bluuebunny/crossref_metadata_2025 huggingface dataset:
Recovery of methanotrophs from disturbance: population dynamics, evenness and functioning
Authors: Ho Adrian , Lüke Claudia , Frenzel Peter
Published: October 2010

Biodiversity is claimed to be essential for ecosystem functioning, but is threatened by anthropogenic disturbances. Prokaryotes have been assumed to be functionally redundant and virtually inextinguishable. However, recent work indicates that microbes may well be sensitive to environmental disturbance. Focusing on methane-oxidizing bacteria as model organisms, we simulated disturbance-induced mortality by mixing native with sterilized paddy soil in two ratios, 1:4 and 1:40, representing moderate and severe die-offs. Disturbed microcosms were compared with an untreated control. Recovery of activity and populations was followed over 4 months by methane uptake measurements, pmoA-qPCR, pmoA-based terminal restriction fragment length polymorphism and a pmoA-based diagnostic microarray. Diversity and evenness of methanotrophs decreased in disturbed microcosms, but functioning was not compromised. We consistently observed distinctive temporal shifts between type I and type II methanotrophs, and a rapid population growth leading to even higher cell numbers comparing disturbed microcosms with the control. Overcompensating mortality suggested that population size in the control was limited by competition with other bacteria. Overall, methanotrophs showed a remarkable ability to compensate for die-offs.
Chemiluminescence and Bioluminescence
Authors: Reschiglian Pierre
Published: October 2010

This complete and well-organized overview of chemiluminescence and bioluminescence is divided into two parts. The first covers historical developments and the fundamental principles of these phenomena before going on to review recent advances and instrumentation. The second part deals with the applications in a variety of research fields including life sciences, drug discovery, diagnostics, environment, agrofood, and forensics. The book is suitable not only for researchers currently employing detection techniques in their research activity, but also for those approaching the subject for the first time. Particular emphasis is placed on the use of chemiluminescence and bioluminescence for the development of a variety of (bio)analytical methods, such as flow-assisted methods, enzyme-, antibody- or gene probe-based assays also in multiplexed formats, miniaturized analytical devices, biosensors, BRET and protein complementation assays, whole-cell biosensors, and bioluminescence molecular imaging. Individual chapters are devoted to the most important and rapidly developing fields including: Instrumentation for Chemiluminescence and Bioluminescence; In vivo Molecular Imaging; Biotechnological Improvements of Bioluminescent Systems; Cell-based Bioluminescent Biosensors, and Miniaturized Analytical Devices Based on Chemiluminescence, Bioluminescence and Electrochemiluminescence. The book also includes a comprehensive collection of recent bibliographic references.
A History of Bioluminescence and Chemiluminescence from Ancient Times to the Present
Authors: Roda Aldo
Published: October 2010

This Chapter reports an overview of the historical development of bioluminescence (BL) and chemiluminescence (CL), starting with the primitive understanding of natural light emission phenomena from BL terrestrial and marine animals and fungi. At that time BL was just described as a fascinating unexplained natural phenomenon and was limited to terms of magic and superstition.

In the course of the Centuries, paralleling the development of other scientific fields, methodological study of BL and CL began, ultimately leading to the exponential growth of knowledge in the last century and half or so. After the first experiments in the late 1800s, the mechanisms of light emission from firefly and marine animals were fully defined in the early 1900s, taking advantage of the background of natural sciences and the advent of the modern chemistry. Again in the late 1800s, the term CL was introduced and in the following years many new CL molecules were synthesised, also modifying the structures of natural BL substrates.

In recent years CL and BL have become fundamental tools in molecular biology and related sciences. In particular, bioanalytical chemistry has greatly benefitted from implementation of CL and BL in a variety of analytical methodologies, such as amplified coupled enzymatic reactions, immunoassays, nucleic acid-based assays, in vivo molecular imaging, cell-based biosensors and in general molecular biology techniques.
The Nature of Chemiluminescent Reactions
Authors: Zomer Gijsbert
Published: October 2010

Chemiluminescence has evolved from being an interested fact, via a promising analytical technique, to a fairly well understood phenomenon. The research during the last two decades has resulted in a much better understanding of the chemistry of chemiluminescence. This has lead to exciting (sic) new systems which are not only interesting from a basic scientific perspective, but also has resulted in commercial exploitation of chemiluminescence in all kinds of applications. This chapter surveys the most important chemiluminescent systems (for example, those involving luminol, dioxetanes, acridan esters, peroxyoxalates), and describes the properties of such chemiluminescent systems and the known or hypothesised molecular mechanisms involved in their chemiluminescence emission.
Progress and Perspectives on Bioluminescence: from Luminous Organisms to Molecular Mechanisms
Authors: Hastings J. Woodland
Published: October 2010

McElroy's discovery of the requirement for ATP in firefly light emission in 1947 marked the onset of biochemical characterizations of many other bioluminescence systems over the subsequent decades, notably bacteria, fungi, dinoflagellates, cypridinids, coelenterates and mollusks, which are described. These, along with many other less-well characterized luminous systems, arose independently in evolution and thus use different luciferins and luciferases. Apparent exceptions to this generalization and their explanations are discussed, along with the nature of photoproteins, which are considered to represent aluciferase reaction intermediate in one case and a chemiluminescence in several others. Luciferins should be defined as luciferase substrates, which after reaction give rise to the species that is responsible for light emission. In cases where there are two substrates, only one is the luciferin. Thus, ATP in the firefly and aldehyde in the bacteria are not luciferins.
Instrumentation for Chemiluminescence and Bioluminescence
Authors: Berthold Fritz , Hennecke Manfred , Wulf Jürgen
Published: October 2010

The most widely used instruments for the measurement of chemiluminescence and bioluminescence are luminometers and low level light imagers.

Luminometers measure single samples in microplates or sample tubes sequentially, while imagers produce quantitative images in one exposure.

The detector of choice for luminometers is the photomultiplier tube, preferably operated as photon counter. To measure flash-type luminescence, luminometers can be equipped with reagent injectors.

CCD's (charge coupled devices) are used in imagers. Besides slow- scan cooled CCD's, modified devices like electron-multiplication CCD's, or CCD's with image intensifier are used in order to obtain higher frame rates.

Imagers are used for objects like small animals, plants, blots, gels, or Petri dishes, but also find use in high- throughput systems, imaging an entire microplate simultaneously.

Fluorescence measuring capabilities are a standard option for imagers, while measurement of bioluminescence and chemiluminescence in single samples is frequently performed in multimode readers, combining luminescence with absorption and different fluorescence measuring capabilities in a single instrument.
“Classical” Applications of Chemiluminescence and Bioluminescence
Authors: Guardigli Massimo , Lundin Arne , Roda Aldo
Published: October 2010

Chemiluminescence and bioluminescence are powerful detection techniques used in such widely different areas as molecular biology, drug discovery, clinical diagnosis, food and hygiene control, environmental and forensic analysis. In this Chapter, analytical applications of chemiluminescence and bioluminescence in batch analytical formats (for examples, tubes or microtiter plates) are reviewed. The first part of the Chapter deals with applications of chemiluminescence, from the detection of hydrogen peroxide in environmental samples to the measurement of enzymes, enzyme substrates and enzyme inhibitors by means of coupled enzymatic reactions, the evaluation of reactive oxygen species production in cells and the assessment of the antioxidant activity of clinical and food samples. The second part of the Chapter is devoted to analytical bioluminescence, especially to ATP-related assays based on the firefly luciferase reaction. The central role of ATP in all living cells makes it possible to detect bacterial or other living cells, which is useful for example for rapid microbiology and hygiene monitoring, and to monitor a wide range of enzymatic reactions, thus allowing the development of diagnostic assays for enzymes and metabolites. Analytical applications of other luciferases, such as bacterial luciferase, are also briefly reported.
Gene Assays Based on Bio(Chemi)luminescence
Authors: Laios Eleftheria , Ioannou Penelope C. , Christopoulos Theodore K.
Published: October 2010

High detectability, wide analytical range and simple instrumentation constitute the unique advantages of bio(chemi)luminometric methods for DNA/RNA detection and quantification. The development of bio(chemi)luminometric assays performed in microtitration wells allows automation and high sample-throughput, features that are necessary for the routine laboratory. This represents a significant advantage over classical gel electrophoresis, blotting and membrane hybridization. This chapter covers the exploitation of bio(chemi)luminescence in: (a) DNA hybridization assays, (b) quantitative polymerase chain reaction (PCR), (c) genotyping of single nucleotide polymorphisms (SNPs), (d) determination of allele burden, as well as (e) strategies for conjugation of reporter molecules. The methods find a wide range of applications in clinical, environmental and food samples. The assay configurations include: (i) immobilization of the target sequence on a solid surface and hybridization with a probe linked to a reporter, (ii) hybridization of the target to an immobilized probe and subsequent linking of the captured target to a reporter and (iii) hybridization of the target with two probes, one of which is immobilized whereas the other is linked to the reporter. Enzymes (such as alkaline phosphatase, peroxidase, and luciferase), photoproteins (e.g. aequorin), expressible DNA fragments, acridinium esters or nanoparticles can serve as reporters. Immobilization of probes or target sequences is accomplished through the biotin/streptavidin or the hapten/antibody interaction. The bridging of probes or targets with the reporter molecules is carried out either directly by chemical conjugation or indirectly through biotin/streptavidin and hapten/antibody interaction. The development of multianalyte assays is an area of intense research effort.
Cell-based Bioluminescent Biosensors
Authors: Turner Kendrick , Raut Nilesh , Pasini Patrizia , Daunert Sylvia , Michelini Elisa , Cevenini Luca , Mezzanotte Laura , Roda Aldo
Published: October 2010

Cell-based biosensors are designed to take advantage of the unique selectivity afforded by biological recognition elements in combination with a protein reporter that generates a measurable signal, i.e., fluorescence, chemiluminescence, bioluminescence, colorimetric or electrochemical. These biosensors are constructed, in general, by transforming a living bacterial cell with an engineered plasmid on which the expression of a reporter protein is under the regulatory control of a promoter/regulatory protein which recognizes an analyte of interest. As a result of this design, the biosensors are capable of rapid, specific/selective, and sensitive measurement in standard as well as miniaturized, rugged, portable platforms. A further benefit of cell-based biosensors is that they provide information regarding the bioavailablility of the analyte in a sample. Cell-based biosensors have been developed using a number of genes for luminescent proteins such as prokaryotic and eukaryotic luciferases, green fluorescent protein (GFP) and its mutants, aequorin, and β-galactosidase. The spectrum of analytes for which cell-based biosensors have been constructed is constantly expanding. Currently, there are biosensors designed to detect general toxicants as well as stress factors and specific analytes or groups of analytes such as metals, inorganic molecules, organic pollutants, antibiotics, sugars, and quorum sensing molecules. Additionally, the development of rugged biosensors, like those based on spore-forming microbes, the miniaturization of cell-based assay formats, and their incorporation onto microfluidics platforms will further expand the applications in on-site environmental/clinical analysis.
Miniaturized Analytical Devices Based on Chemiluminescence, Bioluminescence and Electrochemiluminescence
Authors: Kricka Larry J. , Park Jason Y.
Published: October 2010

Advances in miniaturization technology derived from the microelectronics industry have facilitated the miniaturization of analytical devices. The assays embedded within miniaturized analytical devices utilize a range of detection technologies including electrochemical, colorimetric, and a range of luminescence detection technologies based on fluorescence, chemiluminescence, bioluminescence, and electrochemiluminescence. This chapter reviews the basics of micro-miniature analytical devices (microchips, lab-on-a-chip or micro total analytical systems) and surveys microchip-based assays that utilize chemiluminescence, bioluminescence, and electrochemiluminescence as the detection technology.
Recent Analytical Application Areas of Chemiluminescence and Bioluminescence
Authors: Guardigli Massimo , Mirasoli Mara , Michelini Elisa , Dolci Luisa Stella , Roda Aldo
Published: October 2010

This Chapter deals with applications of CL and BL in topics of significant relevance, which are not described in the previous Chapters of this book. In particular, principle and limitations of the well-known luminol test, based on the catalysis of the luminol CL reaction by blood traces and utilised by forensic scientists in investigations involving violent crime for more than 40 years, are reviewed. Afterwards, the various CL-based methods employed for the rapid and sensitive detection of explosives, from portable explosive analyzers to gas chromatographic and HPLC techniques with CL detection and immunoassays, are described. Finally, examples of application of CL and BL in the study and conservation of cultural heritage are reported, including detection of biodeteriogen agents (bacteria, fungi, yeast, algae and lichens) on artworks by BL imaging of adenosine triphosphate (ATP) and immunolocalization of protein binders in painting cross-sections by CL imaging microscopy.
In Silico Toxicology
Authors: Mekenyan Ovanes
Published: October 2010

In Silico methods to predict toxicity have become increasingly important recently, particularly in light of European legislation such as REACH and the Cosmetics Regulation. They are also being used extensively worldwide e.g. in the USA, Canada, Japan and Australia. In assessing the risk that a chemical may pose to human health or to the environment, focus is now being directed towards exploitation of in silico methods to replace in vivo or in vitro techniques. A prediction of potential toxicity requires several stages: 1) Collation and organisation of data available for the compound, or if this is not available, information for related compounds. 2) An assessment of the quality of the data. 3) Generation of additional information about the compound using computational techniques at various levels of complexity - calculation of physico-chemical properties, 2-D, 3-D / MO descriptors and specific receptor modelling / interaction. 4) Use of an appropriate strategy to predict toxicity - ie a statistically valid method which makes best use of all available information (mechanism of action, activity for related compounds, extrapolation across species and endpoints, likely exposure scenario amounts over time etc). 5) Consideration then needs to be given to how this information is used in the real world ie use of expert systems / tools as relevant to assessors (if sufficiently different to previous) - weight of evidence approaches. 6) Finally evidence should be presented from case studies within this area. No other publication brings together information on all of these areas in one book and this publication is unique in that it provides a logical progression through every one of these key stages and defines the use of computational approaches to predict the environmental toxicity and human health effects of organic chemicals. The volume is aimed at the developers and users of in silico toxicology and provides an analysis of all aspects required for in silico prediction of toxicology, including data collation, quality assessment and computational approaches. The contributions from recognised leaders in each of these areas include evidence of the use and applicability of approaches using real world case studies concerning both environmental and human health effects. The book provides a very useful single source reference for people working in this area including academics, professionals, under- and post-graduate students as well as Governmental Regulatory Scientists involved in chemical risk assessment and REACH.
In Silico Toxicology—An Introduction
Authors: Cronin M. T. D. , Madden J. C.
Published: October 2010

This chapter provides a brief introduction to the term in silico toxicology and the various methods that are available to predict toxicity. The current status and future potential role of in silico techniques are discussed, indicating the key factors that have defined the current state-of–the-art. These factors are diverse and include the need to ensure the safety of chemicals; current legislation; commercial pressures; increased computational power; and public opinion against animal testing. Overall the book provides guidance on how to develop and use in silico models. The topics to be discussed throughout the book are introduced here including: obtaining and assessing data, characterising chemicals in terms of their physico-chemical and structural properties; building models to account for toxicity and taking into consideration any modulating factors (such as external and internal exposure). potential uses for the models
Finding the Data to Develop and Evaluate (Q)SARs and Populate Categories for Toxicity Prediction
Authors: Cronin M. T. D.
Published: October 2010

This chapter describes the sources of data for in silico modelling. It is assumed that the modeller will not normally have the facilities to experimentally determine toxicological data, thus they must rely on existing data. Data can be obtained from in-house sources (e.g. for industry) or from publicly available databases and the scientific literature. For the publicly available data, the sources of toxicologically information and the relevant advantages and disadvantages are defined. The sources include “well-established” datasets and the use of literature searching, through to the use of databases and more global (meta) data portals which call on a number of databases. To use the data collected efficiently, the modeller must define the required endpoint, allow the nature of the data to drive the modelling approach and control the quality of the data and implications for that on in silico models.
Data Quality Assessment for In Silico Methods: A Survey of Approaches and Needs
Authors: Nendza M. , Aldenberg T. , Benfenati E. , Benigni R. , Cronin M.T.D. , Escher S. , Fernandez A. , Gabbert S. , Giralt F. , Hewitt M. , Hrovat M. , Jeram S. , Kroese D. , Madden J. C. , Mangelsdorf I. , Rallo R. , Roncaglioni A. , Rorije E. , Segner H. , Simon-Hettich B. , Vermeire T.
Published: October 2010

As indicated in Chapter 3, there are a large number of potential sources of data now available for modelling purposes. These range from historical literature references for a few compounds to highly curated databases of hundreds of thousands of compounds, available via the internet. Before including any data in an in silico model, the question of data quality must be addressed. Although it is difficult to define the quality of data in absolute terms, it is possible to assess the suitability of data for a given purpose. There are many reasons for variability within data and the degree of error that is acceptable for one model may not be the same as for another. For example generating a global model intended to pre-screen large numbers of compounds does not require the same degree of accuracy as performing an individual risk assessment for a chemical of interest. In this chapter, sources of data variability and error will be discussed and formal methods to score data quality, such as use of the Klimisch criteria, will be described. Examples of data quality issues will be given for specific endpoints relating to both environmental and human health effects. Mathematical approaches (Dempster-Schafer theory and Bayesian networks) demonstrating how this information relating to confidence in the data can be incorporated into in silico models is also discussed.
Statistical Methods for Continuous Measured Endpoints in In Silico Toxicology
Authors: Rowe P. H.
Published: October 2010

This chapter covers three regression techniques-multiple linear, principal components and partial least squares. Toxicity data recorded as continuously varying endpoints can be predicted by these techniques, all of which combine suitably weighted values of one or more chemical descriptors. Throughout the chapter, the need to produce models that are statistically stable, demonstrably predictive and capable of interpretation in biological and chemical terms is emphasised. The identification of non-linearity, interaction and heteroscedacity are discussed and methods to overcome them (use of quadratic terms, cross-products and weighted least squares fitting) are described. Regression diagnostics are explained with coverage of the (often neglected) inspection of residuals and a warning against over-optimistic interpretation of P values when a small number of descriptors have been trawled from a large data set. The problem of testing the true predictive power of regression models is explored, the inadequacy of some cross-validation methods is described and the need for test or evaluation data sets is emphasised. The greatest modelling problem is identified as collinearity among potential predictors. One solution to this problem is the selection of a set of descriptors that includes one representative of each collinear group, rejecting other related descriptors. This can be achieved by best sets, stepwise or genetic algorithms. The alternative is to combine collinear descriptors into principal component or partial least squares scores. It is shown that these techniques can produce stable, interpretable models if used rationally, but in incompetent hands could easily lead to non-interpretable ‘black box’ models.
Statistical Methods for Categorised Endpoints in In Silico Toxicology
Authors: Rowe P. H.
Published: October 2010

In this chapter different statistical approaches to analysing categorical data (Discriminant analysis, k-Nearest Neighbours and logistic regression) are discussed, along with recommendations as to the most appropriate methods for a given query. Discriminant functions are equations that use chemical descriptors to generate scores such that different categories of substance (e.g. toxic and non-toxic) yield maximally separated values. A cut-off point for the scores is then chosen. The cut-off may be selected so that compounds are simply separated according to chemical similarity (either more similar to one group or to the other) or account may be taken of the relative frequency of the two classes ('prior likelihood') to minimise the rate of misclassification or finally account may be taken of the relative costs of false positives and negatives to minimise misclassification costs. For dichotomised data, binary logistic regression uses chemical descriptors to predict the probability that a substance will belong to a particular class. The technique can be extended to predict toxicity recorded on a multi-point ordinal scale. The latter may be considerably more powerful than the binary technique.

k-Nearest Neighbour (k-NN) analysis predicts toxicity on the basis of closeness to other substances of known toxicity, in multi-dimensional space defined by chemical descriptors. Discriminant and k-NN analyses produce visually intuitive presentations when only two descriptors are used. K-NN analysis can tackle difficult patterns of data such as embedded classes that would otherwise be intractable. Used sensibly, both discriminant analysis and logistic regression can produce models capable of chemical and biological interpretation. Logistic regression is powerful, flexible, reasonably free of onerous statistical requirements and probably has the most attractive combination of characteristics, making it a good first choice.
Mechanisms of Toxic Action in In Silico Toxicology
Authors: Roberts D. W.
Published: October 2010

The activity of a compound in any biological endpoint is a function of its chemical identity. In toxicology, biological activity is often interpretable mechanistically in terms of physical chemistry and/or reaction chemistry. This is particularly the case with aquatic toxicology and skin sensitisation, and makes it possible to develop mechanism-based QSARs for these endpoints. In aquatic toxicity both physical chemistry mechanisms, leading to general narcosis or polar narcosis, and reaction chemistry mechanisms are encountered, whereas in skin sensitisation only reaction chemistry mechanisms, in particular electrophilic reactions with skin protein nucleophiles, are encountered. The difference between general and polar narcosis can be explained in terms of different mechanisms of partitioning from water to membranes. For reactive toxicity, both in aquatic toxicity and skin, compounds can be classified into reaction mechanistic applicability domains according to how they react as electrophiles with nucleophiles. For successful reactive toxicity mechanism-based QSAR development it is important to work with compounds in the same reaction mechanistic domain. In the absence of clear knowledge of the identities of the in vivo nucleophilic proteins involved, it is necessary to use reactivity parameters from in chemico data for reaction with model nucleophiles, or from in silico calculations. The scope and limitations of these model reactivity parameters can be assessed from the perspective of the Swain-Scott principle and the hard and soft acids and bases (HSAB) concept. This assessment reinforces the importance of working in the same mechanistic domain, or sub-domains where the domain covers a wide hard-soft range.
Open Source Tools for Read-Across and Category Formation
Authors: Jeliazkova N. , Jaworska J. , Worth A. P.
Published: October 2010

In this chapter, the requirements and challenges for computational tools to support category formation and read-across are summarised. A brief overview of the open source, open data and open standards approaches in chemoinformatics are presented. The opportunities offered by these kinds of “openness” are highlighted, with emphasis on open source applications specifically developed to address challenges posed by the REACH regulation. Structural similarity assessment is currently a common practice in forming categories and applying read-across, and in developing and validating (Q)SARs. The Toxmatch software provides several endpoint-specific similarity measures, with descriptors selected using a training set in combination with data mining methods. The Toxtree software implements several classification schemes for predicting various endpoints and relies primarily on chemical structure, metabolic pathways, physico-chemical properties and descriptors, calculated from chemical structure. In addition to making predictions for individual chemicals, Toxtree can be used to profile the toxicological hazard or mechanistic group of a set of chemicals. Ambit is anopen source software for chemoinformatics data management, which allows storage of a large number of chemical structures and toxicological data and provides a flexible means for exploration of structural and similarity spaces. Several examples of the application of read-across, initiated by an expert-defined search strategy and supported by Ambit search functionalities are described.
Biological Read-Across: Mechanistically-Based Species–Species and Endpoint–Endpoint Extrapolations
Authors: Cronin M. T. D.
Published: October 2010

This chapter describes the development and use of relationships between toxicity data, for the same chemicals, derived from different species. These relationships provide simple models to predict toxicity of, potentially, a higher species from that of a lower species. Approaches to the formation of these models are described, notably inter-species relationships, quantitative structure-activity-activity relationships and prediction models. It is noted that the best extrapolations are for closely related species i.e. within taxa. In addition, forming groups or categories of compounds according to common mechanisms of toxic action improves the correlation for extrapolations from lower to higher species. A freely available software package, Web-ICE, is introduced as a suitable tool to apply these methods.
Expert Systems for Toxicity Prediction
Authors: Dearden J. C.
Published: October 2010

Expert systems offer the facility to predict a toxicity endpoint, as well sometimes as additional relevant information, simply by inputting the chemical structure of a compound. There is now a number of expert systems available, mostly on a commercial basis although a few are free to use or download. This chapter discusses nineteen currently available expert systems, and their performances (if known). Published studies of consensus predictions with these expert systems indicate that these give better results than do individual expert systems.

A test set of compounds with Tetrahymena pyriformis toxicities has been run through the two expert systems known to predict these toxicities; the predictions were quite good, with standard errors of prediction of 0.395 and 0.433 log unit. A further test set of compounds with local lymph node assay skin sensitisation data has been run through seven expert systems, and it was found that consensus predictions were better than were those from any individual expert system.
Integrated Testing Strategies and the Prediction of Toxic Hazard
Authors: Balls M.
Published: October 2010

Over the past 20-30 years there has been a move towards reducing the use of animals in toxicity testing for industrial chemicals, pharmaceuticals, personal care and household products, for economic, scientific and animal welfare reasons. The need for alternatives has been emphasised by the EU REACH regulation, which requires the evaluation of tens of thousands of new and existing chemicals, and also within the pharmaceutical industry owing to the increasing rate at which drugs are being withdrawn from the market due to adverse effects not detected during preclinical testing. Significant effort is being placed into the development of non-animal test procedures using existing data, bioinformatics, in chemico, in silico and in vitro approaches and ethical human studies. Information from these diverse sources needs to be used intelligently and selectively leading to the development of what have become known as Integrated Testing Strategies (ITS). In this chapter factors that need to be considered in the development, evaluation, acceptance and use of ITS will be discussed.
Using In Silico Toxicity Predictions: Case Studies for Skin Sensitisation
Authors: Cronin M. T. D. , Madden J. C.
Published: October 2010

The purpose of this chapter is to demonstrate how predictions from in silico models and other sources can be used to make an overall assessment of toxicity. Two case studies are considered, to predict the skin sensitisation potential of 4-amino-2-nitrophenol and 1,14-tetradecanediol. Predictions were made from various in silico models including Derek for Windows, TIMES-SS, OECD (Q)SAR Application Toolbox and CAESAR. These were compared with existing data and in chemico reactivity data. Overall, greater confidence can be placed in the predictions when they can be combined to give an overall consensus.
pH-Triggered construction of NLO active CMOFs: change in supramolecular assembly, water clusters, helical architectures and their properties
Authors: Saha Rajat , Biswas Susobhan , Mostafa Golam
Published: October 2010

Two different chiral metal–organic frameworks (CMOF), namely, {[Cu2(1,10-phen)2(tartrate)H2O]·8H2O}n(1) and {[Cu(1,10-phen)(H2tartrate)H2O]·6H2O}n(2) have been synthesized by alternating the pH of the reaction media.
Production of recombinant Bombyx mori nucleopolyhedrovirus in silkworm by intrahaemocoelic injection with invasive diaminopimelate auxotrophic Escherichia coli containing BmNPV–Bacmid
Authors: Sun Jingchen , Yao Lunguang , Yao Ning , Xu Hua , Jin Pengfei , Kan Yunchao
Published: October 2010

The present study elaborates a cost‐effective and transfectant‐free method for generating recombinant Bombyx mori (silkworm) nucleopolyhedrovirus in silkworm larvae and pupae by injecting invasive Escherichia coli carrying BmBacmid [BmNPV (B. mori nucleopolyhedrovirus)–Bacmid] into larval haemocoel. Up to 109 PFU (plaque‐forming units)/ml of infective recombinant baculovirus was generated in the silkworm by intrahaemocoelic injection with 106 DAP (diaminopimelic acid) auxotrophic and BmBacmid containing E. coli cells expressing both invasin and listeriolysin. Thus 1 ml of overnight culture of E. coli is sufficient to inject more than 2000 larvae, while DAP costing up to $1 is enough to inject about 4000 larvae. Recombinant proteins can be controlled to be expressed mainly in pupae by adjusting the injection dose, too. In this new method, many original manipulations have been eliminated, including BmBacmid preparation and the subsequent complex transfection procedures. Hence it is a time‐ and cost‐saving means for large‐scale injection of B. mori for recombinant baculovirus production in comparison with the traditional transfection methods, which may play an important role in the industrial development of the BmNPV–silkworm bioreactor.
Identification of binding partners interacting with the α1-N-propeptide of type V collagen
Authors: Symoens Sofie , Renard Marjolijn , Bonod-Bidaud Christelle , Syx Delfien , Vaganay Elisabeth , Malfait Fransiska , Ricard-Blum Sylvie , Kessler Efrat , Van Laer Lut , Coucke Paul , Ruggiero Florence , De Paepe Anne
Published: October 2010

The predominant form of type V collagen is the [α1(V)]2α2(V) heterotrimer. Mutations in COL5A1 or COL5A2, encoding respectively the α1(V)- and α2(V)-collagen chain, cause classic EDS (Ehlers−Danlos syndrome), a heritable connective tissue disorder, characterized by fragile hyperextensible skin and joint hypermobility. Approximately half of the classic EDS cases remain unexplained. Type V collagen controls collagen fibrillogenesis through its conserved α1(V)-N-propeptide domain. To gain an insight into the role of this domain, a yeast two-hybrid screen among proteins expressed in human dermal fibroblasts was performed utilizing the N-propeptide as a bait. We identified 12 interacting proteins, including extracellular matrix proteins and proteins involved in collagen biosynthesis. Eleven interactions were confirmed by surface plasmon resonance and/or co-immunoprecipitation: α1(I)- and α2(I)-collagen chains, α1(VI)-, α2(VI)- and α3(VI)-collagen chains, tenascin-C, fibronectin, PCPE-1 (procollagen C-proteinase enhancer-1), TIMP-1 (tissue inhibitor of metalloproteinases-1), MMP-2 (matrix metalloproteinase 2) and TGF-β1 (transforming growth factor β1). Solid-phase binding assays confirmed the involvement of the α1(V)-N-propeptide in the interaction between native type V collagen and type VI collagen, suggesting a bridging function of this protein complex in the cell-matrix environment. Enzymatic studies showed that processing of the α1(V)-N-propeptide by BMP-1 (bone morphogenetic protein 1)/procollagen C-proteinase is enhanced by PCPE-1. These interactions are likely to be involved in extracellular matrix homoeostasis and their disruption could explain the pathogenetic mechanism in unresolved classic EDS cases.
PKCζ-interacting protein ZIP3 is generated by intronic polyadenylation, and is expressed in the brain and retina of the rat
Authors: Urbanczyk Andreas , Jünemann Anselm , Enz Ralf
Published: October 2010

Scaffold proteins contain multiple protein–protein interaction modules that physically assemble functionally related proteins into larger complexes. ZIPs [PKC (protein kinase C) ζ-interacting proteins] link the enzymatic activity of the atypical PKC isoforms PKCλ/ι or PKCζ to target proteins and are associated with neurodegenerative disorders. In the rat, alternative splicing generates three ZIP variants. Previously, we identified the ZIP3 transcript, containing 13 C-terminal amino acids encoded by intron 4, in the rat CNS (central nervous system). In the present study, we identified intronic polyadenylation signals in rat and human ZIP genes [known as SQSTM1 (sequestosome-1) in humans] and detected the corresponding ZIP3-like transcripts. In addition, we generated ZIP3-specific immune sera and observed expression of the protein in the brain and retina of the adult rat. In the retina, ZIP3 is present in nuclear layers where it co-localizes with PKCζ. An immune serum recognizing all three ZIP isoforms labelled the same cells as the newly generated ZIP3-specific antibodies and, in addition, stained both synaptic layers of the retina. There, ZIPs are localized in axon terminals of rod bipolar cells that also contain ZIP-interacting PKCζ and GABAC (γ-aminobutyric acid type C) receptors. In summary, we detected ZIP3-like transcripts in rat- and human-derived samples and describe the expression of ZIP3 in the rat CNS.
Dysfunction of human subcutaneous fat arterioles in obesity alone or obesity associated with Type 2 diabetes
Authors: Georgescu Adriana , Popov Doina , Constantin Anamaria , Nemecz Miruna , Alexandru Nicoleta , Cochior Daniel , Tudor Aura
Published: October 2010

The aim of the present study was to examine the effects of obesity alone and obesity associated with Type 2 diabetes on the structure, vascular reactivity and response to insulin of isolated human subcutaneous fat arterioles; these effects were correlated with the expression of insulin signalling proteins. Periumbilical subcutaneous adipose tissue was explanted during surgery, small arterioles (internal diameter 220±40 μm) were dissected out and investigated by electron microscopy, myography and immunoblotting. Compared with the subcutaneous arterioles of lean subjects, obesity activated the endothelium, enhanced the accumulation of collagen within vascular wall and increased the sensitivity of adrenergic response; obesity also diminished eNOS (endothelial NO synthase) protein expression, NO production, and endothelium-dependent and insulin-induced vasodilatation, as well as the protein expression of both IRS (insulin receptor substrates)-1 and IRS-2 and of the downstream molecules in the insulin signalling pathway, such as PI3K (phosphoinositide 3-kinase), phospho-Akt and Akt. When obesity was associated with Type 2 diabetes, these changes were significantly augmented. In conclusion, obesity alone or obesity associated with Type 2 diabetes alters human periumbilical adipose tissue arterioles in terms of structure, function and biochemsitry, including diminished eNOS expression and reduced levels of IRS-1, IRS-2, PI3K and Akt in the insulin signalling pathway.
Simulation of a tangential soft x-ray imaging system
Authors: Battaglia D. J. , Shafer M. W. , Unterberg E. A. , Bell R. E. , Hillis D. L. , LeBlanc B. P. , Maingi R. , Sabbagh S. , Stratton B. C.
Published: October 2010

Tangentially viewing soft x-ray (SXR) cameras are capable of detecting nonaxisymmetric plasma structures in magnetically confined plasmas. They are particularly useful for studying stationary perturbations or phenomenon that occur on a timescale faster than the plasma rotation period. Tangential SXR camera diagnostics are planned for the DIII-D and NSTX tokamaks to elucidate the static edge magnetic structure during the application of 3D perturbations. To support the design of the proposed diagnostics, a synthetic diagnostic model was developed using the CHIANTI database to estimate the SXR emission. The model is shown to be in good agreement with the measurements from an existing tangential SXR camera diagnostic on NSTX.
Data processing of absorption spectra from photoionized plasma experiments at Z
Authors: Hall I. M. , Durmaz T. , Mancini R. C. , Bailey J. E. , Rochau G. A.
Published: October 2010

We discuss the processing of x-ray absorption spectra from photoionized plasma experiments at Z. The data was recorded with an imaging spectrometer equipped with two elliptically bent potassium acid phthalate (KAP) crystals. Both time-integrated and time-resolved data were recorded. In both cases, the goal is to obtain the transmission spectra for quantitative analysis of plasma conditions.
Antenna development for high field plasma imaging
Authors: Kong X. , Domier C. W. , Luhmann N. C.
Published: October 2010

Electron cyclotron emission imaging (ECEI) and microwave imaging reflectometry (MIR) are two microwave nonperturbing plasma visualization techniques that employ millimeter-wave imaging arrays with lens-coupled planar antennas, yielding time-resolved images of temperature (via ECEI) and electron density (via MIR) fluctuations within high temperature magnetic fusion plasmas. A series of new planar antennas have been developed that extend this technology to frequencies as high as 220 GHz for use on high field plasma devices with toroidal fields in excess of 3 T. Antenna designs are presented together with theoretical calculations, simulations, and experimental measurements.
On a class of global characteristic problems for the Einstein vacuum equations with small initial data
Authors: Caciotta Giulio , Nicolò Francesco
Published: October 2010

We study a class of global characteristic problems for the Einstein vacuum equations with small initial data. In a previous work [Caciotta and Nicolò, “Global characteristic problem for Einstein vacuum equations with small initial data: (I) The initial data constraints,” Journal of Hyperbolic Differential Equations (JHDE) 2, 201 (2005)], denoted by Paper I, our attention was focused on prescribing the initial data satisfying the constraints imposed by the characteristic problem. In this paper we show how the global existence result can be achieved. This result is heavily based on the global results of Christodoulou and Klainerman [The Global Nonlinear Stability of the Minkowski Space, Princeton Mathematical Series Vol. 41 (Princeton University Press, Princeton, NJ, 1993)] and Klainerman and Nicolò [The Evolution Problem in General Relativity, Progress in Mathematical Physics Vol. 25 (Birkhauser, Boston, MA, 2002)].
2D soft x-ray system on DIII-D for imaging the magnetic topology in the pedestal region
Authors: Shafer M. W. , Battaglia D. J. , Unterberg E. A. , Evans T. E. , Hillis D. L. , Maingi R.
Published: October 2010

A new tangential two-dimensional soft x-ray imaging system (SXRIS) is being designed to examine the edge island structure in the lower X-point region of DIII-D. Plasma shielding and/or amplification of the calculated vacuum islands may play a role in the suppression of edge-localized modes via resonant magnetic perturbations (RMPs). The SXRIS is intended to improve the understanding of three-dimensional (3D) phenomena associated with RMPs. This system utilizes a tangential view with a pinhole imaging system and spectral filtering with beryllium foils. SXR emission is chosen to avoid line radiation and allows suitable signal at the top of a H-mode pedestal where Te∼1–2 keV. A synthetic diagnostic calculation based on 3D SXR emissivity estimates is used to help assess signal levels and resolution of the design. A signal-to-noise ratio of 10 at 1 cm resolution is expected for the perturbed signals, which are sufficient to resolve most of the predicted vacuum island sizes.
The method of Gaussian weighted trajectories. V. On the 1GB procedure for polyatomic processes
Authors: Bonnet L. , Espinosa-García J.
Published: October 2010

In recent years, many chemical reactions have been studied by means of the quasiclassical trajectory (QCT) method within the Gaussian binning (GB) procedure. The latter consists of “quantizing” the final vibrational actions in Bohr spirit by putting strong emphasis on the trajectories reaching the products with vibrational actions close to integer values. A major drawback of this procedure is that if N is the number of product vibrational modes, the amount of trajectories necessary to converge the calculations is ∼10N×larger than with the standard QCT method. Applying it to polyatomic processes is thus problematic. In a recent paper, however, Czakó and Bowman propose to quantize the total vibrational energy instead of the vibrational actions [G. Czakó and J. M. Bowman, J. Chem. Phys. 131, 244302 (2009)], a procedure called 1GB here. The calculations are then only ∼10 times more time consuming than with the standard QCT method, allowing thereby for considerable numerical saving. In this paper, we propose some theoretical arguments supporting the 1GB procedure and check its validity on model test cases as well as the prototype four-atom reaction OH+D2→HOD+D.
Nanowire charging in collisionless plasma
Authors: Shahravan Anaram , Lucas Chris , Matsoukas Themis
Published: October 2010

We calculate the collision cross section of a charged finite cylinder (nanowire) with a beam of ions and electrons in collisionless plasma. We find that, while the shape and area of the cross section has complex dependence on the charge and orientation of the nanowire relative to the charged beam, its orientational average has a remarkably simple form: for attractive interactions, it is a linear function of the electrostatic ratio qjqpe2/4πϵ0L0kT, where qje is the charge of the ions/electrons, qpe is the charge on the cylinder, L0 is the half-length of the nanowire, T is the temperature of the charged species, and ϵ0 is the permittivity of free space. This linearity persists into the repulsive regime up until the cross sectional area is reduced to about 5% of its value for neutral collisions. We calculate the corresponding charging currents and show that the charging behavior of the nanowire in Maxwellian plasma is described by an equivalent sphere whose radius depends only on the aspect ratio of the nanowire. For small aspect ratios, the equivalent sphere has the same surface area as the nanowire.
Spin-degenerate surface and the resonant spin lifetime transistor in wurtzite structures
Authors: Wang Wan-Tsang , Wu C. L. , Chiang J. C. , Lo Ikai , Kao H. F. , Hsu Y. C. , Pang W. Y. , Jang D. J. , Lee Meng-En , Chang Yia-Chung , Chen Chun-Nan
Published: October 2010

Spin-splitting energies of wurtzite AlN and InN are calculated using the linear combination of atomic orbital method, and the data are analyzed utilizing the two-band k⋅p model. It is found that in the k⋅p scheme, a spin-degenerate surface exists in the wurtzite Brillouin zone. Consequently, the D’yakonov-Perel’ spin relaxation mechanism can be effectively suppressed for all spin components in the [001]-grown wurtzite quantum wells (QWs) at a resonant condition through application of appropriate strain or a suitable gate bias. Therefore, wurtzite QWs (e.g., InGaN/AlGaN and GaN/AlGaN) are potential structures for spintronic devices such as the resonant spin lifetime transistor.