bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemometrics in Biospectroscopy
Authors: Kohler Achim , Kristian Afseth Nils , Martens Harald
Published: November 2010

Vibrational spectroscopic techniques have been used for decades for predicting chemical composition of biological samples. For the establishment of prediction models, multivariate calibration techniques are often applied, since the use of single variables or combinations of few variables are not sufficient or robust enough. Multivariate techniques need to handle covariation among variables. We observe an especially high degree of covariation between variables in vibrational spectroscopy: Covariation is present (i) among neighbouring channels providing signals from the same spectral band, (ii) among spectral bands that are due to the same chemical bond, and (iii) finally among chemical bonds that arise from the same biomolecule. Consequently, the underlying dimensions in a given data set are rather few compared to the number of variables (channels) measured, also in cases where the number of samples is quite large. Multivariate methods based on latent variables that relate directly to underlying phenomena and mechanisms, are especially popular in vibrational spectroscopy. By using latent variables, the variations of objects can be studied with respect to these underlying phenomena and variation patterns can be studied in the light of chemical bonds and biomolecules.

Another data modeling issue relates to the preprocessing of spectra: Vibrational spectra of biological materials are plagued by unwanted variability effects such as scatter effects in infrared spectroscopy or fluorescence effects in Raman spectroscopy. Calibration models often become simpler and even better when these effects are removed from the spectra before the calibration model is established. In addition, the interpretation of the results in terms of chemical bands is simpler and more reliable when the spectra are preprocessed.

In this chapter, several issues related to data analysis of vibrational spectra of biological samples are discussed: (i) model‐based preprocessing techniques based on extended multiplicative signal correction (EMSC) are presented. Different variants of EMSC are discussed and a new extension of EMSC especially suited for the correction of fluorescence effects in Raman spectroscopy is introduced. (ii) Different aspects related to multivariate calibration and classification are discussed with a special focus on partial least squares regression (PLSR) and validation.
Infrared Imaging: Principles and Practices
Authors: Sedman Jacqueline , Ghetler Andrew , Enfield Alexander , Ismail Ashraf A.
Published: November 2010

Infrared imaging allows the versatility and the vast information content of infrared spectroscopic techniques to be brought to bear on the chemical characterization of a large variety of ”real‐world“ samples, ranging from biological tissue and cells to manufactured products. In this chapter, the ways in which infrared images are acquired, processed, and interpreted are discussed, with a particular focus on FT‐IR imaging microspectroscopy using MCT focal‐plane‐array detectors. Four categories of infrared imaging applications are presented to illustrate the present and future scope of this relatively new and rapidly evolving technology.
Raman Spectroscopic Imaging
Authors: Treado Patrick J. , Priore Ryan J. , Nelson Matthew P.
Published: November 2010

Raman imaging instrumentation has advanced significantly since the first Raman images were obtained nearly three decades ago. Substantial improvements have been made in point scan, line scan, and widefield Raman imaging platform designs. The focus of this chapter is on Raman imaging instrumentation with respect to food science applications. Current technological approaches used in Raman imaging instrumentation, Raman instrumentation platform types, signal‐enhanced Raman instrumentation, tandem Raman imaging instruments that benefit from orthogonal information obtained from multiple sensor types, and how to assess performance of a Raman imaging instrument are detailed with food science examples. Raman imaging instruments are the tools used to determine where molecular‐specific Raman scatter arises in highly heterogeneous materials. These instruments are used to generate hundreds, thousands, or even millions of independent, spatially resolved Raman spectra from the material of interest. The resulting hyperspectral data cube consists of a series of wavelength‐specific images where each pixel contains a Raman spectrum associated with the material imaged at that location. The Raman spectra in the hypercube are processed to reveal image contrast that is chemical specific without the need for stains, dyes, or contrast agents. Consequently, there is often a reduced burden or even no need for sample preparation unlike many other material analysis tools.
Surface‐EnhancedRaman Spectroscopy: Theory and Application to the Analysis of Chlorpyrifos in Orange Juice
Authors: Shende Chetan , Inscore Frank , Sengupta Atanu , Farquharson Stuart
Published: November 2010

Pesticides are required to increase crop yields and volumes to feed the growing world use population. Unfortunately, many developing countries use an excess of pesticides or those which are banned. Nearly half of the fruit consumed in the USA is imported, and it is estimated that 5% exceeds acceptable pesticide levels. Less than 1% of the food is tested because methods are slow and the equipment is restricted to the laboratory. This chapter describes the use of surface‐enhanced Raman spectroscopy to perform field measurements of pesticides in fruit. Raman spectroscopy provides the necessary specificity to distinguish the numerous pesticides in use, while surface enhancement using silver nanoparticles provides the necessary part‐per‐billion sensitivity. A simple SERS‐active sampling device and field‐usable Raman analyzer were used to measure 50 ppb chlorpyrifos in orange juice within 10 min. This chapter also includes a brief description of SERS theory.
Application of Vibrational Spectroscopy for the Study of Heat‐Induced Changes in Food Components
Authors: Rubio‐Diaz Daniel E. , Rodriguez‐Saona Luis E.
Published: November 2010

Vibrational spectroscopic techniques, including Mid‐IR, NIR, and Raman spectroscopy, are valuable tools for the study of chemical modifications in food constituents. Advances in instrumentation combined with the development of powerful multivariate data analysis make this technology ideal for understanding the effect of heat in major and minor food components. The aim of this review is to compile the current research on applications of spectroscopy to provide detailed information of chemical and structural changes induced by heat treatment based on variations and evolution of vibrational spectra.
Application of Vibrational Spectroscopy to Investigate Radiation‐Induced Changes in Food
Authors: Severcan Feride , Bozkurt Ozlem
Published: November 2010

This chapter is mainly focused on the application of vibrational spectroscopy, namely mid‐infrared, near infrared and Raman spectroscopy, to irradiated food. The chapter begins with an introduction to the basis of radiation and the effects of radiation on biological systems; this is followed by a brief discussion on the usage of radiation in food science and the general spectroscopic methods used in the detection of irradiation. The applications of different chemometric techniques, such as principal component analysis (PCA), partial least squares regression (PLS), canonical variate analysis (CVA), linear discriminant analysis (LDA) and cluster analysis to vibrational spectroscopic data of irradiated food are presented. In addition, the discrimination of radiation dose in food using vibrational spectroscopy together with chemometric methods is described. The application of detailed molecular investigation, such as determination of content, structure, and function of macromolecules, is specifically illustrated in the analysis of hazelnut samples using mid‐IR spectroscopy. Determination of radiation‐induced lipid peroxidation and protein secondary structural alterations in food are discussed. Applications of NIR spectroscopy on irradiated food, such as determination of food quality and the effect of radiation on different food samples are also discussed.
Monitoring Oxidation of Lipids in Edible Oils and Complex Food Systems by Vibrational Spectroscopy
Authors: Ayora‐Cañada Maria José , Domínguez‐Vidal Ana , Lendl Bernhard
Published: November 2010

The potential of near‐infrared (NIR), mid‐infrared (mid‐IR) and Raman spectroscopy for the study of edible oil oxidation is discussed. Major spectral changes observed during oil oxidation are described in detail. The use of two dimensional correlation spectroscopy and multivariate curve resolution methods to aid spectral interpretation and to model the process of lipid oxidation, respectively, is presented. Different methods to assess the extent of oxidation by means of vibrational spectroscopic techniques are critically reviewed. They include methods that measure primary oxidation products, mainly hydroperoxides (peroxide value), as well as, secondary oxidation products like carbonyl compounds. Tests to evaluate the oxidative stability of edible oils by means of infrared spectroscopy are also described. Finally, some selected examples of methods to estimate lipid oxidation extent in foods (like salmon fillets, snacks, etc) are presented.
Raman Spectroscopy for the Study of Molecular Order, Thermodynamics, and Solid–Liquid Transitions in Triacylglycerols
Authors: Da Silva Eric , Rousseau Dérick
Published: November 2010

The use of Raman spectroscopy for the study of the molecular order in triglycerides is explored, with emphasis placed on three key spectroscopic fingerprints: (i) the CH stretching region at 3000–2700 cm−1, (ii) the ester carbonyl (CO) stretching region at 1780–1700 cm−1, and the CC stretching region at ∼1200–1100 cm−1. Triglyceride polymorph and phase‐dependent changes related to the aliphatic chain and glycerol backbone conformation and packing, as well as changes in local environment, are ascertained on the basis of shifts in these bands. In particular, the ester carbonyl stretching region demonstrates clear differences between triglycerides polymorphs, as changes are seen in the number, stretching frequency, and size of the modes present. Besides, phase transition enthalpies are extracted from the Raman spectra of triglycerides studied. This chapter demonstrates that Raman spectroscopy is a viable tool for the characterization of triglycerides.
Applications of Vibrational Spectroscopy to Study Protein Structural Changes in Muscle and Meat Batter Systems
Authors: Herrero Ana M. , Carmona Pedro , Jiménez‐Colmenero Francisco , Ruíz‐Capillas Claudia
Published: November 2010

Proteins are the most important structural and functional components of muscle and meat batter systems. Vibrational spectroscopy provides information to determine protein structural changes of this food, since these spectroscopic techniques are direct, nondestructive or noninvasive, and require small sample quantities. Raman spectroscopy offers structural information about secondary and tertiary protein structure, and infrared spectroscopy provides information particularly on protein secondary structure. This chapter reviews the applications of these techniques to protein structural studies of muscle and meat batter systems including the effects of various processing treatments and the possibilities of protein structural changes to assess muscle food quality.
In situ Fourier Transform Infrared Microspectroscopy and Imaging of Wheat Kernels and Other Grains
Authors: Wetzel David L. , Brewer Lauren R.
Published: November 2010

Revealing the chemical microstructure of wheat kernels and other plant material on a cellular and subcelllular level is the subject of this chapter. The past two decades have been an exciting period involving the technology‐driven emergence of FT‐IR microspectroscopy and hyperspectral imaging. Early spectra were obtained from spatially resolved, localized, single spots within various tissues. Line mapping across borders between botanical parts with a motorized stage revealed distinct differences in their respective chemical populations. The first single aleurone cell 3D imaging and that of its cell walls was an important milestone. Baseline correction imaging software enabled distinction between absorbance and light‐scatter attenuation. Subsequent focal plane array detection provided accelerated data acquisition for imaging and mapping with confocal small image plane‐masked microspectroscopy using the synchrotron, provided spatially resolved detailed images at the diffraction limit. All of these instrumental improvements used in the context of cereal chemistry, an important part of food science, bring the reader to the current state of the art via numerous practical applications that encourage future exploitation of these techniques to satisfy their curiosity.
Applications of Vibrational Spectroscopy to Oilseeds Analysis
Authors: Baranska Malgorzata , Schulz Hartwig , Strehle Marion , Popp Jürgen
Published: November 2010

In this chapter applications of Raman, mid‐infrared and near‐infrared spectroscopy to oilseed analysis is presented. The methods can be successfully used to determine fats, proteins, carbohydrates, and numerous other secondary plant substances occurring in agricultural products. The spectroscopic methods have the potential to supplement existing standard procedures presently used for plant analysis (mainly chromatographic and NMR techniques). In addition, a great advantage of FT‐Raman spectroscopy is shown as a nondestructive method used for analysis of an intact fresh plant tissue without the necessity to perform any sample cleanup preparation.
Quantifying Meat Properties Using Near‐Infrared Spectroscopy
Authors: Burling‐Claridge Robert
Published: November 2010

Meat is a primary source of protein in most parts of the world. Increasing affluence throughout the developing countries has led to a considerable increase in demand, and the concomitantly increased sophistication of consumers has led to a quality requirement being imposed on this increased demand.

Measurement of meat quality is a difficult task. There are many different cuts of meat from a given source, with often only loosely related quality levels. Desirable quality parameters (tenderness, pH, fat content, etc.) are often fundamentally difficult physical properties to define and measure even in controlled laboratory situations. Processing, storage, and handling details have the potential for significant effects on final perceived consumer quality, both positively and negatively. The meat itself is often presented for quality assessment in less than ideal manner, and processing speeds allow very little time for the assessment.

Despite these challenges, it is clear from other natural product supply chains that have adopted a measured‐quality approach, that assured quality will only impact positively for all involved, certainly for the processors, and not least for the final consumer.

Near‐infrared (NIR) spectroscopy could, in principle, be a suitable tool to address this quality requirement. NIR offers much for processors, distributors, and consumers, but it must be admitted that meat is certainly a challenge to measure with acceptable precision, ease, and speed. This chapter discusses those challenges and considerations, and suggests pathways that may allow their resolution, to build commercially viable NIR‐based meat quality measurement systems.
Quality Analysis of Milk by Vibrational Spectroscopy
Authors: Kohler Achim , Afseth Nils Kristian , Jørgensen Kjetil , Randby Åshild , Martens Harald
Published: November 2010

Fourier transform infrared spectroscopy (FTIR) has been used in routine dairy control for many years to measure quality parameters of milk, such as total fat, protein, and lactose. Recently it has been shown that the same instrumentation can be used to predict groups of fatty acids, and even some individual fatty acids, with high precision. When predicting fatty acid profiles by FTIR spectroscopy, the infrared absorption spectrum serves as a biochemical fingerprint containing signals of many functional molecular groups from fatty acids. Owing to the complexity of this information, and since no single functional groups is specific for any fatty acid or group of fatty acids, multivariate techniques using linear or nonlinear transformations are needed to transform these nonselective spectral measurements into selective predictions of the fatty acid profile. For the establishment of these multivariate calibration models, several aspects need to be considered: (i) preprocessing of the measured spectra can often simplify the subsequent multivariate calibration considerably. By preprocessing, nonlinear and additive effects can be removed, and the instrument response linearized. (ii) Another aspect relates to validation of the calibration model. Calibration models need to be validated statistically and chemically, otherwise, the validity of the calibration model may be limited. Statistical validation is done by checking the predictive ability in independent samples with known composition. Chemical validation is–to the extent practically possible–done by interpreting the multivariate calibration model in terms of known spectral features of relevant functional groups. (iii) When predicting more than one quality parameter from FTIR spectra, it is important to study correlation patterns between the quality parameters: strongly intercorrelated analytes are difficult to predict independently.

In this chapter, we summarize result from a three‐year research project, financed by the Norwegian Research Council, where routine FTIR instruments have been calibrated for fatty acid composition in milk by partial least squares regression. Aspects related to preprocessing, multivariate calibration, and validation are discussed using this example.
Applications of Vibrational Spectroscopy to the Study of Cheese and Other Fermented, Solid and Semi‐solid Dairy Products
Authors: Fagan Colette C. , O'Donnell Colm P.
Published: November 2010

Vibrational spectroscopy can be a powerful tool for analysis and quality assurance for cheese, yogurt, and other fermented dairy products. Traditional methods for determining the quality of these products can be labor intensive and expensive, while vibrational spectroscopy can be used rapidly and cost effectively for such applications. This chapter reviews the current state of development of vibrational spectroscopic techniques for process monitoring, quality control, and authenticity determination in cheese and other fermented, solid, and semi‐solid dairy products. Emerging research areas for these technologies are also discussed.
Progression to Fatty Acid Profiling of Edible Fats and Oils Using Vibrational Spectroscopy
Authors: Azizian Hormoz , Kramer John K.G. , Mossoba Magdi M.
Published: November 2010

The contributions of vibrational spectroscopy (FT‐mid‐IR, FT‐Raman, and FT‐NIR) in the analyses of edible fats and oils have been reviewed. The major contributions of FT‐mid‐IR and FT‐Raman have been in structural analysis and for quantitative determination of total unsaturation, trans fat and conjugated linoleic acid (CLA). The current method of choice for fatty acid (FA) determination is GC; however it is time consuming, uses solvents, and FA must be converted to methyl esters before analysis. A rapid spectroscopic method is needed to determine both the FA composition and total trans content to meet current regulatory compliance for labeling purposes. FT‐mid‐IR and FT‐Raman lack the specificity of GC for FA determinations, while FT‐NIR is able to determine the concentration of all FAs using predeveloped spectral models based on accurate GC results. The biological activity of different FA isomers differs; some are harmful while others may have health benefits. This applies specifically to the CLA and trans isomers, since only rumenic acid (9c11t‐CLA) and its precursor vaccenic acid (11t‐18:1) have reported health benefits. Therefore, the current trans regulation may need to be revised to reflect the reality of the scientific evidence. The FT‐NIR method is well equipped to selectively exclude or include specific FAs for labeling purposes because it determines the complete FA composition.
The Analysis of Grapes, Wine, and Other Alcoholic Beverages by Infrared Spectroscopy
Authors: Gishen Mark , Cozzolino Daniel , Dambergs Robert G.
Published: November 2010

Vibrational spectroscopic techniques such as near‐infrared (NIR) and mid‐infrared (mid‐IR) offer possibilities for simple, rapid and cost effective analysis in the wine and other alcoholic beverage industries. This chapter highlights recent applications of vibrational spectroscopy to analyze the composition of grapes, juices, wines, and other alcoholic beverages. A range of challenges and requirements for sample presentation and instrument configurations for optimum performance in analyzing these highly variable and complex matrices are discussed. Applications for grapes and wines include compositional analysis (especially alcoholic content), fermentation monitoring, and authenticity and sensory profiling, some of which also have potential for nondestructive and on‐line testing, including compositional measurement of bottled product in situ. An outline of similar applications for other fermented products, such as beer and sake, is also presented.
Analysis of Caffeine, Sweeteners, and Other Additives in Beverages by Vibrational Spectroscopy
Authors: Garrigues Salvador , Armenta Sergio , de la Guardia Miguel
Published: November 2010

This chapter presents a review of the scientific literature on the use of vibrational spectroscopy, near‐infrared (NIR), mid‐infrared (mid‐IR), and Raman, for the analysis of caffeine, sweeteners, and other additives in beverages and related products. Direct analysis procedures of coffee and tea, for both classification according to precedence or variety and quantitative determination of caffeine, are available. For beverage analysis, caffeine has been determined by direct attenuated total reflection (ATR) measurement or by transmission spectroscopy in the mid‐IR region after extraction with chloroform. Different strategies have been employed for the analysis of sweeteners in beverages and tabletop products, including direct ATR or transmission IR measurements after extraction with an adequate solvent, and also using Raman spectroscopy. Owing to spectral overlapping of characteristic bands of the analytes of interest with other components from beverages and to the high absorption of the sample matrix, many of the developed vibrational‐spectroscopy‐based applications require the use of multivariate calibration through partial least squares (PLS). The future trends for these types of determinations will be based on the use of flow solid‐phase sensors and the automation though flow injection or sequential injection analysis (SIA) approaches.
The Role and Potential of Vibrational Spectroscopy in the Study and Characterization of Traditional and Novel Food Packaging Structures
Authors: Lagaron Jose M. , Lopez‐Rubio A.
Published: November 2010

The suitability and potential of vibrational spectroscopic techniques, in particular mid‐infrared spectroscopy, to study molecular organization and structural changes in packaging materials are discussed in this chapter. Specifically, some examples on the use of these techniques to characterize polymer blends, molecular order, and degradation or crosslinking in polymers are given. Moreover, the interest of using vibrational spectroscopy to study packaging materials also relies on its ability to follow mass transport and migration properties, which is of outstanding importance for food‐packaging applications. Finally, the interest of using vibrational spectroscopy techniques in evaluating novel active packaging applications is highlighted, as these techniques can provide information about the mechanisms of the action of, for instance, antimicrobial polymers, and can also be useful in following the release kinetics of bioactive or functional substances from encapsulating polymeric structures.
Detection of Melamine in Foodstuffs by Vibrational Spectroscopy
Authors: Griffiths Peter R.
Published: November 2010

In this chapter, the detection of melamine in foodstuffs with little or no sample preparation is discussed. First the direct application of mid‐infrared, near‐infrared (NIR) and Raman spectroscopy for the detection of the presence of melamine is discussed. In all three cases, the typical detection limits are between 0.1 and 1%. These detection limits can be reduced by several orders of magnitude by the application of surface‐enhanced Raman spectroscopy. Finally the application of vibrational hyperspectral imaging (HSI) is described. Mid‐infrared HSI was used to detect the presence of melamine cyanurate in feline kidneys, while the presence of a few particles of melamine in a food matrix has been demonstrated by NIR and Raman HSI.
Potential and Challenges of Applying Vibrational Spectroscopy to the Analysis of Trans Fats in Foods for Regulatory Compliance in theUSA
Authors: Mossoba Magdi M. , Moss Julie , Kramer John K.G. , Azizian Hormoz
Published: November 2010

Trans fatty acids are found in a variety of foods like dairy and meat products, but the major dietary sources are products that contain commercially hydrogenated fats. There has been a renewed need for accurate analytical methods for the quantification of total trans fat since declaration of the amount of trans fat present in food products and dietary supplements was made mandatory in many countries. Official capillary GC and IR methodologies are the two most common validated methods used to identify and quantify trans fatty acids for regulatory compliance. The present chapter provides a comprehensive discussion of the IR techniques, including the latest attenuated total reflection (ATR) Fourier transform (FT) IR methodology called thenegative second derivative ATR/FT‐IRmethod, which has been validated in an international collaborative study. This chapter points to potential sources of interferences in the FTIR determination that may lead to inaccurate results, particularly at low trans levels. The presence of high levels of saturated fats may lead to interferences in the FTIR spectra observed for trans triacylglycerols (TAG). TAGs require no derivatization, but have to be melted prior to IR measurement. While GC is currently the method of choice, ATR/FT‐IR spectroscopy is a viable, rapid alternative, and complementary method to GC for a more rapid determination of total trans fats for food‐labeling purposes.
Ammonia Synthesis – Homogeneous
Authors: Hidai Masanobu , Mizobe Yasushi
Published: November 2010

Transformations of molecular nitrogen into ammonia promoted by transition‐metal complexes are summarized. Treatment of transition‐metal salts, mostly those of Groups 4, 5, and 6 metals, with strong reducing agents under N2in aprotic media gives ammonia after hydrolysis of the reaction mixtures, while amorphous V(II) and Mo(III) hydroxides as well as V(II) catecholate complexes react with N2in protic media to afford ammonia and/or hydrazine. The coordinated N2in numerous mononuclear and multinuclear N2complexes can be converted into ammonia and/or hydrazine by treatment with protic acids. Among these complexes, N2complexes of Mo and W with tertiary phosphine coligands are outstanding because the coordinated N2is transformed into ammonia and/or hydrazine in high yields by protonation and the detailed mechanism is revealed by isolation of several intermediates. Furthermore, a tungsten N2complex reacts with a ruthenium H2complex at 55°C to form ammonia, although the reaction is stoichiometric.
Ammonia Synthesis—Homogeneous
Authors: Shibata Yusuke , Seino Hidetake , Mizobe Yasushi , Hidai Masanobu
Published: November 2010

Chemical N2reducing systems to ammonia promoted by the transition metal complexes in solutions have been surveyed. This review includes the ammonia formation facilitated not only by the active transition metal species generatedin situbut, more importantly, by the well‐defined N2complexes. The latter provides the important information about the mechanism for the chemical and biological nitrogen fixation and the clue to the development of new effective catalyst for N2reduction.
Biodesulfurization
Authors: James Grossman Matthew , Regina Durrant Lucia
Published: November 2010

Sulfur is an essential element for all life forms. Sulfur is important for the structure and function of proteins in the form of the sulfur containing amino acids cysteine and methionine. Sulfur groups from sulfur amino acids and prosthetic groups are involved in enzyme catalysis. In addition inorganic sulfur in the form of sulfate, sulfite, elemental sulfur and hydrogen sulfide are used for electron acceptors and donors in energy generating respiratory reactions.

The use of sulfur associated respiratory systems has been commercialized for the the removal of sulfur oxides and hydrogen sulfide from gas streams. The development of sulfur specific biodesulfurization processes has been a long sought after goal to either replace or augment conventional hydrodesulfurization technology in the petroleum refining industry. In addition to these applications, the biochemistry associated with biodesulfurization may have applications in chemical synthesis and biosensors.

The role of sulfur in biology and the research and commercial applications of biodesulfurization systems are reviewed.
Catalyst Characterization—Heterogeneous
Authors: Stavitski Eli , Beale Andrew M. , Weckhuysen Bert M.
Published: November 2010

The study of catalysts under in‐situ conditions enables the catalyst scientist to identify and understand the important steps, e.g., the formation of important reaction intermediates and active sites, and stages in a catalyst?s lifetime, such as activation/deactivation. The development of characterization methods as well as the design and construction of appropriate in‐situ cells and reactor probes are inevitable in order to obtain such insight. Both spectroscopic and scattering techniques have been used in attempt to understand quantitative structure/composition‐activity/selectivity relationships in catalysis. Armed with such detailed knowledge about the catalyst, it is then possible for scientists to design, in a more rational way, new and efficient catalysts for sustainable production of bulk and fine chemicals as well as for the removal of harmful compounds in industrial catalytic processes. This chapter provides an overview of the in‐situ characterization techniques available for investigation of catalytic materials. The possibilities and limitations of the methods are discussed and illustrated with numerous case studies.
Oxidative Dehydrogenation—Biological
Authors: Bartley Glenn E.
Published: November 2010

Carotenoids are photoprotective and colorful pigments necessary for the survival of all photosynthetic organisms. They are vital for the protection of photosynthetic complexes and membranes from reactive oxygen species. Carotenoids also cause the red, yellow, and orange coloration in flowers and vegetables to attract pollinators and vectors for distribution of seeds. The desaturation of carotenoids is essential to impart these photochemical properties to the molecule by increasing the length of the chromophore. This review discusses carotenoid desaturation from a molecular biological perspective. With the cloning of the carotenoid isomerase, most but not all the genes involved are now in the hands of researchers. This review will give the reader knowledge of the overall reaction and up‐to‐date information concerning new developments in carotenoid desaturation.
Mass Spectrometry
Authors: Guttman Charles M.
Published: November 2010

We describe various forms of matrix‐assisted laser desorption/ionization (MALDI) in the determination of the molecular mass distribution (MMD) and the polymer architecture. The time‐o‐flight (TOF) mass spectrometry (MS) system is described in detail this system is the most common in use today for MALDI analysis of synthetic polymers. Because sample preparation poses the major problem in obtaining and analyzing spectra using the TOF/MS methods, we offer detailed descriptions of these methods including those needed to calibrate the mass axis and the signal axis. We also review a variety of applications of MALDI to synthetic polymers such as MMD, molecular composition distribution (MCD) of copolymers, polymer architecture, combinations of MALDI TOF MS with size exclusion chromatography and other forms of polymer chromatography, as well as the use of MALDI in elucidating polymer chemical reactions mechanisms.
Nanocomposites, Polymer–Clay
Authors: Lefebvre Jean‐Marc
Published: November 2010

Polymer clay nanocomposites offer an interesting alternative to conventional polymer filler systems, owing to their distinct behavior for a broad range of properties, in relation to the nanoscale dimensions of the inorganic phase and large interfacial area. Property optimization brings forth unique challenges regarding elaboration routes and structural characterizations at all pertinent scales.
Miscibility
Authors: Arrighi Valeria , Cabral Joao , Cowie John M.G.
Published: November 2010

One of the main goals of polymer scientists is to control the structure and morphology of multicomponent systems to produce materials with novel properties. Understanding the miscibility behavior of polymer–polymer blends is vital, and this requires a knowledge of thermodynamics and the ability to select appropriate methods for the determination of phase behavior. The article provides a brief introduction to some aspects of polymer–polymer miscibility.
Bacteriophage T4
Authors: Mathews Christopher K
Published: November 2010

Bacteriophage T4 and its host bacterium,

Escherichia coli

, can be considered among the earliest model organisms – biological systems that attract large numbers of investigators who, because of technical or conceptual advantages of the system, use the system to investigate processes and mechanisms of general significance in biology. Beginning in the mid‐twentieth century, studies focused on bacteriophage T4 revealed essential features of the molecular nature of genes and genomes, mechanism and fidelity of
deoxyribonucleic acid
(DNA) replication, genetic recombination, DNA repair, control of gene expression, genome organisation, assembly of complex macromolecular structures and pre‐emption of cell metabolism by virus infection. Although much of the molecular biology research community has moved on to eukaryotic model organisms, such as yeast, nematode worms, fruitflies, the plant

Arabidopsis

, zebrafish and mice, bacteriophage T4 continues its service, both as an experimental system and as a source of research reagents and technologies.

Key Concepts:

Bacteriophage T4 presents numerous technical advantages as a model for studying virus reproduction or gene organisation and expression.

Bacteriophage T4 is representative of a large group of closely related phages found in varied environments worldwide.

Bacteriophage T4 is a virulent phage, which always lyses and kills its host bacterium.

The T4 virion has a complex multiprotein structure with a contractile tail that serves both for adsorption to host cells and for intracellular delivery of the viral genome.

Bacteriophage T4 contains a large, linear double‐stranded DNA genome, with chemical modifications of its cytosine residues.

The T4 genome is circularly permuted and terminally redundant with respect to base sequence; these features protect against information loss during replication of a linear DNA.

The T4 genome encodes numerous enzymes, used to support replication of the viral genome and to synthesise deoxyribonucleotides to support the enormous rate of DNA accumulation in infected cells.

T4 uses host cell RNA polymerase for transcription of its own genes, but it modifies the bacterial enzyme, both to prevent its transcription of bacterial genes after infection and to contribute towards a timed viral gene transcription program.

T4 morphogenesis involves separate subassembly pathways for viral heads, tails, tail baseplates and fibers, with the substructures assembling spontaneously.
Transcript Elongation and Termination in Bacteria
Authors: Richardson John P
Published: November 2010

Ribonucleic acid
(RNA) molecules are elongated by the addition of nucleotides to the 3′ end of a nascent RNA by action of
RNA polymerase
. The substrates are the four ribonucleoside triphosphates. The order of their addition is directed by pairing with an unwound part of the template
deoxyribonucleic acid
(DNA) strand and is driven by the release of two of the phosphates as pyrophosphate. The rate of addition varies considerably from one nucleotide to the next, but the overall rate is ∼48 nt s
−1
along genes encoding proteins, synchronised with the rate of translation. The elongation complex is very stable over most sequences. Termination of transcription can occur at an ‘intrinsic’ terminator – a set of sequences where the complex becomes unstable, or at a Rho‐dependent terminator, where the protein Rho acts on the RNA in the transcription complex to mediate its release. The regulation of expression of genes is controlled in many instances by the action of regulatory terminators (attenuators) or by the function of factors that affect the elongation rate and the action of terminators.

Key Concepts:

RNA polymerase unwinds ∼15 bp of DNA so that one strand can serve as a template for the assembly of an RNA transcript.

The elongation complex of RNA polymerase, DNA and nascent RNA is very stable over most DNA sequences, allowing the synthesis of transcripts that are thousands of nucleotides long.

Transcripts encoding protein are elongated with an average rate of 48 nt s
−1
, which is synchronous with the rate of translation.

The rate of step‐wise addition of nucleotides to the nascent RNA varies considerably from position to position on the DNA.

Pauses in the elongation process serves as regulatory points.

At the sequences of an intrinsic terminator the elongation complex becomes unstable allowing spontaneous release of a transcript.

Termination of transcription is mediated in some cases by action of a factor called Rho, which functions by first binding to an exposed transcript followed by acting on the RNA in a reaction powered by ATP hydrolysis.
Nucleolus
Authors: Shaw Peter J
Published: November 2010

The nucleolus is a nuclear substructure where the genes for three of the four ribosomal ribonucleic acids (RNAs) are transcribed and where ribosomal subunits are assembled. Although the nucleolus has been intensively studied for many years, recent progress has been very rapid. We are beginning to understand how the biochemical processes carried out in the nucleolus relate to the observable structure. There is much emerging evidence that the nucleolus is also involved in many other roles, particularly in the biogenesis of RNA‐containing complexes, in stress sensing and in the control of cellular activity and proliferation. Recent observations of nucleolar proteins in living cells have shown that the nucleolus and its components are highly dynamic and that the observed structure is a steady state result of the dynamic diffusion of proteins and other macromolecules throughout the nucleoplasm and nucleolus and their relative residence times in the various locations.

Key Concepts:

The nucleolus is the clearest subnuclear structure in most eukaryotic cells and is the site of rDNA transcription and ribosome biosynthesis.

Most nucleoli show three types of substructural components in standard thin section transmission electron microscopy: fibrillar centres (FC), dense fibrillar component (DFC) and granular component (GC).

The interpretation of nucleolar ultrastructure in functional terms is still not fully understood, but rDNA transcription occurs within the DFC, and the subsequent stages of rRNA processing occur vectorially in enveloping layers as the transcripts move away from the transcription sites.

Nucleoli share factors and, possibly, processes with other subnuclear structures, particularly Cajal bodies.

Most nucleolar proteins are highly dynamic and diffuse freely through the nucleolus and nucleoplasm; ‘nucleolar’ proteins have a residence time in the nucleolus of the order of a few tens of seconds.

The nucleolus is involved in many other nonconventional activities such as biogenesis of other RNP complexes, mRNA surveillance, stress sensing and control of cell proliferation.
Geological Time: History of Ideas
Authors: Bowler Peter J
Published: November 2010

Early estimates of the Earth's age were restricted by literal interpretations of Genesis, but the geological time scale had been greatly extended by the early nineteenth century. The development of stratigraphy encouraged the belief that the Earth's history included a sequence of distinct periods stretching back to a period long before the appearance of humankind. Calculations by nineteenth‐century physicists imposed a limit of at most 100 million years on estimates of the Earth's age, and most geologists accepted this limit. It was only after the discovery of radioactivity that it became possible both to extend the scale of geological time and to develop techniques for providing exact dates.
Diversity of Life through Time
Authors: Simpson Carl , Kiessling Wolfgang
Published: November 2010

Global diversity is the total number of taxa living in the present day or at any time in the geological past. Reconstructing the trajectory of global diversity by compiling data from the fossil record has been a major research agenda for palaeontologists for decades. The goal is to produce an accurate reconstruction of the pattern of global diversity that will ultimately allow us to understand the causes of diversity increases, decreases and transitions in the composition of the biota. The Paleobiology Database, a new large‐scale database based on individual collections of fossil taxa, allows palaeontologists to standardise sampling, thereby controlling for vagaries of the fossil record. Collection‐level data also allows researchers to identify any asynchrony of changes in diversity among regions of the globe, with the ultimate goal of identifying the habitats or environments that support biodiversity growth.

Key Concepts:

Biodiversity is the number of taxa alive in any interval of time.

Given that not all taxa are readily preserved in the fossil record and not all taxa can be counted, trajectories of interpolated changes in biodiversity are more relevant than estimates of extrapolated diversity.

Ancient biodiversity patterns are biased in multiple ways; extreme care must be taken to adjust for biases.

Diversification can be positive and negative; mass depletions of biodiversity are caused by severe and rapid environmental changes, whereas major increases of diversity are more gradual being governed by recoveries from mass extinctions and evolutionary innovations.

Evidence for limits of diversity is increasing in the fossil and molecular records.

Different taxa dominated at different times.

New taxa tend to originate in shallow tropical reef environments.
Nucleus and Nuclear Envelope: Methods for Preparation
Authors: Beckman Marie , Kihlmark Madeleine , Hallberg Einar
Published: November 2010

The cell nucleus of eukaryotic organisms contains the genome surrounded by a nuclear envelope consisting of a double‐lipid membrane with embedded nuclear pores and an underlying nuclear lamina. The uniformity in size and density makes it possible to isolate pure intact nuclei at high yields from tissue homogenates by centrifugation through a sucrose cushion. Nuclear envelopes can be prepared from isolated nuclei by enzymatic degradation of their nucleic acid content. The resulting nuclear envelope preparations contain structurally well‐conserved inner and outer nuclear membranes with attached ribosomes, nuclear pore complexes and nuclear lamina. Reliable methods for preparation of nuclei and nuclear envelopes play an important role in the successful identification of components that are located in nuclei and in nuclear subcompartments.

Key Concepts:

The genetic information in the nucleus of the eukaryotic cell is packaged in the form of chromatin and surrounded by a double‐lipid membrane called the nuclear envelope.

Pure intact nuclei can be isolated at high yields from tissue homogenates, and nuclear envelopes can be prepared from the isolated nuclei.

The preparation of pure nuclei is important for the identification of nuclear and subnuclear components.
History of Plant Ecology
Authors: Hagen Joel B
Published: November 2010

Plant ecology originated during the late nineteenth century in Germany and Scandinavia. Early plant ecologists pursued two broad areas of research: synecology, the study of plant communities and autecology, the study of the adaptation of species to their environments. Plant ecology developed rapidly in Britain and the United States during the first decade of the twentieth century, before animal ecology and other specialties emerged. The study of plant communities, particularly plant succession, became the central focus of ecological research during the first half of the twentieth century. After Second World War, the status of plant ecology as a distinctive area of research declined as new fields such as population ecology and ecosystem ecology gained prominence. However, plant ecologists continued to make substantial contributions to these newer areas of research.

Key Concepts:

Early plant ecologists studied plant communities and the adaptation of species to the physical and biological environments.

Laboratory physiology provided an important intellectual model for the early development of plant ecology.

Plant ecology was the first ecological specialty to emerge, and plant ecologists were largely responsible for establishing the discipline of ecology.

The process of plant succession was an important focus of research for American ecologists during the first half of the twentieth century.

Population genetics and evolutionary theory of the Modern Synthesis strongly influenced the development of population ecology after Second World War.

Population biology combined methods and ideas from population ecology, population genetics and evolutionary theory to study both plant and animal populations.

Ecosystem ecology emphasised the important energy‐capturing role of plants as the photosynthetic producers in terrestrial ecosystems.

Long‐term research carried out by large teams of scientists became a major feature of ecosystem ecology.