bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of aromatic amino acids in protein–nucleic acid recognition
Authors: Baker Christopher M. , Grant Guy H. 
Published: January 2007

AbstractStatistical analysis of structures from the PBD has been used to examine the role that the aromatic amino acids play in protein–nucleic acid recognition. In protein–DNA complexes, the residues Phe and His are found to bind selectively to the DNA chain—Phe to A and T, and His to T and G. The preferred binding modes are identified, and the interactions involving Phe are shown to be important in the transcription process. In protein–RNA complexes, Phe is found to occur far less often and is instead replaced by Trp, which binds selectively to C and G, offering a possible mechanism for differentiation between the two nucleic acids. SASA analysis of the two sets of complexes suggests that all of the aromatic amino acids are more heavily involved in binding than would be expected on the balance of probability. Phe and Tyr occur approximately equal in both sets of data, whereas the proportions of His and Trp vary considerably, supporting the idea that these residues may be involved in differentiating between the two nucleic acids. © 2007 Wiley Periodicals, Inc. Biopolymers 85: 456–470, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Rapid responses of ribosomal RNA synthesis to nutrient shifts
Authors: Suthers Patrick F. , Gourse Richard L. , Yin John 
Published: January 2007

AbstractA major challenge in systems biology is to integrate our mechanistic understanding of gene regulation to predict quantitatively how cells will respond to environmental changes. Living cells respond rapidly to the availability of nutrients in part by altering production of ribosomal RNA (rRNA), a limiting component in the biosynthesis of ribosomes. Studies of rRNA transcription by the RNA polymerase of Escherichia coli have identified regulatory roles for guanosine tetraphosphate (ppGpp), the initiating nucleotide, and the protein DksA. To what extent findings from in vitro studies can be used to quantitatively predict in vivo responses to changing nutrient environments is unknown. We developed a mechanistic mathematical model for rRNA transcriptional responses to such changes. Our model accounts for binding of RNAP to its rRNA promoter to form a closed complex, isomerization from a closed complex to an open complex, reversible incorporation of the initiating NTP (iNTP), transcript elongation, and clearance of the promoter. Further, the model incorporates interactions between ppGpp and DksA with transcription intermediates, and it includes an empirical correction to account for salt effects. The model biophysical parameters were determined using 33 single‐ and multi‐round transcription experiments spanning 487 in vitro measurements. By incorporating in vivo measurements of ppGpp and ATP, the model correctly predicted rRNA production rates for cellular responses to nutrient upshifts, downshifts, and outgrowth into fresh medium. Inclusion of DksA was essential in all three cases. Our work provides a foundation for using data‐driven computational models to predict the kinetics of in vivo transcriptional responses. Biotechnol. Bioeng. 2007; 97: 1230–1245. © 2007 Wiley Periodicals, Inc.
Comparisons of optical pH and dissolved oxygen sensors with traditional electrochemical probes during mammalian cell culture
Authors: Hanson Michael A. , Ge Xudong , Kostov Yordan , Brorson Kurt A. , Moreira Antonio R. , Rao Govind 
Published: January 2007

AbstractSmall‐scale upstream bioprocess development often occurs in flasks and multi‐well plates. These culturing platforms are often not equipped to accurately monitor and control critical process parameters; thus they may not yield conditions representative of manufacturing. In response, we and others have developed optical sensors that enable small‐scale process monitoring. Here we have compared two parameters critical to control in industrial cell culture, pH and dissolved oxygen (DO), measured with our optical sensors versus industrially accepted electrochemical probes. For both optical sensors, agreement with the corresponding electrochemical probe was excellent. The Pearson Correlations between the optical sensors and electrochemical probes were 98.7% and 99.7%, for DO and pH, respectively. Also, we have compared optical pH sensor performance in regular (320 mOsm/kg) and high‐osmolality (450 mOsm/kg) cell culture media to simulate the increase in osmolality in pH‐controlled cultures. Over a pH range of 6.38–7.98 the average difference in pH readings in the two media was 0.04 pH units. In summary, we have demonstrated that these optical sensors agree well with standard electrochemical probes. The accuracy of the optical probes demonstrates their ability to detect potential parameter drift that could have significant impact on growth, production kinetics, and protein product quality. We have also shown that an increase in osmolality that could result from controlling pH or operating the reactor in fed‐batch mode has an insignificant impact on the functionality of the pH patches. Biotechnol. Bioeng. 2007;97: 833–841. © 2007 Wiley Periodicals, Inc.
Cell patterning using magnetite nanoparticles and magnetic force
Authors: Ino Kosuke , Ito Akira , Honda Hiroyuki 
Published: January 2007

AbstractTechnologies for fabricating functional tissue architectures by patterning cells precisely are highly desirable for tissue engineering. Although several cell patterning methods such as microcontact printing and lithography have been developed, these methods require specialized surfaces to be used as substrates, the fabrication of which is time consuming. In the present study, we demonstrated a simple and rapid cell patterning technique, using magnetite nanoparticles and magnetic force, which enables us to allocate cells on arbitrary surfaces. Magnetite cationic liposomes (MCLs) developed in our previous study were used to magnetically label the target cells. When steel plates placed on a magnet were positioned under a cell culture surface, the magnetically labeled cells lined on the surface where the steel plate was positioned. Patterned lines of single cells were achieved by adjusting the number of cells seeded, and complex cell patterns (curved, parallel, or crossing patterns) were successfully fabricated. Since cell patterning using magnetic force may not limit the property of culture surfaces, human umbilical vein endothelial cells (HUVECs) were patterned on Matrigel, thereby forming patterned capillaries. These results suggest that the novel cell patterning methodology, which uses MCLs, is a promising approach for tissue engineering and studying cell–cell interactions in vitro. Biotechnol. Bioeng. 2007; 97: 1309–1317. © 2007 Wiley Periodicals, Inc.
A multi‐step kinetic model for substrate assimilation and bacterial growth: Application to benzene biodegradation
Authors: Bordel S. , Muñoz R. , Díaz L.F. , Villaverde S. 
Published: January 2007

AbstractA multi‐step kinetic model based on the concept of synthesizing unit (SU) was developed for describing benzene biodegradation in Pseudomonas putida F1. The model herein presented considered substrate arrival rates to the SU rather than concentrations, and provided a reasonable good fit of the dynamics of both catechol and biomass concentrations experimentally determined. It was based on very general assumptions and could be applied to any process accumulating metabolic intermediates. Conventional growth models considering a single step can be regarded as a particular case of this multi‐step model. Despite the merits of this model, its applicability strongly depends on the knowledge of the complex induction‐repression and inhibition mechanisms governing the different catabolic steps of the degradation pathway, which in most cases are difficult to elucidate experimentally and/or to model mathematically. In this particular case repression of benzene oxidation by catechol and self‐inhibition of catechol transformation were experimentally confirmed and considered in the simulation, resulting in a good fit (relative average error of 6%) of the experimental data. Biotechnol. Bioeng. 2007; 97: 1098–1107. © 2007 Wiley Periodicals, Inc.
Complexation of Fatty Acids and Fatty Acid‐CoAs with Synthetic O‐Methylated Polysaccharides
Authors: Cheon Hwan‐Sung , Wang Yonghui , Ma Jianguo , Kishi Yoshito 
Published: January 2007

AbstractAn experimentally simple, but highly reproducible and reliable method has been developed to follow the complexation event of fatty acid (FA) and FA‐CoA with polysaccharides. This method was based on the recent discovery of the unique blue‐shifted UV absorption associated with the aggregation of tetraenoic fatty acids (TE‐FAs) in aqueous solution. Complexation was monitored by recording the intensity of UV absorption at 250 nm ([free TE‐FA]) and 303 nm ([complexed TE‐FA]), and the K aggregate of C20 t,t,t,t‐TE‐FA exhibited the ideal property for this purpose. Synthetic 3‐O‐methyl‐D‐mannose‐ and 6‐O‐methyl‐D‐glucose‐containing lipopolysaccharides were found to exhibit a broad range of the binding affinities with C20 t,t,t,t‐TE‐FAs as well as saturated FAs/FA‐CoAs.
Influence of citric acid on calcium sulfate dihydrate crystallization in aqueous media
Authors: Titiz‐Sargut S. , Sayan P. , Avcı B. 
Published: January 2007

AbstractThe crystallization of Calcium sulfate dihydrate produced by the reaction between pure Ca(OH)2 suspension and H2SO4 solution was investigated at different pH values, temperatures and citric acid concentrations. Crystal size distributions, filtration rates and zeta potentials of gypsum were determined as a function of citric acid concentrations at pH 3.5 and 65°C. The influence of citric acid on the morphology of gypsum was also investigated and discussed. The average particle size of gypsum was reached to maximum in the presence of approximately 2500 ppm citric acid concentration, where the minimum cake resistance and maximum filtration rate were obtained. In the presence of citric acid, various crystal morphologies such as tabular, plate‐like, double‐taper leaf‐like and flower‐like, etc., were obtained. The change of morphology is related to the preferential adsorption of citric acid on different crystallographic faces. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Experimental study of bubble generation during β‐BaB2O4 single crystal growth
Authors: Pan X. H. , Jin W. Q. , Ai F. , Liu Y. , Hong Y. 
Published: January 2007

AbstractThe generation of bubble‐inclusions during BaB2O4 (BBO) crystal growth from high temperature solution has been optically observed by an in situ observation technique. It was found that bubbles are formed from the peripheries of some hexagonal defects in the (0001) plane of the growing crystal, which may be caused by the evaporation of the air‐opened interface at the high temperature. In addition, atomic force microscope (AFM) was used to investigate the distribution of bubbles. Results revealed that the bubble generation and distribution depend strongly on the microscopic structure of the interface: on a rough interface, bubbles are easily formed and grow rapidly; however, they are greatly suppressed by step trains on a vicinal interface. In the latter case, the height value of a bubble is close to that of the step, which is in the order of several tens of nanometers. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Synthesis and magnetic properties of lanthanum orthovanadate nanorods
Authors: Wang Nian , Zhang Quanfei , Chen Wen 
Published: January 2007

AbstractIn the present paper, single‐crystalline lanthanum orthovanadate (LaVO4) nanorods were synthesized by an ethylenediaminetetraacetic acid (EDTA)‐mediated hydrothermal method. The resulting products were characterized using XRD, SEM, TEM and HRTEM. The experimental results illustrated that the morphologies and microstructures of LaVO4 nanorods were influenced by EDTA and pH value of the precursor solution. The magnetic properties measurements showed that the magnetocrystalline anisotropy was greatly strengthened by the strong effect of the one‐dimensional anisotropy, and the magnetic properties of LaVO4 nanorods are better than that of LaVO4 nanoparticles. The growth mechanism of LaVO4 nanorods was also discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Crystal structure, thermal and compositional deformations of β‐CsB5O8
Authors: Bubnova R. , Dinnebier R. E. , Filatov S. , Anderson J. 
Published: January 2007

AbstractThe crystal structure of β‐CsB5O8 has been determined from X‐ray powder diffraction data using synchrotron radiation: Pbca, a = 7.8131(3) Å, b = 12.0652(4) Å, c = 14.9582(4) Å, Z = 8, ρcalc = 2.967 g/cm3, R‐p = 0.076, R‐wp = 0.094. β‐CsB5O8 was found to be isostructural with β‐KB5O8 and β‐RbB5O8. The crystal structure consists of a double interlocking framework built up from B‐O pentaborate groups. The crystal structure exhibits a highly anisotropic thermal expansion: αa = 53, αb = 16, αc = 14 · 10‐6/K; the anisotropy may be caused by partial straightening of the screw chains of the pentaborate groups. The similarity of the thermal and compositional (Cs‐Rb‐K substitution) deformations of CsB5O8 is revealed: increasing the radius of the metal by 0.01 Å leads to the same deformations of the crystal structure as increasing the temperature by 35°C. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electrical and magnetotransport properties of La0.7Sr0.3MnO3/TiO2 composites
Authors: Gaur A. , Varma G. D. 
Published: January 2007

AbstractThe composite samples with nominal compositions of (1‐x) La0.7Sr0.3MnO3 + x TiO2 (x = 0, 0.05, 0.10, 0.15 and 0.20) were synthesized via solid state reaction process. The X‐ray diffraction and scanning electronic microscopy observations reveal no reaction between La0.7Sr0.3MnO3 (LSMO) and TiO2 phases. Temperature dependence resistivity measurements show that TiO2 phase shifts the metal‐insulator transition temperature (Tp) towards lower temperature and increases the resistivity. Moreover, the magnetization of the composite samples decreases with TiO2 content. An enhancement in magnetoresistance is observed in the composite samples with x = 0.05 and x = 0.10 at low magnetic fields, which is encouraging for potential application of magnetoresistive materials at low field. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Self‐pumped phase conjugation in CSBN75 crystals
Authors: Gao Ch. Y. , Xia H. R. , Xu J. Q. , Si Sh. Ch. , Ran D. G. , Ling Z. Ch. , Zhang H. J. , Wang J. Y. , Song H. L. 
Published: January 2007

AbstractThe self‐pumped phase conjugation in CSBN75 is studied in this investigation basing on an anti‐traditional method, which using part laser spot to irradiate crystal. With the change of the spot size projected on the crystal, the deformed laser spot that introduced by self‐pumped phase conjugation and its complementary pattern are distinctly displayed on the screen. Tentative analysis is executed in this paper. However, it will be applied in optical information processing with these crystals. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Growth and characterization of semi organic nonlinear optical LHPCL crystals
Authors: Aruna S. , Vimalan M. , Thomas P. C. , Thamizharasan K. , Ambujam K. , Madhavan J. , Sagayaraj P. 
Published: January 2007

AbstractThe growth of single crystals of L‐histidinium perchlorate (LHPCL), a semi organic nonlinear optical material with dimension upto 5 × 6 × 2.5 mm3 is reported. Good optical quality single crystals were grown from aqueous solution by slow solvent evaporation technique. The grown crystals were characterized by single crystal X‐ray diffraction (XRD), FT‐IR and optical transmission studies. Thermal studies confirm that LHPCL has a fairly high thermal stability (272°C) when compared with other members of histidine family. The scanning electron microscopy (SEM) provides information on the quality of the samples and grain distribution over the surface of the sample. The dielectric constant and dielectric loss of the compound were measured at different frequencies, and also at varying temperatures and the results of these experiments are discussed. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Intercalation and anisotropy of optical absorption in MoRe0.005Se1.995 single crystals
Authors: Vora Mihir M. , Vora Aditya M. 
Published: January 2007

AbstractThe optical energy gap of MoRe0.005Se1.995 single crystal has been measured at room temperature near the fundamental absorption method. The incident light was polarized along c‐axis of the crystals. Two and three dimensional models are adopted for generating the results. Direct as well as indirect transitions are involved in the absorption process. The indirect transition was found to be allowed with two phonons involved in the process. The three dimensional model could be used to describe the optical properties of the single crystal of MoRe0.005Se1.995. Also, the optical energy gaps depend upon the amount of the intercalating Re material, which show the anisotropy of the chemical bonds. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Photoacoustic studies on two new organic NLO materials: L‐threonine and L‐prolinium tartrate
Authors: Britto Dhas S. A. Martin , Suresh M. , Raji P. , Ramachandran K. , Natarajan S. 
Published: January 2007

AbstractPhotoacoustic spectroscopy (PAS) is a non‐destructive testing (NDT) tool and used here for analyzing the physical properties such as thermal diffusivity, thermal diffusion length, thermal conductivity and thermal effusivity of L‐Threonine and L‐Prolinium tartrate. These two crystals belong to a group of recently developed NLO materials, in our laboratory. The single crystals of the two compounds were grown by using submerged seed solution growth method. Characterization of the crystals was made by using single crystal X‐ray diffraction. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Selective expression of Bhlhb5 in subsets of early‐born interneurons and late‐born association neurons in the spinal cord
Authors: Liu Ben , Liu Zijing , Chen Tao , Li Hong , Qiang Boqin , Yuan Jiangang , Peng Xiaozhong , Qiu Mengsheng 
Published: January 2007

AbstractAccumulating evidence has suggested that the basic helix‐loop‐helix transcription factors play important roles in controlling neuronal fate specification and differentiation in the developing central nervous system. In this study, we report a detailed immunological study on the expression of Bhlhb5 in embryonic mouse spinal cord with a newly developed antibody. At the early stage of neural development, Bhlhb5 is specifically expressed in dI6 dorsal interneurons and in V1 and V2 ventral interneurons. At late stages of development, Bhlhb5 expression is detected in a subset of late‐born dorsal association interneurons that migrate into the uppermost layer of the dorsal horn. Developmental Dynamics 236:829–835, 2007. © 2007 Wiley‐Liss, Inc.
IL‐18, but not IL‐12, is required for optimal cytokine production by influenza virus‐specific CD8+ T cells
Authors: Denton Alice E. , Doherty Peter C. , Turner Stephen J. , La Gruta Nicole L. 
Published: January 2007

AbstractThe potent innate cytokines IL‐12 and IL‐18 are considered to be important antigen‐independent mediators of IFN‐γ production by NK cells and T lymphocytes. The present analysis addresses the physiological role of IL‐12 and IL‐18 in the generation of virus‐specific CD8+ T cells. Both wt C57BL/6J (B6) mice and mice with disrupted IL‐12p40 (IL‐12p40–/–) or IL‐18 (IL‐18–/–) genes were infected with an influenza A virus and the characteristics of the resultant epitope‐specific CD8+ T cell responses were compared. While IL‐12 appeared to have no notable effect on either virus growth or on CD8+ T cell response profiles, the absence of IL‐18 was associated with delayed virus clearance from the lung and, despite normal numbers, a significantly reduced production of IFN‐γ, TNF‐α, and IL‐2 by epitope‐specific CD8+ T cells. While this cytokine phenotype was broadly maintained in IL‐12p40/IL‐18 double‐knockout mice, no evidence was seen for any additive effect. Together, our results suggest that IL‐18, but not IL‐12, induces optimal, antigen‐specific production of key cytokines by CD8+ T cells for the efficient clearance of influenza virus from the lungs of infected mice.
Combining data from multiple years or areas to improve variogram estimation
Authors: Walter John F. , Christman Mary C. , Hoenig John M. , Mann Roger 
Published: January 2007

AbstractA requirement for geostatistical prediction is estimation of the variogram from the data. Often low sample size is a major impediment to elucidating a variogram even for a highly autocorrelated spatial process. This paper presents a methodology for improving variogram estimation when samples exist from multiple years or regions sharing a similar process for generating spatial autocorrelation. Such samples may come from annual monitoring programs for natural resources or from multiple geologic regions. As each set of samples contains some information on the spatial autocorrelation, combining information through the construction of a combined variogram cloud and binning to obtain a common variogram improves the estimation of the variogram. In both simulations and in real datasets of oyster abundance the method proposed here reduces the likelihood of failing to obtain a variogram from a set of samples and improves the efficiency of variogram estimation. In practice, the benefits obtained by estimating an otherwise elusive variogram generally outweigh the costs of using a slightly incorrect variogram model if different sampling stanzas are combined when they do not share the same spatial autocorrelation. Copyright © 2007 John Wiley & Sons, Ltd.
Simulating meander evolution of the Geul River (the Netherlands) using a topographic steering model
Authors: Moor J. J. W. de , Balen R. T. van , Kasse C. 
Published: January 2007

AbstractActive meandering rivers are capable of reworking and removing large quantities of valuable land. Therefore, understanding the characteristics of meandering rivers and predicting future meander behaviour can be of great value for local authorities. In this study, we apply a topographic steering meander model to the Geul River (southern Netherlands), using field data to calibrate the model. The present channel characteristics of the Geul River were mapped in the field. Cut‐banks were classified as erosive, unstable or stable. The model outcomes were compared with these field data.Several model runs were carried out, using different sets of parameter values. After studying the results and using the field data, we introduced the concept of a variable channel width in the simulation model. In reality, the river has different channel widths varying from 8 to more than 15 m. These widths are a linear function of local curvature. The model runs using a variable channel width show that the model is capable of predicting locations of lateral migration in conformity with observed active lateral migration and erosive banks. With both models, the sediment reworking time of the floodplain can be calculated. Floodplain reworking times of 200–300 years were calculated. In combination with the lateral migration rate, this reworking time is an important element in catchment sediment budget calculations. Copyright © 2007 John Wiley & Sons, Ltd.