scholarly journals Trehalulose Synthase Native and Carbohydrate Complexed Structures Provide Insights into Sucrose Isomerization

2007 ◽  
Vol 282 (38) ◽  
pp. 28126-28136 ◽  
Author(s):  
Stéphanie Ravaud ◽  
Xavier Robert ◽  
Hildegard Watzlawick ◽  
Richard Haser ◽  
Ralf Mattes ◽  
...  
Keyword(s):  
Substrate Recognition ◽  
Three Dimensional ◽  
Enzyme Reaction ◽  
Structural Data ◽  
Side Reactions ◽  
Binding Modes ◽  
Product Specificity ◽  
Reaction Specificity ◽  
First Time ◽  
Enzyme Targeting

Various diseases related to the overconsumption of sugar make a growing need for sugar substitutes. Because sucrose is an inexpensive and readily available d-glucose donor, the industrial potential for enzymatic synthesis of the sucrose isomers trehalulose and/or isomaltulose from sucrose is large. The product specificity of sucrose isomerases that catalyze this reaction depends essentially on the possibility for tautomerization of sucrose, which is required for trehalulose formation. For optimal use of the enzyme, targeting controlled synthesis of these functional isomers, it is necessary to minimize the side reactions. This requires an extensive analysis of substrate binding modes and of the specificity-determining sites in the structure. The 1.6-2.2-Å resolution three-dimensional structures of native and mutant complexes of a trehalulose synthase from Pseudomonas mesoacidophila MX-45 mimic successive states of the enzyme reaction. Combined with mutagenesis studies they give for the first time thorough insights into substrate recognition and processing and reaction specificities of these enzymes. Among the important outcomes of this study is the revelation of an aromatic clamp defined by Phe256 and Phe280 playing an essential role in substrate recognition and in controlling the reaction specificity, which is further supported by mutagenesis studies. Furthermore, this study highlights essential residues for binding the glucosyl and fructosyl moieties. The introduction of subtle changes informed by comparative three-dimensional structural data observed within our study can lead to fundamental modifications in the mode of action of sucrose isomerases and hence provide a template for industrial catalysts.

scholarly journals Cobalt-based magnetic Weyl semimetals with high-thermodynamic stabilities

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Wei Luo ◽  
Yuma Nakamura ◽  
Jinseon Park ◽  
Mina Yoon
Keyword(s):  
Tight Binding ◽  
Three Dimensional ◽  
Interlayer Coupling ◽  
First Principles Calculation ◽  
Optimization Approach ◽  
Binding Model ◽  
Nodal Lines ◽  
Weyl Semimetal ◽  
Topological Quantum ◽  
First Time

AbstractRecent experiments identified Co3Sn2S2 as the first magnetic Weyl semimetal (MWSM). Using first-principles calculation with a global optimization approach, we explore the structural stabilities and topological electronic properties of cobalt (Co)-based shandite and alloys, Co3MM’X2 (M/M’ = Ge, Sn, Pb, X = S, Se, Te), and identify stable structures with different Weyl phases. Using a tight-binding model, for the first time, we reveal that the physical origin of the nodal lines of a Co-based shandite structure is the interlayer coupling between Co atoms in different Kagome layers, while the number of Weyl points and their types are mainly governed by the interaction between Co and the metal atoms, Sn, Ge, and Pb. The Co3SnPbS2 alloy exhibits two distinguished topological phases, depending on the relative positions of the Sn and Pb atoms: a three-dimensional quantum anomalous Hall metal, and a MWSM phase with anomalous Hall conductivity (~1290 Ω−1 cm−1) that is larger than that of Co2Sn2S2. Our work reveals the physical mechanism of the origination of Weyl fermions in Co-based shandite structures and proposes topological quantum states with high thermal stability.

scholarly journals Shell-crossing in a ΛCDM Universe

2020 ◽  
Vol 501 (1) ◽  
pp. L71-L75
Author(s):  
Cornelius Rampf ◽  
Oliver Hahn
Keyword(s):  
Dark Matter ◽  
Perturbation Theory ◽  
Large Scale ◽  
Cold Dark Matter ◽  
Three Dimensional ◽  
Random Initial Data ◽  
Recursion Relations ◽  
Indispensable Tool ◽  
First Time ◽  
Very High

ABSTRACT Perturbation theory is an indispensable tool for studying the cosmic large-scale structure, and establishing its limits is therefore of utmost importance. One crucial limitation of perturbation theory is shell-crossing, which is the instance when cold-dark-matter trajectories intersect for the first time. We investigate Lagrangian perturbation theory (LPT) at very high orders in the vicinity of the first shell-crossing for random initial data in a realistic three-dimensional Universe. For this, we have numerically implemented the all-order recursion relations for the matter trajectories, from which the convergence of the LPT series at shell-crossing is established. Convergence studies performed at large orders reveal the nature of the convergence-limiting singularities. These singularities are not the well-known density singularities at shell-crossing but occur at later times when LPT already ceased to provide physically meaningful results.

scholarly journals Imaging the Human Thyroid Using Three-Dimensional Diffuse Optical Tomography: A Preliminary Study

2021 ◽  
Vol 11 (4) ◽  
pp. 1670
Author(s):  
Tetsuya Mimura ◽  
Shinpei Okawa ◽  
Hiroshi Kawaguchi ◽  
Yukari Tanikawa ◽  
Yoko Hoshi
Keyword(s):  
Optical Tomography ◽  
Tumor Hypoxia ◽  
Three Dimensional ◽  
Diffuse Optical Tomography ◽  
Element Model ◽  
Needle Aspiration ◽  
Human Thyroid ◽  
Tissue Oxygen Saturation ◽  
Preliminary Study ◽  
First Time

Thyroid cancer is usually diagnosed by ultrasound imaging and fine-needle aspiration biopsy. However, diagnosis of follicular thyroid carcinomas (FTC) is difficult because FTC lacks nuclear atypia and a consensus on histological interpretation. Diffuse optical tomography (DOT) offers the potential to diagnose FTC because it can measure tumor hypoxia, while image reconstruction of the thyroid is still challenging mainly due to the complex anatomical features of the neck. In this study, we attempted to solve this issue by creating a finite element model of the human neck excluding the trachea (a void region). By reconstruction of the absorption coefficients at three wavelengths, 3D tissue oxygen saturation maps of the human thyroid are obtained for the first time by DOT.

scholarly journals The on-axis magnetic well and Mercier's criterion for arbitrary stellarator geometries

2021 ◽  
Vol 87 (2) ◽  
Author(s):  
P. Kim ◽  
R. Jorge ◽  
W. Dorland
Keyword(s):  
Magnetic Field ◽  
Original Work ◽  
Three Dimensional ◽  
Radial Distance ◽  
Analytical Form ◽  
One Dimensional ◽  
Modern Notation ◽  
Magnetic Well ◽  
First Time ◽  
Dimensional Integral

A simplified analytical form of the on-axis magnetic well and Mercier's criterion for interchange instabilities for arbitrary three-dimensional magnetic field geometries is derived. For this purpose, a near-axis expansion based on a direct coordinate approach is used by expressing the toroidal magnetic flux in terms of powers of the radial distance to the magnetic axis. For the first time, the magnetic well and Mercier's criterion are then written as a one-dimensional integral with respect to the axis arclength. When compared with the original work of Mercier, the derivation here is presented using modern notation and in a more streamlined manner that highlights essential steps. Finally, these expressions are verified numerically using several quasisymmetric and non-quasisymmetric stellarator configurations including Wendelstein 7-X.

scholarly journals Towards an Improved Model of the Galaxy

1998 ◽  
Vol 11 (1) ◽  
pp. 570-570
Author(s):  
Johan Holmberg ◽  
Lennart Lindegren ◽  
Chris Flynn
Keyword(s):  
Three Dimensional ◽  
Direct Determination ◽  
Galactic Structure ◽  
Open Clusters ◽  
Selection Effects ◽  
Observational Errors ◽  
Red Giant ◽  
Improved Model ◽  
First Time ◽  
Hr Diagram

We use the Hipparcos survey to derive an improved model of the local galactic structure. The availability of parallaxes for all the stars permits direct determination of stellar distributions, eliminating the basic indeterminacy of classical methods based on star counts. Hipparcos gives for the first time a truly three-dimensional view of the solar vicinity, and a complete, homogeneous and highly accurate set of magnitudes and colours. This means that new techniques can be applied in the treatment of the data which place strong constraints on a model that tries to describe the local Galactic structure. Here we investigate how well a static model of low complexitycan describe the Hipparcos observations. The interpretation of the Hipparcos data is complicated by various observational errors and selection effects that are hard to treat correctly. We do not try to correct the data, but instead use a model and subject this model to the same observational errors and selection effects. A model catalogue is created that can be compared with the observed catalogue directly in the observational domain, thereby eliminating the effects from various biases. Many features in the HR diagram are for the first time seen in field stars thanks to Hipparcos, such as the slanted red giant clump, previously seen in rich old open clusters such as Berkeley 18. This and other features ofthe observed HR diagram are well reproduced by the model thanks to the rather detailed modelling of the joint Mv/B — V distribution. Actually, separate distributions were derived for the three different components, disk, thick disk and halo, using the kinematic characteristics of the components to discriminate between them.

scholarly journals Three-Dimensional Structures of Carbohydrates and Where to Find Them

2020 ◽  
Vol 21 (20) ◽  
pp. 7702 ◽  
Author(s):  
Sofya I. Scherbinina ◽  
Philip V. Toukach
Keyword(s):  
Experimental Data ◽  
Molecular Modeling ◽  
Computational Methods ◽  
Three Dimensional ◽  
Structural Diversity ◽  
Structural Data ◽  
Structural Features ◽  
Data Validation ◽  
Data Generation ◽  
Efficient Treatment

Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.

A New Category of Three-Dimensional Chaotic Flows with Identical Eigenvalues

2020 ◽  
Vol 30 (02) ◽  
pp. 2050026 ◽  
Author(s):  
Zahra Faghani ◽  
Fahimeh Nazarimehr ◽  
Sajad Jafari ◽  
Julien C. Sprott
Keyword(s):  
Chaotic Systems ◽  
Autonomous Systems ◽  
Three Dimensional ◽  
Special Property ◽  
Computer Search ◽  
Chaotic Flows ◽  
Stable Equilibria ◽  
Dynamical Properties ◽  
Simple Systems ◽  
First Time

In this paper, some new three-dimensional chaotic systems are proposed. The special property of these autonomous systems is their identical eigenvalues. The systems are designed based on the general form of quadratic jerk systems with 10 terms, and some systems with stable equilibria. Using a systematic computer search, 12 simple chaotic systems with identical eigenvalues were found. We believe that systems with identical eigenvalues are described here for the first time. These simple systems are listed in this paper, and their dynamical properties are investigated.

Mesoscopic characterization of the optical property of antiphase boundaries in CuPt-ordered GaInP2

1999 ◽  
Vol 588 ◽  
Author(s):  
Y. Ohno ◽  
S. Takeda
Keyword(s):  
Optical Property ◽  
Light Emission ◽  
Polarized Light ◽  
Structural Data ◽  
Luminescence Spectra ◽  
Antiphase Boundaries ◽  
Transmission Electron ◽  
Tem Method ◽  
Low Dimensional ◽  
First Time

AbstractWe have developed an apparatus for polarized cathodoluminescence (CL) spectroscopy combined with transmission electron microscopy (TEM), that enables us to obtain simultaneously structural data in higher spatial resolution by TEM and polarized luminescence spectra by CL of the same microscopic area. The polarized-CL/TEM method is very useful to study the optical properties of low-dimensional microstructures in semiconducting materials. We have applied the method to examine the optical property of antiphase boundaries in CuPt-ordered GaInP2 and found, for the first time, the polarized light emission from the APBs whose habit planes are parallel to the (T11) and (1T0) atomic planes.

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.

Diagnosis of COVID-19 using 3D CT scans and vaccination for COVID-19

2021 ◽  
Vol ahead-of-print (ahead-of-print) ◽  
Author(s):  
Gangadhar Ch ◽  
S. Jana ◽  
Sankararao Majji ◽  
Prathyusha Kuncha ◽  
Fantin Irudaya Raj E. ◽  
...  
Keyword(s):  
Virus Isolate ◽  
Research Work ◽  
Three Dimensional ◽  
Ct Scans ◽  
Data Sets ◽  
Content Type ◽  
Infected People ◽  
3D Data ◽  
Ct Classification ◽  
First Time

Purpose For the first time in a decade, a new form of pneumonia virus, coronavirus, COVID-19, appeared in Wuhan, China. To date, it has affected millions of people, killed thousands and resulted in thousands of deaths around the world. To stop the spread of this virus, isolate the infected people. Computed tomography (CT) imaging is very accurate in revealing the details of the lungs and allows oncologists to detect COVID. However, the analysis of CT scans, which can include hundreds of images, may cause delays in hospitals. The use of artificial intelligence (AI) in radiology could help to COVID-19-positive cancer in this manner is the main purpose of the work. Design/methodology/approach CT scans are a medical imaging procedure that gives a three-dimensional (3D) representation of the lungs for clinical purposes. The volumetric 3D data sets can be regarded as axial, coronal and transverse data sets. By using AI, we can diagnose the virus presence. Findings The paper discusses the use of an AI for COVID-19, and CT classification issue and vaccination details of COVID-19 have been detailed in this paper. Originality/value Originality of the work is, all the data can be collected genuinely and did research work doneown methodology.

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