bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data Mining the Arabidopsis Genome Reveals Fifteen 14-3-3 Genes. Expression Is Demonstrated for Two out of Five Novel Genes
Authors: Rosenquist Magnus , Alsterfjord Magnus , Larsson Christer , Sommarin Marianne 
Published: July 2002

AbstractIn plants, 14-3-3 proteins are key regulators of primary metabolism and membrane transport. Although the current dogma states that 14-3-3 isoforms are not very specific with regard to target proteins, recent data suggest that the specificity may be high. Therefore, identification and characterization of all 14-3-3 (GF14) isoforms in the model plant Arabidopsis are important. Using the information now available from The Arabidopsis Information Resource, we found three new GF14 genes. The potential expression of these three genes, and of two additional novel GF14 genes (Rosenquist et al., 2000), in leaves, roots, and flowers was examined using reverse transcriptase-polymerase chain reaction and cDNA library polymerase chain reaction screening. Under normal growth conditions, two of these genes were found to be transcribed. These genes were namedgrf11and grf12, and the corresponding new 14-3-3 isoforms were named GF14omicron and GF14iota, respectively. The gene coding for GF14omicron was expressed in leaves, roots, and flowers, whereas the gene coding for GF14iota was only expressed in flowers. Gene structures and relationships between all members of the GF14 gene family were deduced from data available through The Arabidopsis Information Resource. The data clearly support the theory that two 14-3-3 genes were present when eudicotyledons diverged from monocotyledons. In total, there are 15 14-3-3 genes (grfs 1–15) in Arabidopsis, of which 12 (grfs 1–12) now have been shown to be expressed.
Designed protein G core variants fold to native‐like structures: Sequence selection by ORBIT tolerates variation in backbone specification
Authors: Ross Scott A. , Sarisky Catherine A. , Su Alyce , Mayo Stephen L. 
Published: July 2002

AbstractThe solution structures of two computationally designed core variants of the β1 domain of streptococcal protein G (Gβ1) were solved by 1H NMR methods to assess the robustness of amino acid sequence selection by the ORBIT protein design package under changes in protein backbone specification. One variant has mutations at three of 10 core positions and corresponds to minimal perturbations of the native Gβ1 backbone. The other, with mutations at six of 10 positions, was calculated for a backbone in which the separation between Gβ1's α‐helix and β‐sheet was increased by 15% relative to native Gβ1. Exchange broadening of some resonances and the complete absence of others in spectra of the sixfold mutant bespeak conformational heterogeneity in this protein. The NMR data were sufficiently abundant, however, to generate structures of similar, moderately high quality for both variants. Both proteins adopt backbone structures similar to their target folds. Moreover, the sequence selection algorithm successfully predicted all core κ1 angles in both variants, five of six κ2 angles in the threefold mutant and four of seven κ2 angles in the sixfold mutant. We conclude that ORBIT calculates sequences that fold specifically to a geometry close to the template, even when the template is moderately perturbed relative to a naturally occurring structure. There are apparently limits to the size of acceptable perturbations: In this study, the larger perturbation led to undesired dynamic behavior.
Folding units in calcium vector protein of amphioxus: Structural and functional properties of its amino‐ and carboxy‐terminal halves
Authors: Baladi Sibyl , Tsvetkov Philipp O. , Petrova Tatiana V. , Takagi Takashi , Sakamoto Hiroshi , Lobachov Vladimir M. , Makarov Alexander A. , Cox Jos A. 
Published: July 2002

AbstractMuscle of amphioxus contains large amounts of a four EF‐hand Ca2+‐binding protein, CaVP, and its target, CaVPT. To study the domain structure of CaVP and assess the structurally important determinants for its interaction with CaVPT, we expressed CaVP and its amino (N‐CaVP) and carboxy‐terminal halves (C‐CaVP). The interactive properties of recombinant and wild‐type CaVP are very similar, despite three post‐translational modifications in the wild‐type protein. N‐CaVP does not bind Ca2+, shows a well‐formed hydrophobic core, and melts at 44°C. C‐CaVP binds two Ca2+ with intrinsic dissociation constants of 0.22 and 140 μM (i.e., very similar to the entire CaVP). The metal‐free domain in CaVP and C‐CaVP shows no distinct melting transition, whereas its 1Ca2+ and 2Ca2+ forms melt in the 111°–123°C range, suggesting that C‐CaVP and the carboxy‐ domain of CaVP are natively unfolded in the metal‐free state and progressively gain structure upon binding of 1Ca2+ and 2Ca2+. Thermal denaturation studies provide evidence for interdomain interaction: the apo, 1Ca2+ and 2Ca2+ states of the carboxy‐domain destabilize to different degrees the amino‐domain. Only C‐CaVP forms a Ca2+‐dependent 1:1 complex with CaVPT. Our results suggest that the carboxy‐terminal domain of CaVP interacts with CaVPT and that the amino‐terminal lobe modulates this interaction.
MPtopo: A database of membrane protein topology
Authors: Jayasinghe Sajith , Hristova Kalina , White Stephen H. 
Published: July 2002

AbstractThe reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology‐prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL‐based search engine.
The effect of net charge on the solubility, activity, and stability of ribonuclease Sa
Authors: Shaw Kevin L. , Grimsley Gerald R. , Yakovlev Gennady I. , Makarov Alexander A. , Pace C. Nick 
Published: July 2002

AbstractThe net charge and isoelectric pH (pI) of a protein depend on the content of ionizable groups and their pK values. Ribonuclease Sa (RNase Sa) is an acidic protein with a pI = 3.5 that contains no Lys residues. By replacing Asp and Glu residues on the surface of RNase Sa with Lys residues, we have created a 3K variant (D1K, D17K, E41K) with a pI = 6.4 and a 5K variant (3K + D25K, E74K) with a pI = 10.2. We show that pI values estimated using pK values based on model compound data can be in error by >1 pH unit, and suggest how the estimation can be improved. For RNase Sa and the 3K and 5K variants, the solubility, activity, and stability have been measured as a function of pH. We find that the pH of minimum solubility varies with the pI of the protein, but that the pH of maximum activity and the pH of maximum stability do not.
Excision of a proposed electron transfer pathway in cytochrome c peroxidase and its replacement by a ligand‐binding channel
Authors: Rosenfeld Robin J. , Hays Anna‐Maria A. , Musah Rabi A. , Goodin David B. 
Published: July 2002

AbstractA previously proposed electron transfer (ET) pathway in the heme enzyme cytochrome c peroxidase has been excised from the structure, leaving an open ligand‐binding channel in its place. Earlier studies on cavity mutants of this enzyme have revealed structural plasticity in this region of the molecule. Analysis of these structures has allowed the design of a variant in which the specific section of protein backbone representing a previously proposed ET pathway is accurately extracted from the protein. A crystal structure verified the creation of an open channel that overlays the removed segment, extending from the surface of the protein to the heme at the core of the protein. A number of heterocyclic cations were found to bind to the proximal‐channel mutant with affinities that can be rationalized based on the structures. It is proposed that small ligands bind more weakly to the proximal‐channel mutant than to the W191G cavity due to an increased off rate of the open channel, whereas larger ligands are able to bind to the channel mutant without inducing large conformational changes. The structure of benzimidazole bound to the proximal‐channel mutant shows that the ligand accurately overlays the position of the tryptophan radical center that was removed from the wild‐type enzyme and displaces four of the eight ordered solvent molecules seen in the empty cavity. Ligand binding also caused a small rearrangement of the redesigned protein loop, perhaps as a result of improved electrostatic interactions with the ligand. The engineered channel offers the potential for introducing synthetic replacements for the removed structure, such as sensitizer‐linked substrates. These installed “molecular wires” could be used to rapidly initiate reactions, trap reactive intermediates, or answer unresolved questions about ET pathways.
Diagnostic Checks for Discrete Data Regression Models Using Posterior Predictive Simulations
Authors: Gelman Andrew , Goegebeur Yuri , Tuerlinckx Francis , Van Mechelen Iven van 
Published: July 2002

SUMMARY
Model checking with discrete data regressions can be difficult because the usual methods such as residual plots have complicated reference distributions that depend on the parameters in the model. Posterior predictive checks have been proposed as a Bayesian way to average the results of goodness-of-fit tests in the presence of uncertainty in estimation of the parameters. We try this approach using a variety of discrepancy variables for generalized linear models fitted to a historical data set on behavioural learning. We then discuss the general applicability of our findings in the context of a recent applied example on which we have worked. We find that the following discrepancy variables work well, in the sense of being easy to interpret and sensitive to important model failures: structured displays of the entire data set, general discrepancy variables based on plots of binned or smoothed residuals versus predictors and specific discrepancy variables created on the basis of the particular concerns arising in an application. Plots of binned residuals are especially easy to use because their predictive distributions under the model are sufficiently simple that model checks can often be made implicitly. The following discrepancy variables did not work well: scatterplots of latent residuals defined from an underlying continuous model and quantile–quantile plots of these residuals.
On the Development and Application of the Fast-Response Aerodynamic Probe System in Turbomachines—Part 1: The Measurement System
Authors: Kupferschmied Peter , Ko¨ppel Pascal , Roduner Christian , Gyarmathy Georg 
Published: July 2002

This contribution gives an overview of the current state, performance, and limitations of the fast-response aerodynamic probe measurement system developed at the Turbomachinery Lab of the ETH Zurich. In particular, the following topics are addressed:
• Probe technology: Miniature probes with tip diameter ranging from 0.84 to 1.80 mm (one-sensor and three-sensor probes, respectively) have been developed. New technologies derived from microelectronics and micromechanics have been used to achieve an adequate packaging of the microsensor chips used. Both the sensor packaging and the sensor calibration (time-independent and time-dependent) are crucial issues for the DC accuracy of any measurement.
• Aerodynamic probe calibration: The methods used for the sensor calibration and the aerodynamic probe calibration, the pertinent automated test facilities, and the processing of the output data are briefly presented. Since these miniature probes are also capable of measuring the mean flow temperature, aspects related to the effective recovery factor and the self-heating of the probe tip are treated and some recommendations related to sensor selection are given.
• Measurement system and data evaluation: The early measurement chain described in Gossweiler et al. (1995) has evolved into the fast-response aerodynamic probe system. This automatic system incorporates dedicated measurement concepts for a higher accuracy and a more efficient operation in terms of time and failures. An overview of the data evaluation process is given.
The fast-response aerodynamic probe system has been tested in real-sized turbomachines under industrial conditions within the temperature limits of 140°C imposed by the sensor technology (axial-flow turbofan compressor, axial-flow turbine, centrifugal compressor). These applications confirmed the potential of the system and encouraged its further development. Now, the system is routinely used in the facilities of the Turbomachinery Lab and in occasional measurement campaigns in other laboratories.
Part 2 of this contribution (Roduner et al.) will focus on the application of the fast-response aerodynamic probe system in a transonic centrifugal compressor of the ETH Turbomachinery Laboratory, while Part 3 (Ko¨ppel et al.) treats more sophisticated data analysis methods. [S0889-504X(00)01003-5]
Thermoelastic Stress Analysis: An NDE Tool for Residual Stress
Assessment of Metallic Alloys
Authors: Gyekenyesi A. L. 
Published: July 2002

Abstract
The primary objective of this report involves studying and developing various experimental techniques for accurate measurement of the mean stress effect in thermoelastic stress analysis (TSA, also recognized as SPATE: stress pattern analysis by thermal emission). The analysis of cyclic mean stresses at the coupon level directly relates to the measurement of residual stresses in structures. In a previous study by the authors, it was shown that cyclic mean stresses significantly influenced the TSA results for titanium and nickel-based alloys, although, difficulties were encountered concerning the quantification of the mean stress effect because of large test-to-test variations. This study continues the effort of accurate direct measurements of the mean stress effect by implementing various experimental modifications. In addition, a more in-depth analysis is included which involves analyzing the second harmonic of the temperature response. By obtaining the amplitudes of the first and second harmonics, the stress amplitude and the mean stress at a given point on a structure subjected to a cyclic load can be simultaneously obtained. The rather complex analysis of the temperature response involves obtaining the first and second harmonic amplitudes for 16384 infrared detectors (128×128 focal plane array). Upon establishing a protocol for mean stress measurements in the laboratory using the TSA technique, the next step is to utilize the method to assess residual stress states in complex structures during manufacturing and life.
Twin Web Disk: A Step Beyond Convention
Authors: Cairo R. R. , Sargent K. A. 
Published: July 2002

Abstract
This paper will discuss a study of an innovative design for an advanced turbine rotor that could have a great impact on future engines. The design challenge is to provide a minimum weight turbine rotor system that can withstand beyond state-of-the-art levels of AN2 (turbine annulus area multiplied by speed squared). An AN2 limit has been reached for high-pressure turbine (HPT) disks configured in conventional (single web) geometry with state-of-the-art nickel alloys. The problem has reached the point where increased AN2 has been declared a “break-through” technology. The twin-web disk has the potential to provide this break through. This paper will present the history of this turbine rotor design, analytical results, material/component processing, and concept validation results. All work was performed under an Air Force sponsored program entitled “Composite Ring Reinforced Turbine” (CRRT).
Empirical Evaluation of Convective Heat and Moisture Transport
Coefficients in Porous Cotton Medium
Authors: Ghali Kamel , Ghaddar Nesreen , Jones Byron 
Published: July 2002

Abstract
The air penetration within a porous clothing system on a moving human being is an important physical process that considerably affects the heat and moisture resistance of the textile material. This effect of the coupled convection heat and mass exchange within the clothing system is experimentally investigated and theoretically modeled to determine the heat and mass transfer coefficients between the air penetrating the void space and the solid fiber as a function of the velocity of penetrating air. Experiments were conducted inside environmentally controlled chambers to measure the transient moisture uptake of untreated cotton fabric samples as well as the outer fabric temperature using an infrared pyrometer. The moisture uptake was conducted at three different volumetric flow rates of 0.0067, 0.018 and 0.045 m3/sec/m2 of fabric area to represent airflow penetrations that could result from slow, medium, and vigorous walking, respectively. The theoretical analysis is based on a two-node adsorption model of the fibrous medium. A set of four coupled differential equations were derived describing time-dependent convective heat and mass transfer between the penetrating air and the solid fiber in terms of relevant unknown transport coefficients. The unknown model parameters were adjusted to fit the experimental data. The outer heat and mass transfer coefficients were found to increase with the air penetration flow rate.
Plasma crystal
Authors: Morfill G. E. , Thomas H. 
Published: July 2002

Plasma crystal is the term used to describe the recently discovered ordered state that a colloidal plasma may assume under certain conditions. This state resembles metals, to some extent, with the ‘‘atoms’’ represented by the highly negatively charged and highly ordered colloidal particles and the ‘‘electrons’’ by the mobile plasma ions and electrons—perhaps ‘‘heavy metal’’ might be an appropriate description. Plasma crystals are formed in a colloidal plasma if two conditions are met: (1) The Coulomb coupling parameter (the ratio of the Coulomb energy between neighboring particles to their kinetic energy) exceeds a certain threshold and (2) the lattice parameter (the ratio of the particle separation to the Debye length) is smaller than unity. These conditions are easy to generate in rf discharge plasmas and plasma crystallization then proceeds spontaneously. Plasma crystals have some unique properties, which make them exciting systems to study. (1) In their own right, as a hitherto unknown form of condensed plasma, they may provide many insights into basic plasma physical processes and transport effects. (2) As model systems for the detailed investigation of phase transitions, lattice defects, annealing, doping, etc., they may provide new information for a better understanding of solid state physics. (3) As test systems they may be useful for investigating nonlinear effects in ‘‘nanocrystals’’ (crystals with less than approximately 100 lattice planes).
The unique properties, which enable these investigations and possibly many more, are (1) global charge neutrality, (2) very fast response, (3) very little damping, and (4) easy experimental control and diagnostics, i.e., detailed imaging and high temporal resolution of the dynamics of individual particles (‘‘atoms’’). We present here an overview of recent developments in this new research field.
Upregulation of
ERG
Genes in
Candida
Species by Azoles and Other Sterol Biosynthesis Inhibitors
Authors: Henry Karl W. , Nickels Joseph T. , Edlind Thomas D. 
Published: July 2002

ABSTRACT

Infections due to
Candida albicans
are usually treated with azole antifungals such as fluconazole, but treatment failure is not uncommon especially in immunocompromised individuals. Relatedly, in vitro studies demonstrate that azoles are nonfungicidal, with continued growth at strain-dependent rates even at high azole concentrations. We hypothesized that upregulation of
ERG11
, which encodes the azole target enzyme lanosterol demethylase, contributes to this azole tolerance in
Candida
species. RNA analysis revealed that
ERG11
expression in
C. albicans
is maximal during logarithmic-phase growth and decreases as the cells approach stationary phase. Incubation with fluconazole, however, resulted in a two- to fivefold increase in
ERG11
RNA levels within 2 to 3 h, and this increase was followed by resumption of culture growth.
ERG11
upregulation also occurred following treatment with other azoles (itraconazole, ketoconazole, clotrimazole, and miconazole) and was not dependent on the specific medium or pH. Within 1 h of drug removal
ERG11
upregulation was reversed. Azole-dependent upregulation was not limited to
ERG11
: five of five
ERG
genes tested whose products function upstream and downstream of lanosterol demethylase in the sterol biosynthetic pathway were also upregulated. Similarly,
ERG11
upregulation occurred following treatment of
C. albicans
cultures with terbinafine and fenpropimorph, which target other enzymes in the pathway. These data suggest a common mechanism for global
ERG
upregulation, e.g., in response to ergosterol depletion. Finally, azole-dependent
ERG11
upregulation was demonstrated in three additional
Candida
species (
C. tropicalis
,
C. glabrata
, and
C. krusei
), indicating a conserved response to sterol biosynthesis inhibitors in opportunistic yeasts.
The EmrR Protein Represses the
Escherichia coli emrRAB
Multidrug Resistance Operon by Directly Binding to Its Promoter Region
Authors: Xiong A. , Gottman A. , Park C. , Baetens M. , Pandza S. , Matin A. 
Published: July 2002

ABSTRACT

EmrR negatively regulates the transcription of the multidrug resistance pump-encoding operon,
emrRAB
, by binding to its regulatory region. The binding site spans the promoter and the downstream sequence up to the transcriptional start site of the operon. Structurally unrelated drugs that induce the pump interfere with this binding.
Expression and Characterization of Recombinant Human-Derived
Pneumocystis carinii
Dihydrofolate Reductase
Authors: Ma Liang , Kovacs Joseph A. 
Published: July 2002

ABSTRACT

Dihydrofolate reductase (DHFR) is the target of trimethoprim (TMP), which has been widely used in combination with sulfa drugs for treatment and prophylaxis of
Pneumocystis carinii
pneumonia. While the rat-derived
P. carinii
DHFR has been well characterized, kinetic studies of human-derived
P. carinii
DHFR, which differs from rat-derived
P. carinii
DHFR by 38% in amino acid sequence, have not been reported to date. Here we report on the expression and kinetic characterization of the recombinant human-derived
P. carinii
DHFR. The 618-bp coding sequence of the human-derived
P. carinii
DHFR gene was expressed in
Escherichia coli
. As determined by sodium dodecyl sulfate-polyacrylamide gel eletrophoresis, the purified enzyme had a molecular mass of 25 kDa, consistent with that predicted from the DNA sequence. Kinetic analysis showed that the

K
m

values for dihydrofolate and NADPH were 2.7 ± 0.3 and 14.0 ± 4.3 μM, respectively, which are similar to those reported for rat-derived
P. carinii
DHFR. Inhibition studies revealed that both TMP and pyrimethamine were poor inhibitors of human-derived
P. carinii
DHFR, with

K
i

values of 0.28 ± 0.08 and 0.065 ± 0.005 μM, respectively, while trimetrexate and methotrexate were potent inhibitors, with

K
i

values of 0.23 ± 0.03 and 0.016 ± 0.004 nM, respectively. The availability of purified recombinant enzyme in large quantities should facilitate the identification of antifolate inhibitors with greater potency and higher selectivity for human-derived
P. carinii
DHFR.