Personal computer-based visualization of molecular models by available ray-tracing software

Developed primarily for the graphic arts, ray-tracing algorithms offer a high level of flexibility with reference to photorealistic and surrealistic image rendering. The utility of these programs is further enhanced by portability (i.e., compatibility with a number of operating systems), accessibility through various sources, and low cost. This report documents, through the use of existing software, the application of these ray-tracing attributes to molecular graphics on a desktop computer. This application is especially pertinent in view of rapid speed enhancements in personal computers (PCs), which have enabled molecular modeling and dynamics on these systems. In this regard, ray tracing on a PC provides enhanced capabilities for molecular graphics rendering that are potentially equivalent to those achieved by workstations.     

Recombinant human insulin.

Insulin is a well-characterized peptide that can be produced by recombinant DNA technology for human therapeutic use. A brief overview of insulin production from both traditional mammalian pancreatic extraction and recombinant bacterial and yeast systems is presented, and detection techniques, including electrophoresis, are reviewed. Analytical systems for insulin separation are principally based on reversed-phase chromatography, which resolves the deamidation product(s) (desamido insulin) of insulin, proinsulin, and insulin. Process-scale separation is a multistep process and includes ion exchange, reversed-phase, and size exclusion chromatography. Advantages and/or disadvantages of various separation approaches, as described by the numerous literature references on insulin purification, are presented.     

Recent developments in quantification methods for metallothionein.

The metallothioneins (MT), a family of proteins with relatively low molecular weight (6-7 kDa), are characterised by the intrinsic presence of 20 cysteinyl groups in their structure, which confers unique metal binding properties to the molecule. Since MT are involved in biological roles, quantification of MT remains an important task. To date, a large number of determination methods have been developed. In this paper recent developments, from 1995 to the present, in methodology employed in quantification studies of total MT and MT polymorphism are described. Different fields were taken into consideration, such as (i) separation techniques and hyphenated systems, (ii) electrochemical methods, (iii) immunological methods and (iv) quantification of MT mRNA. The data presented are based on our own and published results. A brief overview of the use of metallothionein as a biomarker is included as a relevant example of the importance of MT quantification. Finally, general problems associated with determination and evaluation of obtained results within the above four topics are mentioned.     

Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware

The timescales of biological processes, primarily those inherent to the molecular mechanisms of disease, are long (>μs) and involve complex interactions of systems consisting of many atoms (>10⁶). Simulating these systems requires an advanced computational approach, and as such, coarse-grained (CG) models have been developed and highly optimised for accelerator hardware, primarily graphics processing units (GPUs). In this review, I discuss the implementation of CG models for biologically relevant systems, and show how such models can be optimised and perform well on GPU-accelerated hardware. Several examples of GPU implementations of CG models for both molecular dynamics and Monte Carlo simulations on purely GPU and hybrid CPU/GPU architectures are presented. Both the hardware and algorithmic limitations of various models, which depend greatly on the application of interest, are discussed.     

Chromatographic methods for the determination of toxicants in faeces

Modern chromatographic techniques and their application in the determination of toxic compounds in faeces are reviewed. Faecal analysis may be of importance in toxicokinetic studies of xenobiotics in order to determine factors such as metabolism, body burden and major routes of elimination. Compounds of interest include various food constituents, drugs and occupational or environmental factors. Further, various mutagenic or carcinogenic compounds which are excreted by faeces have been indicated to represent risk factors for colorectal cancer. In this context, the chromatographic determination of the endogenously generated fecapentaenes and bile acids, both postulated etiological factors in colorectal carcinogenesis, is reviewed. For fecapentaene determination, several high-performance liquid chromatographic (HPLC) methods are available; however, the applicability of some of these methods is limited owing to insufficient separation of various isomeric forms or discrimination between fecapentaenes and their precursors. For the determination of bile acids in faeces, many chromatographic procedures have been reported, and the characteristics of the most relevant methods are compared and discussed. It is concluded that separation by gas chromatography (GC) in combination with mass spectrometry provides the highest selectivity and sensitivity. A relatively rapid alternative analysis for the determination of total and aqueous faecal bile acids is proposed. Further, methods for the determination of polycyclic aromatic hydrocarbons (PAHs) are reviewed. Although the use of radiolabelled PAHs in animal studies has many advantages, it cannot be applied for human biological monitoring and HPLC and GC provide sensitive alternatives. An HPLC method for the determination of non-metabolized PAHs in faeces is described.     

Recent advances in enantiomer separations by affinity capillary electrophoresis using proteins and peptides

Enantiomer separations by capillary electrophoresis (CE), using proteins as chiral selectors--affinity capillary electrophoresis (ACE) with free solutions and capillary electrochromatography (CEC)--with protein immobilized capillaries, are reviewed. The separation principle, recent advances in this field and some interesting topics are presented. In ACE, various enantiomer separations have been already reported using either plasma proteins or egg white ones. Miscellaneous proteins were also explored in the last few years. On the contrary, only a limited number of enantiomer separations have been successfully achieved in CEC. CEC is not yet mature enough to date, and further investigations, such as efficiency, durability and reproducibility of capillaries, will be necessary for the use of routine analyses. The study of enantioselective drug-protein binding is important in pharmaceutical developments. Some applications including high-performance CE/frontal analysis (HPCE/FA) are introduced in this paper.     

Computer graphics in cytologic and pathologic microscopy. Tools for the clinician and researcher

Computer graphics capabilities are becoming practical economically and ergonometrically for the first time on a widespread basis. The factors that have brought this about and the importance of such graphic interfaces to computer technology in the clinical and research laboratory are discussed. The uses of computer graphics in cytologic and pathologic microscopy are reviewed in terms of objectives, types of display and software and hardware display methods, and examples of various types of displays are presented.     

Modeling and measuring urban sustainability in multi-criteria based systems — A challenging issue

This paper addresses how urban sustainability is modeled and the ways criteria-based systems deal with its measurability for an effective and reliable assessment. Twelve sustainability models are reviewed and a subset is briefly presented. More importantly, this research work investigates five national rating systems of sustainable urban development compared with the newly developed CAMSUD system. The comparison focuses on the systems' structure, categorization, technical content and measurability. The main findings about the selected national rating systems thoroughly discussed in the paper are: (i) They all have a tree-like structure, (ii) their conceptualization and categorization follow three or four sustainability pillars models, sustainability topics or spatial scale; (iii) they use either planning-oriented or performance-oriented weighting approaches; (iv) the criteria are defined as sustainability goals, action measures or assignments to be fulfilled; (v) the sustainability items can hardly be juxtaposed since they are differently handled, (vi) overlapping criteria might occur, (vii) similar criteria can be categorized under different categories and this affects the emphasis put on these categories, (viii) all criteria are independently rated with no consideration of mutual interrelationships. In an attempt to solve some of these weaknesses, the newly developed CAMSUD system is introduced as alternative and relies on the following: (i) the system structure is considered as a network, (ii) the conceptualization and categorization is based on spatial scaling as well as on sustainability topics and pillars, (iii) many criteria are directly planning-relevant (23 of 40), (iv) the criteria are defined as sustainability goals rather than action measures and (v) the quantification of criteria is planned as to account for mutual interactions.     

A fast GNU method to draw accurate scientific illustrations for taxonomy

Nowadays only digital figures are accepted by the most important journals of taxonomy. These may be produced by scanning conventional drawings, made with high precision technical ink-pens, which normally use capillary cartridge and various line widths. Digital drawing techniques that use vector graphics, have already been described in literature to support scientists in drawing figures and plates for scientific illustrations; these techniques use many different software and hardware devices. The present work gives step-by-step instructions on how to make accurate line drawings with a new procedure that uses bitmap graphics with the GNU Image Manipulation Program (GIMP). This method is noteworthy: it is very accurate, producing detailed lines at the highest resolution; the raster lines appear as realistic ink-made drawings; it is faster than the traditional way of making illustrations; everyone can use this simple technique; this method is completely free as it does not use expensive and licensed software and it can be used with different operating systems. The method has been developed drawing figures of terrestrial isopods and some examples are here given.     

Student-oriented learning: an inquiry-based developmental biology lecture course

In this junior-level undergraduate course, developmental life cycles exhibited by various organisms are reviewed, with special attention--where relevant--to the human embryo. Morphological features and processes are described and recent insights into the molecular biology of gene expression are discussed. Ways are studied in which model systems, including marine invertebrates, amphibia, fruit flies and other laboratory species are employed to elucidate general principles which apply to fertilization, cleavage, gastrulation and organogenesis. Special attention is given to insights into those topics which will soon be researched with data from the Human Genome Project. The learning experience is divided into three parts: Part I is a in which the Socratic (inquiry) method is employed by the instructor (GMM) to organize a review of classical developmental phenomena; Part II represents an in which students study the details related to the surveys included in Part I as they have been reported in research journals; Part III focuses on a class project--the preparation of a spiral bound on a topic of relevance to human developmental biology (e.g.,Textbook of Embryonal Stem Cells). Student response to the use of the Socratic method increases as the course progresses and represents the most successful aspect of the course.     

The potential of microalgal biotechnology: a review of production and uses of microalgae

An overview of the various aspects, promises and limitations of microalgal biotechnology is presented. The factors of importance in microalgal cultivation as well as the culture systems are briefly described. Microalgal biomasses can fulfil the nutritional requirements of aquatic larvae and organisms. The biochemical composition of algae can be improved by the manipulation of culture conditions. The nutritive value of the microalgal biomasses for human and animal consumption is also commented upon as well as some socio-economical aspects. Among the sources of required nutrients (N, P), wastewaters and manures can upgraded as culture media for microalgae the safety of which has to be evaluated. Harvesting of the biomass is one of the bottlenecks. The various techniques, physical, physico-chemical and biological are outlined and their feasibility and economic interest examined. Microalgal biomasses can be submitted to various technological transformations. Various processes are reviewed in the light of their effects on safety and nutritional value. The possible extraction of fine chemicals and the preparation of protein concentrates is also reported on. The various uses of microalgae lead to a possible competition, to be evaluated, between systems for the production of food, energy and chemicals. The review finally covers the application of genetic manipulation to microalgae.     

Optical properties and structure of tetrapyrroles. A report of a symposium held at the University of Konstanz, FRG, August 12-17, 1984

Many basic life processes such as oxygen transport, electron transport, photosynthesis and plant development, are mediated by tetrapyrroles. It has long been recognized that optical and other physicochemical properties of tetrapyrroles are highly important not only for characterization of the various relevant systems but also to provide a key role in the understanding of their structural and functional aspects. The symposium described below was devoted mainly to recent advances in the optical and molecular properties of biologically important systems, involving both cyclic and open-chain tetrapyrroles. The topics presented and discussed ranged from physics and chemistry to plant biology and medicine. This interdisciplinary character of the meeting conforms with previous symposia also held in Konstanz: Protein-Ligand Interactions (1974) and Transport by Proteins (1978) [see FEBS Lett. (1975) 54, 1-4, and FEBS Lett. (1979) 103, 1-4]. In order to stimulate exchange of ideas, new experimental approaches and techniques, emphasis was placed on the discussions following each presentation, reports of which are also included in the book published. Preprints of the papers presented were distributed some time prior to the symposium. The symposium was mainly supported by the Stiftung Volkswagenwerk and the University of Konstanz. The meeting was based on 29 invited lectures which were divided into four sections.     

Analytical methods to determine phytoestrogenic compounds

The analytical methods for the determination of phytoestrogenic compounds in edible plants, plant products and biological matrices are reviewed. The detection, qualitative and quantitative methods based on different chromatographic separations of gas chromatography (GC), high-performance liquid chromatography (HPLC) and capillary electrophoresis (CE) coupled with various detections by ultraviolet absorption (UV), electrochemical detection (ED), fluorescence detection, mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), as well as non-chromatographic immunoassay are each extensively examined and compared. An overview on phytoestrogen chemistry, bioactivities and health effects, plant precursors, metabolism and sample preparation is also presented.     

Analysis of liposomes by capillary electrophoresis and their use as carrier in electrokinetic chromatography

This contribution reviews work about liposomes in the context of electrically driven separation methods in the capillary format. The discussion covers four topics. The one broaches the application of liposomes as pseudo-stationary phases or carriers in vesicle or liposome electrokinetic chromatography (EKC) in the way as microemulsions and micelles are used; it includes the chromatographic use of liposomal bilayers as stationary phases attached to the wall for capillary electrochromatography (CEC). The second topic is the characterization and separation of liposomes as analytes by capillary electrophoresis (CE). Then the determination of distribution coefficients and binding constants between liposomes and ligands is discussed, and finally work dealing with peptides and proteins are reviewed with lipid bilayers as constituents of the electrically driven separation system.     

Personal computer-based visualization of three-dimensional scalar and vector fields: An application to molecular graphics

A desktop PC-based graphics package, UNIVIS, for visualization of three-dimensional numerical data is described. Apart from routine molecular model visualization, the package provides for a host of other features such as extraction of various surfaces, planar cross-sections of the three-dimensional data, and property texturing. Fast rendering and transparency are the strengths of the present package. These features are comprehensively discussed. The salient features of UNIVIS are presented in the form of visualization of a variety of molecular properties, which are of immense importance in understanding molecular structure and reactivity patterns.     

FRET analysis of domain formation and properties in complex membrane systems

The application of Förster Resonance Energy Transfer (FRET) to the detection and characterization of phase separation in lipid bilayers (both in model systems and in cell membranes) is reviewed. Models describing the rate and efficiency of FRET for both uniform probe distribution and phase separation, and recently reported methods for detection of membrane heterogeneity and determination of phase boundaries, probe partition coefficients and domain size, are presented and critically discussed. Selected recent applications of FRET to one-phase lipid systems, gel/fluid phase separation, liquid ordered/liquid disordered phase separation (lipid rafts), complex systems containing ceramide and cell membranes are presented to illustrate the wealth of information that can be inferred from carefully designed FRET studies of membrane domains.     

The use of X-ray crystallography to determine absolute configuration

Essential background on the determination of absolute configuration by way of single-crystal X-ray diffraction (XRD) is presented. The use and limitations of an internal chiral reference are described. The physical model underlying the Flack parameter is explained. Absolute structure and absolute configuration are defined and their similarities and differences are highlighted. The necessary conditions on the Flack parameter for satisfactory absolute-structure determination are detailed. The symmetry and purity conditions for absolute-configuration determination are discussed. The physical basis of resonant scattering is briefly presented and the insights obtained from a complete derivation of a Bijvoet intensity ratio by way of the mean-square Friedel difference are exposed. The requirements on least-squares refinement are emphasized. The topics of right-handed axes, XRD intensity measurement, software, crystal-structure evaluation, errors in crystal structures, and compatibility of data in their relation to absolute-configuration determination are described. Characterization of the compounds and crystals by the physicochemical measurement of optical rotation, CD spectra, and enantioselective chromatography are presented. Some simple and some complex examples of absolute-configuration determination using combined XRD and CD measurements, using XRD and enantioselective chromatography, and in multiply-twinned crystals clarify the technique. The review concludes with comments on absolute-configuration determination from light-atom structures.     

Optical immunosensing systems--meeting the market needs

Optical immunosensors and sensing systems are biosensors which produce a quantitative measure of the amount of antibody, antigen or hapten present in a complex sample such as serum or whole blood. The market needs for such devices and their associated instrumentation are reviewed. A brief history of the development of optical immunosensors is presented and the performance of the most well-developed optical immunosensors for meeting these market needs is reviewed. One device, the fluorescent capillary fill device (FCFD) is reviewed in detail with respect to it fulfilling the market needs for an optical immunosensor. Areas for the future development of such sensing systems are also discussed.     

代谢物组学方法及其在植物学研究中的应用

代谢物是生物体受遗传控制和环境影响的最终表达产物,以全体代谢物(代谢物组)为研究对象的代谢物组学是继基因组学和蛋白质组学后必然出现的又一门"组学"技术。该文综述了代谢物组的检测、数据的处理和分析等以及这些技术在植物目标分析、基因功能、代谢途径和代谢工程、整合植物学、信号转导等研究中的应用和前景。