bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Blasticidin S Biosynthesis Gene Cluster from Streptomyces griseochromogenes: Sequence Analysis, Organization, and Initial Characterization
Authors: Cone Martha C. , Yin Xihou , Grochowski Laura L. , Parker Morgan R. , Zabriskie T. Mark 
Published: September 2003

AbstractBlasticidin S is a potent antifungal and cytotoxic peptidyl nucleoside antibiotic from Streptomyces griseochromogenes. The mixed biosynthesis of the compound is evident from the three distinct structural components: a cytosine base, an amino deoxyglucuronic acid, and N‐methyl β‐arginine. The blasticidin S biosynthesis gene cluster was cloned from S. griseochromogenes and the pathway heterologously expressed in S. lividans from a cosmid harboring a 36.7‐kb fragment of S. griseochromogenes DNA. The complete DNA sequence of this insert has now been determined and evidence suggests a contiguous 20‐kb section defines the blasticidin S biosynthesis cluster. The predicted functions of several open reading frames are consistent with the expected biochemistry and include an arginine 2,3‐aminomutase, a cytosylglucuronic acid synthase, and a guanidino N‐methyltransferase. Insight into other steps in the assembly of blasticidin S was evident from sequence homology with proteins of known function and heterologous expression of fragments of the cluster. Additionally, the gene that directs the production of free cytosine, blsM, was subcloned and expressed in Escherichia coli. Characterization of BlsM revealed that cytidine monophosphate serves as the precursor to cytosine.
Fluorescent Cellular Sensors of Steroid Receptor Ligands
Authors: Muddana Smita S. , Peterson Blake R. 
Published: September 2003

AbstractSteroid hormone receptors comprise a major class of therapeutic drug targets that control gene expression by binding steroid hormone ligands. These small molecule–protein interactions are typically characterized in living cells by quantification of ligand‐mediated reporter gene expression. As an alternative, non‐transcriptional approach, we constructed fluorescent cellular sensors by expressing yellow fluorescent protein (YFP) fused to the ligand binding domains (LBDs) of estrogen receptor‐alpha (ERα), estrogen receptor‐beta (ERβ), androgen receptor (AR), and the glucocorticoid receptor (GR). These proteins were tethered through a short two amino acid linker and expressed in S. cerevisiae yeast. Recombinant yeast treated with cognate steroid receptor ligands exhibited dose‐dependent fluorescence enhancements that were correlated with known relative receptor binding affinity values. These effects generally paralleled ligand‐mediated receptor dimerization quantified with analogous yeast two‐hybrid transcriptional assays, suggesting that the majority of the observed fluorescence enhancements were conferred by conformational changes coupled with receptor dimerization, such as ligand‐mediated stabilization of protein folding. Remarkably, certain interactions such as the binding of cortisol, progesterone, and dexamethasone to the GR were undetectable with yeast two‐hybrid assays. However, these interactions were detected with the fluorescent cellular sensors, indicating the sensitivity of this system to subtle ligand‐induced conformational effects. These sensors provide a novel, non‐transcriptional, and high‐throughput method to identify and analyze ligands of nuclear hormone receptors.
Synthetic DNA Aptamers to Detect Protein Molecular Variants in a High‐Throughput Fluorescence Quenching Assay
Authors: Fang Xiaohong , Sen Arup , Vicens Marie , Tan Weihong 
Published: September 2003

AbstractReal‐time protein detection in homogeneous solutions is necessary in many biotechnology and biomedical studies. The recent development of molecular aptamers, combined with fluorescence techniques, may provide an easy and efficient approach to protein elucidation. This report describes the development of a fluorescence‐based assay with synthetic DNA aptamers that can detect and distinguish molecular variants of proteins in biological samples in a high‐throughput process. We used an aptamer with high affinity for the B chain of platelet‐derived growth factor (PDGF), labeled it with a fluorophore and a quencher at the two termini, and measured fluorescence quenching by PDGF. The specific quenching can be used to detect PDGF at picomolar concentrations even in the presence of serum and other cell‐derived proteins in cell culture media. This is the first successful application of a synthetic aptamer for the detection of tumor‐related proteins directly from the tumor cells. We also show that three highly related molecular variants of PDGF (AA, AB, and BB dimers) can be distinguished from one another in this single‐step assay, which can be readily adapted to a microtiter plate assay for high‐throughput analysis. The use of fluorescence quenching as a measure of binding between the DNA probe and the target protein eliminates potential false signals that may arise in traditional fluorescence enhancement assays as a result of degradation of the DNA aptamer by contaminating nucleases in biological specimens. This assay is applicable to proteins that are not naturally DNA binding. The excellent specificity, ultrahigh sensitivity, and simplicity of this one‐step assay addresses a growing need for high‐throughput methods that detect changes in the expression of gene products and their variants in cell cultures and biological specimens.
Optimization of Triple‐Helix‐Directed DNA Cleavage by Benzoquinoquinoxaline–Ethylenediaminetetraacetic Acid Conjugates
Authors: Zain Rula , Polverari David , Nguyen Chi‐Hung , Blouquit Yves , Bisagni Emile , Garestier Thérèse , Grierson David S. , Sun Jian‐Sheng 
Published: September 2003

AbstractThe formation of triple‐helical structures of DNA is based on sequence‐specific recognition of oligopyrimidine⋅oligopurine stretches of double‐helical DNA. Triple‐helical structures can be stabilized by DNA‐binding ligands. Benzoquinoquinoxaline (BQQ) derivatives are among the most potent intercalating‐type agents known to stabilize DNA triple‐helical structures. We previously reported the conversion of BQQ into a triplex‐directed DNA cleaving agent, namely BQQ–ethylenediaminetetraacetic acid (EDTA), by coupling of 6‐(3‐aminopropylamino)BQQ to a suitable ethylenediaminetetraacetic acid derivative, and we demonstrated the ability of this conjugate to cause double‐stranded cleavage of DNA at the triplex site. However, this prototype derivative BQQ–EDTA conjugate showed lower affinity towards triplex DNA than BQQ itself. In the light of this observation, and guided by molecular modeling studies, we synthesized a second generation of BQQ–EDTA conjugates based on 6‐[bis(2‐aminoethyl)amino]‐ and 6‐(3,3′‐diamino‐N‐methyldipropylamino)–BQQ derivatives. We confirmed by DNA melting experiments that the new conjugates displayed an increased specific affinity towards triple helices when compared to the previously synthesized BQQ–EDTA. In addition, the efficiency of these new agents in triplex‐specific binding and cleavage was demonstrated by triplex‐directed double‐stranded cleavage of plasmid DNA.
The Structural Plasticity of the C Terminus of p21Cip1 is a Determinant for Target Protein Recognition
Authors: Esteve Vicent , Canela Núria , Rodriguez‐Vilarrupla Aina , Aligué Rosa , Agell Neus , Mingarro Ismael , Bachs Oriol , Pérez‐Payá Enrique 
Published: September 2003

AbstractThe cyclin‐dependent kinase inhibitory protein p21Cip1 might play multiple roles in cell‐cycle regulation through interaction of its C‐terminal domain with a defined set of cellular proteins such as proliferating cell nuclear antigen (PCNA), calmodulin (CaM), and the oncoprotein SET. p21Cip1 could be described as an intrinsically unstructured protein in solution although the C‐terminal domain adopts a well‐defined extended conformation when bound to PCNA. However, the molecular mechanism of the interaction with CaM and the oncoprotein SET is not well understood, partly because of the lack of structural information. In this work, a peptide derived from the C‐terminal domain of p21Cip1 that covers the binding domain of the three above‐mentioned proteins was used to demonstrate that the C‐terminal domain of p21 recognizes multiple ligands through its ability to adopt multiple conformations. The conformation is dictated by tertiary contacts rather than by the primary sequence of the protein. Our results suggest that the C‐terminal domain of p21Cip1 adopts an extended structure when bound to PCNA and probably when bound to the oncoprotein SET, but an α helix when bound to CaM.
Synthesis of N‐Acetyllactosamine Derivatives with Variation in the Aglycon Moiety for the Study of Inhibition of Sialyl Lewis x Expression
Authors: Mong Tony K.‐K. , Lee Lac V. , Brown Jillian R. , Esko Jeffrey D. , Wong Chi‐Huey 
Published: September 2003

AbstractHerein we describe an inhibition study of the sialyl Lewis x (sLex) expression on a human monocytic cell line (U937), using a series of peracetylated N‐Acetyllactosamine (LacNAc) analogues with variation at the aglycon moiety. It was found that the extent of inhibition was related to the hydrophobicity and structure of the aglycon. In general, peracetylated LacNAc analogues with a naphthyl or biphenyl aglycon (3, 4, 6, and 7) were better in suppression of sLex expression than a benzyl derivative (2). Steady‐state kinetic experiments with human α‐1,3‐fucosyltransferases IV and VI (FucT IV and VI, EC 2.4.1.65) revealed that the deacetylated LacNAc‐aglycons with naphthyl (18, 19, and 20) or biphenyl (17) moieties exhibited higher affinity to the fucosyltransferases than aglycon moieties with smaller hydrophobic groups (14, 15, and 16). These results are in agreement with the findings of the U937 cell‐based experiments, and suggest that the higher enzyme affinity LacNAc‐aglycons make better acceptor decoys and, hence, the observed differences in LacNAc‐aglycon inhihitory effects on sLex expression.
NMR Chemical Shift Perturbation Study of the N‐Terminal Domain of Hsp90 upon Binding of ADP, AMP‐PNP, Geldanamycin, and Radicicol
Authors: Dehner Alexander , Furrer Julien , Richter Klaus , Schuster Ioana , Buchner Johannes , Kessler Horst 
Published: September 2003

AbstractHsp90 is one of the most abundant chaperone proteins in the cytosol. In an ATP‐dependent manner it plays an essential role in the folding and activation of a range of client proteins involved in signal transduction and cell cycle regulation. We used NMR shift perturbation experiments to obtain information on the structural implications of the binding of AMP‐PNP (adenylyl‐imidodiphosphate—a non‐hydrolysable ATP analogue), ADP and the inhibitors radicicol and geldanamycin. Analysis of 1H,15N correlation spectra showed a specific pattern of chemical shift perturbations at N210 (ATP binding domain of Hsp90, residues 1–210) upon ligand binding. This can be interpreted qualitatively either as a consequence of direct ligand interactions or of ligand‐induced conformational changes within the protein. All ligands show specific interactions in the binding site, which is known from the crystal structure of the N‐terminal domain of Hsp90. For AMP‐PNP and ADP, additional shift perturbations of residues outside the binding pocket were observed and can be regarded as a result of conformational rearrangement upon binding. According to the crystal structures, these regions are the first α‐helix and the “ATP‐lid” ranging from amino acids 85 to 110. The N‐terminal domain is therefore not a passive nucleotide‐binding site, as suggested by X‐ray crystallography, but responds to the binding of ATP in a dynamic way with specific structural changes required for the progression of the ATPase cycle.
Pyrenemethyl ara‐Uridine‐2′‐carbamate: A Strong Interstrand Excimer in the Major Groove of a DNA Duplex
Authors: Dioubankova Natalia N. , Malakhov Andrei D. , Stetsenko Dmitry A. , Gait Michael J. , Volynsky Pavel E. , Efremov Roman G. , Korshun Vladimir A. 
Published: September 2003

AbstractThe synthesis of new nucleoside derivatives, ara‐uridine‐2′‐carbamates, and their incorporation into synthetic DNA oligomers is described. The modification directs ligands into the major groove of duplex DNA and somewhat destabilizes the duplexes of modified oligonucleotides with complementary DNA or RNA. In the case of pyrenemethyl carbamate modification in DNA–DNA duplexes, the destabilization is considerably reduced. The pyrenemethyl derivative also shows remarkable spectral properties: a 'reversed' absorbance change for pyrene at 350 nm in the course of denaturation of the DNA duplex, as compared to the change seen in the nucleotide absorbance at 260 nm. This derivatization also causes pronounced sequence‐dependent excimer formation in the major groove.
Cover Picture: A Fusion of Disciplines: Chemical Approaches to Exploit Fusion Proteins for Functional Genomics (ChemBioChem 9/2003)
Authors: Johnsson Nils , Johnsson Kai 
Published: September 2003

AbstractThe cover picture shows a living cell inside which a protein is labeled with fluorescein. The labeling is based on the unusual mechanism of the DNA repair protein O6‐alkylguanine‐DNA alkyltransferase (AGT, structure on the right), which irreversibly transfers the alkyl group from O6‐alkylguanine to its reactive cysteine residue. By using O6‐benzylguanine derivatives such as the fluorescein derivative shown, AGT fusion proteins can be covalently labeled in vivo. The method is one example of a growing number of approaches that aim at equipping proteins with functionalities that can not be genetically encoded, which opens up new ways to study proteins in vivo. Further information can be found in the article by N. Johnsson and K. Johnsson on p. 803 ff.
Reversible and Efficient Materials‐based Actuation by Electrolytic Phase Transformation
Authors: Cameron C.G. , Freund M.S. 
Published: September 2003

AbstractElectrolytic phase transformation is presented as a means of inducing reversible actuation in devices operating in a wide range of applications and scales. The device exploits the enormous pressure and volume changes that accompany the electrochemical interconversion between liquid and gas phases. With this method, strains beyond 136,000 % and stresses surpassing 200 MPa can be achieved, offering a level of performance many orders of magnitude beyond that of other materials‐based strategies.
Modeling of Nitrogen and Carbon Dioxide Solubility in Alternative Fuels at High Pressures Using the Soave‐Redlich‐Kwong Equation of State
Authors: Teodorescu M. , Wichterle I. 
Published: September 2003

AbstractIn this paper, the Soave‐Redlich‐Kwong equation of state with quadratic mixing rule has been tested for correlation of vapor‐liquid equilibria (VLE) at high pressures in the binary nitrogen + dimethyl ether, dimethyl ether + methanol, nitrogen + methanol, carbon dioxide + dimethyl ether and carbon dioxide + methanol systems. The interaction parameters kij were evaluated for each binary pair and used for prediction of VLE in the ternary nitrogen + dimethyl ether + methanol and carbon dioxide + dimethyl ether + methanol systems at high pressures. The results of correlation and prediction are discussed.
Operating Characteristics and Performance of a Monolithic Downflow Bubble Column Reactor in Selective Hydrogenation of Butyne‐1,4‐diol
Authors: Marvan H. , Winterbottom J.M. 
Published: September 2003

AbstractThe effects of flow condition, bubble dispersion level, and liquid flow rate on the behavior of a novel monolithic downflow bubble column (M‐DBC) were investigated using a reaction model, the palladium‐catalyzed hydrogenation of butyne‐1,4‐diol. The stable and closely packed homogeneous bubble dispersion present in the bulk region of the M‐DBC allowed effective introduction of the gas‐liquid phase for formation of Taylor flow inside the monolith channels. The condition defined as the minimum level dispersion was required in order to obtain high selectivity towards the intermediate product, cis‐2‐butene‐1,4‐diol. Enhanced reaction rates were obtained at increasing the dispersion level and lowering the liquid flow rate. Comparison with the DBC employing 5 % Pd/C powder catalyst and 1 % Pd‐on‐Raschig‐ring revealed a better performance of the M‐DBC (1 % Pd loading) with the advantage of smaller reaction volume and intensified reaction rate. As an alternative to conventional three‐phase reactors, the M‐DBC was so simple due to its inherent characteristic operation and no specially designed device is required.
Simultaneous Catalytic Removal of Nitrogen Oxides and Soot from Diesel Exhaust Gas over Potassium Modified Iron Oxide
Authors: Kureti S. , Hizbullah K. , Weisweiler W. 
Published: September 2003

AbstractIron oxide modified by potassium, i.e. Fe1.9K0.1O3, exhibits high catalytic performance for the simultaneous conversion of soot and NOx into CO2 and N2. The present study shows that long‐time treatment of the catalyst leads to a drastic decrease in the activity, whereas even the aged catalyst maintains considerable activity. On the other hand, long‐time treatment causes selective N2 formation, i.e. no more formation of the byproduct N2O. This alteration of catalytic performance is likely due to agglomeration of the promoter potassium being present at the surface of catalyst. Detailed experiments were carried out with a more realistic diesel model exhaust gas to confirm that Fe1.9K0.1O3 is a suitable catalyst for the simultaneous removal of soot and NOx between 350 and 480 °C. It was assumed that (CO) intermediates, formed by the catalytic reaction of NOx and oxygen with the soot surface, are the reactive species in NOx‐soot conversion.
Thermal Gasification: A Feasible Solution for Sewage Sludge Valorisation?
Authors: Ferrasse J.‐H. , Seyssiecq I. , Roche N. 
Published: September 2003

AbstractThe proliferation of wastewater treatment plants has become essential to ensure the protection of the natural environment. As a consequence, the production of waste by‐products, namely sewage sludge, has increased together with both the unit efficiency levels and with the number of wastewater treatment plants. Since dumping is no longer allowed in the EU, the processes mainly used to treat sewage sludge are agricultural spreading and incineration. However, due to the constant increase in production, it has became essential to find alternative methods of treatment. Considering the chemical composition of sludge, some new thermal processes of treatment have recently been considered by researchers. Thermal gasification is one method that could be of significant interest. Dried sludge composition is sufficiently close to the that of classical biomass (such as wood, rice, etc.) to make sludge treatment in a gasifier feasible. In this paper we discuss how gasification technologies could be transposed to the treatment and valorisation of sludge. Although this process seems attractive, it will also be demonstarted that much experimentation remains to be conducted on a laboratory and pilot scale.
Gasification – An Opportunity to Design Environmentally Compatible Processes in the Chemical and Pulp & Paper Industry
Authors: Schingnitz M. 
Published: September 2003

AbstractProduction wastes and residues generated in particular in the chemical and pulp & paper industries are currently incinerated or recycled. A stricter environmental legislation and the general prohibition imposed on waste incineration in some countries suggest to open new ways of waste disposal and resource recovery. This work describes how residual and waste materials can not only be disposed of but also converted into a raw gas which can be further processed to obtain valuable materials and synthesis gas in strict compliance with environmental standards by using various modifications of an entrained‐flow gasification technology.
Product Design – The Interaction between Chemistry, Technology and Marketing to Meet Customer Needs
Authors: Rähse W. , Hoffmann S. 
Published: September 2003

AbstractDuring the 1990s the job profile of the process engineer in the chemical industry went through some lasting changes. Interdisciplinary project cooperation became established, aiming at competitive and thus rapid innovative leadership. The development of new or improved products must focus on customer needs. Besides production performance the customer mainly needs good handling properties and aesthetics. Product design includes both these considerations. We describe the career of a product, beginning with the initial idea and ending with the product being launched onto the market. A methodology for establishing and evaluating customers needs plays a key role in this process. Process engineering enables the technical realization while considering economic as well as time restrictions. This requires some creativity – and often the development of new technologies. Moreover, the successful completion of a project requires the staff involved to appreciate and accept their colleagues who come from the fields of either chemistry or business management (marketing and market research.)
Axonal sprouting in the optic nerve is not a prerequisite for successful regeneration
Authors: Dunlop Sarah A. 
Published: September 2003

AbstractAxonal sprouting, the production of axons additional to the parent one, occurs during optic nerve regeneration in goldfish and the frog Rana pipiens, with numbers of regenerate axons exceeding normal values four‐ to sixfold (Murray [1982] J. Comp. Neurol. 209:352–362; Stelzner and Strauss [1986] J. Comp. Neurol. 245:83–103). To determine whether axonal sprouting is a prerequisite for regeneration, the frog Litoria moorei was examined, a species that undergoes successful optic nerve regeneration but with a different time course compared with R. pipiens. Sprouting was assessed, as in goldfish and R. pipiens, from electron microscopic counts between the lesion and chiasm. However, disconnected axons that persist after axotomy would have falsely elevated the counts. The suspected overlap of these two axon populations was confirmed by labeling regenerate axons anterogradely with DiI (1,1′‐dioctadecyl‐3,3,3′,3′‐tetramethylindocarbocyanine perchlorate) and disconnected ones retrogradely with DiA (4‐4‐dihexadecylaminostyrl 1‐N methylpyridinium iodide). Numbers of disconnected axons were estimated after preventing regeneration and subtracted from numbers in regenerate nerves. Throughout, the total number of regenerate axons was approximately one third lower than normal (P < 0.05) supporting a previous finding of minimal axonal sprouting in L. moorei (Dunlop et al. [2002] J. Comp. Neurol. 446:276–287). The validity of the subtractive electron microscopic method was confirmed by retrograde labeling to estimate numbers of retinal ganglion cells whose axons had crossed the lesion; values were approximately one third lower than normal. The data suggest that sprouting is not essential for either axon outgrowth or topographic map refinement. J. Comp. Neurol. 465:319–334, 2003. © 2003 Wiley‐Liss, Inc.