bluuebunny/crossref_metadata_2025 huggingface dataset:
Dimerization of the cytokine receptors gp130 and LIFR analysed in single cells
Authors: Giese Bernd , Roderburg Christoph , Sommerauer Michael , Wortmann Saskia B. , Metz Silke , Heinrich Peter C. , Müller-Newen Gerhard
Published: October 2005

The cytokine receptor gp130 is the shared signalling subunit of the IL-6-type cytokines. Interleukin-6 (IL-6) signals through gp130 homodimers whereas leukaemia inhibitory factor (LIF) exerts its action through a heterodimer of gp130 and the LIF receptor (LIFR). Related haematopoietic receptors such as the erythropoietin receptor have been described as preformed dimers in the plasma membrane. Here we investigated gp130 homodimerization and heterodimerization with the LIFR by fluorescence resonance energy transfer (FRET) and bimolecular fluorescence complementation (BiFC). We detected a FRET signal between YFP- and CFP-tagged gp130 at the plasma membrane of unstimulated cells that does not increase upon IL-6 stimulation. However, FRET between YFP-tagged gp130 and CFP-tagged LIFR considerably increased upon LIF stimulation. Using a BiFC approach that detects stable interactions we show that fluorescence complementation of gp130 constructs tagged with matching `halves' of fluorescent proteins increases upon IL-6 stimulation. Taken together, these findings suggest that transient gp130 homodimers on the plasma membrane are stabilized by IL-6 whereas heterodimerization of gp130 with the LIFR is mainly triggered by the ligand. This view is supported by the observation that the simultaneous action of two IL-6 binding domains on two gp130 molecules is required to efficiently recruit a fluorescent IL-6 (YFP-IL-6) to the plasma membrane.
Interferon-γ selectively increases epithelial permeability to large molecules by activating different populations of paracellular pores
Authors: Watson Christopher J. , Hoare Catherine J. , Garrod David R. , Carlson Gordon L. , Warhurst Geoffrey
Published: October 2005

Impairment of the gut epithelial barrier by agents such as IFNγ may play a key role in the pathogenesis of inflammatory disorders by increasing the paracellular penetration of luminal macromolecules, potentially including bacterial antigens. Owing to limitations of current paracellular probes, little is known about the precise functional changes induced by IFNγ and how these relate to the development of increased macromolecular permeability. Here we investigate how IFNγ modulates this pathway in T84 monolayers using a novel profiling technique that resolves different populations of paracellular pores by simultaneous analysis of 24 permeability probes of defined molecular size. Two types of functional pore present in control monolayers, an abundant restrictive pore with a radius of ∼4.5 Å and a much larger but infrequent, non-restrictive pore, were differentially regulated by IFNγ. Incubation with IFNγ dose-dependently and reversibly increased the frequency of the non-restrictive pores while having no significant effect on the restrictive component. Cytokine-induced increases in β, the descriptor of the non-restrictive pore, correlated closely with increased permeability to large molecules (10 kDa) including E. coli-derived lipopolysaccharide, but not small (0.182 kDa) molecules. This effect was associated with changes in expression of the tight junction proteins occludin and claudin-1. These data suggest that IFNγ selectively increases the transepithelial flux of large molecules by activating specific pathways within the junctional pore. One hypothesis is that this process may be activated in the early stages of the inflammatory response, facilitating the passage of large and potentially antigenic molecules across the gut without gross disruption of the barrier to small molecules.
Proteasomes degrade proteins in focal subdomains of the human cell nucleus
Authors: Rockel Thomas Dino , Stuhlmann Dominik , von Mikecz Anna
Published: October 2005

The ubiquitin proteasome system plays a fundamental role in the regulation of cellular processes by degradation of endogenous proteins. Proteasomes are localized in both, the cytoplasm and the cell nucleus, however, little is known about nuclear proteolysis. Here, fluorogenic precursor substrates enabled detection of proteasomal activity in nucleoplasmic cell fractions (turnover 0.0541 μM/minute) and nuclei of living cells (turnover 0.0472 μM/minute). By contrast, cell fractions of nucleoli or nuclear envelopes did not contain proteasomal activity. Microinjection of ectopic fluorogenic protein DQ-ovalbumin revealed that proteasomal protein degradation occurs in distinct nucleoplasmic foci, which partially overlap with signature proteins of subnuclear domains, such as splicing speckles or promyelocytic leukemia bodies, ubiquitin, nucleoplasmic proteasomes and RNA polymerase II. Our results establish proteasomal proteolysis as an intrinsic function of the cell nucleus.
CZH proteins: a new family of Rho-GEFs
Authors: Meller Nahum , Merlot Sylvain , Guda Chittibabu
Published: October 2005

The Rho family of small GTPases are important regulators of multiple cellular activities and, most notably, reorganization of the actin cytoskeleton. Dbl-homology (DH)-domain-containing proteins are the classical guanine nucleotide exchange factors (GEFs) responsible for activation of Rho GTPases. However, members of a newly discovered family can also act as Rho-GEFs. These CZH proteins include: CDM (Ced-5, Dock180 and Myoblast city) proteins, which activate Rac; and zizimin proteins, which activate Cdc42. The family contains 11 mammalian proteins and has members in many other eukaryotes. The GEF activity is carried out by a novel, DH-unrelated domain named the DOCKER, CZH2 or DHR2 domain. CZH proteins have been implicated in cell migration, phagocytosis of apoptotic cells, T-cell activation and neurite outgrowth, and probably arose relatively early in eukaryotic evolution.
Scale-free networks in cell biology
Authors: Albert Réka
Published: October 2005

A cell's behavior is a consequence of the complex interactions between its numerous constituents, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes, allowing them to respond to and adapt to an ever-changing environment. The large number of components, the degree of interconnectivity and the complex control of cellular networks are becoming evident in the integrated genomic and proteomic analyses that are emerging. It is increasingly recognized that the understanding of properties that arise from whole-cell function require integrated, theoretical descriptions of the relationships between different cellular components. Recent theoretical advances allow us to describe cellular network structure with graph concepts and have revealed organizational features shared with numerous non-biological networks. We now have the opportunity to describe quantitatively a network of hundreds or thousands of interacting components. Moreover, the observed topologies of cellular networks give us clues about their evolution and how their organization influences their function and dynamic responses.
Mitochondrial depolarization following hydrogen sulfide exposure in erythrocytes from a sulfide-tolerant marine invertebrate
Authors: Julian David , April Kelly L. , Patel Shiven , Stein Jenny R. , Wohlgemuth Stephanie E.
Published: October 2005

Sulfide-tolerant marine invertebrates employ a variety of mechanisms to detoxify sulfide once it has entered their bodies, but their integumentary,respiratory epithelium and circulatory cells may still be exposed to toxic sulfide concentrations. To investigate whether sulfide exposure is toxic to mitochondria of a sulfide-tolerant invertebrate, we used the fluorescent dyes JC-1 and TMRM to determine the effect of sulfide exposure on mitochondrial depolarization in erythrocytes from the annelid Glycera dibranchiata. In erythrocytes exposed to 0.11-1.9 mmol l-1 sulfide for 1 h, the dyes showed fluorescence changes consistent with sulfide-induced mitochondrial depolarization. At the highest sulfide concentration, the extent of depolarization was equivalent to that caused by the mitochondrial uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP). Even when induced by as little as 0.3 mmol l-1 sulfide, the depolarization was not reversible over a subsequent 5 h recovery period. The mechanism of toxicity was likely not via inhibition of cytochrome c oxidase (COX),since other COX inhibitors and other mitochondrial electron transport chain inhibitors did not produce similar effects. Furthermore, pharmacological inhibition of the mitochondrial permeability transition pore failed to prevent sulfide-induced depolarization. Finally, increased oxidation of the free radical indicators H2DCFDA and MitoSOX™ in erythrocytes exposed to sulfide suggests that sulfide oxidation increased oxidative stress and superoxide production, respectively. Together, these results indicate that sulfide exposure causes mitochondrial depolarization in cells of a sulfide-tolerant annelid, and that this effect, which differs from the actions of other COX inhibitors, may be via increased free radical damage.
Interactions of visual odometry and landmark guidance during food search in honeybees
Authors: Vladusich Tony , Hemmi Jan M. , Srinivasan Mandyam V. , Zeil Jochen
Published: October 2005

How do honeybees use visual odometry and goal-defining landmarks to guide food search? In one experiment, bees were trained to forage in an optic-flow-rich tunnel with a landmark positioned directly above the feeder. Subsequent food-search tests indicated that bees searched much more accurately when both odometric and landmark cues were available than when only odometry was available. When the two cue sources were set in conflict, by shifting the position of the landmark in the tunnel during test, bees overwhelmingly used landmark cues rather than odometry. In another experiment, odometric cues were removed by training and testing in axially striped tunnels. The data show that bees did not weight landmarks as highly as when odometric cues were available,tending to search in the vicinity of the landmark for shorter periods. A third experiment, in which bees were trained with odometry but without a landmark,showed that a novel landmark placed anywhere in the tunnel during testing prevented bees from searching beyond the landmark location. Two further experiments, involving training bees to relatively longer distances with a goal-defining landmark, produced similar results to the initial experiment. One caveat was that, with the removal of the familiar landmark, bees tended to overshoot the training location, relative to the case where bees were trained without a landmark. Taken together, the results suggest that bees assign appropriate significance to odometric and landmark cues in a more flexible and dynamic way than previously envisaged.
Precision and Accuracy in Ceramic-on-Ceramic Wear Analyses: Influence of Simulator Test Duration
Authors: Richardson H A , Clarke I C , Williams P , Donaldson T , Oonishi H
Published: October 2005

In this, the first report of precision and accuracy in simulator studies, ceramic-ceramic implants with ultra-low wear trends represented a relevant wear model. The effect of test durations was examined in a standard simulator test mode on the quality of the linear regression trends, the average wear estimates, and the amount of noise in the data. Three sets of diametral tolerances were compared in 28 mm diameter alumina implants. The authors' hypothesis was that wear data would be significantly improved with increased test durations. The average wear rates varied little with test duration, the biggest change amounting to only 30 and 15 per cent decreases in the wear estimate by 10 and 14 million cycles respectively. The most satisfactory improvement in the study was the decrease in variance (noise) with increasing duration, ±200 per cent at 5 million cycles reduced to ±55 per cent at 14 million cycles. The quality of the linear regression coefficients improved 150 per cent by 10 million cycles and 250 per cent by 14 million cycles. Overall the ceramic implants with highest diametral tolerances showed the least wear (15 per cent less, but not statistically significant). However, given such low wear rates for alumina liners, it was unlikely that any differences owing to diametral tolerances would be clinically significant in the typical patient.
Effect of Interface Conditions between Ultrahigh Molecular Weight Polyethylene and Polymethyl Methacrylate Bone Cement on the Mechanical Behaviour of Total Shoulder Arthroplasty
Authors: Oosterom R , van Ostayen R A J , Antonelli V , Bersee H E N
Published: October 2005

The aim of this study was to investigate the effect of the interface condition between polymethyl methacrylate (PMMA) bone cement and the ultrahigh molecular weight (UHMWPE) glenoid component on cement stresses and glenoid component tilting in a finite element (FE) model. The background of this research is that most FE models assume bonding between the PMMA bone cement and the UHMWPE component, although it is very doubtful that this bonding is present.

An FE model of a cemented glenoid component was developed and a joint compression force and subluxation force of 725 and 350 N respectively were applied. The maximal principal stresses in the cement layer ranged between 21.30 and 32.18 MPa. Glenoid component tilting ranged between 0.943° and 0.513°.

It was found that the interface condition has a large effect on the maximal principal stresses and glenoid component tilting. Whether adhesion between the UHMWPE component and PMMA bone cement occurs is unknown beforehand and, as a result, design validation using the FE technique should be carried out both by using contact elements in combination with a coefficient of friction as well as by a full bonding at this interface.
A Circumferentially Flanged Tibial Tray Minimizes Bone-Tray Shear Micromotion
Authors: Barker D S , Tanner K E , Ryd L
Published: October 2005

Aseptic loosening of the tibial component is the major complication of total knee arthroplasty. There is an association between early excessive shear micromotion between the bone and the tray of the tibial component and late aseptic loosening. Using non-linear finite element analysis, whether a tibial tray with a circumferentially flanged rim and a mating cut in the proximal tibia could minimize bone-tray shear micromotion was considered. fifteen competing tray designs with various degrees of flange curvature were assessed with the aim of minimizing bone-tray shear micromotion. A trade-off was found between reducing micromotion and increasing peripheral cancellous bone stresses. It was found that, within the limitations of the study, there was a theoretical design that could virtually eliminate micromotion due to axial loads, with minimal bone removal and without the use of screws or pegs.
Stabilizing Synchronization Control of Rotor-Magnetic Bearing Systems
Authors: Xiao Y , Zhu K Y , Zhang C , Tseng K J , Ling K V
Published: October 2005

Active magnetic bearings, which provide non-contact suspension for high-speed rotors, have received increasing attention in recent years. Although the contactless nature of magnetic bearings brings up many advantages over conventional bearings, one of the challenging problems is to stabilize the rotor of the magnetic bearing systems that is very sensitive to outside disturbances and plant uncertainties. In this paper, a stabilizing synchronization design of rotor-magnetic bearing systems is proposed by incorporating cross-coupling technology into the optimal control architecture, which can be decomposed into two problems: a robust optimal control problem to improve the synchronization performance of the rotor in the radial directions and a stability problem. The control scheme is based on minimization of a new quadratic performance index in which the synchronization errors are embedded. Stability of the control scheme is also investigated through the linear quadratic Gaussian (LQG) optimal control technique. Simulations on a compact and efficient flywheel energy storage system with integrated magnetic bearings demonstrate that the proposed approach is very effective to recover the unstable system when the outside disturbances are present.
High Gain Observers for Non-Linear Systems Modelled by Bond Graphs
Authors: Pichardo-Almarza C , Rahmani A , Dauphin-Tanguy G , Delgado M
Published: October 2005

In the present work, a bond graph approach to build full-order high gain observers is shown. The proposed approach is based on the classical techniques to design high gain observers. Simulation results are used to show the performance of the high gain observer in chemical engineering applications as a distillation column modelled by pseudo bond graphs.
Improvements in premixed charge compression ignition combustion and emissions with lower distillation temperature fuels
Authors: Sakai A , Takeyama H , Ogawa H , Miyamoto N
Published: October 2005

The charge mixture in a premixed charge compression ignition (PCCI) engine with direct in-cylinder injection early in the compression stroke is still heterogeneous even at the compression end. Direct injection of a low-volatility fuel, such as diesel fuel, early in the compression stroke results in adhesion of unevaporated fuel on the cylinder liner wall. It may be possible to improve both mixture formation and homogeneity, and decrease wall wetting by using higher-volatility fuels with distillation temperatures lower than the in-cylinder gas temperature early in the compression stroke. This research addressed the potential for improvements in early direct injection type PCCI combustion with a higher-volatility fuel, experimentally and computationally. A normal heptane + isooctane blended fuel with ignitability similar to diesel fuel in PCCI operation was used as the higher-volatility fuel. The experimental results showed that the deterioration in thermal efficiency that occurs with advanced injection timings with ordinary diesel fuel could be eliminated with the higher-volatility fuel without significantly altering the total hydrocarbons (THC) and CO emissions. With early injection timings, the rate of heat release with diesel fuel is smaller than with higher-volatility fuels. This result suggests that with diesel fuel there is significant fuel adhesion to the cylinder liner wall and also absorption into the lubricating oil.
Synthesis and Frictional Properties of Poly(2,3-dihydroxypropyl methacrylate) Brush Prepared by Surface-initiated Atom Transfer Radical Polymerization
Authors: Kobayashi Motoyasu , Takahara Atsushi
Published: October 2005

Surface-initiated atom transfer radical polymerization (ATRP) of (2,2-dimethyl-1,3-dioxolan-4-yl)methyl methacrylate (1) was carried out from an immobilized initiator on a silicon wafer to result in a high-density polymer brush, which was converted to the hydrophilic polymer brush consisting of 2,3-dihyroxypropyl methacrylate (2) units, successively. The poly(2) brush showed low dynamic friction coefficient in water.
Chemical Compositions of Secondary Organic Aerosol from the Ozonolysis of Cyclohexene in the Absence of Seed Particles
Authors: Sato Kei
Published: October 2005

The composition of the aerosol from the ozonolysis of cyclohexene in the absence of seed particles has been investigated by laboratory chamber experiments. The aerosol collected on filters was analyzed by a liquid chromatography/atmospheric pressure chemical ionization-mass spectrometry. Low-molecular weight products, i.e., dicarboxylic acids, oxocarboxylic acids, and hydroxydicarboxylic acids, as well as oligomers with molecular weights more than 200 were found in the aerosol.
An Efficient Method for the Preparation of Carboxamides by Dehydration Condensation Using Tetrakis(1,1,1,3,3,3-hexafluoro-2-propoxy)silane
Authors: Tozawa Takashi , Yamane Yoshinobu , Mukaiyama Teruaki
Published: October 2005

The use of tetraalkoxysilanes, particularly tetrakis(perfluoroalkoxy)silanes, in dehydration condensation of carboxylic acids with amines was investigated. Tetrakis(1,1,1,3,3,3-hexafluoro-2-propoxy)silane, Si[OCH(CF3)2]4, prepared easily from silicon tetrachloride and sodium 1,1,1,3,3,3-hexafluoro-2-propoxide, was found to be an effective dehydrating reagent for preparing various carboxamides in good to high yields from the corresponding carboxylic acids and amines.
Local Environments of Slags: The First Application of 43Ca 3QMAS NMR Technique
Authors: Shimoda Keiji , Tobu Yasuhiro , Kanehashi Koji , Nemoto Takahiro , Saito Koji
Published: October 2005

We first applied 43Ca 3QMAS NMR spectroscopy for 43Ca-enriched model slags. Local environments of Ca2+ ions in slow- and rapid-quench model slags were found to be different each other. The slow-quench slag has well-defined CaO8 polyhedra in a crystalline form, although the rapid-quench slag is considered to have CaO6 octahedral species as a main component.
Control of Selectivity Based on the Diffusion Rates of the Reactants in the Oxidation of Mixed Hydrocarbons with Molecular Oxygen over Silica-coated Pt Catalysts
Authors: Takenaka Sakae , Hori Kunio , Matsune Hideki , Kishida Masahiro
Published: October 2005

Pt metal catalyst covered with silica layers oxidized methane preferentially in the competitive oxidation of methane and isobutane with gaseous oxygen. Selectivity in the competitive oxidation of mixed hydrocarbons over the catalyst was controlled by the diffusion rates of the reactants in the silica layers which wrapped Pt metal particles.
Microwave-induced Fabrication of MFI Zeolite Crystal Films onto Various Metal Oxide Substrates
Authors: Hwang Young Kyu , Lee U-Hwang , Chang Jong-San , Kwon Young-Uk , Park Sang-Eon
Published: October 2005

Thin films comprising oriented and micropatterned Si-MFI molecular sieves have been synthesized with metal oxide nanoparticles as a chemical glue by using microwave irradiation technique and soft lithography which can be applied to uniform coating of micropatterned molecular sieves.
Organic Metals Based on an Asymmetric π Donor PEDT-TSF, (PEDT-TSF)2FeX4 (PEDT-TSF = Pyrazinoethylenedithiotetraselenafulvalene; X = Cl, Br)
Authors: Otsubo Saika , Takahashi Kazuyuki , Cui HengBo , Okano Yoshinori , Kobayashi Hayao
Published: October 2005

(PEDT-TSF)2FeCl4 is the first κ-type organic metal based on an asymmetric π donor with a pyrazine ring, PEDT-TSF. (PEDT-TSF)2FeBr4 has another type of metallic layers composed of unique tetradic PEDT-TSF columns, suggesting that PEDT-TSF is a suitable donor to afford metallic conductors. The extended Hückel tight-binding band examination showed a suitable choice of the atomic orbital parameters to be essential to obtain reasonable results.
Photophysical and Photochemical Properties of The La@C82 Anion
Authors: Fujitsuka Mamoru , Ito Osamu , Maeda Yutaka , Wakahara Takatsugu , Tsuchiya Takahiro , Nakahodo Tsukasa , Akasaka Takeshi , Mizorogi Naomi , Nagase Shigeru
Published: October 2005

Properties of the excited states of the La@C82 anion have been investigated by laser flash photolysis measuring the fluorescence and absorption spectra. Transient absorption bands in the visible and near-IR region observed by the laser excitation of the La@C82 anion were attributed to the excited triplet, which showed high electron-donor ability to viologen dication, yielding La@C82 and viologen radical cation, establishing a reversible photoelectron transfer cycle.
Control of Hydrolysis and Condensation Activities of Thermolysin by Ultrasound Irradiation
Authors: Kawasaki Takayoshi , Hoshino Yu , Ishizu Yukari , Mizushiro Yu , Okahata Yoshio
Published: October 2005

Hydrolysis and condensation reactions of peptides catalyzed by thermolysin can be reversibly controlled by on/off ultrasound irradiation depending on its frequency region.
Predicting RNA folding thermodynamics with a reduced chain representation model
Authors: CAO SONG , CHEN SHI-JIE
Published: October 2005

Based on the virtual bond representation for the nucleotide backbone, we develop a reduced conformational model for RNA. We use the experimentally measured atomic coordinates to model the helices and use the self-avoiding walks in a diamond lattice to model the loop conformations. The atomic coordinates of the helices and the lattice representation for the loops are matched at the loop–helix junction, where steric viability is accounted for. Unlike the previous simplified lattice-based models, the present virtual bond model can account for the atomic details of realistic three-dimensional RNA structures. Based on the model, we develop a statistical mechanical theory for RNA folding energy landscapes and folding thermodynamics. Tests against experiments show that the theory can give much more improved predictions for the native structures, the thermal denaturation curves, and the equilibrium folding/unfolding pathways than the previous models. The application of the model to the P5abc region of Tetrahymena group I ribozyme reveals the misfolded intermediates as well as the native-like intermediates in the equilibrium folding process. Moreover, based on the free energy landscape analysis for each and every loop mutation, the model predicts five lethal mutations that can completely alter the free energy landscape and the folding stability of the molecule.
Ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus display multiple defects in ribosomal functions and sensitivity against erythromycin
Authors: TSAGKALIA AIKATERINI , LEONTIADOU FOTINI , XAPLANTERI MARIA A. , PAPADOPOULOS GEORGIOS , KALPAXIS DIMITRIOS L. , CHOLI-PAPADOPOULOU THEODORA
Published: October 2005

Protein L4 from Thermus thermophilus (TthL4) was heterologously overproduced in Escherichia coli cells. To study the implication of the extended loop of TthL4 in the exit-tunnel and peptidyltransferase functions, the highly conserved E56 was replaced by D or Q, while the semiconserved G55 was changed to E or S. Moreover, the sequence -G55E56- was inverted to -E55G56-. When we incorporated these mutants into E. coli ribosomes and investigated their impact on poly(Phe) synthesis, high variations in the synthetic activity and response to erythromycin of the resulting ribosomes were observed. In the absence of erythromycin, ribosomes harboring mutations G55E and E56D in TthL4 protein were characterized by low activity in synthesizing poly(Phe) and decreased capability in binding tRNA at the A site. On the other hand, ribosomes possessing mutations G55E, G55S, G55E-E56G, or E56Q in TthL4 protein were unexpectedly more sensitive to erythromycin. Evidence in support of these findings was drawn by in vivo experiments, assessing the erythromycin sensitivity of E. coli cells expressing wild-type or mutant TthL4 proteins. Our results emphasize the role of the extended loop of L4 ribosomal protein in the exit-tunnel and peptidyltransferase center functions.
Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures
Authors: WOLF MATTHIAS , ACHTZIGER MARCO , SCHULTZ JÖRG , DANDEKAR THOMAS , MÜLLER TOBIAS
Published: October 2005

Structural genomics meets phylogenetics and vice versa: Knowing rRNA secondary structures is a prerequisite for constructing rRNA alignments for inferring phylogenies, and inferring phylogenies is a precondition to understand the evolution of such rRNA secondary structures. Here, both scientific worlds go together. The rRNA internal transcribed spacer 2 (ITS2) region is a widely used phylogenetic marker. Because of its high variability at the sequence level, correct alignments have to take into account structural information. In this study, we examine the extent of the conservation in structure. We present (1) the homology modeled secondary structure of more than 20,000 ITS2 covering about 14,000 species; (2) a computational approach for homology modeling of rRNA structures, which additionally can be applied to other RNA families; and (3) a database providing about 25,000 ITS2 sequences with their associated secondary structures, a refined ITS2 specific general time reversible (GTR) substitution model, and a scoring matrix, available at http://its2.bioapps.biozentrum.uni-wuerzburg.de.
Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs
Authors: RAYMOND CHRISTOPHER K. , ROBERTS BRIAN S. , GARRETT-ENGELE PHILLIP , LIM LEE P. , JOHNSON JASON M.
Published: October 2005

There has been a surge of interest in the biology of microRNAs and the technology of RNA interference. We describe a simple, robust, inexpensive assay for quantitative analysis of microRNAs and short-interfering RNAs. The method relies on primer extension conversion of RNA to cDNA by reverse transcription followed by quantitative, real-time PCR. Technical parameters critical to the success of the assay are presented. Measurements of microRNA levels are sensitive, with most assays allowing measurements in the femtomolar range, which corresponds to tens of copies per cell or less. The assay has a high dynamic range and provides linear readout over differences in microRNA concentrations that span 6–7 orders of magnitude. The assay is capable of discriminating between related microRNA family members that differ by subtle sequence differences. We used the method for quantitative analysis of six microRNAs across 12 tissue samples. The data confirm striking variation in the patterns of expression of these noncoding regulatory RNAs.
Differences and similarities between Drosophila and mammalian 3′ end processing of histone pre-mRNAs
Authors: DOMINSKI ZBIGNIEW , YANG XIAO-CUI , PURDY MATHEW , MARZLUFF WILLIAM F.
Published: October 2005

We used nuclear extracts from Drosophila Kc cells to characterize 3′ end processing of Drosophila histone pre-mRNAs. Drosophila SLBP plays a critical role in recruiting the U7 snRNP to the pre-mRNA and is essential for processing all five Drosophila histone pre-mRNAs. The Drosophila processing machinery strongly prefers cleavage after a fourth nucleotide following the stem–loop and favors an adenosine over pyrimidines in this position. Increasing the distance between the stem–loop and the HDE does not result in a corresponding shift of the cleavage site, suggesting that in Drosophila processing the U7 snRNP does not function as a molecular ruler. Instead, SLBP directs the cleavage site close to the stem–loop. The upstream cleavage product generated in Drosophila nuclear extracts contains a 3′ OH, and the downstream cleavage product is degraded by a nuclease dependent on the U7 snRNP, suggesting that the cleavage factor has been conserved between Drosophila and mammalian processing. A 2′O-methyl oligonucleotide complementary to the first 17 nt of the Drosophila U7 snRNA was not able to deplete the U7 snRNP from Drosophila nuclear extracts, suggesting that the 5′ end of the Drosophila U7 snRNA is inaccessible. This oligonucleotide selectively inhibited processing of only two Drosophila pre-mRNAs and had no effect on processing of the other three pre-mRNAs. Together, these studies demonstrate that although Drosophila and mammalian histone pre-mRNA processing share common features, there are also significant differences, likely reflecting divergence in the mechanism of 3′ end processing between vertebrates and invertebrates.
MAASE: An alternative splicing database designed for supporting splicing microarray applications
Authors: ZHENG CHRISTINA L. , KWON YOUNG-SOO , LI HAI-RI , ZHANG KUI , COUTINHO-MANSFIELD GABRIELA , YANG CANZHU , NAIR T. MURLIDHARAN , GRIBSKOV MICHAEL , FU XIANG-DONG
Published: October 2005

Alternative splicing is a prominent feature of higher eukaryotes. Understanding of the function of mRNA isoforms and the regulation of alternative splicing is a major challenge in the post-genomic era. The development of mRNA isoform sensitive microarrays, which requires precise splice-junction sequence information, is a promising approach. Despite the availability of a large number of mRNAs and ESTs in various databases and the efforts made to align transcript sequences to genomic sequences, existing alternative splicing databases do not offer adequate information in an appropriate format to aid in splicing array design. Here we describe our effort in constructing the Manually Annotated Alternatively Spliced Events (MAASE) database system, which is specifically designed to support splicing microarray applications. MAASE comprises two components: (1) a manual/computational annotation tool for the efficient extraction of critical sequence and functional information for alternative splicing events and (2) a user-friendly database of annotated events that allows convenient export of information to aid in microarray design and data analysis. We provide a detailed introduction and a step-by-step user guide to the MAASE database system to facilitate future large-scale annotation efforts, integration with other alternative splicing databases, and splicing array fabrication.
Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse
Authors: ZHENG CHRISTINA L. , FU XIANG-DONG , GRIBSKOV MICHAEL
Published: October 2005

Alternative splicing is a major contributor to genomic complexity, disease, and development. Previous studies have captured some of the characteristics that distinguish alternative splicing from constitutive splicing. However, most published work only focuses on skipped exons and/or a single species. Here we take advantage of the highly curated data in the MAASE database (see related paper in this issue) to analyze features that characterize different modes of splicing. Our analysis confirms previous observations about alternative splicing, including weaker splicing signals at alternative splice sites, higher sequence conservation surrounding orthologous alternative exons, shorter exon length, and more frequent reading frame maintenance in skipped exons. In addition, our study reveals potentially novel regulatory principles underlying distinct modes of alternative splicing and a role of a specific class of repeat elements (transposons) in the origin/evolution of alternative exons. These features suggest diverse regulatory mechanisms and evolutionary paths for different modes of alternative splicing.
Contingency Fee Agreements with Represented Persons in Class Actions—An Undesirable Australian Phenomenon
Authors: Morabito Vince
Published: October 2005

Part IVA of the Federal Court of Australia Act 1976 (Cth), which has been regulating class actions in the Federal Court of Australia since 1992, is silent with respect to the crucial issue of whether the lawyers hired by the class representatives may enter into contingency fee agreements with such representatives and/or the persons on whose behalf the class proceedings are instituted, the class members. This silence was attributable to the Australian Government's rejection of the Australian Law Reform Commission's recommendation that the legislative regime governing class actions should expressly authorise and regulate the execution of contingency fee agreements by the class lawyers with the class representatives. As a result of several post–1992 statutes enacted by State Parliaments, lawyers hired by Part IVA plaintiffs have been able to follow the practice of executing contingency fee agreements with, not only the representative plaintiffs, but also the class members. The aim of this paper is to provide a critical analysis of this practice. It undertakes a review of the American and Canadian regimes governing the employment of contingency fee agreements in class proceedings as a part of this analysis.
Lost and Destroyed Evidence: The Search for a Principled Approach to Abuse of Process
Authors: Martinsp Sarah
Published: October 2005

This article examines the situation where evidence which the police were under a duty to obtain or retain, and which could have assisted the defendant's case at trial, is lost or destroyed. Its particular focus is the approach that should be followed when lost or destroyed evidence forms the basis for an application to stay proceedings as an abuse of process. The decision in R (on the application of Ebrahim) v Feltham Magistrates' Court; Mouat v DPP was a significant advance in this regard, for it clarified that the two categories of abuse case—cases where the defendant cannot receive a fair trial (Category 1) and cases where it would be unfair for the defendant to be tried (Category 2)—are analytically distinct, from which it follows that the defendant's right to a fair trial can be violated in the absence of any bad faith on the part of the police. An examination of the cases post- Ebrahim, however, reveals the same regrettable tendency that was evident in the pre- Ebrahim cases, namely a tendency to use the absence of bad faith as a justification for not staying the proceedings in a Category 1 case. On a more principled approach, it is the effects of the conduct of the police with which the court should be primarily concerned when considering whether the defendant can receive a fair trial, and the nature of this conduct which should be the focus when determining whether it would be unfair for the defendant to be tried.
Legal Advice Privilege and the Corporate Client
Authors: Loughrey Joan
Published: October 2005

This article considers the question of which corporate communications attract legal advice privilege. Specifically, it assesses the implications of adopting, on the one hand, a narrow ‘control group’ test and, on the other, a broad ‘dominant purpose’ test for determining the scope of privileged communications. The Court of Appeal's decision in Three Rivers DC v Governor and Company of the Bank of England (No. 5) is compared with approaches adopted in other jurisdictions, particularly the United States. It is concluded that both tests have identifiable shortcomings. However, in light of the human rights implications of applying a broad test, it may be preferable to opt for a restrictive approach to identifying the corporate client in this context.
Closing the Credibility Gap: The Prosecutorial Use of Expert Witness Testimony in Sexual Assault Cases
Authors: Ellison Louise
Published: October 2005

Recent Home Office research indicates that complainants in sexual offence cases still struggle to gain credibility in the eyes of police, prosecutors and jurors. This article examines some of the credibility barriers confronting victims of sexual offences within the criminal process. In the USA, prosecutors have utilised expert witness testimony in an effort to educate jurors and restore credibility to complainants' accounts. This article critically assesses these developments and explores the potential admissibility of ‘educational’ expert witness testimony in criminal courts in England and Wales.
Monitoring Success, Accounting for Failure: The Outcome of Prosecutors' Applications for Special Measures Directions under the Youth Justice and Criminal Evidence Act 1999
Authors: Roberts Paul , Cooper Debbie , Judge Sheelagh
Published: October 2005

This article presents and discusses new empirical data derived from CPS Monitoring of the implementation of special measures for vulnerable and intimidated witnesses (VIWs) pursuant to Part II of the Youth Justice and Criminal Evidence Act 1999. VIW Monitoring was a major undertaking, covering all CPS prosecutions in England and Wales for an entire calendar year. Its results are fully reported elsewhere. Here, we concentrate on one segment of VIW Monitoring data, reporting the outcomes of prosecutors' applications for special measures. Most such applications succeed, but a small minority is rejected, and the characteristics and reasons for these judicial refusals were recorded as part of the Monitoring process. By examining and reflecting upon the circumstances of abortive applications, no less than in contemplating the broader pattern of success which emerges from VIW Monitoring, we may hope to gain a better appreciation of the existing arrangements for securing special measures for vulnerable and intimidated witnesses, and to assess the scope, if any, for further refinements of policy or practice.
Matching Crimes Using Burglars' Modus Operandi: A Test of Three Models
Authors: Ewart B.W. , Oatley G.C. , Burn K.
Published: October 2005

’Hard’ forensic evidence (eg DNA) may be the best means of linking crimes, but it is often absent at burglary crime scenes. Modus operandi information is always present to some degree, but little is known of its significance in matching burglaries. This paper evaluates the ability of three algorithms to match a target crime to the actual offender within a database of 966 offences. The first (RCPA) uses only MO information, the second (RPAL) only temporal and geographic data and a third (COMBIN) is a combination of the two. A score of one indicates a perfect match between the target crime and the case selected by the algorithm. The lowest possible rank is 965 showing that 965 cases were selected before the target offence. The RPAL and COMBIN each achieve a perfect match for 24 per cent of the crimes and succeed in matching over half of the crimes at a score of 10 or less. For prolific offenders, using MO information alone is better than temporal and geographic data, although the best performance is achieved when in combination. Behavioural, spatial and temporal information is collected by many Police Services. The value and means of utilising such data in linking crimes is clearly demonstrated.
Recourse to Executive Coaching: The Mediating Role of Human Resources
Authors: Murphy Steven A.
Published: October 2005

This paper views the proliferation of executive coaching for developmental purposes as a sign of organisational deficits in the areas of leadership, mentoring, and formal training. Key coaching concepts are described in terms of their links to counselling psychology and are compared with foundational development activities to argue that coaching may be a facile response to more serious underlying deficiencies. A police organisation provides an interesting context to illustrate how coaching is uncritically embraced to bridge shortcomings in areas where human resource structures and processes should play a more active mediating role.
Accountable, Responsive and Independent: On the Need for Balance in Police Governance
Authors: Wood Dominic , MacAlister David
Published: October 2005

This paper considers the relevance of police independence in light of developments in police accountability mechanisms in the UK that encourage the police to be more locally responsive. It presents an argument concerning the need for balance in police governance between competing claims and interests. The paper notes the danger of exaggerated forms of accountability arising as a consequence of the inherent tensions within police governance, if the importance of a particular concern is overstated inappropriately at the expense of others. The current focus on being responsive at the expense of recognising the importance of police independence is presented as an example of such a danger. The paper acknowledges the extent to which traditional arguments in support of police independence have been criticised and accepts the need for the police to work interdependently with other bodies within the community. However, it is argued that this should not be interpreted to mean that police independence is redundant. Indeed, it is argued here that the more responsive the police are, the more important their independence becomes.
Should the Law of Theft Extend to Information?
Authors: Christie Anna Louise
Published: October 2005

This article discusses whether the criminal offence of theft should extend to include information or should remain limited to corporeal property. It considers the inherent problems in satisfying the requisite elements of the offence of theft in both Scots law and English law and assesses whether information is classifiable as property for the purposes of theft. The arguments for and against the proposition that information should be capable of being stolen are examined and a case for more comprehensive protection of information through criminal law is put forward. The article finally comments on the probability of legislative reform to remove the legal obstacles and compares the UK position to that of other jurisdictions.
Oral Cancer Plasma Tumor Marker Identified with Bead-Based Affinity-Fractionated Proteomic Technology
Authors: Cheng Ann-Joy , Chen Li-Chiu , Chien Kun-Yi , Chen Yin-Ju , Chang Joseph Tung-Chieh , Wang Hung-Ming , Liao Chun-Ta , Chen I-How
Published: October 2005

Background: There is no plasma marker for detecting oral cancer, one of the most frequent cancers worldwide. We developed a bead-based affinity-fractionated proteomic method to discover a novel plasma marker for oral cancer.

Methods: Affinity purification of heparinized plasma with magnetic beads and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis were used to screen potential oral cancer markers. We compiled MS protein profiles for 57 patients with oral cancer and compared them with profiles from 29 healthy controls. The spectra were analyzed statistically using flexAnalysis™ and ClinProt™ bioinformatic software. In each MS analysis, the peak intensities of interest were normalized with an internal standard (adrenocorticotropic hormone 18–39). For identification, affinity bead–purified plasma protein was subjected to MALDI TOF/TOF analysis followed by Mascot identification of the peptide sequences and a search of the National Center for Biotechnology Information protein database.

Results: To optimize MALDI-TOF analysis based on the best discriminator of the cancer and control spectra, copper-chelated beads were used for plasma protein profiling. The within- and between-run CVs for assays were <4% and 7%, respectively. Six markers that differentiated between cancer and control spectra were found, with mean (SD) molecular masses of 2664 (1), 2850 (1), 3250 (1), 7735 (2), 7927 (2), and 9240 (2) Da. The 2664-Da marker, identified as a fragment of the fibrinogen α-chain, had the highest sensitivity (100%) and specificity (97%) for cancer.

Conclusion: The high specificity and sensitivity of the fibrinogen α-chain fragment suggest that it may be a clinical useful tumor marker.
Role of Hippocampal Cav1.2 Ca2+Channels in NMDA Receptor-Independent Synaptic Plasticity and Spatial Memory
Authors: Moosmang Sven , Haider Nicole , Klugbauer Norbert , Adelsberger Helmuth , Langwieser Nicolas , Müller Jochen , Stiess Michael , Marais Else , Schulla Verena , Lacinova Lubica , Goebbels Sandra , Nave Klaus-Armin , Storm Daniel R. , Hofmann Franz , Kleppisch Thomas
Published: October 2005

Current knowledge about the molecular mechanisms of NMDA receptor (NMDAR)-independent long-term potentiation (LTP) in the hippocampus and its function for memory formation in the behaving animal is limited. NMDAR-independent LTP in the CA1 region is thought to require activity of postsynaptic L-type voltage-dependent Ca2+channels (Cav1.x), but the underlying channel isoform remains unknown. We evaluated the function of the Cav1.2 L-type Ca2+channel for spatial learning, synaptic plasticity, and triggering of learning-associated biochemical processes using a mouse line with an inactivation of theCACNA1C(Cav1.2) gene in the hippocampus and neocortex (Cav1.2HCKO). This model shows (1) a selective loss of protein synthesis-dependent NMDAR-independent Schaffer collateral/CA1 late-phase LTP (L-LTP), (2) a severe impairment of hippocampus-dependent spatial memory, and (3) decreased activation of the mitogen-activated protein kinase (MAPK) pathway and reduced cAMP response element (CRE)-dependent transcription in CA1 pyramidal neurons. Our results provide strong evidence for a role of L-type Ca2+channel-dependent, NMDAR-independent hippocampal L-LTP in the formation of spatial memory in the behaving animal and for a function of the MAPK/CREB (CRE-binding protein) signaling cascade in linking Cav1.2 channel-mediated Ca2+influx to either process.