Determination of structure and methods of analysis

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Modern Methods of Protein Crystal Structure Determination and Structural Analysis of RNA Polymerase

Modern Methods of Protein Crystal Structure Determination and Structural Analysis of RNA Polymerase

X-ray protein structure analysis methods are relatively new and fast developing tools for determination of structure of organic macromolecules. The potential to provide a protein or nucleic acid structure at atomic resolution is one of the clear advantages of this method. The whole process, which leads to the final structure, consists of many steps and can last from weeks to years. For structure determination, usually a few milligrams of protein at a concentration of the order of tens of mg ml -1 is needed. Another part of the process is sample characterisation using dynamic light scattering (DLS), denaturing and native electrophoresis, mass spectroscopy (such as MALDI – Matrix Assisted Laser Desorption Ionization), spectroscopic methods and other biochemical techniques. Then, or in parallel with protein characterisation, crystallization follows. After suitable crystals have been obtained, diffraction experiments take over in the procedure. The last set of steps consists of the methods used to solve and refine the final structure.
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Application of X-ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis

Application of X-ray Diffraction Methods and Molecular Mechanics Simulations to Structure Determination and Cotton Fiber Analysis

SHELXTL is an integrated system of computer programs for the determination and refinement of crystal structures using diffraction data, and provides simple steps for publication of the results. The program XS is used to generate trial structure solutions by calculating the phases of a subset of the hkl reflections from the SAINT output file. The program uses a number of different methods to try and guess the phases, and from them the identity and location of most atoms in the crystal. Hydrogen atoms are not usually found using this program. If XS is successful, then the trial structure generated may be examined by XP, a program for the visualization and editing of molecular structures. After a trial structure has been created, subsequent refinement cycles by XL, a least-square refinement program, and XP will eventually lead to finding all of the atoms. The two most common approaches used by XS to determine phases are direct methods and Patterson methods. Since the structure being investigated contains only small atomic number atoms, direct methods is the proper choice. As mentioned previously, the Direct methods approach is based on statistical analyses of the intensities of the reflections to find the most probable phase relationships. Remember, the phases cannot be determined experimentally and have to be calculated and combined with the experimentally determined amplitudes to give an electron density map. The Direct methods solutions from XS yield a list of positions called Qs. These Qs are peaks of normalized electron density found in the calculated E- map.
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Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Determination of genetic structure of germplasm collections: are traditional hierarchical clustering methods appropriate for molecular marker data?

Abstract Despite the availability of newer approaches, traditional hierarchical clustering remains very popular in genetic diversity studies in plants. However, little is known about its suitability for molecular marker data. We studied the performance of traditional hierarchical clustering techniques using real and simulated molecular marker data. Our study also compared the performance of tradi- tional hierarchical clustering with model-based clustering (STRUCTURE). We showed that the cophenetic correla- tion coefficient is directly related to subgroup differentia- tion and can thus be used as an indicator of the presence of genetically distinct subgroups in germplasm collections. Whereas UPGMA performed well in preserving distances between accessions, Ward excelled in recovering groups. Our results also showed a close similarity between clusters obtained by Ward and by STRUCTURE. Traditional cluster analysis can provide an easy and effective way of determining structure in germplasm collections using molecular marker data, and, the output can be used for sampling core collections or for association studies.
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Determination of Trophic Structure in Selected Freshwater Ecosystems by using Stable Isotope Analysis

Determination of Trophic Structure in Selected Freshwater Ecosystems by using Stable Isotope Analysis

Ten samples in each sampling site were collected for this study. Several dominant families in each study area were collected to represent each trophic level in their food web. Samples of plants that represents the producer; aquatic macroinvertebrates as the primary and secondary consumer; and fish as tertiary consumer were collected randomly in all study sites for stable isotope analysis to compare the trophic levels in the food web. Samples preparation for the analysis was adopted from methods described by Jardine et al. (2003) and Salas and Dudgeon (2001). All collected samples were cleaned, oven dried at 50 o C–60 o C for two days and the tissues were
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In situ structure determination by subtomogram averaging

In situ structure determination by subtomogram averaging

Classification methods that have been reported to deal with heterogeneity can be separated into i) approaches aimed at characterising the heterogeneity of an aligned data set, and ii) algorithms performing classification and alignment simultaneously. In the former group, a fre- quent starting point is the exhaustive computation of the similarity of each pair of aligned subtomograms, giving rise to a covariance matrix. This matrix can be used to feed a Hierarchical Clustering method that locates groups of mutually similar particles [48], or as basis for a Principal Component Analysis [49], a widely used method for complexity reduction that captures the spatial features describing the largest sources of structural variance in the data set. Such features (eigen volumes) appear in order of relevance and can be used to express each particle as a reduced number of coefficients, which can then be clus- tered through k-means. Performance of these methods has been shown to improve significantly by a data-driven tuning of frequency band used to measure particle simi- larity [34].
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Protein 3D structure determination using homology modeling and structure analysis

Protein 3D structure determination using homology modeling and structure analysis

ficult and challenging problem. Basically X- ray crystallography or nuclear magnetic reso- nance (NMR) techniques are used, which are expensive, time consuming and complex proc- ess. Therefore, computational methods/ algorithms including homology modeling, threading, and ab initio are developed. Homol- ogy modeling is the most accurate. It is based on alignment to a known protein structure which is derived experimentally (template). If the similarity of the sequence is greater than 30% then it can act as template.

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Development of nuclear magnetic resonance methods for determination of membrane protein structure

Development of nuclear magnetic resonance methods for determination of membrane protein structure

P a g e | 13 presence of detergent when crystallising can prevent the formation of crystal contacts and can also result in distorted structures due to curvature stress induced by the small diameter of detergent micelles. X-ray crystallography is also more suited to larger multi-spanning membrane proteins as larger proteins crystallise more readily than smaller proteins, as the larger the protein the greater the surface area for which crystal contacts can form that are required for crystal growth. For smaller proteins the surface area is greatly reduced thereby reducing the possibility of forming electrostatic contacts between unit cells in a crystal thereby reducing the possibility of forming diffraction quality crystals for analysis, although in recent years the crystallography of membrane proteins in lipid membranes has become viable by the growth of crystals in lipidic mesophases (also referred to as Lipid cubic phase (LCP) crystallisation (Landau and Rosenbusch 1996; Cherezov 2011; Caffrey, Li et al. 2012). Lipids in the LCP form highly curved bilayers that form cubic lattice structures. First used to obtain high resolution structural data for bacteriorhopdsin (Landau and Rosenbusch 1996) this method has now been used to crystallise a variety of bitopic membrane proteins including GPCRs and helical proteins (Cherezov, Rosenbaum et al. 2007; Jaakola, Griffith et al. 2008; Wu, Chien et al. 2010). Therefore whilst X-ray crystallography is positioned to provide high resolution structures at atomic resolution, the strategies involved in producing viable crystallisation conditions can often result in structures that differ vastly from their native form (Cross, Arseniev et al. 1999).
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STRUCTURAL SAFETY DETERMINATION METHODS UDC =111

STRUCTURAL SAFETY DETERMINATION METHODS UDC =111

The methods providing functional safety have two intertwined areas. Firstly, changing of conditions for three elaborated methods, and secondly, determination of limits which must exceed the design loads. Both in case of stress factors and of load factors the varia- tions of safety factors can be applied, because the purpose is to maintain the elastic char- acter of the structure at design loads. However, the stress factor is usually the functional factor when it is applied in the previously mentioned manner. In this case, when deter- mining the design stress, we observe the cumulative load, without the analysis of func- tional damage regarding the safety factor. Determining the safety degree of the functional damage with the relation method consists in determining the result of S F strength value related to the functional risk, according to the service load L 1 . In the probability method, such value of functional damage probability is determined, which must not be exceeded. This probability concerns the service load which exceeds the functional strength of the structure. In the combined method of probability and relation the minimum relation pro- viding that the given probability of the functional load is not exceeded is determined.
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The determination methods for non ionic surfactants

The determination methods for non ionic surfactants

Shao Bing [25] establishes the NPnEO determination of pseudo-reverse phase chromatography using Capcell Pak C18 column and Waters Spherisorb SW3, improving the reproducibility of the experiment and the separation effect. Mobile phase A and B are respectively ultrapure water and acetonitrile in gradient elution. Fluorescence excitation wavelength is 230 nm, and emission wavelength is 305 nm. Combined with graphitized carbon black solid phase extraction techniques, the method can measure simultaneously NPnEO (EO values up to 28) in 30 min, recoveries are over 90%, the detection limits of standard NPnEO samples (n=1~6) are 10 g/L (S/N=10). The Jialing and Yangtze water samples are measured NPnEO with this method, and the total concentration NPnEO is between 1.99 g/L and 37.28 g/L.
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Statistical analysis of networks with community structure and bootstrap methods for big data

Statistical analysis of networks with community structure and bootstrap methods for big data

Resampling methodology for dependent data such as time series and spatial data have undergone rapid developments since K¨ unsch (1989) and Liu and Singh (1992) introduced the moving block bootstrap independently. The block-based bootstrap and subsampling methods [Politis and Romano (1994)] have been proved to be very useful nonparametric resampling techniques in the inference of regularly spaced time series and spatial data. The block-based resampling/subsampling method- ology, although still applicable and theoretically justified to irregularly spaced time series and spatial data, are practically inconvenient to use. Here we mention Hall (1985), Politis and Romano (1993), Sherman and Carlstein (1994), Sherman (1996), Garcia-Soidan and Hall (1997), Politis et al. (1998), Lahiri (1999), Lahiri et al. (1999), Politis and Sherman (2001), and Nordman and Lahiri (2004), among others for important work along this line. For time series data, the irregularity can occur if there are missing values for a equally-spaced time series, or the time points at which the observation are taken are generated from a one-dimensional point process. In the spatial setting, the irregularly spaced data, which can be in the form of lattice data with an irregular shape of the sampling region, or nonlat- tice data with spatial locations generated from a spatial point process, are quite common.
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Crack Length Determination by Ultrasonic Methods

Crack Length Determination by Ultrasonic Methods

Crack Length From Time-of-Flight Crack length measurement using the technique shown in Figure 1 2 as developed by Silk [5] determines the crack length by the time of flight of the wave d[r]

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METHODS FOR DETERMINATION OF ANTIOXIDANT CAPACITY: A REVIEW

METHODS FOR DETERMINATION OF ANTIOXIDANT CAPACITY: A REVIEW

Total Phenolic Assay by Folin-Ciocalteau reagent: Folin-Ciocalteau (FC) colorimetry is based on early work of Singleton and Rossi’s method of chemical reduction of the reagent, a mixture of tungsten and molybdenum oxides. This method was originally intended for the analysis of proteins like tyrosine 37 containing a phenolic group but later extended by Singleton et al for analyzing the total phenolic content in wine. This method is sensitive, quantitative and relatively independent of the degree of polymerization of phenols but correction for proteins, nucleic acids and ascorbic acid may be required for their interfering action.
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Research on the Structure of Public Fiscal Expenditure Based on the Cluster Analysis Methods

Research on the Structure of Public Fiscal Expenditure Based on the Cluster Analysis Methods

Throughout the related fields of study abroad, mostly to the fiscal expenditure structure is divided into pro- ductive and non-productive expenditure, or further subdivided into constructive spending, consumer spending, as well as science, education spending, agriculture production and spending. Expenditure structure of financial impact of economic growth, the division is essential expenditure structure, and the current study for the division of fiscal expenditure structure often artificial division based on empirical judgment, lack of rigor, factor analysis can solve this problem. This paper attempts to use is the main factor analysis of fiscal expenditure structure is divided. In addition, studies of local government during regional analysis, only will be divided into eastern, cen- tral and west, there is no difference in the classification based on the specific expenditure structure of local gov- ernment finances, the paper cluster analysis on the basis of principal component analysis as a basis for the structure of local government fiscal expenditure divided into five categories, to facilitate targeted policy recom- mendations.
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Comparison of Headwater Stream Origin Determination Methods

Comparison of Headwater Stream Origin Determination Methods

The classification of the predictions is instructive and not intended to be an empirical measure of accuracy. The purpose of this study is to demonstrate how well frequently used data such as DRGs, and DLGs, as well as terrain analysis of elevation data reflect actual findings in the field. The goal of this instructive approach is to explore the usefulness of each data layer and analysis technique rather than empirically validating each stream origin prediction. Moreover, validation of the GPS field determinations alone would require effort and funding beyond the scope of this exploratory study. Therefore, no attempt to quantify omission or commission error is made here. Further, this alternative approach is less of a commentary on the quality of research presented, but more an acknowledgement of the difficulty inherent in quantifying discrete landscape features, such as streams, at a landscape scale.
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Pharmacological analysis and structure determination of
7 methylcyanopindolol–bound b1 adrenergic receptor

Pharmacological analysis and structure determination of 7 methylcyanopindolol–bound b1 adrenergic receptor

Rasmussen SG, Devree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah ST, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, and Kobilka BK (2011b) Crystal structure of the beta(2) adrenergic receptor-Gs protein complex. Nature 477: 549-555.

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Comparative analysis of protein quantification methods for the rapid determination of protein loading in liposomal formulations

Comparative analysis of protein quantification methods for the rapid determination of protein loading in liposomal formulations

Currently, there are a range of techniques available to quantify the protein loading capacities of drug delivery systems (Table 1) [13–19]. Protein quantification techniques can include bicinchoninic acid assay (BCA), variations of high-performance liquid-based chromatography (HPLC) and the use of fluorescently labelled or radio-chemically labelled proteins. Less novel chemical analytical techniques also include the use of the Kjeldahl method to determine the nitrogen content in organic substances. The BCA assay uses peptide bonds in the protein reducing Cu 2+ to Cu + at a rate proportional to the amount of protein present. The bicinchoninic acid reagent then binds with the Cu + , forming a complex which absorbs light around 562 nm wavelength, allowing a direct correlation between protein concentration within a sample and absorbance to be made [20]. Whilst the BCA assay can be utilised for large sample screening given the microplate setup, limitations still exist involving interference from a range of agents, including lipids. Other high throughput methods, such as HPLC, can be used to quantify protein, with many variations of HPLC techniques available [21,22], including reverse phase (RP) HPLC, which is commonly used for protein analysis. Although RP-HPLC and the BCA assay are readily available to most analytical laboratories [23], the use of HPLC-evaporative light scattering detector (HPLC-ELSD) is a good alternative for when the active pharmaceutical ingredient does not have a chromophore, or for impurity analysis [24]. Previous papers from our group have shown the ability to quantify lipids using an HPLC-ELSD system [25], and it is reported to detect analytes at high sensitivity rates [26].
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Stripping voltammetric methods for the determination of aflatoxin compounds

Stripping voltammetric methods for the determination of aflatoxin compounds

Aflatoxin, which is produced by Aspergillus flavus and Aspergillus parasiticus fungi is one of the compounds in the mycotoxin group. The main types of aflatoxins are AFB1, AFB2, AFG1 and AFG2 which have carcinogenic properties and are dangerous to human health. Various techniques have been used for their measurements such as the high performance liquid chromatography (HPLC), enzyme linked immunosorbant assay (ELISA) and radioimmunoassay (RIA) but all these methods have disadvantages such as long analysis time, consume a lot of reagents and expensive. To overcome these problems, the voltammetric technique was proposed in this study using controlled growth mercury drop (CGME) as the working electrode and Britton Robinson buffer (BRB) as the supporting electrolyte. The voltammetric methods were used for investigating the electrochemical properties and the quantitative analysis of aflatoxins at the mercury electrode. The experimental conditions were optimised to obtain the best characterised peak in terms of peak height with analytical validation of the methods for each aflatoxin. The proposed methods were applied for the analysis of aflatoxins in groundnut samples and the results were compared with those obtained by the HPLC technique. All aflatoxins were found to adsorb and undergo irreversible reduction reaction at the working mercury electrode. The optimum experimental parameters for the differential pulse cathodic stripping voltammetry (DPCSV) method were the BRB at pH 9.0 as the supporting electrolyte, initial potential (E i ): -0.1 V, final potential (E f ): -1.4 V, accumulation potential (E acc ): -
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Response Spectrum Analysis Of Single Storey Framed Structure By Numerical Integration Methods

Response Spectrum Analysis Of Single Storey Framed Structure By Numerical Integration Methods

A single storied framed structure is analysis and comparison of all the displacement, velocity, and acceleration by trapezoidal rule and Simpson’s rule method. In this study the mass, stiffness, natural frequency is same for all storey level and other parameters is constant for the entire storey and various time configurations. The mass and stiffens are analysed under the cantilever condition of structures. The theoretical data are calculated using code IS 1893, IS 4326, IS 13920. The theoretical results of trapezoidal rule the maximum deviation of displacement, velocity, and acceleration is 76.29% is higher compare than Simpson's rule in same configuration. In this analyse the final result, displacement, velocity, and acceleration the results are shown in table 1& 2comparison displacement, velocity, and acceleration given in figure 2,3& 4
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The Determination of the Crystal Structure of Potassium Picrate

The Determination of the Crystal Structure of Potassium Picrate

The para nitro group is twisted 6° out of the plane of the benzene ring , apparently due to ionic attraction of the oxygen atoms to neighboring potassium ions... The ortho nitro.[r]

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Ultrasonic determination of the internal structure of solids

Ultrasonic determination of the internal structure of solids

difficulty of accurate object perception in monochromatic illumination and together with the necessity of a wideband signal if good depth resolution was to be obtained in the proposed sy[r]

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