bluuebunny/crossref_metadata_2025 huggingface dataset:
Synthetic DNA Aptamers to Detect Protein Molecular Variants in a High‐Throughput Fluorescence Quenching Assay
Authors: Fang Xiaohong , Sen Arup , Vicens Marie , Tan Weihong
Published: September 2003

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

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

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

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

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

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

The cover picture shows a living cell inside which a protein is labeled with fluorescein. The labeling is based on the unusual mechanism of the DNA repair protein O6‐alkylguanine‐DNA alkyltransferase (AGT, structure on the right), which irreversibly transfers the alkyl group from O6‐alkylguanine to its reactive cysteine residue. By using O6‐benzylguanine derivatives such as the fluorescein derivative shown, AGT fusion proteins can be covalently labeled in vivo. The method is one example of a growing number of approaches that aim at equipping proteins with functionalities that can not be genetically encoded, which opens up new ways to study proteins in vivo. Further information can be found in the article by N. Johnsson and K. Johnsson on p. 803 ff.
Direct Visualization of DNA Duplex Formation on the Surface of a Giant Liposome
Authors: Shohda Koh‐ichiroh , Toyota Taro , Yomo Tetsuya , Sugawara Tadashi
Published: September 2003

(http://dx.doi.org/10.1002/cbic.200300593)
Modeling of Styrene/Butadiene Co‐polymerization in Emulsion with Monte Carlo Simulation
Authors: Ghafelebashi Zarand S.M. , Pourmahdian S. , Afshar Taromi F. , Jabbari E. , Dabir B.
Published: September 2003

Emulsion polymerization is widely used to produce a variety of polymer latices such as paints and adhesives. The Monte Carlo method of simulation has been applied for the first time to styrene/butadiene co‐polymerization in emulsion, in a batch reactor. Polymer particle properties such as molecular weight distribution, particle size distribution, and tri‐ and tetra‐functional branching for emulsion co‐polymerization of styrene‐butadiene are predicted.
Membrane Contactors and Catalytic Membrane Reactors in Process Intensification
Authors: Drioli E. , Criscuoli A. , Curcio E.
Published: September 2003

The design and operation of large plants with steadily increasing production capacity remain the priority of the chemical industry. Since the ninteen eighties, indications regarding a social and economic trend adversely affecting sustainable development, suggested a requirement for the implementation of drastic policy measures. Membrane science and technology has the potential to make a substantial contribution to the development of sustainability pathways, thus providing reliable options for both industrial growth and environmental protection.
Reversible and Efficient Materials‐based Actuation by Electrolytic Phase Transformation
Authors: Cameron C.G. , Freund M.S.
Published: September 2003

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

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

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

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

The proliferation of wastewater treatment plants has become essential to ensure the protection of the natural environment. As a consequence, the production of waste by‐products, namely sewage sludge, has increased together with both the unit efficiency levels and with the number of wastewater treatment plants. Since dumping is no longer allowed in the EU, the processes mainly used to treat sewage sludge are agricultural spreading and incineration. However, due to the constant increase in production, it has became essential to find alternative methods of treatment. Considering the chemical composition of sludge, some new thermal processes of treatment have recently been considered by researchers. Thermal gasification is one method that could be of significant interest. Dried sludge composition is sufficiently close to the that of classical biomass (such as wood, rice, etc.) to make sludge treatment in a gasifier feasible. In this paper we discuss how gasification technologies could be transposed to the treatment and valorisation of sludge. Although this process seems attractive, it will also be demonstarted that much experimentation remains to be conducted on a laboratory and pilot scale.
In‐situ Measurement of Primary Particle Sizes during Carbon Black Production
Authors: Dankers S. , Leipertz A. , Will S. , Arndt J. , Vogel K. , Schraml S. , Hemm A.
Published: September 2003

During the production of carbon black monitoring of primary particle size plays an important role since this parameter determines product properties and is specified accordingly. For process control fast information about this size is absolutely necessary. In the work presented here it was investigated whether time‐resolved laser‐induced incandescence is suitable for on‐line measurement of primary particle sizes of carbon black during the production process. The results obtained experimentally in industrial production and test reactors were compared with values for the specific surface area from laboratory analyses of sampled material.
Gasification – An Opportunity to Design Environmentally Compatible Processes in the Chemical and Pulp & Paper Industry
Authors: Schingnitz M.
Published: September 2003

Production wastes and residues generated in particular in the chemical and pulp & paper industries are currently incinerated or recycled. A stricter environmental legislation and the general prohibition imposed on waste incineration in some countries suggest to open new ways of waste disposal and resource recovery. This work describes how residual and waste materials can not only be disposed of but also converted into a raw gas which can be further processed to obtain valuable materials and synthesis gas in strict compliance with environmental standards by using various modifications of an entrained‐flow gasification technology.
Penetration of Porous Systems by Nonwetting Liquids
Authors: Palzer S. , Sommer K. , Hiebl C.
Published: September 2003

Wetting of porous systems and the corresponding penetration of liquids into single capillaries is one of the most important processes in process engineering. Wetting liquids with a contact angle smaller than 90° are penetrating spontaneously into capillaries. The presented study demonstrates that, under certain conditions, even nonwetting liquids with contact angles larger than 90° can do so. Furthermore, it is shown that the time for such wetting processes can be calculated.
On‐line Determination of Nitrite in Water‐Miscible Cooling Lubricants
Authors: Hantelmann K. , Ulber R.
Published: September 2003

The determination of nitrite in water‐miscible cooling lubricants is problematic in so far as nitrite occurs in an emulsion instead of an aqueous solution. Accordingly, methods like photometry, ion chromatography or gas‐sensitive methods require multistage sample preparations and a large amount of equipment. In this paper, a simple and on‐line processable method for nitrite determination in water‐miscible cooling lubricants is presented. The determination is carried out potentiometrically by using an ion‐selective electrode.
Optimization of Pulse Cleaning Frequency During Bag Filter Operation
Authors: Krammer G. , Kavouras A. , Anzel A.
Published: September 2003

Particle removal from gas streams is effectively accomplished by jet‐pulsed bag filters that are usually operated between two preset pressure differences across the filter, the upper and the lower level. The optimal choice of these pressure levels is given, when the ratio of the time span of a filter cycle and the number of jet pulses per cleaning step reaches a maximum. Experiments were performed in a pilot plant bag filter unit. The analysis of the data obtained allows a simple estimation of the optimal range of operation for a given set of parameters of the pulse cleaning unit.
Rheologically Identical Behavior of Emulsions and Suspensions in Steady Shear Flow: Dimensional Analysis and Experimental Evidence
Authors: Teipel U. , Aksel N.
Published: September 2003

This study presents the key parameters that influence the rheological behavior of emulsions and suspensions subjected to steady shear flow. Emulsions and suspensions with nearly monomodal particle or droplet distributions were experimentally investigated to determine their material behavior in steady shear flow. A comparison of the results revealed that, under special conditions, the emulsions and suspensions subjected to steady shear flow exhibit identical rheological material behavior.
Influence of Droplet Collision on the Design of Flue‐Gas Desulfurization Scrubbers in Power Plant Technology
Authors: Feldkamp M. , Neumann J. , Fahlenkamp H.
Published: September 2003

In power plant technology modern gas scrubbers are used for the flue‐gas desulfurization of coal‐fired plants in order to absorb pollutants such as sulfur dioxide in aqueous solution. For this, the washing liquid is atomized by numerous spray nozzles. The interaction of nozzles and change of droplet spectra has still not been studied systematically. In this work the effect of droplet collision has been investigated. Special simulations performed lead to the conclusion that droplet collision is an important factor in the design of wet scrubbers which contributes to reduce the consumption of washing suspension and pump energy.
Product Design – The Interaction between Chemistry, Technology and Marketing to Meet Customer Needs
Authors: Rähse W. , Hoffmann S.
Published: September 2003

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

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

We studied at the light and electron microscopic levels the nitric oxide–producing neurons in the mouse claustrum. Nicotinamide adenine dinucleotide phosphate (NADPH)‐diaphorase histochemistry and neuronal nitric oxide synthase (nNOS) immunohistochemical staining were used to reveal putative nitrergic neurons. We also analyzed colocalization of nNOS with the inhibitory neurotransmitter γ‐aminobutyric acid (GABA) as well as the ontogenesis of the nNOS‐immunoreactive neurons, providing evidence for different populations of nitrergic neurons in the mouse claustrum. The general staining pattern was similar for the histochemical and the immunohistochemical methods, resulting in neuron and neuropil staining throughout the whole claustrum. We described two populations of nitric oxide–producing neurons in the mouse claustrum on the basis of a different level of nNOS expression. Densely nNOS‐stained neurons were mostly GABA immunoreactive, displayed ultrastructural features typically seen in aspiny neurons, and may originate in the subpallium; they were first seen in the claustrum at embryonic stage 17.5 and probably represent local inhibitory interneurons. Densely stained cells were found from rostral to caudal levels throughout the dorsal claustrum and the endopiriform nucleus. Lightly nNOS‐stained neurons, on the other hand, were more numerous than densely stained ones, especially in the dorsal claustrum. These claustral lightly stained cells, barely observed in the NADPH‐diaphorase reacted sections, were mostly non‐GABAergic, and appeared earlier during ontogenesis than densely stained cells (at embryonic stages 15.5–16.5). We suggest that these neurons are probably projection neurons. J. Comp. Neurol. 465:431–444, 2003. © 2003 Wiley‐Liss, Inc.
Estrogen increases the number of spinophilin‐immunoreactive spines in the hippocampus of young and aged female rhesus monkeys
Authors: Hao Jiandong , Janssen William G.M. , Tang Yong , Roberts Jeffrey A. , McKay Heather , Lasley Bill , Allen Patrick B. , Greengard Paul , Rapp Peter R. , Kordower Jeffrey H. , Hof Patrick R. , Morrison John H.
Published: September 2003

It is well documented that estrogen increases dendritic spine density in CA1 pyramidal cells of young female rats. However, this effect is attenuated in aged rats. We report here a quantitative analysis of estrogen effects on hippocampal spine number as visualized with antispinophilin in young (6–8 years old) and aged (19–23 years old) female rhesus monkeys, a species with a pattern of female endocrine senescence comparable to that of humans. Monkeys were ovariectomized and administered either vehicle or estradiol cypionate 3 months postovariectomy, followed by an additional dose 3 weeks later, with perfusion 24 hours after the last estrogen treatment. Immunolocalization of spinophilin, a spine‐associated protein, was used for quantitative stereologic analyses of total spinophilin‐immunoreactive spine numbers in CA1 stratum radiatum and the inner and outer molecular layers of dentate gyrus. In both young and aged female monkeys, the estrogen‐treated groups had an increase in spinophilin‐immunoreactive spines (37% in young, P < .005; 35% in aged, P < .05) compared with the untreated groups that amounted to more than 1 billion additional immunoreactive spines. The young group also showed a trend toward an estrogen‐induced increase in immunoreactive spines in the dentate gyrus outer molecular layer, but this effect was not statistically significant (P = .097). We conclude that spine number in the rhesus monkey hippocampus is highly responsive to estrogen, yet, unlike the female rat, aged female rhesus monkeys retain the capacity for spine induction in response to estrogen. These data have important implications for cognitive effects of estrogen replacement in postmenopausal women and demonstrate that an estrogen replacement protocol that mimics normal physiological cycles with timed, intermittent peaks can have profound neurobiological effects. J. Comp. Neurol. 465:540–550, 2003. © 2003 Wiley‐Liss, Inc.
Expression of vesicular glutamate transporter 1 in the mouse retina reveals temporal ordering in development of rod vs. cone and ON vs. OFF circuits
Authors: Sherry David M. , Wang Meng M. , Bates Jason , Frishman Laura J.
Published: September 2003

Glutamatergic transmission is crucial to the segregation of ON and OFF pathways in the developing retina. The temporal sequence of maturation of vesicular glutamatergic transmission in rod and cone photoreceptor and ON and OFF bipolar cell terminals is currently unknown. Vesicular glutamate transporters (VGLUTs) that load glutamate into synaptic vesicles are necessary for vesicular glutamatergic transmission. To understand better the formation and maturation of glutamatergic transmission in the rod vs. cone and ON vs. OFF pathways of the retina, we examined the developmental expression of VGLUT1 and VGLUT2 immunocytochemically in the mouse retina. Photoreceptor and bipolar cell terminals showed only VGLUT1‐immunoreactivity (‐IR); no VGLUT2‐IR was present in any synapses of the developing or adult retina. VGLUT1‐IR was first detected in cone photoreceptor terminals at postnatal day 2 (P2), several days before initiation of ribbon synapse formation at P4–P5. Rod terminals showed VGLUT1‐IR by P8, when they invade the outer plexiform layer (OPL) and initiate synaptogenesis. Developing OFF bipolar cell terminals showed VGLUT1‐IR around P8, 2–3 days after bipolar terminals were first identified in the inner plexiform layer (IPL) by labeling for the photoreceptor and bipolar cell terminal marker, synaptic vesicle protein 2B. Although terminals of ON bipolar cells were present in the IPL by P6–P8, most did not show VGLUT1‐IR until P8–P10 and increased dramatically from P12. These data suggest a hierarchical development of glutamatergic transmission in which cone circuits form prior to rod circuits in both the OPL and IPL, and OFF circuits form prior to ON circuits in the IPL. J. Comp. Neurol. 465:480–498, 2003. © 2003 Wiley‐Liss, Inc.
Phylogenetic changes in the expression of delta opioid receptors in spinal cord and dorsal root ganglia
Authors: Mennicken Françoise , Zhang Ji , Hoffert Cyrla , Ahmad Sultan , Beaudet Alain , O'Donnell Dajan
Published: September 2003

To assess the validity of rodent models for investigating the role of delta opioid receptors (DOR) in analgesia, the distribution of DOR binding and mRNA were compared between rodent and primate spinal cord and dorsal root ganglia (DRG), using receptor autoradiography and in situ hybridization, respectively. In mouse and rat spinal cord, [125I]‐deltorphin‐labeled DOR binding sites were detected throughout the gray matter. In contrast, in primate and particularly in human spinal cord, DOR binding was mainly present in laminae I–II, with little to no binding in deeper layers. Accordingly, in rodent spinal cord, DOR mRNA was expressed by a large number of neurons distributed throughout the ventral and dorsal horns, whereas in the primate, DOR expression was significantly lower, as evidenced by a moderate number of labeled cells throughout the gray matter in monkey and by only few labeled cells in human, mainly in Clarke's column and lamina IX. Major species differences in DOR expression were also observed in primary afferent cells bodies. In rat DRG, intense DOR mRNA hybridization was primarily observed over large ganglion cells immunopositive for neurofilament 200. In contrast, in monkey and human DRG, DOR mRNA was primarily detected over small and medium‐sized ganglion cells. These results demonstrate major differences in the expression and distribution of DOR in the spinal cord and DRG between mammalian species. Specifically, they point to a progressive specialization of DOR toward the regulation of primary somatosensory, namely nociceptive, inputs during phylogeny and suggest that the effects of DOR agonists in rodents may not be entirely predictive of their action in humans. J. Comp. Neurol. 465:349–360, 2003. © 2003 Wiley‐Liss, Inc.
Quantitative analysis of axon collaterals of single cells in layer III of the piriform cortex of the guinea pig
Authors: Chen Shaoyun , Murakami Kunio , Oda Satoko , Kishi Kiyoshi
Published: September 2003

Recent physiological and morphological studies suggest that the piriform cortex (PC) functions like the association areas of the neocortex rather than the typical primary sensory area as was previously assumed. The axon connection patterns of single cells are important for understanding the functional organization of the PC. The axon collaterals of three single pyramidal cells and one spiny multipolar cell in layer III of the PC were labeled and quantitatively analyzed by intracellular injections of biocytin in guinea pigs. The individual pyramidal and spiny multipolar cells have highly distributed axon collaterals, which display little tendency for patchy concentrations, within the PC and multiple higher order behavior/reward/contextual‐related areas, such as the prefrontal cortex, amygdaloid nuclei, and entorhinal cortex. For the pyramidal cells, the average length of axonal collaterals is 143 mm; the average number of boutons is 12,930. For the spiny multipolar cell, the length of the axonal collaterals is 88 mm; the number of boutons is 7,052. The pyramidal cells in the anterior subdivision of the PC (APC) have both rostrally and caudally directed intrinsic association fibers, whereas the pyramidal and spiny multipolar cells in the posterior subdivision (PPC) have predominantly caudally directed intrinsic association fibers in the PC. Our results reveal that the connection patterns of single cells in layer III resemble those of pyramidal cells in layer II, suggesting that the PC performs correlative functions analogous to those in the association area of other sensory systems. The rostrally‐to‐caudally directed connections in the APC provide a substrate for the recurrent process, whereas largely caudally directed connections in the PPC suggest the dominance of the feed‐forward process. J. Comp. Neurol. 465:455–465, 2003. © 2003 Wiley‐Liss, Inc.
CD15 immunoreactive amacrine cells in the mouse retina
Authors: Jakobs Tatjana C. , Ben Yixin , Masland Richard H.
Published: September 2003

The mouse retina has become an important model in vision research, mainly because of the wide availability of transgenic animals. In order to study cell function and connectivity in the inner retina, antibodies that differentially stain one cell type, or a small number of cell types, are helpful as markers. Here we characterize the CD15 (3[α1‐3]‐fucosyl‐N‐acetyl‐lactosamine)‐positive cells in the mouse retina using immunofluorescence confocal microscopy and reverse‐transcription polymerase chain reaction. CD15 immunoreactivity was observed in two distinct types of amacrine cells and, faintly, in some cone bipolar cells. Type I CD15+ amacrine cells are GABAergic wide‐field cells that stratify in lamina 3 and 4/5 of the inner plexiform layer. Type II CD15+ amacrine cells are also GABAergic and costratify with the dopaminergic tyrosine hydroxylase‐positive cells in lamina 1 of the inner plexiform layer. The densities of types I and II CD15+ amacrine cells in mid‐periphery were 258 cells/mm2 and 274 cells/mm2. Double labeling with several other markers for amacrine cell types showed that neither type belongs to another previously identified subpopulation of amacrine cells. Single‐cell RT‐PCR showed that CD15+ amacrine cells coexpress several AMPA receptors — GluR1, GluR2, and GluR4 being the most common combination. J. Comp. Neurol. 465:361–371, 2003. © 2003 Wiley‐Liss, Inc.
Localization of B1 bradykinin receptor mRNA in the primate brain and spinal cord: An in situ hybridization study
Authors: Shughrue Paul J. , Ky Betty , Austin Christopher P.
Published: September 2003

The bradykinin 1 and 2 receptors (B1R, B2R) are important mediators of cardiovascular homeostasis, inflammation, and nociception. While B2R is constitutively expressed in many tissues, B1R expression is thought to be absent, but induced under proinflammatory conditions. However, recent data from knockout mice have indicated that B1R acts centrally to mediate nociception, a finding that suggests the constitutive presence of B1R in brain and/or spinal cord. The purpose of the present study was to further elucidate the physiological role of B1R by evaluating the localization of B1R mRNA in the nonhuman primate brain and spinal cord with in situ hybridization. Cryostat sections from monkey brain and spinal cord were hybridized with a [35S]‐labeled riboprobe complementary to B1R mRNA, stringently washed, and apposed to film and emulsion. The results of these studies revealed the presence of B1R mRNA throughout the rostral‐caudal extent of the brain and spinal cord. In particular, labeled cells were seen in the cerebral and entorhinal cortex, dentate gyrus, and pyramidal neurons of the hippocampus, in the thalamus, hypothalamus, amygdala, pontine nuclei, spinal cord, and dorsal root ganglion. Together the present findings offer detailed information about the distribution of B1R mRNA in the primate brain and spinal cord and demonstrate a basal level of expression in the primate nervous system. Moreover, these data provide a foundation for understanding the central actions of kinins and their putative role in mediating a number of processes, including pain and nociception. J. Comp. Neurol. 465:372–384, 2003. © 2003 Wiley‐Liss, Inc.
Comparison of reorganization of the somatosensory system in rats that sustained forelimb removal as neonates and as adults
Authors: Bowlus Theodore H. , Lane Richard D. , Stojic Andrey S. , Johnston Molly , Pluto Charles P. , Chan Michael , Chiaia Nicolas L. , Rhoades Robert W.
Published: September 2003

Studies of sensory pathways in several species indicate that the extent and form of reorganization resulting from deafferentation early in life vs. adulthood are not the same. The reasons for such differences are not well understood. To gain further insight into age‐dependent mechanisms of reorganization, this study compared the consequences of neonatal vs. adult forelimb amputation in rats at multiple levels of the sensory pathway, including primary somatosensory cortex, brainstem, and dorsal root ganglia. At the cortical level, the average area of the functional forelimb‐stump representation from rats amputated as adults was significantly smaller (P < 0.05) than that of neonatally amputated rats (4.3 ± 1.3 mm2 vs. 6.6 ± 1.5 mm2, respectively). At the brainstem level, neonatally amputated rat cuneate neurons possessed the following responsivities: 20% stump responsive, 40% responsive to both stump and hindlimb, 30% responsive to another body region, and 10% unresponsive. In contrast, cuneate neurons of adult amputated rats were 70% stump responsive, 2% responsive to both stump and hindlimb, and 30% unresponsive. A significantly (P < 0.001) greater percentage of the C6‐C8 dorsal root ganglia neurons of adult amputated rats were unresponsive to peripheral stimulation vs. neurons from neonatally amputated rats (48% vs. 16%, respectively). These results indicate that the reorganization that occurs in response to forelimb amputation at birth vs. adulthood is distinctly different at each of these levels of the dorsal column–medial lemniscal pathway. Possible mechanisms to account for these differences are considered. J. Comp. Neurol. 465:335–348, 2003. © 2003 Wiley‐Liss, Inc.
Retinal ganglion cell projections to the hamster suprachiasmatic nucleus, intergeniculate leaflet, and visual midbrain: Bifurcation and melanopsin immunoreactivity
Authors: Morin Lawrence P. , Blanchard Jane H. , Provencio Ignacio
Published: September 2003

The circadian clock in the suprachiasmatic nucleus (SCN) receives direct retinal input via the retinohypothalamic tract (RHT), and the retinal ganglion cells contributing to this projection may be specialized with respect to direct regulation of the circadian clock. However, some ganglion cells forming the RHT bifurcate, sending axon collaterals to the intergeniculate leaflet (IGL) through which light has secondary access to the circadian clock. The present studies provide a more extensive examination of ganglion cell bifurcation and evaluate whether ganglion cells projecting to several subcortical visual nuclei contain melanopsin, a putative ganglion cell photopigment. The results showed that retinal ganglion cells projecting to the SCN send collaterals to the IGL, olivary pretectal nucleus, and superior colliculus, among other places. Melanopsin‐immunoreactive (IR) ganglion cells are present in the hamster retina, and some of these cells project to the SCN, IGL, olivary pretectal nucleus, or superior colliculus. Triple‐label analysis showed that melanopsin‐IR cells bifurcate and project bilaterally to each SCN, but not to the other visual nuclei evaluated. The melanopsin‐IR cells have photoreceptive characteristics optimal for circadian rhythm regulation. However, the presence of moderately widespread bifurcation among ganglion cells projecting to the SCN, and projection by melanopsin‐IR cells to locations distinct from the SCN and without known rhythm function, suggest that this ganglion cell type is generalized, rather than specialized, with respect to the conveyance of photic information to the brain. J. Comp. Neurol. 465:401–416, 2003. © 2003 Wiley‐Liss, Inc.
Deep Start: a hybrid strategy for automated performance problem searches
Authors: Roth Philip C. , Miller Barton P.
Published: September 2003

To attack the problem of scalability of performance diagnosis tools with respect to application code size, we have developed the Deep Start search strategy—a new technique that uses stack sampling to augment an automated search for application performance problems. Our hybrid approach locates performance problems more quickly and finds performance problems hidden from a more straightforward search strategy. The Deep Start strategy uses stack samples collected as a by‐product of normal search instrumentation to selectdeep starters, functions that are likely to be application bottlenecks. With priorities and careful control of the search refinement, our strategy gives preference to experiments on the deep starters and their callees. This approach enables the Deep Start strategy to find application bottlenecks more efficiently and more effectively than a more straightforward search strategy. We implemented the Deep Start search strategy in the Performance Consultant, Paradyn's automated bottleneck detection component. In our tests, Deep Start found half of our test applications' known bottlenecks between 32% and 59% faster than the Performance Consultant's current search strategy, and finished finding bottlenecks between 10% and 61% faster. In addition to improving the search time, Deep Start often found more bottlenecks than the call graph search strategy. Copyright © 2003 John Wiley & Sons, Ltd.
On the optimality of Feautrier's scheduling algorithm
Authors: Vivien Frédéric
Published: September 2003

Feautrier's scheduling algorithm is the most powerful existing algorithm for parallelism detection and extraction, but it has always been known to be suboptimal. However, the question as to whether it may miss some parallelism because of its design has not been answered. We show that this is not the case. Therefore, for an algorithm to find more parallelism than this algorithm, one needs to remove some of the hypotheses underlying its framework. Copyright © 2003 John Wiley & Sons, Ltd.
A self‐stabilizing token‐based k‐out‐of‐ℓ exclusion algorithm
Authors: Datta A. K. , Hadid R. , Villain V.
Published: September 2003

In this paper, we present the first self‐stabilizing solution to the k‐out‐of‐ℓ exclusion problem on a ring. The k‐out‐of‐ℓ exclusion problem is a generalization of the well‐known mutual exclusion problem—there are ℓ units of the shared resources, any process can request k $(1 \leq k \leq \ell)$ units of the shared resources, and no resource unit can be allocated to more than one process at one time. The space requirement of the proposed algorithm is independent of ℓ for all processors except a special processor, called Root. The stabilization time is only 5n, where n is the size of the ring. Copyright © 2003 John Wiley & Sons, Ltd.
Weak communication in single‐hop radio networks: adjusting algorithms to industrial standards
Authors: Jurdziński Tomasz , Kutyłowski Mirosław , Zatopiański Jan
Published: September 2003

Quite often algorithms designed for no‐collision‐detection radio networks use a hidden form of collision detection: it is assumed that a station can simultaneously send and listen. If it cannot hear its own message, apparently the message has been scrambled by another station sending at the same time.

Industrial standard IEEE 802.11 says that a station can either send or listen to a radio channel at a given time, but not both. In order to relate the industrial standard and theoretical algorithms we consider a weak radio network model with no collision detection in which a station cannot simultaneously send and receive signals. Otherwise we talk about a strong model.

In this paper we consider a measure called energy cost (or ‘power consumption’) which is equal to the maximum over all stations of the number of steps in which the station is sending or listening.

We show that computational power of weak and strong single‐hop radio networks differ substantially in the deterministic case: deterministic leader election requires $\Omega(\log n)$ energy cost in the weak model and can be solved by a practical algorithm with $O(\sqrt{\log n})$ energy cost in the strong model. By contrast, we present a very efficient randomized simulation of strong radio networks by weak ones, with preprocessing that requires $O(n)$ steps and has energy cost $O(\log \log n)$. Copyright © 2003 John Wiley & Sons, Ltd.
Performance analysis and qualitative results of an efficient parallel stochastic simulator for a marine host–parasite system
Authors: Langlais M. , Latu G. , Roman J. , Silan P.
Published: September 2003

We are interested in a host–parasite system, i.e. the sea bass–Diplectanum aequans system. A discrete mathematical model is used to describe the dynamics of both populations. Our goal is notably to validate the model in the context of aquaculture. A deterministic numerical simulator and, recently, a stochastic simulator were developed to study this biological system. Parallelization is required because the execution times are too long. The Monte Carlo algorithm of the stochastic simulator and its three levels of parallelism are described. Analysis and performances, up to 256 processors, of a hybrid MPI/OpenMP code are then presented for a cluster of symmetric multi‐processor (SMP) nodes. Qualitative results are given for the host–macroparasite system simulation. Copyright © 2003 John Wiley & Sons, Ltd.