bluuebunny/crossref_metadata_2025 huggingface dataset:
Adsorption of the Bacillus thuringiensis toxin (Cry1Ab) on Na‐montmorillonite and on the clay fractions of different soils
Authors: Pagel‐Wieder Sibylle , Gessler Frank , Niemeyer Jürgen , Schröder Dietmar
Published: March 2004

The adsorption of the toxin from Bacillus thuringiensis (Bt‐toxin), which is synthesized in genetically modified maize, on sterilized Na‐montmorillonite and on H2O2‐treated and untreated clay fractions of three soils from different sites were studied. All adsorption isotherms can be described by a linear isotherm. Although all clay fractions from the different soils show nearly the same mineralogical composition, we found different affinities ranging from k = 47.7 to k = 366.7 of the adsorbates for the Bt‐toxin. The H2O2‐treated clay fractions show no correlation between the adsorption affinity and the amount of soil organic matter. On the other hand, there is a correlation between the content of organic carbon and the adsorption affinity of the untreated clay fractions. This can be explained by the fact that due to the coatings of soil organic matter on aggregates, the Bt‐toxin polymers are not able to adsorb within the clay aggregates.
Composition of the black crusts from the Saint Denis Basilica, France, as revealed by gas chromatography‐mass spectrometry
Authors: Gaviño Maria , Hermosin Bernardo , Vergès‐Belmin Véronique , Nowik Witold , Saiz‐Jimenez Cesareo
Published: March 2004

The organic fraction of black crusts from Saint Denis Basilica, France, is composed of a complex mixture of aliphatic and aromatic compounds. These compounds were studied by two different analytical approaches: tetramethyl ammonium hydroxide (TMAH) thermochemolysis in combination with gas chromatography‐mass spectrometry (GC‐MS), and solvent extraction, fractionation by silica column, and identification of the fraction components by GC‐MS. The first approach, feasible at the micro‐scale level, is able to supply fairly general information on a wide range of compounds. Using the second approach, we were able to separate the complex mixture of compounds into four fractions, enabling a better identification of the extractable compounds. These compounds belong to different classes: aliphatic hydrocarbons (n‐alkanes, n‐alkenes), aliphatic and aromatic carboxylic acids (n‐fatty acids, α,ω‐dicarboxylic acids, and benzenecarboxylic acids), polycyclic aromatic hydrocarbons (PAH), and molecular biomarkers (isoprenoid hydrocarbons, diterpenoids, and triterpenoids). With each approach, similar classes of compounds were identified, although TMAH thermochemolysis failed to identify compounds present at low concentrations in black crusts. The two proposed methodological approaches are complementary, particularly in the study of polar fractions.
Structural elucidation of catechin and epicatechin in sorrel leaf extracts using liquid‐chromatography coupled to diode array‐, fluorescence‐, and mass spectrometric detection
Authors: Stöggl W. M. , Huck C. W. , Bonn Günther K.
Published: March 2004

Flavonoids are natural compounds in medicinal herbs and posses several biological activities important in plant drug design. Especially strong antioxidant effects play an important role against radical oxidative stress causing pathological processes, such as arteriosclerosis or cancer. The aim of this work was to investigate unknown analytes found in sorrel leaf (Rumex acetosa) extracts in order to discover new leading compounds to enable quality control in phytopharmaceuticals made thereof. Therefore compounds of interest were separated after methanolic extraction by reversed‐phase liquid chromatography (RP‐LC) employing silica‐C18 as stationary phase using gradient elution with water (10 mM H3PO4) and acetonitrile as mobile phase. Structural elucidation was carried out by diode array, fluorescence, and mass spectroscopic detection. Photodiode‐array detection allowed the extraction of UV‐absorbance spectra from the peaks of interest. Absorbance maxima were found at 203 and 279 nm with a shoulder at 230 nm. Additionally fluorescence emission and excitation spectra were recorded from the analytes using a fluorescence detector (FLD) after stop flow (λex = 279 nm, λem = 307 nm). The chromatographic reversed‐phase system was coupled to an ion‐trap mass spectrometer (LC‐MS) by using an electrospray ionization interface (ESI). After optimization processes the separation was carried out using an ammonium acetate buffer at pH 5.5. Mass spectrometric detection turned out to be more sensitive in negative mode. Collisionally induced dissociation (CID) was used to obtain fragment ions of structural relevance (LC‐MS/MS). Finally, compounds of interest coming from sorrel leaf (Rumex acetosa) eluting at low acetonitrile concentrations were confirmed to be catechin and epicatechin.
Studying the interactome with the yeast two‐hybrid system and mass spectrometry
Authors: Causier Barry
Published: March 2004

I.
Introduction
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 II.
The Yeast Two‐Hybrid System
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A.  A Brief History
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    1.  Basis of Yeast Two‐Hybrid System
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    2.  Development of the System
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B.  Current Systems
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    1.  The GAL4 and LexA Systems
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    2.  The Sos Recruitment System
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    3.  The Split‐Ubiquitin System
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    4.  The Dual‐Bait System
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    5.  Other Two‐Hybrid Systems
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    6.  Variations on a Theme
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C.  Applications of Yeast Two‐Hybrid
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  III.
Studying Protein Interactions by MS
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 IV.
Genome‐Wide Analysis of Protein–Protein Interactions
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A.  Yeast Two‐Hybrid
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B.  Mass Spectrometry
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C.  Comparison of the Two Approaches
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D.  Placing Interactions in Context
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  V.
Emerging Technologies
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 VI.
Conclusions
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Acknowledgments
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Abbreviations
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References
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Protein interactions are crucial to the life of a cell. The analysis of such interactions is allowing biologists to determine the function of uncharacterized proteins and the genes that encode them. The yeast two‐hybrid system has become one of the most popular and powerful tools to study protein–protein interactions. With the advent of proteomics, the two‐hybrid system has found a niche in interactome mapping. However, it is clear that only by combining two‐hybrid data with that from complementary approaches such as mass spectrometry (MS) can the interactome be analyzed in full. This review introduces the yeast two‐hybrid system to those unfamiliar with the technique, and discusses how it can be used in combination with MS to unravel the network of protein interactions that occur in a cell. © 2004 Wiley Periodicals, Inc., Mass Spec Rev
Biaxial deformation of polyamide‐6: Assessment of orientation by means of infrared trichroism
Authors: Cole K. C. , Depecker C. , Jutigny M. , Lefebvre J.‐M. , Krawczak P.
Published: March 2004

Infrared spectroscopy was used to study the evolution of structure in films of polyamide‐6 drawn on a Cellier tenter frame laboratory tester under conditions of simultaneous equibiaxial stretching and planar uniaxial stretching. The “tilted film” method was used to obtain trichroic spectra corresponding to the machine, transverse, and normal directions, as well the “structural factor” spectrum. From these it was possible to obtain information on the molecular orientation and the evolution of the crystalline structure. The starting films, prepared by melt casting from an extruder on a chilled roll, contained predominantly the mesomorphic β form. The structural factor spectra confirmed that strain‐induced transformation into the α form occurred upon drawing, and that the amount of α form increased with the extent of drawing. The trichroic spectra showed that the molecular orientation was localized mainly, but not exclusively, in the α form. Orientation functions could be determined for both the molecular chain axis and the normal to the hydrogen‐bonded sheets. For both the equibiaxial and planar uniaxial films, these sheets were found to be strongly oriented parallel to the plane of the film, with the degree of orientation increasing with overall draw ratio. For the biaxial samples, the molecular chain orientation was found to be equibiaxial, as expected. Mechanical test results indicated that the chains are evenly distributed in the film plane rather than showing a preference for the two orthogonal draw directions. For the planar uniaxial samples, the chain orientation was predominantly in the draw direction, but some degree of orientation in the transverse direction was also observed. The variation of orientation functions with draw ratio suggested that the α structure evolves in two stages, the first involving chain orientation in the draw direction and the second involving rotation of the sheets into the plane of the film.
Synthesis of unsaturated polyester‐clay nanocomposites using reactive organoclays
Authors: Fu Xiao‐An , Qutubuddin Syed
Published: March 2004

Two polymerizable cationic surfactants, vinylbenzyl n‐alkyldimethyl (n = 12 or 18) ammonium chlorides, were used for functionalization of montmorillonite (MMT) and preparation of unsaturated polyester (UP)‐clay nanocomposites. Polymerizable organophilic clays were prepared by exchanging the sodium ions of MMT with vinylbenzyldodecyldimethyl ammonium chloride (VDAC) or vinylbenzyloctadecyldimethyl ammonium chloride (VOAC) in an aqueous medium. The dispersion of organoclays in UP led to gel formation. UP/VDAC‐MMT resulted in intercalated nanocomposites while UP/VOAC‐MMT formed partially exfoliated nanocomposites. The nanocomposites exhibited higher dynamic modulus than pristine UP.
Curing and pyrolysis of cresol novolac epoxy resins containing [2‐(6‐oxido‐6H‐dibenz(c,e)(1,2)oxaphosphorin‐6‐yl)‐1,4‐naphthalenediol]
Authors: Rwei S.‐P. , Liu A.‐Y. , Liou G.‐S. , Cheng K.‐C. , Guo W.
Published: March 2004

This study investigates the curing kinetics, thermal properties and decomposition kinetics of cresol novolac epoxy (CNE) with two curing agents, 2‐(6‐oxido‐6H dibenz(c,e)(1,2) oxaphosphorin‐6‐yl)‐1,4‐benzenediol (ODOPN), and phenol novolac (PN). In comparison with the conventional PN system, introducing ODOPN, a phosphorus‐containing bulky pendant group, into CNE increases Tg by 33°C, char yield from 30% to 38%, and LOI from 22 to 31. The DSC curing study reveals that the Ea of the CNE/ODOPN epoxy can be obtained by Kissinger's method. The resulting Ea values indicate that the catalytic effect of EMI is insignificant on CNE/ODOPN but is marked on CNE/PN, whose Ea was reduced from 131.5 to 75.6 KJ/mole. This result may be caused by the fact that the symmetric diol attached to the 1 and 4 positions of the naphthalene ring in ODOPN sets up a steadily resonating structure and inhibits the catalytic action. Further investigating the conversion ratio with curing temperature yielded experimental data that agreed closely with Kaiser's model. The orders of the autocatalyzed reaction, m, and the crosslinking reaction, n, are close to 0.5 and 1.0, respectively, independently of the scan rate. Finally, the TGA decomposition study by Ozawa's method demonstrates that the mean Ea declines with the phosphorus content, because the easy decomposition of the phosphorus compound in the initiation stage facilitates the formation of an insulating layer. However, results in this study further reveal an increasing tendency for Ea with decomposition conversion for an ODOPN/PN mixture with the ODOPN content of over 50%, probably because of the retardation of gas diffusion by the insulating layer of phosphorus compound.
Intregrated analysis of the human cardiac transcriptome, proteome and phosphoproteome
Authors: Ruse Cristian I. , Tan Fen‐Lai , Kinter Michael , Bond Meredith
Published: March 2004

Altered expression of different classes of genes has been shown to differentiate between failing and nonfailing human hearts. However, characterization of proteins and the post‐translational modifications that regulate their functions is required for understanding both the physiology of cardiac muscle and the mechanisms leading to pathological states associated with cardiac diseases. We present in this paper, an analysis of the human cardiac transcriptome, proteome and phosphoproteome. Data from two sources (i) experiments performed in our laboratory and (ii) bioinformatics searches of public databases (SWISS‐PROT, NCBI, Cardiac Gene Expression Knowledge Base, Gene Ontology Consortium and Affymetrix) are reported in a relational database that allows user‐designed specific queries. Microarray experiments were performed with Affymetrix Hu95Av2. Cardiac proteins were digested with trypsin. An 11 step cation exchange procedure produced fractions for analysis in separate reversed phase high‐performance liquid chromatography‐tandem mass spectrometry (MS/MS) experiments. Immobilized metal affinity chromatography was used to select the phosphopeptides from the same tryptic peptide mixture. They were then further investigated by MS/MS. Gel‐free approaches were used to detect 267 proteins and 47 phosphopeptides. Our human cardiac database contains 447 entries. We propose the use of this platform, built with data derived from nonfailing hearts, as a template for initiating the effort to characterize the human cardiac proteome and its associated post‐translational modifications.
A proteome reference map for Vibrio cholerae El Tor
Authors: Coelho Ana , de Oliveira Santos Eidy , da Hora Faria Mauro Luiz , de Carvalho Daniela Palermo , Soares Marcia Regina , von Kruger Wanda Maria Almeida , Bisch Paulo Mascarello
Published: March 2004

A proteome reference map has been constructed for Vibrio cholerae El Tor, in the pI range of 4.0 to 7.0. The map is based on two‐dimensional gels (2‐D) and the identification, by peptide mass fingerprint, of proteins in 94 spots, corresponding to 80 abundant proteins. Two strains are compared, strain N16961 and a Latin American El Tor strain C3294. The consensus map contains 340 spots consistently seen with both strains grown in Luria‐Bertani broth (LB) or minimal M9 medium. The results were obtained from nine gels run with 18 cm immobilized pH gradient strips and precast gels. The 2‐D gels were anchored to real N16961 proteins identified by mass spectrometry. Various energy metabolism components and periplasmic ATP‐binding cassette (ABC) transporter proteins were identified among the abundant proteins. Two isoforms of OmpU were found. Five operons are proposed and seven hypothetical proteins were experimentally confirmed. Comparisons are made with protein 2‐D gels for a classical strain and to microarray analysis available for the N16961 El Tor strain. New results were obtained from the proteome analysis, indicating an abundance of periplasmic ABC transporter proteins not found in microarray studies.
A comprehensive approach for establishment of the platform to analyze functions of KIAA proteins: Generation and evaluation of anti‐mKIAA antibodies
Authors: Koga Hisashi , Shimada Kiyo , Hara Yasuhiro , Nagano Mihoko , Kohga Hiroshi , Yokoyama Ryo , Kimura Yayoi , Yuasa Sigeaki , Magae Junji , Inamoto Susumu , Okazaki Noriko , Ohara Osamu
Published: March 2004

Since December 2001 we have been conducting a project to isolate and determine entire sequences of mouse KIAA cDNA clones which encode polypeptides corresponding to human KIAA proteins. The ultimate goal of this project is the elucidation of the functions of KIAA proteins. A critical step in this project is the generation of antibodies based on the cDNA sequence information. Although antibodies are the most optimal tools for biological analysis, the production and isolation of multiple recombinant proteins for an antigen is a rate‐limiting step in antibody production. To address this problem, we established a system utilizing the in vitro recombination‐assisted method and shotgun clones that were generated during the sequencing of mouse KIAA cDNAs (DNA Res. 2003, 10, 129–136). The authenticity of the expressed proteins was confirmed by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry. Another critical step for antibody production is the evaluation of the antibodies. Thus, we also made efforts to develop a systematic approach for evaluation of the titer and the specificity of the antibodies. Using these systems, we have produced and evaluated more than 500 antibodies raised against mouse KIAA proteins to date. We are currently generating antibody arrays for analysis of protein expression profiles. We will verify protein‐protein interactions using immunoprecipitation and tandem mass spectrometry analysis.
Setting up standards and a reference map for the alkaline proteome of the Gram‐positive bacterium Lactococcus lactis
Authors: Drews Oliver , Reil Gerold , Parlar Harun , Görg Angelika
Published: March 2004

Despite the fact that almost 39% of the theoretical expressed proteins of Lactococcus lactis have a predicted isoelectric point above 7, these proteins have not been studied in previous proteome analyses. In the present study, we set up a reference map of alkaline lactococcal proteins by using immobilized pH gradients (IPG) spanning pH 6 to 12 and 9 to 12, and protein identification by matrix‐assisted laser desorption/ionization‐time of flight mass spectrometry (MALDI‐TOF MS). Different electrophoresis systems for isoelectric focusing were evaluated to optimize the first dimension. Best results were obtained by sample application using cup‐loading at the anodic side and increasing the final voltage up to 8000 V for IPGs, using N,N‐dimethylacrylamide as monomer. After two‐dimensional gel electrophoresis of extracts obtained from exponentially growing cells, about 200 protein spots were selected for identification by peptide mass fingerprinting. With MALDI‐TOF MS, 153 proteins were identified that were the products of 85 different genes. Their predicted isoelectric points range from as high as 11.31 to as low as 6.34. Ribosomal proteins, hypothetical proteins and proteins with unknown function represent the largest groups of identified proteins. For further classification, the codon adaptation index (CAI) and grand average of hydropathicity (GRAVY) for each lactococcal protein were calculated. The protein with the lowest CAI identified in this study is the manganese ABC transporter ATP‐binding protein. Less than 10% of the alkaline lactococcal proteins have a smaller CAI. The highest GRAVY for an identified protein is 0.26. The complete in silico data of Lactococcus lactis as well as clickable reference maps are available at www.wzw.tum.de/proteomik/lactis.
Web‐accessible proteome databases for microbial research
Authors: Pleißner Klaus‐Peter , Eifert Till , Buettner Sven , Schmidt Frank , Boehme Martina , Meyer Thomas F. , Kaufmann Stefan H. E. , Jungblut Peter R.
Published: March 2004

The analysis of proteomes of biological organisms represents a major challenge of the post‐genome era. Classical proteomics combines two‐dimensional electrophoresis (2‐DE) and mass spectrometry (MS) for the identification of proteins. Novel technologies such as isotope coded affinity tag (ICAT)‐liquid chromatography/mass spectrometry (LC/MS) open new insights into protein alterations. The vast amount and diverse types of proteomic data require adequate web‐accessible computational and database technologies for storage, integration, dissemination, analysis and visualization. A proteome database system (http://www.mpiib‐berlin.mpg.de/2D‐PAGE) for microbial research has been constructed which integrates 2‐DE/MS, ICAT‐LC/MS and functional classification data of proteins with genomic, metabolic and other biological knowledge sources. The two‐dimensional polyacrylamide gel electrophoresis database delivers experimental data on microbial proteins including mass spectra for the validation of protein identification. The ICAT‐LC/MS database comprises experimental data for protein alterations of mycobacterial strains BCG vs. H37Rv. By formulating complex queries within a functional protein classification database “FUNC_CLASS” for Mycobacterium tuberculosis and Helicobacter pylori the researcher can gather precise information on genes, proteins, protein classes and metabolic pathways. The use of the R language in the database architecture allows high‐level data analysis and visualization to be performed “on‐the‐fly”. The database system is centrally administrated, and investigators without specific bioinformatic competence in database construction can submit their data. The database system also serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. Currently, the database system includes proteome information for six strains of microorganisms.
Proteomic investigation of natural variation between Arabidopsis ecotypes
Authors: Chevalier François , Martin Olivier , Rofidal Valérie , Devauchelle Anne‐Dominique , Barteau Samuel , Sommerer Nicolas , Rossignol Michel
Published: March 2004

Two‐dimensional (2‐D) gel electrophoresis and peptide mass fingerprinting were used to investigate the natural variation in the proteome among 8 Arabidopsis thaliana ecotypes, of which 3 were previously shown to display atypical responses to environmental stress. Comparison of 2‐D maps demonstrated that only one‐quarter of spots was shared by all accessions. On the other hand, only 15% of the 25 majors spots accounting for half the total protein amount could be classified as major spots in all ecotypes. Identification of these major spots demonstrated large differences between the major functions detected. Accordingly, the proteomes appeared to reveal important variations in terms of function between ecotypes. Hierarchical clustering of proteomes according to either the amount of all anonymous spots, that of the 25 major spots or the functions of these major spots identified the same classes of ecotypes, and grouped the three atypical ecotypes. It is proposed that proteome comparison has the capacity to evidence differences in the physiological status of ecotypes. Results are discussed with respect to the possibility to infer such differences from limited comparisons of major proteins. It is concluded that classical proteomics could constitute a powerful tool to mine the biodiversity between ecotypes of a single plant species.
Proteins associated with type II bone morphogenetic protein receptor (BMPR‐II) and identified by two‐dimensional gel electrophoresis and mass spectrometry
Authors: Hassel Sylke , Eichner Annegret , Yakymovych Mariya , Hellman Ulf , Knaus Petra , Souchelnytskyi Serhiy
Published: March 2004

Bone morphogenetic proteins (BMP) are polypeptide growth factors that regulate cell differentiation and proliferation. BMPs bind to type I and type II serine/threonine kinase receptors to initiate intracellular signalling. BMPR‐II is the type II receptor, its mutations lead to hereditary pulmonary hypertension, and knockout of Bmpr‐II results in early embryonic lethality. To identify novel interacting proteins and explore signalling pathways that can be initiated by BMPR‐II, we performed glutathione‐S‐transferase (GST) pull‐down assays with BMPR‐II protein constructs fused to GST and extracts of mouse myoblast C2C12 cells. We generated three constructs which contain different parts of the cytoplasmic region of BMPR‐II: full‐length cytoplasmic part of BMPR‐II, only the kinase domain, or only the C‐terminal tail of BMPR‐II. Proteins which formed complexes with these BMPR‐II constructs were analyzed by two‐dimensional gel electrophoresis (2‐D GE), and specifically interacting proteins were identified by matrix‐assisted laser desorption/ionization‐time of flight‐mass spectrometry (MALDI‐TOF‐MS). We identified 33 interacting proteins; 11 proteins interacted with the C‐terminal tail of BMPR‐II, 4 with full‐length BMPR‐II, and 18 with a short form of the receptor with a deleted tail. Fourteen proteins have assigned functions in various signalling processes, suggesting links of BMP signalling to regulation of MAP kinase pathway, apoptosis, transcription, PKCß, and PKA. Five of the identified proteins are components of the cytoskeleton, and four are enzymes involved in metabolism, e.g., processing of estrogens or lipids. We confirmed interaction of PKCβ and CtBP with BMPR‐II using immunodetection. We showed that the C‐terminal tail of BMPR‐II provides binding sites for a number of regulatory proteins that may initiate Smad‐independent signalling.
No association between pre‐diagnostic plasma C‐reactive protein concentration and subsequent prostate cancer
Authors: Platz Elizabeth A. , De Marzo Angelo M. , Erlinger Thomas P. , Rifai Nader , Visvanathan Kala , Hoffman Sandra C. , Helzlsouer Kathy J.
Published: March 2004

BACKGROUND

We evaluated the association of pre‐diagnostic plasma concentration of C‐reactive protein, a sensitive, but non‐specific indicator of inflammation, with subsequent risk of prostate cancer.

METHODS

Included were 264 histologically confirmed prostate cancer cases and 264 age‐matched controls who were participants in the CLUE II cohort of Washington County, MD. C‐reactive protein was measured using a high‐sensitivity immunoturbidimetric assay. Odds ratios (ORs) and 95% confidence intervals (CI) were estimated from conditional logistic regression models by fourth of the C‐reactive protein distribution with cutpoints based on the controls. The median concentrations from the lowest to highest fourth were 0.41, 1.03, 1.90, and 4.53 mg/L.

RESULTS

Geometric mean plasma concentrations did not differ between the cases (1.24 ± 2.94 mg/L) and controls (1.41 ± 2.97 mg/L; P = 0.16). Compared to the bottom fourth, the ORs (95% CI) of prostate cancer were 1.29 (0.80–2.08), 0.98 (0.61–1.58), and 0.95 (0.57–1.58) for the second, third, and highest fourths (P trend = 0.66). These findings were unchanged after adjusting for body mass index (BMI) and cigarette smoking status or after excluding men with markedly elevated C‐reactive protein, cases diagnosed during the first 2 years of follow‐up, or controls who never had a PSA test. These findings did not differ by stage or grade of prostate cancer.

CONCLUSIONS

Pre‐diagnostic plasma concentration of C‐reactive protein was not associated with subsequent risk of prostate cancer. © 2004 Wiley‐Liss, Inc.
Prostate‐tumor targeting of gene expression by lentiviral vectors containing elements of the probasin promoter
Authors: Yu Duan , Jia William W. , Gleave Martin E. , Nelson Colleen C. , Rennie Paul S.
Published: March 2004

BACKGROUND

Lentiviruses are retroviruses that can infect and stably integrate into the chromatin of non‐dividing cells. The purpose of this study was to determine whether lentiviral vectors containing the probasin (PB) promoter displayed prostate‐specific, androgen‐regulated, and persistent gene expression.

METHODS

Three lentiviral‐PB promoter/enhanced green fluorescent protein (EGFP)‐reporter vectors together with a control lentiviral‐CMV‐EGFP, were tested by microscopy and flowcytometry for expression of EGFP after infection of human prostate cancer cells (LNCaP, PC‐3, PC‐3(hAR), and Du145 cells) and non‐prostate cells (COS‐1, HeLa, HeLa(hAR), and MCF‐7 cells).

RESULTS

All cells infected in vitro with lentiviral‐CMV vectors expressed EGFP, whereas with lentiviral‐PB vectors (the most potent being Lv‐ARR2PB), reporter expression was only observed in LNCaP cells with a small amount seen in androgen‐independent PC‐3 cells. Stable or transient transfection of androgen receptor only raised EGFP expression in prostate‐derived cell lines, but did not change tumor specificity. With Lv‐ARR2PB infected LNCaP cells, androgens regulated EGFP both in vitro and in vivo. After intra‐tumor injection of this vector, EGFP expression was observed in LNCaP tumors, but not in A‐549 lung or CaKi‐2 kidney tumors.

CONCLUSIONS

Lv‐ARR2PB may be an ideal vector for prostate‐tumor targeting and for persistent, hormone‐enhanced expression of a therapeutic gene to treat slow growing prostate tumors. © 2004 Wiley‐Liss, Inc.
Emergency venting requirements for tempered systems considering partial vapor–liquid separation with disengagement parameters greater than unity part I: Model development
Authors: Robert D'Alessandro P.E.
Published: March 2004

Part I of this two‐paper series presents closed‐form analytical expressions for the two‐phase emergency relief requirements of top‐vented vertical cylindrical containers when the fluids involved exhibit partial disengagement. Both churn‐turbulent flow and bubbly flow fluid behaviors, with disengagement parameters greater than unity, are considered. Energy input from either runaway reactions or uncontrolled external heat is included. The methods are limited to systems that are tempered and do not contain noncondensable components. In Part II, the models developed in Part I are applied to specific points along the venting transient, yielding expressions for the required flowrate under emergency conditions. Part II elaborates on the limitations of the models, illustrates the use of the models with numerical examples, and compares the results against previous work. The effect of disengagement parameters greater than unity is illustrated in terms of both the required relieving rate and the mass remaining inside the container when disengagement occurs. © 2004 American Institute of Chemical Engineers Process Saf Prog 23: 1–15, 2004
On the Peierls stress in Al and Cu: An atomistic simulation and comparison with experiment
Authors: Pasianot Roberto C. , Moreno‐Gobbi Ariel
Published: March 2004

An atomistic calculation of the Peierls stress in Al and Cu is undertaken in order to assess consistency with experiments. The measured yield stress extrapolated to 0 K results at least one order of magnitude smaller than the Peierls stress commonly derived from internal friction data. On the theoretical side, some calculations for Al are already available (using different approaches than presently) however none is for Cu. The simulations employ semi‐empirical many‐body interatomic potentials, fitted here to the generalized stacking fault energy surface (calculated elsewhere with ab initio electronic structure methods), as well as others from the literature. After a critical assessment, reasonable agreement is demonstrated between our results and the Peierls stress values derived from internal friction experiments within the framework of the kink pair formation model. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Calculation of thermodynamic properties of Cu and Ag using a self‐consistent statistical method
Authors: Karasevskii A. I. , Lubashenko V. V.
Published: March 2004

The thermal properties of the simple fcc metals Cu and Ag are investigated within a self‐consistent statistical approach. The method is based on a variation procedure calculating a parameter of the quasi‐elastic bond of neighboring atoms. The effective interionic interaction is approximated by the Morse pair potential fitting the experimental values for the lattice constant and the bulk modulus. The electronic contribution to the free energy is estimated within the free‐electron approximation. For both Cu and Ag we compute the temperature dependence of the interatomic distance, the specific heat at constant pressure, and the bulk modulus, and the equation of state at 293 K. Good agreement with experimental data is observed. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Diffusive magnetoresistance and interlayer exchange coupling of the ferromagnet–semiconductor layered systems Fe/GaAs and Fe/Ge
Authors: Perlov A. , Popescu V. , Ebert H.
Published: March 2004

We report results on calculations of the electronic, magnetic and transport properties of Fe/GaAs and Fe/Ge multilayer systems. On the base of the generalized Bloch theorem we have calculated the electronic structure for a set of spin‐spiral structures, which allows us to extract averaged interlayer exchange parameters and their dependence on the width of the semiconductor spacer. The dependence of the dc conductivity and magnetoresistance on the width of the semiconductor layer and the relative angle between the moments of adjacent FM‐layers allowed us to model the dependence of the resistivity on a magnetic field. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The nitrogen–hydrogen–vacancy complex in GaAs
Authors: Ulrici W. , Kiessling F.‐M. , Rudolph P.
Published: March 2004

The local vibrational mode absorption lines at 3079.2 and 983.3 cm−1, measured in semi‐insulating LEC‐grown GaAs, are due to the stretching and wagging mode of one hydrogen bonded to a light impurity atom. The investigation of GaAs grown without boric oxide encapsulant delivers arguments that this impurity atom is nitrogen in the nitrogen‐vacancy (NAs–VGa) defect, which is responsible for the vibrational quadruplet line at 638 cm−1. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
NMR line shape analysis in the incommensurate phase of bis(4‐chlorophenyl)sulfone
Authors: Taye A. , Michel D.
Published: March 2004

High quality single BCPS crystals were used to study the influence of a structurally incommensurate (IC) modulation on the line shape in 35Cl NMR spectra where the phase transition from the normal into the IC phase at ca. 150 K is clearly reflected in the appearance of an asymmetric frequency distribution with edge singularities. The line shape calculations are performed in a temperature range where the validity of the plane wave limit may be assumed. In nice agreement with an X‐ray analysis of the rotational symmetry modes in the IC phase by Zuniga et al., the evaluation of the 35Cl NMR frequency distributions is based on the IC modulation of the Euler angles which describe the orientation of 35Cl NMR quadrupole coupling tensor in the crystal frame. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
ToF‐SIMS studies of nanoporous PMSSQ materials: kinetics and reactions in the processing of low‐K dielectrics for ULSI applications
Authors: Lazzeri P. , Rubloff G. W. , Vanzetti L. , Briber R. M. , Anderle M. , Bersani M. , Park J. J. , Kim H.‐C. , Volksen W. , Miller R. D. , Lin Z.
Published: March 2004

Detailed investigations of spin‐on polymethylsilsesquioxane (PMSSQ)‐based low‐K materials were carried out by means of time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) to identify the reaction kinetics and mechanisms occurring during the manufacturing of nanoporous dielectrics for ULSI applications. Analysis of the static SIMS fingerprints led to the identification of key species related to the PMSSQ oligomers, as well to the observation of features related to the initial functionality of the precursor materials. The intensity variations of the key species with thermal curing reveal the polymerization kinetics of the dielectric precursors. In addition, thermal decomposition and volatilization of the polymethylmethacrylate–dimethylaminoethylmethacrylate copolymer (PMMA‐co‐DMAEMA) porogen was established based on the detection of fragments related to the different moieties of the copolymer molecule. Porogen degradation takes place via cleavage of the DMAEMA co‐monomer at low temperature, followed by volatilization of the residual PMMA‐enriched polymer upon annealing at higher temperature. Several complementary phenomena occurring during the formation of these complex systems can be evaluated by ToF‐SIMS, revealing major features crucial to materials development and the manufacturing of novel low‐dielectric‐constant (K) dielectrics. Copyright © 2004 John Wiley & Sons, Ltd.
Depth profiling of light elements in PAMBE‐grown GaN and helium‐implanted titanium with heavy ion time‐of‐flight elastic recoil detection
Authors: Markwitz A. , Kennedy V. J. , Durbin S.M. , Johnson P. B. , Mücklich A. , Dytlewski N.
Published: March 2004

The heavy ion time‐of‐flight elastic recoil detection analysis (HI‐ERDA) technique was used to investigate the possibility of measuring near‐surface elemental depth profiles of light and mid‐Z elements in thin films of plasma‐assisted molecular beam epitaxy (PAMBE)‐grown GaN and helium‐implanted titanium. The great advantage of HI‐ERDA is the ability to measure mass‐separated elemental depth profiles simultaneously. However for some materials it is not certain whether HI‐ERDA can be used successfully because significant sputtering or other beam‐induced damage may occur. The damage to the surfaces by a 77 MeV iodine beam was assessed using RBS, AFM and profilometry. The results show that for thin PAMBE‐grown polycrystalline GaN films and for titanium that has been heavily implanted with helium a significant modification of the near‐surface region is caused by the probing heavy ion beam. For the PAMBE‐grown GaN films the most significant loss trend is observed for nitrogen. Surprisingly this was not accompanied by a change in surface topology. In contrast, an almost complete removal of the heavily helium‐implanted surface layer was measured for the titanium specimens. The investigation shows that reference measurements with additional techniques such as RBS, AFM and profilometry have to be performed to ascertain sample integrity before HI‐ERDA data can be used. Copyright © 2004 John Wiley & Sons, Ltd.
The cultural production of science in reform‐based physics: Girls' access, participation, and resistance
Authors: Carlone Heidi B.
Published: March 2004

Recent literature in science education suggests that, to transform girls' participation, learning, and identities within school science, we must think about ways to engage girls in different kinds of educational activities that promote broader meanings of science and scientist. This study was designed to examine more deeply this call for a changed science curriculum and its implications for girls' participation, interest, and emerging science identities. In this ethnographic study, I examine the culturally produced meanings of science and scientist in a reform‐based physics classroom that used a curriculum called Active Physics, how these meanings reproduced and contested larger sociohistorical (and prototypical) meanings of science and scientist, and the ways girls participated within and against these meanings. The girls in this upper middle class school were mostly concerned with accessing and maintaining a good student identity (rather than connecting to science in any meaningful way) and resisted promoted meanings of science and scientist that they perceived as threatening to their good student identities. Their embrace of the ways school defined success (via grades and college admission) produced a meaning of Active Physics as a way to get credentials on a transcript and ensured their disconnection from real‐world, meaningful science and science identities. The story of girls' participation and resistance in Active Physics complicates our quest for gender‐fair science and highlights the power of sociohistorical meanings of schooling and science in producing educational subjects. © 2004 Wiley Periodicals, Inc. J Res Sci Teach 41: 392–414, 2004
Blurring the lines for learning: The role of out‐of‐school programs as complements to formal learning
Authors: Pittman Karen J. , Irby Merita , Yohalem Nicole , Wilson‐Ahlstrom Alicia
Published: March 2004

As debates continue over the effectiveness of after‐school programs, we need to create stronger links between schools and out‐of‐school activities. Where do such connections begin? How can we integrate skill‐building and academic competence into the out‐of‐school‐time context?
Processes of adjustment in organized out‐of‐school activities: Opportunities and risks
Authors: Mahoney Joseph L. , Eccles Jacquelynne S. , Larson Reed W.
Published: March 2004

Participation in organized out‐of‐school activities leads to long‐term psychosocial and educational benefits for young people. Now we're learning which features of these activities best support individual children.
The absence of the Isw2p–Itc1p chromatin‐remodelling complex induces mating type‐specific and Flo11p‐independent invasive growth of Saccharomyces cerevisiae
Authors: Trachtulcová Petra , Frýdlová Ivana , Janatová Ivana , Hašek Jiří
Published: March 2004

The Isw2p–Itc1p chromatin remodelling complex of Saccharomyces cerevisiae is a member of the ISWI class of ATPases with a nucleosome spacing activity, involved in regulation of expression of a broad spectrum of genes. Its absence causes derepression of a‐specific genes and aberrant morphology in α‐mating type cells. We report here that the deletion of the ISW2 gene in the originally non‐invasive BY strain induces mating type‐specific invasive growth strongly affected by nitrogen starvation. Although the Flo11 protein was postulated to be critical for haploid invasive growth, we showed that the invasive growth caused by the isw2 and itc1 deletions in α‐mating type cells was Flo11p‐independent. This type of invasive growth was proved to be a consequence of the activation of the pheromone response pathway. Our results suggest that Isw2 and Itc1 proteins do not have the same impact on the described phenomenon. Copyright © 2004 John Wiley & Sons, Ltd.
Domain swapping of a llama VHH domain builds a crystal‐wide β‐sheet structure
Authors: Spinelli Silvia , Desmyter Aline , Frenken Leon , Verrips Theo , Tegoni Mariella , Cambillau Christian
Published: March 2004

Among mammals, camelids have a unique immunological system since they produce functional antibodies devoid of light chains and CH1 domains. To bind antigens, whether they are proteins or haptens, camelids use the single domain VH from their heavy chain (VHH). We report here on such a llama VHH domain (VHH‐R9) which was raised against a hapten, the RR6 red dye. This VHH possesses the shortest complementarity determining region 3 (CDR3) among all the known VHH sequences and nevertheless binds RR6 efficiently with a K
d value of 83 nM. However, the crystal structure of VHH‐R9 exhibits a striking feature: its CDR3 and its last β‐strand (β9) do not follow the immunoglobulin VH domain fold, but instead extend out of the VHH molecular boundary and associate with a symmetry‐related molecule. The two monomers thus form a domain‐swapped dimer which establishes further contacts with symmetry‐related molecules and build a crystal‐wide β‐sheet structure. The driving force of the dimer formation is probably the strain induced by the short CDR3 together with the cleavage of the first seven residues.
LRRC8 involved in B cell development belongs to a novel family of leucine‐rich repeat proteins
Authors: Kubota Keiko , Kim Ji Yoo , Sawada Akihisa , Tokimasa Sadao , Fujisaki Hiroyuki , Matsuda-Hashii Yoshiko , Ozono Keiichi , Hara Junichi
Published: March 2004

In a previous study, we isolated a novel gene, LRRC8 (leucine‐rich repeat‐containing 8), in a girl with congenital agammaglobulinemia. We have now identified four unknown LRRC8‐like genes, named TA‐LRRP, AD158, LRRC5, and FLJ23420. Their predicted structures are very similar to each other, and highly conserved between humans and the mouse. All five genes encode proteins consisting of 16 extracellular leucine‐rich repeats (LRRs), all of which have four transmembrane regions except for FLJ23420. These genes belong to a novel family, designated the LRRC8 family, within the superfamily of LRR proteins. TA‐LRRP, AD158, and LRRC5 might be implicated in proliferation and activation of lymphocytes and monocytes.
Kinetic analysis of operator binding by the E. coli methionine repressor highlights the role(s) of electrostatic interactions
Authors: Lawrenson Isobel D. , Stockley Peter G.
Published: March 2004

MetJ is a member of the ribbon‐helix‐helix class of DNA‐binding proteins whose affinity for operators is apparently controlled by an unprecedented long‐range electrostatic effect from the tertiary sulphur atom of its co‐repressor, S‐adenosyl methionine. We report here the results of kinetic assays of DNA binding with MetJ mutant proteins having altered net charges. The results (a) suggest that MetJ locates its operators via a sliding mechanism, (b) support the idea that electrostatic steering is important in the initial DNA binding event and (c) highlight the sensitivity of this system to electrostatic effects.
Editorial
Authors: BALME CHRISTOPHER
Published: March 2004

The first issue of the journal in 2004, and the first under my editorship, is devoted to a special focus on ‘Postdramatic Theatre’. While this term may not be familiar to many readers, the phenomenon it embraces most certainly is. Coined by the German theatre studies scholar, Hans-Thies Lehmann in his book Postdramatisches Theater,1 the concept refers to tendencies and experiments defining theatre outside the paradigm of the dramatic text. Also known, somewhat imprecisely, as postmodern theatre, it questions fundamentally the very tenets of the dramatic theatre. Postdramatic performances usually eschew clear coordinates of narrative and character and require therefore considerable effort on the part of the spectator. For this reason, it has been termed, in the words of New York theatre critic Elinor Fuchs, ‘spectator's response theatre: we write our own script out of the “pieces of culture” offered’.2 Like Lehmann, Fuchs tries to find an over-arching frame within which to make sense of the manifold experiments in theatre and performance that were taking place in the 1980s. Whereas Lehmann sees postdramatic theatre primarily as a question of form and history which affect the configuration of time, space and mediality of theatre, Fuchs regards the same developments as a response to the massive critique of Western models of subjectivity that we associate with terms such as poststructuralism and deconstruction.
Look who's Looking!: Perspective and the Paradox of Postdramatic Subjectivity
Authors: BLEEKER MAAIKE
Published: March 2004

In his Postdramatisches Theater Lehmann compares the effect of the dramatic theatre to that of perspective in painting. Both are structured according to an aesthetic logic that can be characterized as teleological. On the contemporary post-dramatic stage, this logic is deconstructed or rejected. In my text, I take a closer look at this comparison of drama and perspective in Lehmann's text. I confront Lehmann's account of the postdramatic theatre with the work of Dutch theatre director Gerardjan Rijnders. Rijndesr's work draws attention to the inevitably of the subjectivity involved in every vision of the world, even when this world seems to be shown ‘as it is’ in itself. As I will argue, it is precisely the relationship between what is seen and the subjective point of view from where it is seen that is obscured in Lehmann's account of the similarities between drama and perspective.
Dining with the Perpetrators. Eva Diamantstein's Performative Exploration of the Role of Women in National Socialism
Authors: KLÖCK ANJA I.
Published: March 2004

Eva Diamantstein's play and production of Nachtmahl (Supper) premiered during the Spielart Theatre Festival in Munich, Germany, in November 2001, and subsequently toured to Frankfurt am Main, Hamburg and Vienna in 2002. Both a research project and a theatrical enterprise, Nachtmahl is based on the biographies of four women who actively participated in various Nazi projects. Seated at a long table and having a four-course dinner together with the female characters, the spectators gradually discover their histories while the theatre becomes a dynamic space of coexistences, in which the continuities between past and present acquire a material and experiential quality. By situating Nachtmahl within the historiographical strategies crystallizing around women and National Socialism, the author discusses the production's use of social rituals, strategies of domination and intimidation and mechanisms of collective communication. The production explores how culturally conditioned strategies of exoneration function as devices for separating oneself from a seemingly distanced past.