bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring the fate of autologous and allogeneic mesenchymal progenitor cells injected into the superficial digital flexor tendon of horses: Preliminary study
Authors: GUEST D. J. , SMITH M. R. W. , ALLEN W. R. 
Published: February 2008

SummaryAutologous mesenchymal progenitor cells (MPCs) purified from bone marrow aspirates are being used in the treatment of superficial digital flexor tendon (SDFT) injuries in the horse with promising results. In this study the fate of autologous and allogeneic MPCs following injection into the SDFT was monitored by stable transfection of MPCs with green fluorescent protein (GFP). Small lesions were created manually in one forelimb SDFT of 2 horses and injected with autologous MPCs, allogeneic MPCs or bone marrow supernatant alone.Post mortemexaminations performed after 10 or 34 days revealed GFP labelled cells located mainly within injected lesions, but with a small proportion integrated into the crimp pattern of adjacent healthy areas of tendon. Furthermore, there was no visible cell mediated immune response to allogeneic MPCs in either of the host horses.
The efficacy of a commercial ELISA as an alternative to virus neutralisation test for the detection of antibodies to EAV
Authors: DUTHIE S. , MILLS H. , BURR P. 
Published: February 2008

SummaryInfection with equine arteritis virus is a notifiable disease with sporadic occurrence in the UK. As stallions may harbour the virus after infection, horses are screened for exposure by serological testing prior to breeding. The virus neutralisation test is considered the ‘gold standard’ serological screening test, but it is time‐consuming and labour intensive; consequently there is a move towards more rapid screening methodology. In this study, a commercially available EVA antibody ELISA is assessed. The ELISA performed poorly with a sensitivity of 26% and a specificity of 96% in the samples analysed. It was concluded that this ELISA would be of little value for reducing sample turnaround time. The study emphasises the need for in‐house validation of commercially available kits.
Identification and Characterization of Oxylipid‐Protein and Peptide Conjugates by Mass Spectrometry
Authors: Chung Woon‐Gye , Maier Claudia S. 
Published: February 2008

AbstractThe modification of proteins by reactive products of lipid peroxidation is associated with a large number of diseases and biological aging; thus, methods that enable the characterization of oxylipid‐protein and/or peptide conjugates are highly in demand. This unit outlines a chemical labeling approach to identifying and characterizing proteins modified by lipid peroxidation products. It also outlines two approaches for mass spectrometry–based identification and detailed characterization of oxylipid conjugates. The first combines chemical labeling of oxylipid‐protein conjugates using an aldehyde‐specific biotinylation reagent, electrophoretic separation, and mass spectrometry–based identification of the biotinylated proteins. In the second approach, protein extracts are treated with the aldehyde‐specific reagent, proteolyzed using trypsin, and the biotinylated peptides are enriched using immobilized monomeric avidin. The enriched peptide fractions are submitted to tandem mass spectrometry for determining the peptide sequence information, site of the modification, and chemical nature of the oxylipid. Curr. Protoc. Toxicol. 35:17.9.1‐17.9.19. © 2008 by John Wiley & Sons, Inc.
Detection and Analysis of Protein‐Protein Interactions of Organellar and Prokaryotic Proteomes by Blue Native and Colorless Native Gel Electrophoresis
Authors: Krause Frank , Seelert Holger 
Published: February 2008

AbstractNative gels enable the analysis of protein complexes on a proteome‐wide scale in a single experiment. The protocols described in this unit are based on separation of protein complexes by blue native polyacrylamide electrophoresis (BN‐PAGE), the most versatile native gel system, and the closely related milder colorless native PAGE (CN‐PAGE). Both BN‐PAGE and CN‐PAGE are described on analytical to preparative scales. In addition, methods for subsequent analysis of protein complexes are given, including electroelution from native gels as well as denaturing and native two‐dimensional PAGE. Finally, the removal of Coomassie dye from electroeluted proteins is detailed along with a discussion of fundamental considerations for the solubilization of membrane protein complexes from various biological samples, which are exemplified for mitochondria, chloroplasts (thylakoids), and cyanobacteria. Curr. Protoc. Protein Sci. 51:14.11.1‐14.11.36. © 2008 by John Wiley & Sons, Inc.
Characterization of Mouse Hematopoietic Stem and Progenitor Cells
Authors: Miller Cindy L. , Dykstra Brad , Eaves Connie J. 
Published: February 2008

AbstractThe unit describes functional assays for the quantification of mouse hematopoietic stem cells and progenitor cells. The competitive repopulating unit (CRU) assay detects transplantable mouse hematopoietic stem cells with the capacity to regenerate all of the blood cell lineages for extended time periods in vivo. The long‐term culture‐initiating cell (LTC‐IC) assay, founded on the bone marrow long‐term culture system, measures primitive hematopoietic progenitors based on their capacity to produce myeloid progeny for at least four weeks. Colony‐forming cell (CFC) assays, performed in semisolid medium cultures to assess mouse pre‐B, megakaryocyte, erythroid, granulocyte‐monocyte, and multipotential hematopoietic progenitors are also described. These assays are powerful tools for evaluating human stem cell (HSC) and progenitor content in various hematopoietic tissues, during development as well as in the adult animal, and in cell populations manipulated ex vivo. Curr. Protoc. Immunol. 80:22B.2.1‐22B.2.31. © 2008 by John Wiley & Sons, Inc.
Monoclonal Antibodies to Human Cell Surface Antigens
Authors: Beare Alice , Stockinger Hannes , Zola Heddy , Nicholson Ian 
Published: February 2008

AbstractMany of the leukocyte cell surface molecules are known by “CD” numbers. In this Appendix, a short introduction describes the history and the use of CD nomenclature and provides a few key references to enable access to the wider literature. This is followed by a table that lists all human molecules with approved CD names, tabulating alternative names, key structural features, cellular expression, major known functions, and usefulness of the molecules or antibodies against them in research or clinical applications. Curr. Protoc. Immunol. 80:A.4A.1‐A.4A.73. © 2008 by John Wiley & Sons, Inc.
Amino Acids: Chemical Properties
Authors: Dwyer Donard S. 
Published: February 2008

Abstract

A complete understanding of protein folding, protein recognition, enzyme catalysis, and allosteric regulation will require intimate knowledge about the fundamental physico‐chemical properties of amino acids. This article will summarize the chemistry of the 20 naturally occurring amino acids with special emphasis on the relationship to protein folding and biologic activity. The major features of the amino acids are classified into three categories, which are as follows: 1) physico‐chemical properties, 2) biologic properties, and 3) electronic properties. Cross‐correlations among more than 34 different parameters revealed that these measures segregate into four main properties that are largely independent, as follows: 1) steric effects (polarizability), 2) hydrophilicity (H
p
index), 3) inductive effects, and 4) field effects. Advances in quantum chemistry, nuclear magnetic resonance (NMR) analysis, and theoretic physics encourage efforts to derive all‐electronic expressions for the fundamental properties of amino acids that will provide mechanistic insights into protein structure and function.
Antibiotics: Bacterial Resistance
Authors: Wright Gerard D 
Published: February 2008

Abstract
Microbes have evolved a myriad of mechanisms to overcome the toxic effects of antibiotics, which include the production of enzymes that modify or degrade antibiotics, complex membrane‐associated efflux systems that can pump antibiotics out of the cell, modification of antibiotic targets, and the production of immunity proteins. The biochemical logic of resistance is often intimately linked with the mode of action of the antibiotics. As a result, chemical biology approaches for understanding resistance not only have application in our understanding of this phenomenon, but also they can guide the generation and deployment of new antibiotics. In this review, a survey of the chemical strategies employed by bacteria to resist antibiotics is presented with an emphasis on the molecular mechanisms of resistance enzymes and proteins.
Cell Cycle: Regulation
Authors: McAndrew Christopher W. , Gastwirt Randy F. , Donoghue Daniel J. 
Published: February 2008

Abstract
Normal regulation of the cell cycle ensures the passage of genetic material without mutations and aberrations. Proper completion of each phase is critical to the initiation of the following phase, and the pathways that cell division occur in an ordered, sequential, and irreversible procession. The two major cell‐cycle events that are regulated tightly are DNA replication and cell division. Progression through each phase transition is regulated by extracellular signaling, transcription factors, cyclin‐dependent kinases (CDKs), and checkpoints, which prevent uncontrolled cell division. Cyclin/CDK complexes are the primary factors responsible for the timely order of cell‐cycle progression, which include entry into S phase, initiation of DNA replication, and mitotic entry. Each phase of the cell cycle and the different cyclin/CDK complexes, as well as other important factors that regulate cell‐cycle progression and checkpoints, will be discussed.
Unraveling Cell Division Mechanisms with Small‐Molecule Inhibitors
Authors: Lampson Michael A. , Kapoor Tarun M. 
Published: February 2008

Abstract
Cell division is the process by which a cell creates two genetically identical daughter cells. To maintain genomic integrity, a complex and highly regulated sequence of events ensures that the replicated chromosomes are partitioned equally between the daughter cells. For more than 50 years, strategies designed around small‐molecule inhibitors have played a critical role in advancing our understanding of this essential process. Here we introduce a series of questions in the biology of cell division and illustrate how small molecules have been used to design experiments to address these questions. Because of the highly dynamic nature of cell division, the temporal control over protein function that is possible with small molecules has been valuable particularly in dissecting biologic mechanisms.
Chaperones, Molecular
Authors: Ellis R. John 
Published: February 2008

Abstract
The generic tendency of proteins to aggregate into nonfunctional, and sometimes cytotoxic, structures poses a universal problem for all types of cells. This problem is exacerbated by the high total concentrations of macromolecules found within most intracellular compartments, but it is solved by the actions of certain proteins that function as molecular chaperones. Different chaperones act by distinct mechanisms on both the folding of polypeptide chains and their subsequent assembly into oligomeric structures. Many chaperones, but not all, are also stress (or heat shock) proteins because the need for a chaperone function increases under stress conditions that cause proteins to unfold.
Chlorophylls and Carotenoids, Chemistry of
Authors: Scheer Hugo 
Published: February 2008

AbstractChlorophylls and carotenoids are essential pigments of photosynthesis, in which they have complementary functions for capturing light and transducing it to biochemical energy and for protecting against its deleterious effects. Carotenoids are also present in most other organisms where they have, besides photoprotection, a variety of other functions. Typical structures of both types of pigments are reviewed in this article as well as their functions, chemical properties, spectroscopy, biosynthesis, and applications.
CoA‐Dependent Enzymes, Chemistry of
Authors: Drueckhammer Dale G. 
Published: February 2008

AbstractCoenzyme A (CoA) and its thioesters play a diverse array of roles in biologic systems. The enzymes that catalyze reactions of CoA are of interest for a variety of reasons, including, but not limited to, their potential as drug targets. The enzymology of CoA biosynthesis is now well understood, and the genes for all of the enzymes involved have been identified. Thioesters are inherently reactive toward acyl transfer reactions and toward reactions involving deprotonation of the α‐carbon, and these are the primary reactivity patterns in enzyme‐catalyzed reactions of CoA thioesters. CoA utilizing enzymes have been widely studied mechanistically and structurally. Analogs of the natural CoA thioester substrates have been widely used in these studies, including thioesters of unnatural or uncommon acyl groups as well as a large number of analogs in which the thioester is replaced with alternative functionality. Recent technical applications of CoA have included the tagging of carrier protein domains and carrier protein fusions with tagged phosphopantetheine derivatives transferred enzymatically from the corresponding tagged CoA derivatives using promiscuous phosphopantetheinyl transferases.
Endocytosis: Receptor‐Mediated
Authors: Peterson Blake R. 
Published: February 2008

Abstract
Specific receptors on the surface of mammalian cells actively internalize cell‐impermeable ligands by the mechanism of receptor‐mediated endocytosis (RME). This process is critical for the acquisition of nutrients, signal transduction, development, neurotransmission, and cellular homeostasis. Binding of ligands to internalizing receptors on the plasma membrane results in clustering of the complex in clathrin‐coated pits or other dynamic membrane regions. Invagination of these regions yields intracellular vesicles that fuse to form membrane‐sealed endosomes. Receptors typically dissociate from ligands in these acidic compartments, which allows the free receptor to cycle back to the cell surface, whereas ligands are often degraded on delivery to lysosomes, which liberates amino acids and other nutrients. By mimicking endogenous ligands, certain protein toxins, viruses, and other pathogens exploit RME to enter the cytoplasm or reach other intracellular destinations. Similarly, artificial delivery systems that mimic ligands or receptors can enhance efficiently the cellular uptake of impermeable molecules, including drugs, proteins, and nucleic acids. Advances in small‐molecule probes, structural biology, and genetic methods are beginning to illuminate the complex mechanisms of this process at the molecular level.
Enzyme Catalysis: Chemical Strategies
Authors: Bugg Timothy D.H. 
Published: February 2008

Abstract
This article will describe the different chemical strategies used by enzymes to achieve rate acceleration in the reactions that they catalyze. The concept of transition state stabilization applies to all types of catalysts. Because enzyme‐catalyzed reactions are contained within an active site of a protein, proximity effects caused by the high effective concentrations of reactive groups are important for enzyme‐catalyzed reactions, and, depending on how solvent‐exposed the active site is, substrate desolvation may be important also. Examples of acid–base catalysis and covalent (nucleophilic) catalysis will be illustrated as well as examples of “strain” or substrate destabilization, which is a type of catalysis observed rarely in chemical catalysis. Some more advanced topics then will be mentioned briefly: the stabilization of reactive intermediates in enzyme active sites and the possible involvement of protein dynamics and hydrogen tunneling in enzyme catalysis.
Enzyme Inhibition
Authors: Silverman Richard B. 
Published: February 2008

AbstractThis article describes various approaches to inhibition of enzyme catalysis. Reversible inhibition includes competitive, uncompetitive, mixed inhibition, noncompetitive inhibition, transition state, and slow tight‐binding inhibition. Irreversible inhibition approaches include affinity labeling and mechanism‐based enzyme inhibition. The kinetics of the various inhibition approaches are summarized, and examples of each type of inhibition are presented.
Epigenetic Modifications
Authors: Huertas Dori , Esteller Manel 
Published: February 2008

Abstract
Epigenetic modifications play a fundamental role in chromatin structure and function. Histone modifications and DNA methylation regulate important biologic processes such as heterochromatin formation, genomic imprinting, X‐chromosome inactivation, and transcriptional activation and silencing. Epigenetic mechanisms are responsible for a considerable part of the phenotype of complex organisms. The understanding of epigenetic modifications in chromatin may offer some clues to solve the mechanisms of cellular identity, tumorigenesis, stem cell plasticity, regeneration, and aging. These processes are of interest in the fields of human biology and human diseases. Here, we describe the principal components involved in epigenetic modifications, such as the enzymes that modify chromatin, the protein domains that recognize modified chromatin, some best‐characterized downstream effectors, and the tools and techniques for studying epigenetics. However, the biological mechanism of the majority of components is still poorly understood, and the analysis of these components is fundamental to our understanding of epigenetics.
Fatty Acid Desaturases, Chemistry of
Authors: Buist Peter H. 
Published: February 2008

AbstractThe mid‐chain dehydrogenation of saturated fatty acyl derivatives is carried out by a large family of O2‐dependent, nonheme diiron‐containing enzymes known as desaturases. Both soluble and membrane‐bound desaturases have been characterized. The mechanism of desaturation is thought to involve the stepwisesynremoval of vicinal hydrogen atoms via a short‐lived carbon‐centered radical intermediate. The most common desaturase inserts a (Z)‐double bond between the C9,10 carbons of a stearoyl thioester; however, many variations of this prototypical reaction have been discovered. Accounting for this diversity in terms of subtle alterations in active‐site architecture constitutes a new frontier for research in this area.
Forward Chemical Genetics
Authors: Chang Young‐Tae 
Published: February 2008

AbstractWith the successful results of the Human Genome Project, we are now faced with the problem of handling numerous gene targets whose functions remain to be studied; this challenge is being undertaken by the field known as functional genomics. Chemical genetics is an emerging new paradigm to attack this challenging problem, of which there are two approaches: forward and reverse. Although reverse chemical genetics uses a “cause‐to‐effect” approach, forward chemical genetics uses an “effect‐to‐cause” approach. As opposed to conventional genetics where gene knock‐outs or overexpression, forward chemical genetics uses a small‐molecule library to produce a novel phenotype that eventually is employed in the elucidation of gene function. Compared with conventional genetics, chemical genetics holds several unique advantages. A successful forward genetic study provides not only knowledge about a novel gene's function, but also it provides a small moleculeON/OFFswitch that can regulate biologic processes. These small molecules will be extremely useful biologic probes as well as potential new drug candidates. Three main components make up forward chemical genetics: 1) chemical toolbox generation, 2) phenotypic screening, and 3) target identification. Although all three components require additional refinement, target identification poses the greatest challenge. Herein, the general concepts of chemical genetics, with a focus on the forward approach, and the technical overviews for each component are described.
Glycan Biosynthesis in Mammals
Authors: Meledeo M. Adam , Yarema Kevin J. 
Published: February 2008

AbstractMammalian glycosylation, the process by which a cellular complement of glycans of dazzling complexity is produced, involves a minimum of 1% of the genome (in humans) and is the dominant postsynthetic modification of both proteins and lipids endowing these molecules with an extended range of structure and function. This article provides a brief outline of the metabolic process by which monosaccharides—the raw material for the construction of complex oligosaccharides—are converted into high energy nucleotide sugar “building blocks” that are in turn assembled into four major classes of mammalians carbohydrates: glycoproteins, glycolipids, GPI anchored structures, and polysaccharides. Finally, the article concludes with a brief discussion of modern methods for manipulating glycans in living cells and in animals–using synthetic, molecular biology, and “chemical biology” approaches—as early steps toward developing sugar‐based medicines.
Glycosylation of Proteins in the Golgi Apparatus
Authors: Desko Marguerite M. , Kohler Jennifer J. 
Published: February 2008

AbstractOligosaccharides are essential for interactions of cells with their environments. These complex carbohydrates are often found covalently attached to proteins embedded in eukaryotic cell membranes. Protein glycosylation is heterogeneous; this heterogeneity stems from the biosynthesis of these polymers. As proteins destined for secretion or cell‐surface presentation traffic through the endoplasmic reticulum and the Golgi apparatus, they are modified with sugars in a stepwise fashion by enzymes called glycosyltransferases. The differential expression of these enzymes leads to a multiplicity of specific oligosaccharides both among and within cells because not all cells contain all enzymes and because not all substrate proteins will encounter every enzyme. Although myriad oligosaccharides are found attached to proteins, most of these diverse structures can be grouped into several classes of glycans. In this article, we will discuss some of the most common forms of Golgi protein glycosylation: mucin‐typeO‐linked glycosylation,N‐linked glycosylation, and the formation of glycosaminoglycans. In addition, we will briefly consider some less common, but essential, forms of glycosylation.
Glycosyltransferases, Chemistry of
Authors: Weadge Joel T. , Palcic Monica M. 
Published: February 2008

Abstract
Glycosyltransferases (GTs) form glycosidic bonds by catalyzing the transfer of saccharides from a donor to a wide variety of acceptors. The donors used by GTs are sugars conjugated to nucleotides, phosphates, or lipid phosphates; whereas acceptors consist of carbohydrates, proteins, lipids, DNA, and numerous small molecules such as antibiotics, flavonols, steroids, and so on. Together, the products of these reactions comprise the most diverse and abundant class of natural compounds found in nature. Numerous GTs are needed to synthesize these compounds because the formation of each distinct glycosidic linkage requires a different enzyme. The abundance of these enzymes is emphasized by the fact that GTs constitute 1% of the genes in all genomes sequenced. They are ubiquitous in every kingdom of life and in all compartments of the cell. Currently, over 32,000 GT ORFs have been classified into 90 families on the basis of amino acid sequence similarity. The structures for 64 GTs have been determined to date and generally reveal conserved architectures of a GT‐A or GT‐B fold, although other folds have been observed and are predicted. These crystal structures, together with biochemical data, have provided insight into the catalytic mechanism. GTs generally exhibit strict regio/stereospecificity and transfer with either retention or inversion of configuration at the anomeric carbon of the donor sugar. The importance of characterizing the precise activity of these enzymes is exemplified by the many genetic disorders that have been linked to aberrant glycosylation.