scholarly journals Diagnosed Three-Dimensional Axisymmetric Structure of the Mulhall Tornado on 3 May 1999

2005 ◽  
Vol 62 (7) ◽  
pp. 2373-2393 ◽  
Author(s):  
Wen-Chau Lee ◽  
Joshua Wurman
Keyword(s):  
Cell Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Necessary Condition ◽  
Maximum Pressure ◽  
Wind Fields ◽  
Tangential Wind ◽  
Axisymmetric Structure ◽  
Perturbation Pressure ◽  
First Time

Abstract On 3 May 1999, an unusually large tornado that caused F4-level damage and killed several people was intercepted by the Doppler on Wheels (DOW) mobile radar near Mulhall, Oklahoma, from a range of 4 to 9 km, resulting in high-resolution volumetric data every 55 s up to 1.5-km altitude over a period of 14 min. For the first time, the evolution and three-dimensional structure of a tornado were deduced using the ground-based velocity track display (GBVTD) technique. After the circulation center was determined, the tangential wind and radial wind were derived from the GBVTD technique at each radius and height. In addition, the axisymmetric vertical velocity, angular momentum, vorticity, and perturbation pressure were deduced from the tangential and radial wind fields. This study focuses on the axisymmetric aspects of this tornado. The primary circulation of the Mulhall tornado consisted of an 84 m s−1 peak axisymmetric tangential wind with the radius of maximum wind (RMW) ranging from 500 to 1000 m. The secondary circulation exhibited a two-cell structure characterized by a central downdraft surrounded by an annular updraft near the RMW. The calculated maximum pressure deficit from a 3-km radius to the tornado center at 50-m altitude was −80 hPa. The maximum vorticity during the first 8 min of observation was located inside the RMW away from the tornado center. This vorticity profile satisfied the necessary condition of barotropic instability. As the tornado weakened afterward, the vorticity monotonically increased toward the center. The computed swirl ratios were between 2 and 6, consistent with the observed multiple vortex radar signatures and the vorticity pattern. Swirl ratios were generally smaller during the weakening phase.

scholarly journals Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum

2013 ◽  
Vol 288 (23) ◽  
pp. 16460-16475 ◽  
Author(s):  
Linda J. Olson ◽  
Ramiro Orsi ◽  
Solana G. Alculumbre ◽  
Francis C. Peterson ◽  
Ivan D. Stigliano ◽  
...  
Keyword(s):  
Endoplasmic Reticulum ◽  
Three Dimensional ◽  
Binding Pocket ◽  
Dimensional Structure ◽  
Mannose Residue ◽  
Glucosidase Ii ◽  
Mannose 6 Phosphate ◽  
First Time ◽  
Conserved Residue

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit. GIIβ participates in the endoplasmic reticulum localization of GIIα and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIβ MRH domain by NMR spectroscopy. It adopts a β-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIβ but not in other MRHs that influences GII glucose trimming activity.

Rational humanization of the powerful antithrombotic anti-GPIbα antibody: 6B4

2006 ◽  
Vol 96 (11) ◽  
pp. 671-684 ◽  
Author(s):  
Alexandre Fontayne ◽  
Karen Vanhoorelbeke ◽  
Inge Pareyn ◽  
Isabel Van Rompaey ◽  
Muriel Meiring ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Three Dimensional ◽  
Vector System ◽  
Dimensional Structure ◽  
Fab Fragment ◽  
Variable Regions ◽  
Significant Prolongation ◽  
Von Willebrand ◽  
First Time

SummaryFab-fragments of the monoclonal antibody 6B4, raised against human glycoprotein Ibα (GPIbα), have a powerful antithrombotic effect in baboons by blocking the GPIbα binding site for von Willebrand factor (VWF), without significant prolongation of the skin bleeding time. In order to bring this antibody to the clinic,we here humanized for the first time an anti-human GPIbα by variable-domain resurfacing guided by computer modeling. First, the genes coding for the variable regions of the heavy and light chains of 6B4 were cloned and sequenced. Based on this,a three-dimensional structure of the Fv-fragment was constructed by using homology-based modeling, and with this and comparison with antibodies with known structure,”murine” putative immunogenic residues which are exposed, were changed for “human-like” residues. The humanized Fab-fragment, h6B4-Fab, was constructed in the pKaneo vector system, expressed and purified and showed in vitro an unaltered, even slightly higher binding affinity for its antigen than the murine form as determined by different ELISA set-ups and surface plasmon resonance. Finally, injection of doses of 0.1 to 1.5 mg/kg of h6B4-Fab in baboons showed that both pharmacokinetics and ex-vivo bio-activity of the molecule were to a large extent preserved.In conclusion, the method used here to humanize 6B4 by resurfacing resulted in a fully active derivative, which is now ready for further development.

Structural modeling and role of HAX-1 as a positive allosteric modulator of human serine protease HtrA2

2019 ◽  
Vol 476 (20) ◽  
pp. 2965-2980
Author(s):  
Lalith K. Chaganti ◽  
Shubhankar Dutta ◽  
Raja Reddy Kuppili ◽  
Mriganka Mandal ◽  
Kakoli Bose
Keyword(s):  
Pdz Domain ◽  
Limited Proteolysis ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Multifunctional Protein ◽  
Promising Therapeutic Target ◽  
Wide Range ◽  
Structural Details ◽  
Structural Architecture ◽  
First Time

Abstract HAX-1, a multifunctional protein involved in cell proliferation, calcium homeostasis, and regulation of apoptosis, is a promising therapeutic target. It regulates apoptosis through multiple pathways, understanding of which is limited by the obscurity of its structural details and its intricate interaction with its cellular partners. Therefore, using computational modeling, biochemical, functional enzymology and spectroscopic tools, we predicted the structure of HAX-1 as well as delineated its interaction with one of it pro-apoptotic partner, HtrA2. In this study, three-dimensional structure of HAX-1 was predicted by threading and ab initio tools that were validated using limited proteolysis and fluorescence quenching studies. Our pull-down studies distinctly demonstrate that the interaction of HtrA2 with HAX-1 is directly through its protease domain and not via the conventional PDZ domain. Enzymology studies further depicted that HAX-1 acts as an allosteric activator of HtrA2. This ‘allosteric regulation’ offers promising opportunities for the specific control and functional modulation of a wide range of biological processes associated with HtrA2. Hence, this study for the first time dissects the structural architecture of HAX-1 and elucidates its role in PDZ-independent activation of HtrA2.

scholarly journals Evaluation of the Hurricane Research Division Doppler Radar Analysis Software Using Synthetic Data

2013 ◽  
Vol 30 (6) ◽  
pp. 1055-1071 ◽  
Author(s):  
Sylvie Lorsolo ◽  
John Gamache ◽  
Altug Aksoy
Keyword(s):  
Doppler Radar ◽  
Three Dimensional ◽  
Synthetic Data ◽  
Vertical Component ◽  
Radar Data ◽  
Weather Research And Forecasting ◽  
Analysis Software ◽  
Wind Fields ◽  
Research Division ◽  
Tangential Wind

Abstract The Hurricane Research Division Doppler radar analysis software provides three-dimensional analyses of the three wind components in tropical cyclones. Although this software has been used for over a decade, there has never been a complete and in-depth evaluation of the resulting analyses. The goal here is to provide an evaluation that will permit the best use of the analyses, but also to improve the software. To evaluate the software, analyses are produced from simulated radar data acquired from an output of a Hurricane Weather Research and Forecasting (HWRF) model nature run and are compared against the model “truth” wind fields. Comparisons of the three components of the wind show that the software provides analyses of good quality. The tangential wind is best retrieved, exhibiting an overall small mean error of 0.5 m s−1 at most levels and a root-mean-square error less than 2 m s−1. The retrieval of the radial wind is also quite accurate, exhibiting comparable errors, although the accuracy of the tangential wind is generally better. Some degradation of the retrieval quality is observed at higher altitude, mainly due to sparser distribution of data in the model. The vertical component of the wind appears to be the most challenging to retrieve, but the software still provides acceptable results. The tropical cyclone mean azimuthal structure and wavenumber structure are found to be very well captured. Sources of errors inherent to airborne Doppler measurements and the effects of some of the simplifications used in the simulation methodology are also discussed.

scholarly journals Dual-Doppler Analysis of Winds and Vorticity Budget Terms near a Tornado

2007 ◽  
Vol 135 (6) ◽  
pp. 2392-2405 ◽  
Author(s):  
Joshua Wurman ◽  
Yvette Richardson ◽  
Curtis Alexander ◽  
Stephen Weygandt ◽  
Peng Fei Zhang
Keyword(s):  
Three Dimensional ◽  
Wind Fields ◽  
Vertical Vorticity ◽  
Model Predictions ◽  
Vorticity Budget ◽  
Vorticity Generation ◽  
Tornadic Storms ◽  
First Time ◽  
Vector Wind ◽  
Single Set

Abstract Three-dimensional dual-Doppler observations with unprecedented finescale spatial and temporal resolution are used to characterize the vector wind field and vorticity generation terms in and near a weak, short-lived tornado. The beam widths of the two Doppler on Wheels (DOW) mobile radars, at the range of the tornado, are 250 m with gate lengths of 75 m, resulting in a resolution of less than 107 m3. One of the DOWs collected data during the 240 s prior to the formation of the tornado, enabling examination of the genesis process. A single set of volumetric scans suitable for dual-Doppler analyses were completed by both DOWs, permitting the calculation of vertical and horizontal vorticity, divergence, and stretching and tilting terms in the vorticity budget of the large but weak tornado and its surroundings, but no local tendency terms. Analyses of the dual-Doppler vector wind fields document, for the first time in a supercellular tornado, revealed several structures expected to be associated with tornadoes, including the tilting of horizontal vorticity into the vertical near the tornado, and stretching of vertical vorticity in the region of the tornado. The analyses are compared to conceptual and computer models of tornadic storms, confirming the existence of various phenomena and processes, although some model predictions, particularly those concerning the distribution of horizontal vorticity, could not be verified through these analyses. The observed magnitudes of stretching of vertical vorticity and tilting of horizontal vorticity are consistent with those necessary for generating the observed vorticity near the tornado.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of theEscherichia colicommon pilus chaperone EcpB

2015 ◽  
Vol 71 (6) ◽  
pp. 676-679 ◽  
Author(s):  
James A. Garnett ◽  
Mamou Diallo ◽  
Steve J. Matthews
Keyword(s):  
Heavy Atom ◽  
Three Dimensional ◽  
Solid Surfaces ◽  
Dimensional Structure ◽  
Molecular Replacement ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
The Common ◽  
First Time

Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. InEscherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space groupP3121 orP3221, with unit-cell parametersa=b= 62.65,c= 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.

scholarly journals Can Climate Models Capture the Structure of Extratropical Cyclones?

2010 ◽  
Vol 23 (7) ◽  
pp. 1621-1635 ◽  
Author(s):  
Jennifer L. Catto ◽  
Len C. Shaffrey ◽  
Kevin I. Hodges
Keyword(s):  
Relative Humidity ◽  
Vertical Velocity ◽  
Climate Models ◽  
Potential Temperature ◽  
Three Dimensional ◽  
Conveyor Belt ◽  
Dimensional Structure ◽  
Extratropical Cyclones ◽  
Wind Fields ◽  
Wind Speeds

Abstract Composites of wind speeds, equivalent potential temperature, mean sea level pressure, vertical velocity, and relative humidity have been produced for the 100 most intense extratropical cyclones in the Northern Hemisphere winter for the 40-yr ECMWF Re-Analysis (ERA-40) and the high resolution global environment model (HiGEM). Features of conceptual models of cyclone structure—the warm conveyor belt, cold conveyor belt, and dry intrusion—have been identified in the composites from ERA-40 and compared to HiGEM. Such features can be identified in the composite fields despite the smoothing that occurs in the compositing process. The surface features and the three-dimensional structure of the cyclones in HiGEM compare very well with those from ERA-40. The warm conveyor belt is identified in the temperature and wind fields as a mass of warm air undergoing moist isentropic uplift and is very similar in ERA-40 and HiGEM. The rate of ascent is lower in HiGEM, associated with a shallower slope of the moist isentropes in the warm sector. There are also differences in the relative humidity fields in the warm conveyor belt. In ERA-40, the high values of relative humidity are strongly associated with the moist isentropic uplift, whereas in HiGEM these are not so strongly associated. The cold conveyor belt is identified as rearward flowing air that undercuts the warm conveyor belt and produces a low-level jet, and is very similar in HiGEM and ERA-40. The dry intrusion is identified in the 500-hPa vertical velocity and relative humidity. The structure of the dry intrusion compares well between HiGEM and ERA-40 but the descent is weaker in HiGEM because of weaker along-isentrope flow behind the composite cyclone. HiGEM’s ability to represent the key features of extratropical cyclone structure can give confidence in future predictions from this model.

scholarly journals The Lagrangian structure of ozone mini-holes and potential vorticity anomalies in the Northern Hemisphere

2002 ◽  
Vol 20 (6) ◽  
pp. 835-846 ◽  
Author(s):  
P. M. James ◽  
D. Peters
Keyword(s):  
Northern Hemisphere ◽  
Potential Vorticity ◽  
Middle Atmosphere ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Synoptic Scale ◽  
Lagrangian Analysis ◽  
Band Pass ◽  
First Time ◽  
Middle Stratosphere

Abstract. An ozone mini-hole is a synoptic-scale area of strongly reduced column total ozone, which undergoes a growth-decay cycle in association with baroclinic weather systems. The tracks of mini-hole events recorded during the TOMS observation period over the Northern Hemisphere provide a database for building anomaly fields of various meteorological parameters, following each mini-hole center in a Lagrangian sense. The resulting fields provide, for the first time, a complete mean Lagrangian picture of the three-dimensional structure of typical ozone mini-holes in the Northern Hemisphere. Mini-holes are shown to be associated with anomalous warm anticyclonic flow in the upper troposphere and cold cyclonic anomalies in the middle stratosphere. Ascending air columns occur upstream and descent downstream of the mini-hole centers. Band-pass filtering is used to reveal the transient synoptic nature of mini-holes embedded within larger scale circulation anomalies. Significant correlations between ozone and Ertel’s potential vorticity on isentropes (IPV) both near the tropopause and in the middle stratosphere are shown and then utilized by reconstructing the Lagrangian analysis to follow local IPV anomalies instead of ozone minima. By using IPV as a proxy for ozone, the geopotential anomaly dipolar structure in the vertical characteristic of mini-holes is shown to result from a superposition of two largely independent dynamical components, stratospheric and tropospheric, typically operating on different time scales. Hence, ozone mini-holes may be viewed primarily as phenomena of coincidence.Key words. Meteorology and atmospheric dynamics (middle atmosphere dynamics; synoptic-scale meteorology)

Geometric morphometrics to interpret the endophytic egg-laying behavior of Odonata (Insecta) from the Eocene of Patagonia, Argentina

2019 ◽  
Vol 93 (06) ◽  
pp. 1126-1136 ◽  
Author(s):  
Eugenia Romero-Lebrón ◽  
Raquel M. Gleiser ◽  
Julián F. Petrulevičius
Keyword(s):  
Geometric Morphometrics ◽  
Relative Position ◽  
Fossil Record ◽  
Oviposition Behavior ◽  
Three Dimensional ◽  
Egg Laying ◽  
Dimensional Structure ◽  
Early Eocene ◽  
Single Female ◽  
First Time

AbstractAlthough the order Odonata has a rich fossil record, many questions about its reproductive biology remain unanswered. There are two strategies of egg laying among odonates, exophytic and endophytic, the latter being one of the most revealing vestiges of plant–insect association in the fossil record. We assessed whether geometric morphometrics based on elliptical series of Fourier allow expression of variability of shape in traces of Odonata eggs within a leaf of Eucalyptus chubutensis (Berry) González (in part), González, 2009 (Myrtaceae) from Laguna del Hunco (Chubut, Argentina) (early Eocene) and whether this variability is consistent with the ichnotaxonomy of this material. We found that the largest variation corresponds to the compression of the shape while the remaining two components reflect variations in the apex position and its curvature, which changed according to the relative position of the traces in the leaf. There was no evidence that the hardness of the leaf would affect the shape of the egg trace. We postulate that these traces could have been produced by one single female: Variations in the pattern observable in the fossil of an originally three-dimensional structure are consistent with differences in the position of the eggs inserted by a single female who has flexed her abdomen to insert the eggs as she approaches the apex of the leaf (behavior observed also in extant dragonflies). For the first time, endophytic egg traces are analyzed with geometrical morphometrics, and this allows us to make inferences on the oviposition behavior of a female that lived around 52 million years ago.

scholarly journals High pressure crystallization and crystallography of glucose isomerase

2014 ◽  
Vol 70 (a1) ◽  
pp. C1190-C1190
Author(s):  
Yoshihisa Suzuki ◽  
Masayuki Tsukamoto ◽  
Takahisa Fujiwara ◽  
Yuuta Uehara
Keyword(s):  
High Pressure ◽  
3D Structure ◽  
Three Dimensional ◽  
Protein Molecule ◽  
Glucose Isomerase ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Value Of It ◽  
First Time

Crystallization of protein is still a "bottleneck" for the three-dimensional (3D) structure analysis of a protein molecule. Therefore, the study on the acceleration of the crystallization is important. Visuri et al. repoted, for the first time, that the crystallization of glucose isomerase (GI) crystals was significantly enhanced with increasing pressure [1], while they did not discuss further effects of pressure on the crystallization. We measured solubilities, growth rates of a crystal face, step velocities and two-dimensional (2D) nucleation rates, three-dimensional (3D) nucleation rates of the GI crystal under high pressure. From these results, we found the negative molar volume change of crystallization delta V, the decrease in a step ledge surface energy and the increase in a step kinetic coefficient with increasing pressure. Activation volume of crystallization delta V‡ was discussed and the absolute value of it was almost half of that of delta V [2]. X-ray crystallography is also very important to study how the three dimensional structure of protein is related to its function under high pressure at atomic level. Kundrot et al. analyzed the crystal structure of lysozyme at 100 MPa using a beryllium (Be) cell. The crystal was prepared under 0.1 MPa. Charron et al. reported that thaumatin crystals grown under 150 MPa were analyzed under 0.1 MPa. Although Kundrot et al. concluded that the protein structure under high pressure was compressed, they could not estimate the influence of the bond structure of the crystal at 0.1 MPa on the compressed structure. In Charron's case, the thaumatin structures in crystals prepared under 0.1 MPa and 150 MPa were almost identical, when they did X-ray analyses of both crystals at 0.1 MPa. From these two results, we considered that compression of the crystals was reversible. We conducted both Kundrot's and Charron's methods for GI using a stand-alone type Be vessel [3]. We found that (1) GI molecule was reversibly compressed under high pressure, (2) the distributions of water sites around GI molecules were almost identical in the range of pressures from 0.1 to 100 MPa.

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