bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biosynthesis and Elongation of Short- and Medium-Chain-Length Fatty Acids
Authors: van der Hoeven Rutger S. , Steffens John C. 
Published: July 2002

AbstractShort- and medium-chain-length fatty acids (FAs) are important constituents of a wide array of natural products. Branched and straight short-chain-length FAs originate from branched chain amino acid metabolism, and serve as primers for elongation in FA synthase-like reactions. However, a recent model proposes that the one-carbon extension reactions that utilize 2-oxo-3-methylbutyric acid in leucine biosynthesis also catalyze a repetitive one-carbon elongation of short-chain primers to medium-chain-length FAs. The existence of such a mechanism would require a novel form of regulation to control carbon flux between amino acid and FA biosynthesis. A critical re-analysis of the data used to support this pathway fails to support the hypothesis for FA elongation by one-carbon extension cycles of α-ketoacids. Therefore, we tested the hypothesis experimentally using criteria that distinguish between one- and two-carbon elongation mechanisms: (a) isotopomer patterns in terminal carbon atom pairs of branched and straight FAs resulting from differential labeling with [13C]acetate; (b) [13C]threonine labeling patterns in odd- and even chain length FAs; and (c) differential sensitivity of elongation reactions to inhibition by cerulenin. All three criteria indicated that biosynthesis of medium-chain length FAs is mediated primarily by FA synthase-like reactions.
Specific Combinations of Zein Genes and Genetic Backgrounds Influence the Transcription of the Heavy-Chain Zein Genes in Maizeopaque-2 Endosperms
Authors: Ciceri Pietro , Castelli Silvana , Lauria Massimiliano , Lazzari Barbara , Genga Annamaria , Bernard Loris , Sturaro Monica , Viotti Angelo 
Published: July 2002

Abstract
The transcript levels of heavy-chain zein genes (zH1and zH2) and the occurrence of the zH polypeptides in different opaque-2 (o2) lines were investigated by RNA-blot analyses and by sodium dodecylsulfate-polyacrylamide gel electrophoresis or two-dimensional gel electrophoresis protein fractionations. Four mutant alleleso2R, o2T, o2It, and o2-676 introgressed into different genetic backgrounds (GBs) were considered. The mono-dimensional gel electrophoresis zein pattern can be either conserved or different among the various GBs carrying the same o2 allele. Likewise, in the identicalGB carrying different o2 alleles, the zein pattern can be either conserved or differentially affected by the different mutant allele. Zein protein analysis of reciprocal crosses between lines with different o2 alleles or the sameo2 showed in some case a more than additive zH pattern in respect to the o2 parent lines. Electrophoretic mobility shift assay approaches, with O2-binding oligonucleotide and endosperm extracts from the above o2 lines, failed to reveal o2-specific retarded band in any of the o2 extracts. The results suggest that the promoter of some zH1 andzH2 contains motif(s) that can respond to factors other than O2.
The Involvement of a Cysteine Proteinase in the Nodule Development in Chinese Milk Vetch Infected with Mesorhizobium huakuii subsp. rengei
Authors: Naito Yuki , Fujie Makoto , Usami Shoji , Murooka Yoshikatsu , Yamada Takashi 
Published: July 2002

Abstract
Cys proteinases play important roles in plant cell development and senescence. A cDNA, AsNODf32, obtained by differential screening of a nodule cDNA library of the leguminous plant Chinese milk vetch (Astragalus sinicus), represents a nodule-specific Cys proteinase similar to that reported for the actinorhizal Alnus glutinosa-Flankia symbiosis. A characteristic feature of this proteinase is the presence of a putative vacuolar targetting signal, LQDA, within its propeptide. Expression of the AsNODf32 gene, which was studied on northern blots and in situ hybridization, showed good correlation with the onset of nodule senescence. In situ hybridization studies revealed thatAsNODf32 was expressed in senescent-infected tissue at the base of the nodule, as well as in interzone II-III of the infected nodules. In addition to degrading old nodule tissues and bacteroids, AsNODf32 protein may be required as a component of tissue remodeling during nodule development.
Roles of dimerization in folding and stability of ketosteroid isomerase from Pseudomonas putida biotype B
Authors: Kim Do‐Hyung , Nam Gyu Hyun , Jang Do Soo , Yun Sunggoo , Choi Gildon , Lee Hee Cheon , Choi Kwan Yong 
Published: July 2002

AbstractEquilibrium and kinetic analyses have been performed to elucidate the roles of dimerization in folding and stability of KSI from Pseudomonas putida biotype B. Folding was reversible in secondary and tertiary structures as well as in activity. Equilibrium unfolding transition, as monitored by fluorescence and ellipticity measurements, could be modeled by a two‐state mechanism without thermodynamically stable intermediates. Consistent with the two‐state model, one dimensional (1D) NMR spectra and gel‐filtration chromatography analysis did not show any evidence for a folded monomeric intermediate. Interestingly enough, Cys 81 located at the dimeric interface was modified by DTNB before unfolding. This inconsistent result might be explained by increased dynamic motion of the interface residues in the presence of urea to expose Cys 81 more frequently without the dimer dissociation. The refolding process, as monitored by fluorescence change, could best be described by five kinetic phases, in which the second phase was a bimolecular step. Because <30% of the total fluorescence change occurred during the first step, most of the native tertiary structure may be driven to form by the bimolecular step. During the refolding process, negative ellipticity at 225 nm increased very fast within 80 msec to account for >80% of the total amplitude. This result suggests that the protein folds into a monomer containing most of the α‐helical structures before dimerization. Monitoring the enzyme activity during the refolding process could estimate the activity of the monomer that is not fully active. Together, these results stress the importance of dimerization in the formation and maintenance of the functional native tertiary structure.
Stabilizing interactions in the dimer interface of α‐subunit in Escherichia coli RNA polymerase: A graph spectral and point mutation study
Authors: Kannan Natarajan , Chander Preethi , Ghosh Pallavi , Vishveshwara Saraswathi , Chatterji Dipankar 
Published: July 2002

AbstractThe formation of α2 dimer in Escherichia coli core RNA polymerase (RNAP) is thought to be the first step toward the assembly of the functional enzyme. A large number of evidences indicate that the α‐subunit dimerizes through its N‐terminal domain (NTD). The crystal structures of the α‐subunit NTD and that of a homologous Thermus aquaticus core RNAP are known. To identify the stabilizing interactions in the dimer interface of the α‐NTD of E. coli RNAP, we identified side‐chain clusters by using the crystal structure coordinates of E. coli α‐NTD. A graph spectral algorithm was used to identify side‐chain clusters. This algorithm considers the global nonbonded side‐chain interactions of the residues for the clustering procedure and is unique in identifying residues that make the largest number of interactions among the residues that form clusters in a very quantitative way. By using this algorithm, a nine‐residue cluster consisting of polar and hydrophobic residues was identified in the subunit interface adjacent to the hydrophobic core. The residues forming the cluster are relatively rigid regions of the interface, as measured by the thermal factors of the residues. Most of the cluster residues in the E. coli enzyme were topologically and sequentially conserved in the T. aquaticus RNAP crystal structure. Residues 35F and 46I were predicted to be important in the stability of the α‐dimer interface, with 35F forming the center of the cluster. The predictions were tested by isolating single‐point mutants α‐F35A and α‐I46S on the dimer interface, which were found to disrupt dimerization. Thus, the identified cluster at the edge of the dimer interface seems to be a vital component in stabilizing the α‐NTD.
Effect of polymorphisms on ligand binding by mouse major urinary proteins
Authors: Darwish Marie Amr , Veggerby Christina , Robertson Duncan H.L. , Gaskell Simon J. , Hubbard Simon J. , Martinsen Line , Hurst Jane L. , Beynon Robert J. 
Published: July 2002

AbstractMouse urine contains an abundance of major urinary proteins, lipocalins, whose roles include slow release of semiochemicals. These proteins are highly polymorphic, with small sequence differences between individual members. In this study, we purified to homogeneity four of these proteins from two strains of inbred mice and characterized them by mass spectrometry. This analysis has led to the discovery of another variant in this group of proteins. Three of the polymorphic variants that map to the surface have no effect on the binding of a fluorescent probe in the binding cavity, but the fourth, characterized by a Phe to Val substitution in the cavity, shows a substantially lower affinity and fluorescence yield for the probe. These results are interpreted in light of the known crystal structure of the protein and molecular modeling calculations, which rationalize the experimental findings. This work raises the possibility that the calyx‐binding site can show specificity for different ligands, the implications of which on pheromone binding and chemical communication are discussed.
Thermal and urea‐induced unfolding in T7 RNA polymerase: Calorimetry, circular dichroism and fluorescence study
Authors: Griko Yuri , Sreerama Narasimha , Osumi‐Davis Patricia , Woody Robert W. , Woody A‐Young Moon 
Published: July 2002

AbstractStructural changes in T7 RNA polymerase (T7RNAP) induced by temperature and urea have been studied over a wide range of conditions to obtain information about the structural organization and the stability of the enzyme. T7RNAP is a large monomeric enzyme (99 kD). Calorimetric studies of the thermal transitions in T7RNAP show that the enzyme consists of three cooperative units that may be regarded as structural domains. Interactions between these structural domains and their stability strongly depend on solvent conditions. The unfolding of T7RNAP under different solvent conditions induces a highly stable intermediate state that lacks specific tertiary interactions, contains a significant amount of residual secondary structure, and undergoes further cooperative unfolding at high urea concentrations. Circular dichroism (CD) studies show that thermal unfolding leads to an intermediate state that has increased β‐sheet and reduced α‐helix content relative to the native state. Urea‐induced unfolding at 25°C reveals a two‐step process. The first transition centered near 3 M urea leads to a plateau from 3.5 to 5.0 M urea, followed by a second transition centered near 6.5 M urea. The CD spectrum of the enzyme in the plateau region, which is similar to that of the enzyme thermally unfolded in the absence of urea, shows little temperature dependence from 15° to 60°C. The second transition leads to a mixture of poly(Pro)II and unordered conformations. As the temperature increases, the ellipticity at 222 nm becomes more negative because of conversion of poly(Pro)II to the unordered conformation. Near‐ultraviolet CD spectra at 25°C at varying concentrations of urea are consistent with this picture. Both thermal and urea denaturation are irreversible, presumably because of processes that follow unfolding.
Nanostructure, Effective Properties, and Deformation Pattern of the Cochlear Outer Hair Cell Cytoskeleton
Authors: Spector Alexander A. , Ameen Mohammed , Charalambides Panos G. , Popel Aleksander S. 
Published: July 2002

AbstractWe consider the mechanical properties of the outer hair cell cytoskeleton. The cytoskeleton is represented as a set of microdomains of different sizes and orientations composed of actin filaments and spectrin crosslinks. An intermediate material between domains is also introduced. The domain characteristics are randomly generated and the histograms of the cytoskeleton stiffness moduli are obtained. We solve an inverse problem and estimate the stiffness of the crosslink and connective molecule in the intermediate material. We discovered a pattern of highly inhomogeneous deformation of the cytoskeleton where the circumferential strain is primarily determined by the deformation of the intermediate material.
Delay-independent Stability of Uncertain Control Systems
Authors: Tuzcu Ilhan , Ahmadian Mehdi 
Published: July 2002

Abstract
This paper will provide a study of the delay-independent stability of uncertain control systems, represented by a family of quasipolynomials with single time-delays. The uncertain systems that are considered here are delay differential systems whose parameters are known only by their lower and upper bounds. The results are given in the form of necessary and sufficient conditions along with the assumptions for the quasipolynomial families considered. The conditions are transformed into convenient forms, which provide analytical expressions that can be easily checked by commercially available computing tools. For uncertain systems represented by families of quasipolynomials, it is shown that the delay independent stability for the extreme values of parameters is not sufficient for the delay independent stability of the entire family. In addition, the family must satisfy some conditions for the interior values of each parameter within specially constructed frequency ranges. The implementation of the theorem that is suggested is demonstrated on an example system that includes a single degree of freedom system with an active vibration absorber, namely the Delayed Resonator.
Experimental Analysis of Thermal Instability in Natural Convection
Between Horizontal Parallel Plates Uniformly Heated
Authors: Manca O. , Morrone B. , Nardini S. 
Published: July 2002

Abstract
An experimental investigation of natural convection between horizontal, heated, parallel plates in air was carried out by visualizing the flow and measuring the air temperature. Grashof numbers, based on the plate spacing, varied in the 1.22×105-1.06×106 range. Flow patterns and probable onset of secondary motions were observed for three heating modes: (1) both plates heated, (2) upper plate heated and lower one unheated, and (3) upper plate unheated and lower one heated. The main flow pattern resembled a C shape (C loop) for all modes. In fact, the flow penetrated inside the cavity close to the leading edge of the lower plate and exited from the upper part, by reversing its motion between the plates. When the lower plate was heated, flow visualization showed that secondary flows were added to the C loop main flow. Such secondary structures arose as thermals, then changed into longitudinal vortices and, in the upper region of the open-ended cavity, a chaotic motion was detected. The existence of these structures was confirmed by measurements of instantaneous temperature values. They showed that the greater the Grashof number the more chaotic the flow in the outflow branch of the C loop when the lower plate was heated and the upper one was unheated. [S0022-1481(00)01801-6]
Buoyancy-Driven Flow Reversal Phenomena in Radially Rotating
Serpentine Ducts
Authors: Hwang J. J. , Wang W.-J. , Chen Cha'o Kuang 
Published: July 2002

Abstract
Convective characteristics are analyzed numerically in a rotating multipass square duct connecting with 180-deg sharp returns. Isoflux is applied to each duct wall and periodic conditions are used between the entrance and exit of a typical two-pass module. Emphasis is placed on the phenomenon of buoyancy-driven reversed flow in the serpentine duct. Predictions reveal that the radial distance from the rotational axis to the location of flow separation in the radial-outward duct decreases with increasing the Richardson number. In addition, the local buoyancy that is required to yield the radial flow reversal increases with increasing the rotation number. This buoyancy-driven reversed flow in the radial-outward duct always results in local hot spots in the cooling channels. The critical buoyancy for the initiation of flow reversal is therefore concluded for the design purpose. [S0022-1481(00)01101-4]
Abstract: Low-aberration deflection system for microfabrication
Authors: Owen G. , Nixon W. C. 
Published: July 2002

A theoretical design has previously been proposed for a low-aberration magnetic deflection system.1 This has now been translated into practice. Specially shaped interleaved deflection coils have been constructed that give rise to low values of all the aberration coefficients except for distortion and field curvature. The latter aberration is corrected electrically. Since the sole effect of distortion is to destroy the linearity between coil excitation and beam deflection, no correction for this aberration has been incorporated at present. A combined electrical and mechanical centering procedure has been developed and implemented. The deflection system has been tested and found to increase the diameter of an on-axis spot by a maximum of 1.2 μm over a 3×3-mm working field at an angular aperture of 8 mrad. This compares well with the theoretically predicted value of 1.3 μm. The spot diameter has been taken as the 1% to 99% rise distance of the transmitted beam current as the spot was scanned across an edge.
The theoretical work has been extended to show that under certain conditions it is, in principle, possible to eliminate the noncorrectable aberrations completely.
Abstract: Theory of lenslet interactions in a fly’s eye lens
Authors: Harte K. J. 
Published: July 2002

In an electron-optical fly’s eye lens, comprised of several parallel plates with arrays of aligned holes, the field at each lenslet is distorted by the fields of the surrounding lenslets. This interaction sets a limit on how closely packed the array can be (or how large the lenslet holes can be for a given spacing) and therefore has a direct bearing on performance. In this paper a method is developed for calculating the effect of the interaction for arbitrary lens geometry.
First, from the symmetry of the environment of each lenslet, Neumann boundary conditions are derived on the bounding polygon between lenslets. These boundary conditions are expanded in a Fourier-perturbation series about the circle which is the zeroth harmonic of the polygon. Laplace’s equation is then solved within the bounding circle for each harmonic to first-order in the perturbation theory, for example by numerical relaxation. Second- and higher-order solutions can be similarly obtained if necessary. From the zeroth Fourier component of the resulting axial potential, Gaussian properties of the lenslet are obtained, along with the spherical aberration coefficient. The next nonvanishing harmonic (fourth for a square array of lenslets, sixth for an hexagonal array) determines a corresponding aberration coefficient, which describes the major effect of lenslet interactions on the focused spot. Higher-order aberration coefficients are calculated from higher-harmonic potentials, if needed.
Finally, as an example, the method is applied to a three-element einzel lens with a square array of lenslets. Fourfold aberrations, which are the dominant interaction effect, are found to be significant if the hole diameter in the center element is greater than about 70% of the lenslet spacing, in rough agreement with experimental results. At this diameter such aberrations amount to roughly one tenth of the spherical aberration.
Abstract: Determination of ion-implanted profiles using the MOS capacitance–voltage technique
Authors: Edwards J. R. , Marr G. 
Published: July 2002

In this paper, the application of the MOS capacitance–voltage technique for the determination of ion-implanted impurity profiles is described experimentally and theoretically for moderate (1011–1012 ions/cm2) ion implants.
The experimental vehicle was a large-geometry p-channel IGFET (250×250 μm) which was implanted with boron ions at an energy of 120 keV through the gate region (500 Å Al2O3 + 1000 Å SiO2). This results in a doping profile with a peak approximately 1700 Å beneath the Si–SiO2 interface and an effective Debye length the order of 500 Å. Since the application of a gate voltage results in a maximum surface depletion width which is less than the boron profile depth, a reverse bias was applied between the source-drain diffusions and the substrate in order to sweep out the inversion electrons that otherwise would shield the surface electric field. The resulting gate to source-drain capacitance curve in the surface depletion region was used to determine the implanted profile with the Kennedy–O’Brien majority carrier correction factor included. This was also compared to a theoretical Gaussian implant profile based on theoretical values for range and straggle.
To examine the validity of the experimental results, a theoretical study was made using the following method: (1) Assume a Gaussian profile. (2) From the above, calculate the semiconductor capacitance. (3) Use the capacitance to calculate an ’’effective’’ profile. (4) Compare the ’’effective’’ profile with the Gaussian profile. This comparison showed that the measured profile can be determined with resolution substantially less than a Debye length.
Based on this work, it is concluded that the substrate-biased MOS transistor capacitance of an ion-implanted depletion-mode IGFET is a practical method which can be used for process control of the peak of the implant to an accuracy which is better than a Debye length.