Characterization and mass spectral analysis of some grayanotoxin derivatives

The mass spectra of grayanotoxin III and some of its mono-, di, and tri-ester derivatives are discussed. Some of the physiological responses of this compound class are also presented. The extraction of this material from a natural source is discussed as well as the schemes for ester derivatization and spectral characterization of all compounds studied. High resolution mass spectral analysis and comparison of the mass spectra of similar compounds were used to define possible fragmentation mechanisms.     

Structure of bonito heart ferricytochrome c and some remarks on molecular interaction in its crystalline state.

The structure analysis of bonito heart ferricytochrome c was carried out at 2.8 A resolution by X-ray diffraction. The overall features of the molecule are virtually identical with those of bonito ferrocytochromes c and other cytochromes c. In the present work, the modes of molecular packing among cytochromes c were also compared by means of intermolecular distance maps. Some differences in the structures of ferro- and ferricytochrome c may exist on the surface of the molecules.     

Direct separation of albendazole sulfoxide enantiomers by liquid chromatography on a chiral column deriving from (S)-N-(3,5-dinitrobenzoyl) tyrosine: application to enantiomeric assays on plasma samples

The direct enantiomeric resolution of albendazole sulfoxide (SOABZ), an anthelmintic drug belonging to the benzimidazole class, is reported on a chiral stationary phase (CSP) synthesized by covalent binding of (S)-N-(3,5-dinitrobenzoyl)tyrosine-O-(2-propen-1-yl) methyl ester on a gamma-mercaptopropyl-silanized silica gel. A comparison with the resolution achieved on commercially available Pirkle-type CSPs obtained from N-(3,5-dinitrobenzoyl) derivatives of (R)-phenyglycine or (S)-phenylalanine is described. Some structurally related chiral sulfoxides including oxfendazole (SOFBZ) are also studied. Optimization of the mobile phase nature and composition is investigated showing that a hexane-dioxane-ethanol ternary mixture affords an almost baseline resolution (Rs = 1.25); however, in this case, albendazole sulfone (SO2ABZ) is eluted between the two sulfoxide enantiomers; accordingly, a hexane-ethanol mobile phase would be preferred for biological samples containing both metabolites. The influence of temperature on the resolution is depicted with a hexane-ethanol mobile phase. Finally, application to the enantiomeric assays of SOABZ in plasmatic extracts of rat, sheep, bovin, and man after oral administration of albendazole (sulfoxidized to SOABZ and SO2ABZ) is reported. Some distortions in the enantiomeric ratios are evidenced depending on the species.     

High-resolution crystallography and drug design

Ultra-high-resolution X-ray crystallography of macromolecules (i.e. resolution better than 0.8 Angstroms) is a rising field that promises to provide new insight into the structure-function relationships of biomacromolecules. The picture emerging from macromolecular structures at this resolution is far more complex than previously understood, requiring for its study improved tools for structure refinement, analysis and annotation. Some of these problems were highlighted during the recent High Resolution Drug Design Meeting (Bischenberg-Strasbourg, France, 13-16 May 2004). We will review here some of the results and discussions that took place during that meeting and elaborate on the trends and challenges ahead in this emerging new field of research.     

Assignment of methylene proton resonances in NMR spectra of embryonic and transformed cells to plasma membrane triglyceride

Some biological characteristics of cancer cells and solid tumors are identifiable by the high resolution NMR relaxation behavior of their nonaqueous components. Chemical analysis and two-dimensional scalar correlated (COSY) NMR spectroscopy show these resonances arise from neutral lipid in the plasma membrane. Triglyceride is shown to be the main plasma membrane component giving rise to the NMR spectrum, while soluble nonmembrane components account for 90% of the remaining resonances in the spectrum of intact cells. The presence of triglyceride has been detected by chemical analysis in highly purified plasma membranes from two different cell lines. The COSY spectra of cancer cells are comparable with that obtained for the triglyceride-rich very low density human lipoprotein.     

How to measure CT image quality: Variations in CT-numbers,uniformity and low contrast resolution for a CT quality assurance phantom

PurposeQuality assurance (QA) phantoms for testing different image quality parameters in computed tomography (CT) are commercially available. Such phantoms are also used as reference for acceptance in the specifications of CT-scanners. The aim of this study was to analyze the characteristics of the most commonly used QA phantom in CT: Catphan 500/504/600.MethodsNine different phantoms were scanned on the same day, on one CT-scanner with the same parameter settings. Interphantom variations in CT-number values, image uniformity and low contrast resolution were evaluated for the phantoms. Comparisons between manual image analysis and results obtained from the automatic evaluation software QAlite were performed.ResultsSome interphantom variations were observed in the low contrast resolution and the CT-number modules of the phantoms. Depending on the chosen regulatory framework, the variations in CT-numbers can be interpreted as substantial. The homogenous modules were found more invariable. However, the automatic image analysis software QAlite measures image uniformity differently than recommended in international standards, and will not necessarily give results in agreement with these standards.ConclusionsIt is important to consider the interphantom variations in relation to ones framework, and to be aware of which phantom is used to study CT-numbers and low contrast resolution for a specific scanner. Comparisons with predicted values from manual and acceptance values should be performed with care and consideration. If automatic software-based evaluations are to be used, users should be aware that large differences can exist for the image uniformity testing.     

Studying cellular architecture in three dimensions with improved resolution: Ta replicas revisited

Metal replicas have been used for surface analysis of biological structures with a variety of spatial resolutions. Platinum (Pt) has been the metal of choice because it provides very stable replicas and images of high contrast. Some other metals, such as tantalum (Ta) have been reported to provide better resolution on isolated macromolecular complexes and cellular structures. Our goal is to study the gain in detail with Ta and to evaluate if it provides enough detail and resolution to assist in the study of complex volumes of intact cellular structures obtained by methods that reach molecular resolution. To this purpose Pt and Ta replicas of cellular structures and viruses have been studied by transmission electron microscopy (TEM). Replicas of Ta show new details on the surface of two types of isolated viral particles such as 100 nm bunyaviruses and large, > 300 nm, vaccinia virus (VV). Inside cells, the structural pieces that build VV immature particles are visualized only in Ta replicas. Looking for smaller intracellular complexes, new details are also seen in nuclear pores from Ta replicas. Additional masses, most likely representing the cargo during transport, are distinguished in some of the pores. Visualization of proteins in plasma membranes strongly suggests that detail and resolution of Ta replicas are similar to those estimated for 3D maps currently obtained by electron tomography of viruses and cells.     

光学相干层析成像技术在内窥镜中的应用

光学相干层析成像(optical coherence tomography,OCT)技术是继X射线成像、核磁共振成像、超声成像等之后的一种新型的成像技术,其可光纤化的特点使得它易于医用电子内窥镜相结合。OCT内窥镜技术可实现对人体内部器官的高速率、高分辨率、无损伤、实时成像。主要介绍了OCT技术的种类、基本原理以及包括探测深度和纵向分辨率等的参数;简述了OCT内窥镜的发展历史以及最新成果,重点分析了光源对OCT内窥镜的影响。总结了OCT内窥镜的主要应用。     

Low temperature column chromatography: application to microsomal hydroxylating system.

A chromatography device working at subzero temperature is described. Some results concerning resolution of microsomal hydroxylating system are given, after solubilisation and chromatography at ?20°C.     

Can local energy minimization refine the PDB structures of different resolution universally?

Local energy minimization was statistically tested as the refinement strategy for PDB structure pairs of different resolution. The 13 pairs of structures with the only difference being the resolution were extracted from PDB and represented structures of 11 identical proteins obtained with different x-ray diffraction techniques. The rmsd distribution was calculated for these pairs before and after local energy minimization of each structure. MMFF94 was used for energy calculations and the quasi-Newtonian method was used for local energy minimization. By comparison of these two rmsd distributions, the local energy minimization was proved to statistically increase the structural differences in pairs, so it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in the multidimensional space of atomic coordinates. For these randomized structures the rmsd distribution was calculated and compared with the one for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by x-ray analysis for PDB. Some other results we obtained exploring the energy surface near these conformations are also presented. These results are expected to be useful for the development of new protein refinement strategies based on energy minimization.     

High spatial resolution analysis of fungal cell biochemistry--bridging the analytical gap using synchrotron FTIR spectromicroscopy.

Fungi impact humans and the environment in many ways, for good and ill. Some fungi support the growth of terrestrial plants or are used in biotechnology, and yet others are established or emerging pathogens. In some cases, the same organism may play different roles depending on the context or the circumstance. A better understanding of the relationship between fungal biochemical composition as related to the fungal growth environment is essential if we are to support or control their activities. Synchrotron FTIR (sFTIR) spectromicroscopy of fungal hyphae is a major new tool for exploring cell composition at a high spatial resolution. Brilliant synchrotron light is essential for this analysis due to the small size of fungal hyphae. sFTIR biochemical characterization of subcellular variation in hyphal composition will allow detailed exploration of fungal responses to experimental treatments and to environmental factors.     

High spatial resolution analysis of fungal cell biochemistry – bridging the analytical gap using synchrotron FTIR spectromicroscopy

Fungi impact humans and the environment in many ways, for good and ill. Some fungi support the growth of terrestrial plants or are used in biotechnology, and yet others are established or emerging pathogens. In some cases, the same organism may play different roles depending on the context or the circumstance. A better understanding of the relationship between fungal biochemical composition as related to the fungal growth environment is essential if we are to support or control their activities. Synchrotron FTIR (sFTIR) spectromicroscopy of fungal hyphae is a major new tool for exploring cell composition at a high spatial resolution. Brilliant synchrotron light is essential for this analysis due to the small size of fungal hyphae. sFTIR biochemical characterization of subcellular variation in hyphal composition will allow detailed exploration of fungal responses to experimental treatments and to environmental factors.     

Inhibition of aggregation by media selection,sample loading and elution in size exclusion chromatographic refolding of denatured bovine carbonic anhydrase B

The effects of gel media, sample application and elution flowrate on the activity recovery and aggregation in refolding of bovine carbonic anhydrase B (CAB) by size exclusion chromatography (SEC) were investigated. Variation in aggregation was demonstrated visibly by the comparison of refolding profiles under different operating conditions. Some principles with regard to practical application were proposed. Meanwhile, the analysis of relationship between peak resolution and activity recovery provided evidences for the mechanism of size exclusion chromatography protein refolding.     

寡核苷酸阵列比较基因组杂交技术及其应用

阵列-比较基因组杂交技术（array comparative genomic hybridization, array CGH）能在全基因组水平和/或高分辨率基础上检测染色体拷贝数的变化,主要应用于遗传学和肿瘤学研究。Array CGH中微阵列探针通常是PCR扩增的BAC克隆或cDNA分子。最近几年,寡核苷酸阵列比较基因组杂交（oligonucleotide array CGH, oaCGH）逐渐开始应用。oaCGH与BAC array CGH比较,具有操作更简便、探针设计更灵活、分辨率更高等多项优点,预计oaCGH将逐步取代利用BAC克隆片段或cDNA分子的array CGH。oaCGH的应用及其与其它高通量检测技术的结合将促进新的癌症相关基因、肿瘤耐药基因的发现。本文综述了现有主要oaCGH平台在空间分辨率、探针长度、灵敏度、特异性等方面的特点及其应用,概括了oaCGH近年来的进展。     

Linkage between quantitative trait loci and marker loci: resolution power of three statistical approaches in single marker analysis

This paper presents a comparison of three methods of parameter estimation in analysis of linkage between a quantitative trait locus (QTL) and a marker locus: maximum likelihood, mean square for trait cumulative distribution function, and method of moments, employing simulated backcross data. The sensitivity of estimates to violation of assumptions of normality and equal variances were also studied. Some measures of discrepancy between the trait distributions in the QTL groups are considered to evaluate the potential dependence of the resolution capacity of the QTL substitution effect with respect to trait mean value and variance.     

Computer‐automated bird detection and counts in high‐resolution aerial images: a review

Bird surveys conducted using aerial images can be more accurate than those using airborne observers, but can also be more time‐consuming if images must be analyzed manually. Recent advances in digital cameras and image‐analysis software offer unprecedented potential for computer‐automated bird detection and counts in high‐resolution aerial images. We review the literature on this subject and provide an overview of the main image‐analysis techniques. Birds that contrast sharply with image backgrounds (e.g., bright birds on dark ground) are generally the most amenable to automated detection, in some cases requiring only basic image‐analysis software. However, the sophisticated analysis capabilities of modern object‐based image analysis software provide ways to detect birds in more challenging situations based on a variety of attributes including color, size, shape, texture, and spatial context. Some techniques developed to detect mammals may also be applicable to birds, although the prevalent use of aerial thermal‐infrared images for detecting large mammals is of limited applicability to birds because of the low pixel resolution of thermal cameras and the smaller size of birds. However, the increasingly high resolution of true‐color cameras and availability of small unmanned aircraft systems (drones) that can fly at very low altitude now make it feasible to detect even small shorebirds in aerial images. Continued advances in camera and drone technology, in combination with increasingly sophisticated image analysis software, now make it possible for investigators involved in monitoring bird populations to save time and resources by increasing their use of automated bird detection and counts in aerial images. We recommend close collaboration between wildlife‐monitoring practitioners and experts in the fields of remote sensing and computer science to help generate relevant, accessible, and readily applicable computer‐automated aerial photographic census techniques.     

Characterization of normal and rearranged human chromosomes by simultaneous Q- and R-banding with chromomycin A3

Simultaneous Q- and R-type banding patterns in human chromosomes have been achieved by staining with chromomycin A3. Some peculiarities of these patterns as compared to the patterns induced by other fluorochromes are described. The resolution power of this technique in analyzing structural rearrangements of human chromosomes is discussed.     

Ruby-Helix: an implementation of helical image processing based on object-oriented scripting language

Helical image analysis in combination with electron microscopy has been used to study three-dimensional structures of various biological filaments or tubes, such as microtubules, actin filaments, and bacterial flagella. A number of packages have been developed to carry out helical image analysis. Some biological specimens, however, have a symmetry break (seam) in their three-dimensional structure, even though their subunits are mostly arranged in a helical manner. We refer to these objects as "asymmetric helices". All the existing packages are designed for helically symmetric specimens, and do not allow analysis of asymmetric helical objects, such as microtubules with seams. Here, we describe Ruby-Helix, a new set of programs for the analysis of "helical" objects with or without a seam. Ruby-Helix is built on top of the Ruby programming language and is the first implementation of asymmetric helical reconstruction for practical image analysis. It also allows easier and semi-automated analysis, performing iterative unbending and accurate determination of the repeat length. As a result, Ruby-Helix enables us to analyze motor-microtubule complexes with higher throughput to higher resolution.     

Growth During the Bacterial Cell Cycle: Analysis of Cell Size Distribution

Cell volume distributions were determined electronically for steady-state cultures of Escherichia coli, Bacillus megaterium, Bacillus subtilis, and Salmonella typhimurium by use of a Coulter transducer-multichannel analyzer system of good resolution. All of the cell volume distributions had the same general shape, even though cultures were grown at widely different rates. Some results were independent of any particular growth model. Both the variability in the volumes of dividing cells and the fraction of constricted and unseparated doublet cells increased with growth rate. The greater separation to single cells at slow growth rates is in agreement with the general finding that filamentous and hyphal forms are greatly reduced in slowly growing chemostat cultures. The distributions were fitted equally well by simple models which assumed that cell growth was either linear or exponential throughout the entire cell cycle. It is concluded that methods of determining growth rate by analysis of distributions of bacterial volumes do not yet have sufficient resolution to distinguish between a variety of alternative models for growth of bacteria.