Computerized sequence-based predictive methods: their use in the conformational characterization of proteins and in the analysis of their homologies a practical case employing lysozyme and α-lactalbumin

The percolating morphology is adopted as a reference conceptualization to evaluate the “fractality” effect on the transport phenomena in disordered systems. The relevance of this approach is demonstrated using two practical case studies: conducting polymers and porous media. In the first case, a conceptual model for conducting polymers is proposed in terms of a random resistor network subjected to percolation disorder. The effect of topological and morphological disorder on the conducting behavior of an idealized system is investigated and some insights, are given as to the way in which conducting polymers could be designed. In the second case, the examination of effective transport properties in percolation-like porous structures enables us to reinterpret the classical guidelines for the characterization of fluid flow through porous beds.

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Integrated approach for the molecular characterization of edited plants obtained via Agrobacterium tumefaciens-mediated gene transfer

European Food Research and Technology ◽

10.1007/s00217-021-03881-0 ◽

2021 ◽

Author(s):

Lorenza Dalla Costa ◽

Daniela Vinciguerra ◽

Lisa Giacomelli ◽

Umberto Salvagnin ◽

Stefano Piazza ◽

...

Keyword(s):

Agrobacterium Tumefaciens ◽

Gene Transfer ◽

Molecular Characterization ◽

Good Practice ◽

Integrated Approach ◽

Digital Pcr ◽

Plant Genome ◽

Practical Case ◽

Knock Out

AbstractAgrobacterium tumefaciens-mediated gene transfer—actually the most used method to engineer plants—may lead to integration of multiple copies of T-DNA in the plant genome, as well as to chimeric tissues composed of modified cells and wild type cells. A molecular characterization of the transformed lines is thus a good practice to select the best ones for further investigation. Nowadays, several quantitative and semi-quantitative techniques are available to estimate the copy number (CN) of the T-DNA in genetically modified plants. In this study, we compared three methods based on (1) real-time polymerase chain reaction (qPCR), (2) droplet digital PCR (ddPCR), and (3) next generation sequencing (NGS), to carry out a molecular characterization of grapevine edited lines. These lines contain a knock-out mutation, obtained via CRISPR/Cas9 technology, in genes involved in plant susceptibility to two important mildew diseases of grapevine. According to our results, qPCR and ddPCR outputs are largely in agreement in terms of accuracy, especially for low CN values, while ddPCR resulted more precise than qPCR. With regard to the NGS analysis, the CNs detected with this method were often not consistent with those calculated by qPCR and ddPCR, and NGS was not able to discriminate the integration points in three out of ten lines. Nevertheless, the NGS method can positively identify T-DNA truncations or the presence of tandem/inverted repeats, providing distinct and relevant information about the transgene integration asset. Moreover, the expression analysis of Cas9 and single guide RNA (sgRNA), and the sequencing of the target site added new information to be related to CN data. This work, by reporting a practical case-study on grapevine edited lines, explores pros and cons of the most advanced diagnostic techniques available for the precocious selection of the proper transgenic material. The results may be of interest both to scientists developing new transgenic lines, and to laboratories in charge of GMO control.

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Characterization of Heavy Oils. 2. Definition of a Significant Characterizing Parameter To Ensure the Reliability of Predictive Methods for PVT Calculations

Industrial & Engineering Chemistry Research ◽

10.1021/ie00044a039 ◽

1995 ◽

Vol 34 (5) ◽

pp. 1873-1881 ◽

Cited By ~ 10

Author(s):

Jean-Noeel Jaubert ◽

Evelyne Neau

Keyword(s):

Heavy Oils ◽

Predictive Methods ◽

Definition Of

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Morphological Characterization of Mycobacteriophage R1

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051281 ◽

1974 ◽

Vol 32 ◽

pp. 254-255

Author(s):

B. L. Soloff ◽

T. A. Rado

Keyword(s):

Carbon Source ◽

Stationary Phase ◽

Growth Phase ◽

Minimal Medium ◽

Morphological Characterization ◽

Logarithmic Growth Phase ◽

Complete Lysis ◽

Lysogenic Culture ◽

Logarithmic Growth

Mycobacteriophage R1 was originally isolated from a lysogenic culture of M. butyricum. The virus was propagated on a leucine-requiring derivative of M. smegmatis, 607 leu−, isolated by nitrosoguanidine mutagenesis of typestrain ATCC 607. Growth was accomplished in a minimal medium containing glycerol and glucose as carbon source and enriched by the addition of 80 μg/ ml L-leucine. Bacteria in early logarithmic growth phase were infected with virus at a multiplicity of 5, and incubated with aeration for 8 hours. The partially lysed suspension was diluted 1:10 in growth medium and incubated for a further 8 hours. This permitted stationary phase cells to re-enter logarithmic growth and resulted in complete lysis of the culture.

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AEM analysis of crystallization in Ti-based amorphous alloys

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100075142 ◽

1983 ◽

Vol 41 ◽

pp. 270-271

Author(s):

A.R. Pelton ◽

A.F. Marshall ◽

Y.S. Lee

Keyword(s):

Magnetic Properties ◽

Amorphous Alloys ◽

Amorphous Materials ◽

Isothermal Annealing ◽

Amorphous Matrix ◽

Nucleation And Growth ◽

Current Interest ◽

Amorphous Films ◽

Electrical And Magnetic Properties

Amorphous materials are of current interest due to their desirable mechanical, electrical and magnetic properties. Furthermore, crystallizing amorphous alloys provides an avenue for discerning sequential and competitive phases thus allowing access to otherwise inaccessible crystalline structures. Previous studies have shown the benefits of using AEM to determine crystal structures and compositions of partially crystallized alloys. The present paper will discuss the AEM characterization of crystallized Cu-Ti and Ni-Ti amorphous films.Cu60Ti40: The amorphous alloy Cu60Ti40, when continuously heated, forms a simple intermediate, macrocrystalline phase which then transforms to the ordered, equilibrium Cu3Ti2 phase. However, contrary to what one would expect from kinetic considerations, isothermal annealing below the isochronal crystallization temperature results in direct nucleation and growth of Cu3Ti2 from the amorphous matrix.

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Characterization of Coherent, Ordered Precipitates in Nickel-Base Alloys

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071168 ◽

1973 ◽

Vol 31 ◽

pp. 144-145

Author(s):

B. H. Kear ◽

J. M. Oblak

Keyword(s):

Stable Phase ◽

Nickel Base Superalloy ◽

Alloy 718 ◽

Commercial Alloy ◽

Precipitate Morphology ◽

Continuous Precipitation ◽

Nickel Base ◽

Base Superalloy ◽

Strengthening Precipitate

A nickel-base superalloy is essentially a Ni/Cr solid solution hardened by additions of Al (Ti, Nb, etc.) to precipitate a coherent, ordered phase. In most commercial alloy systems, e.g. B-1900, IN-100 and Mar-M200, the stable precipitate is Ni3 (Al,Ti) γ′, with an LI2structure. In A lloy 901 the normal precipitate is metastable Nis Ti3 γ′ ; the stable phase is a hexagonal Do2 4 structure. In Alloy 718 the strengthening precipitate is metastable γ″, which has a body-centered tetragonal D022 structure.Precipitate MorphologyIn most systems the ordered γ′ phase forms by a continuous precipitation re-action, which gives rise to a uniform intragranular dispersion of precipitate particles. For zero γ/γ′ misfit, the γ′ precipitates assume a spheroidal.

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The Use of Advanced Analytical Techniques for Characterization of the Chemical, Physical, and Crystallographic Nature of a Surface

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100071107 ◽

1973 ◽

Vol 31 ◽

pp. 132-133 ◽

Cited By ~ 1

Author(s):

R. E. Herfert

Keyword(s):

Surface Characterization ◽

Analytical Techniques ◽

X Ray Diffraction ◽

Depth Of Penetration ◽

X Ray ◽

The Past ◽

Transmission Electron ◽

Scanning Electron

Studies of the nature of a surface, either metallic or nonmetallic, in the past, have been limited to the instrumentation available for these measurements. In the past, optical microscopy, replica transmission electron microscopy, electron or X-ray diffraction and optical or X-ray spectroscopy have provided the means of surface characterization. Actually, some of these techniques are not purely surface; the depth of penetration may be a few thousands of an inch. Within the last five years, instrumentation has been made available which now makes it practical for use to study the outer few 100A of layers and characterize it completely from a chemical, physical, and crystallographic standpoint. The scanning electron microscope (SEM) provides a means of viewing the surface of a material in situ to magnifications as high as 250,000X.

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Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074768 ◽

1983 ◽

Vol 41 ◽

pp. 194-195

Author(s):

D. F. Blake ◽

L. F. Allard ◽

D. R. Peacor

Keyword(s):

High Resolution ◽

Marine Invertebrates ◽

Sea Urchins ◽

Structural Features ◽

Sea Stars ◽

High Resolution Tem ◽

Relationship Of ◽

The Relationship ◽

Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

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Some applications of electron beam microanalysis techniques in VLSI process evaluation

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010007463x ◽

1983 ◽

Vol 41 ◽

pp. 160-161

Author(s):

Simon Thomas

Keyword(s):

Integrated Circuits ◽

Process Evaluation ◽

Large Scale ◽

Technology Development ◽

Analytical Techniques ◽

Successful Implementation ◽

Analysis Of Failures ◽

Characterization Of Materials ◽

Circuits Vlsi

Trends in the technology development of very large scale integrated circuits (VLSI) have been in the direction of higher density of components with smaller dimensions. The scaling down of device dimensions has been not only laterally but also in depth. Such efforts in miniaturization bring with them new developments in materials and processing. Successful implementation of these efforts is, to a large extent, dependent on the proper understanding of the material properties, process technologies and reliability issues, through adequate analytical studies. The analytical instrumentation technology has, fortunately, kept pace with the basic requirements of devices with lateral dimensions in the micron/ submicron range and depths of the order of nonometers. Often, newer analytical techniques have emerged or the more conventional techniques have been adapted to meet the more stringent requirements. As such, a variety of analytical techniques are available today to aid an analyst in the efforts of VLSI process evaluation. Generally such analytical efforts are divided into the characterization of materials, evaluation of processing steps and the analysis of failures.

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Irradiation behavior of pyrolytic silicon carbide

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074288 ◽

1983 ◽

Vol 41 ◽

pp. 72-73

Author(s):

R. J. Lauf

Keyword(s):

Silicon Carbide ◽

Fission Products ◽

Thermodynamics And Kinetics ◽

Neutron Fluences ◽

Fuel Particles ◽

Sic Coatings ◽

Irradiation Behavior ◽

Kinetics Of ◽

Htgr Fuel

Fuel particles for the High-Temperature Gas-Cooled Reactor (HTGR) contain a layer of pyrolytic silicon carbide to act as a miniature pressure vessel and primary fission product barrier. Optimization of the SiC with respect to fuel performance involves four areas of study: (a) characterization of as-deposited SiC coatings; (b) thermodynamics and kinetics of chemical reactions between SiC and fission products; (c) irradiation behavior of SiC in the absence of fission products; and (d) combined effects of irradiation and fission products. This paper reports the behavior of SiC deposited on inert microspheres and irradiated to fast neutron fluences typical of HTGR fuel at end-of-life.

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