bluuebunny/crossref_metadata_2025 huggingface dataset:
Room-temperature ferromagnetism in well-aligned Zn1−xCoxO nanorods
Authors: Wu Jih-Jen , Liu Sai-Chang , Yang Ming-Hsun
Published: August 2004

Diluted magnetic semiconductor Zn1−xCoxO nanorods with a Curie temperature higher than 350K have been synthesized by in situ doping of Co in ZnO nanorods using a simple thermal chemical vapor deposition method. Structural analyses indicated that the nanorod possesses the single-crystalline wurtzite structure and there is no segregated cluster of impurity phase appearing throughout the nanorod. The transparence of the Zn1−xCoxO nanorods in the visible region has been examined by UV-visible absorption. The fundamental absorptions of the Zn1−xCoxO nanorods estimated from the absorption spectra do not reveal pronounced difference from that of pure ZnO nanorods.
GaSe crystals for broadband terahertz wave detection
Authors: Liu Kai , Xu Jingzhou , Zhang X.-C.
Published: August 2004

We report experimental results of using GaSe crystals for the broadband detection of terahertz (THz) waves from 100GHzto30THz. In comparison, the THz wave field amplitude measured with a GaSe crystal exceeds that detected by a ZnTe crystal with a comparable detection bandwidth. The central frequency is tunable by varying the angle between the incident THz radiation and the crystal surface normal.
Many-body optical gain of GaInNAs∕GaAs strained quantum-well lasers
Authors: Park Seoung-Hwan
Published: August 2004

Optical properties of strained GaInNAs∕GaAs quantum wells (QWs) are investigated using the multiband effective-mass theory. We also take into account the many-body effects on the optical gain spectrum. It is observed that the transition energy decreases with increasing In or N mole fraction. The theoretical transition energies show very good agreement with the experimental results for several compositions and well widths. The optical gain is shown to increase with increasing compressive or tensile strain. The increase of the transverse electric optical gain is attributed to the fact that the subband energy spacing increases with the strain. On the other hand, the increase of the transverse magnetic optical gain is mainly due to the increases of the optical matrix element. The threshold current density rapidly decreases with increasing well width and begins to saturate near the well width of 80Å. In the case of a QW structure with relatively short cavity length (Lcav=800μm), it is found that the threshold current density is minimum near 80Å. We see that there is a universal relation governing the dependence of the band-gap renormalization on carrier density and the relation is close to ΔEg∝n2D1∕3.
Hollow metallic microspheres produced by spark erosion
Authors: Berkowitz A. E. , Harper H. , Smith David J. , Hu Hao , Jiang Qian , Solomon Virgil C. , Radousky H. B.
Published: August 2004

Hollow spherical particles of Ni, CoFe, the ferromagnetic shape memory alloy Ni49Mn30Ga21, and the giant magnetostrictive alloy Fe83Ga17, with diameters up to several tens of microns were produced by spark erosion, using liquid nitrogen as the dielectric liquid. In contrast, the particles were primarily solid when the dielectric liquid was argon. The wall thicknesses of the hollow particles depended on the elemental composition. Different models are considered to account for the formation of the spark-eroded hollow spheres, and some of the potential benefits to be derived from their use are described.
Poling-assisted bleaching of metal-doped nanocomposite glass
Authors: Deparis Olivier , Kazansky Peter G. , Abdolvand Amin , Podlipensky Alexander , Seifert Gerhard , Graener Heinrich
Published: August 2004

Thermal poling of soda-lime glass which was doped with spherical or ellipsoidal silver nanoparticles has revealed what we believe to be a phenomenon of general interest in the physics of nanocomposite materials: The field-assisted dissolution of metal nanoparticles embedded in glass. Macroscopically, this phenomenon manifested itself as poling-assisted bleaching of the glass in the sense that the glass became more (or even completely) transparent under the anode. The phenomenon is physically interpreted in terms of the ionization of metal nanoclusters followed by the removal of ions from the clusters and their drift in the depth, under the action of the extremely high electric field which is created underneath the anodic surface during poling. The underlying physical mechanism is expected to offer unique opportunities for the control of structural and optical properties of nanocomposite glasses.
Acoustic imaging and collimating by slabs of sonic crystalsmade from arrays of rigid cylinders in air
Authors: Chen Liang-Shan , Kuo Chao-Hsien , Ye Zhen
Published: August 2004

We show some properties of the acoustic propagation in two-dimensional sonic crystals, formed by parallel rigid cylinders placed in air. The transmission through slabs of sonic crystals and the associated band structures are considered. It is shown that within partial band gaps, the waves tend to be collimated or guided into the direction in which the propagation is allowed. Such a feature also prevails in the situations in which deaf bands appear. We show that within the partial band gaps, a stable imaging effect can be obtained for flat sonic crystal slabs, in analogy to the cases with photonic crystals.
Estimating the diameter∕thickness of a pipe using the primary wave velocity of a hollow cylindrical guided wave
Authors: Nishino Hideo , Takemoto Mikio , Chubachi Noriyoshi
Published: August 2004

A method for measuring the diameter/thickness (d∕t) of a pipe using a characteristic of a hollow cylindrical guided wave (HCGW) is presented. The HCGW is an ultrasonic guided wave propagating along a pipe. In the first part of this letter, we briefly show that the primary wave (first-arriving wave packet from an impulse source) of the HCGW achieves a faster group velocity for a larger d∕t. Experimental verifications were carried out for aluminum pipes (several different d∕t’s) using a laser ultrasonic method to generate the HCGW. The experimental results are in fairly good agreement with the theoretical prediction described.
The role of thermally-induced internal stresses on the tunabilityof textured barium strontium titanate films
Authors: Sharma A. , Ban Z.-G. , Alpay S. P. , Mantese J. V.
Published: August 2004

The tunability of highly textured thin films of barium strontium titanate (Ba0.5Sr0.5TiO3, BST) is analyzed theoretically using a Landau–Devonshire thermodynamic model. The relative dielectric constant of BST films is determined as functions of the applied external electric field, deposition temperature, and the thermal expansion coefficient of the substrate. Our analysis shows that tunability is highly dependent upon thermally induced strains within the material. Both tension and compression produce deleterious tuning response. However, this effect can be minimized through judicious choices of deposition temperature and appropriate substrate material.
Hopping versus bulk conductivity in transparent oxides: 12CaO∙7Al2O3
Authors: Medvedeva J. E. , Freeman A. J.
Published: August 2004

First-principles calculations of the mayenite-based oxide, [Ca12Al14O32]2+(2e−), reveal the mechanism responsible for its high conductivity. A detailed comparison of the electronic and optical properties of this material with those of the recently discovered transparent conducting oxide, H-doped UV-activated Ca12Al14O33, allowed us to conclude that the enhanced conductivity in [Ca12Al14O32]2+(2e−) is achieved by elimination of the Coulomb blockade of the charge carriers. This results in a transition from variable range-hopping behavior with a Coulomb gap in H-doped UV-irradiated Ca12Al14O33, to bulk conductivity in [Ca12Al14O32]2+(2e−). Further, the high degree of delocalization of the conduction electrons obtained in [Ca12Al14O32]2+(2e−) indicates that it cannot be classified as an electride, as originally suggested.
Instant curvature measurement for microcantilever sensors
Authors: Jeon Sangmin , Thundat Thomas
Published: August 2004

A multiple-point deflection technique has been developed for the instant measurement of microcantilever curvature. Eight light-emitting diodes are focused on various positions of a gold-coated silicon cantilever through optical fibers, and temperature change or chemical adsorption induces cantilever bending. The deflection at each point on the cantilever is measured with subnanometer precision by a position-sensitive detector, and thus the curvature of the cantilever is obtained.
Magneto-Seebeck coefficient of a bismuth microwire arrayin a magnetic field
Authors: Hasegawa Y. , Ishikawa Y. , Komine T. , Huber T. E. , Suzuki A. , Morita H. , Shirai H.
Published: August 2004

The enhancement of the magneto-Seebeck coefficient of a bismuth microwire array under a magnetic field is measured at temperatures from 45to295K. The measured magneto-Seebeck coefficient exhibits a peak at a certain magnitude of magnetic field, with the peak shifting to higher magnetic fields and becoming broader with increasing temperature. The results show that the magneto-Seebeck coefficient can be improved by approximately 20% by applying an appropriate external magnetic field and temperature. The Boltzmann equation with a relaxation-time approximation is solved numerically to determine the magnetic field and temperature dependences of the magneto-Seebeck coefficient for the bismuth microwire array. The experimental results are compared with calculations, and the two sets of results are shown to be in very good agreement, clarifying the mechanisms contributing to the magneto-Seebeck coefficient for bismuth. The wire array structure is thus suitable for enhancing the thermoelectric properties of materials in a magnetic field.
Traveling-wave thermoacoustic electric generator
Authors: Backhaus S. , Tward E. , Petach M.
Published: August 2004

Traveling-wave thermoacoustic heat engines have been demonstrated to convert high-temperature heat to acoustic power with high efficiency without using moving parts. Electrodynamic linear alternators and compressors have demonstrated high acoustic-to-electric transduction efficiency as well as long maintenance-free lifetimes. By optimizing a small-scale traveling-wave thermoacoustic engine for use with an electrodynamic linear alternator, we have created a traveling-wave thermoacoustic electric generator; a power conversion system suitable for demanding applications such as electricity generation aboard spacecraft.
In
As
∕
Ga
As
self-assembled quantum-dot lasers grown by metalorganic chemical vapor deposition—Effects of postgrowth annealing on stacked InAs quantum dots
Authors: Tatebayashi Jun , Arakawa Yasuhiko , Hatori Nobuaki , Ebe Hiroji , Sugawara Mitsuru , Sudo Hisao , Kuramata Akito
Published: August 2004

We investigated the effects of postgrowth annealing on stacked InAs∕GaAs quantum dots. The blueshift in emission energy by postgrowth annealing depends on the temperature of postgrowth annealing and the growth conditions of stacked InAs quantum dots, such as a spacer thickness or a stacking number. We can control the peak wavelength of stacked InAs quantum dots by changing the temperature of postgrowth annealing and the growth conditions of stacked InAs quantum dots. We achieved continuous-wave lasing with a threshold current of 16.4mA at the wavelength of 1.245μm from five layer vertically aligned InAs quantum dots whose upper cladding layer was grown at 600°C.
Effect of metal electrodes on the performance of polymer:fullerene bulk heterojunction solar cells
Authors: Mihailetchi V. D. , Koster L. J. A. , Blom P. W. M.
Published: August 2004

An increase in the workfunction of the metal top electrode leads to a reduction of the open-circuit voltage, short-circuit current, and power conversion efficiency of organic bulk-heterojunction solar cells. It has been demonstrated that the photocurrent obtained from an active layer comprised of a blend of poly(2-methoxy-5-(3′,7′-dimethyloctyloxy)-p-phenylenevinylene) (OC1C10-PPV) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM), with lithium fluoride topped aluminum, silver, gold, or palladium electrodes, shows a universal behavior when scaled against the effective voltage across the device. Indeed, model calculations confirm that the dependence of the photocurrent on the effective voltage is responsible for the observed variation in performance of each different electrode. Consequently, for any given metal, only the device’s open-circuit voltage is required in order to be able to predict the remaining solar cell parameters.
Optical gain in homoepitaxial GaN
Authors: Juršėnas S. , Kurilčik N. , Kurilčik G. , Miasojedovas S. , Žukauskas A. , Suski T. , Perlin P. , Leszczynski M. , Prystawko P. , Grzegory I.
Published: August 2004

Optical gain in GaN epilayers, grown by metalorganic chemical-vapor deposition technique on bulk GaN substrates is studied by means of time-resolved luminescence spectroscopy at room temperature. Both stimulated emission and carrier recombination rate are analyzed under high photoexcitation conditions that are close to laser operation regime. Homoepitaxial GaN shows a high value of optical gain coefficient g=7200cm−1 estimated under intense pulsed excitation by a variable stripe method. For comparison, a GaN epilayer grown under identical conditions on sapphire shows a significantly lower value, g=2300cm−1. Larger values of the optical gain coefficient achieved in homoepitaxial GaN are due to the lower density of nonradiative traps. This is proved by the carrier capture time that is estimated right after exhaustion of the inverted population, and has values of τe=970 and 195ps for homo- and heterolayers, respectively.
Amelioration of proteolipid protein 139–151-induced encephalomyelitis in SJL mice by modified amino acid copolymers and their mechanisms
Authors: Stern Joel N. H. , Illés Zsolt , Reddy Jayagopala , Keskin Derin B. , Sheu Eric , Fridkis-Hareli Masha , Nishimura Hiroyuki , Brosnan Celia F. , Santambrogio Laura , Kuchroo Vijay K. , Strominger Jack L.
Published: August 2004

Copolymer 1 [Cop1, glatiramer acetate, Copaxone, poly(Y,E,A,K)n] is widely used in the treatment of relapsing/remitting multiple sclerosis in which it reduces the frequency of relapses by ≈30%. In the present study, copolymers with modified amino acid compositions (based on the binding motif of myelin basic protein 85–99 to HLA-DR2) have been developed with the aim of suppressing multiple sclerosis more effectively. The enhanced efficacy of these copolymers in experimental autoimmune encephalomyelitis (EAE) induced in SJL/J mice with proteolipid protein 139–151 was demonstrated by using three protocols: (i) simultaneous administration of autoantigen and copolymer (termed prevention), (ii) pretreatment with copolymers (vaccination), or (iii) administration of copolymers after disease onset (treatment). Strikingly, in the treatment protocol administration of soluble VWAK and FYAK after onset of disease led to stasis of its progression and suppression of histopathological evidence of EAE. The mechanisms by which these effects are achieved have been examined in several types of assays: binding of copolymers to I-Asin competition with proteolipid protein 139–151 (blocking), cytokine production by T cells (T helper 2 polarization), and transfer of protection by CD3+splenocytes or, notably, by copolymer-specific T cell lines (induction of regulatory T cells). The generation of these copolymer-specific regulatory T cells that secrete IL-4 and IL-10 and are independent of the immunizing autoantigen is very prominent among the multiple mechanisms that account for the observed suppressive effect of copolymers in EAE.
Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution
Authors: Hwang Dick G. , Green Phil
Published: August 2004

We describe a model of neutral DNA evolution that allows substitution rates at a site to depend on the two flanking nucleotides (“context”), the branch of the phylogenetic tree, and position within the sequence and implement it by using a flexible and computationally efficient Bayesian Markov chain Monte Carlo approach. We then apply this approach to characterize phylogenetic variation in context-dependent substitution patterns in a 1.7-megabase genomic region in 19 mammalian species. In contrast to other substitution types, CpG transition substitutions have accumulated in a relatively clock-like fashion. More broadly, our results support the notion that context-dependent DNA replication errors, cytosine deamination, and biased gene conversion are major sources of naturally occurring mutations whose relative contributions have varied in mammalian evolution as a result of changes in generation times, effective population sizes, and recombination rates.
Tetrodotoxin-sensitive Na
+
channels and muscarinic and purinergic receptors identified in human erythroid progenitor cells and red blood cell ghosts
Authors: Hoffman Joseph F. , Dodson Alicia , Wickrema Amittha , Dib-Hajj Sulayman D.
Published: August 2004

This article concerns the identification of different types of voltage-gated Na
+
channels and of muscarinic and purinergic receptors that are expressed in human erythroid precursor cells and red cell ghosts. We analyzed, by RT-PCR, RNA that was extracted from purified and synchronously growing human erythroid progenitor cells, differentiating from erythroblasts to reticulocytes in 7 to 14 days. These extracts were free of white cell and platelet contamination. Two types of voltage-gated, tetrodotoxin-sensitive Na
+
channels were found. These were Na
v
1.4 and Na
v
1.7, the former known to be present in skeletal muscle and the latter in peripheral nerve. By using a pan Na
+
channel antibody and Western blotting, an immunoreactive channel was detected in ghosts of human red blood cells, consistent with the expression of these two channels. The transcripts for four of the five known subtypes of muscarinic receptors were also identified, including subtypes M2, M3, M4, and M5, whereas subtype M1 was not found. Expression was also detected for the purinergic type receptors P2X
1
, P2X
4
, P2X
7
, and P2Y
1
whereas types P2Y
2
, P2Y
4
, and P2Y
6
were not found. We also searched for but did not find transcripts for hBNP-1, a type 1b human brain sodium phosphate cotransporter, and cystic fibrosis transmembrane conductance regulator (CFTR). Implications regarding the presence of these different types of channels and receptors in human red blood cells and their functional significance are discussed.
Single-molecule study of RuvAB-mediated Holliday-junction migration
Authors: Dawid A. , Croquette V. , Grigoriev M. , Heslot F.
Published: August 2004

Branch migration of Holliday junctions is an important step of genetic recombination and DNA repair. In
Escherichia coli
, this process is driven by the RuvAB complex acting as a molecular motor. Using magnetic tweezers, we studied the RuvAB-directed migration of individual Holliday junctions formed between two ≈6-kb DNA molecules of identical sequence, and we measured the migration rate at 37°C and 1 mM ATP. We directly demonstrate that RuvAB is a highly processive DNA motor protein that is able to drive continuous and unidirectional branch migration of Holliday junctions at a well defined average speed over several kilobases through homologous sequences. We observed directional inversions of the migration at the DNA molecule boundaries leading to forth-and-back migration of the branch point and allowing us to measure the migration rate in the presence of negative or positive loads. The average migration rate at zero load was found to be ≈43 bp/sec. Furthermore, the load dependence of the migration rate is small, within the force range of –3.4 pN (hindering force) to +3.4 pN (assisting force).
De novo
design of catalytic proteins
Authors: Kaplan J. , DeGrado W. F.
Published: August 2004

The
de novo
design of catalytic proteins provides a stringent test of our understanding of enzyme function, while simultaneously laying the groundwork for the design of novel catalysts. Here we describe the design of an O
2
-dependent phenol oxidase whose structure, sequence, and activity are designed from first principles. The protein catalyzes the two-electron oxidation of 4-aminophenol (
k
cat
/
K
M
= 1,500 M
·1
·min
·1
) to the corresponding quinone monoimine by using a diiron cofactor. The catalytic efficiency is sensitive to changes of the size of a methyl group in the protein, illustrating the specificity of the design.
Humoral immune response to native eukaryotic prion protein correlates with anti-prion protection
Authors: Polymenidou Magdalini , Heppner Frank L. , Pellicioli Erica C. , Urich Eduard , Miele Gino , Braun Nathalie , Wopfner Franziska , Schätzl Hermann M. , Becher Burkhard , Aguzzi Adriano
Published: August 2004

Prion diseases are characterized by the deposition of an abnormal form (termed PrP
Sc
) of the cellular prion protein (PrP
C
). Because antibodies to PrP
C
can antagonize deposition of PrP
Sc
in cultured cells and mice, they may be useful for anti-prion therapy. However, induction of protective anti-prion immune responses in WT animals may be hindered by host tolerance. Here, we studied the cellular and molecular basis of tolerance to PrP
C
. Immunization of
Prnp
o/o
mice with bacterially expressed PrP (PrP
REC
) resulted in vigorous humoral immune responses to PrP
REC
and native cell-surface PrP
C
. Instead, WT mice yielded antibodies that failed to recognize native PrP
C
despite immunoreactivity with PrP
REC
, even after immunization with PrP-PrP polyprotein and/or upon administration of anti-OX40 antibodies. Consequently, immunized WT mice experienced insignificantly delayed prion pathogenesis upon peripheral prion challenge. Anti-PrP immune responses in
Prnp
o/o
mice were completely abrogated by transgenic expression of PrP
C
in B cells, T cells, neurons, or hepatocytes, but only moderately reduced by expression in myelinating cells, despite additional thymic
Prnp
transcription in each case. We conclude that tolerance to PrP
C
can coexist with immunoreactivity to PrP
REC
and does not depend on thymic PrP
C
expression. Its circumvention might represent an important step toward the development of effective anti-prion immunotherapy.
Localization of RNAs to the Mitochondrial Cloud inXenopusOocytes through Entrapment and Association with Endoplasmic Reticulum
Authors: Chang Patrick , Torres Jan , Lewis Raymond A. , Mowry Kimberly L. , Houliston Evelyn , King Mary Lou
Published: August 2004

The germ cell lineage in Xenopus is specified by the inheritance of germ plasm, which originates within a distinct “mitochondrial cloud” (MC) in previtellogenic oocytes. Germ plasm contains localized RNAs implicated in germ cell development, including Xcat2 and Xdazl. To understand the mechanism of the early pathway through which RNAs localize to the MC, we applied live confocal imaging and photobleaching analysis to oocytes microinjected with fluorescent Xcat2 and Xdazl RNA constructs. These RNAs dispersed evenly throughout the cytoplasm through diffusion and then became progressively immobilized and formed aggregates in the MC. Entrapment in the MC was not prevented by microtubule disruption and did not require localization to germinal granules. Immobilized RNA constructs codistributed and showed coordinated movement with densely packed endoplasmic reticulum (ER) concentrated in the MC, as revealed with Dil16(3) labeling and immunofluorescence analysis. Vg1RBP/Vera protein, which has been implicated in linking late pathway RNAs to vegetal ER, was shown to bind specifically both wild-type Xcat2 3′ untranslated region and localization-defective constructs. We found endogenous Vg1RBP/Vera and Vg1RBP/Vera-green fluorescent protein to be largely excluded from the MC but subsequently to codistribute with Xcat2 and ER at the vegetal cortex. We conclude that germ line RNAs localize into the MC through a diffusion/entrapment mechanism involving Vg1RBP/Vera-independent association with ER.
Intracellular Macromolecular Mobility Measured by Fluorescence Recovery after Photobleaching with Confocal Laser Scanning Microscopes
Authors: Braga José , Desterro Joana M.P. , Carmo-Fonseca Maria
Published: August 2004

Fluorescence recovery after photobleaching (FRAP) is a widely used tool for estimating mobility parameters of fluorescently tagged molecules in cells. Despite the widespread use of confocal laser scanning microscopes (CLSMs) to perform photobleaching experiments, quantitative data analysis has been limited by lack of appropriate practical models. Here, we present a new approximate FRAP model for use on any standard CLSM. The main novelty of the method is that it takes into account diffusion of highly mobile molecules during the bleach phase. In fact, we show that by the time the first postbleach image is acquired in a CLSM a significant fluorescence recovery of fast-moving molecules has already taken place. The model was tested by generating simulated FRAP recovery curves for a wide range of diffusion coefficients and immobile fractions. The method was further validated by an experimental determination of the diffusion coefficient of fluorescent dextrans and green fluorescent protein. The new FRAP method was used to compare the mobility rates of fluorescent dextrans of 20, 40, 70, and 500 kDa in aqueous solution and in the nucleus of living HeLa cells. Diffusion coefficients were lower in the nucleoplasm, particularly for higher molecular weight dextrans. This is most likely caused by a sterical hindrance effect imposed by nuclear components. Decreasing the temperature from 37 to 22°C reduces the dextran diffusion rates by ∼30% in aqueous solution but has little effect on mobility in the nucleoplasm. This suggests that spatial constraints to diffusion of dextrans inside the nucleus are insensitive to temperature.
VOZ; Isolation and Characterization of Novel Vascular Plant Transcription Factors with a One-Zinc Finger from Arabidopsis thaliana
Authors: Mitsuda Nobutaka , Hisabori Toru , Takeyasu Kunio , Sato Masa H.
Published: August 2004

A 38-bp pollen-specific cis-acting region of the AVP1 gene is involved in the expression of the Arabidopsis thaliana V-PPase during pollen development. Here, we report the isolation and structural characterization of AtVOZ1 and AtVOZ2, novel transcription factors that bind to the 38-bp cis-acting region of A. thaliana V-PPase gene, AVP1. AtVOZ1 and AtVOZ2 show 53% amino acid sequence similarity. Homologs of AtVOZ1 and AtVOZ2 are found in various vascular plants as well as a moss, Physcomitrella patens. Promoter-β-glucuronidase reporter analysis shows that AtVOZ1 is specifically expressed in the phloem tissue and AtVOZ2 is strongly expressed in the root. In vivo transient effector-reporter analysis in A. thaliana suspension-cultured cells demonstrates that AtVOZ1 and AtVOZ2 function as transcriptional activators in the Arabidopsis cell. Two conserved regions termed Domain-A and Domain-B were identified from an alignment of AtVOZ proteins and their homologs of O. sativa and P. patens. AtVOZ2 binds as a dimer to the specific palindromic sequence, GCGTNx7ACGC, with Domain-B, which is comprised of a functional novel zinc coordinating motif and a conserved basic region. Domain-B is shown to function as both the DNA-binding and the dimerization domains of AtVOZ2. From highly the conservative nature among all identified VOZ proteins, we conclude that Domain-B is responsible for the DNA binding and dimerization of all VOZ-family proteins and designate it as the VOZ-domain.
Genome-Wide Analysis of Arabidopsis Pentatricopeptide Repeat Proteins Reveals Their Essential Role in Organelle Biogenesis[W]
Authors: Lurin Claire , Andreés Charles , Aubourg Seébastien , Bellaoui Mohammed , Bitton Freédeérique , Bruyère Cleémence , Caboche Michel , Debast Ceédrig , Gualberto Joseé , Hoffmann Beate , Lecharny Alain , Le Ret Monique , Martin-Magniette Marie-Laure , Mireau Hakim , Peeters Nemo , Renou Jean-Pierre , Szurek Boris , Taconnat Ludivine , Small Ian
Published: August 2004

The complete sequence of the Arabidopsis thaliana genome revealed thousands of previously unsuspected genes, many of which cannot be ascribed even putative functions. One of the largest and most enigmatic gene families discovered in this way is characterized by tandem arrays of pentatricopeptide repeats (PPRs). We describe a detailed bioinformatic analysis of 441 members of the Arabidopsis PPR family plus genomic and genetic data on the expression (microarray data), localization (green fluorescent protein and red fluorescent protein fusions), and general function (insertion mutants and RNA binding assays) of many family members. The basic picture that arises from these studies is that PPR proteins play constitutive, often essential roles in mitochondria and chloroplasts, probably via binding to organellar transcripts. These results confirm, but massively extend, the very sparse observations previously obtained from detailed characterization of individual mutants in other organisms.
Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis[W]
Authors: Sunkar Ramanjulu , Zhu Jian-Kang
Published: August 2004

MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are small noncoding RNAs that have recently emerged as important regulators of mRNA degradation, translational repression, and chromatin modification. In Arabidopsis thaliana, 43 miRNAs comprising 15 families have been reported thus far. In an attempt to identify novel and abiotic stress regulated miRNAs and siRNAs, we constructed a library of small RNAs from Arabidopsis seedlings exposed to dehydration, salinity, or cold stress or to the plant stress hormone abscisic acid. Sequencing of the library and subsequent analysis revealed 26 new miRNAs from 34 loci, forming 15 new families. Two of the new miRNAs from three loci are members of previously reported miR171 and miR319 families. Some of the miRNAs are preferentially expressed in specific tissues, and several are either upregulated or downregulated by abiotic stresses. Ten of the miRNAs are highly conserved in other plant species. Fifty-one potential targets with diverse function were predicted for the newly identified miRNAs based on sequence complementarity. In addition to miRNAs, we identified 102 other novel endogenous small RNAs in Arabidopsis. These findings suggest that a large number of miRNAs and other small regulatory RNAs are encoded by the Arabidopsis genome and that some of them may play important roles in plant responses to environmental stresses as well as in development and genome maintenance.
Functional Specialization amongst the Arabidopsis Toc159 Family of Chloroplast Protein Import Receptors[W]
Authors: Kubis Sybille , Patel Ramesh , Combe Jonathan , Beédard Jocelyn , Kovacheva Sabina , Lilley Kathryn , Biehl Alexander , Leister Dario , Riéos Gabino , Koncz Csaba , Jarvis Paul
Published: August 2004

The initial stages of preprotein import into chloroplasts are mediated by the receptor GTPase Toc159. In Arabidopsis thaliana, Toc159 is encoded by a small gene family: atTOC159, atTOC132, atTOC120, and atTOC90. Phylogenetic analysis suggested that at least two distinct Toc159 subtypes, characterized by atToc159 and atToc132/atToc120, exist in plants. atTOC159 was strongly expressed in young, photosynthetic tissues, whereas atTOC132 and atTOC120 were expressed at a uniformly low level and so were relatively prominent in nonphotosynthetic tissues. Based on the albino phenotype of its knockout mutant, atToc159 was previously proposed to be a receptor with specificity for photosynthetic preproteins. To elucidate the roles of the other isoforms, we characterized Arabidopsis knockout mutants for each one. None of the single mutants had strong visible phenotypes, but toc132 toc120 double homozygotes appeared similar to toc159, indicating redundancy between atToc132 and atToc120. Transgenic complementation studies confirmed this redundancy but revealed little functional overlap between atToc132/atToc120 and atToc159 or atToc90. Unlike toc159, toc132 toc120 caused structural abnormalities in root plastids. Furthermore, when proteomics and transcriptomics were used to compare toc132 with ppi1 (a receptor mutant that is specifically defective in the expression, import, and accumulation of photosynthetic proteins), major differences were observed, suggesting that atToc132 (and atToc120) has specificity for nonphotosynthetic proteins. When both atToc159 and the major isoform of the other subtype, atToc132, were absent, an embryo-lethal phenotype resulted, demonstrating the essential role of Toc159 in the import mechanism.
Homologs of Plant PsbP and PsbQ Proteins Are Necessary for Regulation of Photosystem II Activity in the CyanobacteriumSynechocystis6803[W]
Authors: Thornton Leeann E. , Ohkawa Hiroshi , Roose Johnna L. , Kashino Yasuhiro , Keren Nir , Pakrasi Himadri B.
Published: August 2004

The mechanism of oxygen evolution by photosystem II (PSII) has remained highly conserved during the course of evolution from ancestral cyanobacteria to green plants. A cluster of manganese, calcium, and chloride ions, whose binding environment is optimized by PSII extrinsic proteins, catalyzes this water-splitting reaction. The accepted view is that in plants and green algae, the three extrinsic proteins are PsbO, PsbP, and PsbQ, whereas in cyanobacteria, they are PsbO, PsbV, and PsbU. Our previous proteomic analysis established the presence of a PsbQ homolog in the cyanobacterium Synechocystis 6803. The current study additionally demonstrates the presence of a PsbP homolog in cyanobacterial PSII. Both psbP and psbQ inactivation mutants exhibited reduced photoautotrophic growth as well as decreased water oxidation activity under CaCl2-depleted conditions. Moreover, purified PSII complexes from each mutant had significantly reduced activity. In cyanobacteria, one PsbQ is present per PSII complex, whereas PsbP is significantly substoichiometric. These findings indicate that both PsbP and PsbQ proteins are regulators that are necessary for the biogenesis of optimally active PSII in Synechocystis 6803. The new picture emerging from these data is that five extrinsic PSII proteins, PsbO, PsbP, PsbQ, PsbU, and PsbV, are present in cyanobacteria, two of which, PsbU and PsbV, have been lost during the evolution of green plants.
The Oxylipin Signal Jasmonic Acid Is Activated by an Enzyme That Conjugates It to Isoleucine in Arabidopsis[W]
Authors: Staswick Paul E. , Tiryaki Iskender
Published: August 2004

Despite its importance in a variety of plant defense responses, our understanding of how jasmonic acid (JA) functions at the biochemical level is limited. Several amino acid conjugates of JA were tested for their ability to complement the JA-insensitive Arabidopsis thaliana mutant jar1-1. Unlike free JA, JA-Ile inhibited root growth in jar1-1 to the same extent as in the wild type, whereas JA-Val, JA-Leu, and JA-Phe were ineffective inhibitors in both genotypes. Thin-layer chromatography and gas chromatography–mass spectrometry (GC-MS) analysis of products produced in vitro by recombinant JAR1 demonstrated that this enzyme forms JA-amido conjugates with several amino acids, including JA-Ile. JA-Val, -Leu, -Ile, and -Phe were each quantified in Arabidopsis seedlings by GC-MS. JA-Ile was found at 29.6 pmole g−1 fresh weight (FW) in the wild type but was more than sevenfold lower in two jar1 alleles. JA-Leu, -Val, and -Phe were present at only low levels in both genotypes. Expression of wild-type JAR1 in transgenic jar1-1 plants restored sensitivity to JA and elevated JA-Ile to the same level as in the wild type. The ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) conjugated to JA was also found in plant tissue at 18.4 pmole g−1 FW. JA-ACC was determined not be an effective jasmonate root inhibitor, and surprisingly, was twofold higher in the mutants than in the wild type. This suggests that another JA-conjugating enzyme(s) is present in Arabidopsis. Synthesis of JA-ACC might provide a mechanism to coregulate the availability of JA and ACC for conversion to the active hormones JA-Ile and ethylene, respectively. We conclude that JAR1 is a JA-amino synthetase that is required to activate JA for optimal signaling in Arabidopsis. Plant hormone activation by conjugation to amino acids and the enzymes involved in their formation were previously unknown.
A new framework for the estimation of control parameters in metabolic pathways using lin‐log kinetics
Authors: Wu Liang , Wang Weiming , van Winden Wouter A. , van Gulik Walter M. , Heijnen Joseph J.
Published: August 2004

The control properties of biochemical pathways can be described by control coefficients and elasticities, as defined in the framework of metabolic control analysis. The determination of these parameters using the traditional metabolic control analysis relationships is, however, limited by experimental difficulties (e.g. realizing and measuring small changes in biological systems) and lack of appropriate mathematical procedures (e.g. when the more practical large changes are made). In this paper, the recently developed lin‐log approach is proposed to avoid the above‐mentioned problems and is applied to estimate control parameters from measurements obtained in steady state experiments. The lin‐log approach employs approximative linear‐logarithmic kinetics parameterized by elasticities and provides analytical solutions for fluxes and metabolite concentrations when large changes are made. Published flux and metabolite concentration data are used, obtained from a reconstructed section of glycolysis converting 3‐phosphoglycerate to pyruvate [Giersch, C. (1995) Eur. J. Biochem. 227, 194–201]. With the lin‐log approach, all data from different experiments can be combined to give realistic elasticity and flux control coefficient estimates by linear regression. Despite the large changes, a good agreement of fluxes and metabolite concentrations is obtained between the measured and calculated values according to the lin‐log model. Furthermore, it is shown that the lin‐log approach allows a rigorous statistical evaluation to identify the optimal reference state and the optimal model structure assumption. In conclusion, the lin‐log approach addresses practical problems encountered in the traditional metabolic control analysis‐based methods by introducing suitable nonlinear kinetics, thus providing a novel framework with improved procedures for the estimation of elasticities and control parameters from large perturbation experiments.
Functional properties of the protein disulfide oxidoreductase from the archaeon Pyrococcus furiosus
Authors: Pedone Emilia , Ren Bin , Ladenstein Rudolf , Rossi Mosè , Bartolucci Simonetta
Published: August 2004

Protein disulfide oxidoreductases are ubiquitous redox enzymes that catalyse dithiol–disulfide exchange reactions with a CXXC sequence motif at their active site. A disulfide oxidoreductase, a highly thermostable protein, was isolated from Pyrococcus furiosus (PfPDO), which is characterized by two redox sites (CXXC) and an unusual molecular mass. Its 3D structure at high resolution suggests that it may be related to the multidomain protein disulfide‐isomerase (PDI), which is currently known only in eukaryotes. This work focuses on the functional characterization of PfPDO as well as its relation to the eukaryotic PDIs. Assays of oxidative, reductive, and isomerase activities of PfPDO were performed, which revealed that the archaeal protein not only has oxidative and reductive activity, but also isomerase activity. On the basis of structural data, two single mutants (C35S and C146S) and a double mutant (C35S/C146S) of PfPDO were constructed and analyzed to elucidate the specific roles of the two redox sites. The results indicate that the CPYC site in the C‐terminal half of the protein is fundamental to reductive/oxidative activity, whereas isomerase activity requires both active sites. In comparison with PDI, the ATPase activity was tested for PfPDO, which was found to be cation‐dependent with a basic pH optimum and an optimum temperature of 90 °C. These results and an investigation on genomic sequence databases indicate that PfPDO may be an ancestor of the eukaryotic PDI and belongs to a novel protein disulfide oxidoreductase family.
Functional characterization of the evolutionarily divergent fern plastocyanin
Authors: Navarro José A. , Lowe Christian E. , Amons Reinout , Kohzuma Takamitsu , Canters Gerard W. , De la Rosa Miguel A. , Ubbink Marcellus , Hervás Manuel
Published: August 2004

Plastocyanin (Pc) is a soluble copper protein that transfers electrons from cytochrome b6f to photosystem I (PSI), two protein complexes that are localized in the thylakoid membranes in chloroplasts. The surface electrostatic potential distribution of Pc plays a key role in complex formation with the membrane‐bound partners. It is practically identical for Pcs from plants and green algae, but is quite different for Pc from ferns. Here we report on a laser flash kinetic analysis of PSI reduction by Pc from various eukaryotic and prokaryotic organisms. The reaction of fern Pc with fern PSI fits a two‐step kinetic model, consisting of complex formation and electron transfer, whereas other plant systems exhibit a mechanism that requires an additional intracomplex rearrangement step. The fern Pc interacts inefficiently with spinach PSI, showing no detectable complex formation. This can be explained by assuming that the unusual surface charge distribution of fern Pc impairs the interaction. Fern PSI behaves in a similar way as spinach PSI in reaction with other Pcs. The reactivity of fern Pc towards several soluble c‐type cytochromes, including cytochrome f, has been analysed by flavin‐photosensitized laser flash photolysis, demonstrating that the specific surface motifs for the interaction with cytochrome f are conserved in fern Pc.
Morphology of the long and short uveal nerves in the human eye
Authors: May Chr. Albrecht
Published: August 2004

The aim of this study was to examine the architecture of the uveal nerves in the sclera and suprachoroid of human eyes. Eyes from 17 adult human donors were investigated. The uveal nerves in different regions (retrobulbar, intrascleral, suprachoroidal, pars plana) were prepared and studied by light and electron microscopy. In addition, immunohistochemistry was performed for various neuronal markers. The long uveal nerves showed a characteristic suprachoroidal location with no branches supplying the choroid. It was found that typically they are composed of myelinated (75%) and non‐myelinated (25%) nerve fibres. They mainly contain aminergic and sensory nerve fibres. A separate set of cholinergic non‐myelinated nerve fibre bundles runs parallel with these long uveal nerves. The short uveal nerves supply the suprachoroidal nerve plexus with approximately 13% of their nerve fibres. The nerves and the branches supplying the choroid appear as mixed nerves containing sympathetic, parasympathetic and sensory axons. This study therefore provides new information about the quantity, type and distribution of myelinated and non‐myelinated nerve fibres in the posterior uvea of the human eye.
Does the degree of laminarity correlate with site‐specific differences in collagen fibre orientation in primary bone? An evaluation in the turkey ulna diaphysis
Authors: Skedros John G. , Hunt Kenneth J.
Published: August 2004

de Margerie hypothesized that preferred orientations of primary vascular canals in avian primary cortical bone mediate important mechanical adaptations. Specifically, bones that receive habitual compression, tension or bending stresses typically have cortices with a low laminarity index (LI) (i.e. relatively lower cross‐sectional areas of circularly (C) orientated primary vascular canals, and relatively higher areas of canals with radial (R), oblique (O) or longitudinal (L) orientations. By contrast, bones subject to habitual torsion have a high LI (i.e. relatively higher C‐orientated canal area) [LI, based on percentage vascular canal area, = C/(C + R + O + L)]. Regional variations in predominant collagen fibre orientation (CFO) may be the adaptive characteristic mediated by LI. Using turkey ulnae, we tested the hypothesis that site‐specific variations in predominant CFO and LI are strongly correlated. Mid‐diaphyseal cross‐sections (100 ± 5 µm) from subadult and adult bones were evaluated for CFO and LI using circularly polarized light images of cortical octants. Results showing significant differences between mean LI of subadult (40.0% ± 10.7%) and adult (50.9% ± 10.4%) (P < 0.01) bones suggest that adult bones experience more prevalent/predominant torsion. Alternatively, this relationship may reflect differences in growth rates. High positive correlations between LI and predominant CFO (subadults: r = 0.735; adults: r = 0.866; P < 0.001) suggest that primary bone can exhibit potentially adaptive material variations that are independent of secondary osteon formation.
Expression of amyloid precursor protein‐like molecule in astroglial cells of the subventricular zone and rostral migratory stream of the adult rat forebrain
Authors: Yasuoka Katsunori , Hirata Kazuho , Kuraoka Akio , He Jian‐wen , Kawabuchi Masaru
Published: August 2004

In adult mammals, new neurons in the subventricular zone (SVZ) of the lateral ventricle (LV) migrate tangentially through the rostral migratory stream (RMS) to the olfactory bulb (OB), where they mature into local interneurons. Using a monoclonal antibody for the β‐amyloid precursor protein (APP) (mAb 22C11), which is specific for the amino‐terminal region of the secreted form of APP and recognizes all APP isoforms and APP‐related proteins, immunoreactivity was detected in specific subpopulations of cells in the SVZ and RMS of the adult rat forebrain. In the SVZ, APP‐like immunoreactivity was detected in the ependymal cells lining the LV and some of the subependymal cells. The latter were regarded as astrocytes, because they were positive for the glial markers, S‐100 protein (S‐100) and glial fibrillary acidic protein (GFAP). APP‐like immunoreactive astrocytes exhibited strong labelling of the perinuclear cytoplasm and often possessed a long, fine process similar to that found with radial glia. The process extended to an APP‐like immunoreactive meshwork in the RMS that consisted of cytoplasmic processes of astrocytes forming ‘glial tubes’. Double‐immunofluorescent labelling with a highly polysialylated neural cell adhesion molecule (PSA‐NCAM) confirmed that the APP‐like immunoreactive astrocytes in the SVZ and meshwork in the RMS made close contact with PSA‐NCAM‐immunopositive neuroblasts, suggesting an interaction between APP‐containing cells and neuroblasts. This region of the adult brain is a useful in vivo model to investigate the role of APP in neurogenesis.
Environmental control of flowering and sex expression in Carex flava
Authors: Heide Ola M.
Published: August 2004

The environmental control of flowering and sex expression has been studied under controlled environment conditions in three populations of the sedge Carex flava L. A dual floral induction requirement was demonstrated in all populations. Low temperature (< 12°C) was obligatory for, and short photoperiods strongly enhanced, primary induction and inflorescence initiation. Stem elongation and inflorescence development were promoted by long photoperiods, although most plants developed stunted flower stems also under short day (SD) conditions. Growth vigour, abundance of flowering and primary induction requirements varied widely among the populations, with critical exposure times for full flowering varying from less than 9 to about 12 weeks in SD at 9°C, and from about 9 to more than 15 weeks in long days (LD). Sex expression in the normally male terminal spike was shifted towards femaleness by marginal or incomplete primary induction. Primary induction in LD resulted in a complete change to entirely female inflorescences, whereas marginal induction in SD resulted in a similar sex reversal in some plants. The results are discussed in relation to environmental and hormonal factors known to modify sex expression in flowering plants and the significance of the results to Carex systematics and classification.