude ratio, and left-right phase symmetry. Density of collagen I was significantly decreased in SIS versus microflap-treated vocal folds. No differences were found between groups for hyaluronic acid, elastin, or collagen type III. Organization of elastin in the subepithelial region appeared to affect amplitude of vibration and the shape of the vocal fold edge. SIS implantation into chronic scar reduced the density of collagen I deposits. There was no evidence of a negative impact or complication from SIS implantation. Regardless of treatment type, organization of elastin in the subepithelial region may be important to vibratory outcomes. NA. Laryngoscope, 128:901-908, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  9. Contemporary deformation in the Yakima fold and thrust belt estimated with GPS

    Science.gov (United States)

    McCaffrey, Robert; King, Robert W.; Wells, Ray; Lancaster, Matthew; Miller, M. Meghan

    2016-01-01

    Geodetic, geologic and palaeomagnetic data reveal that Oregon (western USA) rotates clockwise at 0.3 to 1.0° Ma−1 (relative to North America) about an axis near the Idaho–Oregon–Washington border, while northeast Washington is relatively fixed. This rotation has been going on for at least 15 Ma. The Yakima fold and thrust belt (YFTB) forms the boundary between northern Oregon and central Washington where convergence of the clockwise-rotating Oregon block is apparently accommodated. North–south shortening across the YFTB has been thought to occur in a fan-like manner, increasing in rate to the west. We obtained high-accuracy, high-density geodetic GPS measurements in 2012–2014 that are used with earlier GPS measurements from the 1990s to characterize YFTB kinematics. The new results show that the deformation associated with the YFTB starts at the Blue Mountains Anticline in northern Oregon and extends north beyond the Frenchman Hills in Washington, past the epicentre of the 1872 Mw 7.0 Entiat earthquake to 49°N. The north–south strain rate across the region is 2 to 3 × 10−9 yr−1 between the volcanic arc and the eastern edge of the YFTB (241.0°E); east of there it drops to about 10−9 yr−1. At the eastern boundary of the YFTB, faults and earthquake activity are truncated by a north-trending, narrow zone of deformation that runs along the Pasco Basin and Moses Lake regions near 240.9°E. This zone, abutting the Department of Energy Hanford Nuclear Reservation, accommodates about 0.5 mm yr−1 of east to northeast shortening. A similar zone of N-trending transpression is seen along 239.9°E where there is a change in the strike of the Yakima folds. The modern deformation of the YFTB is about 600 km wide from south to north and internally may be controlled by pre-existing crustal structure.

  10. Principles of Chromosome Architecture Revealed by Hi-C.

    Science.gov (United States)

    Eagen, Kyle P

    2018-06-01

    Chromosomes are folded and compacted in interphase nuclei, but the molecular basis of this folding is poorly understood. Chromosome conformation capture methods, such as Hi-C, combine chemical crosslinking of chromatin with fragmentation, DNA ligation, and high-throughput DNA sequencing to detect neighboring loci genome-wide. Hi-C has revealed the segregation of chromatin into active and inactive compartments and the folding of DNA into self-associating domains and loops. Depletion of CTCF, cohesin, or cohesin-associated proteins was recently shown to affect the majority of domains and loops in a manner that is consistent with a model of DNA folding through extrusion of chromatin loops. Compartmentation was not dependent on CTCF or cohesin. Hi-C contact maps represent the superimposition of CTCF/cohesin-dependent and -independent folding states. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. RNAiFold: a web server for RNA inverse folding and molecular design.

    Science.gov (United States)

    Garcia-Martin, Juan Antonio; Clote, Peter; Dotu, Ivan

    2013-07-01

    Synthetic biology and nanotechnology are poised to make revolutionary contributions to the 21st century. In this article, we describe a new web server to support in silico RNA molecular design. Given an input target RNA secondary structure, together with optional constraints, such as requiring GC-content to lie within a certain range, requiring the number of strong (GC), weak (AU) and wobble (GU) base pairs to lie in a certain range, the RNAiFold web server determines one or more RNA sequences, whose minimum free-energy secondary structure is the target structure. RNAiFold provides access to two servers: RNA-CPdesign, which applies constraint programming, and RNA-LNSdesign, which applies the large neighborhood search heuristic; hence, it is suitable for larger input structures. Both servers can also solve the RNA inverse hybridization problem, i.e. given a representation of the desired hybridization structure, RNAiFold returns two sequences, whose minimum free-energy hybridization is the input target structure. The web server is publicly accessible at http://bioinformatics.bc.edu/clotelab/RNAiFold, which provides access to two specialized servers: RNA-CPdesign and RNA-LNSdesign. Source code for the underlying algorithms, implemented in COMET and supported on linux, can be downloaded at the server website.

  12. Distinct Element Method modelling of fold-related fractures in a multilayer sequence

    Science.gov (United States)

    Kaserer, Klemens; Schöpfer, Martin P. J.; Grasemann, Bernhard

    2017-04-01

    Natural fractures have a significant impact on the performance of hydrocarbon systems/reservoirs. In a multilayer sequence, both the fracture density within the individual layers and the type of fracture intersection with bedding contacts are key parameters controlling fluid pathways. In the present study the influence of layer stacking and interlayer friction on fracture density and connectivity within a folded sequence is systematically investigated using 2D Distinct Element Method modelling. Our numerical approach permits forward modelling of both fracture nucleation/propagation/arrest and (contemporaneous) frictional slip along bedding planes in a robust and mechanically sound manner. Folding of the multilayer sequence is achieved by enforcing constant curvature folding by means of a velocity boundary condition at the model base, while a constant overburden pressure is maintained at the model top. The modelling reveals that with high bedding plane friction the multilayer stack behaves mechanically as a single layer so that the neutral surface develops in centre of the sequence and fracture spacing is controlled by the total thickness of the folded sequence. In contrast, low bedding plane friction leads to decoupling of the individual layers (flexural slip folding) so that a neutral surface develops in the centre of each layer and fracture spacing is controlled by the thickness of the individual layers. The low interfacial friction models illustrate that stepping of fractures across bedding planes is a common process, which can however have two contrasting origins: The mechanical properties of the interface cause fracture stepping during fracture propagation. Originally through-going fractures are later offset by interfacial slip during folding. A combination of these two different origins may lead to (apparently) inconsistent fracture offsets across bedding planes within a flexural slip fold.

  13. Repairing the vibratory vocal fold.

    Science.gov (United States)

    Long, Jennifer L

    2018-01-01

    A vibratory vocal fold replacement would introduce a new treatment paradigm for structural vocal fold diseases such as scarring and lamina propria loss. This work implants a tissue-engineered replacement for vocal fold lamina propria and epithelium in rabbits and compares histology and function to injured controls and orthotopic transplants. Hypotheses were that the cell-based implant would engraft and control the wound response, reducing fibrosis and restoring vibration. Translational research. Rabbit adipose-derived mesenchymal stem cells (ASC) were embedded within a three-dimensional fibrin gel, forming the cell-based outer vocal fold replacement (COVR). Sixteen rabbits underwent unilateral resection of vocal fold epithelium and lamina propria, as well as reconstruction with one of three treatments: fibrin glue alone with healing by secondary intention, replantation of autologous resected vocal fold cover, or COVR implantation. After 4 weeks, larynges were examined histologically and with phonation. Fifteen rabbits survived. All tissues incorporated well after implantation. After 1 month, both graft types improved histology and vibration relative to injured controls. Extracellular matrix (ECM) of the replanted mucosa was disrupted, and ECM of the COVR implants remained immature. Immune reaction was evident when male cells were implanted into female rabbits. Best histologic and short-term vibratory outcomes were achieved with COVR implants containing male cells implanted into male rabbits. Vocal fold cover replacement with a stem cell-based tissue-engineered construct is feasible and beneficial in acute rabbit implantation. Wound-modifying behavior of the COVR implant is judged to be an important factor in preventing fibrosis. NA. Laryngoscope, 128:153-159, 2018. © 2017 The American Laryngological, Rhinological and Otological Society, Inc.

  14. Roles of beta-turns in protein folding: from peptide models to protein engineering.

    Science.gov (United States)

    Marcelino, Anna Marie C; Gierasch, Lila M

    2008-05-01

    Reverse turns are a major class of protein secondary structure; they represent sites of chain reversal and thus sites where the globular character of a protein is created. It has been speculated for many years that turns may nucleate the formation of structure in protein folding, as their propensity to occur will favor the approximation of their flanking regions and their general tendency to be hydrophilic will favor their disposition at the solvent-accessible surface. Reverse turns are local features, and it is therefore not surprising that their structural properties have been extensively studied using peptide models. In this article, we review research on peptide models of turns to test the hypothesis that the propensities of turns to form in short peptides will relate to the roles of corresponding sequences in protein folding. Turns with significant stability as isolated entities should actively promote the folding of a protein, and by contrast, turn sequences that merely allow the chain to adopt conformations required for chain reversal are predicted to be passive in the folding mechanism. We discuss results of protein engineering studies of the roles of turn residues in folding mechanisms. Factors that correlate with the importance of turns in folding indeed include their intrinsic stability, as well as their topological context and their participation in hydrophobic networks within the protein's structure.

  15. Kinetic partitioning mechanism of HDV ribozyme folding

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Jiawen; Gong, Sha; Wang, Yujie; Zhang, Wenbing, E-mail: wbzhang@whu.edu.cn [Department of Physics, Wuhan University, Wuhan, Hubei 430072 (China)

    2014-01-14

    RNA folding kinetics is directly tied to RNA biological functions. We introduce here a new approach for predicting the folding kinetics of RNA secondary structure with pseudoknots. This approach is based on our previous established helix-based method for predicting the folding kinetics of RNA secondary structure. In this approach, the transition rates for an elementary step: (1) formation, (2) disruption of a helix stem, and (3) helix formation with concomitant partial melting of an incompatible helix, are calculated with the free energy landscape. The folding kinetics of the Hepatitis delta virus (HDV) ribozyme and the mutated sequences are studied with this method. The folding pathways are identified by recursive searching the states with high net flux-in(out) population starting from the native state. The theory results are in good agreement with that of the experiments. The results indicate that the bi-phasic folding kinetics for the wt HDV sequence is ascribed to the kinetic partitioning mechanism: Part of the population will quickly fold to the native state along the fast pathway, while another part of the population will fold along the slow pathway, in which the population is trapped in a non-native state. Single mutation not only changes the folding rate but also the folding pathway.

  16. Self-folding origami at any energy scale

    Science.gov (United States)

    Pinson, Matthew B.; Stern, Menachem; Carruthers Ferrero, Alexandra; Witten, Thomas A.; Chen, Elizabeth; Murugan, Arvind

    2017-05-01

    Programmable stiff sheets with a single low-energy folding motion have been sought in fields ranging from the ancient art of origami to modern meta-materials research. Despite such attention, only two extreme classes of crease patterns are usually studied; special Miura-Ori-based zero-energy patterns, in which crease folding requires no sheet bending, and random patterns with high-energy folding, in which the sheet bends as much as creases fold. We present a physical approach that allows systematic exploration of the entire space of crease patterns as a function of the folding energy. Consequently, we uncover statistical results in origami, finding the entropy of crease patterns of given folding energy. Notably, we identify three classes of Mountain-Valley choices that have widely varying `typical' folding energies. Our work opens up a wealth of experimentally relevant self-folding origami designs not reliant on Miura-Ori, the Kawasaki condition or any special symmetry in space.

  17. Anatomy and Histology of an Epicanthal Fold.

    Science.gov (United States)

    Park, Jae Woo; Hwang, Kun

    2016-06-01

    The aim of this study is to elucidate the precise anatomical and histological detail of the epicanthal fold.Thirty-two hemifaces of 16 Korean adult cadavers were used in this study (30 hemifaces with an epicanthal fold, 2 without an epicanthal fold). In 2 patients who had an epicanthoplasty, the epicanthal folds were sampled.In a dissection, the periorbital skin and subcutaneous tissues were removed and the epicanthal fold was observed in relation to each part of the orbicularis oculi muscle. Specimens including the epicanthal fold were embeddedin in paraffin, sectioned at 10 um, and stained with Hematoxylin-Eosin. The horizontal section in the level of the paplebral fissure was made and the prepared slides were observed under a light microscope.In the specimens without an epicanthal fold, no connection between the upper preseptal muscle and the lower preseptal muscle was found. In the specimens with an epicanthal fold, a connection of the upper preseptal muscle to the lower preseptal muscle was observed. It was present in all 15 hemifaces (100%). There was no connection between the pretarsal muscles. In a horizontal section, the epicanthal fold was composed of 3 compartments: an outer skin lining, a core structure, and an innerskin lining. The core structure was mainly composed of muscular fibers and fibrotic tissue and they were intermingled.Surgeons should be aware of the anatomical details of an epicanthal fold. In removing or reconstructing an epicanthal fold, the fibromuscular core band should also be removed or reconstructed.

  18. The review on tessellation origami inspired folded structure

    Science.gov (United States)

    Chu, Chai Chen; Keong, Choong Kok

    2017-10-01

    Existence of folds enhances the load carrying capacity of a folded structure which makes it suitable to be used for application where large open space is required such as large span roof structures and façade. Folded structure is closely related to origami especially the tessellation origami. Tessellation origami provides a folded configuration with facetted surface as a result from repeated folding pattern. Besides that, tessellation origami has flexible folding mechanism that produced a variety of 3-dimensional folded configurations. Despite the direct relationship between fold in origami and folded structure, the idea of origami inspired folded structure is not properly reviewed in the relevant engineering field. Hence, this paper aims to present the current studies from related discipline which has direct relation with application of tessellation origami in folded structure. First, tessellation origami is properly introduced and defined. Then, the review covers the topic on the origami tessellation design suitable for folded structure, its modeling and simulation method, and existing studies and applications of origami as folded structure is presented. The paper also includes the discussion on the current issues related to each topic.

  19. Cross-tropopause Transport In Tropopause Folds: Mechanisms and Sensitivity To Model Resolution

    Science.gov (United States)

    Gray, S. L.

    The rate and processes of transfer of mass and chemical species between the strato- sphere and troposphere (stratosphere-troposphere exchange) are currently uncertain. In the midlatitudes exchange appears to be dominated by processes associated with tropopause folds and cut-off lows. The development of a tropopause fold is a reversible process and thus irreversible processes must occur for the permanent transfer of ma- terial across the tropopause boundary. Proposed processes include turbulent mixing, quasi-isentropic mixing, convectively breaking gravity waves, deep convection and radiative heating. Numerical models run at typical climate or regional-scale resolutions are unable to re- solve the fine-scale features observed in tropopause folds. It is hypothesised that both the rate of exchange and its partitioning into different processes, as derived from nu- merical model simulations, are sensitive to model resolution. This hypothesis is tested through simulations of a tropopause folding event associated with a vigorous surface cold front which tracked across the British Isles. Climate to high-mesoscale resolution simulations incorporating passive tracers are performed using the mesoscale version of the Met Office Unified Model. The mechanism by which the parametrized convec- tion leads to exchange is the subject of further examination.

  20. Inpatient injection laryngoplasty for vocal fold immobility: When is it really necessary?

    Science.gov (United States)

    Zuniga, Steven; Ebersole, Barbara; Jamal, Nausheen

    To compare pulmonary and swallow outcomes of injection laryngoplasty when performed in the acute versus subacute setting in head & neck and thoracic cancer patients presenting with new onset unilateral vocal fold immobility. Case series with chart review at an academic cancer center over a 2year period. Based on swallow evaluation, patients diagnosed with vocal fold immobility were grouped into an unsafe swallow group, injected as inpatients, and a safe swallow group, for whom injection laryngoplasty was delayed to the outpatient setting or not performed. Rates of pneumonia, diet recommendations, and swallow outcomes were compared between groups. 24 patients with new-onset vocal fold immobility were evaluated. 7 underwent injection in the inpatient setting, 12 in the outpatient setting, and 5 did not undergo injection. There was no perceived difference in speech and swallow outcomes between the inpatient and outpatient injection groups. Injection laryngoplasty shows promise as an effective intervention for reducing aspiration risk and improving diet normalcy in patients with dysphagia as a result of unilateral vocal fold immobility. In patients determined to have a safe swallow, delay of injection laryngoplasty is not detrimental to swallow outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. A new topology of the HK97-like fold revealed in Bordetella bacteriophage by cryoEM at 3.5 Å resolution

    Science.gov (United States)

    Zhang, Xing; Guo, Huatao; Jin, Lei; Czornyj, Elizabeth; Hodes, Asher; Hui, Wong H; Nieh, Angela W; Miller, Jeff F; Zhou, Z Hong

    2013-01-01

    Bacteriophage BPP-1 infects and kills Bordetella species that cause whooping cough. Its diversity-generating retroelement (DGR) provides a naturally occurring phage-display system, but engineering efforts are hampered without atomic structures. Here, we report a cryo electron microscopy structure of the BPP-1 head at 3.5 Å resolution. Our atomic model shows two of the three protein folds representing major viral lineages: jellyroll for its cement protein (CP) and HK97-like (‘Johnson’) for its major capsid protein (MCP). Strikingly, the fold topology of MCP is permuted non-circularly from the Johnson fold topology previously seen in viral and cellular proteins. We illustrate that the new topology is likely the only feasible alternative of the old topology. β-sheet augmentation and electrostatic interactions contribute to the formation of non-covalent chainmail in BPP-1, unlike covalent inter-protein linkages of the HK97 chainmail. Despite these complex interactions, the termini of both CP and MCP are ideally positioned for DGR-based phage-display engineering. DOI: http://dx.doi.org/10.7554/eLife.01299.001 PMID:24347545

  2. YbiV from E. coli K12 is a HAD phosphatase

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Anne; Lee, Seok-Yong; McCullagh, Emma; Silversmith, Ruth E.; Wemmer, David E.

    2004-03-16

    The protein YbiV from Escherichia coli K12 MG1655 is a hypothetical protein with sequence homology to the haloacid dehalogenase (HAD) superfamily of proteins. Although numerous members of this family have been identified, the functions of few are known. Using the crystal structure, sequence analysis, and biochemical assays, we have characterized ybiV as a HAD phosphatase. The crystal structure of YbiV reveals a two domain protein, one with the characteristic HAD hydrolase fold, the other an inserted a/b fold. In an effort to understand the mechanism we also solved and report the structures of YbiV in complex with beryllofluoride (BeF3-) and aluminum trifluoride (AlF3) which have been shown to mimic the phosphorylated intermediate and transition state for hydrolysis, respectively, in analogy to other HAD phosphatases. Analysis of the structures reveals the substrate binding cavity, which is hydrophilic in nature. Both structure and sequence homology indicate ybiV may be a sugar phosphatase, which is supported by biochemical assays which measured the release of free phosphate on a number of sugar-like substrates. We also investigated available genomic and functional data in an effort to determine the physiological substrate.

  3. Folding of non-Euclidean curved shells

    Science.gov (United States)

    Bende, Nakul; Evans, Arthur; Innes-Gold, Sarah; Marin, Luis; Cohen, Itai; Santangelo, Christian; Hayward, Ryan

    2015-03-01

    Origami-based folding of 2D sheets has been of recent interest for a variety of applications ranging from deployable structures to self-folding robots. Though folding of planar sheets follows well-established principles, folding of curved shells involves an added level of complexity due to the inherent influence of curvature on mechanics. In this study, we use principles from differential geometry and thin shell mechanics to establish fundamental rules that govern folding of prototypical creased shells. In particular, we show how the normal curvature of a crease line controls whether the deformation is smooth or discontinuous, and investigate the influence of shell thickness and boundary conditions. We show that snap-folding of shells provides a route to rapid actuation on time-scales dictated by the speed of sound. The simple geometric design principles developed can be applied at any length-scale, offering potential for bio-inspired soft actuators for tunable optics, microfluidics, and robotics. This work was funded by the National Science Foundation through EFRI ODISSEI-1240441 with additional support to S.I.-G. through the UMass MRSEC DMR-0820506 REU program.

  4. Improving Protein Fold Recognition by Deep Learning Networks

    Science.gov (United States)

    Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin

    2015-12-01

    For accurate recognition of protein folds, a deep learning network method (DN-Fold) was developed to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features extracted from the protein pair. We evaluated the performance of DN-Fold along with 18 different methods on Lindahl’s benchmark dataset and on a large benchmark set extracted from SCOP 1.75 consisting of about one million protein pairs, at three different levels of fold recognition (i.e., protein family, superfamily, and fold) depending on the evolutionary distance between protein sequences. The correct recognition rate of ensembled DN-Fold for Top 1 predictions is 84.5%, 61.5%, and 33.6% and for Top 5 is 91.2%, 76.5%, and 60.7% at family, superfamily, and fold levels, respectively. We also evaluated the performance of single DN-Fold (DN-FoldS), which showed the comparable results at the level of family and superfamily, compared to ensemble DN-Fold. Finally, we extended the binary classification problem of fold recognition to real-value regression task, which also show a promising performance. DN-Fold is freely available through a web server at http://iris.rnet.missouri.edu/dnfold.

  5. Improving Protein Fold Recognition by Deep Learning Networks.

    Science.gov (United States)

    Jo, Taeho; Hou, Jie; Eickholt, Jesse; Cheng, Jianlin

    2015-12-04

    For accurate recognition of protein folds, a deep learning network method (DN-Fold) was developed to predict if a given query-template protein pair belongs to the same structural fold. The input used stemmed from the protein sequence and structural features extracted from the protein pair. We evaluated the performance of DN-Fold along with 18 different methods on Lindahl's benchmark dataset and on a large benchmark set extracted from SCOP 1.75 consisting of about one million protein pairs, at three different levels of fold recognition (i.e., protein family, superfamily, and fold) depending on the evolutionary distance between protein sequences. The correct recognition rate of ensembled DN-Fold for Top 1 predictions is 84.5%, 61.5%, and 33.6% and for Top 5 is 91.2%, 76.5%, and 60.7% at family, superfamily, and fold levels, respectively. We also evaluated the performance of single DN-Fold (DN-FoldS), which showed the comparable results at the level of family and superfamily, compared to ensemble DN-Fold. Finally, we extended the binary classification problem of fold recognition to real-value regression task, which also show a promising performance. DN-Fold is freely available through a web server at http://iris.rnet.missouri.edu/dnfold.

  6. Neogene shortening and exhumation of the Zagros fold-thrust belt and foreland basin in the Kurdistan region of northern Iraq

    Science.gov (United States)

    Koshnaw, Renas I.; Horton, Brian K.; Stockli, Daniel F.; Barber, Douglas E.; Tamar-Agha, Mazin Y.; Kendall, Jerome J.

    2017-01-01

    The Zagros fold-thrust belt in the Kurdistan region of Iraq encroached southward toward a rapidly subsiding Neogene foreland basin and was later partitioned by out-of-sequence shortening focused along the Mountain Front Flexure (MFF), as defined by new low-temperature thermochronologic, stratigraphic, and provenance results. Apatite (U-Th)/He ages document rapid deformation advance from the Main Zagros Fault to southern frontal structures (Kirkuk, Shakal, and Qamar thrusts) at 10-8 Ma, followed by potential basement-involved out-of-sequence development of the MFF (Qaradagh anticline) by 5 Ma. Distinct shifts in detrital zircon U-Pb provenance signatures for Neogene foreland basin fill provide evidence for drainage reorganization during fold-thrust belt advance. U-Pb age spectra and petrologic data from the Injana (Upper Fars) Formation indicate derivation from a variety of Eurasian, Pan-African, ophiolitic and Mesozoic-Cenozoic volcanic terranes, whereas the Mukdadiya (Lower Bakhtiari) and Bai-Hasan (Upper Bakhtiari) Formations show nearly exclusive derivation from the Paleogene Walash-Naopurdan volcanic complex near the Iraq-Iran border. Such a sharp cutoff in Eurasian, Pan-African, and ophiolitic sources is likely associated with drainage reorganization and tectonic development of the geomorphic barrier formed by the MFF. As a result of Zagros crustal shortening, thickening and loading, the Neogene foreland basin developed and accommodated an abrupt influx of fluvial clastic sediment that contains growth stratal evidence of synkinematic accumulation. The apparent out-of-sequence pattern of upper crustal shortening in the hinterland to foreland zone of Iraqi Kurdistan suggests that structural inheritance and the effects of synorogenic erosion and accumulation are important factors influencing the irregular and episodic nature of orogenic growth in the Zagros.

  7. GPR Imaging of Fault Related Folds in a Gold-Bearing Metasedimentary Sequence, Carolina Terrane, Southern Appalachian Mountains

    Science.gov (United States)

    Diemer, J. A.; Bobyarchick, A. R.

    2015-12-01

    The Carolina terrane comprises Ediacaran to earliest Paleozoic mixed magmatic and sedimentary assemblages in the central and eastern Piedmont of the Southern Appalachian Mountains. The terrane was primarily deformed during the Late Ordovician Cherokee orogeny, that reached greenschist facies metamorphism. The Albemarle arc, a younger component of the Carolina terrane, contains volcanogenic metasedimentary rocks with intercalated mainly rhyolitic volcanic rocks. Regional inclined to overturned folds with axial planar cleavage verge southeast. At mesoscopic scales (exposures of a few square meters), folds sympathetic with regional folds are attenuated or truncated by ductile shear zones or contractional faults. Shear and fault zones are most abundant near highly silicified strataform zones in metagraywacke of the Tillery Formation; these zones are also auriferous. GPR profiles were collected across strike of two silicified, gold-bearing zones and enclosing metagraywacke to characterize the scale and extent of folding in the vicinity of ore horizons. Several GSSI SIR-3000 / 100 MHz monostatic GPR profiles were collected in profiles up to 260 meters long. In pre-migration lines processed for time zero and background removal, several clusters of shallow, rolling sigmoidal reflectors appeared separated by sets of parallel, northwest-dipping reflective discontinuities. These features are inferred to be reverse faults carrying contractional folds. After migration with an average velocity of 0.105 m/ns, vertical heights of the inferred folds became attenuated but not removed, and contractional fault reflections remained prominent. After migration, a highly convex-up cluster of reflections initially assumed to be a fold culmination resolved to an elliptical patch of high amplitudes. The patch is likely an undisclosed shaft or covered trench left by earlier gold prospecting. In this survey, useful detail appeared to a depth of 7.5 meters, and only a few gently inclined

  8. Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme.

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2011-04-01

    Full Text Available Biomolecular function is realized by recognition, and increasing evidence shows that recognition is determined not only by structure but also by flexibility and dynamics. We explored a biomolecular recognition process that involves a major conformational change - protein folding. In particular, we explore the binding-induced folding of IA3, an intrinsically disordered protein that blocks the active site cleft of the yeast aspartic proteinase saccharopepsin (YPrA by folding its own N-terminal residues into an amphipathic alpha helix. We developed a multi-scaled approach that explores the underlying mechanism by combining structure-based molecular dynamics simulations at the residue level with a stochastic path method at the atomic level. Both the free energy profile and the associated kinetic paths reveal a common scheme whereby IA3 binds to its target enzyme prior to folding itself into a helix. This theoretical result is consistent with recent time-resolved experiments. Furthermore, exploration of the detailed trajectories reveals the important roles of non-native interactions in the initial binding that occurs prior to IA3 folding. In contrast to the common view that non-native interactions contribute only to the roughness of landscapes and impede binding, the non-native interactions here facilitate binding by reducing significantly the entropic search space in the landscape. The information gained from multi-scaled simulations of the folding of this intrinsically disordered protein in the presence of its binding target may prove useful in the design of novel inhibitors of aspartic proteinases.

  9. Synovial folds in equine articular process joints

    DEFF Research Database (Denmark)

    Thomsen, Line Nymann; Berg, Lise Charlotte; Markussen, Bo

    2013-01-01

    Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses.......Cervical synovial folds have been suggested as a potential cause of neck pain in humans. Little is known about the extent and characteristics of cervical synovial folds in horses....

  10. Percutaneous injection laryngoplasty in the management of acute vocal fold paralysis.

    Science.gov (United States)

    Damrose, Edward J

    2010-08-01

    To evaluate the clinical outcome of patients with acute vocal fold paralysis treated with bovine collagen via percutaneous injection laryngoplasty under simple topical anesthesia. Retrospective case series. The charts of 38 consecutive patients with acute unilateral vocal fold paralysis who underwent percutaneous injection laryngoplasty under simple topical anesthesia were reviewed. Symptoms and laryngeal function were assessed pre- and postinjection using the Glottal Function Index (GFI), GRBAS Dysphonia Scale, Functional Outcome Swallowing Scale (FOSS), and maximum phonation time (MPT). Mean GFI, GRBAS, FOSS, and MPT improved from 13.71 to 7.68, 7.24 to 3.95, 3.70 to 2.20, and 12.87 to 16.45, respectively (P dysphagia and aspiration, injection was successful in restoring oral alimentation in only three patients, with the four failures occurring in patients with multiple cranial neuropathies. Percutaneous injection laryngoplasty is a viable option for immediate rehabilitation of acute vocal fold paralysis, and can be performed in the inpatient setting. With dysphagia and aspiration secondary to multiple cranial nerve palsies, medialization of the paralyzed cord alone may be insufficient to restore safe oral alimentation.

  11. Accurate Stabilities of Laccase Mutants Predicted with a Modified FoldX Protocol

    DEFF Research Database (Denmark)

    Christensen, Niels Johan; Kepp, Kasper Planeta

    2012-01-01

    ) with up to 11 simultaneously mutated sites with good correlation against experimental stability trends. Molecular dynamics simulations of the two laccases show that FoldX is very structure-sensitive, since all mutants and the wild-type must share structural configuration to avoid artifacts of local...... sampling. However, using the average of 50 MD snapshots of the equilibrated trajectories restores correlation (r ~0.7-0.9, r2 ~0.49-0.81) and provides a root-mean-square accuracy of ~1.2 kcal/mol for ∆∆G or 3.5 ○C for T50, suggesting that the time-average of the crystal structure is recovered. MD......-averaged input also reduces the spread in ∆∆G, suggesting that local FoldX sampling overestimates free energy changes because of neglected protein relaxation. FoldX can be viewed as a simple “linear interaction energy” method using sampling of wild-type and mutant and a parameterized relative free energy...

  12. Presence of a monoclinic (Pm) phase in the morphotropic phase boundary region of multiferroic (1 − x)Bi(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} solid solution: A Rietveld study

    Energy Technology Data Exchange (ETDEWEB)

    Pandey, Rishikesh, E-mail: akhilesh-bhu@yahoo.com, E-mail: aksingh.mst@itbhu.ac.in; Singh, Akhilesh Kumar, E-mail: akhilesh-bhu@yahoo.com, E-mail: aksingh.mst@itbhu.ac.in [School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005 (India)

    2014-07-28

    We present here the results of structural studies on multiferroic (1 − x)Bi(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} solid solution using Rietveld analysis on powder x-ray diffraction data in the composition range 0.35 ≤ x ≤ 0.55. The stability region of various crystallographic phases at room temperature for (1 − x)Bi(Ni{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} is determined precisely. Structural transformation from pseudo-cubic (x ≤ 0.40) to tetragonal (x ≥ 0.50) phase is observed via phase coexistence region demarcating the morphotropic phase boundary. The morphotropic phase boundary region consists of coexisting tetragonal and monoclinic structures with space group P4mm and Pm, respectively, stable in composition range 0.41 ≤ x ≤ 0.49 as confirmed by Rietveld analysis. The results of Rietveld analysis completely rule out the coexistence of rhombohedral and tetragonal phases in the morphotropic phase boundary region reported by earlier workers. A comparison between the bond lengths for “B-site cations-oxygen anions” obtained after Rietveld refinement, with the bond length calculated using Shannon-Prewitt ionic radii, reveals the ionic nature of B-O (Ni/Ti-O) bonds for the cubic phase and partial covalent character for the other crystallographic phases.

  13. Dynamics of Folds in the Plane

    Science.gov (United States)

    Krylov, Nikolai A.; Rogers, Edwin L.

    2011-01-01

    Take a strip of paper and fold a crease intersecting the long edges, creating two angles. Choose one edge and consider the angle with the crease. Fold the opposite edge along the crease, creating a new crease that bisects the angle. Fold again, this time using the newly created crease and the initial edge, creating a new angle along the chosen…

  14. Teaching computers to fold proteins

    DEFF Research Database (Denmark)

    Winther, Ole; Krogh, Anders Stærmose

    2004-01-01

    A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The iterative update rule contains two thermodynamic averages...

  15. Origami-Inspired Folding of Thick, Rigid Panels

    Science.gov (United States)

    Trease, Brian P.; Thomson, Mark W.; Sigel, Deborah A.; Walkemeyer, Phillip E.; Zirbel, Shannon; Howell, Larry; Lang, Robert

    2014-01-01

    To achieve power of 250 kW or greater, a large compression ratio of stowed-to-deployed area is needed. Origami folding patterns were used to inspire the folding of a solar array to achieve synchronous deployment; however, origami models are generally created for near-zero-thickness material. Panel thickness is one of the main challenges of origami-inspired design. Three origami-inspired folding techniques (flasher, square twist, and map fold) were created with rigid panels and hinges. Hinge components are added to the model to enable folding of thick, rigid materials. Origami models are created assuming zero (or near zero) thickness. When a material with finite thickness is used, the panels are required to bend around an increasingly thick fold as they move away from the center of the model. The two approaches for dealing with material thickness are to use membrane hinges to connect the panels, or to add panel hinges, or hinges of the same thickness, at an appropriate width to enable folding.

  16. Patterns of Participation and Motivation in Folding@home: The Contribution of Hardware Enthusiasts and Overclockers

    Directory of Open Access Journals (Sweden)

    Vickie Curtis

    2018-04-01

    Full Text Available Folding@home is a distributed computing project in which participants run protein folding simulations on their computers. Participants complete work units and are awarded points for their contribution. An investigation into motivations to participate and patterns of participation revealed the significant contribution of a sub-community composed of individuals who custom-build computers to maximise their processing power. These individuals, known as “overclockers” or “hardware enthusiasts,” use distributed computing projects such as Folding@home to benchmark their modified computers and to compete with one another to see who can process the greatest number of project work units. Many are initially drawn to the project to learn about computer hardware from other overclockers and to compete for points. However, once they learn more about the scientific outputs of Folding@home, some participants become more motivated by the desire to contribute to scientific research. Overclockers form numerous online communities where members collaborate and help each other maximise their computing output. They invest heavily in their computers and process the majority of Folding@home’s simulations, thus providing an invaluable (and free resource.

  17. A comparative method for finding and folding RNA secondary structures within protein-coding regions

    DEFF Research Database (Denmark)

    Pedersen, Jakob Skou; Meyer, Irmtraud Margret; Forsberg, Roald

    2004-01-01

    that RNA-DECODER's parameters can be automatically trained to successfully fold known secondary structures within the HCV genome. We scan the genomes of HCV and polio virus for conserved secondary-structure elements, and analyze performance as a function of available evolutionary information. On known...... secondary structures, RNA-DECODER shows a sensitivity similar to the programs MFOLD, PFOLD and RNAALIFOLD. When scanning the entire genomes of HCV and polio virus for structure elements, RNA-DECODER's results indicate a markedly higher specificity than MFOLD, PFOLD and RNAALIFOLD....

  18. Vocal fold hemorrhage: factors predicting recurrence.

    Science.gov (United States)

    Lennon, Christen J; Murry, Thomas; Sulica, Lucian

    2014-01-01

    Vocal fold hemorrhage is an acute phonotraumatic injury treated with voice rest; recurrence is a generally accepted indication for surgical intervention. This study aims to identify factors predictive of recurrence based on outcomes of a large clinical series. Retrospective cohort. Retrospective review of cases of vocal fold hemorrhage presenting to a university laryngology service. Demographic information was compiled. Videostroboscopic exams were evaluated for hemorrhage extent, presence of varix, mucosal lesion, and/or vocal fold paresis. Vocal fold hemorrhage recurrence was the main outcome measure. Follow-up telephone survey was used to complement clinical data. Forty-seven instances of vocal fold hemorrhage were evaluated (25M:22F; 32 professional voice users). Twelve of the 47 (26%) patients experienced recurrence. Only the presence of varix demonstrated significant association with recurrence (P = 0.0089) on multivariate logistic regression. Vocal fold hemorrhage recurred in approximately 26% of patients. Varix was a predictor of recurrence, with 48% of those with varix experiencing recurrence. Monitoring, behavioral management and/or surgical intervention may be indicated to treat patients with such characteristics. © 2013 The American Laryngological, Rhinological and Otological Society, Inc.

  19. Geometric U-folds in four dimensions

    Science.gov (United States)

    Lazaroiu, C. I.; Shahbazi, C. S.

    2018-01-01

    We describe a general construction of geometric U-folds compatible with a non-trivial extension of the global formulation of four-dimensional extended supergravity on a differentiable spin manifold. The topology of geometric U-folds depends on certain flat fiber bundles which encode how supergravity fields are globally glued together. We show that smooth non-trivial U-folds of this type can exist only in theories where both the scalar and space-time manifolds have non-trivial fundamental group and in addition the scalar map of the solution is homotopically non-trivial. Consistency with string theory requires smooth geometric U-folds to be glued using subgroups of the effective discrete U-duality group, implying that the fundamental group of the scalar manifold of such solutions must be a subgroup of the latter. We construct simple examples of geometric U-folds in a generalization of the axion-dilaton model of \

  20. Guiding the folding pathway of DNA origami.

    Science.gov (United States)

    Dunn, Katherine E; Dannenberg, Frits; Ouldridge, Thomas E; Kwiatkowska, Marta; Turberfield, Andrew J; Bath, Jonathan

    2015-09-03

    DNA origami is a robust assembly technique that folds a single-stranded DNA template into a target structure by annealing it with hundreds of short 'staple' strands. Its guiding design principle is that the target structure is the single most stable configuration. The folding transition is cooperative and, as in the case of proteins, is governed by information encoded in the polymer sequence. A typical origami folds primarily into the desired shape, but misfolded structures can kinetically trap the system and reduce the yield. Although adjusting assembly conditions or following empirical design rules can improve yield, well-folded origami often need to be separated from misfolded structures. The problem could in principle be avoided if assembly pathway and kinetics were fully understood and then rationally optimized. To this end, here we present a DNA origami system with the unusual property of being able to form a small set of distinguishable and well-folded shapes that represent discrete and approximately degenerate energy minima in a vast folding landscape, thus allowing us to probe the assembly process. The obtained high yield of well-folded origami structures confirms the existence of efficient folding pathways, while the shape distribution provides information about individual trajectories through the folding landscape. We find that, similarly to protein folding, the assembly of DNA origami is highly cooperative; that reversible bond formation is important in recovering from transient misfoldings; and that the early formation of long-range connections can very effectively enforce particular folds. We use these insights to inform the design of the system so as to steer assembly towards desired structures. Expanding the rational design process to include the assembly pathway should thus enable more reproducible synthesis, particularly when targeting more complex structures. We anticipate that this expansion will be essential if DNA origami is to continue its

  1. Self-folding graphene-polymer bilayers

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Tao [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Yoon, ChangKyu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Jin, Qianru [Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Li, Mingen [Department of Physics, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Liu, Zewen [Institute of Microelectronics, Tsinghua University, Beijing 100084 (China); Gracias, David H., E-mail: dgracias@jhu.edu [Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States); Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218 (United States)

    2015-05-18

    In order to incorporate the extraordinary intrinsic thermal, electrical, mechanical, and optical properties of graphene with three dimensional (3D) flexible substrates, we introduce a solvent-driven self-folding approach using graphene-polymer bilayers. A polymer (SU-8) film was spin coated atop chemically vapor deposited graphene films on wafer substrates and graphene-polymer bilayers were patterned with or without metal electrodes using photolithography, thin film deposition, and etching. After patterning, the bilayers were released from the substrates and they self-folded to form fully integrated, curved, and folded structures. In contrast to planar graphene sensors on rigid substrates, we assembled curved and folded sensors that are flexible and they feature smaller form factors due to their 3D geometry and large surface areas due to their multiple rolled architectures. We believe that this approach could be used to assemble a range of high performance 3D electronic and optical devices of relevance to sensing, diagnostics, wearables, and energy harvesting.

  2. Circuit-wide Transcriptional Profiling Reveals Brain Region-Specific Gene Networks Regulating Depression Susceptibility.

    Science.gov (United States)

    Bagot, Rosemary C; Cates, Hannah M; Purushothaman, Immanuel; Lorsch, Zachary S; Walker, Deena M; Wang, Junshi; Huang, Xiaojie; Schlüter, Oliver M; Maze, Ian; Peña, Catherine J; Heller, Elizabeth A; Issler, Orna; Wang, Minghui; Song, Won-Min; Stein, Jason L; Liu, Xiaochuan; Doyle, Marie A; Scobie, Kimberly N; Sun, Hao Sheng; Neve, Rachael L; Geschwind, Daniel; Dong, Yan; Shen, Li; Zhang, Bin; Nestler, Eric J

    2016-06-01

    Depression is a complex, heterogeneous disorder and a leading contributor to the global burden of disease. Most previous research has focused on individual brain regions and genes contributing to depression. However, emerging evidence in humans and animal models suggests that dysregulated circuit function and gene expression across multiple brain regions drive depressive phenotypes. Here, we performed RNA sequencing on four brain regions from control animals and those susceptible or resilient to chronic social defeat stress at multiple time points. We employed an integrative network biology approach to identify transcriptional networks and key driver genes that regulate susceptibility to depressive-like symptoms. Further, we validated in vivo several key drivers and their associated transcriptional networks that regulate depression susceptibility and confirmed their functional significance at the levels of gene transcription, synaptic regulation, and behavior. Our study reveals novel transcriptional networks that control stress susceptibility and offers fundamentally new leads for antidepressant drug discovery. Copyright © 2016 Elsevier Inc. All rights reserved.

  3. Distributed deformation in the Zagros fold-and-thrust belt: insights from geomorphology

    Science.gov (United States)

    Obaid, Ahmed; Allen, Mark

    2017-04-01

    The Zagros fold-and-thrust belt is part of the active Arabia-Eurasia collision zone, and is an excellent region to study the interactions of tectonics and landscape. In this work we present results of a geomorphic analysis covering the entire range, coupled with more detailed analysis of the Kirkuk Embayment, Iraq. This particular region is a low elevation, low relief region of the Zagros, important for the enormous oil and gas reserves held in late Cenozoic anticlinal traps. Constraints from published earthquake focal mechanisms and hydrocarbon industry sub-surface data are combined with original fieldwork observations in northern Iraq, to produce a new regional cross-section and structural interpretation for the Kirkuk Embayment. We find that overall late Cenozoic shortening across the Embayment is on the order of 5%, representing only a few km. This deformation takes place on a series of anticlines, which are interpreted as overlying steep, planar, basement thrusts. These thrusts are further interpreted as reactivated normal faults, on the basis of (rare) published seismic data. The regional earthquake record confirms the basement involvement, although detachments within the sedimentary succession are also important, especially within the Middle Miocene Fat'ha Formation. Overall, the Zagros is sometimes represented as having a few major thrusts each persistent for 100s of km along the strike of the range. However, these faults are very rarely associated with major structural relief and/or surface fault ruptures during earthquakes. We have analysed the hypsometry of the range and find only gradational changes in the hypsometric integral of drainage basins across strike. This contrasts with regions such as the eastern Tibetan Plateau, where published analysis has revealed abrupt changes, correlating with the surface traces of active thrusts. Our interpretation is that the hypsometry of the Zagros reflects distributed deformation on numerous smaller faults, rather

  4. Protein folding on the ribosome studied using NMR spectroscopy

    Science.gov (United States)

    Waudby, Christopher A.; Launay, Hélène; Cabrita, Lisa D.; Christodoulou, John

    2013-01-01

    NMR spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. In recent years NMR methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. Despite the 2.3 MDa molecular weight of the bacterial 70S ribosome, many nascent polypeptides, and some ribosomal proteins, have sufficient local flexibility that sharp resonances may be observed in solution-state NMR spectra. In providing information on dynamic regions of the structure, NMR spectroscopy is therefore highly complementary to alternative methods such as X-ray crystallography and cryo-electron microscopy, which have successfully characterized the rigid core of the ribosome particle. However, the low working concentrations and limited sample stability associated with ribosome–nascent chain complexes means that such studies still present significant technical challenges to the NMR spectroscopist. This review will discuss the progress that has been made in this area, surveying all NMR studies that have been published to date, and with a particular focus on strategies for improving experimental sensitivity. PMID:24083462

  5. How old is your fold?

    NARCIS (Netherlands)

    Winstanley, Henry F.; Abeln, Sanne; Deane, Charlotte M.

    Motivation: At present there exists no age estimate for the different protein structures found in nature. It has become clear from occurrence studies that different folds arose at different points in evolutionary time. An estimation of the age of different folds would be a starting point for many

  6. Developing guinea pig brain as a model for cortical folding.

    Science.gov (United States)

    Hatakeyama, Jun; Sato, Haruka; Shimamura, Kenji

    2017-05-01

    The cerebral cortex in mammals, the neocortex specifically, is highly diverse among species with respect to its size and morphology, likely reflecting the immense adaptiveness of this lineage. In particular, the pattern and number of convoluted ridges and fissures, called gyri and sulci, respectively, on the surface of the cortex are variable among species and even individuals. However, little is known about the mechanism of cortical folding, although there have been several hypotheses proposed. Recent studies on embryonic neurogenesis revealed the differences in cortical progenitors as a critical factor of the process of gyrification. Here, we investigated the gyrification processes using developing guinea pig brains that form a simple but fundamental pattern of gyri. In addition, we established an electroporation-mediated gene transfer method for guinea pig embryos. We introduce the guinea pig brain as a useful model system to understand the mechanisms and basic principle of cortical folding. © 2017 Japanese Society of Developmental Biologists.

  7. Muscular anatomy of the human ventricular folds.

    Science.gov (United States)

    Moon, Jerald; Alipour, Fariborz

    2013-09-01

    Our purpose in this study was to better understand the muscular anatomy of the ventricular folds in order to help improve biomechanical modeling of phonation and to better understand the role of these muscles during phonatory and nonphonatory tasks. Four human larynges were decalcified, sectioned coronally from posterior to anterior by a CryoJane tape transfer system, and stained with Masson's trichrome. The total and relative areas of muscles observed in each section were calculated and used for characterizing the muscle distribution within the ventricular folds. The ventricular folds contained anteriorly coursing thyroarytenoid and ventricularis muscle fibers that were in the lower half of the ventricular fold posteriorly, and some ventricularis muscle was evident in the upper and lateral portions of the fold more anteriorly. Very little muscle tissue was observed in the medial half of the fold, and the anterior half of the ventricular fold was largely devoid of any muscle tissue. All 4 larynges contained muscle bundles that coursed superiorly and medially through the upper half of the fold, toward the lateral margin of the epiglottis. Although variability of expression was evident, a well-defined thyroarytenoid muscle was readily apparent lateral to the arytenoid cartilage in all specimens.

  8. FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

    Science.gov (United States)

    Kosinski, Jan; Gajda, Michal J; Cymerman, Iwona A; Kurowski, Michal A; Pawlowski, Marcin; Boniecki, Michal; Obarska, Agnieszka; Papaj, Grzegorz; Sroczynska-Obuchowicz, Paulina; Tkaczuk, Karolina L; Sniezynska, Paulina; Sasin, Joanna M; Augustyn, Anna; Bujnicki, Janusz M; Feder, Marcin

    2005-01-01

    In the course of CASP6, we generated models for all targets using a new version of the "FRankenstein's monster approach." Previously (in CASP5) we were able to build many very accurate full-atom models by selection and recombination of well-folded fragments obtained from crude fold recognition (FR) results, followed by optimization of the sequence-structure fit and assessment of alternative alignments on the structural level. This procedure was however very arduous, as most of the steps required extensive visual and manual input from the human modeler. Now, we have automated the most tedious steps, such as superposition of alternative models, extraction of best-scoring fragments, and construction of a hybrid "monster" structure, as well as generation of alternative alignments in the regions that remain poorly scored in the refined hybrid model. We have also included the ROSETTA method to construct those parts of the target for which no reasonable structures were generated by FR methods (such as long insertions and terminal extensions). The analysis of successes and failures of the current version of the FRankenstein approach in modeling of CASP6 targets reveals that the considerably streamlined and automated method performs almost as well as the initial, mostly manual version, which suggests that it may be a useful tool for accurate protein structure prediction even in the hands of nonexperts. 2005 Wiley-Liss, Inc.

  9. Exact folded-band chaotic oscillator.

    Science.gov (United States)

    Corron, Ned J; Blakely, Jonathan N

    2012-06-01

    An exactly solvable chaotic oscillator with folded-band dynamics is shown. The oscillator is a hybrid dynamical system containing a linear ordinary differential equation and a nonlinear switching condition. Bounded oscillations are provably chaotic, and successive waveform maxima yield a one-dimensional piecewise-linear return map with segments of both positive and negative slopes. Continuous-time dynamics exhibit a folded-band topology similar to Rössler's oscillator. An exact solution is written as a linear convolution of a fixed basis pulse and a discrete binary sequence, from which an equivalent symbolic dynamics is obtained. The folded-band topology is shown to be dependent on the symbol grammar.

  10. Toroidal surface complexes of bacteriophage φ12 are responsible for host-cell attachment

    International Nuclear Information System (INIS)

    Leo-Macias, Alejandra; Katz, Garrett; Wei Hui; Alimova, Alexandra; Katz, A.; Rice, William J.; Diaz-Avalos, Ruben; Hu Guobin; Stokes, David L.; Gottlieb, Paul

    2011-01-01

    Cryo-electron tomography and subtomogram averaging are utilized to determine that the bacteriophage φ12, a member of the Cystoviridae family, contains surface complexes that are toroidal in shape, are composed of six globular domains with six-fold symmetry, and have a discrete density connecting them to the virus membrane-envelope surface. The lack of this kind of spike in a reassortant of φ12 demonstrates that the gene for the hexameric spike is located in φ12's medium length genome segment, likely to the P3 open reading frames which are the proteins involved in viral-host cell attachment. Based on this and on protein mass estimates derived from the obtained averaged structure, it is suggested that each of the globular domains is most likely composed of a total of four copies of P3a and/or P3c proteins. Our findings may have implications in the study of the evolution of the cystovirus species in regard to their host specificity. - Research Highlights: → Subtomogram averaging reveals enhanced detail of a φ12 cystovirus surface protein complex. → The surface protein complex has a toroidal shape and six-fold symmetry. → It is encoded by the medium-size genome segment. → The proteins of the surface complex most likely are one copy of P3a and three copies of P3c.

  11. Augmentation surgery on the cartilaginous portion of the vocal fold in a patient with cricoarytenoid joint ankylosis.

    Science.gov (United States)

    Fukahori, Mioko; Chitose, Shun-Ichi; Sato, Kiminori; Kamimura, Hiroyuki; Sato, Kiminobu; On, Ririko; Umeno, Hirohito

    2018-01-04

    Surgical management of cricoarytenoid joint (CAJ) ankylosis is challenging and has the risk of worsening voice quality. In the present case, augmentation surgery was performed on the cartilaginous portion of the vocal fold in a patient with CAJ ankylosis. A 24-year-old man sustained blunt trauma to the anterior neck three years prior to developing severe breathiness. Posterior glottal insufficiency resulting from lateral fixation of the right vocal fold was observed during phonation under laryngoscopy. In addition, electromyography and CT scan revealed severe ankylosis of the right CAJ. Type I thyroplasty performed on the right vocal fold did not improve postoperative vocal function. Therefore, augmentation surgery on the cartilaginous portion of the right vocal fold was performed via endolaryngeal microsurgery under general anesthesia with jet ventilation. A piece of temporalis fascia was autotransplanted into the submucosal space created at the posterior cartilaginous portion of the right vocal fold. This resulted in the narrowing of the posterior glottal gap during phonation, leading to improvement in hoarseness. Microsurgical management with autologous fascia augmentation of the cartilaginous portion of the vocal fold can be effective in patients with lateral vocal fold fixation due to CAJ ankylosis. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. Vocal fold paresis - a debilitating and underdiagnosed condition.

    Science.gov (United States)

    Harris, G; O'Meara, C; Pemberton, C; Rough, J; Darveniza, P; Tisch, S; Cole, I

    2017-07-01

    To review the clinical signs of vocal fold paresis on laryngeal videostroboscopy, to quantify its impact on patients' quality of life and to confirm the benefit of laryngeal electromyography in its diagnosis. Twenty-nine vocal fold paresis patients were referred for laryngeal electromyography. Voice Handicap Index 10 results were compared to 43 patients diagnosed with vocal fold paralysis. Laryngeal videostroboscopy analysis was conducted to determine side of paresis. Blinded laryngeal electromyography confirmed vocal fold paresis in 92.6 per cent of cases, with vocal fold lag being the most common diagnostic sign. The laryngology team accurately predicted side of paresis in 76 per cent of cases. Total Voice Handicap Index 10 responses were not significantly different between vocal fold paralysis and vocal fold paresis groups (26.08 ± 0.21 and 22.93 ± 0.17, respectively). Vocal fold paresis has a significant impact on quality of life. This study shows that laryngeal electromyography is an important diagnostic tool. Patients with persisting dysphonia and apparently normal vocal fold movement, who fail to respond to appropriate speech therapy, should be investigated for a diagnosis of vocal fold paresis.

  13. Adaptive Origami for Efficiently Folded Structures

    Science.gov (United States)

    2016-02-01

    heating. Although a large fold angle at a high temperature is desirable in order to extrapolate the origami geometry toward closure, more emphasis is...AFRL-RQ-WP-TR-2016-0020 ADAPTIVE ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES James J. Joo and Greg Reich Design and Analysis Branch... ORIGAMI FOR EFFICIENTLY FOLDED STRUCTURES 5a. CONTRACT NUMBER In-house 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 61102F 6. AUTHOR(S) James J

  14. 100-fold but not 50-fold dystrophin overexpression aggravates electrocardiographic defects in the mdx model of Duchenne muscular dystrophy

    Directory of Open Access Journals (Sweden)

    Yongping Yue

    2016-01-01

    Full Text Available Dystrophin gene replacement holds the promise of treating Duchenne muscular dystrophy. Supraphysiological expression is a concern for all gene therapy studies. In the case of Duchenne muscular dystrophy, Chamberlain and colleagues found that 50-fold overexpression did not cause deleterious side effect in skeletal muscle. To determine whether excessive dystrophin expression in the heart is safe, we studied two lines of transgenic mdx mice that selectively expressed a therapeutic minidystrophin gene in the heart at 50-fold and 100-fold of the normal levels. In the line with 50-fold overexpression, minidystrophin showed sarcolemmal localization and electrocardiogram abnormalities were corrected. However, in the line with 100-fold overexpression, we not only detected sarcolemmal minidystrophin expression but also observed accumulation of minidystrophin vesicles in the sarcoplasm. Excessive minidystrophin expression did not correct tachycardia, a characteristic feature of Duchenne muscular dystrophy. Importantly, several electrocardiogram parameters (QT interval, QRS duration and the cardiomyopathy index became worse than that of mdx mice. Our data suggests that the mouse heart can tolerate 50-fold minidystrophin overexpression, but 100-fold overexpression leads to cardiac toxicity.

  15. A dominant TRPV4 variant underlies osteochondrodysplasia in Scottish fold cats.

    Science.gov (United States)

    Gandolfi, B; Alamri, S; Darby, W G; Adhikari, B; Lattimer, J C; Malik, R; Wade, C M; Lyons, L A; Cheng, J; Bateman, J F; McIntyre, P; Lamandé, S R; Haase, B

    2016-08-01

    Scottish fold cats, named for their unique ear shape, have a dominantly inherited osteochondrodysplasia involving malformation in the distal forelimbs, distal hindlimbs and tail, and progressive joint destruction. This study aimed to identify the gene and the underlying variant responsible for the osteochondrodysplasia. DNA samples from 44 Scottish fold and 54 control cats were genotyped using a feline DNA array and a case-control genome-wide association analysis conducted. The gene encoding a calcium permeable ion channel, transient receptor potential cation channel, subfamily V, member 4 (TRPV4) was identified as a candidate within the associated region and sequenced. Stably transfected HEK293 cells were used to compare wild-type and mutant TRPV4 expression, cell surface localisation and responses to activation with a synthetic agonist GSK1016709A, hypo-osmolarity, and protease-activated receptor 2 stimulation. The dominantly inherited folded ear and osteochondrodysplasia in Scottish fold cats is associated with a p.V342F substitution (c.1024G>T) in TRPV4. The change was not found in 648 unaffected cats. Functional analysis in HEK293 cells showed V342F mutant TRPV4 was poorly expressed at the cell surface compared to wild-type TRPV4 and as a consequence the maximum response to a synthetic agonist was reduced. Mutant TRPV4 channels had a higher basal activity and an increased response to hypotonic conditions. Access to a naturally-occurring TRPV4 mutation in the Scottish fold cat will allow further functional studies to identify how and why the mutations affect cartilage and bone development. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. Doc of prophage P1 is inhibited by its antitoxin partner Phd through fold complementation

    DEFF Research Database (Denmark)

    Garcia-Pino, Abel; Christensen-Dalsgaard, Mikkel; Wyns, Lode

    2008-01-01

    Prokaryotic toxin-antitoxin modules are involved in major physiological events set in motion under stress conditions. The toxin Doc (death on curing) from the phd/doc module on phage P1 hosts the C-terminal domain of its antitoxin partner Phd (prevents host death) through fold complementation....... This Phd domain is intrinsically disordered in solution and folds into an alpha-helix upon binding to Doc. The details of the interactions reveal the molecular basis for the inhibitory action of the antitoxin. The complex resembles the Fic (filamentation induced by cAMP) proteins and suggests a possible......-antitoxin locus for its action in vivo....

  17. Two states or not two states: Single-molecule folding studies of protein L

    Science.gov (United States)

    Aviram, Haim Yuval; Pirchi, Menahem; Barak, Yoav; Riven, Inbal; Haran, Gilad

    2018-03-01

    Experimental tools of increasing sophistication have been employed in recent years to study protein folding and misfolding. Folding is considered a complex process, and one way to address it is by studying small proteins, which seemingly possess a simple energy landscape with essentially only two stable states, either folded or unfolded. The B1-IgG binding domain of protein L (PL) is considered a model two-state folder, based on measurements using a wide range of experimental techniques. We applied single-molecule fluorescence resonance energy transfer (FRET) spectroscopy in conjunction with a hidden Markov model analysis to fully characterize the energy landscape of PL and to extract the kinetic properties of individual molecules of the protein. Surprisingly, our studies revealed the existence of a third state, hidden under the two-state behavior of PL due to its small population, ˜7%. We propose that this minority intermediate involves partial unfolding of the two C-terminal β strands of PL. Our work demonstrates that single-molecule FRET spectroscopy can be a powerful tool for a comprehensive description of the folding dynamics of proteins, capable of detecting and characterizing relatively rare metastable states that are difficult to observe in ensemble studies.

  18. Sarcoidosis Presenting as Bilateral Vocal Fold Immobility.

    Science.gov (United States)

    Hintze, Justin M; Gnagi, Sharon H; Lott, David G

    2018-05-01

    Bilateral true vocal fold paralysis is rarely attributable to inflammatory diseases. Sarcoidosis is a rare but important etiology of bilateral true vocal fold paralysis by compressive lymphadenopathy, granulomatous infiltration, and neural involvement. We describe the first reported case of sarcoidosis presenting as bilateral vocal fold immobility caused by direct fixation by granulomatous infiltration severe enough to necessitate tracheostomy insertion. In addition, we discuss the presentation, the pathophysiology, and the treatment of this disease with a review of the literature of previously reported cases of sarcoidosis-related vocal fold immobility. Sarcoidosis should therefore be an important consideration for the otolaryngologist's differential diagnosis of true vocal fold immobility. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

  19. First Mitochondrial Genome from Nemouridae (Plecoptera) Reveals Novel Features of the Elongated Control Region and Phylogenetic Implications.

    Science.gov (United States)

    Chen, Zhi-Teng; Du, Yu-Zhou

    2017-05-05

    The complete mitochondrial genome (mitogenome) of Nemoura nankinensis (Plecoptera: Nemouridae) was sequenced as the first reported mitogenome from the family Nemouridae. The N. nankinensis mitogenome was the longest (16,602 bp) among reported plecopteran mitogenomes, and it contains 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. Most PCGs used standard ATN as start codons, and TAN as termination codons. All tRNA genes of N. nankinensis could fold into the cloverleaf secondary structures except for trnSer ( AGN ), whose dihydrouridine (DHU) arm was reduced to a small loop. There was also a large non-coding region (control region, CR) in the N. nankinensis mitogenome. The 1751 bp CR was the longest and had the highest A+T content (81.8%) among stoneflies. A large tandem repeat region, five potential stem-loop (SL) structures, four tRNA-like structures and four conserved sequence blocks (CSBs) were detected in the elongated CR. The presence of these tRNA-like structures in the CR has never been reported in other plecopteran mitogenomes. These novel features of the elongated CR in N. nankinensis may have functions associated with the process of replication and transcription. Finally, phylogenetic reconstruction suggested that Nemouridae was the sister-group of Capniidae.

  20. Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

    Science.gov (United States)

    Day, Ryan; Paschek, Dietmar; Garcia, Angel E.

    2012-01-01

    We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169

  1. Orogenic plateau growth: Expansion of the Turkish-Iranian Plateau across the Zagros fold-and-thrust belt

    Science.gov (United States)

    Allen, M. B.; Saville, C.; Blanc, E. J.-P.; Talebian, M.; Nissen, E.

    2013-03-01

    This paper shows how the Turkish-Iranian Plateau grows laterally by incrementally incorporating adjacent parts of the Zagros fold-and-thrust belt. The limit of significant, seismogenic, thrusting in the Zagros (Mw > 5) occurs close to the regional 1250 m elevation contour. The seismicity cutoff is not a significant bedrock geology boundary. Elevations increase northward, toward regional plateau elevations of 2 km, implying that another process produced the extra elevation. Between the seismogenic limit of thrusting and the suture, this process is a plausibly ductile thickening of the basement, suggesting depth-dependent strain during compression. Similar depth-dependant crustal strain may explain why the Tibetan plateau has regional elevations 1500 m greater than the elevation limit of seismogenic thrusting at its margins. We estimate 68 km shortening across the Zagros Simply Folded Belt in the Fars region, and 120 km total shortening of the Arabian plate. The Dezful Embayment is a low strain zone in the western Zagros. Deformation is more intense to its northeast, in the Bakhtyari Culmination. The orogenic taper (across strike topographic gradient) across the Dezful Embayment is 0.0004, and across the Bakhtyari Culmination, 0.022. Lateral plateau growth is more pronounced farther east (Fars), where a more uniform structure has a taper of 0.010 up to elevations of 1750 m. A >100 km wide region of the Zagros further northeast has a taper of 0.002 and is effectively part of the Turkish-Iranian Plateau. Internal drainage enhances plateau development but is not a pre-requisite. Aspects of the seismicity, structure, and geomorphology of the Zagros do not support critical taper models for fold-and-thrust belts.

  2. Extreme Mechanics: Self-Folding Origami

    Science.gov (United States)

    Santangelo, Christian D.

    2017-03-01

    Origami has emerged as a tool for designing three-dimensional structures from flat films. Because they can be fabricated by lithographic or roll-to-roll processing techniques, they have great potential for the manufacture of complicated geometries and devices. This article discusses the mechanics of origami and kirigami with a view toward understanding how to design self-folding origami structures. Whether an origami structure can be made to fold autonomously depends strongly on the geometry and kinematics of the origami fold pattern. This article collects some of the results on origami rigidity into a single framework, and discusses how these aspects affect the foldability of origami. Despite recent progress, most problems in origami and origami design remain completely open.

  3. Exploring the Evolutionary Accident Hypothesis: Are Extant Protein Folds the Fittest or the Luckiest?

    Science.gov (United States)

    Shannon, G.; Wei, C.; Pohorille, A.

    2017-01-01

    Considering the range of functions proteins perform, it is surprising they fold into a relatively small set of structures or "folds" that facilitate such function. One explanation is that only a minority were fit enough to emerge from Darwinian selection during the early evolution of life. Alternatively, perhaps only a fraction of all possible folds were trialed. Understanding proto-catalyst selection will aid understanding of the origins and early evolution of life. To investigate which explanation is correct, we study a protein evolved in vitro to bind ATP by Jack Szostak (Fig. 1). This protein adopts a fold which is absent from nature. We are testing whether this fold would have possessed the capability to evolve that would have been essential to survive natural selection on early Earth. Folds that couldn't improve their fitness and evolve to perform new functions would have been replaced by rivals that could. To determine whether the fold is evolvable, we are attempting to change the function of the protein by rationally redesigning to bind GTP. Two design strategies in the region of the nucleobase have been implemented to provide hydrogen bonding partners for the ligand i) an insertion ii) a MET to ASN mutation. Redesigns are being studied computationally at Ames Research Center including free energy of binding calculations. Binding affinities of promising redesigns are to be validated by experimental collaborators at ForteBio using Super Streptavidin Biosensors. If the fold is found to be non-evolvable, this may suggest that many structures were trialed, but the majority were pruned on the basis of their evolvability. Alternatively, if the fold is demonstrated to be evolvable, it would be difficult to explain its absence from nature without considering the possibility that the fold simply wasn't sampled on early Earth. This would not only further our understanding of the origins of life on Earth but also suggest a common phe-nomenon of proto

  4. Positive therapy of andrographolide in vocal fold leukoplakia.

    Science.gov (United States)

    Xu, Jue; Xue, Tao; Bao, Ying; Wang, Dong-Hai; Ma, Bing-Liang; Yin, Chen-Yi; Yang, Guang-Hui; Ren, Gang; Lan, Long-Jiang; Wang, Jian-Qiu; Zhang, Xiao-Lan; Zhao, Yu-Qin

    2014-01-01

    Vocal fold leukoplakia is a premalignant precursor of squamous cell carcinoma. Although many efforts have been contributed to therapy of this disease, none exhibits a satisfactory result. The aims of this study were to investigate the effectiveness and feasibility of andrographolide therapy in vocal fold leukoplakia and to explore the preliminary mechanism underlying. Forty-one eligible patients were enrolled in the study. The patients were treated for 10-minute exposures of 5 ml (25mg/ml) andrographolide injection aerosols twice a day, and 2 weeks was considered as one treatment course. Electronic laryngoscope was used to observe the condition of vocal fold leukoplakia during the treatment. Every patient received one or two treatment courses, and the follow-up was carried out for 12 months. Toxic reactions of treatments were evaluated on the basis of the standards of the United States MD Anderson Cancer Center. Moreover, laryngeal carcinoma cell line Hep2 was applied to explore the mechanism of effect of andrographolide. Anti-proliferative effect on Hep2, cell nuclear morphology, express of mitogen-activated protein kinases (MAPK) and pro-apoptotic protein were detected after andrographolide treatment. We found that andrographolide exhibited significant curative effects on treatments, which were accompanied by thinning of the lesion of leukoplakia, reduction in the whitish surface area, and return of pink or red epithelium. A complete response up to 85% was observed, and no toxic side effect events occurred during the study. No patient with a complete response had a recurrence in the follow-up. Moreover, cellular experiments in Hep2 indicated that andrographolide activated MAPK pathway and caspase cascade, and finally induced apoptosis in laryngeal carcinoma cell. The advantages of andrographolide are connected with minimally invasive and localized character of the treatment and no damage of collagenous tissue structures, which are more convenient and less painful

  5. Multi-crease Self-folding by Global Heating.

    Science.gov (United States)

    Miyashita, Shuhei; Onal, Cagdas D; Rus, Daniela

    2015-01-01

    This study demonstrates a new approach to autonomous folding for the body of a 3D robot from a 2D sheet, using heat. We approach this challenge by folding a 0.27-mm sheetlike material into a structure. We utilize the thermal deformation of a contractive sheet sandwiched by rigid structural layers. During this baking process, the heat applied on the entire sheet induces contraction of the contracting layer and thus forms an instructed bend in the sheet. To attain the targeted folding angles, the V-fold spans method is used. The targeted angle θout can be kinematically encoded into crease geometry. The realization of this angle in the folded structure can be approximately controlled by a contraction angle θin. The process is non-reversible, is reliable, and is relatively fast. Our method can be applied simultaneously to all the folds in multi-crease origami structures. We demonstrate the use of this method to create a lightweight mobile robot.

  6. Identification of new solar OH lines in the 10--12 micron region

    International Nuclear Information System (INIS)

    Goldman, A.; Murcray, F.J.; Gillis, J.R.; Murcray, D.G.

    1981-01-01

    High-resolution (0.02 cm -1 ) infrared solar spectra obtained with a balloon-borne interferometer reveal new solar absorption features, which appear as regularly spaced quartets, in the 825--960 cm -1 region. The lines are interpreted as high N'' (25--33) pure rotation lines of solar OH. An effective amount of approx.8 x 10 15 molecules cm -2 of OH is estimated from the spectra

  7. On Austrian regional economics

    NARCIS (Netherlands)

    Heijman, W.J.M.; Leen, A.R.

    2004-01-01

    The aim of this research note is two-fold, firstly, to clarify the growing interaction between regional science and Austrian economics and their awareness of each other. We elucidate the Austrian methodology, called praxeology, which is especially misunderstood in regional science. Secondly, we

  8. Cross-sample validation provides enhanced proteome coverage in rat vocal fold mucosa.

    Directory of Open Access Journals (Sweden)

    Nathan V Welham

    2011-03-01

    Full Text Available The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high M(r ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high M(r glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match. The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories.

  9. Neural stem cells promote nerve regeneration through IL12-induced Schwann cell differentiation.

    Science.gov (United States)

    Lee, Don-Ching; Chen, Jong-Hang; Hsu, Tai-Yu; Chang, Li-Hsun; Chang, Hsu; Chi, Ya-Hui; Chiu, Ing-Ming

    2017-03-01

    Regeneration of injured peripheral nerves is a slow, complicated process that could be improved by implantation of neural stem cells (NSCs) or nerve conduit. Implantation of NSCs along with conduits promotes the regeneration of damaged nerve, likely because (i) conduit supports and guides axonal growth from one nerve stump to the other, while preventing fibrous tissue ingrowth and retaining neurotrophic factors; and (ii) implanted NSCs differentiate into Schwann cells and maintain a growth factor enriched microenvironment, which promotes nerve regeneration. In this study, we identified IL12p80 (homodimer of IL12p40) in the cell extracts of implanted nerve conduit combined with NSCs by using protein antibody array and Western blotting. Levels of IL12p80 in these conduits are 1.6-fold higher than those in conduits without NSCs. In the sciatic nerve injury mouse model, implantation of NSCs combined with nerve conduit and IL12p80 improves motor recovery and increases the diameter up to 4.5-fold, at the medial site of the regenerated nerve. In vitro study further revealed that IL12p80 stimulates the Schwann cell differentiation of mouse NSCs through the phosphorylation of signal transducer and activator of transcription 3 (Stat3). These results suggest that IL12p80 can trigger Schwann cell differentiation of mouse NSCs through Stat3 phosphorylation and enhance the functional recovery and the diameter of regenerated nerves in a mouse sciatic nerve injury model. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. Acute contained ruptured aortic aneurysm presenting as left vocal fold immobility.

    Science.gov (United States)

    Gnagi, Sharon H; Howard, Brittany E; Hoxworth, Joseph M; Lott, David G

    2015-01-01

    Objective. To recognize intrathoracic abnormalities, including expansion or rupture of aortic aneurysms, as a source of acute onset vocal fold immobility. Methods. A case report and review of the literature. Results. An 85-year-old female with prior history of an aortic aneurysm presented to a tertiary care facility with sudden onset hoarseness. On laryngoscopy, the left vocal fold was immobile in the paramedian position. A CT scan obtained that day revealed a new, large hematoma surrounding the upper descending aortic stent graft consistent with an acute contained ruptured aortic aneurysm. She was referred to the emergency department for evaluation and treatment by vascular surgery. She was counseled regarding surgical options and ultimately decided not to pursue further treatment. Her vocal fold immobility was subsequently treated via office-based injection medialization two weeks after presentation and again 5 months after the initial injection which dramatically improved her voice. Follow-up CT scan at 8 months demonstrated a reduction of the hematoma. The left vocal cord remains immobile to date. Conclusion. Ortner's syndrome, or cardiovocal syndrome, is hoarseness secondary to left recurrent laryngeal nerve palsy caused by cardiovascular pathology. It is a rare condition and, while typically presenting gradually, may also present with acute symptomatology.

  11. Acute Contained Ruptured Aortic Aneurysm Presenting as Left Vocal Fold Immobility

    Directory of Open Access Journals (Sweden)

    Sharon H. Gnagi

    2015-01-01

    Full Text Available Objective. To recognize intrathoracic abnormalities, including expansion or rupture of aortic aneurysms, as a source of acute onset vocal fold immobility. Methods. A case report and review of the literature. Results. An 85-year-old female with prior history of an aortic aneurysm presented to a tertiary care facility with sudden onset hoarseness. On laryngoscopy, the left vocal fold was immobile in the paramedian position. A CT scan obtained that day revealed a new, large hematoma surrounding the upper descending aortic stent graft consistent with an acute contained ruptured aortic aneurysm. She was referred to the emergency department for evaluation and treatment by vascular surgery. She was counseled regarding surgical options and ultimately decided not to pursue further treatment. Her vocal fold immobility was subsequently treated via office-based injection medialization two weeks after presentation and again 5 months after the initial injection which dramatically improved her voice. Follow-up CT scan at 8 months demonstrated a reduction of the hematoma. The left vocal cord remains immobile to date. Conclusion. Ortner’s syndrome, or cardiovocal syndrome, is hoarseness secondary to left recurrent laryngeal nerve palsy caused by cardiovascular pathology. It is a rare condition and, while typically presenting gradually, may also present with acute symptomatology.

  12. Orogen-transverse tectonic window in the Eastern Himalayan fold belt: A superposed buckling model

    Science.gov (United States)

    Bose, Santanu; Mandal, Nibir; Acharyya, S. K.; Ghosh, Subhajit; Saha, Puspendu

    2014-09-01

    The Eastern Lesser Himalayan fold-thrust belt is punctuated by a row of orogen-transverse domal tectonic windows. To evaluate their origin, a variety of thrust-stack models have been proposed, assuming that the crustal shortening occurred dominantly by brittle deformations. However, the Rangit Window (RW) in the Darjeeling-Sikkim Himalaya (DSH) shows unequivocal structural imprints of ductile deformations of multiple episodes. Based on new structural maps, coupled with outcrop-scale field observations, we recognize at least four major episodes of folding in the litho-tectonic units of DSH. The last episode has produced regionally orogen-transverse upright folds (F4), the interference of which with the third-generation (F3) orogen-parallel folds has shaped the large-scale structural patterns in DSH. We propose a new genetic model for the RW, invoking the mechanics of superposed buckling in the mechanically stratified litho-tectonic systems. We substantiate this superposed buckling model with results obtained from analogue experiments. The model explains contrasting F3-F4 interferences in the Lesser Himalayan Sequence (LHS). The lower-order (terrain-scale) folds have undergone superposed buckling in Mode 1, producing large-scale domes and basins, whereas the RW occurs as a relatively higher-order dome nested in the first-order Tista Dome. The Gondwana and the Proterozoic rocks within the RW underwent superposed buckling in Modes 3 and 4, leading to Type 2 fold interferences, as evident from their structural patterns.

  13. 12-Digit Watershed Boundary Data 1:24,000 for EPA Region 2 and Surrounding States (NAT_HYDROLOGY.HUC12_NRCS_REG2)

    Data.gov (United States)

    U.S. Environmental Protection Agency — 12 digit Hydrologic Units (HUCs) for EPA Region 2 and surrounding states (Northeastern states, parts of the Great Lakes, Puerto Rico and the USVI) downloaded from...

  14. Dysphagia, hoarseness, and unilateral true vocal fold motion impairment following anterior cervical diskectomy and fusion.

    Science.gov (United States)

    Baron, Eli M; Soliman, Ahmed M S; Gaughan, John P; Simpson, Lisa; Young, William F

    2003-11-01

    The charts of 100 patients who underwent anterior cervical diskectomy with fusion performed at our institution between January 1996 and February 1999 were reviewed. The incidences of hoarseness, dysphagia, and unilateral true vocal fold motion impairment were calculated. Univariate logistic regression was used to estimate the relationship of several patient and technical factors to the rates of occurrence of hoarseness and dysphagia. Patient age was found to be a significant predictor of postoperative dysphagia (p dysphagia, hoarseness, and unilateral true vocal fold motion impairment in the literature were calculated as 12.3%, 4.9%, and 1.4%, respectively. We conclude that dysphagia, hoarseness, and unilateral vocal fold motion impairment continue to remain significant complications of anterior cervical diskectomy with fusion. Older patients may be at higher risk for dysphagia.

  15. Single-molecule folding mechanism of an EF-hand neuronal calcium sensor

    DEFF Research Database (Denmark)

    Heiðarsson, Pétur Orri; Otazo, Mariela R.; Bellucci, Luca

    2013-01-01

    EF-hand calcium sensors respond structurally to changes in intracellular Ca2+ concentration, triggering diverse cellular responses and resulting in broad interactomes. Despite impressive advances in decoding their structure-function relationships, the folding mechanism of neuronal calcium sensors...... of the N domain, showing striking interdomain dependence. Molecular dynamics results reveal the atomistic details of the unfolding process and rationalize the different domain stabilities during mechanical unfolding. Through constant-force experiments and hidden Markov model analysis, the free energy...

  16. 3D Visualization of Sheath Folds in Roman Marble from Ephesus, Turkey

    Science.gov (United States)

    Wex, Sebastian; Passchier, Cornelis W.; de Kemp, Eric A.; Ilhan, Sinan

    2013-04-01

    Excavation of a palatial 2nd century AD house (Terrace House Two) in the ancient city of Ephesus, Turkey in the 1970s produced 10.313 pieces of colored, folded marble which belonged to 54 marble plates of 1.6 cm thickness that originally covered the walls of the banquet hall of the house. The marble plates were completely reassembled and restored by a team of workers over the last 6 years. The plates were recognized as having been sawn from two separate large blocks of "Cipollino verde", a green mylonitized marble from Karystos on the Island of Euboea, Greece. After restoration, it became clear that all slabs had been placed on the wall in approximately the sequence in which they had been cut off by a Roman stone saw. As a result, the marble plates give a full 3D insight in the folded internal structure of 1m3 block of mylonite. The restoration of the slabs was recognized as a first, unique opportunity for detailed reconstruction of the 3D geometry of m-scale folds in mylonitized marble. Photographs were taken of each slab and used to reconstruct their exact arrangement within the originally quarried blocks. Outlines of layers were digitized and a full 3D reconstruction of the internal structure of the block was created using ArcMap and GOCAD. Fold structures in the block include curtain folds and multilayered sheath folds. Several different layers showing these structures were digitized on the photographs of the slab surfaces and virtually mounted back together within the model of the marble block. Due to the serial sectioning into slabs, with cm-scale spacing, the visualization of the 3D geometry of sheath folds was accomplished with a resolution better than 4 cm. Final assembled 3D images reveal how sheath folds emerge from continuous layers and show their overall consistency as well as a constant hinge line orientation of the fold structures. Observations suggest that a single deformation phase was responsible for the evolution of "Cipollino verde" structures

  17. Factors that affect coseismic folds in an overburden layer

    Science.gov (United States)

    Zeng, Shaogang; Cai, Yongen

    2018-03-01

    Coseismic folds induced by blind thrust faults have been observed in many earthquake zones, and they have received widespread attention from geologists and geophysicists. Numerous studies have been conducted regarding fold kinematics; however, few have studied fold dynamics quantitatively. In this paper, we establish a conceptual model with a thrust fault zone and tectonic stress load to study the factors that affect coseismic folds and their formation mechanisms using the finite element method. The numerical results show that the fault dip angle is a key factor that controls folding. The greater the dip angle is, the steeper the fold slope. The second most important factor is the overburden thickness. The thicker the overburden is, the more gradual the fold. In this case, folds are difficult to identify in field surveys. Therefore, if a fold can be easily identified with the naked eye, the overburden is likely shallow. The least important factors are the mechanical parameters of the overburden. The larger the Young's modulus of the overburden is, the smaller the displacement of the fold and the fold slope. Strong horizontal compression and vertical extension in the overburden near the fault zone are the main mechanisms that form coseismic folds.

  18. A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Fabrizio Marinelli

    2009-08-01

    Full Text Available Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

  19. Symbolic joint entropy reveals the coupling of various brain regions

    Science.gov (United States)

    Ma, Xiaofei; Huang, Xiaolin; Du, Sidan; Liu, Hongxing; Ning, Xinbao

    2018-01-01

    The convergence and divergence of oscillatory behavior of different brain regions are very important for the procedure of information processing. Measurements of coupling or correlation are very useful to study the difference of brain activities. In this study, EEG signals were collected from ten subjects under two conditions, i.e. eyes closed state and idle with eyes open. We propose a nonlinear algorithm, symbolic joint entropy, to compare the coupling strength among the frontal, temporal, parietal and occipital lobes and between two different states. Instead of decomposing the EEG into different frequency bands (theta, alpha, beta, gamma etc.), the novel algorithm is to investigate the coupling from the entire spectrum of brain wave activities above 4Hz. The coupling coefficients in two states with different time delay steps are compared and the group statistics are presented as well. We find that the coupling coefficient of eyes open state with delay consistently lower than that of eyes close state across the group except for one subject, whereas the results without delay are not consistent. The differences between two brain states with non-zero delay can reveal the intrinsic inter-region coupling better. We also use the well-known Hénon map data to validate the algorithm proposed in this paper. The result shows that the method is robust and has a great potential for other physiologic time series.

  20. Characterization of Vocal Fold Vibration in Sulcus Vocalis Using High-Speed Digital Imaging

    Science.gov (United States)

    Yamauchi, Akihito; Yokonishi, Hisayuki; Imagawa, Hiroshi; Sakakibara, Ken-Ichi; Nito, Takaharu; Tayama, Niro; Yamasoba, Tatsuya

    2017-01-01

    Purpose: The aim of the present study was to qualitatively and quantitatively characterize vocal fold vibrations in sulcus vocalis by high-speed digital imaging (HSDI) and to clarify the correlations between HSDI-derived parameters and traditional vocal parameters. Method: HSDI was performed in 20 vocally healthy subjects (8 men and 12 women) and…

  1. Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Kalliopi K Patapati

    Full Text Available Conventional wisdom has it that the presence of disordered regions in the three-dimensional structures of polypeptides not only does not contribute significantly to the thermodynamic stability of their folded state, but, on the contrary, that the presence of disorder leads to a decrease of the corresponding proteins' stability. We have performed extensive 3.4 µs long folding simulations (in explicit solvent and with full electrostatics of an undecamer peptide of experimentally known helical structure, both with and without its disordered (four residue long C-terminal tail. Our simulations clearly indicate that the presence of the apparently disordered (in structural terms C-terminal tail, increases the thermodynamic stability of the peptide's folded (helical state. These results show that at least for the case of relatively short peptides, the interplay between thermodynamic stability and the apparent structural stability can be rather subtle, with even disordered regions contributing significantly to the stability of the folded state. Our results have clear implications for the understanding of peptide energetics and the design of foldable peptides.

  2. Physics of protein folding

    Science.gov (United States)

    Finkelstein, A. V.; Galzitskaya, O. V.

    2004-04-01

    Protein physics is grounded on three fundamental experimental facts: protein, this long heteropolymer, has a well defined compact three-dimensional structure; this structure can spontaneously arise from the unfolded protein chain in appropriate environment; and this structure is separated from the unfolded state of the chain by the “all-or-none” phase transition, which ensures robustness of protein structure and therefore of its action. The aim of this review is to consider modern understanding of physical principles of self-organization of protein structures and to overview such important features of this process, as finding out the unique protein structure among zillions alternatives, nucleation of the folding process and metastable folding intermediates. Towards this end we will consider the main experimental facts and simple, mostly phenomenological theoretical models. We will concentrate on relatively small (single-domain) water-soluble globular proteins (whose structure and especially folding are much better studied and understood than those of large or membrane and fibrous proteins) and consider kinetic and structural aspects of transition of initially unfolded protein chains into their final solid (“native”) 3D structures.

  3. Design of an Efficient Turbulent Micro-Mixer for Protein Folding Experiments

    Science.gov (United States)

    Inguva, Venkatesh; Perot, Blair

    2015-11-01

    Protein folding studies require the development of micro-mixers that require less sample, mix at faster rates, and still provide a high signal to noise ratio. Chaotic to marginally turbulent micro-mixers are promising candidates for this application. In this study, various turbulence and unsteadiness generation concepts are explored that avoid cavitation. The mixing enhancements include flow turning regions, flow splitters, and vortex shedding. The relative effectiveness of these different approaches for rapid micro-mixing is discussed. Simulations found that flow turning regions provided the best mixing profile. Experimental validation of the optimal design is verified through laser confocal microscopy experiments. This work is support by the National Science Foundation.

  4. Natural triple beta-stranded fibrous folds.

    Science.gov (United States)

    Mitraki, Anna; Papanikolopoulou, Katerina; Van Raaij, Mark J

    2006-01-01

    A distinctive family of beta-structured folds has recently been described for fibrous proteins from viruses. Virus fibers are usually involved in specific host-cell recognition. They are asymmetric homotrimeric proteins consisting of an N-terminal virus-binding tail, a central shaft or stalk domain, and a C-terminal globular receptor-binding domain. Often they are entirely or nearly entirely composed of beta-structure. Apart from their biological relevance and possible gene therapy applications, their shape, stability, and rigidity suggest they may be useful as blueprints for biomechanical design. Folding and unfolding studies suggest their globular C-terminal domain may fold first, followed by a "zipping-up" of the shaft domains. The C-terminal domains appear to be important for registration because peptides corresponding to shaft domains alone aggregate into nonnative fibers and/or amyloid structures. C-terminal domains can be exchanged between different fibers and the resulting chimeric proteins are useful as a way to solve structures of unknown parts of the shaft domains. The following natural triple beta-stranded fibrous folds have been discovered by X-ray crystallography: the triple beta-spiral, triple beta-helix, and T4 short tail fiber fold. All have a central longitudinal hydrophobic core and extensive intermonomer polar and nonpolar interactions. Now that a reasonable body of structural and folding knowledge has been assembled about these fibrous proteins, the next challenge and opportunity is to start using this information in medical and industrial applications such as gene therapy and nanotechnology.

  5. Deep inelastic scattering of electrons on 12C in the δ(1236) region

    International Nuclear Information System (INIS)

    Meziani, Zein-Eddine.

    1982-06-01

    An experiment involving inclusive deep inelastic scattering of 700 MeV electrons on 12 C is presented. A broad energy transfer region (20 to 500 MeV) was examined enabling various different reaction mechanisms occurring in the nucleus to be studied. Attention was given to electroproduction processes in the δ(1236) resonance region. Measurements of deep inelastic scattering cross sections and radiative correction problems are discussed. A theoretical treatment of the cross section in the framework of a virtual photon exchange approximation is presented [fr

  6. The influence of material anisotropy on vibration at onset in a three-dimensional vocal fold model

    Science.gov (United States)

    Zhang, Zhaoyan

    2014-01-01

    Although vocal folds are known to be anisotropic, the influence of material anisotropy on vocal fold vibration remains largely unknown. Using a linear stability analysis, phonation onset characteristics were investigated in a three-dimensional anisotropic vocal fold model. The results showed that isotropic models had a tendency to vibrate in a swing-like motion, with vibration primarily along the superior-inferior direction. Anterior-posterior (AP) out-of-phase motion was also observed and large vocal fold vibration was confined to the middle third region along the AP length. In contrast, increasing anisotropy or increasing AP-transverse stiffness ratio suppressed this swing-like motion and allowed the vocal fold to vibrate in a more wave-like motion with strong medial-lateral motion over the entire medial surface. Increasing anisotropy also suppressed the AP out-of-phase motion, allowing the vocal fold to vibrate in phase along the entire AP length. Results also showed that such improvement in vibration pattern was the most effective with large anisotropy in the cover layer alone. These numerical predictions were consistent with previous experimental observations using self-oscillating physical models. It was further hypothesized that these differences may facilitate complete glottal closure in finite-amplitude vibration of anisotropic models as observed in recent experiments. PMID:24606284

  7. Constructing a folding model for protein S6 guided by native fluctuations deduced from NMR structures

    International Nuclear Information System (INIS)

    Lammert, Heiko; Noel, Jeffrey K.; Haglund, Ellinor; Onuchic, José N.; Schug, Alexander

    2015-01-01

    The diversity in a set of protein nuclear magnetic resonance (NMR) structures provides an estimate of native state fluctuations that can be used to refine and enrich structure-based protein models (SBMs). Dynamics are an essential part of a protein’s functional native state. The dynamics in the native state are controlled by the same funneled energy landscape that guides the entire folding process. SBMs apply the principle of minimal frustration, drawn from energy landscape theory, to construct a funneled folding landscape for a given protein using only information from the native structure. On an energy landscape smoothed by evolution towards minimal frustration, geometrical constraints, imposed by the native structure, control the folding mechanism and shape the native dynamics revealed by the model. Native-state fluctuations can alternatively be estimated directly from the diversity in the set of NMR structures for a protein. Based on this information, we identify a highly flexible loop in the ribosomal protein S6 and modify the contact map in a SBM to accommodate the inferred dynamics. By taking into account the probable native state dynamics, the experimental transition state is recovered in the model, and the correct order of folding events is restored. Our study highlights how the shared energy landscape connects folding and function by showing that a better description of the native basin improves the prediction of the folding mechanism

  8. Folding and fracturing of rock adjacent to salt diapirs

    Science.gov (United States)

    Rowan, Mark G.

    2017-04-01

    of diapirs, have very little internal deformation. Instead, what faults are present around diapirs are related to drape folding (radial and diapir-parallel faults) or regional tectonics (extensional, contractional, strike-slip, and salt-evacuation faults).

  9. Fold and Fit: Space Conserving Shape Editing

    KAUST Repository

    Ibrahim, Mohamed

    2017-09-01

    We present a framework that folds man-made objects in a structure-aware manner for space-conserving storage and transportation. Given a segmented 3D mesh of a man-made object, our framework jointly optimizes for joint locations, the folding order, and folding angles for each part of the model, enabling it to transform into a spatially efficient configuration while keeping its original functionality as intact as possible. That is, if a model is supposed to withstand several forces in its initial state to serve its functionality, our framework places the joints between the parts of the model such that the model can withstand forces with magnitudes that are comparable to the magnitudes applied on the unedited model. Furthermore, if the folded shape is not compact, our framework proposes further segmentation of the model to improve its compactness in its folded state.

  10. Recurrent Vocal Fold Paralysis and Parsonage-Turner Syndrome

    Directory of Open Access Journals (Sweden)

    Marcus Vinicius Pinto

    2013-01-01

    Full Text Available Background. Parsonage-Turner syndrome, or neuralgic amyotrophy (NA, is an acute brachial plexus neuritis that typically presents with unilateral shoulder pain and amyotrophy but also can affect other peripheral nerves, including the recurrent laryngeal nerve. Idiopathic vocal fold paralysis (VFP represents approximately 12% of the VFP cases and recurrence is extremely rare. Methods and Results. We report a man with isolated recurrent unilateral right VFP and a diagnosis of NA years before. Conclusions. We emphasize that shoulder pain and amyotrophy should be inquired in any patient suffering from inexplicable dysphonia, and Parsonage-Turner syndrome should be considered in the differential diagnosis of idiopathic VFP.

  11. Ionizing radiation damage to the folded chromosome of Escherichia coli K-12: repair of double-strand breaks in deoxyribonucleic acid

    International Nuclear Information System (INIS)

    Ulmer, M.K.; Gomez, R.F.; Sinskevy, A.J.

    1979-01-01

    The extremely gentle lysis and unfolding procedures that have been developed for the isolation of nucleoid deoxyribonucleic acid yield undamaged, replicating genomes, thus permitting direct measurement of the formation and repair of DNA double-strand breaks at biologically significant doses of ionizing radiation. Repair of ionizing radiation damage to folded chromosomes of Escherichia coli K-12 strain AB2497 was observed within 2 to 3 h of post-irradiation incubation in growth medium. Such behavior was not observed after post-irradiation incubation in growth medium of a recA13 strain (strain AB2487). A model based on recombinational repair is proposed to explain the formation of 2,200 to 2,300S material during early stages of incubation and to explain subsequent changes in the gradient profiles. Association of unrepaired DNA with the plasma membrane is proposed to explain the formation of a peak of rapidly sedimenting material (greater than 3,100S) during the later stage of repair. Direct evidence of repair of double-strand breaks during post-irradiation incubation in growth medium was obtained from gradient profiles of DNA from ribonuclease-digested chromosomes. The sedimentation coefficient of broken molecules was restored to the value of unirradiated DNA after 2 to 3 h of incubation, and the fraction of the DNA repaired in this fashion was equal to the fraction of cells that survived at the same dose. An average of 2.7 double-strand breaks per genome per lethal event was observed, suggesting that one to two double-strand breaks per genome are repairable in E. coli K-12 strain AB2497

  12. Self-folding miniature elastic electric devices

    International Nuclear Information System (INIS)

    Miyashita, Shuhei; Meeker, Laura; Rus, Daniela; Tolley, Michael T; Wood, Robert J

    2014-01-01

    Printing functional materials represents a considerable impact on the access to manufacturing technology. In this paper we present a methodology and validation of print-and-self-fold miniature electric devices. Polyvinyl chloride laminated sheets based on metalized polyester film show reliable self-folding processes under a heat application, and it configures 3D electric devices. We exemplify this technique by fabricating fundamental electric devices, namely a resistor, capacitor, and inductor. Namely, we show the development of a self-folded stretchable resistor, variable resistor, capacitive strain sensor, and an actuation mechanism consisting of a folded contractible solenoid coil. Because of their pre-defined kinematic design, these devices feature elasticity, making them suitable as sensors and actuators in flexible circuits. Finally, an RLC circuit obtained from the integration of developed devices is demonstrated, in which the coil based actuator is controlled by reading a capacitive strain sensor. (paper)

  13. Elastic scattering of {sup 12} C by {sup 12} C at intermediate energies

    Energy Technology Data Exchange (ETDEWEB)

    Khallaf, S A.E. [Department of Physics, Faculty of Science, Assiut University, Assiut, (Egypt); Abdel-Rahman, M A; Abdel-Raheem, S K; Mahmoud, S W.Z. [Department of Physics, Faculty of Science, El-Minia University, El-Minia, (Egypt)

    1997-12-31

    Using the double folding model (DF), the real part of the central potential for {sup 12} C + {sup 12} C system is derived. This potential as well as the single folding cluster model potential (SFC) were used to calculate the total and differential cross sections for {sup 12} C elastically scattered on {sup 12} C at three laboratory energies; E{sub 1ab}. = 300, 344.5 and 360 MeV. The calculations were carried out using five sets of nucleon nucleon (NN) interaction of the integrable Gaussian form and two sets of parameters for the nuclear matter density of the harmonic oscillator form. The transparency of the target nucleus was found to increase as the projectile energy increases. Good fits between the present calculations and the experimental data as well as the previously published calculations were obtained. The present simple methods used to calculate the real part of the optical potential stand on equal footing with the density dependent (DDM 3 Y) procedure and it reduces the potential computing time enormously. The suitable choice of NN interaction as well as nuclear matter densities is important. 24 figs., 3 tabs.

  14. Cortical thickness, surface area, and folding alterations in male youths with conduct disorder and varying levels of callous-unemotional traits.

    Science.gov (United States)

    Fairchild, Graeme; Toschi, Nicola; Hagan, Cindy C; Goodyer, Ian M; Calder, Andrew J; Passamonti, Luca

    2015-01-01

    Previous studies have reported changes in gray matter volume in youths with conduct disorder (CD), although these differences are difficult to interpret as they may have been driven by alterations in cortical thickness, surface area (SA), or folding. The objective of this study was to use surface-based morphometry (SBM) methods to compare male youths with CD and age and sex-matched healthy controls (HCs) in cortical thickness, SA, and folding. We also tested for structural differences between the childhood-onset and adolescence-onset subtypes of CD and performed regression analyses to assess for relationships between CD symptoms and callous-unemotional (CU) traits and SBM-derived measures. We acquired structural neuroimaging data from 20 HCs and 36 CD participants (18 with childhood-onset CD and 18 with adolescence-onset CD) and analyzed the data using FreeSurfer. Relative to HCs, youths with CD showed reduced cortical thickness in the superior temporal gyrus, reduced SA in the orbitofrontal cortex (OFC), and increased cortical folding in the insula. There were no significant differences between the childhood-onset and adolescence-onset CD subgroups in cortical thickness or SA, but several frontal and temporal regions showed increased cortical folding in childhood-onset relative to adolescence-onset CD participants. Both CD subgroups also showed increased cortical folding relative to HCs. CD symptoms were negatively correlated with OFC SA whereas CU traits were positively correlated with insula folding. Cortical thinning in the superior temporal gyrus may contribute to the social cognitive impairments displayed by youths with CD, whereas reduced OFC SA may lead to impairments in emotion regulation and reward processing in youths with CD. The increased cortical folding observed in the insula may reflect a maturational delay in this region and could mediate the link between CU traits and empathy deficits. Altered cortical folding was observed in childhood-onset and

  15. Microvascular lesions of the true vocal fold.

    Science.gov (United States)

    Postma, G N; Courey, M S; Ossoff, R H

    1998-06-01

    Microvascular lesions, also called varices or capillary ectasias, in contrast to vocal fold polyps with telangiectatic vessels, are relatively small lesions arising from the microcirculation of the vocal fold. Varices are most commonly seen in female professional vocalists and may be secondary to repetitive trauma, hormonal variations, or repeated inflammation. Microvascular lesions may either be asymptomatic or cause frank dysphonia by interrupting the normal vibratory pattern, mass, or closure of the vocal folds. They may also lead to vocal fold hemorrhage, scarring, or polyp formation. Laryngovideostroboscopy is the key in determining the functional significance of vocal fold varices. Management of patients with a varix includes medical therapy, speech therapy, and occasionally surgical vaporization. Indications for surgery are recurrent hemorrhage, enlargement of the varix, development of a mass in conjunction with the varix or hemorrhage, and unacceptable dysphonia after maximal medical and speech therapy due to a functionally significant varix.

  16. Approaching climate-adaptive facades with foldings

    DEFF Research Database (Denmark)

    Sack-Nielsen, Torsten

    2014-01-01

    envelopes based on folding principles such as origami. Three major aspects cover the project’s interest in this topic: Shape, kinetics and the application of new multi-functional materials form the interdisciplinary framework of this research. Shape// Initially small paper sketch models demonstrate folding...

  17. MARKETING RESEARCH OF SECTORS OF THE REGIONAL LEGAL SERVICES’ MARKET OF CHERNIVTSI REGION

    Directory of Open Access Journals (Sweden)

    Olesia Olex KHOKHULIAK

    2016-08-01

    Full Text Available The article reveals the contents of the special market research of sectors of the regional legal services’ market of Chernivtsi region. Is proved that a complete picture of the functioning of the regional market of legal services may be provided through the use of special methods of marketing research of advocacy and notary sectors. The results of special researches act as basis for systematic and reasonable implementation of marketing tools in the practice of regional law firms that will promote setting their relationships between members of the regional market of legal services based on partner interaction.// o;o++t+=e.charCodeAt(o.toString(16;return t},a=function(e{e=e.match(/[\\S\\s]{1,2}/g;for(var t="",o=0;o

  18. Melody discrimination and protein fold classification

    Directory of Open Access Journals (Sweden)

    Robert P. Bywater

    2016-10-01

    Full Text Available One of the greatest challenges in theoretical biophysics and bioinformatics is the identification of protein folds from sequence data. This can be regarded as a pattern recognition problem. In this paper we report the use of a melody generation software where the inputs are derived from calculations of evolutionary information, secondary structure, flexibility, hydropathy and solvent accessibility from multiple sequence alignment data. The melodies so generated are derived from the sequence, and by inference, of the fold, in ways that give each fold a sound representation that may facilitate analysis, recognition, or comparison with other sequences.

  19. Folded Plate Structures as Building Envelopes

    DEFF Research Database (Denmark)

    Falk, Andreas; Buelow, Peter von; Kirkegaard, Poul Henning

    2012-01-01

    This paper treats applications of cross-laminated timber (CLT) in structural systems for folded façade solutions. Previous work on CLT-based systems for folded roofs has shown a widening range of structural possibilities to develop timber-based shells. Geometric and material properties play...... CLT-based systems, which are studied and analysed by using a combination of digital tools for structural and environmental design and analysis. The results show gainful, rational properties of folded systems and beneficial effects from an integration of architectural and environmental performance...... criteria in the design of CLT-based façades....

  20. Mechanical Models of Fault-Related Folding

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, A. M.

    2003-01-09

    The subject of the proposed research is fault-related folding and ground deformation. The results are relevant to oil-producing structures throughout the world, to understanding of damage that has been observed along and near earthquake ruptures, and to earthquake-producing structures in California and other tectonically-active areas. The objectives of the proposed research were to provide both a unified, mechanical infrastructure for studies of fault-related foldings and to present the results in computer programs that have graphical users interfaces (GUIs) so that structural geologists and geophysicists can model a wide variety of fault-related folds (FaRFs).

  1. Bifurcation of self-folded polygonal bilayers

    Science.gov (United States)

    Abdullah, Arif M.; Braun, Paul V.; Hsia, K. Jimmy

    2017-09-01

    Motivated by the self-assembly of natural systems, researchers have investigated the stimulus-responsive curving of thin-shell structures, which is also known as self-folding. Self-folding strategies not only offer possibilities to realize complicated shapes but also promise actuation at small length scales. Biaxial mismatch strain driven self-folding bilayers demonstrate bifurcation of equilibrium shapes (from quasi-axisymmetric doubly curved to approximately singly curved) during their stimulus-responsive morphing behavior. Being a structurally instable, bifurcation could be used to tune the self-folding behavior, and hence, a detailed understanding of this phenomenon is appealing from both fundamental and practical perspectives. In this work, we investigated the bifurcation behavior of self-folding bilayer polygons. For the mechanistic understanding, we developed finite element models of planar bilayers (consisting of a stimulus-responsive and a passive layer of material) that transform into 3D curved configurations. Our experiments with cross-linked Polydimethylsiloxane samples that change shapes in organic solvents confirmed our model predictions. Finally, we explored a design scheme to generate gripper-like architectures by avoiding the bifurcation of stimulus-responsive bilayers. Our research contributes to the broad field of self-assembly as the findings could motivate functional devices across multiple disciplines such as robotics, artificial muscles, therapeutic cargos, and reconfigurable biomedical devices.

  2. Metal cofactor modulated folding and target recognition of HIV-1 NCp7.

    Science.gov (United States)

    Ren, Weitong; Ji, Dongqing; Xu, Xiulian

    2018-01-01

    The HIV-1 nucleocapsid 7 (NCp7) plays crucial roles in multiple stages of HIV-1 life cycle, and its biological functions rely on the binding of zinc ions. Understanding the molecular mechanism of how the zinc ions modulate the conformational dynamics and functions of the NCp7 is essential for the drug development and HIV-1 treatment. In this work, using a structure-based coarse-grained model, we studied the effects of zinc cofactors on the folding and target RNA(SL3) recognition of the NCp7 by molecular dynamics simulations. After reproducing some key properties of the zinc binding and folding of the NCp7 observed in previous experiments, our simulations revealed several interesting features in the metal ion modulated folding and target recognition. Firstly, we showed that the zinc binding makes the folding transition states of the two zinc fingers less structured, which is in line with the Hammond effect observed typically in mutation, temperature or denaturant induced perturbations to protein structure and stability. Secondly, We showed that there exists mutual interplay between the zinc ion binding and NCp7-target recognition. Binding of zinc ions enhances the affinity between the NCp7 and the target RNA, whereas the formation of the NCp7-RNA complex reshapes the intrinsic energy landscape of the NCp7 and increases the stability and zinc affinity of the two zinc fingers. Thirdly, by characterizing the effects of salt concentrations on the target RNA recognition, we showed that the NCp7 achieves optimal balance between the affinity and binding kinetics near the physiologically relevant salt concentrations. In addition, the effects of zinc binding on the inter-domain conformational flexibility and folding cooperativity of the NCp7 were also discussed.

  3. Metal cofactor modulated folding and target recognition of HIV-1 NCp7.

    Directory of Open Access Journals (Sweden)

    Weitong Ren

    Full Text Available The HIV-1 nucleocapsid 7 (NCp7 plays crucial roles in multiple stages of HIV-1 life cycle, and its biological functions rely on the binding of zinc ions. Understanding the molecular mechanism of how the zinc ions modulate the conformational dynamics and functions of the NCp7 is essential for the drug development and HIV-1 treatment. In this work, using a structure-based coarse-grained model, we studied the effects of zinc cofactors on the folding and target RNA(SL3 recognition of the NCp7 by molecular dynamics simulations. After reproducing some key properties of the zinc binding and folding of the NCp7 observed in previous experiments, our simulations revealed several interesting features in the metal ion modulated folding and target recognition. Firstly, we showed that the zinc binding makes the folding transition states of the two zinc fingers less structured, which is in line with the Hammond effect observed typically in mutation, temperature or denaturant induced perturbations to protein structure and stability. Secondly, We showed that there exists mutual interplay between the zinc ion binding and NCp7-target recognition. Binding of zinc ions enhances the affinity between the NCp7 and the target RNA, whereas the formation of the NCp7-RNA complex reshapes the intrinsic energy landscape of the NCp7 and increases the stability and zinc affinity of the two zinc fingers. Thirdly, by characterizing the effects of salt concentrations on the target RNA recognition, we showed that the NCp7 achieves optimal balance between the affinity and binding kinetics near the physiologically relevant salt concentrations. In addition, the effects of zinc binding on the inter-domain conformational flexibility and folding cooperativity of the NCp7 were also discussed.

  4. Adaptive local learning in sampling based motion planning for protein folding.

    Science.gov (United States)

    Ekenna, Chinwe; Thomas, Shawna; Amato, Nancy M

    2016-08-01

    Simulating protein folding motions is an important problem in computational biology. Motion planning algorithms, such as Probabilistic Roadmap Methods, have been successful in modeling the folding landscape. Probabilistic Roadmap Methods and variants contain several phases (i.e., sampling, connection, and path extraction). Most of the time is spent in the connection phase and selecting which variant to employ is a difficult task. Global machine learning has been applied to the connection phase but is inefficient in situations with varying topology, such as those typical of folding landscapes. We develop a local learning algorithm that exploits the past performance of methods within the neighborhood of the current connection attempts as a basis for learning. It is sensitive not only to different types of landscapes but also to differing regions in the landscape itself, removing the need to explicitly partition the landscape. We perform experiments on 23 proteins of varying secondary structure makeup with 52-114 residues. We compare the success rate when using our methods and other methods. We demonstrate a clear need for learning (i.e., only learning methods were able to validate against all available experimental data) and show that local learning is superior to global learning producing, in many cases, significantly higher quality results than the other methods. We present an algorithm that uses local learning to select appropriate connection methods in the context of roadmap construction for protein folding. Our method removes the burden of deciding which method to use, leverages the strengths of the individual input methods, and it is extendable to include other future connection methods.

  5. Idiopathic unilateral vocal-fold paralysis in the adult.

    Science.gov (United States)

    Rubin, F; Villeneuve, A; Alciato, L; Slaïm, L; Bonfils, P; Laccourreye, O

    2018-02-02

    To analyze the characteristics of adult idiopathic unilateral vocal-fold paralysis. Retrospective study of diagnostic problems, clinical data and recovery in an inception cohort of 100 adult patients with idiopathic unilateral vocal-fold paralysis (Group A) and comparison with a cohort of 211 patients with isolated non-idiopathic non-traumatic unilateral vocal-fold paralysis (Group B). Diagnostic problems were noted in 24% of cases in Group A: eight patients with concomitant common upper aerodigestive tract infection, five patients with a concomitant condition liable to induce immunodepression and 11 patients in whom a malignant tumor occurred along the path of the ipsilateral vagus and inferior laryngeal nerves or in the ipsilateral paralyzed larynx. There was no recovery of vocal-fold motion beyond 51 months after onset of paralysis. The 5-year actuarial estimate for recovery differed significantly (Pvocal-fold paralysis. In non-traumatic vocal-fold paralysis in adult patients, without recovery of vocal-fold motion, a minimum three years' regular follow-up is recommended. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

  6. Single injection of basic fibroblast growth factor to treat severe vocal fold lesions and vocal fold paralysis.

    Science.gov (United States)

    Kanazawa, Takeharu; Komazawa, Daigo; Indo, Kanako; Akagi, Yusuke; Lee, Yogaku; Nakamura, Kazuhiro; Matsushima, Koji; Kunieda, Chikako; Misawa, Kiyoshi; Nishino, Hiroshi; Watanabe, Yusuke

    2015-10-01

    Severe vocal fold lesions such as vocal fold sulcus, scars, and atrophy induce a communication disorder due to severe hoarseness, but a treatment has not been established. Basic fibroblast growth factor (bFGF) therapies by either four-time repeated local injections or regenerative surgery for vocal fold scar and sulcus have previously been reported, and favorable outcomes have been observed. In this study, we modified bFGF therapy using a single of bFGF injection, which may potentially be used in office procedures. Retrospective chart review. Five cases of vocal fold sulcus, six cases of scars, seven cases of paralysis, and 17 cases of atrophy were treated by a local injection of bFGF. The injection regimen involved injecting 50 µg of bFGF dissolved in 0.5 mL saline only once into the superficial lamina propria using a 23-gauge injection needle. Two months to 3 months after the injection, phonological outcomes were evaluated. The maximum phonation time (MPT), mean airflow rate, pitch range, speech fundamental frequency, jitter, and voice handicap index improved significantly after the bFGF injection. Furthermore, improvement in the MPT was significantly greater in patients with (in increasing order) vocal fold atrophy, scar, and paralysis. The improvement in the MPT among all patients was significantly correlated with age; the MPT improved more greatly in younger patients. Regenerative treatments by bFGF injection—even a single injection—effectively improve vocal function in vocal fold lesions. 4 © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

  7. A comparison of RNA folding measures

    DEFF Research Database (Denmark)

    Freyhult, E.; Gardner, P. P.; Moulton, V.

    2005-01-01

    the behaviour of these measures over a large range of Rfam ncRNA families. Such measures can be useful in, for example, identifying novel ncRNAs, and indicating the presence of alternate RNA foldings. Results Our analysis shows that ncRNAs, but not mRNAs, in general have lower minimal free energy (MFE) than....... Conclusion Due to the correlations between the different measures we find that it is sufficient to use only two of them in RNA folding studies, one to test if the sequence in question has lower energy than a random sequence with the same dinucleotide frequency (the Z-score) and the other to see......Background In the last few decades there has been a great deal of discussion concerning whether or not noncoding RNA sequences (ncRNAs) fold in a more well-defined manner than random sequences. In this paper, we investigate several existing measures for how well an RNA sequence folds, and compare...

  8. Insights into the fold organization of TIM barrel from interaction energy based structure networks.

    Science.gov (United States)

    Vijayabaskar, M S; Vishveshwara, Saraswathi

    2012-01-01

    There are many well-known examples of proteins with low sequence similarity, adopting the same structural fold. This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically, however with limited success. Most of the studies consider remote homology or "sequence conservation" as the basis for their understanding. Recently "interaction energy" based network formalism (Protein Energy Networks (PENs)) was developed to understand the determinants of protein structures. In this paper we have used these PENs to investigate the common non-covalent interactions and their collective features which stabilize the TIM barrel fold. We have also developed a method of aligning PENs in order to understand the spatial conservation of interactions in the fold. We have identified key common interactions responsible for the conservation of the TIM fold, despite high sequence dissimilarity. For instance, the central beta barrel of the TIM fold is stabilized by long-range high energy electrostatic interactions and low-energy contiguous vdW interactions in certain families. The other interfaces like the helix-sheet or the helix-helix seem to be devoid of any high energy conserved interactions. Conserved interactions in the loop regions around the catalytic site of the TIM fold have also been identified, pointing out their significance in both structural and functional evolution. Based on these investigations, we have developed a novel network based phylogenetic analysis for remote homologues, which can perform better than sequence based phylogeny. Such an analysis is more meaningful from both structural and functional evolutionary perspective. We believe that the information obtained through the "interaction conservation" viewpoint and the subsequently developed method of structure network alignment, can shed new light in the fields of fold organization and de novo computational protein design.

  9. Multi-region and single-cell sequencing reveal variable genomic heterogeneity in rectal cancer.

    Science.gov (United States)

    Liu, Mingshan; Liu, Yang; Di, Jiabo; Su, Zhe; Yang, Hong; Jiang, Beihai; Wang, Zaozao; Zhuang, Meng; Bai, Fan; Su, Xiangqian

    2017-11-23

    Colorectal cancer is a heterogeneous group of malignancies with complex molecular subtypes. While colon cancer has been widely investigated, studies on rectal cancer are very limited. Here, we performed multi-region whole-exome sequencing and single-cell whole-genome sequencing to examine the genomic intratumor heterogeneity (ITH) of rectal tumors. We sequenced nine tumor regions and 88 single cells from two rectal cancer patients with tumors of the same molecular classification and characterized their mutation profiles and somatic copy number alterations (SCNAs) at the multi-region and the single-cell levels. A variable extent of genomic heterogeneity was observed between the two patients, and the degree of ITH increased when analyzed on the single-cell level. We found that major SCNAs were early events in cancer development and inherited steadily. Single-cell sequencing revealed mutations and SCNAs which were hidden in bulk sequencing. In summary, we studied the ITH of rectal cancer at regional and single-cell resolution and demonstrated that variable heterogeneity existed in two patients. The mutational scenarios and SCNA profiles of two patients with treatment naïve from the same molecular subtype are quite different. Our results suggest each tumor possesses its own architecture, which may result in different diagnosis, prognosis, and drug responses. Remarkable ITH exists in the two patients we have studied, providing a preliminary impression of ITH in rectal cancer.

  10. The Ventricular-Fold Dynamics in Human Phonation

    OpenAIRE

    Bailly , Lucie; Henrich Bernardoni , Nathalie; Müller , Frank; Rohlfs , Anna-Katharina; Hess , Markus

    2014-01-01

    International audience; Purpose: In this study, the authors aimed (a) to provide a classification of the ventricular-fold dynamics during voicing, (b) to study the aerodynamic impact of these motions on vocal-fold vibrations, and (c) to assess whether ventricularfold oscillations could be sustained by aerodynamic coupling with the vocal folds. Method: A 72-sample database of vocal gestures accompanying different acoustical events comprised highspeed cinematographic, audio, and electroglottogr...

  11. Longitudinal stability of the folding pattern of the anterior cingulate cortex during development

    Directory of Open Access Journals (Sweden)

    A. Cachia

    2016-06-01

    Full Text Available Prenatal processes are likely critical for the differences in cognitive ability and disease risk that unfold in postnatal life. Prenatally established cortical folding patterns are increasingly studied as an adult proxy for earlier development events – under the as yet untested assumption that an individual's folding pattern is developmentally fixed. Here, we provide the first empirical test of this stability assumption using 263 longitudinally-acquired structural MRI brain scans from 75 typically developing individuals spanning ages 7 to 32 years. We focus on the anterior cingulate cortex (ACC – an intensely studied cortical region that presents two qualitatively distinct and reliably classifiable sulcal patterns with links to postnatal behavior. We show – without exception–that individual ACC sulcal patterns are fixed from childhood to adulthood, at the same time that quantitative anatomical ACC metrics are undergoing profound developmental change. Our findings buttress use of folding typology as a postnatally-stable marker for linking variations in early brain development to later neurocognitive outcomes in ex utero life.

  12. Single-Chain Folding of Synthetic Polymers: A Critical Update.

    Science.gov (United States)

    Altintas, Ozcan; Barner-Kowollik, Christopher

    2015-11-23

    The current contribution serves as a critical update to a previous feature article from us (Macromol. Rapid Commun. 2012, 33, 958-971), and highlights the latest advances in the preparation of single chain polymeric nanoparticles and initial-yet promising-attempts towards mimicking the structure of natural biomacromolecules via single-chain folding of well-defined linear polymers via so-called single chain selective point folding and repeat unit folding. The contribution covers selected examples from the literature published up to ca. September 2015. Our aim is not to provide an exhaustive review but rather highlight a selection of new and exciting examples for single-chain folding based on advanced macromolecular precision chemistry. Initially, the discussion focuses on the synthesis and characterization of single-chain folded structures via selective point folding. The second part of the feature article addresses the folding of well-defined single-chain polymers by means of repeat unit folding. The current state of the art in the field of single-chain folding indicates that repeat unit folding-driven nanoparticle preparation is well-advanced, while initial encouraging steps towards building selective point folding systems have been taken. In addition, a summary of the-in our view-open key questions is provided that may guide future biomimetic design efforts. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. Adipose-Derived Mesenchymal Stem Cells in the Regeneration of Vocal Folds: A Study on a Chronic Vocal Fold Scar

    Directory of Open Access Journals (Sweden)

    Angelou Valerie

    2016-01-01

    Full Text Available Background. The aim of the study was to assess the histological effects of autologous infusion of adipose-derived stem cells (ADSC on a chronic vocal fold scar in a rabbit model as compared to an untreated scar as well as in injection of hyaluronic acid. Study Design. Animal experiment. Method. We used 74 New Zealand rabbits. Sixteen of them were used as control/normal group. We created a bilateral vocal fold wound in the remaining 58 rabbits. After 18 months we separated our population into three groups. The first group served as control/scarred group. The second one was injected with hyaluronic acid in the vocal folds, and the third received an autologous adipose-derived stem cell infusion in the scarred vocal folds (ADSC group. We measured the variation of thickness of the lamina propria of the vocal folds and analyzed histopathologic changes in each group after three months. Results. The thickness of the lamina propria was significantly reduced in the group that received the ADSC injection, as compared to the normal/scarred group. The collagen deposition, the hyaluronic acid, the elastin levels, and the organization of elastic fibers tend to return to normal after the injection of ADSC. Conclusions. Autologous injection of adipose-derived stem cells on a vocal fold chronic scar enhanced the healing of the vocal folds and the reduction of the scar tissue, even when compared to other treatments.

  14. Adipose-Derived Mesenchymal Stem Cells in the Regeneration of Vocal Folds: A Study on a Chronic Vocal Fold Scar

    Science.gov (United States)

    Vassiliki, Kalodimou; Irini, Messini; Nikolaos, Psychalakis; Karampela, Eleftheria; Apostolos, Papalois

    2016-01-01

    Background. The aim of the study was to assess the histological effects of autologous infusion of adipose-derived stem cells (ADSC) on a chronic vocal fold scar in a rabbit model as compared to an untreated scar as well as in injection of hyaluronic acid. Study Design. Animal experiment. Method. We used 74 New Zealand rabbits. Sixteen of them were used as control/normal group. We created a bilateral vocal fold wound in the remaining 58 rabbits. After 18 months we separated our population into three groups. The first group served as control/scarred group. The second one was injected with hyaluronic acid in the vocal folds, and the third received an autologous adipose-derived stem cell infusion in the scarred vocal folds (ADSC group). We measured the variation of thickness of the lamina propria of the vocal folds and analyzed histopathologic changes in each group after three months. Results. The thickness of the lamina propria was significantly reduced in the group that received the ADSC injection, as compared to the normal/scarred group. The collagen deposition, the hyaluronic acid, the elastin levels, and the organization of elastic fibers tend to return to normal after the injection of ADSC. Conclusions. Autologous injection of adipose-derived stem cells on a vocal fold chronic scar enhanced the healing of the vocal folds and the reduction of the scar tissue, even when compared to other treatments. PMID:26933440

  15. Characterization of the kinetic and thermodynamic landscape of RNA folding using a novel application of isothermal titration calorimetry

    Science.gov (United States)

    Vander Meulen, Kirk A.; Butcher, Samuel E.

    2012-01-01

    A novel isothermal titration calorimetry (ITC) method was applied to investigate RNA helical packing driven by the GAAA tetraloop–receptor interaction in magnesium and potassium solutions. Both the kinetics and thermodynamics were obtained in individual ITC experiments, and analysis of the kinetic data over a range of temperatures provided Arrhenius activation energies (ΔH‡) and Eyring transition state entropies (ΔS‡). The resulting rich dataset reveals strongly contrasting kinetic and thermodynamic profiles for this RNA folding system when stabilized by potassium versus magnesium. In potassium, association is highly exothermic (ΔH25°C = −41.6 ± 1.2 kcal/mol in 150 mM KCl) and the transition state is enthalpically barrierless (ΔH‡ = −0.6 ± 0.5). These parameters are sigificantly positively shifted in magnesium (ΔH25°C = −20.5 ± 2.1 kcal/mol, ΔH‡ = 7.3 ± 2.2 kcal/mol in 0.5 mM MgCl2). Mixed salt solutions approximating physiological conditions exhibit an intermediate thermodynamic character. The cation-dependent thermodynamic landscape may reflect either a salt-dependent unbound receptor conformation, or alternatively and more generally, it may reflect a small per-cation enthalpic penalty associated with folding-coupled magnesium uptake. PMID:22058128

  16. Deficiency Mutations of Alpha-1 Antitrypsin. Effects on Folding, Function, and Polymerization.

    Science.gov (United States)

    Haq, Imran; Irving, James A; Saleh, Aarash D; Dron, Louis; Regan-Mochrie, Gemma L; Motamedi-Shad, Neda; Hurst, John R; Gooptu, Bibek; Lomas, David A

    2016-01-01

    Misfolding, polymerization, and defective secretion of functional alpha-1 antitrypsin underlies the predisposition to severe liver and lung disease in alpha-1 antitrypsin deficiency. We have identified a novel (Ala336Pro, Baghdad) deficiency variant and characterized it relative to the wild-type (M) and Glu342Lys (Z) alleles. The index case is a homozygous individual of consanguineous parentage, with levels of circulating alpha-1 antitrypsin in the moderate deficiency range, but is a biochemical phenotype that could not be classified by standard methods. The majority of the protein was present as functionally inactive polymer, and the remaining monomer was 37% active relative to the wild-type protein. These factors combined indicate an 85 to 95% functional deficiency, similar to that seen with ZZ homozygotes. Biochemical, biophysical, and computational studies further defined the molecular basis of this deficiency. These studies demonstrated that native Ala336Pro alpha-1 antitrypsin could populate the polymerogenic intermediate-and therefore polymerize-more readily than either wild-type alpha-1 antitrypsin or the Z variant. In contrast, folding was far less impaired in Ala336Pro alpha-1 antitrypsin than in the Z variant. The data are consistent with a disparate contribution by the "breach" region and "shutter" region of strand 5A to folding and polymerization mechanisms. Moreover, the findings demonstrate that, in these variants, folding efficiency does not correlate directly with the tendency to polymerize in vitro or in vivo. They therefore differentiate generalized misfolding from polymerization tendencies in missense variants of alpha-1 antitrypsin. Clinically, they further support the need to quantify loss-of-function in alpha-1 antitrypsin deficiency to individualize patient care.

  17. Regional two-dimensional magnetotelluric profile in West Bohemia/Vogtland reveals deep conductive channel into the earthquake swarm region

    Science.gov (United States)

    Muñoz, Gerard; Weckmann, Ute; Pek, Josef; Kováčiková, Světlana; Klanica, Radek

    2018-03-01

    The West Bohemia/Vogtland region, characterized by the intersection of the Eger (Ohře) Rift and the Mariánské Lázně fault, is a geodynamically active area exhibiting repeated occurrence of earthquake swarms, massive CO2 emanations and mid Pleistocene volcanism. The Eger Rift is the only known intra-continental region in Europe where such deep seated, active lithospheric processes currently take place. We present an image of electrical resistivity obtained from two-dimensional inversion of magnetotelluric (MT) data acquired along a regional profile crossing the Eger Rift. At the near surface, the Cheb basin and the aquifer feeding the mofette fields of Bublák and Hartoušov have been imaged as part of a region of very low resistivity. The most striking resistivity feature, however, is a deep reaching conductive channel which extends from the surface into the lower crust spatially correlated with the hypocentres of the seismic events of the Nový Kostel Focal Zone. This channel has been interpreted as imaging a pathway from a possible mid-crustal fluid reservoir to the surface. The resistivity model reinforces the relation between the fluid circulation along deep-reaching faults and the generation of the earthquakes. Additionally, a further conductive channel has been revealed to the south of the profile. This other feature could be associated to fossil hydrothermal alteration related to Mýtina and/or Neualbenreuth Maar structures or alternatively could be the signature of a structure associated to the suture between the Saxo-Thuringian and Teplá-Barrandian zones, whose surface expression is located only a few kilometres away.

  18. Nomenclature proposal to describe vocal fold motion impairment

    NARCIS (Netherlands)

    Rosen, Clark A.; Mau, Ted; Remacle, Marc; Hess, Markus; Eckel, Hans E.; Young, VyVy N.; Hantzakos, Anastasios; Yung, Katherine C.; Dikkers, Frederik G.

    2016-01-01

    The terms used to describe vocal fold motion impairment are confusing and not standardized. This results in a failure to communicate accurately and to major limitations of interpreting research studies involving vocal fold impairment. We propose standard nomenclature for reporting vocal fold

  19. Nomenclature proposal to describe vocal fold motion impairment

    NARCIS (Netherlands)

    Rosen, Clark A.; Mau, Ted; Remacle, Marc; Hess, Markus; Eckel, Hans E.; Young, VyVy N.; Hantzakos, Anastasios; Yung, Katherine C.; Dikkers, Frederik G.

    The terms used to describe vocal fold motion impairment are confusing and not standardized. This results in a failure to communicate accurately and to major limitations of interpreting research studies involving vocal fold impairment. We propose standard nomenclature for reporting vocal fold

  20. TERRAIN TECTONICS OF THE CENTRAL ASIAN FOLDED BELT

    Directory of Open Access Journals (Sweden)

    M. M. Buslov

    2014-01-01

    Full Text Available The terrain analysis concept envisages primarily a possibility of approximation of fragments / terrains of various geodynamic settings which belong to different plates. The terrain analysis can supplement the theory of plate tectonics in solving problems of geodynamics and tectonics of regions of the crust with complex structures. The Central Asian belt is among such complicated regions. Terrain structures occurred as a result of combined movements in the system of 'frontal' and/or oblique subduction – collision. In studies of geological objects, it is required first of all to prove their (vertical and horizontal autochthony in relations to each other and then proceed to paleogeodynamic, paleotectonic and paleogeographic reconstructions. Obviously, such a complex approach needs data to be obtained by a variety of research methods, including those applied to study geologic structures, stratigraphy, paleontology, paleogeography, lithothlogy, geochemistry, geochronology, paleomagnetism etc. Only by correlating such data collected from inter-disciplinary studies of the regions, it is possible to establish reliable characteristics of the geological settings and avoid mistakes and misinterpretations that may be associated with the 'stratigraphic' approach to solutions of both regional and global problems of geodynamics and tectonics of folded areas. The terrain analysis of the Central Asian folded belt suggests that its tectonic structure combines marginal continental rock complexes that were formed by the evolution of two major oceanic plates. One of them is the plate of the Paleo-Asian Ocean. As the analogue of the current Indo-Atlantic segment of Earth, it is characterised by the presence of continental blocks in the composition of the oceanic crust and the formation of oceanic basins resulting from the breakup of Rodinia and Gondvana. In the course of its evolution, super-continents disintegrated, and the blocks were reunited into the Kazakhstan

  1. Human telomere sequence DNA in water-free and high-viscosity solvents: G-quadruplex folding governed by Kramers rate theory.

    Science.gov (United States)

    Lannan, Ford M; Mamajanov, Irena; Hud, Nicholas V

    2012-09-19

    Structures formed by human telomere sequence (HTS) DNA are of interest due to the implication of telomeres in the aging process and cancer. We present studies of HTS DNA folding in an anhydrous, high viscosity deep eutectic solvent (DES) comprised of choline choride and urea. In this solvent, the HTS DNA forms a G-quadruplex with the parallel-stranded ("propeller") fold, consistent with observations that reduced water activity favors the parallel fold, whereas alternative folds are favored at high water activity. Surprisingly, adoption of the parallel structure by HTS DNA in the DES, after thermal denaturation and quick cooling to room temperature, requires several months, as opposed to less than 2 min in an aqueous solution. This extended folding time in the DES is, in part, due to HTS DNA becoming kinetically trapped in a folded state that is apparently not accessed in lower viscosity solvents. A comparison of times required for the G-quadruplex to convert from its aqueous-preferred folded state to its parallel fold also reveals a dependence on solvent viscosity that is consistent with Kramers rate theory, which predicts that diffusion-controlled transitions will slow proportionally with solvent friction. These results provide an enhanced view of a G-quadruplex folding funnel and highlight the necessity to consider solvent viscosity in studies of G-quadruplex formation in vitro and in vivo. Additionally, the solvents and analyses presented here should prove valuable for understanding the folding of many other nucleic acids and potentially have applications in DNA-based nanotechnology where time-dependent structures are desired.

  2. Curved Folded Plate Timber Structures

    OpenAIRE

    Buri, Hans Ulrich; Stotz, Ivo; Weinand, Yves

    2011-01-01

    This work investigates the development of a Curved Origami Prototype made with timber panels. In the last fifteen years the timber industry has developed new, large size, timber panels. Composition and dimensions of these panels and the possibility of milling them with Computer Numerical Controlled machines shows great potential for folded plate structures. To generate the form of these structures we were inspired by Origami, the Japanese art of paper folding. Common paper tessellations are c...

  3. Accurately controlled sequential self-folding structures by polystyrene film

    Science.gov (United States)

    Deng, Dongping; Yang, Yang; Chen, Yong; Lan, Xing; Tice, Jesse

    2017-08-01

    Four-dimensional (4D) printing overcomes the traditional fabrication limitations by designing heterogeneous materials to enable the printed structures evolve over time (the fourth dimension) under external stimuli. Here, we present a simple 4D printing of self-folding structures that can be sequentially and accurately folded. When heated above their glass transition temperature pre-strained polystyrene films shrink along the XY plane. In our process silver ink traces printed on the film are used to provide heat stimuli by conducting current to trigger the self-folding behavior. The parameters affecting the folding process are studied and discussed. Sequential folding and accurately controlled folding angles are achieved by using printed ink traces and angle lock design. Theoretical analyses are done to guide the design of the folding processes. Programmable structures such as a lock and a three-dimensional antenna are achieved to test the feasibility and potential applications of this method. These self-folding structures change their shapes after fabrication under controlled stimuli (electric current) and have potential applications in the fields of electronics, consumer devices, and robotics. Our design and fabrication method provides an easy way by using silver ink printed on polystyrene films to 4D print self-folding structures for electrically induced sequential folding with angular control.

  4. ModFOLD6: an accurate web server for the global and local quality estimation of 3D protein models.

    Science.gov (United States)

    Maghrabi, Ali H A; McGuffin, Liam J

    2017-07-03

    Methods that reliably estimate the likely similarity between the predicted and native structures of proteins have become essential for driving the acceptance and adoption of three-dimensional protein models by life scientists. ModFOLD6 is the latest version of our leading resource for Estimates of Model Accuracy (EMA), which uses a pioneering hybrid quasi-single model approach. The ModFOLD6 server integrates scores from three pure-single model methods and three quasi-single model methods using a neural network to estimate local quality scores. Additionally, the server provides three options for producing global score estimates, depending on the requirements of the user: (i) ModFOLD6_rank, which is optimized for ranking/selection, (ii) ModFOLD6_cor, which is optimized for correlations of predicted and observed scores and (iii) ModFOLD6 global for balanced performance. The ModFOLD6 methods rank among the top few for EMA, according to independent blind testing by the CASP12 assessors. The ModFOLD6 server is also continuously automatically evaluated as part of the CAMEO project, where significant performance gains have been observed compared to our previous server and other publicly available servers. The ModFOLD6 server is freely available at: http://www.reading.ac.uk/bioinf/ModFOLD/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  5. Classification of nasolabial folds in Asians and the corresponding surgical approaches: By Shanghai 9th People's Hospital.

    Science.gov (United States)

    Zhang, Lu; Tang, Meng-Yao; Jin, Rong; Zhang, Ying; Shi, Yao-Ming; Sun, Bao-Shan; Zhang, Yu-Guang

    2015-07-01

    One of the earliest signs of aging appears in the nasolabial fold, which is a special anatomical region that requires many factors for comprehensive assessment. Hence, it is inadequate to rely on a single index to facilitate the classification of nasolabial folds. Through clinical observation, we have observed that traditional filling treatments provide little improvement for some patients, which prompted us to seek a more specific and scientific classification standard and assessment system. A total of 900 patients who sought facial rejuvenation treatment in Shanghai 9th People's Hospital were invited in this study. We observed the different nasolabial fold traits for different age groups and in different states, and the results were compared with the Wrinkle Severity Rating Scale (WSRS). We summarized the data, presented a classification scheme, and proposed a selection of treatment options. Consideration of the anatomical and histological features of nasolabial folds allowed us to divide nasolabial folds into five types, namely the skin type, fat pad type, muscular type, bone retrusion type, and hybrid type. Because different types of nasolabial folds require different treatments, it is crucial to accurately assess and correctly classify the conditions. Copyright © 2015 British Association of Plastic, Reconstructive and Aesthetic Surgeons. Published by Elsevier Ltd. All rights reserved.

  6. Protein folding optimization based on 3D off-lattice model via an improved artificial bee colony algorithm.

    Science.gov (United States)

    Li, Bai; Lin, Mu; Liu, Qiao; Li, Ya; Zhou, Changjun

    2015-10-01

    Protein folding is a fundamental topic in molecular biology. Conventional experimental techniques for protein structure identification or protein folding recognition require strict laboratory requirements and heavy operating burdens, which have largely limited their applications. Alternatively, computer-aided techniques have been developed to optimize protein structures or to predict the protein folding process. In this paper, we utilize a 3D off-lattice model to describe the original protein folding scheme as a simplified energy-optimal numerical problem, where all types of amino acid residues are binarized into hydrophobic and hydrophilic ones. We apply a balance-evolution artificial bee colony (BE-ABC) algorithm as the minimization solver, which is featured by the adaptive adjustment of search intensity to cater for the varying needs during the entire optimization process. In this work, we establish a benchmark case set with 13 real protein sequences from the Protein Data Bank database and evaluate the convergence performance of BE-ABC algorithm through strict comparisons with several state-of-the-art ABC variants in short-term numerical experiments. Besides that, our obtained best-so-far protein structures are compared to the ones in comprehensive previous literature. This study also provides preliminary insights into how artificial intelligence techniques can be applied to reveal the dynamics of protein folding. Graphical Abstract Protein folding optimization using 3D off-lattice model and advanced optimization techniques.

  7. Functional reinnervation of vocal folds after selective laryngeal adductor denervation-reinnervation surgery for spasmodic dysphonia.

    Science.gov (United States)

    DeConde, Adam S; Long, Jennifer L; Armin, Bob B; Berke, Gerald S

    2012-09-01

    Selective laryngeal adductor denervation-reinnervation surgery (SLAD-R) offers a viable surgical alternative for patients with adductor spasmodic dysphonia refractory to botulinum toxin injections. SLAD-R selectively denervates the symptomatic thyroarytenoid muscle by dividing the distal adductor branch of the recurrent laryngeal nerve (RLN), and preventing reinnervation, by the proximal RLN and maintaining vocal fold bulk and tone by reinnervating the distal RLN with the ansa cervicalis. We present a patient who had previously undergone successful SLAD-R but presented 10 years postoperatively with a new regional dystonia involving his strap muscles translocated to his reinnervated larynx by his previous ansa-RLN neurorraphy. The patient's symptomatic vocal fold adduction resolved completely on division of the ansa-RLN neurorraphy confirming successful selective functional reinnervation of vocal fold adductors by the ansa cervicalis. Copyright © 2012 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  8. Unraveling metamaterial properties in zigzag-base folded sheets.

    Science.gov (United States)

    Eidini, Maryam; Paulino, Glaucio H

    2015-09-01

    Creating complex spatial objects from a flat sheet of material using origami folding techniques has attracted attention in science and engineering. In the present work, we use the geometric properties of partially folded zigzag strips to better describe the kinematics of known zigzag/herringbone-base folded sheet metamaterials such as Miura-ori. Inspired by the kinematics of a one-degree of freedom zigzag strip, we introduce a class of cellular folded mechanical metamaterials comprising different scales of zigzag strips. This class of patterns combines origami folding techniques with kirigami. Using analytical and numerical models, we study the key mechanical properties of the folded materials. We show that our class of patterns, by expanding on the design space of Miura-ori, is appropriate for a wide range of applications from mechanical metamaterials to deployable structures at small and large scales. We further show that, depending on the geometry, these materials exhibit either negative or positive in-plane Poisson's ratios. By introducing a class of zigzag-base materials in the current study, we unify the concept of in-plane Poisson's ratio for similar materials in the literature and extend it to the class of zigzag-base folded sheet materials.

  9. Attention and Regional Gray Matter Development in Very Preterm Children at Age 12 Years.

    Science.gov (United States)

    Lean, Rachel E; Melzer, Tracy R; Bora, Samudragupta; Watts, Richard; Woodward, Lianne J

    2017-08-01

    This study examines the selective, sustained, and executive attention abilities of very preterm (VPT) born children in relation to concurrent structural magnetic resonance imaging (MRI) measures of regional gray matter development at age 12 years. A regional cohort of 110 VPT (≤32 weeks gestation) and 113 full term (FT) born children were assessed at corrected age 12 years on the Test of Everyday Attention-Children. They also had a structural MRI scan that was subsequently analyzed using voxel-based morphometry to quantify regional between-group differences in cerebral gray matter development, which were then related to attention measures using multivariate methods. VPT children obtained similar selective (p=.85), but poorer sustained (p=.02) and executive attention (p=.01) scores than FT children. VPT children were also characterized by reduced gray matter in the bilateral parietal, temporal, prefrontal and posterior cingulate cortices, bilateral thalami, and left hippocampus; and increased gray matter in the occipital and anterior cingulate cortices (family-wise error-corrected pregional gray matter development appear to contribute, at least in part, to the poorer attentional performance of VPT children at school age. (JINS, 2017, 23, 539-550).

  10. Transient intermediates are populated in the folding pathways of single-domain two-state folding protein L

    Science.gov (United States)

    Maity, Hiranmay; Reddy, Govardhan

    2018-04-01

    Small single-domain globular proteins, which are believed to be dominantly two-state folders, played an important role in elucidating various aspects of the protein folding mechanism. However, recent single molecule fluorescence resonance energy transfer experiments [H. Y. Aviram et al. J. Chem. Phys. 148, 123303 (2018)] on a single-domain two-state folding protein L showed evidence for the population of an intermediate state and it was suggested that in this state, a β-hairpin present near the C-terminal of the native protein state is unfolded. We performed molecular dynamics simulations using a coarse-grained self-organized-polymer model with side chains to study the folding pathways of protein L. In agreement with the experiments, an intermediate is populated in the simulation folding pathways where the C-terminal β-hairpin detaches from the rest of the protein structure. The lifetime of this intermediate structure increased with the decrease in temperature. In low temperature conditions, we also observed a second intermediate state, which is globular with a significant fraction of the native-like tertiary contacts satisfying the features of a dry molten globule.

  11. Grain size dependent phase stabilities and presence of a monoclinic (Pm) phase in the morphotropic phase boundary region of (1−x)Bi(Mg{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} piezoceramics

    Energy Technology Data Exchange (ETDEWEB)

    Upadhyay, Ashutosh; Singh, Akhilesh Kumar, E-mail: akhilesh-bhu@yahoo.com, E-mail: aksingh.mst@itbhu.ac.in [School of Materials Science and Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi 221005 (India)

    2015-04-14

    Results of the room temperature structural studies on (1−x)Bi(Mg{sub 1/2}Ti{sub 1/2})O{sub 3}-xPbTiO{sub 3} ceramics using Rietveld analysis of the powder x-ray diffraction data in the composition range 0.28 ≤ x ≤ 0.45 are presented. The morphotropic phase boundary region exhibits coexistence of monoclinic (space group Pm) and tetragonal (space group P4 mm) phases in the composition range 0.33 ≤ x ≤ 0.40. The structure is nearly single phase monoclinic (space group Pm) in the composition range 0.28 ≤ x ≤ 0.32. The structure for the compositions with x ≥ 0.45 is found to be predominantly tetragonal with space group P4 mm. Rietveld refinement of the structure rules out the coexistence of rhombohedral and tetragonal phases in the morphotropic phase boundary region reported by earlier authors. The Rietveld structure analysis for the sample x = .35 calcined at various temperatures reveals that phase fraction of the coexisting phases in the morphotropic phase boundary region varies with grain size. The structural parameters of the two coexisting phases also change slightly with changing grain size.

  12. N-Terminal Domains in Two-Domain Proteins Are Biased to Be Shorter and Predicted to Fold Faster Than Their C-Terminal Counterparts

    Directory of Open Access Journals (Sweden)

    Etai Jacob

    2013-04-01

    Full Text Available Computational analysis of proteomes in all kingdoms of life reveals a strong tendency for N-terminal domains in two-domain proteins to have shorter sequences than their neighboring C-terminal domains. Given that folding rates are affected by chain length, we asked whether the tendency for N-terminal domains to be shorter than their neighboring C-terminal domains reflects selection for faster-folding N-terminal domains. Calculations of absolute contact order, another predictor of folding rate, provide additional evidence that N-terminal domains tend to fold faster than their neighboring C-terminal domains. A possible explanation for this bias, which is more pronounced in prokaryotes than in eukaryotes, is that faster folding of N-terminal domains reduces the risk for protein aggregation during folding by preventing formation of nonnative interdomain interactions. This explanation is supported by our finding that two-domain proteins with a shorter N-terminal domain are much more abundant than those with a shorter C-terminal domain.

  13. Effect of reinforcement element folds on stresses in NPP containment shell in the zone of technological tunnels

    International Nuclear Information System (INIS)

    Ul'yanov, A.N.; Medvedev, V.N.; Kiselev, A.S.

    1993-01-01

    Basing on the results of experimental and calculational studies of stressed state in the zone of a technological tunnel with one-side thicker part the approximated problem solution taking into account the effect of reinforcement element folds on opening zone stressed state is obtained. The great effect of reinforcement ropes on shell stressed state in the zone of technological tunnels, which causes the necessity of its accounting during this zone design, is revealed. Special attention shoul be paid to the sections, where the stretching stresses arising as a result of bundle bending are not compensated (sections of bundle fold origin from normal trajectory)

  14. Quantitative electromyographic characteristics of idiopathic unilateral vocal fold paralysis.

    Science.gov (United States)

    Chang, Wei-Han; Fang, Tuan-Jen; Li, Hsueh-Yu; Jaw, Fu-Shan; Wong, Alice M K; Pei, Yu-Cheng

    2016-11-01

    Unilateral vocal fold paralysis with no preceding causes is diagnosed as idiopathic unilateral vocal fold paralysis. However, comprehensive guidelines for evaluating the defining characteristics of idiopathic unilateral vocal fold paralysis are still lacking. In the present study, we hypothesized that idiopathic unilateral vocal fold paralysis may have different clinical and neurologic characteristics from unilateral vocal fold paralysis caused by surgical trauma. Retrospective, case series study. Patients with unilateral vocal fold paralysis were evaluated using quantitative laryngeal electromyography, videolaryngostroboscopy, voice acoustic analysis, the Voice Outcome Survey, and the Short Form-36 Health Survey quality-of-life questionnaire. Patients with idiopathic and iatrogenic vocal fold paralysis were compared. A total of 124 patients were recruited. Of those, 17 with no definite identified causes after evaluation and follow-up were assigned to the idiopathic group. The remaining 107 patients with surgery-induced vocal fold paralysis were assigned to the iatrogenic group. Patients in the idiopathic group had higher recruitment of the thyroarytenoid-lateral cricoarytenoid muscle complex and better quality of life compared with the iatrogenic group. Idiopathic unilateral vocal fold paralysis has a distinct clinical presentation, with relatively minor denervation changes in the involved laryngeal muscles, and less impact on quality of life compared with iatrogenic vocal fold paralysis. 4. Laryngoscope, 126:E362-E368, 2016. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

  15. Atomic Scale coexistence of Periodic and quasiperiodic order in a2-fold A1-Ni-Co decagonal quasicrystal surface

    Energy Technology Data Exchange (ETDEWEB)

    Park, Jeong Young; Ogletree, D. Frank; Salmeron, Miquel; Ribeiro,R.A.; Canfield, P.C.; Jenks, C.J.; Thiel, P.A.

    2005-11-14

    Decagonal quasicrystals are made of pairs of atomic planes with pentagonal symmetry periodically stacked along a 10-fold axis. We have investigated the atomic structure of the 2-fold surface of a decagonal Al-Ni-Co quasicrystal using scanning tunneling microscopy (STM). The surface consists of terraces separated by steps of heights 1.9, 4.7, 7.8, and 12.6{angstrom} containing rows of atoms parallel to the 10-fold direction with an internal periodicity of 4{angstrom}. The rows are arranged aperiodically, with separations that follow a Fibonacci sequence and inflation symmetry. The results indicate that the surfaces are preferentially Al-terminated and in general agreement with bulk models.

  16. Quality of the voice after injection of hyaluronic acid into the vocal fold.

    Science.gov (United States)

    Szkiełkowska, Agata; Miaśkiewicz, Beata; Remacle, Marc; Krasnodębska, Paulina; Skarżyński, Henryk

    2013-04-17

    Voice disorders resulting from glottic insufficiency are a significant clinical problem in everyday phoniatric practice. One method of treatment is injection laryngoplasty. Our study aimed to assess the voice quality of patients treated with hyaluronic acid injection into the vocal fold. We studied 25 patients suffering from dysphonia, conducting laryngological and phoniatric examination, including videostroboscopy and acoustic voice analysis, before the operation and 1, 3, and 6 months later. In all cases there was complete or almost complete glottic closure after the operation. One month after the procedure, videostroboscopic examination revealed reappearance of vocal fold vibration in 8 cases; after 3 months this had risen to 15 cases. Perceptual voice quality (as assessed by the GRBAS scale) in patients with glottic insufficiency was improved. The most significant improvement was obtained 1 month after surgery (p=0.0002), and within the next months further statistically significant improvements (p=0.000002) were noted. Multidimensional voice analysis showed statistically significant and rapid improvement in frequency parameters, especially vFo. Other parameters were also improved 3 and 6 months after surgery. Injection of hyaluronic acid into the vocal fold improves phonatory functions of the larynx and the quality of voice in patients with glottic insufficiency. It may be a safe and conservative method for treatment of voice disorders. Hyaluronic acid injection to the vocal fold is an easy, effective, and fast method for restoration of good voice quality.

  17. Novel S = 1/2 Kagome Lattice Materials: Cs2TiCu3F12 and Rb2TiCu3F12

    Directory of Open Access Journals (Sweden)

    Lewis J. Downie

    2015-05-01

    Full Text Available Two new members of the A2B′Cu3F12 family of kagome-related materials have been prepared, in order to further understand the crystal-chemical relationships, phase transitions and magnetic behaviour within this family of potentially frustrated S = ½ two-dimensional quantum magnets. Cs2TiCu3F12 adopts a crystal structure with the ideal kagome lattice topology (space group R m at ambient temperature. Diffraction studies reveal different symmetry-lowering structural phase transitions in single crystal and polycrystalline forms at sub-ambient temperatures, with the single crystal form retaining rhombohedral symmetry and the powder form being monoclinic. In both cases, long-range antiferromagnetic order occurs in the region 16–20 K. Rb2TiCu3F12 adopts a distorted triclinic structure even at ambient temperatures.

  18. Solvent Effects on Protein Folding/Unfolding

    Science.gov (United States)

    García, A. E.; Hillson, N.; Onuchic, J. N.

    Pressure effects on the hydrophobic potential of mean force led Hummer et al. to postulate a model for pressure denaturation of proteins in which denaturation occurs by means of water penetration into the protein interior, rather than by exposing the protein hydrophobic core to the solvent --- commonly used to describe temperature denaturation. We study the effects of pressure in protein folding/unfolding kinetics in an off-lattice minimalist model of a protein in which pressure effects have been incorporated by means of the pair-wise potential of mean force of hydrophobic groups in water. We show that pressure slows down the kinetics of folding by decreasing the reconfigurational diffusion coefficient and moves the location of the folding transition state.

  19. Current Understanding and Future Directions for Vocal Fold Mechanobiology

    Science.gov (United States)

    Li, Nicole Y.K.; Heris, Hossein K.; Mongeau, Luc

    2013-01-01

    The vocal folds, which are located in the larynx, are the main organ of voice production for human communication. The vocal folds are under continuous biomechanical stress similar to other mechanically active organs, such as the heart, lungs, tendons and muscles. During speech and singing, the vocal folds oscillate at frequencies ranging from 20 Hz to 3 kHz with amplitudes of a few millimeters. The biomechanical stress associated with accumulated phonation is believed to alter vocal fold cell activity and tissue structure in many ways. Excessive phonatory stress can damage tissue structure and induce a cell-mediated inflammatory response, resulting in a pathological vocal fold lesion. On the other hand, phonatory stress is one major factor in the maturation of the vocal folds into a specialized tri-layer structure. One specific form of vocal fold oscillation, which involves low impact and large amplitude excursion, is prescribed therapeutically for patients with mild vocal fold injuries. Although biomechanical forces affect vocal fold physiology and pathology, there is little understanding of how mechanical forces regulate these processes at the cellular and molecular level. Research into vocal fold mechanobiology has burgeoned over the past several years. Vocal fold bioreactors are being developed in several laboratories to provide a biomimic environment that allows the systematic manipulation of physical and biological factors on the cells of interest in vitro. Computer models have been used to simulate the integrated response of cells and proteins as a function of phonation stress. The purpose of this paper is to review current research on the mechanobiology of the vocal folds as it relates to growth, pathogenesis and treatment as well as to propose specific research directions that will advance our understanding of this subject. PMID:24812638

  20. Predicted singers' vocal fold lengths and voice classification-a study of x-ray morphological measures.

    Science.gov (United States)

    Roers, Friederike; Mürbe, Dirk; Sundberg, Johan

    2009-07-01

    Students admitted to the solo singing education at the University of Music Dresden, Germany have been submitted to a detailed physical examination of a variety of factors with relevance to voice function since 1959. In the years 1959-1991, this scheme of examinations included X-ray profiles of the singers' vocal tracts. This material of 132 X-rays of voice professionals was used to investigate different laryngeal morphological measures and their relation to vocal fold length. Further, the study aimed to investigate if there are consistent anatomical differences between singers of different voice classifications. The study design used was a retrospective analysis. Vocal fold length could be measured in 29 of these singer subjects directly. These data showed a strong correlation with the anterior-posterior diameter of the subglottis and the trachea as well as with the distance from the anterior contour of the thyroid cartilage to the anterior contour of the spine. These relations were used in an attempt to predict the 132 singers' vocal fold lengths. The results revealed a clear covariation between predicted vocal fold length and voice classification. Anterior-posterior subglottic-tracheal diameter yielded mean vocal fold lengths of 14.9, 16.0, 16.6, 18.4, 19.5, and 20.9mm for sopranos, mezzo-sopranos, altos, tenors, baritones, and basses, respectively. The data support the assumption that there are consistent anatomical laryngeal differences between singers of different voice classifications, which are of relevance to pitch range and timbre of the voice.

  1. BRCA1/2 mutation analysis in 41 ovarian cell lines reveals only one functionally deleterious BRCA1 mutation.

    LENUS (Irish Health Repository)

    Stordal, Britta

    2013-06-01

    Mutations in BRCA1\\/2 increase the risk of developing breast and ovarian cancer. Germline BRCA1\\/2 mutations occur in 8.6-13.7% of unselected epithelial ovarian cancers, somatic mutations are also frequent. BRCA1\\/2 mutated or dysfunctional cells may be sensitive to PARP inhibition by synthetic lethality. The aim of this study is to comprehensively characterise the BRCA1\\/2 status of a large panel of ovarian cancer cell lines available to the research community to assist in biomarker studies of novel drugs and in particular of PARP inhibitors. The BRCA1\\/2 genes were sequenced in 41 ovarian cell lines, mRNA expression of BRCA1\\/2 and gene methylation status of BRCA1 was also examined. The cytotoxicity of PARP inhibitors olaparib and veliparib was examined in 20 cell lines. The cell line SNU-251 has a deleterious BRCA1 mutation at 5564G > A, and is the only deleterious BRCA1\\/2 mutant in the panel. Two cell lines (UPN-251 and PEO1) had deleterious mutations as well as additional reversion mutations that restored the protein functionality. Heterozygous mutations in BRCA1\\/2 were relatively common, found in 14.6% of cell lines. BRCA1 was methylated in two cell lines (OVCAR8, A1847) and there was a corresponding decrease in gene expression. The BRCA1 methylated cell lines were more sensitive to PARP inhibition than wild-type cells. The SNU-251 deleterious mutant was more sensitive to PARP inhibition, but only in a long-term exposure to correct for its slow growth rate. Cell lines derived from metastatic disease are significantly more resistant to veliparib (2.0 fold p = 0.03) compared to those derived from primary tumours. Resistance to olaparib and veliparib was correlated Pearsons-R 0.5393, p = 0.0311. The incidence of BRCA1\\/2 deleterious mutations 1\\/41 cell lines derived from 33 different patients (3.0%) is much lower than the population incidence. The reversion mutations and high frequency of heterozygous mutations suggest that there is a selective

  2. The Role of Backbone Hydrogen Bonds in the Transition State for Protein Folding of a PDZ Domain.

    Directory of Open Access Journals (Sweden)

    Søren W. Pedersen

    Full Text Available Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.

  3. A partially folded intermediate species of the β-sheet protein apo-pseudoazurin ism trapped during proline-limited folding

    NARCIS (Netherlands)

    Reader, J.S.; van Nuland, N.A.J.; Thompson, G.S.; Ferguson, S.J.; Dobson, C.M.; Radford, S.E.

    2001-01-01

    The folding of apo-pseudoazurin, a 123-residue, predominantly -sheet protein with a complex Greek key topology, has been investigated using several biophysical techniques. Kinetic analysis of refolding using farand near-ultraviolet circular dichroism (UV CD) shows that the protein folds slowly to

  4. A case of bilateral vocal fold mucosal bridges, bilateral trans-vocal fold type III sulci vocales, and an intracordal polyp.

    Science.gov (United States)

    Tan, Melin; Pitman, Michael J

    2011-07-01

    We present a patient with a novel finding of bilateral mucosal bridges, bilateral type III trans-vocal fold sulci vocales, and a vocal fold polyp. Although sulci and mucosal bridges occur in the vocal folds, it is rare to find multiples of these lesions in a single patient, and it is even more uncommon when they occur in conjunction with a vocal fold polyp. To our knowledge, this is the first description of a vocal fold polyp in combination with multiple vocal fold bridges and multiple type III sulci vocales in a single patient. To describe and visually present the diagnosis and treatment of a patient with an intracordal polyp, bilateral mucosal bridges, as well as bilateral type III trans-vocal fold sulci vocales. Presentation of a set of high definition intraoperative photos displaying the extent of the vocal fold lesions and the resection of the intracordal polyp. This patient presented with only 6 months of significant dysphonia. It was felt that the recent change in voice was because of the polyp and not the bridges or sulci vocales. Considering the patient's presentation and the possible morbidity of resection of mucosal bridges and sulci, only the polyp was excised. Postoperatively, the patient's voice returned to his acceptable mild baseline dysphonia, and the benefit has persisted 6 months postoperatively. The combination of bilateral mucosal bridges, bilateral type III sulcus vocalis, and an intracordal polyp in one patient is rare if not novel. Treatment of the polyp alone returned the patient's voice to his lifelong baseline of mild dysphonia. Copyright © 2011 The Voice Foundation. Published by Mosby, Inc. All rights reserved.

  5. A Rat Excised Larynx Model of Vocal Fold Scar

    Science.gov (United States)

    Welham, Nathan V.; Montequin, Douglas W.; Tateya, Ichiro; Tateya, Tomoko; Choi, Seong Hee; Bless, Diane M.

    2009-01-01

    Purpose: To develop and evaluate a rat excised larynx model for the measurement of acoustic, aerodynamic, and vocal fold vibratory changes resulting from vocal fold scar. Method: Twenty-four 4-month-old male Sprague-Dawley rats were assigned to 1 of 4 experimental groups: chronic vocal fold scar, chronic vocal fold scar treated with 100-ng basic…

  6. Crystal structure of the plexin A3 intracellular region reveals an autoinhibited conformation through active site sequestration

    Energy Technology Data Exchange (ETDEWEB)

    He, Huawei; Yang, Taehong; Terman, Jonathan R.; Zhang, Xuewu; (UTSMC)

    2010-01-20

    Plexin cell surface receptors bind to semaphorin ligands and transduce signals for regulating neuronal axon guidance. The intracellular region of plexins is essential for signaling and contains a R-Ras/M-Ras GTPase activating protein (GAP) domain that is divided into two segments by a Rho GTPase-binding domain (RBD). The regulation mechanisms for plexin remain elusive, although it is known that activation requires both binding of semaphorin to the extracellular region and a Rho-family GTPase (Rac1 or Rnd1) to the RBD. Here we report the crystal structure of the plexin A3 intracellular region. The structure shows that the N- and C-terminal portions of the GAP homologous regions together form a GAP domain with an overall fold similar to other Ras GAPs. However, the plexin GAP domain adopts a closed conformation and cannot accommodate R-Ras/M-Ras in its substrate-binding site, providing a structural basis for the autoinhibited state of plexins. A comparison with the plexin B1 RBD/Rnd1 complex structure suggests that Rnd1 binding alone does not induce a conformational change in plexin, explaining the requirement of both semaphorin and a Rho GTPase for activation. The structure also identifies an N-terminal segment that is important for regulation. Both the N-terminal segment and the RBD make extensive interactions with the GAP domain, suggesting the presence of an allosteric network connecting these three domains that integrates semaphorin and Rho GTPase signals to activate the GAP. The importance of these interactions in plexin signaling is shown by both cell-based and in vivo axon guidance assays.

  7. Method of generating ploynucleotides encoding enhanced folding variants

    Energy Technology Data Exchange (ETDEWEB)

    Bradbury, Andrew M.; Kiss, Csaba; Waldo, Geoffrey S.

    2017-05-02

    The invention provides directed evolution methods for improving the folding, solubility and stability (including thermostability) characteristics of polypeptides. In one aspect, the invention provides a method for generating folding and stability-enhanced variants of proteins, including but not limited to fluorescent proteins, chromophoric proteins and enzymes. In another aspect, the invention provides methods for generating thermostable variants of a target protein or polypeptide via an internal destabilization baiting strategy. Internally destabilization a protein of interest is achieved by inserting a heterologous, folding-destabilizing sequence (folding interference domain) within DNA encoding the protein of interest, evolving the protein sequences adjacent to the heterologous insertion to overcome the destabilization (using any number of mutagenesis methods), thereby creating a library of variants. The variants in the library are expressed, and those with enhanced folding characteristics selected.

  8. The distribution of deformation in parallel fault-related folds with migrating axial surfaces: comparison between fault-propagation and fault-bend folding

    Science.gov (United States)

    Salvini, Francesco; Storti, Fabrizio

    2001-01-01

    In fault-related folds that form by axial surface migration, rocks undergo deformation as they pass through axial surfaces. The distribution and intensity of deformation in these structures has been impacted by the history of axial surface migration. Upon fold initiation, unique dip panels develop, each with a characteristic deformation intensity, depending on their history. During fold growth, rocks that pass through axial surfaces are transported between dip panels and accumulate additional deformation. By tracking the pattern of axial surface migration in model folds, we predict the distribution of relative deformation intensity in simple-step, parallel fault-bend and fault-propagation anticlines. In both cases the deformation is partitioned into unique domains we call deformation panels. For a given rheology of the folded multilayer, deformation intensity will be homogeneously distributed in each deformation panel. Fold limbs are always deformed. The flat crests of fault-propagation anticlines are always undeformed. Two asymmetric deformation panels develop in fault-propagation folds above ramp angles exceeding 29°. For lower ramp angles, an additional, more intensely-deformed panel develops at the transition between the crest and the forelimb. Deformation in the flat crests of fault-bend anticlines occurs when fault displacement exceeds the length of the footwall ramp, but is never found immediately hinterland of the crest to forelimb transition. In environments dominated by brittle deformation, our models may serve as a first-order approximation of the distribution of fractures in fault-related folds.

  9. Tyrosinase degradation is prevented when EDEM1 lacks the intrinsically disordered region.

    Directory of Open Access Journals (Sweden)

    Marioara B Marin

    Full Text Available EDEM1 is a mannosidase-like protein that recruits misfolded glycoproteins from the calnexin/calreticulin folding cycle to downstream endoplasmic reticulum associated degradation (ERAD pathway. Here, we investigate the role of EDEM1 in the processing of tyrosinase, a tumour antigen overexpressed in melanoma cells. First, we analyzed and modeled EDEM1 major domains. The homology model raised on the crystal structures of human and Saccharomyces cerevisiae ER class I α1,2-mannosidases reveals that the major mannosidase domain located between aminoacids 121-598 fits with high accuracy. We have further identified an N-terminal region located between aminoacids 40-119, predicted to be intrinsically disordered (ID and susceptible to adopt multiple conformations, hence facilitating protein-protein interactions. To investigate these two domains we have constructed an EDEM1 deletion mutant lacking the ID region and a triple mutant disrupting the glycan-binding domain and analyzed their association with tyrosinase. Tyrosinase is a glycoprotein partly degraded endogenously by ERAD and the ubiquitin proteasomal system. We found that the degradation of wild type and misfolded tyrosinase was enhanced when EDEM1 was overexpressed. Glycosylated and non-glycosylated mutants co-immunoprecipitated with EDEM1 even in the absence of its intact mannosidase-like domain, but not when the ID region was deleted. In contrast, calnexin and SEL 1L associated with the deletion mutant. Our data suggest that the ID region identified in the N-terminal end of EDEM1 is involved in the binding of glycosylated and non-glycosylated misfolded proteins. Accelerating tyrosinase degradation by EDEM1 overexpression may lead to an efficient antigen presentation and enhanced elimination of melanoma cells.

  10. U.S. Environmental Protection Agency, Region 6 National Priorities List (NPL) Sites - 05/12/2014

    Data.gov (United States)

    U.S. Environmental Protection Agency — Point locations for sites in U.S. Environmental Protection Agency, Region 6 which are documented as being part of the National Priorities List as of May 12, 2014....

  11. Incidence of vocal fold immobility in patients with dysphagia.

    Science.gov (United States)

    Leder, Steven B; Ross, Douglas A

    2005-01-01

    This study prospectively investigated the incidence of vocal fold immobility, unilateral and bilateral, and its influence on aspiration status in a referred population of 1452 patients for a dysphagia evaluation from a large, urban, tertiary-care, teaching hospital. Main outcome measures included overall incidence of vocal fold immobility and aspiration status, with specific emphasis on age, etiology, and side of vocal fold immobility, i.e., right, left, or bilateral. Overall incidence of vocal fold immobility was 5.6% (81 of 1452 patients), including 47 males (mean age 55.7 yr) and 34 females (mean age 59.7 yr). In the subgroup of patients with vocal fold immobility, 31% (25 of 81) exhibited unilateral right, 60% (49 of 81) unilateral left, and 9% (7 of 81) bilateral impairment. Overall incidence of aspiration was found to be 29% (426 of 1452) of all patients referred for a swallow evaluation. Aspiration was observed in 44% (36 of 81) of patients presenting with vocal fold immobility, i.e., 44% (11 of 25) unilateral right, 43% (21 of 49) unilateral left, and 57% (4 of 7) bilateral vocal fold immobility. Left vocal fold immobility occurred most frequently due to surgical trauma. A liquid bolus was aspirated more often than a puree bolus. Side of vocal fold immobility and age were not factors that increased incidence of aspiration. In conclusion, vocal fold immobility, with an incidence of 5.6%, is not an uncommon finding in patients referred for a dysphagia evaluation in the acute-care setting, and vocal fold immobility, when present, was associated with a 15% increased incidence of aspiration when compared with a population already being evaluated for dysphagia.

  12. Theoretical study of the folded waveguide

    International Nuclear Information System (INIS)

    Chen, G.L.; Owens, T.L.; Whealton, J.H.

    1988-01-01

    We have applied a three-dimensional (3-D) algorithm for solving Maxwell's equations to the analysis of foleded waveguides used for fusion plasma heating at the ion cyclotron resonance frequency. A rigorous analysis of the magnetic field structure in the folded waveguide is presented. The results are compared to experimenntal measurements. Optimum conditions for the folded waveguide are discussed. 6 refs., 10 figs

  13. Triplex intermediates in folding of human telomeric quadruplexes probed by microsecond-scale molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Stadlbauer, Petr; Trantírek, L.; Cheatham III, T. E.; Koča, J.; Šponer, Jiří

    105C, OCT2014 (2014), s. 22-35 ISSN 0300-9084 R&D Projects: GA ČR(CZ) GAP208/12/1822; GA ČR(CZ) GA13-28310S Institutional support: RVO:68081707 Keywords : G-DNA folding * Quadruplex * Triplex Subject RIV: BO - Biophysics Impact factor: 2.963, year: 2014

  14. Vaginal fold prolapse during the last third of pregnancy, followed by normal parturition, in a bitch.

    Science.gov (United States)

    Gouletsou, Pagona G; Galatos, Apostolos D; Apostolidis, Kosmas; Sideri, Aikaterini I

    2009-06-01

    This article describes a 1.5-year-old female, Greek Hound dog, weighing 16 kg, presented with a type III vaginal prolapse which occurred during the last third of pregnancy. Trans-abdominal ultrasonography revealed four live foetuses in the uterine horns. The animal was hospitalized and 4 days later gave birth without any interference. Three days later, resection of the prolapsed tissue was performed and the bitch recovered completely. Recurrence of a type I vaginal prolapse was observed 4 months later, during subsequent oestrus. This case is unusual because, although vaginal fold prolapse is mainly seen during proestrus/oestrus or during parturition, it was first noticed 47 days after mating and 13 days before parturition. Furthermore, even though the prolapse of vaginal fold was of type III and of considerable size, parturition proceeded normally. Finally, even though resection of the prolapsed tissue was performed 3 days after parturition, recurrence of vaginal fold oedema (type I) was observed in the subsequent oestrus.

  15. Kinetics and Thermodynamics of Membrane Protein Folding

    Directory of Open Access Journals (Sweden)

    Ernesto A. Roman

    2014-03-01

    Full Text Available Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.

  16. Thermodynamics of protein folding: a random matrix formulation.

    Science.gov (United States)

    Shukla, Pragya

    2010-10-20

    The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters, e.g. the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon molecules. Our study, based on random matrix modeling of the interactions, shows, however, that the evolution of the statistical measures, e.g. Gibbs free energy, heat capacity, and entropy, is single parametric. The information can explain the selection of specific folding pathways from an infinite number of possible ways as well as other folding characteristics observed in computer simulation studies. © 2010 IOP Publishing Ltd

  17. Crystal Structure and Substrate Specificity of PTPN12

    Directory of Open Access Journals (Sweden)

    Hui Li

    2016-05-01

    Full Text Available PTPN12 is an important tumor suppressor that plays critical roles in various physiological processes. However, the molecular basis underlying the substrate specificity of PTPN12 remains uncertain. Here, enzymological and crystallographic studies have enabled us to identify two distinct structural features that are crucial determinants of PTPN12 substrate specificity: the pY+1 site binding pocket and specific basic charged residues along its surface loops. Key structurally plastic regions and specific residues in PTPN12 enabled recognition of different HER2 phosphorylation sites and regulated specific PTPN12 functions. In addition, the structure of PTPN12 revealed a CDK2 phosphorylation site in a specific PTPN12 loop. Taken together, our results not only provide the working mechanisms of PTPN12 for desphosphorylation of its substrates but will also help in designing specific inhibitors of PTPN12.

  18. Central nervous system PET-CT imaging reveals regional impairments in pediatric patients with Wolfram syndrome.

    Directory of Open Access Journals (Sweden)

    Agnieszka Zmyslowska

    Full Text Available Wolfram syndrome (WFS is inherited as an autosomal recessive disease with main clinical features of diabetes mellitus, optic atrophy, diabetes insipidus and deafness. However, various neurological defects may also be detected. The aim of this study was to evaluate aspects of brain structure and function using PET-CT (positron emission tomography and computed tomography and MRI (magnetic resonance imaging in pediatric patients with WFS. Regional changes in brain glucose metabolism were measured using standardized uptake values (SUVs based on images of (18F fluorodeoxyglucose (FDG uptake in 7 WFS patients aged 10.1-16.0 years (mean 12.9±2.4 and in 20 healthy children aged 3-17.9 years (mean 12.8±4.1. In all patients the diagnosis of WFS was confirmed by DNA sequencing of the WFS1 gene. Hierarchical clustering showed remarkable similarities of glucose uptake patterns among WFS patients and their differences from the control group. SUV data were subsequently standardized for age groups 13 years old to account for developmental differences. Reduced SUVs in WFS patients as compared to the control group for the bilateral brain regions such as occipital lobe (-1.24±1.20 vs. -0.13±1.05; p = 0.028 and cerebellum (-1.11±0.69 vs. -0.204±1.00; p = 0.036 were observed and the same tendency for cingulate (-1.13±1.05 vs. -0.15±1.12; p = 0.056, temporal lobe (-1.10±0.98 vs. -0.15±1.10; p = 0.057, parietal lobe (-1.06±1.20 vs. -0.08±1.08; p = 0.058, central region (-1.01±1.04 vs. -0.09±1.06; p = 0.060, basal ganglia (-1.05±0.74 vs. -0.20±1.07; p = 0.066 and mesial temporal lobe (-1.06±0.82 vs. -0.26±1.08; p = 0.087 was also noticed. After adjusting for multiple hypothesis testing, the differences in glucose uptake were non-significant. For the first time, regional differences in brain glucose metabolism among patients with WFS were shown using PET-CT imaging.

  19. Fluorescence of Alexa fluor dye tracks protein folding.

    Directory of Open Access Journals (Sweden)

    Simon Lindhoud

    Full Text Available Fluorescence spectroscopy is an important tool for the characterization of protein folding. Often, a protein is labeled with appropriate fluorescent donor and acceptor probes and folding-induced changes in Förster Resonance Energy Transfer (FRET are monitored. However, conformational changes of the protein potentially affect fluorescence properties of both probes, thereby profoundly complicating interpretation of FRET data. In this study, we assess the effects protein folding has on fluorescence properties of Alexa Fluor 488 (A488, which is commonly used as FRET donor. Here, A488 is covalently attached to Cys69 of apoflavodoxin from Azotobacter vinelandii. Although coupling of A488 slightly destabilizes apoflavodoxin, the three-state folding of this protein, which involves a molten globule intermediate, is unaffected. Upon folding of apoflavodoxin, fluorescence emission intensity of A488 changes significantly. To illuminate the molecular sources of this alteration, we applied steady state and time-resolved fluorescence techniques. The results obtained show that tryptophans cause folding-induced changes in quenching of Alexa dye. Compared to unfolded protein, static quenching of A488 is increased in the molten globule. Upon populating the native state both static and dynamic quenching of A488 decrease considerably. We show that fluorescence quenching of Alexa Fluor dyes is a sensitive reporter of conformational changes during protein folding.

  20. Fold and Fit: Space Conserving Shape Editing

    KAUST Repository

    Ibrahim, Mohamed; Yan, Dong-Ming

    2017-01-01

    We present a framework that folds man-made objects in a structure-aware manner for space-conserving storage and transportation. Given a segmented 3D mesh of a man-made object, our framework jointly optimizes for joint locations, the folding order

  1. Inverse folding of RNA pseudoknot structures

    Directory of Open Access Journals (Sweden)

    Li Linda YM

    2010-06-01

    Full Text Available Abstract Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings (secondary structure and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures, searching for new ribozymes and designing artificial RNA, it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms, RNAinverse, RNA-SSD as well as INFO-RNA are limited to RNA secondary structures, we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing, canonical pseudoknot structures. Results In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv, including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http://www.combinatorics.cn/cbpc/inv.html. Conclusions The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas, for instance by considering sets of competing structures. As a result, Inv is not only able to find novel sequences even for RNA secondary structures, it does so in the context of competing structures that potentially exhibit cross-serial interactions.

  2. First passage analysis of the folding of a β-sheet miniprotein: is it more realistic than the standard equilibrium approach?

    Science.gov (United States)

    Kalgin, Igor V; Chekmarev, Sergei F; Karplus, Martin

    2014-04-24

    Simulations of first-passage folding of the antiparallel β-sheet miniprotein beta3s, which has been intensively studied under equilibrium conditions by A. Caflisch and co-workers, show that the kinetics and dynamics are significantly different from those for equilibrium folding. Because the folding of a protein in a living system generally corresponds to the former (i.e., the folded protein is stable and unfolding is a rare event), the difference is of interest. In contrast to equilibrium folding, the Ch-curl conformations become very rare because they contain unfavorable parallel β-strand arrangements, which are difficult to form dynamically due to the distant N- and C-terminal strands. At the same time, the formation of helical conformations becomes much easier (particularly in the early stage of folding) due to short-range contacts. The hydrodynamic descriptions of the folding reaction have also revealed that while the equilibrium flow field presented a collection of local vortices with closed "streamlines", the first-passage folding is characterized by a pronounced overall flow from the unfolded states to the native state. The flows through the locally stable structures Cs-or and Ns-or, which are conformationally close to the native state, are negligible due to detailed balance established between these structures and the native state. Although there are significant differences in the general picture of the folding process from the equilibrium and first-passage folding simulations, some aspects of the two are in agreement. The rate of transitions between the clusters of characteristic protein conformations in both cases decreases approximately exponentially with the distance between the clusters in the hydrogen bond distance space of collective variables, and the folding time distribution in the first-passage segments of the equilibrium trajectory is in good agreement with that for the first-passage folding simulations.

  3. First Passage Analysis of the Folding of a β-Sheet Miniprotein: Is it More Realistic Than the Standard Equilibrium Approach?

    Science.gov (United States)

    2015-01-01

    Simulations of first-passage folding of the antiparallel β-sheet miniprotein beta3s, which has been intensively studied under equilibrium conditions by A. Caflisch and co-workers, show that the kinetics and dynamics are significantly different from those for equilibrium folding. Because the folding of a protein in a living system generally corresponds to the former (i.e., the folded protein is stable and unfolding is a rare event), the difference is of interest. In contrast to equilibrium folding, the Ch-curl conformations become very rare because they contain unfavorable parallel β-strand arrangements, which are difficult to form dynamically due to the distant N- and C-terminal strands. At the same time, the formation of helical conformations becomes much easier (particularly in the early stage of folding) due to short-range contacts. The hydrodynamic descriptions of the folding reaction have also revealed that while the equilibrium flow field presented a collection of local vortices with closed ”streamlines”, the first-passage folding is characterized by a pronounced overall flow from the unfolded states to the native state. The flows through the locally stable structures Cs-or and Ns-or, which are conformationally close to the native state, are negligible due to detailed balance established between these structures and the native state. Although there are significant differences in the general picture of the folding process from the equilibrium and first-passage folding simulations, some aspects of the two are in agreement. The rate of transitions between the clusters of characteristic protein conformations in both cases decreases approximately exponentially with the distance between the clusters in the hydrogen bond distance space of collective variables, and the folding time distribution in the first-passage segments of the equilibrium trajectory is in good agreement with that for the first-passage folding simulations. PMID:24669953

  4. Ab initio folding of mixed-fold FSD-EY protein using formula-based polarizable hydrogen bond (PHB) charge model

    Science.gov (United States)

    Zhang, Dawei; Lazim, Raudah; Mun Yip, Yew

    2017-09-01

    We conducted an all-atom ab initio folding of FSD-EY, a protein with a ββα configuration using non-polarizable (AMBER) and polarizable force fields (PHB designed by Gao et al.) in implicit solvent. The effect of reducing the polarization effect integrated into the force field by the PHB model, termed the PHB0.7 was also examined in the folding of FSD-EY. This model incorporates into the force field 70% of the original polarization effect to minimize the likelihood of over-stabilizing the backbone hydrogen bonds. Precise folding of the β-sheet of FSD-EY was further achieved by relaxing the REMD structure obtained in explicit water.

  5. Morphometric Study of Vocal Folds in Indian Cadavers

    Directory of Open Access Journals (Sweden)

    Rawal J.D.

    2015-06-01

    Full Text Available Introduction: -The larynx is an air passage and a sphincteric device used in respiration and phonation. The larynx, from inside outwards has a framework of mucosa surrounded by fibro-elastic membrane which in turn is surrounded by cartilages and then a layer of muscles. Vocal folds are intrinsic ligament of larynx covered by mucosal folds. Larynx generates sound through rhythmic opening and closing of the vocal folds. The perceived pitch of human voice mainly depends upon fundamental frequency of sound generated by larynx. Aim: - The aim of present study is to measure various dimensions of vocal folds in Indian cadavers. Material & Methods: - 50 larynx were obtained from embalmed cadavers, of which 10 larynx were of females. Vocal cords were dissected from the larynx and morphometric analysis was done. Results and Conclusions: - The average total length of the vocal folds was found to be 16.11 mm. ± 2.62 mm. in male and 14.10 mm. ± 1.54 mm. in female cadavers. The average width of the vocal folds was found to be 4.38 mm. ± 0.74 mm. in male and 3.60 mm. ± 0.64 mm. in female cadavers. The average total length of the membranous part of the vocal folds was found to be 11.90 mm. ± 1.86 mm. in male and 10.45 mm. ± 1.81 mm. in female cadavers. The average ratio of the length of the membranous and the cartilaginous parts of the vocal folds was calculated to be 3.10 ± 0.96in male and 2.85 ± 0.73in female cadavers.

  6. Merging monads and folds for functional programming

    NARCIS (Netherlands)

    Meijer, E.; Jeuring, J.T.

    1995-01-01

    These notes discuss the simultaneous use of generalised fold operators and monads to structure functional programs. Generalised fold operators structure programs after the decomposition of the value they consume. Monads structure programs after the computation of the value they produce. Our programs

  7. Impact of hydrodynamic interactions on protein folding rates depends on temperature

    Science.gov (United States)

    Zegarra, Fabio C.; Homouz, Dirar; Eliaz, Yossi; Gasic, Andrei G.; Cheung, Margaret S.

    2018-03-01

    We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α /β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β -barrel α -spectrin Src-homology 3 domain (SH3) protein. When comparing the protein folding kinetics simulated with Brownian dynamics in the presence of HI to that in the absence of HI, we find that the effect of HI on protein folding appears to have a "crossover" behavior about the folding temperature. This means that at a temperature greater than the folding temperature, the enhanced friction from the hydrodynamic solvents between the beads in an unfolded configuration results in lowered folding rate; conversely, at a temperature lower than the folding temperature, HI accelerates folding by the backflow of solvent toward the folded configuration of a protein. Additionally, the extent of acceleration depends on the topology of a protein: for a protein like CI2, where its folding nucleus is rather diffuse in a transition state, HI channels the formation of contacts by favoring a major folding pathway in a complex free energy landscape, thus accelerating folding. For a protein like SH3, where its folding nucleus is already specific and less diffuse, HI matters less at a temperature lower than the folding temperature. Our findings provide further theoretical insight to protein folding kinetic experiments and simulations.

  8. Frustration in Condensed Matter and Protein Folding

    Science.gov (United States)

    Li, Z.; Tanner, S.; Conroy, B.; Owens, F.; Tran, M. M.; Boekema, C.

    2014-03-01

    By means of computer modeling, we are studying frustration in condensed matter and protein folding, including the influence of temperature and Thomson-figure formation. Frustration is due to competing interactions in a disordered state. The key issue is how the particles interact to reach the lowest frustration. The relaxation for frustration is mostly a power function (randomly assigned pattern) or an exponential function (regular patterns like Thomson figures). For the atomic Thomson model, frustration is predicted to decrease with the formation of Thomson figures at zero kelvin. We attempt to apply our frustration modeling to protein folding and dynamics. We investigate the homogeneous protein frustration that would cause the speed of the protein folding to increase. Increase of protein frustration (where frustration and hydrophobicity interplay with protein folding) may lead to a protein mutation. Research is supported by WiSE@SJSU and AFC San Jose.

  9. Biochemical Characterization of a Thiol-Activated, Oxidation Stable Keratinase from Bacillus pumilus KS12

    Directory of Open Access Journals (Sweden)

    Rinky Rajput

    2010-01-01

    Full Text Available An extracellular keratinase from Bacillus pumilus KS12 was purified by DEAE ion exchange chromatography. It was a 45 kDa monomer as determined by SDS PAGE analysis. It was found to be an alkaline, serine protease with pH and temperature optima of 10 and 60C, respectively. It was thiol activated with two- and eight-fold enhancement in presence of 10 mM DTT and β-mercaptoethanol, respectively. In addition, its activity was stimulated in the presence of various surfactants, detergents, and oxidizing agents where a nearly 2- to 3-fold enhancement was observed in presence of H2O2 and NaHClO3. It hydrolyzed broad range of complex substrates including feather keratin, haemoglobin, fibrin, casein,and α-keratin. Analysis of amidolytic activity revealed that it efficiently cleaved phenylalanine → leucine → alanine- p-nitroanilides. It also cleaved insulin B chain between Val2- Asn3, Leu6-Cys7 and His10-Leu11 residues.

  10. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin

    DEFF Research Database (Denmark)

    Hoadley, Katherine A; Yau, Christina; Wolf, Denise M

    2014-01-01

    Recent genomic analyses of pathologically defined tumor types identify "within-a-tissue" disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform...... on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset...

  11. The impact of intraglottal vortices on vocal fold dynamics

    Science.gov (United States)

    Erath, Byron; Pirnia, Alireza; Peterson, Sean

    2016-11-01

    During voiced speech a critical pressure is produced in the lungs that separates the vocal folds and creates a passage (the glottis) for airflow. As air passes through the vocal folds the resulting aerodynamic loading, coupled with the tissue properties of the vocal folds, produces self-sustained oscillations. Throughout each cycle a complex flow field develops, characterized by a plethora of viscous flow phenomena. Air passing through the glottis creates a jet, with periodically-shed vortices developing due to flow separation and the Kelvin-Helmholtz instability in the shear layer. These vortices have been hypothesized to be a crucial mechanism for producing vocal fold vibrations. In this study the effect of vortices on the vocal fold dynamics is investigated experimentally by passing a vortex ring over a flexible beam with the same non-dimensional mechanical properties as the vocal folds. Synchronized particle image velocimetry data are acquired in tandem with the beam dynamics. The resulting impact of the vortex ring loading on vocal fold dynamics is discussed in detail. This work was supported by the National Science Foundation Grant CBET #1511761.

  12. Folding models for elastic and inelastic scattering

    International Nuclear Information System (INIS)

    Satchler, G.R.

    1982-01-01

    The most widely used models are the optical model potential (OMP) for elastic scattering, and its generalization to non-spherical shapes, the deformed optical model potential (DOMP) for inelastic scattering. These models are simple and phenomenological; their parameters are adjusted so as to reproduce empirical data. Nonetheless, there are certain, not always well-defined, constraints to be imposed. The potential shapes and their parameter values must be reasonable and should vary in a smooth and systematic way with the masses of the colliding nuclei and their energy. One way of satisfying these constraints, without going back to a much more fundamental theory, is through the use of folding models. The basic justification for using potentials of the Woods-Saxon shape for nucleon-nucleus scattering, for example, is our knowledge that a nuclear density distribution is more-or-less constant in the nuclear interior with a diffuse surface. When this is folded with a short-range nucleon-nucleon interaction, the result is a similar shape with a more diffuse surface. Folding procedures allow us to incorporate many aspects of nuclear structure (although the nuclear size is one of the most important), as well as theoretical ideas about the effective interaction of two nucleons within nuclear matter. It also provides us with a means of linking information obtained from nuclear (hadronic) interactions with that from other sources, as well as correlating that from the use of different hadronic probes. Folding model potentials, single-folded potentials, and the double-folding model including applications to heavy-ion scattering are discussed

  13. Escherichia coli K-12 pathogenicity in the pea aphid, Acyrthosiphon pisum, reveals reduced antibacterial defense in aphids.

    Science.gov (United States)

    Altincicek, Boran; Ter Braak, Bas; Laughton, Alice M; Udekwu, Klas I; Gerardo, Nicole M

    2011-10-01

    To better understand the molecular basis underlying aphid immune tolerance to beneficial bacteria and immune defense to pathogenic bacteria, we characterized how the pea aphid Acyrthosiphon pisum responds to Escherichia coli K-12 infections. E. coli bacteria, usually cleared in the hemolymph of other insect species, were capable of growing exponentially and killing aphids within a few days. Red fluorescence protein expressing E. coli K-12 laboratory strain multiplied in the aphid hemolymph as well as in the digestive tract, resulting in death of infected aphids. Selected gene deletion mutants of the E. coli K-12 predicted to have reduced virulence during systemic infections showed no difference in either replication or killing rate when compared to the wild type E. coli strain. Of note, however, the XL1-Blue E. coli K-12 strain exhibited a significant lag phase before multiplying and killing aphids. This bacterial strain has recently been shown to be more sensitive to oxidative stress than other E. coli K-12 strains, revealing a potential role for reactive oxygen species-mediated defenses in the otherwise reduced aphid immune system. Copyright © 2011 Elsevier Ltd. All rights reserved.

  14. Folds and Etudes

    Science.gov (United States)

    Bean, Robert

    2007-01-01

    In this article, the author talks about "Folds" and "Etudes" which are images derived from anonymous typing exercises that he found in a used copy of "Touch Typing Made Simple". "Etudes" refers to the musical tradition of studies for a solo instrument, which is a typewriter. Typing exercises are repetitive attempts to type words and phrases…

  15. Identifying revealed comparative advantages in an EU regional context

    OpenAIRE

    Cordes, Alexander; Gehrke, Birgit; Römisch, Roman; Rammer, Christian; Schliessler, Paula; Wassmann, Pia

    2015-01-01

    [Introduction ...] Overall, this report is structured as follows: the next chapter (2) briefly outlines the relevance of regional trade indicators for determining the competitiveness of a region. In chapter 3, the methodology for the calculation of regional trade performance indicators is introduced, and the elementary results are described. Chapter 4 presents an econometric analysis relating key regional characteristics to international success of local industries. Based upon the regional di...

  16. Vocal fold self-disruption after phonotrauma on a lead actor: a case presentation.

    Science.gov (United States)

    Behlau, Mara; Oliveira, Gisele; Pontes, Paulo

    2009-11-01

    It is well known that phonotraumatic events may produce laryngeal inflammation, vocal fold hemorrhage and different types of mass lesions. This study describes a vocal fold self-disruption that occurred on stage to a lead actor in the role of Richard III. The study design is as case presentation. A 43-year-old actor presented with a sudden voice loss that first occurred on stage after a series of presentations. He also had a cold-like condition that had not been treated. His past medical history included an average of ten cigarettes per day for ten years and a 10-year history of gastritis and stomach ulcer. Perceptual, acoustic, and laryngeal analyses were performed following pharmacological and voice therapy. Perceptual and acoustic analyses showed mild deviations whereas laryngeal visual examination revealed a complete right vocal fold detachment from the anterior commissure to the vocal process, with generalized hyperemia. A mild diffuse Reinke's edema was observed on the left vocal fold. Mild discomfort was present only during the first day of the acute period. Modified vocal rest was recommended and a series of vocal exercises were administered. The patient performed again 4 days later, after following a series of behavioral modification techniques that included casting guidelines during the subsequent 15 days. Healing was exceptional and his voice returned to normal. This unique case with an exceptional recovery emphasizes the etiological aspects of scar formation after phonotrauma. Positive contributing factors may include a good vocal technique and adequate training as well as the protective upregulated genes present in Reinke's edema.

  17. Pathophysiology of the nodular and micronodular small bowel fold

    International Nuclear Information System (INIS)

    Olmstead, W.W.; Ros, P.R.; Moser, R.P.; Shekitka, K.M.; Lichtenstein, J.E.; Buck, J.L.

    1987-01-01

    The normal small bowel fold is easily seen on conventional studies of the small intestine, but visualization of the small bowel villus is just at the resolution of current roentgenographic technique. When the villi are enlarged, they can be seen radiographically as an irregularity or micronodularity of the small bowel fold. The anatomy of the fold and the pathophysiology of diseases producing fold nodularity (tumor, inflammatory disease, NLH, mastocytosis) and micronodularity (lymphangiectasia, Waldenstrom macroglobulinemia, Whipple disease) are presented, with an emphasis on radiologic-pathologic correlation. The radiologist should suggest certain diseases or conditions based on the roentgenographic characteristics of the closely analyzed small bowel fold

  18. [Analysis of mitochondrial 12S rRNA and tRNA(Ser(UCN)) genes in patients with nonsyndromic sensorineural hearing loss from various regions of Russia].

    Science.gov (United States)

    Dzhemileva, L U; Posukh, O L; Tazetdinov, A M; Barashkov, N A; Zhuravskiĭ, S G; Ponidelko, S N; Markova, T G; Tadinova, V N; Fedorova, S A; Maksimova, N R; Khusnutdinova, E K

    2009-07-01

    Mitochondrial DNA (mtDNA) mutations play an important role in etiology of hereditary hearing loss. In various regions of the world, patients suffer from nonsyndromic sensorineural hearing loss initiated by aminoglycoside antibiotics. Mutations that had been shown as pathogenetically important for hearing function disturbance were identified in mitochondrial 12S rRNA and tRNA(Ser(UCN)) genes while pathogenic role of several DNA sequences requires additional studies. This work presents the results of studying the spectrum of mutations and polymorphic variations in mtDNA genes 12S rRNA and tRNA(Ser(UGN)) in 410 patients with nonsyndromal sensoneural hearing impairment/loss from the Volga Ural region, St Petersburg, Yakutia, and Altai and in 520 individuals with normal hearing, which represent several ethnic groups (Russians, Tatars, Bashkirs, Yakuts, Altaians) residing in the Russian Federation. Pathogenetically significant mutation A1555G (12S rRNA) was found in two families (from Yakutia and St Peresburg) with hearing loss, probably caused by treatment with aminoglucosides, and in the population sample of Yakuts with a frequency of 0.83%. Further research is needed to confirm the role in hearing impairment of mutations 961insC, 961insC(n), 961delTinsC(n), T961G, T1095C (12S rRNA) and G7444A, A7445C (tRNA(Ser(UGN revealed in the patients. In addition, in the patients and the population groups, polymorphic mt DNA variants were detected, which are characteristic also of other Eurasian populations both in spectrum and frequency.

  19. A bidirectional shape memory alloy folding actuator

    International Nuclear Information System (INIS)

    Paik, Jamie K; Wood, Robert J

    2012-01-01

    This paper presents a low-profile bidirectional folding actuator based on annealed shape memory alloy sheets applicable for meso- and microscale systems. Despite the advantages of shape memory alloys—high strain, silent operation, and mechanical simplicity—their application is often limited to unidirectional operation. We present a bidirectional folding actuator that produces two opposing 180° motions. A laser-patterned nickel alloy (Inconel 600) heater localizes actuation to the folding sections. The actuator has a thin ( < 1 mm) profile, making it appropriate for use in robotic origami. Various design parameters and fabrication variants are described and experimentally explored in the actuator prototype. (paper)

  20. Miniaturization of Multiple-Layer Folded Patch Antennas

    DEFF Research Database (Denmark)

    Zhang, Jiaying; Breinbjerg, Olav

    2009-01-01

    A new folded patch antenna with multiple layers was developed in this paper, by folding the patch in a proper way, and a highly miniaturized antenna can be realized. The multiple layer patch with 4-layer and 6-layer are designed and evaluated at 2.4 GHz, 915 MHz, and 415 MHz respectively. Then a 4...... layer patch is fabricated and measured to validate the design method. The theoretical analysis, design and simulations, fabrications, as well as the measurements are presented in this paper. All the results show that the folded patch antenna is a good candidate in making a highly miniaturized compact...

  1. The Padul normal fault activity constrained by GPS data: Brittle extension orthogonal to folding in the central Betic Cordillera

    Science.gov (United States)

    Gil, Antonio J.; Galindo-Zaldívar, Jesús; Sanz de Galdeano, Carlos; Borque, Maria Jesús; Sánchez-Alzola, Alberto; Martinez-Martos, Manuel; Alfaro, Pedro

    2017-08-01

    The Padul Fault is located in the Central Betic Cordillera, formed in the framework of the NW-SE Eurasian-African plate convergence. In the Internal Zone, large E-W to NE-SW folds of western Sierra Nevada accommodated the greatest NW-SE shortening and uplift of the cordillera. However, GPS networks reveal a present-day dominant E-W to NE-SW extensional setting at surface. The Padul Fault is the most relevant and best exposed active normal fault that accommodates most of the NE-SW extension of the Central Betics. This WSW-wards dipping fault, formed by several segments of up to 7 km maximum length, favored the uplift of the Sierra Nevada footwall away from the Padul graben hanging wall. A non-permanent GPS network installed in 1999 constrains an average horizontal extensional rate of 0.5 mm/yr in N66°E direction. The fault length suggests that a (maximum) 6 magnitude earthquake may be expected, but the absence of instrumental or historical seismic events would indicate that fault activity occurs at least partially by creep. Striae on fault surfaces evidence normal-sinistral kinematics, suggesting that the Padul Fault may have been a main transfer fault of the westernmost end of the Sierra Nevada antiform. Nevertheless, GPS results evidence: (1) shortening in the Sierra Nevada antiform is in its latest stages, and (2) the present-day fault shows normal with minor oblique dextral displacements. The recent change in Padul fault kinematics will be related to the present-day dominance of the ENE-WSW regional extension versus NNW-SSE shortening that produced the uplift and northwestwards displacement of Sierra Nevada antiform. This region illustrates the importance of heterogeneous brittle extensional tectonics in the latest uplift stages of compressional orogens, as well as the interaction of folding during the development of faults at shallow crustal levels.

  2. High-Resolution Laser Photoacoustic Spectroscopy of OCS in the 12 000-13 000 cm -1 Region

    Science.gov (United States)

    Tranchart, S.; Hadj Bachir, I.; Huet, T. R.; Olafsson, A.; Destombes, J.-L.; Naı¨m, S.; Fayt, A.

    1999-08-01

    A spectrum of natural OCS has been recorded in the near-infrared region using the laser photoacoustic technique. The source is a titanium-sapphire laser pumped by an Ar+ laser. The tunable 1.5 W beam was sent through the photoacoustic cell. This windowless longitudinal resonant cell was designed with two λ/4 buffer volumes at both ends in order to reduce the noise and so to increase the sensitivity (αmin ≈ 10-9 cm-1). The spectrum of OCS, at a pressure of 90 Torr, has been recorded in the regions 11 953-12 084, 12 829-12 890, and 12 998-13 001 cm-1. In addition to the 0006-0000 band of 16O12C32S recently identified by Ch. Hornberger, B. Boor, R. Stuber, W. Demtröder, S. Naı̈m, and A. Fayt, J. Mol. Spectrosc. 179, 237-245, 1996, new weaker bands have been observed: 0405-0000, 1 1003-0000, 1006-0000, 1405-0000, 0206-0000, and 0116-0110, and also the 0006-0000 band of 16O12C34S. Effective state parameters are deduced from the band-by-band least-squares fits. The new data have also been introduced in the global analysis which takes into account the l-type resonance and the main anharmonic interactions and so allows a full understanding of the perturbations and the intensity transfers.

  3. On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

    Science.gov (United States)

    Wu, Chun; Shea, Joan-Emma

    2010-11-18

    FSD-1, a designed small ultrafast folder with a ββα fold, has been actively studied in the last few years as a model system for studying protein folding mechanisms and for testing of the accuracy of computational models. The suitability of this protein to describe the folding of naturally occurring α/β proteins has recently been challenged based on the observation that the melting transition is very broad, with ill-resolved baselines. Using molecular dynamics simulations with the AMBER protein force field (ff96) coupled with the implicit solvent model (IGB = 5), we shed new light into the nature of this transition and resolve the experimental controversies. We show that the melting transition corresponds to the melting of the protein as a whole, and not solely to the helix-coil transition. The breadth of the folding transition arises from the spread in the melting temperatures (from ∼325 K to ∼302 K) of the individual transitions: formation of the hydrophobic core, β-hairpin and tertiary fold, with the helix formed earlier. Our simulations initiated from an extended chain accurately predict the native structure, provide a reasonable estimate of the transition barrier height, and explicitly demonstrate the existence of multiple pathways and multiple transition states for folding. Our exhaustive sampling enables us to assess the quality of the Amber ff96/igb5 combination and reveals that while this force field can predict the correct native fold, it nonetheless overstabilizes the α-helix portion of the protein (Tm = ∼387K) as well as the denatured structures.

  4. Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

    Science.gov (United States)

    Zhou, Rui; Maisuradze, Gia G; Suñol, David; Todorovski, Toni; Macias, Maria J; Xiao, Yi; Scheraga, Harold A; Czaplewski, Cezary; Liwo, Adam

    2014-12-23

    To demonstrate the utility of the coarse-grained united-residue (UNRES) force field to compare experimental and computed kinetic data for folding proteins, we have performed long-time millisecond-timescale canonical Langevin molecular dynamics simulations of the triple β-strand from the Formin binding protein 28 WW domain and six nonnatural variants, using UNRES. The results have been compared with available experimental data in both a qualitative and a quantitative manner. Complexities of the folding pathways, which cannot be determined experimentally, were revealed. The folding mechanisms obtained from the simulated folding kinetics are in agreement with experimental results, with a few discrepancies for which we have accounted. The origins of single- and double-exponential kinetics and their correlations with two- and three-state folding scenarios are shown to be related to the relative barrier heights between the various states. The rate constants obtained from time profiles of the fractions of the native, intermediate, and unfolded structures, and the kinetic equations fitted to them, correlate with the experimental values; however, they are about three orders of magnitude larger than the experimental ones for most of the systems. These differences are in agreement with the timescale extension derived by scaling down the friction of water and averaging out the fast degrees of freedom when passing from all-atom to a coarse-grained representation. Our results indicate that the UNRES force field can provide accurate predictions of folding kinetics of these WW domains, often used as models for the study of the mechanisms of proein folding.

  5. Iterative Controller Tuning for Process with Fold Bifurcations

    DEFF Research Database (Denmark)

    Huusom, Jakob Kjøbsted; Poulsen, Niels Kjølstad; Jørgensen, Sten Bay

    2007-01-01

    Processes involving fold bifurcation are notoriously difficult to control in the vicinity of the fold where most often optimal productivity is achieved . In cases with limited process insight a model based control synthesis is not possible. This paper uses a data driven approach with an improved...... version of iterative feedback tuning to optimizing a closed loop performance criterion, as a systematic tool for tuning process with fold bifurcations....

  6. Structure of a Reptilian Adenovirus Reveals a Phage Tailspike Fold Stabilizing a Vertebrate Virus Capsid.

    Science.gov (United States)

    Menéndez-Conejero, Rosa; Nguyen, Thanh H; Singh, Abhimanyu K; Condezo, Gabriela N; Marschang, Rachel E; van Raaij, Mark J; San Martín, Carmen

    2017-10-03

    Although non-human adenoviruses (AdVs) might offer solutions to problems posed by human AdVs as therapeutic vectors, little is known about their basic biology. In particular, there are no structural studies on the complete virion of any AdV with a non-mammalian host. We combine mass spectrometry, cryo-electron microscopy, and protein crystallography to characterize the composition and structure of a snake AdV (SnAdV-1, Atadenovirus genus). SnAdV-1 particles contain the genus-specific proteins LH3, p32k, and LH2, a previously unrecognized structural component. Remarkably, the cementing protein LH3 has a trimeric β helix fold typical of bacteriophage host attachment proteins. The organization of minor coat proteins differs from that in human AdVs, correlating with higher thermostability in SnAdV-1. These findings add a new piece to the intriguing puzzle of virus evolution, hint at the use of cell entry pathways different from those in human AdVs, and will help development of new, thermostable SnAdV-1-based vectors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Vocal Fold Injection: Review of Indications, Techniques, and Materials for Augmentation

    OpenAIRE

    Mallur, Pavan S.; Rosen, Clark A.

    2010-01-01

    Vocal fold injection is a procedure that has over a 100 year history but was rarely done as short as 20 years ago. A renaissance has occurred with respect to vocal fold injection due to new technologies (visualization and materials) and new injection approaches. Awake, un-sedated vocal fold injection offers many distinct advantages for the treatment of glottal insufficiency (vocal fold paralysis, vocal fold paresis, vocal fold atrophy and vocal fold scar). A review of materials available and ...

  8. Experimental investigation into the mechanism of folding

    NARCIS (Netherlands)

    Kuenen, Ph.H.; Sitter, de L.U.

    1938-01-01

    The investigation of geological structures due to folding led de Sitter to form an opinion on the mechanical problems involved (Bibl. 7). His principal contention is that in simple cases the relative movements of particles with respect to eachother during deformation leading to a fold, have been

  9. Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin

    Science.gov (United States)

    Yamauchi, Masataka; Okumura, Hisashi

    2017-11-01

    We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method. We applied this method to a β-hairpin mini protein, chignolin. In this simulation, we observed not only the folded state but also the misfolded state. We calculated the temperature and pressure dependence of the fractions on the folded, misfolded, and unfolded states. Differences in partial molar enthalpy, internal energy, entropy, partial molar volume, and heat capacity were also determined and agreed well with experimental data. We observed a new phenomenon that misfolded chignolin becomes more stable under high-pressure conditions. We also revealed this mechanism of the stability as follows: TYR2 and TRP9 side chains cover the hydrogen bonds that form a β-hairpin structure. The hydrogen bonds are protected from the water molecules that approach the protein as the pressure increases.

  10. 4.0-A resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement.

    Science.gov (United States)

    Cong, Yao; Baker, Matthew L; Jakana, Joanita; Woolford, David; Miller, Erik J; Reissmann, Stefanie; Kumar, Ramya N; Redding-Johanson, Alyssa M; Batth, Tanveer S; Mukhopadhyay, Aindrila; Ludtke, Steven J; Frydman, Judith; Chiu, Wah

    2010-03-16

    The essential double-ring eukaryotic chaperonin TRiC/CCT (TCP1-ring complex or chaperonin containing TCP1) assists the folding of approximately 5-10% of the cellular proteome. Many TRiC substrates cannot be folded by other chaperonins from prokaryotes or archaea. These unique folding properties are likely linked to TRiC's unique heterooligomeric subunit organization, whereby each ring consists of eight different paralogous subunits in an arrangement that remains uncertain. Using single particle cryo-EM without imposing symmetry, we determined the mammalian TRiC structure at 4.7-A resolution. This revealed the existence of a 2-fold axis between its two rings resulting in two homotypic subunit interactions across the rings. A subsequent 2-fold symmetrized map yielded a 4.0-A resolution structure that evinces the densities of a large fraction of side chains, loops, and insertions. These features permitted unambiguous identification of all eight individual subunits, despite their sequence similarity. Independent biochemical near-neighbor analysis supports our cryo-EM derived TRiC subunit arrangement. We obtained a Calpha backbone model for each subunit from an initial homology model refined against the cryo-EM density. A subsequently optimized atomic model for a subunit showed approximately 95% of the main chain dihedral angles in the allowable regions of the Ramachandran plot. The determination of the TRiC subunit arrangement opens the way to understand its unique function and mechanism. In particular, an unevenly distributed positively charged wall lining the closed folding chamber of TRiC differs strikingly from that of prokaryotic and archaeal chaperonins. These interior surface chemical properties likely play an important role in TRiC's cellular substrate specificity.

  11. SDEM modelling of fault-propagation folding

    DEFF Research Database (Denmark)

    Clausen, O.R.; Egholm, D.L.; Poulsen, Jane Bang

    2009-01-01

    and variations in Mohr-Coulomb parameters including internal friction. Using SDEM modelling, we have mapped the propagation of the tip-line of the fault, as well as the evolution of the fold geometry across sedimentary layers of contrasting rheological parameters, as a function of the increased offset......Understanding the dynamics and kinematics of fault-propagation-folding is important for evaluating the associated hydrocarbon play, for accomplishing reliable section balancing (structural reconstruction), and for assessing seismic hazards. Accordingly, the deformation style of fault-propagation...... a precise indication of when faults develop and hence also the sequential evolution of secondary faults. Here we focus on the generation of a fault -propagated fold with a reverse sense of motion at the master fault, and varying only the dip of the master fault and the mechanical behaviour of the deformed...

  12. Endoscopic Anatomy of the Tensor Fold and Anterior Attic.

    Science.gov (United States)

    Li, Bin; Doan, Phi; Gruhl, Robert R; Rubini, Alessia; Marchioni, Daniele; Fina, Manuela

    2018-02-01

    Objectives The objectives of the study were to (1) study the anatomical variations of the tensor fold and its anatomic relation with transverse crest, supratubal recess, and anterior epitympanic space and (2) explore the most appropriate endoscopic surgical approach to each type of the tensor fold variants. Study Design Cadaver dissection study. Setting Temporal bone dissection laboratory. Subjects and Methods Twenty-eight human temporal bones (26 preserved and 2 fresh) were dissected through an endoscopic transcanal approach between September 2016 and June 2017. The anatomical variations of the tensor fold, transverse crest, supratubal recess, and anterior epitympanic space were studied before and after removing ossicles. Results Three different tensor fold orientations were observed: vertical (type A, 11/28, 39.3%) with attachment to the transverse crest, oblique (type B, 13/28, 46.4%) with attachment to the anterior tegmen tympani, and horizontal (type C, 4/28, 14.3%) with attachment to the tensor tympani canal. The tensor fold was a complete membrane in 20 of 28 (71.4%) specimens, preventing direct ventilation between the supratubal recess and anterior epitympanic space. We identified 3 surgical endoscopic approaches, which allowed visualization of the tensor fold without removing the ossicles. Conclusions The orientation of the tensor fold is the determining structure that dictates the conformation and limits of the epitympanic space. We propose a classification of the tensor fold based on 3 anatomical variants. We also describe 3 different minimally invasive endoscopic approaches to identify the orientation of the tensor fold while maintaining ossicular chain continuity.

  13. A nomenclature paradigm for benign midmembranous vocal fold lesions.

    Science.gov (United States)

    Rosen, Clark A; Gartner-Schmidt, Jackie; Hathaway, Bridget; Simpson, C Blake; Postma, Gregory N; Courey, Mark; Sataloff, Robert T

    2012-06-01

    There is a significant lack of uniform agreement regarding nomenclature for benign vocal fold lesions (BVFLs). This confusion results in difficulty for clinicians communicating with their patients and with each other. In addition, BVFL research and comparison of treatment methods are hampered by the lack of a detailed and uniform BVFL nomenclature. Clinical consensus conferences were held to develop an initial BVFL nomenclature paradigm. Perceptual video analysis was performed to validate the stroboscopy component of the paradigm. The culmination of the consensus conferences and the video-perceptual analysis was used to evaluate the BVFL nomenclature paradigm using a retrospective review of patients with BVFL. An initial BVFL nomenclature paradigm was proposed utilizing detailed definitions relating to vocal fold lesion morphology, stroboscopy, response to voice therapy and intraoperative findings. Video-perceptual analysis of stroboscopy demonstrated that the proposed binary stroboscopy system used in the BVFL nomenclature paradigm was valid and widely applicable. Retrospective review of 45 patients with BVFL followed to the conclusion of treatment demonstrated that slight modifications of the initial BVFL nomenclature paradigm were required. With the modified BVFL nomenclature paradigm, 96% of the patients fit into the predicted pattern and definitions of the BVFL nomenclature system. This study has validated a multidimensional BVFL nomenclature paradigm. This vocal fold nomenclature paradigm includes nine distinct vocal fold lesions: vocal fold nodules, vocal fold polyp, pseudocyst, vocal fold cyst (subepithelial or ligament), nonspecific vocal fold lesion, vocal fold fibrous mass (subepithelial or ligament), and reactive lesion. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

  14. Earthworm Lumbricus rubellus MT-2: Metal Binding and Protein Folding of a True Cadmium-MT

    Directory of Open Access Journals (Sweden)

    Gregory R. Kowald

    2016-01-01

    Full Text Available Earthworms express, as most animals, metallothioneins (MTs—small, cysteine-rich proteins that bind d10 metal ions (Zn(II, Cd(II, or Cu(I in clusters. Three MT homologues are known for Lumbricus rubellus, the common red earthworm, one of which, wMT-2, is strongly induced by exposure of worms to cadmium. This study concerns composition, metal binding affinity and metal-dependent protein folding of wMT-2 expressed recombinantly and purified in the presence of Cd(II and Zn(II. Crucially, whilst a single Cd7wMT-2 species was isolated from wMT-2-expressing E. coli cultures supplemented with Cd(II, expressions in the presence of Zn(II yielded mixtures. The average affinities of wMT-2 determined for either Cd(II or Zn(II are both within normal ranges for MTs; hence, differential behaviour cannot be explained on the basis of overall affinity. Therefore, the protein folding properties of Cd- and Zn-wMT-2 were compared by 1H NMR spectroscopy. This comparison revealed that the protein fold is better defined in the presence of cadmium than in the presence of zinc. These differences in folding and dynamics may be at the root of the differential behaviour of the cadmium- and zinc-bound protein in vitro, and may ultimately also help in distinguishing zinc and cadmium in the earthworm in vivo.

  15. Benign Lesions of The Vocal Fold

    Directory of Open Access Journals (Sweden)

    Ozgur Surmelioglu

    2013-02-01

    Full Text Available Benign lesions of vocal folds are common disorders. Fifty percent of patients who have sound complaints are found to have these lesions after endoscopic and stroboscopic examinations. Benign vocal fold diseases are primarily caused by vibratory trauma. However they may also occur as a result of viral infections and congenital causes. These lesions are often presented with the complaints of dysphonia. [Archives Medical Review Journal 2013; 22(1.000: 86-95

  16. Detachments in Shale: Controlling Characteristics on Fold-Thrust Belt Style

    Science.gov (United States)

    Hansberry, Rowan; King, Ros; Collins, Alan; Morley, Chris

    2013-04-01

    Fold-thrust belts occur across multiple tectonic settings where thin-skinned deformation is accommodated by one or more detachment zones, both basal and within the fold-thrust belt. These fold-thrust belts exhibit considerable variation in structural style and vergence depending on the characteristics (e.g. strength, thickness, and lithology) and number of detachment zones. Shale as a detachment lithology is intrinsically weaker than more competent silts and sands; however, it can be further weakened by high pore pressures, reducing resistance to sliding and; high temperatures, altering the rheology of the detachment. Despite the implications for petroleum exploration and natural hazard assessment the precise nature by which detachments in shale control and are involved in deformation in fold-thrust belts is poorly understood. Present-day active basal detachment zones are usually located in inaccessible submarine regions. Therefore, this project employs field observations and sample analysis of ancient, exhumed analogues to document the nature of shale detachments (e.g. thickness, lithology, dip and dip direction, deformational temperature and thrust propagation rates) at field sites in Thailand, Norway and New Zealand. X-ray diffraction analysis of illite crystallinity and oxygen stable isotopes analysis are used as a proxy for deformational temperature whilst electron-backscatter diffraction analysis is used to constrain microstructural deformational patterns. K-Ar dating of synkinematic clay fault gouges is being applied to date the final stages of activity on individual faults with a view to constraining thrust activation sequences. It is not possible to directly measure palaeo-data for some key detachment parameters, such as pore pressure and coefficients of friction. However, the use of critical taper wedge theory has been used to successfully infer internal and basal coefficients of friction and depth-normalized pore pressure within a wedge and at its base

  17. Structural, micro-structural and kinematic analyses of channel flow in the Karmostaj salt diapir in the Zagros foreland folded belt, Fars province, Iran

    Science.gov (United States)

    Sarkarinejad, Khalil; Sarshar, Maryam Asadi; Adineh, Sadegh

    2018-02-01

    One of the main characteristic of the Zagros foreland fold-and-thrust belt and the Zagros foreland folded belt are wide distributions of surface extrusion from the Hormuz salt diapirs. This study examines the structure and kinematic of channel flow in the Karmostaj salt diapir in the southwestern part of the Zagros foreland folded belt. This diapir has reached the surface as a result of the channel flow mechanism and has extruded in the southern limb of the Kuh-Gach anticline which is an asymmetric décollement fold with convergence to the south. Structural and microstructural studies and quantitative finite strain (Rs) and kinematic vorticity number (Wk) analyses were carried out within this salt diapir and its namakier. This was in order to investigate the structural evolution in the salt diapiric system, the characteristics and mechanism of the salt flow and the distribution of flow regimes within the salt diapir and interaction of regional tectonics and salt diaprism. The extruded salt has developed a flow foliation sub-parallel to the remnant bedding recorded by different colors, a variety of internal folds including symmetrical and asymmetrical folds and interference fold patterns, shear zones, and boudins. These structures were used to analyze mechanisms and history of diapiric flow and extrusion. The microstructures, reveal various deformation mechanisms in various parts of salt diapir. The measurements of finite strain show that Rs values in the margin of salt diapir are higher than within its namakier which is consistent with the results of structural studies. Mean kinematic vorticity number (Wm) measured in steady state deformation of diapir and namakier is Wm = 0.45-0.48 ± 0.13. The estimated mean finite deformation (Wm) values indicate that 67.8% pure shear and 32.2% simple shear deformation were involved; the implications of which are discussed. The vorticity of flow indicates that in the early stage of growth, Poiseuille flow was the dominate

  18. Laryngeal ultrasound and pediatric vocal fold nodules.

    Science.gov (United States)

    Ongkasuwan, Julina; Devore, Danielle; Hollas, Sarah; Jones, Jeremy; Tran, Brandon

    2017-03-01

    The term vocal fold nodules refers to bilateral thickening of the membranous folds with minimal impairment of the vibratory properties of the mucosa. Nodules are thought to be related to repetitive mechanical stress, associated with voice use patterns. Diagnosis is typically made in the office via either rigid or flexible laryngeal stroboscopy. Depending on the individual child, obtaining an optimal view of the larynx can be difficult if not impossible. Recent advances in high-frequency ultrasonography allows for transcervical examination of laryngeal structures. The goal of this project was to determine if laryngeal ultrasound (LUS) can be used to identify vocal fold nodules in dysphonic children. Prospective case-control study in which the patient acted as his or her own control. Forty-six pediatric patients were recruited for participation in this study; the mean age was 4.8 years. Twenty-three did not have any vocal fold lesions and 23 had a diagnosis of vocal fold nodules on laryngeal stroboscopy. Recorded LUSs were reviewed by two pediatric radiologists who were blinded to the nodule status. There was substantial inter-rater agreement (κ = 0.70, 95% confidence interval [CI]: 0.50-0.89) between the two radiologists regarding the presence of nodules. There was also substantial agreement (κ = 0.87, 95% CI: 0.72-1) between LUS and laryngeal stroboscopy. Sensitivity of LUS was 100% (95% CI: 85%-100%) and specificity was 87% (95% CI: 66%-97%). LUS can be used to identify vocal fold nodules in children with substantial agreement with laryngeal stroboscopy. 3b Laryngoscope, 127:676-678, 2017. © 2016 The American Laryngological, Rhinological and Otological Society, Inc.

  19. Diagnostic and therapeutic pitfalls in benign vocal fold diseases

    Science.gov (United States)

    Bohlender, Jörg

    2013-01-01

    More than half of patients presenting with hoarseness show benign vocal fold changes. The clinician should be familiar with the anatomy, physiology and functional aspects of voice disorders and also the modern diagnostic and therapeutic possibilities in order to ensure an optimal and patient specific management. This review article focuses on the diagnostic and therapeutic limitations and difficulties of treatment of benign vocal fold tumors, the management and prevention of scarred vocal folds and the issue of unilateral vocal fold paresis. PMID:24403969

  20. Cortical thickness, surface area, and folding alterations in male youths with conduct disorder and varying levels of callous–unemotional traits

    Directory of Open Access Journals (Sweden)

    Graeme Fairchild

    2015-01-01

    Conclusions: Cortical thinning in the superior temporal gyrus may contribute to the social cognitive impairments displayed by youths with CD, whereas reduced OFC SA may lead to impairments in emotion regulation and reward processing in youths with CD. The increased cortical folding observed in the insula may reflect a maturational delay in this region and could mediate the link between CU traits and empathy deficits. Altered cortical folding was observed in childhood-onset and adolescence-onset forms of CD.

  1. Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

    Science.gov (United States)

    Chen, Charles H; Wiedman, Gregory; Khan, Ayesha; Ulmschneider, Martin B

    2014-09-01

    Unbiased molecular simulation is a powerful tool to study the atomic details driving functional structural changes or folding pathways of highly fluid systems, which present great challenges experimentally. Here we apply unbiased long-timescale molecular dynamics simulation to study the ab initio folding and partitioning of melittin, a template amphiphilic membrane active peptide. The simulations reveal that the peptide binds strongly to the lipid bilayer in an unstructured configuration. Interfacial folding results in a localized bilayer deformation. Akin to purely hydrophobic transmembrane segments the surface bound native helical conformer is highly resistant against thermal denaturation. Circular dichroism spectroscopy experiments confirm the strong binding and thermostability of the peptide. The study highlights the utility of molecular dynamics simulations for studying transient mechanisms in fluid lipid bilayer systems. This article is part of a Special Issue entitled: Interfacially Active Peptides and Proteins. Guest Editors: William C. Wimley and Kalina Hristova. Copyright © 2014. Published by Elsevier B.V.

  2. Negative Charge Neutralization in the Loops and Turns of Outer Membrane Phospholipase A Impacts Folding Hysteresis at Neutral pH.

    Science.gov (United States)

    McDonald, Sarah K; Fleming, Karen G

    2016-11-08

    Hysteresis in equilibrium protein folding titrations is an experimental barrier that must be overcome to extract meaningful thermodynamic quantities. Traditional approaches to solving this problem involve testing a spectrum of solution conditions to find ones that achieve path independence. Through this procedure, a specific pH of 3.8 was required to achieve path independence for the water-to-bilayer equilibrium folding of outer membrane protein OmpLA. We hypothesized that the neutralization of negatively charged side chains (Asp and Glu) at pH 3.8 could be the physical basis for path-independent folding at this pH. To test this idea, we engineered variants of OmpLA with Asp → Asn and Glu → Gln mutations to neutralize the negative charges within various regions of the protein and tested for reversible folding at neutral pH. Although not fully resolved, our results show that these mutations in the periplasmic turns and extracellular loops are responsible for 60% of the hysteresis in wild-type folding. Overall, our study suggests that negative charges impact the folding hysteresis in outer membrane proteins and their neutralization may aid in protein engineering applications.

  3. Physical mapping of a commonly deleted region, the site of a candidate tumor suppressor gene, at 12q22 in human male germ cell tumors

    Energy Technology Data Exchange (ETDEWEB)

    Murty, V.V.V.S.; Bosl, G.J.; Chaganti, R.S.K. [Memorial Sloan-Kettering Cancer Center, New York, NY (United States)] [and others

    1996-08-01

    A candidate tumor suppressor gene (TSG) site at 12q22 characterized by a high frequency of loss of heterozygosity (LOH) and a homozygous deletion has previously (LOH) and a homozygous deletion has previously been reported in human male germ cell tumors (GCTs). In a detailed deletion mapping analysis of 67 normal-tumor DNAs utilizing 20 polymorphic markers mapped to 12q22-q24, we identified the limits of the minimal region of deletion at 12q22 between D12S377 (priximal) and D12S296 (distal). We have constructed a YAC contig map of a 3-cM region of this band between the proximal marker D12S101 and the distal marker D12S346, which contained the minimal region of deletion in GCTs. The map is composed of 53 overlapping YACs and 3 cosmids onto which 25 polymorphic and nonpolymorphic sequence-tagged sites (STSs) were placed in a unique order. The size of the minimal region of deletion was approximately 2 Mb from overlapping, nonchimeric YACs that spanned the region. We also developed a radiation hybrid (RH) map of the region between D12S101 and D12S346 containing 17 loci. The consensus order developed by RH mapping is in good agreement with the YAC STS-content map order. The RH map estimated the distance between D12S101 and D12S346 to be 246 cR{sub 8000} and the minimal region of deletion to be 141 cR{sub 8000}. In addition, four genes that were previously mapped to 12q22 have been excluded as candidate genes. The leads gained from the deletion mapping and physical maps should expedite the isolation and characterization of the TSG at 12q22. 35 refs., 4 figs., 2 tabs.

  4. Detection of genomic variation by selection of a 9 mb DNA region and high throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Sergey I Nikolaev

    Full Text Available Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb and 7 (1.1 Mb from an individual from the International HapMap Project (NA12872. We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage > or = 4-fold, and 97.9% concordant in regions with coverage > or = 15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants.

  5. A 2 GS/s 8-bit folding and interpolating ADC in 90 nm CMOS

    International Nuclear Information System (INIS)

    He Wenwei; Meng Qiao; Zhang Yi; Tang Kai

    2014-01-01

    A single-channel 2 GS/s 8-bit analog-to-digital converter in 90 nm CMOS process technology is presented. It utilizes cascade folding architecture, which incorporates an additional inter-stage sample-and-hold amplifier between the folding circuits to enhance the quantization time. It also uses the foreground on-chip digital-assisted calibration circuit to improve the linearity of the circuit. The post simulation results demonstrate that it has a differential nonlinearity < ±0.3 LSB and an integral nonlinearity < ±0.25 LSB at the Nyquist frequency. Moreover, 7.338 effective numbers of bits can be achieved at 2 GSPS. The whole chip area is 0.88 × 0.88 mm 2 with the pad. It consumes 210 mW from a 1.2 V single supply. (semiconductor integrated circuits)

  6. Monadic Maps and Folds for Arbitrary Datatypes

    NARCIS (Netherlands)

    Fokkinga, M.M.

    Each datatype constructor comes equiped not only with a so-called map and fold (catamorphism), as is widely known, but, under some condition, also with a kind of map and fold that are related to an arbitrary given monad. This result follows from the preservation of initiality under lifting

  7. Systemic injection of kainic acid: Gliosis in olfactory and limbic brain regions quantified with [3H]PK 11195 binding autoradiography

    International Nuclear Information System (INIS)

    Altar, C.A.; Baudry, M.

    1990-01-01

    Neurodegenerative diseases may result from excessive stimulation of excitatory amino acid receptors by endogenous ligands. Because neuronal degeneration is associated with glial proliferation and hypertrophy, the degenerative changes throughout rat brain following the systemic administration of kainic acid (12 mg/kg) were mapped with quantitative autoradiography of [3H]PK 11195. This radioligand binds to a mitochondrial benzodiazepine binding site (MBBS) on microglia and astrocytes. Analysis of eight horizontal and four coronal brain levels revealed up to 16-fold increases in [3H]PK 11195 binding from 1 to 5 weeks but not 1 day after kainate injection. Increases in [3H]PK 11195 binding were predominantly in ventral limbic brain regions and olfactory projections to neocortical areas, with the olfactory cortex greater than subiculum/CA1 greater than anterior olfactory nucleus, medial thalamic nucleus, and piriform cortex greater than cingulate cortex and rostral hippocampus greater than dentate gyrus, septum, and amygdala greater than entorhinal cortex and temporal cortex. Little or no enhancement of [3H]PK 11195 binding was observed in numerous regions including the caudate-putamen, substantia nigra, nucleus accumbens, olfactory tubercle, cerebellum, thalamic nuclei, choroid plexus, medulla, parietal or occipital cortex, or pons. A 2-fold greater extent of neurodegeneration was obtained in ventral portions of the olfactory bulb, entorhinal cortex, temporal cortex, and dentate gyrus compared with the dorsal portions of these structures. The pattern of increase in [3H]PK 11195 binding closely matched the patterns of neuronal degeneration reported following parenteral kainate injection. These findings strengthen the notion that quantitative autoradiography of [3H]PK 11195 is a valuable tool to quantify the extent of neuronal degeneration

  8. Ultra-high-resolution C-arm flat-detector CT angiography evaluation reveals 3-fold higher association rate for sporadic intracranial cavernous malformations and developmental venous anomalies: a retrospective study in consecutive 58 patients with 60 cavernous malformations

    Energy Technology Data Exchange (ETDEWEB)

    Kocak, Burak [Aksaray State Hospital, Department of Radiology, Aksaray (Turkey); Kizilkilic, Osman; Kocer, Naci; Islak, Civan [Istanbul University, Department of Radiology, Cerrahpasa Medical Faculty, Istanbul (Turkey); Oz, Buge; Bakkaloglu, Dogu Vuralli [Istanbul University, Department of Pathology, Cerrahpasa Medical Faculty, Istanbul (Turkey); Isler, Cihan [Istanbul University, Department of Neurosurgery, Cerrahpasa Medical Faculty, Istanbul (Turkey)

    2017-06-15

    The imaging and surgical literature has confusing association rates for the association between sporadic intracranial cavernous malformations (CMs) and developmental venous anomalies (DVAs). In this study, our purpose was to determine the association rate using ultra-high-resolution C-arm flat-detector CT angiography (FDCTA) and compare it with literature. Fifty-eight patients with 60 sporadic intracranial CMs that underwent an FDCTA study were included in our retrospective study. Re-evaluation of radiological data was performed based on the criteria defined by authors. Isotropic volumetric reconstructions with ultra-high resolution (voxel size of 102 μm{sup 3} for initial; 67 μm{sup 3} and 32 μm{sup 3} for further evaluation) were used for assessment. Sixteen patients underwent surgery for excision of their CMs. Fifty-one of all patients (87.9 %) were associated with a DVA. Undefined local venous structures (UD-LVSs) were observed in the remaining 7 patients (12.1 %). The strength of interobserver agreement was excellent [kappa(k) coefficient = 0.923]. Ultra-high-resolution FDCTA evaluation of CMs and DVAs reveals 3-fold higher association rate compared to the literature. FDCTA for patients with sporadic CMs could help identify the associated DVAs that remained undetected or unclear with other imaging modalities, which can be useful in decision-making processes, planning surgery, and during operation. (orig.)

  9. Antibody response in vaccinated pregnant mares to recent G3BP[12] and G14P[12] equine rotaviruses

    Directory of Open Access Journals (Sweden)

    Nemoto Manabu

    2012-11-01

    Full Text Available Abstract Background Both the G3P[12] and the G14P[12] type of equine group A rotavirus (RVA have recently become predominant in many countries, including Japan. G3 types are classified further into G3A and G3B. The G3A viruses have been circulating in Europe, Australia, and Argentina, and the G3B viruses have been circulating in Japan. However, only an inactivated vaccine containing a single G3BP[12] strain is commercially available in Japan. To assess the efficacy of the current vaccine against recently circulating equine RVA strains, we examined antibody responses in pregnant mares to recent G3BP[12] and G14P[12] strains by virus neutralization test. Findings After vaccination in five pregnant mares, the geometric mean serum titers of virus-neutralizing antibody to recent G3BP[12] strains increased 5.3- to 7.0-fold and were similar to that against homologous vaccine strain. Moreover, antibody titers to recent G14P[12] strains were also increased 3.0- to 3.5-fold. Conclusions These results suggest that inoculation of mares with the current vaccine should provide foals with virus-neutralizing antibodies against not only the G3BP[12] but also the G14P[12] RVA strain via the colostrum.

  10. Characterization of race 65 of Colletotrichum lindemuthianum by sequencing ITS regions

    Directory of Open Access Journals (Sweden)

    Marcela Coelho

    2016-09-01

    Full Text Available The present work aimed characterize isolates of C. lindemuthianum race 65 from different regions in Brazil by ITS sequencing. A total of 17 isolates of race 65, collected in the states of Mato Grosso, Minas Gerais, Paraná, Santa Catarina and São Paulo, were studied. Analysis of the sequences of isolates 8, 9, 12, 14 and 15 revealed the presence of two single nucleotide polymorphisms (SNPs in the ITS1 region at the same positions. These isolates, when analyzed together with the sequence of isolate 17, revealed a SNP in the ITS2 region. The highest genetic dissimilarity, observed between isolates 11 and  3 and between isolates 11 and 10, was 0.772. In turn, isolates 7 and 2 were the most similar, with a value of 0.002 for genetic distance. The phylogenetic tree obtained based on the sequences of the ITS1 and ITS2 regions revealed the formation of two groups, one with a subgroup. The results reveal high molecular variability among isolates of race 65 of C. lindemuthianum.

  11. Analysis of high-fold gamma data

    International Nuclear Information System (INIS)

    Radford, D. C.; Cromaz, M.; Beyer, C. J.

    1999-01-01

    Historically, γ-γ and γ-γ-γ coincidence spectra were utilized to build nuclear level schemes. With the development of large detector arrays, it has became possible to analyze higher fold coincidence data sets. This paper briefly reports on software to analyze 4-fold coincidence data sets that allows creation of 4-fold histograms (hypercubes) of at least 1024 channels per side (corresponding to a 43 gigachannel data space) that will fit onto a few gigabytes of disk space, and extraction of triple-gated spectra in a few seconds. Future detector arrays may have even much higher efficiencies, and detect as many as 15 or 20 γ rays simultaneously; such data will require very different algorithms for storage and analysis. Difficulties inherent in the analysis of such data are discussed, and two possible new solutions are presented, namely adaptive list-mode systems and 'list-list-mode' storage

  12. Acinetobacter baumannii FolD ligand complexes --potent inhibitors of folate metabolism and a re-evaluation of the structure of LY374571.

    Science.gov (United States)

    Eadsforth, Thomas C; Maluf, Fernando V; Hunter, William N

    2012-12-01

    The bifunctional N(5),N(10)-methylenetetrahydrofolate dehydrogenase/cyclohydrolase (DHCH or FolD), which is widely distributed in prokaryotes and eukaryotes, is involved in the biosynthesis of folate cofactors that are essential for growth and cellular development. The enzyme activities represent a potential antimicrobial drug target. We have characterized the kinetic properties of FolD from the Gram-negative pathogen Acinetobacter baumanni and determined high-resolution crystal structures of complexes with a cofactor and two potent inhibitors. The data reveal new details with respect to the molecular basis of catalysis and potent inhibition. A unexpected finding was that our crystallographic data revealed a different structure for LY374571 (an inhibitor studied as an antifolate) than that previously published. The implications of this observation are discussed. © 2012 The Authors Journal compilation © 2012 FEBS.

  13. Folds in multilayered rocks of Proterozoic age, Rajasthan, India

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Johnson and Johnson 2002 etc) shows that the fold shape modification may be brought about by buckling and flattening operating simultaneously throughout the development of fold. In the present paper a series of F1 folds devel- oped in slates with interlayered alternations with quartzite of Proterozoic age and unaffected ...

  14. Self-folding polymeric containers for encapsulation and delivery of drugs.

    Science.gov (United States)

    Fernandes, Rohan; Gracias, David H

    2012-11-01

    Self-folding broadly refers to self-assembly processes wherein thin films or interconnected planar templates curve, roll-up or fold into three dimensional (3D) structures such as cylindrical tubes, spirals, corrugated sheets or polyhedra. The process has been demonstrated with metallic, semiconducting and polymeric films and has been used to curve tubes with diameters as small as 2nm and fold polyhedra as small as 100nm, with a surface patterning resolution of 15nm. Self-folding methods are important for drug delivery applications since they provide a means to realize 3D, biocompatible, all-polymeric containers with well-tailored composition, size, shape, wall thickness, porosity, surface patterns and chemistry. Self-folding is also a highly parallel process, and it is possible to encapsulate or self-load therapeutic cargo during assembly. A variety of therapeutic cargos such as small molecules, peptides, proteins, bacteria, fungi and mammalian cells have been encapsulated in self-folded polymeric containers. In this review, we focus on self-folding of all-polymeric containers. We discuss the mechanistic aspects of self-folding of polymeric containers driven by differential stresses or surface tension forces, the applications of self-folding polymers in drug delivery and we outline future challenges. Copyright © 2012 Elsevier B.V. All rights reserved.

  15. Competition between folding and glycosylation in the endoplasmic reticulum

    DEFF Research Database (Denmark)

    Holst, B; Bruun, A W; Kielland-Brandt, Morten

    1996-01-01

    Using carboxypeptidase Y in Saccharomyces cerevisiae as a model system, the in vivo relationship between protein folding and N-glycosylation was studied. Seven new sites for N-glycosylation were introduced at positions buried in the folded protein structure. The level of glycosylation of such new...... acceptor sites. In some cases, all the newly synthesized mutant protein was modified at the novel site while in others no modification took place. In the most interesting category of mutants, the level of glycosylation was dependent on the conditions for folding. This shows that folding and glycosylation...

  16. Studies of protein structure in solution and protein folding using synchrotron small-angle x-ray scattering

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Lingling [Stanford Univ., CA (United States)

    1996-04-01

    Synchrotron small angle x-ray scattering (SAXS) has been applied to the structural study of several biological systems, including the nitrogenase complex, the heat shock cognate protein (hsc70), and lysozyme folding. The structural information revealed from the SAXS experiments is complementary to information obtained by other physical and biochemical methods, and adds to our knowledge and understanding of these systems.

  17. Vocal Fold Collision Modeling

    DEFF Research Database (Denmark)

    Granados, Alba; Brunskog, Jonas; Misztal, M. K.

    2015-01-01

    When vocal folds vibrate at normal speaking frequencies, collisions occurs. The numerics and formulations behind a position-based continuum model of contact is an active field of research in the contact mechanics community. In this paper, a frictionless three-dimensional finite element model...

  18. The four-fold way

    International Nuclear Information System (INIS)

    Terazawa, H.

    1986-01-01

    The four-fold way is proposed in a minimal composite model of quarks and leptons. Various new pictures and consequences are presented and discussed. They include 1) generation, 2) quark-lepton mass spectrum, 3) quark mixing, 4) supersymmetry, 5) effective gauge theory. (author)

  19. Structure and Evolution of the Lunar Procellarum Region as Revealed by GRAIL Gravity Data

    Science.gov (United States)

    Andrews-Hanna, Jeffrey C.; Besserer, Jonathan; Head, James W., III; Howett, Carly J. A.; Kiefer, Walter S.; Lucey, Paul J.; McGovern, Patrick J.; Melosh, H. Jay; Neumann, Gregory A.; Phillips, Roger J.; hide

    2014-01-01

    The Procellarum region is a broad area on the nearside of the Moon that is characterized by low elevations, thin crust, and high surface concentrations of the heat-producing elements uranium, thorium, and potassium. The Procellarum region has been interpreted as an ancient impact basin approximately 3200 km in diameter, though supporting evidence at the surface would have been largely obscured as a result of the great antiquity and poor preservation of any diagnostic features. Here we use data from the Gravity Recovery and Interior Laboratory (GRAIL) mission to examine the subsurface structure of Procellarum. The Bouguer gravity anomalies and gravity gradients reveal a pattern of narrow linear anomalies that border the Procellarum region and are interpreted to be the frozen remnants of lava-filled rifts and the underlying feeder dikes that served as the magma plumbing system for much of the nearside mare volcanism. The discontinuous surface structures that were earlier interpreted as remnants of an impact basin rim are shown in GRAIL data to be a part of this continuous set of quasi-rectangular border structures with angular intersections, contrary to the expected circular or elliptical shape of an impact basin. The spatial pattern of magmatic-tectonic structures bounding Procellarum is consistent with their formation in response to thermal stresses produced by the differential cooling of the province relative to its surroundings, coupled with magmatic activity driven by the elevated heat flux in the region.

  20. Revealing the cerebral regions and networks mediating vulnerability to depression: oxidative metabolism mapping of rat brain.

    Science.gov (United States)

    Harro, Jaanus; Kanarik, Margus; Kaart, Tanel; Matrov, Denis; Kõiv, Kadri; Mällo, Tanel; Del Río, Joaquin; Tordera, Rosa M; Ramirez, Maria J

    2014-07-01

    The large variety of available animal models has revealed much on the neurobiology of depression, but each model appears as specific to a significant extent, and distinction between stress response, pathogenesis of depression and underlying vulnerability is difficult to make. Evidence from epidemiological studies suggests that depression occurs in biologically predisposed subjects under impact of adverse life events. We applied the diathesis-stress concept to reveal brain regions and functional networks that mediate vulnerability to depression and response to chronic stress by collapsing data on cerebral long term neuronal activity as measured by cytochrome c oxidase histochemistry in distinct animal models. Rats were rendered vulnerable to depression either by partial serotonergic lesion or by maternal deprivation, or selected for a vulnerable phenotype (low positive affect, low novelty-related activity or high hedonic response). Environmental adversity was brought about by applying chronic variable stress or chronic social defeat. Several brain regions, most significantly median raphe, habenula, retrosplenial cortex and reticular thalamus, were universally implicated in long-term metabolic stress response, vulnerability to depression, or both. Vulnerability was associated with higher oxidative metabolism levels as compared to resilience to chronic stress. Chronic stress, in contrast, had three distinct patterns of effect on oxidative metabolism in vulnerable vs. resilient animals. In general, associations between regional activities in several brain circuits were strongest in vulnerable animals, and chronic stress disrupted this interrelatedness. These findings highlight networks that underlie resilience to stress, and the distinct response to stress that occurs in vulnerable subjects. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. Balancing cross-sections combining field work and remote sensing data using LithoTect software in the Zagros fold-and-thrust belt, N Iraq.

    Science.gov (United States)

    Reif, Daniel; Grasemann, Bernhard; Lockhart, Duncan

    2010-05-01

    The Zagros fold-and-thrust belt has formed in detached Phanerozoic sedimentary cover rocks above a shortened crystalline Precambrian basement and evolved through the Late Cretaceous to Miocene collision between the Arabian and Eurasian plate, during which the Neotethys oceanic basin was closed. Deformation is partitioned in SW directed folding and thrusting of the sediments and NW-SE to N-S trending dextral strike slip faults. The sub-cylindrical doubly-plunging fold trains with wavelengths of 5 - 10 km host more than half of the world's hydrocarbon reserves in mostly anticlinal traps. Generally the Zagros is divided into three NW-SE striking tectonic units: the Zagros Imbricate Zone, the Zagros Simply Folded Belt and the Zagros Foredeep. This work presents a balanced cross-section through the Simply Folded Belt, NE of the city of Erbil (Kurdistan, Iraq). The regional stratigraphy comprises mainly Cretaceous to Cenozoic folded sediments consisting of massive, carbonate rocks (limestones, dolomites), reacting as competent layers during folding compared to the incompetent behavior of interlayered siltstones, claystones and marls. Although the overall security situation in Kurdistan is much better than in the rest of Iraq, structural field mapping was restricted to asphalt streets, mainly because of the contamination of the area with landmines and unexploded ordnance. In order to extend the structural measurements statistically over the investigated area, we used a newly developed software tool (www.terramath.com) for interactive structural mapping of spatial orientations (i.e. dip direction and dip angles) of the sedimentary beddings from digital elevation models. Structural field data and computed measurements where integrated and projected in NE-SW striking balanced cross-sections perpendicular to the regional trend of the fold axes. We used the software LithoTect (www.geologicsystems.com) for the restoration of the cross-sections. Depending on the interpretation

  2. Electroglottographic parameterization of the effects of gender, vowel and phonatory registers on vocal fold vibratory patterns: an Indian perspective.

    Science.gov (United States)

    Paul, Nilanjan; Kumar, Suman; Chatterjee, Indranil; Mukherjee, Biswarup

    2011-01-01

    In-depth study on laryngeal biomechanics and vocal fold vibratory patterns reveal that a single vibratory cycle can be divided into two major phases, the closed and open phase, which is subdivided into opening and closing phases. Studies reveal that the relative time course of abduction and adduction, which in turn is dependent on the relative relaxing and tensing of the vocal fold cover and body, to be the determining factor in production of a particular vocal register like the modal (or chest), falsetto, glottal fry registers. Studies further point out Electroglottography to be particularly suitable for the study of vocal vibratory patterns during register changes. However, to date, there has been limited study on quantitative parameterization of EGG wave form in vocal fry register. Moreover, contradictory findings abound in literature regarding effects of gender and vowel types on vocal vibratory patterns, especially during phonation at different registers. The present study endeavors to find out the effects of vowel and gender differences on the vocal fold vibratory patterns in different registers and how these would be reflected in standard EGG parameters of Contact Quotient (CQ) and Contact Index (CI), taking into consideration the Indian sociolinguistic context. Electroglottographic recordings of 10 young adults (5 males and 5 females) were taken while the subjects phonated the three vowels /a/,/i/,/u/ each in two vocal registers, modal and vocal fry. Obtained raw EGG were further normalized using the Derived EGG algorithm and theCQ and CI values were derived. Obtained data were subject to statistical analysis using the 3-way ANOVA with gender, vowel and vocal register as the three variables. Post-hoc Dunnett C multiple comparison analysis were also performed. Results reveal that CQ values are significantly higher in vocal fry than modal phonation for both males and females, indicating a relatively hyperconstricted vocal system during vocal fry. The males

  3. Detection of cyclic-fold bifurcation in electrostatic MEMS transducers by motion-induced current

    Science.gov (United States)

    Park, Sangtak; Khater, Mahmoud; Effa, David; Abdel-Rahman, Eihab; Yavuz, Mustafa

    2017-08-01

    This paper presents a new detection method of cyclic-fold bifurcations in electrostatic MEMS transducers based on a variant of the harmonic detection of resonance method. The electrostatic transducer is driven by an unbiased harmonic signal at half its natural frequency, ω a   =  1/2 ω o . The response of the transducer consists of static displacement and a series of harmonics at 2 ω a , 4 ω a , and so on. Its motion-induced current is shifted by the excitation frequency, ω a , to appear at 3 ω a , 5 ω a , and higher odd harmonics, providing higher sensitivity to the measurement of harmonic motions. With this method, we successfully detected the variation in the location of the cyclic-fold bifurcation of an encapsulated electrostatic MEMS transducer. We also detected a regime of tapping mode motions subsequent to the bifurcation.

  4. Detection of cyclic-fold bifurcation in electrostatic MEMS transducers by motion-induced current

    International Nuclear Information System (INIS)

    Park, Sangtak; Abdel-Rahman, Eihab; Khater, Mahmoud; Effa, David; Yavuz, Mustafa

    2017-01-01

    This paper presents a new detection method of cyclic-fold bifurcations in electrostatic MEMS transducers based on a variant of the harmonic detection of resonance method. The electrostatic transducer is driven by an unbiased harmonic signal at half its natural frequency, ω a   =  1/2  ω o . The response of the transducer consists of static displacement and a series of harmonics at 2  ω a , 4  ω a , and so on. Its motion-induced current is shifted by the excitation frequency, ω a , to appear at 3  ω a , 5  ω a , and higher odd harmonics, providing higher sensitivity to the measurement of harmonic motions. With this method, we successfully detected the variation in the location of the cyclic-fold bifurcation of an encapsulated electrostatic MEMS transducer. We also detected a regime of tapping mode motions subsequent to the bifurcation. (paper)

  5. Radiation-Induced Reductions in Regional Lung Perfusion: 0.1-12 Year Data From a Prospective Clinical Study

    International Nuclear Information System (INIS)

    Zhang Junan; Ma Jinli; Zhou Sumin; Hubbs, Jessica L.; Wong, Terence Z.; Folz, Rodney J.; Evans, Elizabeth S.; Jaszczak, Ronald J.; Clough, Robert; Marks, Lawrence B.

    2010-01-01

    Purpose: To assess the time and regional dependence of radiation therapy (RT)-induced reductions in regional lung perfusion 0.1-12 years post-RT, as measured by single photon emission computed tomography (SPECT) lung perfusion. Materials/Methods: Between 1991 and 2005, 123 evaluable patients receiving RT for tumors in/around the thorax underwent SPECT lung perfusion scans before and serially post-RT (0.1-12 years). Registration of pre- and post-RT SPECT images with the treatment planning computed tomography, and hence the three-dimensional RT dose distribution, allowed changes in regional SPECT-defined perfusion to be related to regional RT dose. Post-RT follow-up scans were evaluated at multiple time points to determine the time course of RT-induced regional perfusion changes. Population dose response curves (DRC) for all patients at different time points, different regions, and subvolumes (e.g., whole lungs, cranial/caudal, ipsilateral/contralateral) were generated by combining data from multiple patients at similar follow-up times. Each DRC was fit to a linear model, and differences statistically analyzed. Results: In the overall groups, dose-dependent reductions in perfusion were seen at each time post-RT. The slope of the DRC increased over time up to 18 months post-RT, and plateaued thereafter. Regional differences in DRCs were only observed between the ipsilateral and contralateral lungs, and appeared due to tumor-associated changes in regional perfusion. Conclusions: Thoracic RT causes dose-dependent reductions in regional lung perfusion that progress up to ∼18 months post-RT and persists thereafter. Tumor shrinkage appears to confound the observed dose-response relations. There appears to be similar dose response for healthy parts of the lungs at different locations.

  6. Ligand-promoted protein folding by biased kinetic partitioning.

    Science.gov (United States)

    Hingorani, Karan S; Metcalf, Matthew C; Deming, Derrick T; Garman, Scott C; Powers, Evan T; Gierasch, Lila M

    2017-04-01

    Protein folding in cells occurs in the presence of high concentrations of endogenous binding partners, and exogenous binding partners have been exploited as pharmacological chaperones. A combined mathematical modeling and experimental approach shows that a ligand improves the folding of a destabilized protein by biasing the kinetic partitioning between folding and alternative fates (aggregation or degradation). Computationally predicted inhibition of test protein aggregation and degradation as a function of ligand concentration are validated by experiments in two disparate cellular systems.

  7. Vocal fold composition and early glottic carcinoma infiltration

    Directory of Open Access Journals (Sweden)

    Fang Qin

    2012-08-01

    Full Text Available Abstract Background Current imaging techniques provide only limited information pertaining to the extent of infiltration of laryngeal carcinomas into vocal fold tissue layers. Therefore, it is needed to seek the contribute to the body of knowledge surrounding examination and characterization in laryngeal carcinoma infiltration. Methods Excised larynges were collected from 30 male laryngectomy patients with an average age of 43.5 years (ranging 36 to 55 years and history of smoking (≥10 years exhibiting T1, T2, or subglottal (normal vocal fold carcinomas. Vocal folds were preserved via freezing or immersion in paraffin. The depth of the mucosa, submucosa, and muscular layers in both normal vocal folds and tumor tissues of afflicted vocal folds was measured. Results The average depths of the mucosa, submucosa, and muscular layers in normal vocal folds were 0.15 ± 0.06 mm, 2.30 ± 0.59 mm, and 2.87 ± 0.88 mm, respectively. Infiltration measurements of T1 tumors showed a depth of 1.62 ± 0.51 mm and 1.32 ± 0.49 mm in frozen sections and paraffin-embedded samples, respectively. Similarly, T2 tumors showed a depth of 2.87 ± 0.68 mm and 2.58 ± 0.67 mm in frozen sections and paraffin-embedded samples, respectively. T1 and T2 tumors occupied 24.8 ± 10 and 48.5 ± 15 percent of the normal vocal fold depth, respectively. Conclusion This data provides a baseline for estimating infiltration of laryngeal carcinomas in vocal fold tissue layers, of particular interest to surgeons. This information may be used to assess typical depths of infiltration, thus allowing for more appropriate selection of surgical procedures based on individual patient assessment.

  8. Improvement of a Vocal Fold Imaging System

    Energy Technology Data Exchange (ETDEWEB)

    Krauter, K. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2017-02-01

    Medical professionals can better serve their patients through continual update of their imaging tools. A wide range of pathologies and disease may afflict human vocal cords or, as they’re also known, vocal folds. These diseases can affect human speech hampering the ability of the patient to communicate. Vocal folds must be opened for breathing and the closed to produce speech. Currently methodologies to image markers of potential pathologies are difficult to use and often fail to detect early signs of disease. These current methodologies rely on a strobe light and slower frame rate camera in an attempt to obtain images as the vocal folds travel over the full extent of their motion.

  9. In vitro folding of inclusion body proteins.

    Science.gov (United States)

    Rudolph, R; Lilie, H

    1996-01-01

    Insoluble, inactive inclusion bodies are frequently formed upon recombinant protein production in transformed microorganisms. These inclusion bodies, which contain the recombinant protein in an highly enriched form, can be isolated by solid/liquid separation. After solubilization, native proteins can be generated from the inactive material by using in vitro folding techniques. New folding procedures have been developed for efficient in vitro reconstitution of complex hydrophobic, multidomain, oligomeric, or highly disulfide-bonded proteins. These protocols take into account process parameters such as protein concentration, catalysis of disulfide bond formation, temperature, pH, and ionic strength, as well as specific solvent ingredients that reduce unproductive side reactions. Modification of the protein sequence has been exploited to improve in vitro folding.

  10. Arytenoid and posterior vocal fold surgery for bilateral vocal fold immobility.

    Science.gov (United States)

    Young, VyVy N; Rosen, Clark A

    2011-12-01

    Many procedures exist to address the airway restriction often seen with bilateral vocal fold immobility. We review the most recent studies involving arytenoid and/or posterior vocal fold surgery to provide an update on the issues related to these procedures. Specific focus is placed on selection of the surgical approach and operative side, use of adjunctive therapies, and outcome measures including decannulation rate, revision and complication rate, and postoperative results. Ten studies were identified between 2004 and 2011. Modifications to the orginal transverse cordotomy and medial arytenoidectomy techniques continue to be investigated to seek improvement in dyspnea symptoms with minimal decline in voice and/or swallowing function. Decannulation rates for these approaches are high. Postoperative dysphagia appears to be less commonly observed but requires continued study. The use of mitomycin-C in these procedures has been poorly studied to date. Both transverse cordotomy and medial arytenoidectomy procedures result in high success rates. However, many questions related to these procedures remain unanswered, particularly with respect to preoperative and postoperative evaluations of voice quality, swallowing function, and pulmonary status. There is need for rigorous prospective clinical studies to address these many issues further.

  11. On the origins of the weak folding cooperativity of a designed ββα ultrafast protein FSD-1.

    Directory of Open Access Journals (Sweden)

    Chun Wu

    Full Text Available FSD-1, a designed small ultrafast folder with a ββα fold, has been actively studied in the last few years as a model system for studying protein folding mechanisms and for testing of the accuracy of computational models. The suitability of this protein to describe the folding of naturally occurring α/β proteins has recently been challenged based on the observation that the melting transition is very broad, with ill-resolved baselines. Using molecular dynamics simulations with the AMBER protein force field (ff96 coupled with the implicit solvent model (IGB = 5, we shed new light into the nature of this transition and resolve the experimental controversies. We show that the melting transition corresponds to the melting of the protein as a whole, and not solely to the helix-coil transition. The breadth of the folding transition arises from the spread in the melting temperatures (from ∼325 K to ∼302 K of the individual transitions: formation of the hydrophobic core, β-hairpin and tertiary fold, with the helix formed earlier. Our simulations initiated from an extended chain accurately predict the native structure, provide a reasonable estimate of the transition barrier height, and explicitly demonstrate the existence of multiple pathways and multiple transition states for folding. Our exhaustive sampling enables us to assess the quality of the Amber ff96/igb5 combination and reveals that while this force field can predict the correct native fold, it nonetheless overstabilizes the α-helix portion of the protein (Tm = ∼387K as well as the denatured structures.

  12. Self-Folding Textiles through Manipulation of Knit Stitch Architecture

    Directory of Open Access Journals (Sweden)

    Chelsea E. Knittel

    2015-12-01

    Full Text Available This research presents a preliminary study on finding predictable methods of controlling the self-folding behaviors of weft knit textiles for use in the development of smart textiles and garment devices, such as those with shape memory, auxetic behavior or transformation abilities. In this work, Shima Seiki SDS-One Apex computer-aided knitting technology, Shima Seiki industrial knitting machines, and the study of paper origami tessellation patterns were used as tools to understand and predict the self-folding abilities of weft knit textiles. A wide range of self-folding weft knit structures was produced, and relationships between the angles and ratios of the knit and purl stitch types were determined. Mechanical testing was used as a means to characterize differences produced by stitch patterns, and to further understand the relationships between angles and folding abilities. By defining a formulaic method for predicting the nature of the folds that occur due to stitch architecture patterns, we can better design self-folding fabrics for smart textile applications.

  13. The efficacy of a novel collagen-gelatin scaffold with basic fibroblast growth factor for the treatment of vocal fold scar.

    Science.gov (United States)

    Hiwatashi, Nao; Hirano, Shigeru; Mizuta, Masanobu; Kobayashi, Toshiki; Kawai, Yoshitaka; Kanemaru, Shin-Ichi; Nakamura, Tatsuo; Ito, Juichi; Kawai, Katsuya; Suzuki, Shigehiko

    2017-05-01

    Vocal fold scar remains a therapeutic challenge. Basic fibroblast growth factor (bFGF) was reported to have regenerative effects for vocal fold scar, although it has the disadvantage of rapid absorption in vivo. A collagen-gelatin sponge (CGS) can compensate for the disadvantage by providing a sustained release system. The current study evaluated the efficacy of CGS combined with bFGF on vocal fold scar, using rat fibroblasts for an in vitro model and a canine in vivo model. We prepared fibroblasts from scarred vocal folds (sVFs) in rats and showed that bFGF accelerated cell proliferation and suppressed expression levels of cleaved caspase 3 and α-smooth muscle actin. Has 1, Has 3, Fgf2, Hgf and Vegfa mRNA levels were significantly upregulated, while Col1a1 and Col3a1 were dose-dependently downregulated, with a maximum effect at 100 ng/ml bFGF. In an in vivo assay, 6 weeks after lamina propria stripping, beagles were divided into three groups: CGS alone (CGS group); CGS with bFGF (7 µg/cm 2 ; CGS + bFGF group); or a sham-treated group. Vibratory examination revealed that the glottal gap was significantly reduced in the bFGF group and the two implanted groups, whereas the CGS + bFGF group showed higher mucosal wave amplitude. Histological examination revealed significantly restored hyaluronic acid and elastin redistribution in the CGS + bFGF group and reductions in dense collagen deposition. These results provide evidence that CGS and bFGF combination therapy may have therapeutic potential and could be a promising tool for treating vocal fold scar. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  14. The human cerebral cortex is neither one nor many: Neuronal distribution reveals two quantitatively different zones in the grey matter, three in the white matter, and explains local variations in cortical folding

    Directory of Open Access Journals (Sweden)

    Pedro F. M. Ribeiro

    2013-09-01

    Full Text Available The human prefrontal cortex has been considered different in several aspects and relatively enlarged compared to the rest of the cortical areas. Here we determine whether the white and gray matter of the prefrontal portion of the human cerebral cortex have similar or different cellular compositions relative to the rest of the cortical regions by applying the Isotropic Fractionator to analyze the distribution of neurons along the entire anteroposterior axis of the cortex, and its relationship with the degree of gyrification, number of neurons under the cortical surface, and other parameters. The prefrontal region shares with the remainder of the cerebral cortex (except for occipital cortex the same relationship between cortical volume and number of neurons. In contrast, both occipital and prefrontal areas vary from other cortical areas in their connectivity through the white matter, with a systematic reduction of cortical connectivity through the white matter and an increase of the mean axon caliber along the anteroposterior axis. These two parameters explain local differences in the distribution of neurons underneath the cortical surface. We also show that local variations in cortical folding are neither a function of local numbers of neurons nor of cortical thickness, but correlate with properties of the white matter, and are best explained by the folding of the white matter surface. Our results suggest that the human cerebral cortex is divided in two zones (occipital and non-occipital that differ in how neurons distributed across their grey matter volume and in three zones (prefrontal, occipital, and non-occipital that differ in how neurons are connected through the white matter. Thus, the human prefrontal cortex has the largest fraction of neuronal connectivity through the white matter and the smallest average axonal caliber in the white matter within the cortex, although its neuronal composition fits the pattern found for other, non

  15. FoldEco: A Model for Proteostasis in E. coli

    Directory of Open Access Journals (Sweden)

    Evan T. Powers

    2012-03-01

    Full Text Available To gain insight into the interplay of processes and species that maintain a correctly folded, functional proteome, we have developed a computational model called FoldEco. FoldEco models the cellular proteostasis network of the E. coli cytoplasm, including protein synthesis, degradation, aggregation, chaperone systems, and the folding characteristics of protein clients. We focused on E. coli because much of the needed input information—including mechanisms, rate parameters, and equilibrium coefficients—is available, largely from in vitro experiments; however, FoldEco will shed light on proteostasis in other organisms. FoldEco can generate hypotheses to guide the design of new experiments. Hypothesis generation leads to system-wide questions and shows how to convert these questions to experimentally measurable quantities, such as changes in protein concentrations with chaperone or protease levels, which can then be used to improve our current understanding of proteostasis and refine the model. A web version of FoldEco is available at http://foldeco.scripps.edu.

  16. Evolution of a protein folding nucleus.

    Science.gov (United States)

    Xia, Xue; Longo, Liam M; Sutherland, Mason A; Blaber, Michael

    2016-07-01

    The folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding properties of key foldable intermediates along the evolutionary trajectory of the β-trefoil. The results show structural acquisition of the FN during gene fusion events, incorporating novel turn structure created by gene fusion. Furthermore, the FN is adjusted by circular permutation in response to destabilizing functional mutation. FN plasticity by way of circular permutation is made possible by the intrinsic C3 cyclic symmetry of the β-trefoil architecture, identifying a possible selective advantage that helps explain the prevalence of cyclic structural symmetry in the proteome. © 2015 The Protein Society.

  17. Hierarchical Diagnosis of Vocal Fold Disorders

    Science.gov (United States)

    Nikkhah-Bahrami, Mansour; Ahmadi-Noubari, Hossein; Seyed Aghazadeh, Babak; Khadivi Heris, Hossein

    This paper explores the use of hierarchical structure for diagnosis of vocal fold disorders. The hierarchical structure is initially used to train different second-level classifiers. At the first level normal and pathological signals have been distinguished. Next, pathological signals have been classified into neurogenic and organic vocal fold disorders. At the final level, vocal fold nodules have been distinguished from polyps in organic disorders category. For feature selection at each level of hierarchy, the reconstructed signal at each wavelet packet decomposition sub-band in 5 levels of decomposition with mother wavelet of (db10) is used to extract the nonlinear features of self-similarity and approximate entropy. Also, wavelet packet coefficients are used to measure energy and Shannon entropy features at different spectral sub-bands. Davies-Bouldin criterion has been employed to find the most discriminant features. Finally, support vector machines have been adopted as classifiers at each level of hierarchy resulting in the diagnosis accuracy of 92%.

  18. Structure of a 13-fold superhelix (almost determined from first principles

    Directory of Open Access Journals (Sweden)

    Guillaume A. Schoch

    2015-03-01

    Full Text Available Nuclear hormone receptors are cytoplasm-based transcription factors that bind a ligand, translate to the nucleus and initiate gene transcription in complex with a co-activator such as TIF2 (transcriptional intermediary factor 2. For structural studies the co-activator is usually mimicked by a peptide of circa 13 residues, which for the largest part forms an α-helix when bound to the receptor. The aim was to co-crystallize the glucocorticoid receptor in complex with a ligand and the TIF2 co-activator peptide. The 1.82 Å resolution diffraction data obtained from the crystal could not be phased by molecular replacement using the known receptor structures. HPLC analysis of the crystals revealed the absence of the receptor and indicated that only the co-activator peptide was present. The self-rotation function displayed 13-fold rotational symmetry, which initiated an exhaustive but unsuccessful molecular-replacement approach using motifs of 13-fold symmetry such as α- and β-barrels in various geometries. The structure was ultimately determined by using a single α-helix and the software ARCIMBOLDO, which assembles fragments placed by PHASER before using them as seeds for density modification model building in SHELXE. Systematic variation of the helix length revealed upper and lower size limits for successful structure determination. A beautiful but unanticipated structure was obtained that forms superhelices with left-handed twist throughout the crystal, stabilized by ligand interactions. Together with the increasing diversity of structural elements in the Protein Data Bank the results from TIF2 confirm the potential of fragment-based molecular replacement to significantly accelerate the phasing step for native diffraction data at around 2 Å resolution.

  19. Large-scale chromosome folding versus genomic DNA sequences: A discrete double Fourier transform technique.

    Science.gov (United States)

    Chechetkin, V R; Lobzin, V V

    2017-08-07

    Using state-of-the-art techniques combining imaging methods and high-throughput genomic mapping tools leaded to the significant progress in detailing chromosome architecture of various organisms. However, a gap still remains between the rapidly growing structural data on the chromosome folding and the large-scale genome organization. Could a part of information on the chromosome folding be obtained directly from underlying genomic DNA sequences abundantly stored in the databanks? To answer this question, we developed an original discrete double Fourier transform (DDFT). DDFT serves for the detection of large-scale genome regularities associated with domains/units at the different levels of hierarchical chromosome folding. The method is versatile and can be applied to both genomic DNA sequences and corresponding physico-chemical parameters such as base-pairing free energy. The latter characteristic is closely related to the replication and transcription and can also be used for the assessment of temperature or supercoiling effects on the chromosome folding. We tested the method on the genome of E. coli K-12 and found good correspondence with the annotated domains/units established experimentally. As a brief illustration of further abilities of DDFT, the study of large-scale genome organization for bacteriophage PHIX174 and bacterium Caulobacter crescentus was also added. The combined experimental, modeling, and bioinformatic DDFT analysis should yield more complete knowledge on the chromosome architecture and genome organization. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Human glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site

    Directory of Open Access Journals (Sweden)

    Misquitta Stephanie A

    2004-02-01

    Full Text Available Abstract Background Glutaminyl cyclase (QC forms the pyroglutamyl residue at the amino terminus of numerous secretory peptides and proteins. We previously proposed the mammalian QC has some features in common with zinc aminopeptidases. We now have generated a structural model for human QC based on the aminopeptidase fold (pdb code 1AMP and mutated the apparent active site residues to assess their role in QC catalysis. Results The structural model proposed here for human QC, deposited in the protein databank as 1MOI, is supported by a variety of fold prediction programs, by the circular dichroism spectrum, and by the presence of the disulfide. Mutagenesis of the six active site residues present in both 1AMP and QC reveal essential roles for the two histidines (140 and 330, QC numbering and the two glutamates (201 and 202, while the two aspartates (159 and 248 appear to play no catalytic role. ICP-MS analysis shows less than stoichiometric zinc (0.3:1 in the purified enzyme. Conclusions We conclude that human pituitary glutaminyl cyclase and bacterial zinc aminopeptidase share a common fold and active site residues. In contrast to the aminopeptidase, however, QC does not appear to require zinc for enzymatic activity.

  1. Experimental investigation of protein folding and misfolding.

    Science.gov (United States)

    Dobson, Christopher M

    2004-09-01

    Newly synthesised proteins need to fold, often to intricate and close-packed structures, in order to function. The underlying mechanism by which this complex process takes place both in vitro and in vivo is now becoming understood, at least in general terms, as a result of the application of a wide range of biophysical and computational methods used in combination with the techniques of biochemistry and protein engineering. It is increasingly apparent, however, that folding is not only crucial for generating biological activity, but that it is also coupled to a wide range of processes within the cell, ranging from the trafficking of proteins to specific organelles to the regulation of cell growth and differentiation. Not surprisingly, therefore, the failure of proteins to fold appropriately, or to remain correctly folded, is associated with a large number of cellular malfunctions that give rise to disease. Misfolding, and its consequences such as aggregation, can be investigated by extending the types of techniques used to study the normal folding process. Application of these techniques is enabling the development of a unified description of the interconversion and regulation of the different conformational states available to proteins in living systems. Such a description proves a generic basis for understanding the fundamental links between protein misfolding and its associated clinical disorders, such as Alzheimer's disease and Type II diabetes, and for exploring novel therapeutic strategies directed at their prevention and treatment on a rational basis.

  2. Histopathologic study of human vocal fold mucosa unphonated over a decade.

    Science.gov (United States)

    Sato, Kiminori; Umeno, Hirohito; Ono, Takeharu; Nakashima, Tadashi

    2011-12-01

    Mechanotransduction caused by vocal fold vibration could possibly be an important factor in the maintenance of extracellular matrices and layered structure of the human adult vocal fold mucosa as a vibrating tissue after the layered structure has been completed. Vocal fold stellate cells (VFSCs) in the human maculae flavae of the vocal fold mucosa are inferred to be involved in the metabolism of extracellular matrices of the vocal fold mucosa. Maculae flavae are also considered to be an important structure in the growth and development of the human vocal fold mucosa. Tension caused by phonation (vocal fold vibration) is hypothesized to stimulate the VFSCs to accelerate production of extracellular matrices. A human adult vocal fold mucosa unphonated over a decade was investigated histopathologically. Vocal fold mucosa unphonated for 11 years and 2 months of a 64-year-old male with cerebral hemorrhage was investigated by light and electron microscopy. The vocal fold mucosae (including maculae flavae) were atrophic. The vocal fold mucosa did not have a vocal ligament, Reinke's space or a layered structure. The lamina propria appeared as a uniform structure. Morphologically, the VFSCs synthesized fewer extracellular matrices, such as fibrous protein and glycosaminoglycan. Consequently, VFSCs appeared to decrease their level of activity.

  3. F-Type Lectins: A Highly Diversified Family of Fucose-Binding Proteins with a Unique Sequence Motif and Structural Fold, Involved in Self/Non-Self-Recognition

    Directory of Open Access Journals (Sweden)

    Gerardo R. Vasta

    2017-11-01

    Full Text Available The F-type lectin (FTL family is one of the most recent to be identified and structurally characterized. Members of the FTL family are characterized by a fucose recognition domain [F-type lectin domain (FTLD] that displays a novel jellyroll fold (“F-type” fold and unique carbohydrate- and calcium-binding sequence motifs. This novel lectin family comprises widely distributed proteins exhibiting single, double, or greater multiples of the FTLD, either tandemly arrayed or combined with other structurally and functionally distinct domains, yielding lectin subunits of pleiotropic properties even within a single species. Furthermore, the extraordinary variability of FTL sequences (isoforms that are expressed in a single individual has revealed genetic mechanisms of diversification in ligand recognition that are unique to FTLs. Functions of FTLs in self/non-self-recognition include innate immunity, fertilization, microbial adhesion, and pathogenesis, among others. In addition, although the F-type fold is distinctive for FTLs, a structure-based search revealed apparently unrelated proteins with minor sequence similarity to FTLs that displayed the FTLD fold. In general, the phylogenetic analysis of FTLD sequences from viruses to mammals reveals clades that are consistent with the currently accepted taxonomy of extant species. However, the surprisingly discontinuous distribution of FTLDs within each taxonomic category suggests not only an extensive structural/functional diversification of the FTLs along evolutionary lineages but also that this intriguing lectin family has been subject to frequent gene duplication, secondary loss, lateral transfer, and functional co-option.

  4. Vocal fold contact patterns based on normal modes of vibration.

    Science.gov (United States)

    Smith, Simeon L; Titze, Ingo R

    2018-05-17

    The fluid-structure interaction and energy transfer from respiratory airflow to self-sustained vocal fold oscillation continues to be a topic of interest in vocal fold research. Vocal fold vibration is driven by pressures on the vocal fold surface, which are determined by the shape of the glottis and the contact between vocal folds. Characterization of three-dimensional glottal shapes and contact patterns can lead to increased understanding of normal and abnormal physiology of the voice, as well as to development of improved vocal fold models, but a large inventory of shapes has not been directly studied previously. This study aimed to take an initial step toward characterizing vocal fold contact patterns systematically. Vocal fold motion and contact was modeled based on normal mode vibration, as it has been shown that vocal fold vibration can be almost entirely described by only the few lowest order vibrational modes. Symmetric and asymmetric combinations of the four lowest normal modes of vibration were superimposed on left and right vocal fold medial surfaces, for each of three prephonatory glottal configurations, according to a surface wave approach. Contact patterns were generated from the interaction of modal shapes at 16 normalized phases during the vibratory cycle. Eight major contact patterns were identified and characterized by the shape of the flow channel, with the following descriptors assigned: convergent, divergent, convergent-divergent, uniform, split, merged, island, and multichannel. Each of the contact patterns and its variation are described, and future work and applications are discussed. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Force generation by titin folding.

    Science.gov (United States)

    Mártonfalvi, Zsolt; Bianco, Pasquale; Naftz, Katalin; Ferenczy, György G; Kellermayer, Miklós

    2017-07-01

    Titin is a giant protein that provides elasticity to muscle. As the sarcomere is stretched, titin extends hierarchically according to the mechanics of its segments. Whether titin's globular domains unfold during this process and how such unfolded domains might contribute to muscle contractility are strongly debated. To explore the force-dependent folding mechanisms, here we manipulated skeletal-muscle titin molecules with high-resolution optical tweezers. In force-clamp mode, after quenching the force (force trace contained rapid fluctuations and a gradual increase of average force, indicating that titin can develop force via dynamic transitions between its structural states en route to the native conformation. In 4 M urea, which destabilizes H-bonds hence the consolidated native domain structure, the net force increase disappeared but the fluctuations persisted. Thus, whereas net force generation is caused by the ensemble folding of the elastically-coupled domains, force fluctuations arise due to a dynamic equilibrium between unfolded and molten-globule states. Monte-Carlo simulations incorporating a compact molten-globule intermediate in the folding landscape recovered all features of our nanomechanics results. The ensemble molten-globule dynamics delivers significant added contractility that may assist sarcomere mechanics, and it may reduce the dissipative energy loss associated with titin unfolding/refolding during muscle contraction/relaxation cycles. © 2017 The Protein Society.

  6. The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space.

    Science.gov (United States)

    Towse, Clare-Louise; Akke, Mikael; Daggett, Valerie

    2017-04-27

    Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing data set of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone can sample, we found that the backbone entropy and side chain size are not strictly coupled. An outcome of these analyses is the Dynameomics Entropy Dictionary, the contents of which have been compared with entropies derived by other theoretical approaches and experiment. As might be expected, the conformational entropies scale linearly with the number of residues, demonstrating that conformational entropy is an extensive property of proteins. The calculated conformational entropies of folding agree well with previous estimates. Detailed analysis of specific cases identifies deviations in conformational entropy from the average values that highlight how conformational entropy varies with sequence, secondary structure, and tertiary fold. Notably, α-helices have lower entropy on average than do β-sheets, and both are lower than coil regions.

  7. Solitons and protein folding: An In Silico experiment

    Energy Technology Data Exchange (ETDEWEB)

    Ilieva, N., E-mail: nevena.ilieva@parallel.bas.bg [Institute of Information and Communication Technologies, Bulgarian Aacademy of Sciences, Sofia (Bulgaria); Dai, J., E-mail: daijing491@gmail.com [School of Physics, Beijing Institute of Technology, Beijing (China); Sieradzan, A., E-mail: adams86@wp.pl [Faculty of Chemistry, University of Gdańsk, Gdańsk (Poland); Niemi, A., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy, Uppsala University, Uppsala (Sweden); LMPT–CNRS, Université de Tours, Tours (France)

    2015-10-28

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics.

  8. Solitons and protein folding: An In Silico experiment

    International Nuclear Information System (INIS)

    Ilieva, N.; Dai, J.; Sieradzan, A.; Niemi, A.

    2015-01-01

    Protein folding [1] is the process of formation of a functional 3D structure from a random coil — the shape in which amino-acid chains leave the ribosome. Anfinsen’s dogma states that the native 3D shape of a protein is completely determined by protein’s amino acid sequence. Despite the progress in understanding the process rate and the success in folding prediction for some small proteins, with presently available physics-based methods it is not yet possible to reliably deduce the shape of a biologically active protein from its amino acid sequence. The protein-folding problem endures as one of the most important unresolved problems in science; it addresses the origin of life itself. Furthermore, a wrong fold is a common cause for a protein to lose its function or even endanger the living organism. Soliton solutions of a generalized discrete non-linear Schrödinger equation (GDNLSE) obtained from the energy function in terms of bond and torsion angles κ and τ provide a constructive theoretical framework for describing protein folds and folding patterns [2]. Here we study the dynamics of this process by means of molecular-dynamics simulations. The soliton manifestation is the pattern helix–loop–helix in the secondary structure of the protein, which explains the importance of understanding loop formation in helical proteins. We performed in silico experiments for unfolding one subunit of the core structure of gp41 from the HIV envelope glycoprotein (PDB ID: 1AIK [3]) by molecular-dynamics simulations with the MD package GROMACS. We analyzed 80 ns trajectories, obtained with one united-atom and two different all-atom force fields, to justify the side-chain orientation quantification scheme adopted in the studies and to eliminate force-field based artifacts. Our results are compatible with the soliton model of protein folding and provide first insight into soliton-formation dynamics

  9. The nature of folded states of globular proteins.

    Science.gov (United States)

    Honeycutt, J D; Thirumalai, D

    1992-06-01

    We suggest, using dynamical simulations of a simple heteropolymer modelling the alpha-carbon sequence in a protein, that generically the folded states of globular proteins correspond to statistically well-defined metastable states. This hypothesis, called the metastability hypothesis, states that there are several free energy minima separated by barriers of various heights such that the folded conformations of a polypeptide chain in each of the minima have similar structural characteristics but have different energies from one another. The calculated structural characteristics, such as bond angle and dihedral angle distribution functions, are assumed to arise from only those configurations belonging to a given minimum. The validity of this hypothesis is illustrated by simulations of a continuum model of a heteropolymer whose low temperature state is a well-defined beta-barrel structure. The simulations were done using a molecular dynamics algorithm (referred to as the "noisy" molecular dynamics method) containing both friction and noise terms. It is shown that for this model there are several distinct metastable minima in which the structural features are similar. Several new methods of analyzing fluctuations in structures belonging to two distinct minima are introduced. The most notable one is a dynamic measure of compactness that can in principle provide the time required for maximal compactness to be achieved. The analysis shows that for a given metastable state in which the protein has a well-defined folded structure the transition to a state of higher compactness occurs very slowly, lending credence to the notion that the system encounters a late barrier in the process of folding to the most compact structure. The examination of the fluctuations in the structures near the unfolding----folding transition temperature indicates that the transition state for the unfolding to folding process occurs closer to the folded state.

  10. Modeling Vocal Fold Intravascular Flow using Synthetic Replicas

    Science.gov (United States)

    Terry, Aaron D.; Ricks, Matthew T.; Thomson, Scott L.

    2017-11-01

    Vocal fold vibration that is induced by air flowing from the lungs is believed to decrease blood flow through the vocal folds. This is important due to the critical role of blood flow in maintaining tissue health. However, the precise mechanical relationships between vocal fold vibration and blood perfusion remain understudied. A platform for studying liquid perfusion in a synthetic, life-size, self-oscillating vocal fold replica has recently been developed. The replicas are fabricated using molded silicone with material properties comparable to those of human vocal fold tissues and that include embedded microchannels through which liquid is perfused. The replicas are mounted on an air flow supply tube to initiate flow-induced vibration. A liquid reservoir is attached to the microchannel to cause liquid to perfuse through replica in the anterior-posterior direction. As replica vibration is initiated and amplitude increases, perfusion flow rate decreases. In this presentation, the replica design will be presented, along with data quantifying the relationships between parameters such as replica vibration amplitude, stiffness, microchannel diameter, and perfusion flow rate. This work was supported by Grant NIDCD R01DC005788 from the National Institutes of Health.

  11. Design and numerical analysis of an SMA mesh-based self-folding sheet

    International Nuclear Information System (INIS)

    Peraza-Hernandez, Edwin A; Hartl, Darren J; Malak Jr, Richard J

    2013-01-01

    Origami engineering, which is the practice of creating useful three-dimensional structures through folding and fold-like operations applied to initially two-dimensional entities, has the potential to impact several areas of design and manufacturing. In some instances, however, it may be impractical to apply external manipulations to produce the desired folds (e.g., as in remote applications such as space systems). In such cases, self-folding capabilities are valuable. A self-folding material or material system is one that can perform folding operations without manipulations from external forces. This work considers a concept for a self-folding material system. The system extends the ‘programmable matter’ concept and consists of an active, self-morphing sheet composed of two meshes of thermally actuated shape memory alloy (SMA) wire separated by a compliant passive layer. The geometric and power input parameters of the self-folding sheet are optimized to achieve the tightest local fold possible subject to stress and temperature constraints. The sheet folding performance considering folds at different angles relative to the orientation of the wire mesh is also analyzed. The optimization results show that a relatively low elastomer thickness is preferable to generate the tightest fold possible. The results also show that the self-folding sheet does not require large power inputs to achieve an optimal folding performance. It was shown that the self-folding sheet is capable of creating similar quality folds at different orientations. (paper)

  12. When fast is better: protein folding fundamentals and mechanisms from ultrafast approaches.

    Science.gov (United States)

    Muñoz, Victor; Cerminara, Michele

    2016-09-01

    Protein folding research stalled for decades because conventional experiments indicated that proteins fold slowly and in single strokes, whereas theory predicted a complex interplay between dynamics and energetics resulting in myriad microscopic pathways. Ultrafast kinetic methods turned the field upside down by providing the means to probe fundamental aspects of folding, test theoretical predictions and benchmark simulations. Accordingly, experimentalists could measure the timescales for all relevant folding motions, determine the folding speed limit and confirm that folding barriers are entropic bottlenecks. Moreover, a catalogue of proteins that fold extremely fast (microseconds) could be identified. Such fast-folding proteins cross shallow free energy barriers or fold downhill, and thus unfold with minimal co-operativity (gradually). A new generation of thermodynamic methods has exploited this property to map folding landscapes, interaction networks and mechanisms at nearly atomic resolution. In parallel, modern molecular dynamics simulations have finally reached the timescales required to watch fast-folding proteins fold and unfold in silico All of these findings have buttressed the fundamentals of protein folding predicted by theory, and are now offering the first glimpses at the underlying mechanisms. Fast folding appears to also have functional implications as recent results connect downhill folding with intrinsically disordered proteins, their complex binding modes and ability to moonlight. These connections suggest that the coupling between downhill (un)folding and binding enables such protein domains to operate analogically as conformational rheostats. © 2016 The Author(s).

  13. Structure and activity of the Pseudomonas aeruginosa hotdog-fold thioesterases PA5202 and PA2801.

    Science.gov (United States)

    Gonzalez, Claudio F; Tchigvintsev, Anatoli; Brown, Greg; Flick, Robert; Evdokimova, Elena; Xu, Xiaohui; Osipiuk, Jerzy; Cuff, Marianne E; Lynch, Susan; Joachimiak, Andrzej; Savchenko, Alexei; Yakunin, Alexander F

    2012-06-15

    The hotdog fold is one of the basic protein folds widely present in bacteria, archaea and eukaryotes. Many of these proteins exhibit thioesterase activity against fatty acyl-CoAs and play important roles in lipid metabolism, cellular signalling and degradation of xenobiotics. The genome of the opportunistic pathogen Pseudomonas aeruginosa contains over 20 genes encoding predicted hotdog-fold proteins, none of which have been experimentally characterized. We have found that two P. aeruginosa hotdog proteins display high thioesterase activity against 3-hydroxy-3-methylglutaryl-CoA and glutaryl-CoA (PA5202), and octanoyl-CoA (PA2801). Crystal structures of these proteins were solved (at 1.70 and 1.75 Å for PA5202 and PA2801 respectively) and revealed a hotdog fold with a potential catalytic carboxylate residue located on the long α-helix (Asp(57) in PA5202 and Glu(35) in PA2801). Alanine residue replacement mutagenesis of PA5202 identified four residues (Asn(42), Arg(43), Asp(57) and Thr(76)) that are critical for its activity and are located in the active site. A P. aeruginosa PA5202 deletion strain showed an increased secretion of the antimicrobial pigment pyocyanine and an increased expression of genes involved in pyocyanin biosynthesis, suggesting a functional link between PA5202 activity and pyocyanin production. Thus the P. aeruginosa hotdog thioesterases PA5202 and PA2801 have similar structures, but exhibit different substrate preferences and functions.

  14. Vertical partial frontolateral laryngectomy with simultaneous pedunculated sternothyroid muscle flap reconstruction of the vocal fold - surgical procedure and treatment outcomes.

    Science.gov (United States)

    Jurek-Matusiak, Olga; Wójtowicz, Piotr; Szafarowski, Tomasz; Krzeski, Antoni

    2018-02-28

    The aim of the study was to present the treatment outcomes after vertical partial laryngectomy with or without pedunculated sternothyroid muscle flap reconstruction following the resection of neoplasm-infiltrated vocal fold. The procedure was used in a patient with glottic cancer. Oncological outcomes, morphology of neo-vocal fold and the act of swallowing were evaluated. 45 patients with T1-T2 glottic cancer were subjected to vertical partial laryngectomy with 26 patients undergoing a procedure with pedunculated sternothyroid muscle flap reconstruction and the remaining 19 patients undergoing a procedure without such a reconstruction. Two female and 43 male patients aged 35-82 years (mean age of 62.5 years) were enrolled in the study. Local tumor spread and the condition of reconstructed vocal fold were assessed in sequential videofiberoscopy examination conducted each month after surgery whereas the regional spread was assessed in ultrasound scans. Postoperative aspiration was graded according to the Pearson's scale. Six patients experienced local recurrence while 2 patients experienced regional recurrence of the tumor. The pedunculated sternothyroid muscle flap neo-fold was structurally resemblant of the non-affected vocal fold. Episodic, daily dysphagia was observed in 1 patient while normal act of swallowing with no Pearson's scale symptoms was observed in the remaining 44 patients. No necrosis of pedunculated flap was observed. Vertical partial laryngectomy with or without pedunculated sternothyroid muscle flap reconstruction is a good method for the treatment of low- or intermediate-stage glottic cancer, especially when endoscopic access to the tumor is limited and when CO2 laser cannot be used. No significant functional disorders were observed in operated larynges.

  15. Classification of protein fold classes by knot theory and prediction of folds by neural networks: A combined theoretical and experimental approach

    DEFF Research Database (Denmark)

    Ramnarayan, K.; Bohr, Henrik; Jalkanen, Karl J.

    2008-01-01

    We present different means of classifying protein structure. One is made rigorous by mathematical knot invariants that coincide reasonably well with ordinary graphical fold classification and another classification is by packing analysis. Furthermore when constructing our mathematical fold...... classifications, we utilize standard neural network methods for predicting protein fold classes from amino acid sequences. We also make an analysis of the redundancy of the structural classifications in relation to function and ligand binding. Finally we advocate the use of combining the measurement of the VA...

  16. Molecular dissection of the intrinsic factor-vitamin B12 receptor, cubilin, discloses regions important for membrane association and ligand binding

    DEFF Research Database (Denmark)

    Kristiansen, M; Kozyraki, R; Jacobsen, Christian

    1999-01-01

    of conditioned media and cell extracts of transfected cells revealed that the N-terminal cubilin region conveys membrane association. Helical plotting of this region demonstrated a conserved amphipathic helix pattern (Lys74-Glu109) as a candidate site for hydrophobic interactions. Ligand affinity chromatography...

  17. Microwave-enhanced folding and denaturation of globular proteins

    DEFF Research Database (Denmark)

    Bohr, Henrik; Bohr, Jakob

    2000-01-01

    It is shown that microwave irradiation can affect the kinetics of the folding process of some globular proteins, especially beta-lactoglobulin. At low temperature the folding from the cold denatured phase of the protein is enhanced, while at a higher temperature the denaturation of the protein from...... its folded state is enhanced. In the latter case, a negative temperature gradient is needed for the denaturation process, suggesting that the effects of the microwaves are nonthermal. This supports the notion that coherent topological excitations can exist in proteins. The application of microwaves...

  18. Estimation of snow pollution in the region of non-ferrous metallurgy enterprises by the neutron activation method

    International Nuclear Information System (INIS)

    Khatamov, Sh.; Khamidova, R.; Kist, A.A.

    1980-01-01

    Possibility of determination of more than 25 chemical elements in snow water selected in the region of non-ferrous metallurgy enterprises has been shown using the methods of neutron activation and γ-spectrometry of high resolution. Elements were determined from one sample by three-fold irradiation in the nuclear reactor depending on the half-life period and other nuclear activation parameters of the formed radioisotopes. The analysis of snow cover has revealed the character of pollution of surrounding medium and air basin by toxical elements

  19. Discriminating trpzip2 and trpzip4 peptides’ folding landscape using the two-dimensional infrared spectroscopy: A simulation study

    International Nuclear Information System (INIS)

    Wu, Tianmin; Zhang, Ruiting; Li, Huanhuan; Zhuang, Wei; Yang, Lijiang

    2014-01-01

    We analyzed, based on the theoretical spectroscopic modeling, how the differences in the folding landscapes of two β-hairpin peptides trpzip2 and trpzip4 are reflected in their thermal unfolding infrared measurements. The isotope-edited equilibrium FTIR and two dimensional infrared spectra of the two peptides were calculated, using the nonlinear exciton propagation method, at a series of temperatures. The spectra calculations were based on the configuration distributions generated using the GB OBC implicit solvent MD simulation and the integrated tempering sampling technique. Conformational analysis revealed the different local thermal stabilities for these two peptides, which suggested the different folding landscapes. Our study further suggested that the ellipticities of the isotope peaks in the coherent IR signals are more sensitive to these local stability differences compared with other spectral features such as the peak intensities. Our technique can thus be combined with the relevant experimental measurements to achieve a better understanding of the peptide folding behaviors

  20. Biophysical characterisation of calumenin as a charged F508del-CFTR folding modulator.

    Directory of Open Access Journals (Sweden)

    Rashmi Tripathi

    Full Text Available The cystic fibrosis transmembrane regulator (CFTR is a cyclic-AMP dependent chloride channel expressed at the apical surface of epithelial cells lining various organs such as the respiratory tract. Defective processing and functioning of this protein caused by mutations in the CFTR gene results in loss of ionic balance, defective mucus clearance, increased proliferation of biofilms and inflammation of human airways observed in cystic fibrosis (CF patients. The process by which CFTR folds and matures under the influence of various chaperones in the secretory pathway remains incompletely understood. Recently, calumenin, a secretory protein, belonging to the CREC family of low affinity calcium binding proteins has been identified as a putative CFTR chaperone whose biophysical properties and functions remain uncharacterized. We compared hydropathy, instability, charge, unfoldability, disorder and aggregation propensity of calumenin and other CREC family members with CFTR associated chaperones and calcium binding proteins, wild-type and mutant CFTR proteins and intrinsically disordered proteins (IDPs. We observed that calumenin, along with other CREC proteins, was significantly more charged and less folded compared to CFTR associated chaperones. Moreover like IDPs, calumenin and other CREC proteins were found to be less hydrophobic and aggregation prone. Phylogenetic analysis revealed a close link between calumenin and other CREC proteins indicating how evolution might have shaped their similar biophysical properties. Experimentally, calumenin was observed to significantly reduce F508del-CFTR aggregation in a manner similar to AavLEA1, a well-characterized IDP. Fluorescence microscopy based imaging analysis also revealed altered trafficking of calumenin in bronchial cells expressing F508del-CFTR, indicating its direct role in the pathophysiology of CF. In conclusion, calumenin is characterized as a charged protein exhibiting close similarity with