bluuebunny/crossref_metadata_2025 huggingface dataset:
Seismic base‐isolation by use of a telescoping stepping mechanism
Authors: Martinez‐Rodrigo Maria D. , Luco J. Enrique
Published: December 2004

A new base‐isolation mechanism corresponding to a variance of the stepping A‐shaped frame is proposed and its seismic performance is investigated numerically for strong ground accelerations with peak values in the range from 0.5 to 1g. In its simplest two‐dimensional form, the system consists of a frame with two telescoping legs pinned at the apex at a sharp angle. The legs are attached to the foundation through a spring and a damper acting in parallel. Both the springs and viscous dampers have bilinear characteristics that make them very stiff in compression but very soft in tension. As the structure rocks sideways, the length of the loaded leg remains essentially constant while the length of the unloaded leg increases. When the ground acceleration changes direction, the process is reversed. The resulting system has three main characteristics: (i) as the structure steps on a rigid leg, the maximum acceleration that can be transmitted to the superstructure is limited to a value which is approximately independent of the amplitude of the ground motion; (ii) there is a systematic lifting of the superstructure with kinetic energy being systematically transformed into potential energy during the strong phase of the ground motion; and (iii) the system is slowly self‐centering at the end of the earthquake. The seismic performance of the system is evaluated for a tall bridge pier and for a smaller frame that could be used in a multi‐story building. The results obtained for the 1940 El Centro ground motion scaled to 1g and for the near‐field Rinaldi ground motion recorded during the Northridge earthquake show that substantial reductions of the absolute acceleration can be obtained with reasonable relative displacements of the superstructure and small strokes in the isolation devices. Copyright © 2004 John Wiley & Sons, Ltd.
A Green's function approach to deriving non‐reflecting boundary conditions in molecular dynamics simulations
Authors: Karpov E. G. , Wagner G. J. , Liu Wing Kam
Published: December 2004

Computer simulations of atomic scale processes in solids are often associated with the issue of spurious reflection of elastic waves at the boundaries of a molecular dynamics domain. In this paper, we propose an approach to emulate non‐reflecting boundary conditions in atomistic simulations of crystalline solids. Harmonic response of the outer, non‐simulated, region is accurately represented by a memory function, related to the lattice dynamics Green's function. The outward wave flow is cancelled due to work done by the corresponding response forces. Performance of method, dependent on a series of method parameters, is illustrated on a benchmark problem. Copyright © 2004 John Wiley & Sons, Ltd.
Electrosynthesis and characterization of o‐phenylenediamine oligomers
Authors: Angélica del Valle M , Díaz Fernando R , Bodini Mario E , Alfonso Geraldo , Soto Giovanny M , Borrego Euddy D
Published: December 2004

The contribution of electrochemical methods to the development of conducting polymers has been most relevant, although the electropolymerization mechanism has not yet been totally elucidated. The formation of a high‐density oligomeric region in the electrode–solution interface has been clearly established as formed by oligomers with different chain lengths. It has been confirmed that, depending on the variables governing the process (applied potential, electrolysis time, concentration, etc), it is possible to control to some extent the oligomer to be generated. In this present work, the electrosynthesis of oligomers of o‐phenylenediamine is proposed. A saturated solution of the monomer was electrolysed at 0.95 V versus SCE over 1 min, using stainless steel as the working electrode material. Under these conditions, a mixture of the dimer and tetramer, relatively easy to separate by thin layer chromatography, was deposited. The products were characterized by mass spectrometry, UV–vis spectroscopy, elemental analysis and 1H NMR spectroscopy. This approach allows the synthesis of oligomers in a fast and simple way. In addition, the product is directly obtained on the electrode surface, hence making its separation and purification very straightforward. Copyright © 2004 Society of Chemical Industry
Dependency of the shape memory properties of a polyurethane upon thermomechanical cyclic conditions
Authors: Hu Jin Lian , Ji Feng Long , Wong Yuen Wah
Published: December 2004

The relationship between the shape memory properties and thermomechanical cyclic conditions was investigated with a type of shape memory polyurethane (SMPU). The thermal and dynamic mechanical properties of the polyurethane were examined by using differential scanning calorimetry (DSC) and dynamic mechanical analysis (DMA). It was found that the SMPU exhibited good shape memory effects (SMEs) at deformation temperatures ranging from Tg to Tg + 25 °C. The strain recovery ratios increased with the increase of deformation speed and with the decrease in maximum strain. The recovery ratios also increased with increasing fixing speed. Therefore, in practical applications, in order to obtain better SMEs, the SMPU should be cooled to its frozen state as soon as possible after being deformed at a high temperature. The ‘fixity’ dramatically increased with the decrease in fixing temperature. To obtain optimal SMEs, the polymer has to be reheated up to the temperature at which the polymer deformed. In addition, the recovery ratios of the SMPU could increase slightly with the increase of recovery time. Copyright © 2004 Society of Chemical Industry
Density functional theory study of palladium‐catalyzed aryl‐nitrogen and aryl‐oxygen bond formation
Authors: Cundari Thomas R. , Deng Jun
Published: December 2004

A density functional theory study of the kinetics and thermodynamics of Pd‐phosphine‐catalyzed heteroatom bond formation $${\rm ArX} + {\rm REH}_n \mathrel{\mathop{\kern0pt\longrightarrow}\limits_{{\rm [Pd]}}} {\rm ArE}({\rm H})_{n - 1} {\rm R} + {\rm HX}$$ was carried out. Individual steps in the catalytic cycle—ArX oxidative addition, REHn coordination, HX loss and ArE(H)n−1R reductive elimination and β‐hydride elimination—were investigated. The effects of modification of the ligand (PH3 versus PMe3), leaving group (X = Cl versus X = Br), heteroatom substrate (REHn = H2O and NH3), aryl (Ar = phenyl, p‐cyanophenyl, p‐aminophenyl, pyridyl) and metal coordination number (Pd(PH3) versus Pd(PH3)2) were investigated. Copyright © 2004 John Wiley & Sons, Ltd.
Neutral polymer slow mode and its rheological correlate
Authors: O'Connell Robert , Hanson Helen , Phillies George D. J.
Published: December 2004

Quasi‐elastic light scattering spectroscopy intensity–intensity autocorrelation functions [S(k,t)] and static light scattering intensities of 1 MDa hydroxypropylcellulose in aqueous solutions were measured. With increasing polymer concentration, over a narrow concentration range, S(k,t) gained a slow relaxation. The transition concentration for the appearance of the slow mode (ct) was also the transition concentration for the solution‐like/melt‐like rheological transition (c+) at which the solution shear viscosity [ηp(c)] passed over from a stretched exponential to a power‐law concentration dependence. To a good approximation, we found ct[η] ≈ c+[η] ≈ 4, [η] being the intrinsic viscosity. The appearance of the slow mode did not change the light scattering intensity (I): from a concentration lower than ct to a concentration greater than ct, I/c fell uniformly with increasing concentration. The slow mode thus did not arise from the formation of compact aggregates of polymer chains. If the polymer slow mode arose from long‐lived structures that were not concentration fluctuations, the structures involved much of the dissolved polymer. At 25 °C, the mean relaxation rate of the slow mode approximately matched the relaxation rate for the diffusion of 0.2‐μm‐diameter optical probes observed with the same scattering vector. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 323–333, 2005
Phosphorylation of glycosyl‐phosphatidylinositol by phosphatidylinositol 3‐kinase changes its properties as a substrate for phospholipases
Authors: Jones David R. , Pañeda Covadonga , Villar Ana Victoria , Alonso Alicia , Goñi Félix M. , Bütikofer Peter , Brodbeck Urs , Shepherd Peter R. , Varela-Nieto Isabel
Published: December 2004

Phosphatidylinositol 3‐kinases (PI3K) phosphorylate the 3‐position of the inositol ring of phosphatidylinositol‐4,5‐bisphosphate to produce phosphatidylinositol‐3,4,5‐trisphosphate. It is not clear whether PI3K can phosphorylate the inositol group in other biomolecules. We sought to determine whether PI3K was able to use glycosyl‐phosphatidylinositol (GPI) as a substrate. This phospholipid may exist either in free form (GPIfree) or forming a lipid anchor (GPIanchor) for the attachment of extracellular proteins to the plasma membrane. We demonstrate the specific PI3K‐mediated phosphorylation of the inositol 3‐hydroxyl group within both types of GPI by incubating this phospholipid with immunoprecipitated PI3K. The phosphorylated product behaves in HPLC as a derivative of a PI3K lipid product. To our knowledge, this is the first demonstration that PI3K uses lipid substrates other than phosphoinositides. Further, we show that this has potential functional consequences. When GPIfree is phosphorylated, it becomes a poorer substrate for GPI‐specific phospholipase D, but a better substrate for phosphatidylinositol‐specific phospholipase C. These phosphorylation events may constitute the basis of a previously undescribed signal transduction mechanism.
Zinc‐α2‐glycoprotein, a lipid mobilizing factor, is expressed and secreted by human (SGBS) adipocytes
Authors: Bao Yi , Bing Chen , Hunter Leif , Jenkins John R. , Wabitsch Martin , Trayhurn Paul
Published: December 2004

Zinc‐α2‐glycoprotein (ZAG), a lipid mobilizing factor, is expressed in mouse adipose tissue and is markedly upregulated in mice with cancer cachexia. We have explored whether ZAG is expressed and secreted by human adipocytes, using SGBS cells, and examined the regulation of ZAG expression. ZAG mRNA was detected by RT‐PCR in mature human adipocytes and in SGBS cells post‐, but not pre‐, differentiation to adipocytes. Relative ZAG mRNA levels increased rapidly after differentiation of SGBS cells, peaking at day 8 post‐induction. ZAG protein was evident in differentiated adipocytes (by day 3) and also detected in the culture medium (by day 6) post‐induction. The PPARγ agonist rosiglitazone induced a 3‐fold increase in ZAG mRNA level, while TNF‐α led to a 4‐fold decrease. Human adipocytes express and secrete ZAG, with ZAG expression being regulated particularly through TNF‐α and the PPARγ nuclear receptor. ZAG is a novel adipokine, which may be involved in the local regulation of adipose tissue function.
The co‐translational folding and interactions of nascent protein chains: a new approach using fluorescence resonance energy transfer
Authors: Johnson Arthur E.
Published: December 2004

During protein biosynthesis, a nascent protein is exposed to multiple environments and proteins both inside and outside the ribosome that influence nascent chain folding and trafficking. Fluorescence resonance energy transfer between two dyes incorporated into a single nascent chain using aminoacyl‐tRNA analogs can directly and selectively monitor changes in nascent chain conformation. This approach recently revealed the existence and functional ramifications of ribosome‐mediated folding of nascent membrane proteins inside the ribosome and can be extended to characterize the effects of chaperones and other proteins and ligands on nascent protein folding, interactions, assembly, and avoidance of misfolding and degradation.
Different role of functional domains of hTR in DNA binding to telomere and telomerase reconstruction
Authors: Yeo M. , Rha S.Y. , Jeung H.C. , Shen X.H. , Yang S.H. , An S.W. , Roh J.K. , Chung H.C.
Published: December 2004

Even if template sequence of hTR played an essential role in telomere binding, a 326 nucleotide fragment of hTR containing template, pseudoknot, and CR4–5 domains is critical for both binding with telomeric DNA and reconstitution of telomerase activity. A functional study with antisense oligonucleotides suggested that targeted disruption of the template region efficiently abrogated both telomeric DNA binding and telomerase activity, whereas disruption of the CR4–5 region induced only loss of telomerase activity. hTR interacts with telomeric DNA via structural region composed of the template, pseudoknot, and CR4–5 domains, however, each structural domain plays a distinct role in telomere binding and telomerase activity reconstitution.
IkB‐α‐specific transcript regulation by the C‐terminal end of c‐Rel
Authors: Iwai Kazuyuki , Lee Byung Rho , Hashiguchi Masaaki , Fukushima Atsuki , Iwashima Makio
Published: December 2004

The NF‐kB family transcription factor c‐Rel is a critical molecule for inducing expression of cytokine genes by T cells. Here, we report that a deletion of the C‐terminal end, similar to the deletion in the highly oncogenic chicken v‐Rel gene, renders c‐Rel hyperactive toward cytokine gene promoters. At the same time, this mutation dramatically reduced c‐Rel activity in induction of IkB‐α mRNA expression. Moreover, ectopic expression of IkB‐α, along with the C‐terminal truncated c‐Rel, abrogates hyperactivity of this mutant. IkB‐α co‐expression did not affect the function of wild‐type c‐Rel. The data demonstrate that the C‐terminal end of c‐Rel has specific activity for IkB‐α mRNA expression and is dispensable for IL‐2 gene expression.
Reproduction and seasonal occurrence of the copper shark, Carcharhinus brachyurus, from north Patagonia, Argentina
Authors: Lucifora Luis O. , Menni Roberto C. , Escalante Alicia H.
Published: December 2004

The copper shark, Carcharhinus brachyurus, is the only member of its genus with a preferred habitat in temperate waters, and it usually gives birth in the cooler extremes of its range. Maturation patterns, reproductive condition, monthly sex ratios, and seasonal occurrence of copper sharks were analysed, mostly from Anegada Bay (Argentina), a presumed nursery area for the species. Males mature between 200 and 220 cm total length (LT), with a 50% size at maturity (L50) of 216.18 cm LT. Females mature between 215 and 223 cm LT (with an L50 of 222.16 cm LT). Maturity off Argentina is at a slightly smaller size than off South Africa and Australia. There is no sexual dimorphism in size at maturity. Only two pregnant females, each carrying 16 advanced embryos, were caught. The hepatosomatic index (IH) of adult males showed significant monthly changes, related possibly to an increase in the gonadosomatic index (IG). IH and IG of adult females showed no significant trend throughout the fishing season. The IH of adult females was significantly correlated with maximum diameter of ovarian follicles. Small translucent ovarian follicles in two gravid females indicated that ovarian and gestation cycles run sequentially, with maturation of oocytes subsequent to parturition. Neither newborns nor significant numbers of females bearing term embryos were recorded, and there was no evidence of a copper shark primary nursery area in Anegada Bay. However, most copper sharks in Anegada Bay were large juveniles and sub-adults. The species is found off Argentina from October to late March, but they do not move southwards to Anegada Bay until December, and they leave the bay again by April. These movements appear to be related more to water temperature rather than to migration of potential prey. Monthly variation in sex ratios is associated mainly with fluctuations in the sex ratios of juveniles.
Closed mitral valvotomy in pregnancy and labor
Authors: Aggarwal N. , Suri V. , Goyal A. , Malhotra S. , Manoj R. , Dhaliwal R.S.
Published: December 2004

Objective

To study the feasibility and benefits of closed mitral valvotomy (CMV) during pregnancy.

Design

Prospective study from 2000 through 2003 to study the effect on maternal condition and perinatal outcome of closed mitral valvotomy during pregnancy were evaluated.

Methods

Eight pregnant women with severe mitral stenosis refractory to medical therapy had closed mitral valvotomy at different stages of pregnancy (one during labor).

Results

All patients improved clinically (according to the New York Heart Association classification), and the mitral valve area increased. There was no mortality or major morbidity.

Conclusion

Closed mitral valvotomy offers excellent results and is cost effective during pregnancy. It is still the procedure of choice in poor countries when balloon mitral valvotomy (BMV) is not affordable.
Product architecture assessment: a tool to link product, process, and supply chain design decisions
Authors: Fixson Sebastian K.
Published: December 2004

Increasingly heterogeneous markets, together with shorter product life cycles, are forcing many companies to simultaneously compete in the three domains of product, process, and supply chain. Dependencies among decisions across these domains make this competitive situation very complex. To address this complexity, three‐dimensional concurrent engineering (3D‐CE) has been suggested ([Fine, C.H., 1998. Clockspeed—Winning Industry Control in the Age of Temporary Advantage. Perseus Books, Reading, MA.]). Applying 3D‐CE requires an operationalization of one of its core elements: the product architecture. In this paper, I develop a multi‐dimensional framework that enables comprehensive product architecture assessments. The framework builds on existing product characteristic concepts such as component commonality, product platforms, and product modularity. The framework's utility is illustrated with two example products, showing how individual product architecture dimensions link decisions across different domains. This framework can be used to focus advice for product design on product architecture dimensions that are critical for a given operational strategy, to assess advantages and limitations of operational strategies in conjunction with given product architectures, or to develop dynamic capabilities such as planning effective product–operation strategy combinations.
Entrepreneurial orientation as a basis for classification within a service industry: the case of retail pharmacy industry
Authors: Jambulingam Thanigavelan , Kathuria Ravi , Doucette William R.
Published: December 2004

To date, service classification research has primarily taken a macro view, creating service typologies or taxonomies by using dimensions such as customer contact or degree of labor intensity. Such classification schemes, though helpful in deciphering critical management issues and positioning strategies between service industries, tend to treat an entire industry, such as airlines, as a single homogenous entity. However, organizations in the same industry often use intangible resources, such as entrepreneurial orientation processes, to compete with one another. Resource‐advantage theory suggests that organizations utilize intangible resources to build long‐term strategies and a sustainable competitive advantage leading to superior performance. We developed organization clusters based on entrepreneurial orientation as intangible resources to classify organizations within a retailing industry. Using data from the retail pharmacy industry, we tested if the entrepreneurial orientations of the resultant groups within the pharmacy industry were related to their perception of the environment, organizational factors, and performance outcomes. The operationalization of the construct of entrepreneurial orientation is one of the contributions of the study.
Cell traffic between donor and recipient following rat limb allograft
Authors: Muramatsu Keiichi , Kurokawa Yoko , You‐Xin Song , Bishop Allen T. , Doi Kazuteru
Published: December 2004

Although cell traffic from the graft into the recipient and from the recipient into the graft had been noticed in allogeneic organ transplantation, little is known following whole‐limb allografting. This study was conducted to define cell migration between donor and recipient. Sixty‐seven vascularized hind limb allotransplantations were performed in rat sex‐mismatched pairs and the recipient animals were treated with FK506 immunosuppression. The ratio of donor and recipient cells was evaluated by semi‐quantitative PCR using the specific primers of the Y‐chromosome. Allografted limbs had no rejection episode until the final assessment. The male recipient cells were detected in female limb grafts not at 1 week but at 48 weeks after transplantation. The male donor cells were detected in the humerus and tibia in the female recipient but not in the gastrocnemius muscle and leg skin. Our results demonstrated that recipient‐derived cells gradually migrated into the grafted bone, muscle and skin cells with the duration of time. Donor‐derived cells migrated into the healthy bones but not into the healthy muscle and skin. Because active regeneration occurs in the grafted limb to compensate graft damage secondary to ischemia and operative intervention, recipient‐derived cells may mediate a muscular and dermo‐epidermal renewal. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Development of an individual‐specific autoantibody (ISA) protein microarray
Authors: Lebrun Stewart J. , Suquilanda Edgar , Petchpud Wasinee N.
Published: December 2004

We have developed an ISA (individual‐specific autoantibody) identification method to identify biological samples based on an individual's unique class of autoantibodies. This method involved the presentation of human proteins derived from crude lysates after SDS/PAGE separation and transferance to a solid support. In the present study, ISA strips are produced and developed on a new protein microarray. In making the ISA strips, it was found that variation in protein migration during electrophoresis and strip‐manufacturing quality control limit the reliability of the assay. Therefore it was decided to semi‐purify and separate proteins by column chromatography in large batches and to develop an ISA‐specific protein microarray. It was found that this ISA protein microarray approximates a similar serum titre as the ISA strip and is predicted to circumvent the batch‐to‐batch production issues related to SDS/PAGE.
Multiplex PCR–single‐base extension genotyping of multiple glutathione S‐transferase polymorphisms
Authors: Faber Ana , Ferreira Guilherme N. M. , Silva Susana N. , Rueff José , Gaspar Jorge
Published: December 2004

Identification of genetic polymorphisms has recently gained increased interest, since they can be used as markers to identify the genes that predispose to disease. This emerging role of genetic polymorphism in clinical association has created the need for high‐throughput genotyping methodologies. The present study describes the development of an SBE (single‐base extension) methodology for the parallel identification of genetic polymorphisms in glutathione S‐transferase genes, a superfamily of phase II drug‐metabolizing enzymes. Oligonucleotide PCR primers were designed for simultaneous amplification of GSTM1, GSTP1 and GSTT1 gene loci SBE primers were also designed to be specific for each loci and to stop one nucleotide 5′‐upstream of the polymorphic location. A specific tag was associated with each SBE primer to guarantee further discrimination by length. After simultaneous amplification of the target gene loci from genomic DNA extracted from human blood samples, SBE reactions were performed with fluorescently labelled dideoxynucleotide triphosphates. Individual genotypes were identified after separation of each tag‐SBE probe by PAGE. The multiplex/SBE methodology was validated with previously genotyped DNA samples extracted from 21 individuals and it was used in a blind assay to genotype additional 64 individuals. The results show that SBE leads to the same results as the current ‘gold standard’ restriction‐fragment‐length‐polymorphism‐based genotyping methodologies, since SBE is a robust and accurate genotyping methodology that enables the parallel identification of multiple polymorphisms in the same reaction.
Batch cooling crystallization and pressure filtration of sulphathiazole: the influence of solvent composition
Authors: Häkkinen Antti , Pöllänen Kati , Karjalainen Milja , Rantanen Jukka , Louhi‐Kultanen Marjatta , Nyström Lars
Published: December 2004

Currently there is a great interest in new process analytical approaches to increase the process understanding of pharmaceutical unit operations. In the present study, the influence of the solvent composition on the material properties and, further, on the filtration characteristics, of different crystal suspensions obtained through an unseeded batch‐cooling‐crystallization process was studied. Sulphathiazole, which is an antibiotic agent with multiple polymorphic forms, was produced by performing laboratory‐scale cooling crystallization experiments from five different mixtures of water and propan‐1‐ol (n‐propanol). The size, shape and polymorphic composition of the crystals produced were characterized with a scanning electron microscope, with a novel automated image analyser and with an X‐ray powder diffractometer. All of the monitored crystal properties were found to clearly differ between the samples obtained from different solvents. The crystals produced in the batch‐cooling‐crystallization experiments were separated from the crystallizing solvents using a batch‐type pressure Nutsche filter, and the filtration characteristics of the suspensions were evaluated on the basis of average filter‐cake porosities and average specific cake resistances, which were determined from the experimentally obtained filtration data. Comparison between the calculated filtration characteristics revealed that considerable differences existed between the different suspensions, and it could therefore be concluded that the pressure‐filtration process was influenced by the composition of the crystallizing solvent. The filterability of all the studied sulphathiazole suspensions was considered to be rather good on the basis of the relatively low cake porosities (0.51–0.63), which were accompanied with low average specific cake resistances [(8.7×107)–(1.2×109) m/kg].
Thermostable β‐cyclodextrin conjugates of two similar plant amine oxidases and their properties
Authors: Šebela Marek , Kopečný David , Lamplot Zbyněk , Havliš Jan , Thomas Henrik , Shevchenko Andrej
Published: December 2004

Syntheses of conjugates of garden pea (Pisum sativum) and grass pea (Lathyrus sativus) amine oxidases (PSAO and GPAO respectively) with BCD (β‐cyclodextrin), performed to improve the thermostability of the enzymes, are described in the present study. Periodate‐oxidized BCD reacted with the enzyme proteins via free primary amino groups in a buffered solution containing cyanoborohydride as a reductant. Although the specific activities of PSAO and GPAO partially decreased after modification, Km values determined for the best diamine substrates remained almost unchanged. Both the BCD conjugates could be incubated at 65 °C for 30 min without considerable inactivation, and the residual activity remained detectable even after incubation at 75 °C. The conjugates contained approx. 30% of neutral sugars. Molecular masses of BCD–PSAO and BCD–GPAO (180 kDa), as estimated by gel‐permeation chromatography, were higher compared with the value of 145 kDa for the native enzymes. This was in good correlation with the number of modified lysine residues determined by a spectrophotometric method. Peptide mass fingerprints of tryptic digests of BCD–PSAO and BCD–GPAO were less specific than those of the native enzymes when compared with the database sequence of PSAO. As a consequence of the modification, many unidentified peaks were observed in the digests of the studied conjugates that were not seen in the digests of native PSAO and GPAO. Only some of these peaks overlapped between BCD–PSAO and BCD–GPAO. The BCD conjugates described in the present study represent suitable candidates for biotechnological applications, e.g. in analyses using biosensors, which might benefit from increased storage stability and amine oxidation at high temperatures.
A vaccination strategy consisting of Semliki‐Forest‐virus (SFV) DNA prime and fowlpox‐virus boost significantly protects mice from a recombinant (HIV‐1) vaccinia‐virus infection
Authors: Quintana‐Vázquez Diógenes , Vázquez‐Blomquist Dania M. , Rodríguez Ernesto Galbán , Buch Antonieta M. Herrera , Cano Carlos A. Duarte
Published: December 2004

The use of DNA vectors based on the SFV (Semliki Forest virus) replicon have not been reported in the modality of DNA prime virus boost. In the present study, SFV DNA vectors (DNA vectors based on the SFV replicon) bearing the HIV‐1 TAB9 multiepitopic polypeptide minigene were evaluated as priming DNA immunogens followed by a recombinant fowlpox expressing the TAB9 mutiepitope (FPTAB9LZ) boost. The results indicated that mice primed with pSFV(k)tab9 and boosted with FPTAB9LZ significantly decreased the HIV‐1 recombinant (VVTAB13, a recombinant vaccinia virus expressing the TAB13 multiepitope) vaccinia virus replication, compared with groups given pSFV(k)tab9 vector and FPTAB9LZ virus alone. Additionally, the viral titre in ovary correlated with the number of specific γ‐interferon‐secreting T‐cells in spleen. These results support the possible use of SFV DNA vectors in prime‐boost approaches implemented in therapeutic/prophylactic treatments for infectious diseases such as HIV‐1.
Insulin activates the rat sterol-regulatory-element-binding protein 1c (SREBP-1c) promoter through the combinatorial actions of SREBP, LXR, Sp-1 and NF-Y cis-acting elements
Authors: CAGEN Lauren M. , DENG Xiong , WILCOX Henry G. , PARK Edwards A. , RAGHOW Rajendra , ELAM Marshall B.
Published: December 2004

The enhanced synthesis of fatty acids in the liver and adipose tissue in response to insulin is critically dependent on the transcription factor SREBP-1c (sterol-regulatory-element-binding protein 1c). Insulin increases the expression of the SREBP-1c gene in intact liver and in hepatocytes cultured in vitro. To learn the mechanism of this stimulation, we analysed the activation of the rat SREBP-1c promoter and its truncated or mutated congeners driving a luciferase reporter gene in transiently transfected rat hepatocytes. The rat SREBP-1c promoter contains binding sites for LXR (liver X receptor), Sp1, NF-Y (nuclear factor-Y) and SREBP itself. We have found that each of these sites is required for the full stimulatory response of the SREBP-1c promoter to insulin. Mutation of either the putative LXREs (LXR response elements) or the SRE (sterol response element) in the proximal SREBP-1c promoter reduced the stimulatory effect of insulin by about 50%. Insulin and the LXR agonist TO901317 increased the association of SREBP-1 with the SREBP-1c promoter. Ectopic expression of LXRα or SREBP-1c increased activity of the SREBP-1c promoter, and this effect is further enhanced by insulin. The Sp1 and NF-Y sites adjacent to the SRE are also required for full activation of the SREBP-1c promoter by insulin. We propose that the combined actions of the SRE, LXREs, Sp1 and NF-Y elements constitute an insulin-responsive cis-acting unit of the SREBP-1c gene in the liver.
A cryptic matrix targeting signal of the yeast ADP/ATP carrier normally inserted by the TIM22 complex is recognized by the TIM23 machinery
Authors: VERGNOLLE Maïlys A. S. , SAWNEY Helen , JUNNE Tina , DOLFINI Luisita , TOKATLIDIS Kostas
Published: December 2004

The yeast ADP/ATP carrier (AAC) is a mitochondrial protein that is targeted to the inner membrane via the TIM10 and TIM22 translocase complexes. AAC is devoid of a typical mitochondrial targeting signal and its targeting and insertion are thought to be guided by internal amino acid sequences. Here we show that AAC contains a cryptic matrix targeting signal that can target up to two thirds of the N-terminal part of the protein to the matrix. This event is coordinated by the TIM23 translocase and displays all the features of the matrix-targeting pathway. However, in the context of the whole protein, this signal is ‘masked’ and rendered non-functional as the polypeptide is targeted to the inner membrane via the TIM10 and TIM22 translocases. Our data suggest that after crossing the outer membrane the whole polypeptide chain of AAC is necessary to commit the precursor to the TIM22-mediated inner membrane insertion pathway.
Contribution of the two conserved tryptophan residues to the catalytic and structural properties of Proteus mirabilis glutathione S-transferase B1-1
Authors: ALLOCATI Nerino , MASULLI Michele , PIETRACUPA Marilena , FAVALORO Bartolo , FEDERICI Luca , DI ILIO Carmine
Published: December 2004

PmGSTB1-1 (Proteus mirabilis glutathione S-transferase B1-1) has two tryptophan residues at positions 97 and 164 in each monomer. Structural data for this bacterial enzyme indicated that Trp97 is positioned in the helix α4, whereas Trp164 is located at the bottom of the helix α6 in the xenobiotic-binding site. To elucidate the role of the two tryptophan residues they were replaced by site-directed mutagenesis. Trp97 and Trp164 were mutated to either phenylalanine or alanine. A double mutant was also constructed. The effects of the replacement on the activity, structural properties and antibiotic-binding capacity of the enzymes were examined. On the basis of the results obtained, Trp97 does not seem to be involved in the enzyme active site and structural stabilization. In contrast, different results were achieved for Trp164 mutants. Conservative substitution of the Trp164 with phenylalanine enhanced enzyme activity 10-fold, whereas replacement with alanine enhanced enzyme activity 17-fold. Moreover, the catalytic efficiency for both GSH and 1-chloro-2,4-dinitrobenzene substrates improved. In particular, the catalytic efficiency for 1-chloro-2,4-dinitrobenzene improved for both W164F (Trp164→Phe) and W164A by factors of 7- and 22-fold respectively. These results are supported by molecular graphic analysis. In fact, W164A presented a more extensive substrate-binding pocket that could allow the substrates to be better accommodated. Furthermore, both Trp164 mutants were significantly more thermolabile than wild-type, suggesting that the substitution of this residue affects the overall stability of the enzyme. Taken together, these results indicate that Trp164 is an important residue of PmGSTB1-1 in the catalytic process as well as for protein stability.
The BIR domain of IAP-like protein 2 is conformationally unstable: implications for caspase inhibition
Authors: SHIN Hwain , RENATUS Martin , ECKELMAN Brendan P. , NUNES Viviane A. , SAMPAIO Claudio A. M. , SALVESEN Guy S.
Published: December 2004

Several IAP (inhibitor of apoptosis) proteins regulate cell fate decisions, and the X-linked IAP (XIAP) does so in part by inhibiting caspases, proteases that execute the apoptotic pathway. A tissue-specific homologue of XIAP, known as ILP2 (IAP-like protein 2), has previously been implicated in the control of apoptosis in the testis by direct inhibition of caspase 9. In examining this protein we found that the putative caspase 9 interaction domain is a surprisingly weak inhibitor and is also conformationally unstable. Comparison with the equivalent domain in XIAP demonstrated that the instability is due to the lack of a linker segment N-terminal to the inhibitory BIR (baculovirus IAP repeat) domain. Fusion of a 9-residue linker from XIAP to the N-terminus of ILP2 restored tight caspase 9 inhibition, dramatically increased conformational stability and allowed crystallization of the ILP2 BIR domain in a form strikingly similar to the XIAP third BIR domain. We conclude that ILP2 is an unstable protein, and cannot inhibit caspase 9 in a physiological way on its own. We speculate that ILP2 requires assistance from unidentified cellular factors to be an effective inhibitor of apoptosis in vivo.
Engineering ML-IAP to produce an extraordinarily potent caspase 9 inhibitor: implications for Smac-dependent anti-apoptotic activity of ML-IAP
Authors: VUCIC Domagoj , FRANKLIN Matthew C. , WALLWEBER Heidi J. A. , DAS Kanad , ECKELMAN Brendan P. , SHIN Hwain , ELLIOTT Linda O. , KADKHODAYAN Saloumeh , DESHAYES Kurt , SALVESEN Guy S. , FAIRBROTHER Wayne J.
Published: December 2004

ML-IAP (melanoma inhibitor of apoptosis) is a potent anti-apoptotic protein that is strongly up-regulated in melanoma and confers protection against a variety of pro-apoptotic stimuli. The mechanism by which ML-IAP regulates apoptosis is unclear, although weak inhibition of caspases 3 and 9 has been reported. Here, the binding to and inhibition of caspase 9 by the single BIR (baculovirus IAP repeat) domain of ML-IAP has been investigated and found to be significantly less potent than the ubiquitously expressed XIAP (X-linked IAP). Engineering of the ML-IAP-BIR domain, based on comparisons with the third BIR domain of XIAP, resulted in a chimeric BIR domain that binds to and inhibits caspase 9 significantly better than either ML-IAP-BIR or XIAP-BIR3. Mutational analysis of the ML-IAP-BIR domain demonstrated that similar enhancements in caspase 9 affinity can be achieved with only three amino acid substitutions. However, none of these modifications affected binding of the ML-IAP-BIR domain to the IAP antagonist Smac (second mitochondrial activator of caspases). ML-IAP-BIR was found to bind mature Smac with low nanomolar affinity, similar to that of XIAP-BIR2-BIR3. Correspondingly, increased expression of ML-IAP results in formation of a ML-IAP–Smac complex and disruption of the endogenous interaction between XIAP and mature Smac. These results suggest that ML-IAP might regulate apoptosis by sequestering Smac and preventing it from antagonizing XIAP-mediated inhibition of caspases, rather than by direct inhibition of caspases.
K+ channel types targeted by synthetic OSK1, a toxin fromOrthochirus scrobiculosusscorpion venom
Authors: MOUHAT Stéphanie , VISAN Violeta , ANANTHAKRISHNAN S. , WULFF Heike , ANDREOTTI Nicolas , GRISSMER Stephan , DARBON Hervé , DE WAARD Michel , SABATIER Jean-Marc
Published: December 2004

OSK1 (α-KTx3.7) is a 38-residue toxin cross-linked by three disulphide bridges that was initially isolated from the venom of the Asian scorpion Orthochirus scrobiculosus. OSK1 and several structural analogues were produced by solid-phase chemical synthesis, and were tested for lethality in mice and for their efficacy in blocking a series of 14 voltage-gated and Ca2+-activated K+ channels in vitro. In the present paper, we report that OSK1 is lethal in mice by intracerebroventricular injection, with a LD50 (50% lethal dose) value of 2 μg/kg. OSK1 blocks Kv1.1, Kv1.2, Kv1.3 channels potently and KCa3.1 channel moderately, with IC50 values of 0.6, 5.4, 0.014 and 225 nM respectively. Structural analogues of OSK1, in which we mutated positions 16 (Glu16→Lys) and/or 20 (Lys20→Asp) to amino acid residues that are conserved in all other members of the α-KTx3 toxin family except OSK1, were also produced and tested. Among the OSK1 analogues, [K16,D20]-OSK1 (OSK1 with Glu16→Lys and Lys20→Asp mutations) shows an increased potency on Kv1.3 channel, with an IC50 value of 0.003 nM, without loss of activity on KCa3.1 channel. These data suggest that OSK1 or [K16,D20]-OSK1 could serve as leads for the design and production of new immunosuppressive drugs.
Investigation of structure of liquid 2,2,2 trifluoroethanol: Neutron diffraction, molecular dynamics, and ab initio quantum chemical study
Authors: Bakó Imre , Radnai Tamás , Bellisent Funel Marie Claire
Published: December 2004

The molecular conformation and intermolecular H bonding in liquid 2,2,2 trifluoroethanol (TFE) have been studied by neutron diffraction with hydrogen/deuterium isotopic substitution at room temperature. For comparison, conformations of molecules and their dimers in the gas phase have also been calculated, based on the density functional theory. Energies, geometry, and vibrational frequencies of dimers were analyzed. Diffraction data analyzed by the “Monte Carlo determination of g(r)” (MCGR) method resulted in a molecular structure in agreement with the findings from gas phase electron diffraction experiments and density functional calculations. The intermolecular structure functions were compared to the same functions obtained from a molecular dynamics simulation. All of the composite radial distribution functions are in good agreement with the simulation results. According to our calculation the hydrogen-bonded aggregation size is smaller in pure liquid TFE than in pure liquid ethanol.
Combined coupled-cluster and many-body perturbation theories
Authors: Hirata So , Fan Peng-Dong , Auer Alexander A. , Nooijen Marcel , Piecuch Piotr
Published: December 2004

Various approximations combining coupled-cluster (CC) and many-body perturbation theories have been derived and implemented into the parallel execution programs that take into account the spin, spatial (real Abelian), and permutation symmetries and that are applicable to closed- and open-shell molecules. The implemented models range from the CCSD(T), CCSD[T], CCSD(2)T, CCSD(2)TQ, and CCSDT(2)Q methods to the completely renormalized (CR) CCSD(T) and CCSD[T] approaches, where CCSD (CCSDT) stands for the CC method with connected single and double (single, double, and triple) cluster operators, and subscripted or parenthesized 2, T, and Q indicate the perturbation order or the excitation ranks of the cluster operators included in the corrections. The derivation and computer implementation have been automated by the algebraic and symbolic manipulation program TENSOR CONTRACTION ENGINE (TCE). The TCE-synthesized subroutines generate the tensors with the highest excitation rank in a blockwise manner so that they need not be stored in their entirety, while enabling the efficient reuse of other precalculated intermediate tensors defined by prioritizing the memory optimization as well as operation minimization. Consequently, the overall storage requirements for the corrections due to connected triple and quadruple cluster operators scale as O(n4) and O(n6), respectively (n being a measure of the system size). For systems with modest multireference character of their wave functions, we found that the order of accuracy is CCSD<CR-CCSD(T)≈CCSD(2)T≈CCSD(T)<CCSDT≈CCSD(2)TQ<CCSDT(2)Q, whereas CR-CCSD(T) is more effective in cases of larger quasidegeneracy. The operation costs of the TCE-generated CCSD(2)TQ and CCSDT(2)Q codes scale as rather steep O(n9), while the TCE-generated CCSD(T), CCSD(2)T, and CR-CCSD(T) codes are near operation minimum [a noniterative O(n7)]. The perturbative correction part of the CCSD(T)/cc-pVDZ calculations for azulene exhibited a 45-fold speedup upon a 64-fold increase in the number of processors from 8 to 512.
Path-integral Monte Carlo simulations for electronic dynamics on molecular chains. I. Sequential hopping and super exchange
Authors: Mühlbacher Lothar , Ankerhold Joachim , Escher Charlotte
Published: December 2004

An improved real-time quantum Monte Carlo procedure is presented and applied to describe the electronic transfer dynamics along molecular chains. The model consists of discrete electronic sites coupled to a thermal environment which is integrated out exactly within the path integral formulation. The approach is numerically exact and its results reduce to known analytical findings (Marcus theory, golden rule) in proper limits. Special attention is paid to the role of superexchange and sequential hopping at lower temperatures in symmetric donor-bridge-acceptor systems. In contrast to previous approximate studies, superexchange turns out to play a significant role only for extremely high-lying bridges where the transfer is basically frozen or for extremely low temperatures where for weaker dissipation a description in terms of rate constants is no longer feasible. For bridges with increasing length an algebraic decrease of the yield is found for short as well as for long bridges. The approach can be extended to electronic systems with more complicated topologies including impurities and in presence of external time-dependent forces.
Vibrational molecular quantum computing: Basis set independence and theoretical realization of the Deutsch–Jozsa algorithm
Authors: Tesch Carmen M. , de Vivie-Riedle Regina
Published: December 2004

The phase of quantum gates is one key issue for the implementation of quantum algorithms. In this paper we first investigate the phase evolution of global molecular quantum gates, which are realized by optimally shaped femtosecond laser pulses. The specific laser fields are calculated using the multitarget optimal control algorithm, our modification of the optimal control theory relevant for application in quantum computing. As qubit system we use vibrational modes of polyatomic molecules, here the two IR-active modes of acetylene. Exemplarily, we present our results for a Π gate, which shows a strong dependence on the phase, leading to a significant decrease in quantum yield. To correct for this unwanted behavior we include pressure on the quantum phase in our multitarget approach. In addition the accuracy of these phase corrected global quantum gates is enhanced. Furthermore we could show that in our molecular approach phase corrected quantum gates and basis set independence are directly linked. Basis set independence is also another property highly required for the performance of quantum algorithms. By realizing the Deutsch–Jozsa algorithm in our two qubit molecular model system, we demonstrate the good performance of our phase corrected and basis set independent quantum gates.
Taxonomy of nucleation and growth processes in isotropic systems
Authors: Bahadur Ranjit , McClurg Richard B.
Published: December 2004

We construct a taxonomy of transient behavior for one component coupled nucleation and growth based on linear and nonlinear stability analysis of a two species model. The two species are the condensable species and the condensed droplets or particles, respectively. Our model reproduces previously reported asymptotically stable and oscillatory transient nucleation behavior. Additionally, we show previously unreported possibilities of multiple stationary states and combinations of stationary states with limit cycles. We predict that multiple stationary states may be observed under near critical conditions. Estimates of suitable conditions for experimental verification are given for several systems of interest.
The effects of isotope substitution and nuclear spin modifications on the spectra of complexes of tetracene with hydrogen molecules in ultracold 0.37 K He droplets
Authors: Lindinger A. , Toennies J. P. , Vilesov A. F.
Published: December 2004

The van der Waals complexes consisting of single tetracene chromophore molecules with an attached H2, HD, or a D2 molecule have been assembled inside cold (0.37 K), large (≈1.5×104 atoms) helium droplets. Their laser-induced fluorescence spectra exhibit typically three well isolated fairly sharp [δν(full width at half maximum)≈0.5 cm−1] bands in the spectral region 22220–22300 cm−1. Their positions differ for each isotopomer and also are different for each of the ortho- and para-spin modifications. The common feature (except for D2) with the largest redshift at about 30 cm−1, found also in other related free complexes, is attributed to a strongly bound site above one of the two central benzene rings. The other major features come in pairs spaced 3 cm−1 apart and are not found in similar gas phase studies. This doublet is assigned to a less tightly bound peripheral site with either slightly different configurations or states of the aduct or possibly the He atoms which are stabilized by the surrounding helium bath. The common feature and one branch of the doublet exhibit a pronounced narrow fine structure with spacings of only 0.1 cm−1, which is nearly the same for all complexes as well as for the bare chromophore, and maybe be due to partially resolved rotational structure of the bands.