bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalyst Characterization—Heterogeneous
Authors: Stavitski Eli , Beale Andrew M. , Weckhuysen Bert M. 
Published: November 2010

AbstractThe 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

AbstractCarotenoids 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

AbstractWe 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

AbstractPolymer 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

Abstract
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

Abstract

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

Abstract

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

AbstractThe 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

AbstractEarly 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

Abstract

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

Abstract

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

AbstractPlant 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.
Root Nodules (Legume–RhizobiumSymbiosis)
Authors: Brewin Nicholas J 
Published: November 2010

AbstractRoot nodule symbiosis enables nitrogen‐fixing bacteria to convert atmospheric nitrogen into a form that is directly available for plant growth. Biological nitrogen fixation provides a built‐in supply of nitrogen fertiliser for many legume crops such as peas, beans and clover. Legumes (Fabales) interact with single‐celled Gram‐negative bacteria, collectively termed rhizobia, whereas members of three other Rosid orders (Fagales, Cucurbitales and Rosales) interact with Gram‐positive filamentous actinobacteria of the genusFrankia. In legumes, infection proceeds through intercellular and trans‐cellular channels termed infection threads. At the same time, cells in the root cortex are induced to divide and generate the tissues of the nodule. Nitrogen fixation normally takes place within specialised bacteroid cells enclosed within organelle‐like cytoplasmic compartments termed symbiosomes. The anatomy and physiology of root nodules both reflect a high degree of structural and metabolic integration between plant and microbial symbionts.Key Concepts:Legumes (family Fabales) develop root nodules that harbourRhizobiumbacteria (rhizobia).Endosymbiotic bacteria (bacteroids) convert nitrogen to ammonia (biological nitrogen fixation).Legume crops restore fertility to agricultural soils by capturing nitrogen from the atmosphere.The legume–Rhizobiumsymbiosis provides one‐fifth of all nitrogen inputs into global agriculture.Symbiosis is based on metabolic exchange for mutual benefit: exchanges of oxygen, carbon and nitrogen are tightly regulated.Legumes only form a nitrogen‐fixing symbiosis with single‐celled bacteria collectively termedRhizobium. However, other (related) groups of flowering plants form a root nodule symbiosis with filamentous actinobacteria of the genusFrankia.Some of the invasion processes adopted byRhizobiumandFrankiaare shared with a mineral‐scavenging symbiosis involving arbuscular mycorrhizal fungi that originated over 400 Ma.Colonisation of host cells byRhizobiumusually involves specialised invasion structures termed ‘infection threads’ and specialised organelle‐like compartments termed ‘symbiosomes’.During evolution, there has been horizontal transfer of the genes that specify the capability for nodulation and symbiotic nitrogen fixation between diverse groups of soil bacteria.
Pseudogenes and Their Evolution
Authors: Podlaha Ondrej , Zhang Jianzhi 
Published: November 2010

Abstract

Pseudogenes are relics of former genes that no longer possess biological functions. They are abundant in the genomes of complex organisms such as vertebrates and flowering plants and provide a useful resource for studying mutation rates and neutral evolutionary patterns. Processed pseudogenes can be regarded as fossilised footprints of past gene expression, permitting a peek into ancient transcriptomes. Occasionally adaptive, pseudogenisation is usually a neutral process. Yet, it can have a substantial impact on future evolution by limiting or opening certain evolutionary possibilities. Studies of pseudogenisation may help date key phenotypic changes in evolution and understand the genetic basis of phenotypic evolution. Recent studies found some pseudogenes to possess apparent functions in gene regulation, creating a difficulty in defining pseudogenes.

Key Concepts:

Pseudogenes are relatives of functional genes that have lost their functions.

Most pseudogenes arise from degenerated replicates of functional genes produced by either DNA‐mediated gene duplication or RNA‐mediated retroposition.

Processed pseudogenes arise from retroposition and their copy numbers are positively correlated with the germline expression levels of their parent genes. Thus, they may be regarded as fossilised footprints of past gene expression for studying ancient transcriptomes.

Most pseudogenes evolve neutrally and thus have been used to study the rates and patterns of mutations.

The human and mouse genomes contain nearly as many pseudogenes as functional genes.

The number of pseudogenes in a genome, compared to that of functional genes, varies substantially among organisms.

Pseudogenisation is usually a neutral process; yet, it can have significant impacts on future evolution by either limiting or opening certain evolutionary possibilities.

Pseudogenisation may occasionally be adaptive when the expression of a gene becomes deleterious, due to changes of the genetic background or environment.

Some apparent pseudogenes have been found to possess regulatory functions, causing a difficulty in defining pseudogenes.
DNA
Profiling in Ecology
Authors: Hamilton Matthew J , Sadowsky Michael J 
Published: November 2010

Abstract

Deoxyribonucleic acid
(DNA) profiling uses various molecular biological techniques to identify, classify, and study the ecology and evolution of organisms based on differences in DNA sequence. These differences in DNA sequence are known as polymorphisms, which may be as simple as a single nucleotide at a given nucleotide position within the genome or as complex as variant numbers of tandem repeat sequences or the presence of an interspersed repetitive element. Individuals, populations or species‐specific DNA polymorphisms are used as targets to generate fingerprint patterns suitable for the differentiation of individuals and populations. Data generated by DNA profiling methods are used to provide quantitative or qualitative information for population genetics, human diseases, diversity, phylogeny, epidemiological, forensics and conservation management purposes.

Key Concepts:

DNA profiling methodologies allow for the classification of organisms based on polymorphisms in DNA sequences at a given loci.

DNA profiling methods that can be used to detect single nucleotide and repetitive element polymorphisms include: amplified and restriction fragment length polymorphisms (AFLP/RFLP), multilocus fingerprinting using hybridisation, random amplified polymorphic DNA and denaturing gradient and pulse field gel electrophoresis (DGGE/PFGE).

DNA profiling patterns can be used to identify individuals, determine kinship and genealogy, examine inbreeding, and bottlenecks and differentiate populations.