bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chloroplast Division and Morphology Are Differentially Affected by Overexpression of FtsZ1 and FtsZ2 Genes in Arabidopsis,
Authors: Stokes Kevin D. , McAndrew Rosemary S. , Figueroa Rubi , Vitha Stanislav , Osteryoung Katherine W. 
Published: July 2002

Abstract
In higher plants, two nuclear gene families, FtsZ1and FtsZ2, encode homologs of the bacterial protein FtsZ, a key component of the prokaryotic cell division machinery. We previously demonstrated that members of both gene families are essential for plastid division, but are functionally distinct. To further explore differences between FtsZ1 and FtsZ2 proteins we investigated the phenotypes of transgenic plants overexpressingAtFtsZ1-1 or AtFtsZ2-1, Arabidopsis members of the FtsZ1 and FtsZ2 families, respectively. Increasing the level of AtFtsZ1-1 protein as little as 3-fold inhibited chloroplast division. Plants with the most severe plastid division defects had 13- to 26-fold increases in AtFtsZ1-1 levels over wild type, and some of these also exhibited a novel chloroplast morphology. Quantitative immunoblotting revealed a correlation between the degree of plastid division inhibition and the extent to which the AtFtsZ1-1 protein level was elevated. In contrast, expression of an AtFtsZ2-1 sense transgene had no obvious effect on plastid division or morphology, though AtFtsZ2-1 protein levels were elevated only slightly over wild-type levels. This may indicate that AtFtsZ2-1 accumulation is more tightly regulated than that of AtFtsZ1-1. Plants expressing the AtFtsZ2-1transgene did accumulate a form of the protein smaller than those detected in wild-type plants. AtFtsZ2-1 levels were unaffected by increased or decreased accumulation of AtFtsZ1-1 and vice versa, suggesting that the levels of these two plastid division proteins are regulated independently. Taken together, our results provide additional evidence for the functional divergence of the FtsZ1 andFtsZ2 plant gene families.
Sugar Coordinately and Differentially Regulates Growth- and Stress-Related Gene Expression via a Complex Signal Transduction Network and Multiple Control Mechanisms
Authors: Ho Shin-Lon , Chao Yu-Chan , Tong Wu-Fu , Yu Su-May 
Published: July 2002

Abstract
In plants, sugars are required to sustain growth and regulate gene expression. A large set of genes are either up- or down-regulated by sugars; however, whether there is a common mechanism and signal transduction pathway for differential and coordinated sugar regulation remain unclear. In the present study, the rice (Oryza sativa cv Tainan 5) cell culture was used as a model system to address this question. Sucrose and glucose both played dual functions in gene regulation as exemplified by the up-regulation of growth-related genes and down-regulation of stress-related genes. Sugar coordinately but differentially activated or repressed gene expression, and nuclear run-on transcription and mRNA half-life analyses revealed regulation of both the transcription rate and mRNA stability. Although coordinately regulated by sugars, these growth- and stress-related genes were up-regulated or down-regulated through hexokinase-dependent and/or hexokinase-independent pathways. We also found that the sugar signal transduction pathway may overlap the glycolytic pathway for gene repression. α-Amylase and the stress-related genes identified in this study were coordinately expressed under sugar starvation, suggesting a convergence of the nutritional and environmental stress signal transduction pathways. Together, our studies provide a new insight into the complex signal transduction network and mechanisms of sugar regulation of growth and stress-related genes in plants.
Inventory of the Superfamily of P-Type Ion Pumps in Arabidopsis
Authors: Axelsen Kristian B. , Palmgren Michael G. 
Published: July 2002

AbstractA total of 45 genes encoding for P-type ATPases have been identified in the complete genome sequence of Arabidopsis. Thus, this plant harbors a primary transport capability not seen in any other eukaryotic organism sequenced so far. The sequences group in all five subfamilies of P-type ATPases. The most prominent subfamilies are P1B ATPases (heavy metal pumps; seven members), P2A and P2B ATPases (Ca2+ pumps; 14 in total), P3A ATPases (plasma membrane H+pumps; 12 members including a truncated pump, which might represent a pseudogene or an ATPase-like protein with an alternative function), and P4 ATPases (12 members). P4 ATPases have been implicated in aminophosholipid flipping but it is not known whether this is a direct or an indirect effect of pump activity. Despite this apparent plethora of pumps, Arabidopsis appears to be lacking Na+ pumps and secretory pathway (PMR1-like) Ca2+-ATPases. A cluster of Arabidopsis heavy metal pumps resembles bacterial Zn2+/Co2+/Cd2+/Pb2+transporters. Two members of the cluster have extended C termini containing putative heavy metal binding motifs. The complete inventory of P-type ATPases in Arabidopsis is an important starting point for reverse genetic and physiological approaches aiming at elucidating the biological significance of these pumps.
Comprehensive Expression Profile Analysis of the Arabidopsis Hsp70 Gene Family
Authors: Sung Dong Yul , Vierling Elizabeth , Guy Charles L. 
Published: July 2002

Abstract
We isolated cDNA clones for two nuclear-encoded, organellar members of the Arabidopsis hsp70 gene family, mtHsc70-2(AF217458) and cpHsc70-2 (AF217459). Together with the completion of the genome sequence, the hsp70 family in Arabidopsis consists of 14 members unequally distributed among the five chromosomes. To establish detailed expression data of this gene family, a comprehensive reverse transcriptase-polymerase chain reaction analysis for 11 hsp70s was conducted including analysis of organ-specific and developmental expression and expression in response to temperature extremes. All hsp70s showed 2- to 20-fold induction by heat shock treatment except cpHsc70-1 andmtHsc70-1, which were unchanged or repressed. The expression profiles in response to low temperature treatment were more diverse than those evoked by heat shock treatment. Both mitochondrial and all cytosolic members of the family except Hsp70bwere strongly induced by low temperature, whereas endoplasmic reticulum and chloroplast members were not induced or were slightly repressed. Developmentally regulated expression of the heat-inducibleHsp70 in mature dry seed and roots in the absence of temperature stress suggests prominent roles in seed maturation and root growth for this member of the hsp70 family. This reverse transcriptase-polymerase chain reaction analysis establishes the complex differential expression pattern for the hsp70s in Arabidopsis that portends specialized functions even among members localized to the same subcellular compartment.
Enhanced Accumulation of BiP in Transgenic Plants Confers Tolerance to Water Stress
Authors: Alvim Fátima C. , Carolino Sônia M.B. , Cascardo Júlio C.M. , Nunes Cristiano C. , Martinez Carlos A. , Otoni Wagner C. , Fontes Elizabeth P.B. 
Published: July 2002

AbstractThe binding protein (BiP) is an important component of endoplasmic reticulum stress response of cells. Despite extensive studies in cultured cells, a protective function of BiP against stress has not yet been demonstrated in whole multicellular organisms. Here, we have obtained transgenic tobacco (Nicotiana tabacum L. cv Havana) plants constitutively expressing elevated levels of BiP or its antisense cDNA to analyze the protective role of this endoplasmic reticulum lumenal stress protein at the whole plant level. Elevated levels of BiP in transgenic sense lines conferred tolerance to the glycosylation inhibitor tunicamycin during germination and tolerance to water deficit during plant growth. Under progressive drought, the leaf BiP levels correlated with the maintenance of the shoot turgidity and water content. The protective effect of BiP overexpression against water stress was disrupted by expression of an antisense BiP cDNA construct. Although overexpression of BiP prevented cellular dehydration, the stomatal conductance and transpiration rate in droughted sense leaves were higher than in control and antisense leaves. The rate of photosynthesis under water deficit might have caused a degree of greater osmotic adjustment in sense leaves because it remained unaffected during water deprivation, which was in marked contrast with the severe drought-induced decrease in the CO2 assimilation in control and antisense leaves. In antisense plants, the water stress stimulation of the antioxidative defenses was higher than in control plants, whereas in droughted sense leaves an induction of superoxide dismutase activity was not observed. These results suggest that overexpression of BiP in plants may prevent endogenous oxidative stress.
The Yttrium Oxide Fluoride Solid Solution Described as a Composite Modulated System
Authors: Schmid S. 
Published: July 2002

Single-crystal X-ray diffraction data (Mo Kα radiation) are used to determine the structure of the Δ = 0.174 member of a (YO1 − ΔFΔ)F1 + Δ, 0.12 ≤ Δ ≤ 0.22, wide-range non-stoichiometric solid solution in the yttrium oxide fluoride system. The structure is refined as a composite modulated structure composed of two mutually incommensurable Q and H substructures with overall superspace-group symmetry Acmm(0,0,1.174..)0s0. The Q substructure has lattice parameters a = 5.415 (2), bQ
= 5.534 (2) and cQ
= 5.525 (2) Å, and superspace-group symmetry Acmm(0,0,1.174..)0s0. The H substructure has lattice parameters a = 5.415 (2), bH
= 1/2bQ
= 2.767 (1) and cH
= 4.696 (2) Å, and superspace-group symmetry Pmcm(0,1/2,0.8518...)s00. Refinement on 338 unique reflections converged to R = 0.025, while a previous conventional superstructure refinement led to R = 0.101. This lowering of the R factor goes hand-in-hand with a substantial reduction in the number of refined parameters.
Two crystal forms of ModE, the molybdate-dependent transcriptional regulator from Escherichia coli
Authors: Hall D. R. , Gourley D. G. , Duke E. M. H. , Leonard G. A. , Anderson L. A. , Pau R. N. , Boxer D. H. , Hunter W. N. 
Published: July 2002

The molybdenum-responsive ModE regulatory protein from Escherichia coli has been purified and used in crystallization trials. Two crystal forms have been observed. Form I is tetragonal, P41212 (or enantiomorph), with a = b = 72.3, c = 246.2 Å and diffracts to medium resolution. Form II is orthorhombic, P21212, with a = 82.8, b = 127.9, c = 64.0 Å and diffraction has been observed beyond 2.8 Å resolution. Structural analysis, in combination with ongoing biochemical characterization, will assist the elucidation of the structure–activity relationship in regulating the uptake of molybdate in bacteria.
Crystallographic analysis of the dsDNA bacteriophage HK97 mature empty capsid
Authors: Wikoff William R. , Duda Robert L. , Hendrix Roger W. , Johnson John E. 
Published: July 2002

HK97 is a member of the Siphovirus family of dsDNA bacteriophages. It is similar in architecture to bacteriophage λ, the type member of this family, with an icosahedral capsid of triangulation number T = 7. No high-resolution structural information is available for the dsDNA phages, and HK97 is the only dsDNA bacteriophage capsid to produce crystals which diffract X-rays. At 650 Å in diameter, the large size of the particle and resultant large unit cell create crystallographic challenges. The empty Head II (mature) particles were expressed in Escherichia coli and assembled in vitro, but they have the same morphology as the mature HK97 capsid. Previously reported Head II crystals diffracting to 3.5 Å resolution are examined here in detail. Although the cell dimensions suggest an orthorhombic lattice, further analysis demonstrated that the space group was monoclinic. This has been confirmed by the present study. Images were recorded on the F1 beamline at CHESS and they were processed and scaled, resulting in a data set with a cumulative completeness of 65% and a scaling R factor of 7.7% to 7 Å. The cell dimensions after post-refinement were a = 580, b = 626, c = 788 Å, β = 90.0°. From the particle dimensions determined by cryo-electron microscopy (cryo-EM), there were determined to be two particles per unit cell. Systematic absences of even reflections along the 0k0 lattice line indicate that the space group is P21. The rotation function was used to determine the orientation of the particles in the unit cell and to confirm the space group. An icosahedral twofold axis is approximately, but not exactly, aligned with the crystallographic screw (b) axis. An icosahedral twofold axis orthogonal to the one approximately parallel to the b axis, is rotated 18° away from the a axis. The centers of the two particles must be positioned close to the minimum-energy packing arrangement for spheres, which places one particle at (1\over4, 0, 1\over4) and the other particle at (3\over4, 1\over2, 3\over4). The particle position and orientation were confirmed by calculating a Patterson function. The particles interact closely along icosahedral threefold axes, which occurs both along the crystallographic a axis and along the b axis. The particle dimensions derived from this packing arrangement agree well with those determined by cryo-EM and image reconstruction. The cryo-EM reconstruction will be used as a model to initiate phase determination; structure determination at 7 Å is under way.
Crystallization and preliminary X-ray analysis of Saccharomyces cerevisiae Ypd1p, a key intermediate in phosphorelay signal transduction
Authors: Lee Myong Gyong , Lee Jae Young , Song Hyun Kyu , Suh Se Won 
Published: July 2002

Ypd1p, a 167-residue protein from Saccharomyces cerevisiae, plays a key role in osmosensing phosphorelay signal transduction. It forms part of a multistep phosphorelay system which also includes Sln1p hybrid histidine kinase and two response regulators, Ssk1p and Skn7p. It has been overexpressed in soluble form in Escherichia coli with a His6-tag at its C-terminus. The recombinant protein has been crystallized at room temperature using ammonium sulfate and lithium sulfate as precipitants. Native diffraction data have been collected to 2.3 Å using synchrotron radiation. The crystals are triclinic, belonging to the space group P1, with unit-cell parameters a = 65.78, b = 66.74, c = 65.75 Å, α = 106.60, β = 106.48, γ = 115.53°. The asymmetric unit contains four molecules of the monomeric recombinant Ypd1p, with a corresponding Vm
of 2.75 Å3 Da−1 and a solvent content of 55.3%.
Crystallization and preliminary X-ray diffraction studies on the N-utilizing substance-B (NusB) from Mycobacterium tuberculosis
Authors: Gopal B. , Cox R. A. , Colston M. J. , Dodson G. G. , Smerdon S. J. , Haire L. F. 
Published: July 2002

N-utilizing substance B (NusB) is a protein which forms part of a complex assembly in transcriptional antitermination in Mycobacterium tuberculosis. It forms a heterodimer with the product of the NusE gene (identical to the ribosomal protein S10) and mediates the process of transcriptional antitermination by forming the core complex with the nut site of the ribosomal RNA along with other protein factors. NusB has been cloned and overexpressed in Escherichia coli and crystallized using the hanging-drop vapour-diffusion method. The space group is P212121, with unit-cell parameters a = 46.6, b = 64.2, c = 90.1 Å. A native data set complete to 1.6 Å resolution has been collected from a single crystal.
Tris(N-cyclohexyl-N-methyldithiocarbamato-S)antimony(III)
Authors: Baba Ibrahim , Ibrahim Sukeria , Farina Yang , Othman A. Hamid , Razak Ibrahim Abdul , Fun Hoong-Kun , Ng Seik Weng 
Published: July 2002

In the title compound, [Sb(C8H14NS2)3], the dithiocarbamate groups chelate to the Sb atom in an anisobidentate manner [Sb—S = 2.530 (1) and 2.975 (1) Å]. The Sb atom lies on a threefold axis and the lone pair is also stereochemically active.
A normalized root‐mean‐spuare distance for comparing protein three‐dimensional structures
Authors: Carugo Oliviero , Pongor Sándor 
Published: July 2002

AbstractThe degree of similarity of two protein three‐dimensional structures is usually measured with the root‐mean‐square distance between equivalent atom pairs. Such a similarity measure depends on the dimension of the proteins, that is, on the number of equivalent atom pairs. The present communication presents a simple procedure to make the root‐mean‐square distances between pairs of three‐dimensional structures independent of their dimensions. This normalization may be useful in evolutionary and fold classification studies as well as in simple comparisons between different structural models.
Time Series Modelling of Childhood Diseases: A Dynamical Systems Approach
Authors: Finkenstädt Bärbel F. , Grenfell Bryan T. 
Published: July 2002

SUMMARY
A key issue in the dynamical modelling of epidemics is the synthesis of complex mathematical models and data by means of time series analysis. We report such an approach, focusing on the particularly well-documented case of measles. We propose the use of a discrete time epidemic model comprising the infected and susceptible class as state variables. The model uses a discrete time version of the susceptible–exposed–infected–recovered type epidemic models, which can be fitted to observed disease incidence time series. We describe a method for reconstructing the dynamics of the susceptible class, which is an unobserved state variable of the dynamical system. The model provides a remarkable fit to the data on case reports of measles in England and Wales from 1944 to 1964. Morever, its systematic part explains the well-documented predominant biennial cyclic pattern. We study the dynamic behaviour of the time series model and show that episodes of annual cyclicity, which have not previously been explained quantitatively, arise as a response to a quicker replenishment of the susceptible class during the baby boom, around 1947.
Proton Exchange Membrane Fuel Cell System Model for Automotive
Vehicle Simulation and Control
Authors: Boettner Daisie D. , Paganelli Gino , Guezennec Yann G. , Rizzoni Giorgio , Moran Michael J. 
Published: July 2002

Abstract
This paper describes a proton exchange membrane (PEM) fuel cell system model for automotive applications that includes an air compressor, cooling system, and other auxiliaries. The fuel cell system model has been integrated into a vehicle performance simulator that determines fuel economy and allows consideration of control strategies. Significant fuel cell system efficiency improvements may be possible through control of the air compressor and other auxiliaries. Fuel cell system efficiency results are presented for two limiting air compressor cases: ideal control and no control. Extension of the present analysis to hybrid configurations consisting of a fuel cell system and battery is currently under study.
The New Genomics: Global Views of Biology
Authors: Lander Eric S. 
Published: July 2002

What will happen after a complete sequence of the human genome is available? Eric Lander argues that it will be the beginning of a new phase of research. He presents 10 goals for the future that are related to a global view of biology.
The author is at the Whitehead Institute for Biomedical Research and the Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA.
Antibiotic Susceptibility Pattern of
Mycobacterium marinum
Authors: Aubry Alexandra , Jarlier Vincent , Escolano Sylvie , Truffot-Pernot Chantal , Cambau Emmanuelle 
Published: July 2002

ABSTRACT

In vitro activities of 17 antibiotics against 53 clinical strains of
Mycobacterium marinum
, an atypical mycobacterium responsible for cutaneous infections, were determined using the reference agar dilution method. Rifampin and rifabutin were the most active drugs (MICs at which 90% of the isolates tested were inhibited [MIC
90
s], 0.5 and 0.6 μg/ml, respectively). MICs of minocycline (MIC
90
, 4 μg/ml), doxycycline (MIC
90
, 16 μg/ml), clarithromycin (MIC
90
, 4 μg/ml), sparfloxacin (MIC
90
, 2 μg/ml), moxifloxacin (MIC
90
, 1 μg/ml), imipenem (MIC
90
, 8 μg/ml), sulfamethoxazole (MIC
90
, 8 μg/ml) and amikacin (MIC
90
, 4 μg/ml) were close to the susceptibility breakpoints. MICs of isoniazid, ethambutol, trimethoprim, azithromycin, ciprofloxacin, ofloxacin, and levofloxacin were above the concentrations usually obtained in vivo. For each drug, the MIC
50
, geometric mean MIC, and modal MIC were very close, showing that all the strains had a similar susceptibility pattern. Percent agreement (within ±1 log
2
dilution) between MICs yielded by the Etest method and by the agar dilution method used as reference were 83, 59, 43, and 24% for minocycline, rifampin, clarithromycin, and sparfloxacin, respectively. Reproducibility with the Etest was low, in contrast to that with the agar dilution method. In conclusion,
M. marinum
is a naturally multidrug-resistant species for which the agar dilution method is more accurate than the Etest for antibiotic susceptibility testing.
Efficacy of Ravuconazole in Treatment of Mucosal Candidosis in SCID Mice
Authors: Clemons Karl V. , Stevens David A. 
Published: July 2002

ABSTRACT

A model of orogastric candidosis in SCID mice, which mimics disease seen in AIDS patients, was used to evaluate ravuconazole in comparison with fluconazole for treatment. Mice were infected orally with
Candida albicans
and received either no treatment or oral treatment once daily for 12 days with 1, 5, or 25 mg of ravuconazole per kg of body weight per day, 5 or 25 mg of fluconazole per kg per day, or diluent (10% dimethyl sulfoxide in 0.5% carboxymethyl cellulose). The numbers of
C. albicans
CFU in the esophagus, stomach, small intestine, and cecum on day 25 in mice given no treatment and diluent were equivalent. Both doses of fluconazole significantly reduced numbers of CFU in all four tissues but were equivalent to each other. Ravuconazole showed dose-responsive improvement of clearance of CFU. Ravuconazole at 25 mg/kg was superior in reduction of numbers of CFU in all tissues to controls or 25 mg of fluconazole per kg and to other regimens in at least three tissues. Fluconazole at 25 mg/kg cured no infection in any tissue, whereas 25 mg of ravuconazole/kg cleared infection in all tissues from 50% of mice. Ravuconazole has good efficacy and the potential to cure mucosal candidosis in the absence of a functional immune response.
In Vitro Activities of Posaconazole, Itraconazole, Voriconazole, Amphotericin B, and Fluconazole against 37 Clinical Isolates of Zygomycetes
Authors: Sun Qiu N. , Fothergill Annette W. , McCarthy Dora I. , Rinaldi Michael G. , Graybill John R. 
Published: July 2002

ABSTRACT
In vitro antifungal susceptibility testing results of a new antifungal triazole, posaconazole (POS), were compared to results with amphotericin B (AMB), itraconazole (ITC), voriconazole (VRC), and fluconazole (FLC) against clinical agents of zygomycosis. The MICs of POS at which 50% and 90% of the isolates were inhibited were 0.25 and 4 μg/ml, respectively. POS was significantly more active than VRC and FLC and slightly more active than ITC. The results suggest that POS has significant potential for clinical development against the zygomycetes.