bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA Polymerases
Authors: Paschal Beth M. , McReynolds Larry A. , Noren Christopher J. , Nichols Nicole M. 
Published: October 2008

AbstractThis unit describes DNA‐dependent, RNA‐dependent, and template‐independent RNA polymerases. DNA‐dependent RNA polymerases include the related bacteriophage T7, T3, and SP6 polymerases, the most commonly used RNA polymerases for in vitro transcription reactions. Reaction conditions to produce preparative quantities of transcribed RNA and labeled RNA probes are covered, as are the major applications of these reactions. Limitations of the E. coli RNA polymerase for these applications are also presented. The properties of the phi6 RNA‐dependent RNA polymerase (RdRp) and its use in RNAi experiments are also introduced. Poly(A) polymerase, a template‐independent polymerase, catalyzes the incorporation of AMP residues onto the free 3′‐hydroxyl terminus of RNA, utilizing ATP as a precursor. Specific reaction conditions of poly(A) polymerase, as well as applications including RNA tailing and 3′ end labeling, are discussed. Curr. Protoc. Mol. Biol. 84:3.8.1‐3.8.8. © 2008 by John Wiley & Sons, Inc.
DNA Repair Enzymes
Authors: Evans Thomas C. , Nichols Nicole M. 
Published: October 2008

AbstractIn vivo DNA damage impacts the genetic stability of an organism; therefore, multiple pathways utilizing a large number of enzymes have evolved to repair DNA damage. This unit focuses on enzymes involved in base excision repair (BER). The BER enzymes possessing N‐glycosylase activity can find and remove a wide variety of damaged bases in a sea of normal bases. The combination of unique substrate specificity, accuracy, and robust in vitro activity of many of these enzymes has led to their use in various experimental techniques, including site‐specific DNA cleavage. The enzymes described in this unit are active on many substrates including oxidized purines and pyrimidines, alkylated bases, abasic sites, pyrimidine dimers, deaminated cytosines, and deaminated adenines. Curr. Protoc. Mol. Biol. 84:3.9.1‐3.9.12. © 2008 by John Wiley & Sons, Inc.
PolyPhred Analysis Software for Mutation Detection from Fluorescence‐Based Sequence Data
Authors: Montgomery Kate T. , Iartchouck Oleg , Li Li , Loomis Stephanie , Obourn Vanessa , Kucherlapati Raju 
Published: October 2008

AbstractThe ability to search for genetic variants that may be related to human disease is one of the most exciting consequences of the availability of the sequence of the human genome. Large cohorts of individuals exhibiting certain phenotypes can be studied and candidate genes resequenced. However, the challenge of analyzing sequence data from many individuals with accuracy, speed, and economy is great. This unit describes one set of software tools: Phred, Phrap, PolyPhred, and Consed. Coverage includes the advantages and disadvantages of these analysis tools, details for obtaining and using the software, and the results one may expect. The software is being continually updated to permit further automation of mutation analysis. Currently, however, at least some manual review is required if one wishes to identify 100% of the variants in a sample set. Curr. Protoc. Hum. Genet. 59:7.16.1‐7.16.21. © 2008 by John Wiley & Sons, Inc.
Assessment of Histone Acetylation Levels in Relation to Cell Cycle Phase
Authors: Ronzoni Simona , Faretta Mario , Ballarini Marco , Pelicci PierGiuseppe , Minucci Saverio 
Published: October 2008

AbstractHistone acetylation affects chromatin structural organization, thus regulating gene expression and DNA‐related cellular events. Levels of histone acetylation are tightly modulated in normal cells and frequently altered in tumors. Consequently, histone deacetylase inhibitors are currently being tested in clinical trials as anticancer drugs. Presented here is a protocol for measuring the degree of cellular histone tail acetylation, alone or in combination with DNA content to simultaneously evaluate cell ploidy and/or cell cycle progression. The procedure can also be employed to stain peripheral blood samples in order to assess mean histone acetylation levels in patients treated with histone deacetylase inhibitors. Curr. Protocol. Cytom. 46:7.35.1‐7.35.8. © 2008 by John Wiley & Sons, Inc.
Whole Blood Processing for Measurement of Signaling Proteins by Flow Cytometry
Authors: Chow Sue , Hedley David , Shankey T. Vincent 
Published: October 2008

AbstractSignal transduction pathways link external stimuli with cellular responses, which normally regulate cell proliferation, death, and differentiation. The study of signal transduction was revolutionized through the development of phospho‐specific antibodies that recognize proteins only when they are phosphorylated at specific sites. As discussed by Nolan and co‐workers (UNIT here), one of the unique features of flow cytometry is its ability to perform correlated measurements of multiple phosphorylation states at the single cell level. This provides insight into the complexity of signaling networks that is not obtained by standard biochemical techniques. Furthermore, in combination with other phenotypic markers, flow cytometry can measure alterations in signaling pathways in subpopulations of cells. This clearly has wide potential for studying disorders of the hematopoietic and immune systems. Curr. Protocol. Cytom. 46:9.27.1‐9.27.19. © 2008 by John Wiley & Sons, Inc.
Isolation and Manipulation of Mouse Trophoblast Stem Cells
Authors: Himeno Emi , Tanaka Satoshi , Kunath Tilo 
Published: October 2008

AbstractThe isolation of stable trophoblast stem (TS) cell lines from early mouse embryos has provided a useful cell culture model to study trophoblast development. TS cells are derived from pre‐implantation blastocysts or from the extraembryonic ectoderm of early post‐implantation embryos. The derivation and maintenance of mouse TS cells is dependent upon continuous fibroblast growth factor (FGF) signaling. Gene expression analysis, differentiation in culture, and chimera formation show that TS cells accurately model the mouse trophoblast lineage. This unit describes how to derive, maintain, and manipulate TS cells, including DNA transfection and chimera formation. Curr. Protoc. Stem Cell Biol. 7:1E.4.1‐1E.4.27. © 2008 by John Wiley & Sons, Inc.
Contraction of free liquid ligaments
Authors: Li Ri , Ashgriz Nasser , Chandra Sanjeev , Andrews John R. 
Published: October 2008

AbstractThis article presents an experimental and theoretical study on the contraction of free, stable, and inviscid liquid ligaments under the action of surface tension forces. The ligament is considered as two blobs of arbitrary initial sizes connected by a central column with a constant and uniform radius. Based on the conservation of mass, momentum, and energy, a theoretical model is developed to predict the ligament length as a function of time, thereby predicting the lifetime of the ligament. The theoretical results are compared with our experimental measurements of the transient length of liquid ligaments ejected from an inkjet printhead, showing good agreement. © 2008 American Institute of Chemical Engineers AIChE J, 2008
Acanthoscurrin fragment 101–132: Total synthesis at 60°C of a novel difficult sequence
Authors: Remuzgo César , Andrade Gustavo F. S. , Temperini Márcia L. A. , Miranda M. Terêsa M. 
Published: October 2008

AbstractGlycine‐rich proteins (GRPs) serve a variety of biological functions. Acanthoscurrin is an antimicrobial GRP isolated from hemocytes of the Brazilian spider Acanthoscurria gomesiana. Aiming to contribute to the knowledge of the secondary structure and stepwise solid‐phase synthesis of GRPs' glycine‐rich domains, we attempted to prepare G101GGLGGGRGGGYG113GGGGYGGGYG123 GGY126GGGKYK132‐NH2, acanthoscurrin C‐terminal amidated fragment. Although a theoretical prediction did not indicate high aggregation potential for this peptide, repetitive incomplete aminoacylations were observed after incorporating Tyr126 to the growing peptide‐MBHA resin (Boc chemistry) at 60°C. The problem was not solved by varying the coupling reagents or solvents, adding chaotropic salts to the reaction media or changing the resin/chemistry (Rink amide resin/Fmoc chemistry). Some improvement was made when CLEAR amide resin (Fmoc chemistry) was used, as it allowed for obtaining fragment G113–K132. NIR‐FT‐Raman spectra collected for samples of the growing peptide‐MBHA, ‐Rink amide resin and ‐CLEAR amide resin revealed the presence of β‐sheet structures. Only the combination of CLEAR‐amide resin, 60°C, Fmoc‐(Fmoc‐Hmb)Gly‐OH and LiCl (the last two used alternately) was able to inhibit the phenomenon, as proven by NIR‐FT‐Raman analysis of the growing peptide‐resin, allowing the total synthesis of desired fragment Gly101–K132. In summary, this work describes a new difficult sequence, contributes to understanding stepwise solid‐phase synthesis of this type of peptide and shows that, at least while protected and linked to a resin, this GRP's glycine‐rich motif presents an early tendency to assume β‐sheet structures. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 92: 65–75, 2009.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Oxidation of Diiron and Triiron Sulfurdithiolato Complexes: Mimics for the Active Site of [FeFe]‐Hydrogenase
Authors: Windhager Jochen , Seidel Raphael A. , Apfel Ulf‐Peter , Görls Helmar , Linti Gerald , Weigand Wolfgang 
Published: October 2008

AbstractThe oxidation of the hexacarbonyl(1,3‐dithiolato‐S,S′)diiron complexes 4a–4c with varying amounts of dimethyldioxirane (DMD) was systematically studied. The chemoselectivity of the oxidation products depended upon the substituent R (R=H, Me, 1/2 (CH2)5). For R=H, four oxidation products, 6a–6d, have been obtained. In the case of R=Me, three products, 7a–7c, were formed, and for R=1/2 (CH2)5, only complex 8 was observed. These observations are due to steric and electronic effects caused by the substituent R. Additionally, oxidation of the triiron complex 5 with DMD was performed to yield the products 9a and 9b. X‐Ray diffraction analyses were performed for 6a–6d, 7a, and 7c, as well as for 9a and 9b. The electronic properties were determined by density‐functional theory (DFT) calculations.
Cytotoxicity and Cellular Accumulation of Palladium(II) Complexes of Tetracyclines
Authors: de Paula Flávia C. S. , Guerra Wendell , Silva Iara R. , Silveira Josianne N. , Botelho Françoise Vasconcelos , Vieira Leda Q. , Pereira‐Maia Elene C. 
Published: October 2008

AbstractWe studied the cytotoxic effect and the uptake of PdII complexes of doxycycline (Dox), [Pd(Dox)Cl2] (1), and tetracycline (Tc), [Pd(Tc)Cl2] (2), in chronic myelogenous leukemia cells. The effect of the compounds on macrophage viability was also investigated. Compound 1 is more effective than compound 2 in inhibiting the growth of K562 cells with the IC50 values of 14.44 and 34.54 μM, respectively. There is a good correlation between cell‐growth inhibition and intracellular metal concentrations, determined by inductively coupled plasma atomic emission spectroscopy (ICP‐AES). Incubation of the cells with equitoxic concentrations of both compounds yields approximately the same intracellular Pd concentration. At the IC50 doses, intracellular concentration is ca. 33×10−16 mol/cell for both compounds 1 and 2. This suggests that more [Pd(Tc)Cl2] is needed to produce a cytotoxic effect, because it enters cells more slowly. Both compounds up to 16 μM did not affect the viability of mouse peritoneal macrophages after a 48‐h incubation. After 72 h of incubation, the IC50 values are 22 for [Pd(Dox)Cl2] and 40 μM for [Pd(Tc)Cl2]. Therefore, the cytotoxic effect in cancer cells exhibited by both compounds is higher than their effect in macrophages.
Imaging Target mRNA and siRNA‐Mediated Gene Silencing In Vivo with Ribozyme‐Based Reporters
Authors: So Min‐Kyung , Gowrishankar Gayatri , Hasegawa Sumitaka , Chung June‐Key , Rao Jianghong 
Published: October 2008

AbstractNoninvasive imaging of specific mRNAs in living subjects promises numerous biological and medical applications. Common strategies use fluorescently or radioactively labelled antisense probes to detect target mRNAs through a hybridization mechanism, but have met with limited success in living animals. Here we present a novel molecular imaging approach based on the group I intron of Tetrahymena thermophila for imaging mRNA molecules in vivo. Engineered trans‐splicing ribozyme reporters contain three domains, each of which is designed for targeting, splicing, and reporting. They can transduce the target mRNA into a reporter mRNA, leading to the production of reporter enzymes that can be noninvasively imaged in vivo. We have demonstrated this ribozyme‐mediated RNA imaging method for imaging a mutant p53 mRNA both in single cells and noninvasively in living mice. After optimization, the ribozyme reporter increases contrast for the transiently expressed target by 180‐fold, and by ten‐fold for the stably expressed target. siRNA‐mediated specific gene silencing of p53 expression has been successfully imaged in real time in vivo. This new ribozyme‐based RNA reporter system should open up new avenues for in vivo RNA imaging and direct imaging of siRNA inhibition.
A Type I/Type III Polyketide Synthase Hybrid Biosynthetic Pathway for the Structurally Unique ansa Compound Kendomycin
Authors: Wenzel Silke C. , Bode Helge B. , Kochems Irene , Müller Rolf 
Published: October 2008

AbstractKendomycin is a bioactive polyketide that is produced by various Streptomyces strains. It displays strong antibiotic activities against a wide range of bacteria and exhibits remarkable cytotoxic effects on the growth of several human cancer cell lines. In this study we cloned the corresponding biosynthetic locus from the producer Streptomyces violaceoruber (strain 3844‐33C). Our analysis shows that a mixed type I/type III polyketide synthase pathway is responsible for the formation of the fully carbogenic macrocyclic scaffold of kendomycin, which is unprecedented among all of the ansa compounds that have been isolated so far. Heterologous expression of a gene set in Streptomyces coelicolor shows that 3,5‐dihydroxybenzoic acid is an intermediate in the starter unit biosynthesis that is initiated by the type III polyketide synthase. The identification of the kendomycin biosynthetic gene cluster sets the stage to study a novel chain termination mechanism by a type I PKS that leads to carbocycle formation and provides the starting material for the heterologous expression of the entire pathway, and the production of novel derivatives by genetic engineering.
A Novel Ni4 Complex Exhibiting Microsecond Quantum Tunneling of the Magnetization
Authors: Aromí Guillem , Bouwman Elisabeth , Burzurí Enrique , Carbonera Chiara , Krzystek J. , Luis Fernando , Schlegel Christoph , van Slageren Joris , Tanase Stefania , Teat Simon J. 
Published: October 2008

AbstractA highly asymmetric NiII cluster [Ni4(OH)(OMe)3(Hphpz)4(MeOH)3](MeOH) (1) (H2phpz=3‐methyl‐5‐(2‐hydroxyphenyl)pyrazole) has been prepared and its structure determined by means of single‐crystal X‐ray diffraction by using synchrotron radiation. Variable‐temperature bulk‐magnetization measurements show that the complex exhibits intramolecular‐ferromagnetic interactions leading to a spin ground state S=4 with close‐lying excited states. Magnetization and high‐frequency EPR measurements suggest the presence of sizable Ising‐type magnetic anisotropy, with zero‐field splitting parameters D=−0.263 cm−1 and E=0.04 cm−1 for the spin ground state, and an isotropic g value of 2.25. The presence of both axial and transverse anisotropy was confirmed through low‐temperature specific heat determinations down to 300 mK, but no slow relaxation of the magnetization was observed by AC measurements down to 1.8 K. Interestingly, AC susceptibility measurements down to temperatures as low as 23 mK showed no indication of slow relaxation of the magnetization in 1. Thus, despite the presence of an anisotropy barrier (U≈4.21 cm−1 for the purely axial limit), the magnetization relaxation remains extremely fast down to the lowest temperatures. The estimated quantum tunneling rate, Γ>0.667 MHz, makes this complex a prime candidate for observation of coherent tunneling of the magnetization.
Geräte und Anlagen für neue Lacke mit nanoskaligem Zirkondioxid
Authors: Veith M. , Altherr A. , Klook M. 
Published: October 2008

AbstractFür die Herstellung und Verarbeitung nanoskaliger Partikel wie z. B. ZrO2kann nicht immer auf Geräte, Anlagen oder Methoden nach dem Stand der Technik zurückgegriffen werden. Aus diesem Grund müssen für den Syntheseweg, von der Fällung über die Kristallisation bis zum fertigen Produkt, eigens konstruierte Anlagen bzw. speziell umgebaute Maschinen verwendet werden. Der Fokus des Beitrags liegt hierbei auf einem eigens konstruierten kontinuierlichen Autoklaven (Rohrreaktor) und einer speziell umgebauten Kugelmühle.
Herstellung von Nanostrukturen mittels Atomlagenabscheidung
Authors: Langner A. , Knez M. , Gösele U. 
Published: October 2008

AbstractDie kontrollierte Manipulation von Materialien auf einer Größenskala bis in den Nanometerbereich ist heutzutage ein wesentlicher Bestandteil moderner Technologie. Dieser Übersichtsartikel behandelt eine Methode, die zum kontrollierten Dickenwachstum von Elementen und Verbindungen auf zahlreichen Substraten verwendet wird.
Polymere für Funktionale Oberflächen: Nanostrukturen und Selbstorganisation
Authors: Stamm M. 
Published: October 2008

AbstractPolymere bieten eine große Vielfalt an chemischen Grundbausteinen und Architekturen, die die Werkstoffeigenschaften bestimmen. Weitgehend unabhängig von den Materialeigenschaften im Innern lassen sich durch nanoskopisch dünne Filme an der Oberfläche neue Funktionalitäten erzeugen, die die Gebrauchseigenschaften ganz entscheidend beeinflussen können. Hierbei spielt häufig nur eine nanoskopisch dünne Oberflächenschicht eine Rolle, an der die Struktur, Ordnung und Konformation der Polymere interessante Gestaltungsmöglichkeiten bieten. Prominentes Beispiel ist die Ultrahydrophobie in Verbindung mit der Selbstreinigung der Oberfläche, die durch eine Kombination von Struktur und Chemie der Oberfläche mit geeigneten Polymeren synthetisch erzeugt werden kann. Im Folgenden werden einige Beispiele von nanostrukturierten Oberflächen diskutiert, an denen durch zunehmende Organisation der Polymere unterschiedliche Funktionalitäten erzeugt werden können. Der Baukasten der Polymere bietet hier noch ungeahnte Möglichkeiten.
Einfluss der Reinigung und Funktionalisierung von Kohlenstoff‐Nanoröhren auf deren katalytische Eigenschaften in der Direct Methanol Fuel Cell‐Anode
Authors: Drillet J.‐F. , Bueb H. , Dittmeyer R. , Dettlaff‐Weglikowska U. , Roth S. 
Published: October 2008

AbstractKohlenstoff‐VulcanXC72 gilt derzeit als Standard‐Katalysatorträger in der Niedertemperatur‐Brennstoffzelle. Aufgrund seiner relativ niedrigen spezifischen Oberfläche sowie seiner Korrosionsanfälligkeit ist man zurzeit auf der Suche nach Ersatzmaterialien. In diesem Beitrag wird über den Einsatz von Kohlenstoff‐Nanoröhren als PtRu‐Katalysatorträger in der DMFC‐Anode berichtet. Nach chemischer Vorbehandlung der Kohlenstoff‐Nanoröhren in Luft bei 300 °C bzw. in konzentrierter Salpetersäure wurde eine Zellleistung von 152 bzw. 157 mW cm–2 bei einer anodischen und kathodischen Pt‐Beladung von 1 mg cm–2 ermittelt. Dies entspricht einer um ca. 10 % höheren Leistung im Vergleich zu einer Membran‐Elektroden‐Einheit (MEE) mit einer PtRu‐Vulcan‐Anode.
Nanotechnologie – Zwerge erobern den Alltag
Authors: Krug Harald F. 
Published: October 2008

AbstractDie verschiedenen Bereiche der Nanotechnologie bringen neue Entwicklungen sowie neue Materialien in neuen Anwendungen mit sich und damit werden auch Mensch und Umwelt mit diesen neuen Materialien in Kontakt kommen. Wann immer die Nutzung von Chemikalien oder Nanomaterialien mit einer möglicherweise erhöhten Exposition von Mensch und Umwelt einhergeht, müssen wir aufmerksam sein und auch die Möglichkeit prüfen, ob dieser Kontakt eventuell negative Folgen haben kann. Sowohl die Gesundheit des Menschen aber auch die Erhaltung der Ökosysteme sollten dabei höchste Priorität besitzen. Daher wird seit einiger Zeit auch intensiv auf dem Gebiet der Nanotoxikologie geforscht, um die Nutzung der Nanomaterialien sicher und nachhaltig zu gestalten. Der Bericht soll einen Überblick nicht nur über die nationalen, sondern auch über die europaweiten Aktivitäten geben, die zur Nachhaltigkeit der Nanotechnologien beitragen sollen.
Polymere Nanofasern durch Elektrospinnen – Materialien für neue Anwendungen
Authors: Agarwal S. , Greiner A. , Wendorff J. H. 
Published: October 2008

AbstractVliese aus Nanofasern, die in vielfältiger Art und Weise aus verschiedensten Polymeren durch Elektrospinnen hierzu verarbeitet werden, lassen sich ebenfalls durch Elektrospinnen herstellen. Unterschiedliche Additive wie z. B. Katalysatoren, Farbstoffe, Nanopartikel, Medikamente, Viren, Bakterien etc. steigern die Funktionalität elektrogesponnener Nanofasern deutlich. Mit geeigneten Elektrospinn‐Anlagen können Nanofaservliese für verschiedene technische Anwendungen wie z. B. im Bereich der Filtration bzw. der Schutztextilien hergestellt werden. Dabei lassen sich Ergebnisse aus der Grundlagenforschung in entsprechende technische Produkte übertragen.
Polymere Nanokomposite mit anorganischen Funktionsfüllstoffen
Authors: Wagenknecht U. , Kretzschmar B. , Pötschke P. , Costa F. R. , Pegel S. , Stöckelhuber K. W. , Heinrich G. 
Published: October 2008

AbstractPolymer/Partikel‐Nanokomposite sind eine Stoffklasse, die seit ca. 15 Jahren intensives Interesse in Forschung und Industrie gefunden hat. Neben erfolgreichen Anwendungen sind auch eine Reihe der ursprünglichen Erwartungen nicht erfüllt oder erfordern noch erheblichen Entwicklungsaufwand. Beispielgebend werden für drei der wichtigsten Füllstoffgruppen –Schichtsilicate, Kohlenstoff‐Nanoröhren und Layered Double Hydroxides – die Füllstoffe selbst, die Herstellung und die Eigenschaften der Nanokomposite sowie deren Anwendungspotenzial dargestellt.
Pleomorphic adenoma with predominant plasmocytoid myoepithelial cells: A diagnostic pitfall in aspiration cytology. Case report and review of the literature
Authors: Pusztaszeri Marc , Braunschweig Richard , Mihaescu Anca 
Published: October 2008

AbstractFine‐needle aspiration (FNA) biopsy of the salivary gland is a sensitive and specific diagnostic tool. However, diagnostic problems are sometimes encountered in interpreting some cases, not only in differentiating benign from malignant cases but also in the specific classification of these neoplasms. We report a case of a pleomorphic adenoma with predominant plasmocytoid myoepithelial cells arising in minor salivary glands from the hard palate in a 78‐year‐old patient, which was falsely diagnosed as a carcinoma on liquid‐based cytology (ThinPrep (TP)). The differential diagnosis of salivary gland tumors with predominant myoepithelial cells on FNA biopsy is discussed. Diagn. Cytopathol. 2009. © 2008 Wiley‐Liss, Inc.