bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preparation of 2′‐Deoxy‐2′‐Methylseleno‐Modified Phosphoramidites and RNA
Authors: Micura Ronald , Höbartner Claudia , Rieder Renate , Kreutz Christoph , Puffer Barbara , Lang Kathrin , Moroder Holger 
Published: January 2007

AbstractThe derivatization of nucleic acids with selenium is a useful approach to facilitate phase determination during three‐dimensional structural analysis by X‐ray crystallography. This unit describes (1) the synthesis and characterization of 2′‐deoxy‐2′‐methylseleno (2′‐Se‐methyl) nucleosides and their corresponding 3′‐O‐(2‐cyanoethyl)‐N,N‐diisopropylphosphoramidite derivatives, (2) the site‐specific incorporation of 2′‐Se‐methyl ribonucleosides into oligoribonucleotides by chemical RNA solid‐phase synthesis, and (3) the enzymatic ligation of Se‐containing RNA oligonucleotides to produce a biologically relevant RNA sequence.
Using Morpholinos to Control Gene Expression
Authors: Moulton Jon D. 
Published: January 2007

AbstractMorpholino oligonucleotides are stable, uncharged, water‐soluble molecules used to block complementary sequences of RNA, preventing processing, read‐through, or protein binding at those sites. Morpholinos are typically used to block translation of mRNA and to block splicing of pre‐mRNA, though they can block other interactions between biological macromolecules and RNA. Morpholinos are effective, specific, and lack non‐antisense effects. They work in any cell that transcribes and translates RNA, but must be delivered into the nuclear/cytosolic compartment to be effective. Morpholinos form stable base pairs with complementary nucleic acid sequences but apparently do not bind to proteins to a significant extent. They are not recognized by any proteins and do not undergo protein‐mediated catalysis; nor do they mediate RNA cleavage by RNase H or the RISC complex. This work focuses on techniques and background for using Morpholinos.
Analysis and Management of Microarray Gene Expression Data
Authors: Grant Gregory R. , Manduchi Elisabetta , Stoeckert Christian J. 
Published: January 2007

AbstractMicroarray experiments require careful planning and choice of analysis tools in order to get the most out of the data generated, especially considering the associated significant cost and effort. Microarray experiments also require careful documentation, often residing in local databases and/or submitted to public repositories. An often bewildering assortment of choices is available for experimental design, data preprocessing, data analysis (e.g., differential gene expression, classification), and data management. This unit covers the basic steps and common applications for planning, data processing, and data management of microarray experiments, and provides guidance to making choices based on the goals and practical realities of the experiment, as well as the authors' experience in this area.
Evaluation of Glucose Homeostasis
Authors: Heikkinen Sami , Argmann Carmen A. , Champy Marie‐France , Auwerx Johan 
Published: January 2007

AbstractObesity and dyslipidemia are often found in association with insulin resistance (IR). These components combined with hypertension characterize the most common endocrine disorder in humans, the metabolic syndrome. Thus, in addition to profiling body weight evolution and lipid metabolites, glucose tolerance (a reflection of IR) and insulin sensitivity should also be considered as part of any metabolic phenotyping protocol. The ability to measure IR and glucose tolerance is important not only in the quest to fully understand the pathogenesis of the metabolic syndrome in the mouse, but also to test the effects of potential interventions. This unit presents a variety of tests used for this purpose, including direct blood glucose measurements, insulin measurement by ELISA, the homeostatic model assessment, glucose tolerance and insulin sensitivity tests, and the euglycemic clamp.
Techniques for Mammalian Cell Tissue Culture
Authors: Phelan Mary C. 
Published: January 2007

AbstractThis unit opens with detailed discussions on the latest principles of sterile technique and preparation of culture media. Step‐by‐step protocols describe trypsinizing and subculturing monolayer cultures, passaging suspension cultures, freezing and thawing cells, counting cells using a hemacytometer, and preparing cells for transport.
Population‐Based Case‐Control Association Studies
Authors: Hancock Dana B. , Scott William K. 
Published: January 2007

AbstractThis unit provides an overview of the design and analysis of population‐based case‐control studies of genetic risk factors for complex disease. Considerations specific to genetic studies are emphasized. The unit reviews basic study designs, differentiating case‐control studies from others, discusses selection of genetic markers for use in studies, introduces basic methods of analysis of case‐control data, and discusses measures of association and impact. Controlling for confounding (including population stratification), consideration of multiple loci, and haplotype analysis are briefly discussed. Readers are referred to basic texts on epidemiology for more details on general conduct of case‐control studies.
Using BLAST for Performing Sequence Alignment
Authors: Healy Matthew D. 
Published: January 2007

AbstractBLAST is a widely used genetic sequence comparison program developed at the National Center for Biotechnology Information (NCBI). In this unit, three Basic Protocols and one Support Protocol are provided for general‐purpose BLAST searches on the NCBI and ENSEMBL Web‐accessible BLAST servers. Key parameters affecting how the search algorithm works are reviewed, with advice on modifying search parameters for specific situations. Many other public and private Web sites offer BLAST interfaces which may differ from those described in this unit, but the general principles will be similar. The Support Protocol describes how to obtain sequences in various formats from NCBI for use in BLAST searches. It is emphasized that no algorithm can be a substitute for biological understanding; performing a BLAST search takes only a few minutes but understanding the implications of the results takes much longer.
Preparation of Cells from Formalin‐Fixed, Paraffin‐Embedded Tissue for Use in Fluorescence In Situ Hybridization (FISH) Experiments
Authors: Weremowicz Stanislawa , Schofield Deborah E 
Published: January 2007

AbstractNumerical and structural chromosome abnormalities can be accurately detected in cells from archived tissues using fluorescence in situ hybridization (FISH). This unit describes two common approaches to performing FISH in formalin‐fixed, paraffin‐embedded tissue. The first approach utilizes 4 to 6 µm tissue sections in cases for which preserving tissue morphology is necessary, and the second involves extraction of intact nuclei from 50 µm tissue sections. To interpret FISH results using 4 to 6 µm sections, an adequate number of nuclei must be evaluated to perform statistical analysis. Evaluation of 30 to 50 nuclei from the single cell suspension generally gives an interpretable result.
Standard Safety Practices for Sorting of Unfixed Cells
Authors: Schmid Ingrid , Lambert Claude , Ambrozak David , Perfetto Stephen P. 
Published: January 2007

AbstractCell sorting of viable biological specimens has become widespread in laboratories involved in basic and clinical research. As these samples can contain infectious agents, precautions to protect instrument operators and the environment from hazards arising from the use of sorters are paramount. This unit presents a revised and updated version of the biosafety guidelines for sorting of unfixed cells established in 1977 by the International Society of Analytical Cytology (ISAC), whose recommendations have become recognized worldwide as the standard practices and safety precautions for laboratories performing viable cell‐sorting experiments. The unit contains background information on the biohazard potential of sorting and the hazard classification of infectious agents as well as recommendations on (1) sample handling, (2) operator training and personal protection, (3) laboratory design, (4) cell sorter setup, maintenance, and decontamination, and (5) testing the instrument for the efficiency of aerosol containment.
Optimized Whole‐Blood Assay for Measurement of ZAP‐70 Protein Expression
Authors: Shankey T. Vincent , Forman Meryl , Scibelli Paul 
Published: January 2007

AbstractChronic lymphocytic leukemia (CLL) is characterized by a clonal expansion of small lymphocytes commonly expressing cell surface markers (CD5 and CD19) that are consistent with a population of B lymphocytes. This unit describes a technique to measure ZAP‐70 protein expression in whole‐blood specimens from CLL samples. The protocols presented include an optimized fixation/permeabilization technique that allows labeling of cell surface markers and intracellular ZAP‐70 protein with significantly improved signal‐to‐noise ratio, an optimized combination of antibodies‐fluorophores to maximize ZAP‐70 expression levels, standardized methodology for instrument setup, including compensation, to improve inter‐ and intra‐laboratory reproducibility, and a method to index ZAP‐70 protein expression levels to internal positive and negative cell populations. Residual normal T and B cells function as internal positive and negative controls. These are used to index ZAP‐70 protein expression levels in the CLL population.
Isolation of Myelin
Authors: Larocca Jorge N. , Norton Williams T. 
Published: January 2007

AbstractThe methods used to prepare myelin involve homogenization of the tissue in isotonic sucrose solution, followed by the isolation of myelin membranes by a series of steps that include density gradient centrifugation and differential centrifugation. Homogenization of nervous tissue in isotonic sucrose causes the myelin sheath to peel from the axon and form relatively large myelin vesicles. The large size of the myelin vesicles, together with the fact that myelin membrane has a lower density than other biological membranes, make differential centrifugation and density gradient centrifugation the main tools for the isolation of this membrane. Three protocols are outlined in this unit: isolation of a highly‐purified myelin fraction from the central nervous system (CNS); separation of a highly‐purified CNS myelin fraction into subfractions of different densities; and isolation of myelin from the peripheral nervous system (PNS).
Preparation of Extracellular Matrices Produced by Cultured and Primary Fibroblasts
Authors: Beacham Dorothy A. , Amatangelo Michael D. , Cukierman Edna 
Published: January 2007

AbstractFibroblasts secrete and organize extracellular matrix (ECM), which provides structural support for their adhesion, migration, and tissue organization, besides regulating cellular functions such as growth and survival. Cell‐to‐matrix interactions are vital for vertebrate development. Disorders in these processes have been associated with fibrosis, developmental malformations, cancer, and other diseases. This unit describes a method for preparing a three‐dimensional matrix derived from NIH‐3T3 cells; the matrix is three‐dimensions, cell and debris free, and attached to a two‐dimensional culture surface. Cell adhesion and spreading are normal on these matrices. This matrix can also be compressed into a two‐dimensional matrix and solubilized to study the matrix biochemically.
Identification and Analysis of Multiprotein Complexes Through Chemical Crosslinking
Authors: Melcher Karsten , Chen Hung‐Ta 
Published: January 2007

AbstractChemical crosslinking provides information about protein‐protein interactions in the context of intact protein complexes; therefore, it is particularly suited to the analysis of multiprotein complexes. Rather than a single distinct technique, chemical crosslinking represents a smorgasbord of techniques that differ significantly both in chemistry and in scope. This unit will attempt to guide the reader through the complexities of crosslinking to find the most suitable approach for a given biological question. Sample protocols for two crosslinking methods considered to be particularly useful for the analysis of large multiprotein complexes are provided: His6‐mediated crosslinking and photoinducible label transfer crosslinking.
The Fluorescent Protein Color Palette
Authors: Olenych Scott G. , Claxton Nathan S. , Ottenberg Gregory K. , Davidson Michael W. 
Published: January 2007

AbstractAdvances in fluorescent protein development over the past 10 years have led to fine‐tuning of the Aequorea victoria jellyfish color palette in the emission color range from blue to yellow, while a significant amount of progress has been achieved with reef coral species in the generation of monomeric fluorescent proteins emitting in the orange to far‐red spectral regions. It is not inconceivable that near‐infrared fluorescent proteins loom on the horizon. Expansion of the fluorescent protein family to include optical highlighters and FRET biosensors further arms this ubiquitous class of fluorophores with biological probes capable of photoactivation, photoconversion, and detection of molecular interactions beyond the resolution limits of optical microscopy. The success of these endeavors certainly suggests that almost any biological parameter can be investigated using the appropriate fluorescent protein–based application.
Using the NCBI Map Viewer to Browse Genomic Sequence Data
Authors: Wolfsberg Tyra G. 
Published: January 2007

AbstractThis unit includes an introduction to the Map Viewer, which describes how to perform a simple text‐based search of genome annotations to view the genomic context of a gene, navigate along a chromosome, zoom in and out, and change the displayed maps to hide and show information. It also describes some of NCBI's sequence‐analysis tools, which are provided as links from the Map Viewer. The Alternate Protocols describe different ways to query the genome sequence, and also illustrate additional features of the Map Viewer. Alternate Protocol 1 shows how to perform and interpret the results of a BLAST search against the human genome. Alternate Protocol 2 demonstrates how to retrieve a list of all genes between two STS markers. Finally, Alternate Protocol 3 shows how to find all annotated members of a gene family
Using the Ensembl Genome Server to Browse Genomic Sequence Data
Authors: Fernández‐Suárez Xosé M. , Schuster Michael K. 
Published: January 2007

AbstractThe Ensembl genome Web browser (http://www.ensembl.org) provides a comprehensive source of automatic annotation of the human genome sequence (as well as other species of biomedical interest), with confirmed gene predictions that have been integrated with external data sources. This unit describes how to use the Ensembl browser, how to find your gene or protein of interest and get information and external links about them, and how to use the comparative genomic data.
Structure‐Based pKa Calculations Using Continuum Electrostatics Methods
Authors: Fitch Carolyn A. , García‐Moreno E. Bertrand 
Published: January 2007

AbstractElectrostatic free energy is useful for correlating structure with function in proteins in which ionizable groups play essential functional roles. To this end, the pKa values of ionizable groups must be known and their molecular determinants must be understood. Structure‐based calculations of electrostatic energies and pKa values are necessary for this purpose. This unit describes protocols for pKa calculations with continuum electrostatics methods based on the numerical solution of the linearized Poisson‐Boltzmann equation by the method of finite differences. Critical discussion of key parameters, approximations, and shortcomings of these methods is included. Two protocols are described for calculations with methods modified empirically to maximize agreement between measured and calculated pKa values. Applied judiciously, these methods can contribute useful and novel insight into properties of surface ionizable groups in proteins.
Common File Formats
Authors: Leonard Shonda A. , Littlejohn Timothy G. , Baxevanis Andreas D. 
Published: January 2007

AbstractThis appendix discusses a few of the file formats frequently encountered in bioinformatics. Specifically, it reviews the rules for generating FASTA files and provides guidance for interpreting NCBI descriptor lines, commonly found in FASTA files. In addition, it reviews the construction of GenBank, Phylip, MSF and Nexus files.
Do better stories make better memories? Narrative quality and memory accuracy in preschool children
Authors: Kulkofsky Sarah , Wang Qi , Ceci Stephen J. 
Published: January 2007

AbstractThe present study examines how the quality of children's narratives relates to the accuracy of those narratives. Sixty‐one 3‐ to 5‐year‐olds played a novel game with a researcher in their schools. Children were questioned in an interview that included an open‐ended free recall prompt followed by a series of directed questions. Children's narratives were coded for volume, complexity and cohesion as well as for accuracy. Correlational results showed that overall, narrative skills enable the reporting of more information, while decreasing the proportion of information that was accurate. These results appeared to be driven by a quantity‐accuracy trade‐off; in an ensuing regression analysis with all narrative variables entered into the model, volume was associated with decreases in accuracy while narrative cohesion was associated with increases in accuracy. We discuss the results in terms of their relationship to the development of autobiographical memory as well as implications for forensic contexts. Copyright © 2007 John Wiley & Sons, Ltd.
Low‐Operating‐Voltage Organic Transistors Made of Bifunctional Self‐Assembled Monolayers
Authors: Mottaghi M. , Lang P. , Rodriguez F. , Rumyantseva A. , Yassar A. , Horowitz G. , Lenfant S. , Tondelier D. , Vuillaume D. 
Published: January 2007

AbstractSelf‐assembled monolayers (SAMs) are molecular assemblies that spontaneously form on an appropriate substrate dipped into a solution of an active surfactant in an organic solvent. Organic field‐effect transistors are described, built on an SAM made of bifunctional molecules comprising a short alkyl chain linked to an oligothiophene moiety that acts as the active semiconductor. The SAM is deposited on a thin oxide layer (alumina or silica) that serves as a gate insulator. Platinum–titanium source and drain electrodes (either top‐ or bottom‐contact configuration) are patterned by using electron‐beam (e‐beam) lithography, with a channel length ranging between 20 and 1000 nm. In most cases, ill‐defined current–voltage (I–V) curves are recorded, attributed to a poor electrical contact between platinum and the oligothiophene moiety. However, a few devices offer well‐defined curves with a clear saturation, thus allowing an estimation of the mobility: 0.0035 cm2 V–1 s–1 for quaterthiophene and 8 × 10–4 cm2 V–1 s–1 for terthiophene. In the first case, the on–off ratio reaches 1800 at a gate voltage of –2 V. Interestingly, the device operates at room temperature and very low bias, which may open the way to applications where low consumption is required.
Transparent Mesoporous Nanocomposite Films for Self‐Cleaning Applications
Authors: Allain E. , Besson S. , Durand C. , Moreau M. , Gacoin T. , Boilot J.‐P. 
Published: January 2007

AbstractA versatile approach is studied for the elaboration of TiO2 based photocatalytic coatings for self‐cleaning applications on transparent substrates. The basic principle of the synthesis relies on the use of preformed TiO2 colloidal particles that are further dispersed within a transparent silica binder with a mesoporous structure. Film porosity in the nanometer range is controlled by achieving the sol–gel silica condensation around self‐organized micellar assemblies of a templating copolymer surfactant. The latter also acts as a stabilizer for the TiO2 particles, thus preserving their high dispersion within the film so that excellent optical properties are maintained even for high TiO2 loading (up to 50 %). Studies of photodegradation kinetics show that such mesoporous films are at least 15 times more active than films synthesized with a usual microporous silica binder. Moreover, the measured quantum‐yield efficiency (1.1 %) is found to be among the highest reported up to now. Improved photoactivity of the films is discussed as resulting from the closer proximity between the organic molecules and the surface of the TiO2 crystallites as well as the improved diffusion rate of water and oxygen through the interconnected pore network.
Thioether‐bridged Mesoporous Organosilicas: Mesophase Transformations Induced by the Bridged Organosilane Precursor
Authors: Liu J. , Yang Q. , Zhang L. , Jiang D. , Shi X. , Yang J. , Zhong H. , Li C. 
Published: January 2007

AbstractThe achievement of structural control over thioether‐bridged mesoporous organosilicas is reported. The mesoporous materials have been synthesized by co‐condensation of bis[3‐(triethoxysilyl)propyl]tetrasulfide (TESPTS) and tetramethoxysilane (TMOS) in acetic acid/sodium acetate buffer solution (HAc–NaAc, pH 4.4), using the nonionic surfactant P123 as a template. The mesostructure of the material is mainly controlled by the molar ratio of TESPTS/TMOS in the initial gel mixture. A mesophase transformation, progressing from a highly ordered 2D hexagonal structure via a vesiclelike structure to a mesostructured cellular foam, can be clearly observed when the molar ratio of TESPTS/TMOS is increased in increments. Solid‐state NMR results show that TESPTS is not completely hydrolyzed and condensed at the applied buffer conditions. At low concentrations, the unhydrolyzed TESPTS can penetrate into the core of the surfactant micelles and change the packing parameter of the P123 surfactant. Above a certain concentration, the TESPTS can form a microemulsion with P123 surfactant molecules. Therefore, the vesiclelike structure or cellular foam structure can be synthesized by simply controlling the molar ratio of TESPTS/TMOS. This approach provides a novel method for the facile synthesis of organic–inorganic hybrid materials with a controllable mesostructure under mild synthetic conditions.
Long K‐Doped Titania and Titanate Nanowires on Ti Foil and FTO/Quartz Substrates for Solar‐Cell Applications
Authors: Cheung K. Y. , Yip C. T. , Djurišić A. B. , Leung Y. H. , Chan W. K. 
Published: January 2007

AbstractPotassium‐doped titania and titanate nanowires are fabricated by moisture‐assisted direct oxidation of titanium. The influence of the fabrication conditions on nanowire structure and morphology is investigated. It is shown that the presence of potassium is essential for nanowire formation, while the nanowire structure and morphology are strongly dependent on the fabrication temperature. The longest nanowires (ca. 10 μm) are obtained at 650 °C. At this substrate temperature, nanowires could be produced over a large substrate area both by oxidation of the Ti foil as well as by depositing a Ti film on the substrate (quartz or fluorine‐doped tin oxide (FTO)/quartz). Photovoltaic cells based on these nanowires are fabricated. The cell performance is dependent on the nanowire fabrication temperature and the substrate used, as well as on the annealing environment. Short‐circuit current densities of Isc = 3.05 mA cm–2 and Isc = 4.97 mA cm–2 could be obtained for Ti foil and FTO/quartz substrates, respectively, while the corresponding power‐conversion efficiencies are η = 0.93 % and η = 1.88 % (under AM 1.5 illumination, 100 mW cm–2; AM: air mass).