bluuebunny/crossref_metadata_2025 huggingface dataset:
Pressure-induced structural transition in AlN nanowires
Authors: Shen L. H. , Li X. F. , Ma Y. M. , Yang K. F. , Lei W. W. , Cui Q. L. , Zou G. T.
Published: October 2006

The structural transition of AlN nanowires was investigated under pressures up to 51.1GPa by in situ angle dispersive high-pressure x-ray diffraction using synchrotron radiation source and a diamond anvil cell. A pressure-induced wurtzite to rocksalt phase transition starts at 24.9GPa and completes at 45.4GPa. The high-pressure behaviors of AlN nanowires differing from the bulk and nanocrystal AlN might arise from the intrinsic geometry in nanowires.
Probing deep level centers in GaN epilayers with variable-frequency capacitance-voltage characteristics of Au∕GaN Schottky contacts
Authors: Wang R. X. , Xu S. J. , Shi S. L. , Beling C. D. , Fung S. , Zhao D. G. , Yang H. , Tao X. M.
Published: October 2006

Under identical preparation conditions, Au∕GaN Schottky contacts were prepared on two kinds of GaN epilayers with significantly different background electron concentrations and mobility as well as yellow emission intensities. Current-voltage (I-V) and variable-frequency capacitance-voltage (C-V) characteristics show that the Schottky contacts on the GaN epilayer with a higher background carrier concentration and strong yellow emission exhibit anomalous reverse-bias I-V and C-V characteristics. This is attributed to the presence of deep level centers. Theoretical simulation of the low-frequency C-V curves leads to a determination of the density and energy level position of the deep centers.
Highly ordered graphene for two dimensional electronics
Authors: Hass J. , Feng R. , Li T. , Li X. , Zong Z. , de Heer W. A. , First P. N. , Conrad E. H. , Jeffrey C. A. , Berger C.
Published: October 2006

With expanding interest in graphene-based electronics, it is crucial that high quality graphene films be grown. Sublimation of Si from the 4H-SiC(0001) (Si-terminated) surface in ultrahigh vacuum is a demonstrated method to produce epitaxial graphene sheets on a semiconductor. In this letter the authors show that graphene grown from the SiC(0001¯) (C-terminated) surface are of higher quality than those previously grown on SiC(0001). Graphene grown on the C face can have structural domain sizes more than three times larger than those grown on the Si face while at the same time reducing SiC substrate disorder from sublimation by an order of magnitude.
Composite-microlens-array-enabled microfluidic sorting
Authors: Sun Y. Y. , Ong L. S. , Yuan X.-C.
Published: October 2006

We propose a simple, reliable and cost-effective method for microfluidic sorting of microparticles using an optical potential landscape projected by a composite microlens array (MLA). The MLA enables a high power efficient approach to forming composite shape and size of the projected pattern. Sorting particles by size is demonstrated both theoretically and experimentally.
Polymer field-effect transistor gated via a poly(styrenesulfonic acid) thin film
Authors: Said Elias , Crispin Xavier , Herlogsson Lars , Elhag Sami , Robinson Nathaniel D. , Berggren Magnus
Published: October 2006

A polyanionic proton conductor, named poly(styrenesulfonic acid) (PSSH), is used to gate an organic field-effect transistor (OFET) based on poly(3-hexylthiophene) (P3HT). Upon applying a gate bias, large electric double layer capacitors (EDLCs) are formed quickly at the gate-PSSH and P3HT-PSSH interfaces due to proton migration in the polyelectrolyte. This type of robust transistor, called an EDLC-OFET, displays fast response (<1ms) and operates at low voltages (<1V). The results presented are relevant for low-cost printed polymer electronics.
High critical current densities observed in PrBa2Cu3O7−δ∕YBa2Cu3O7−δ∕PrBa2Cu3O7−δ ultrathin film constrictions
Authors: Peroz Ch. , Villégier J. C. , Dégardin A. F. , Guillet B. , Kreisler A. J.
Published: October 2006

An original process has been developed for fabricating 0.45×0.45μm2 constrictions with normal metal banks using stacked YBa2Cu3O7−δ and PrBa2Cu3O7−δ ultrathin films. High values of critical temperature Tc≈89K and critical current densities Jc≈2×107A∕cm2 at 77K were measured on 17nm thick YBa2Cu3O7−δ, after the complete fabrication on MgO substrate. The observed robust superconducting properties of the device under applied magnetic field are attributed to large edge barriers opposed to vortex entry inside the nanobridge section. As there is no apparent degradation of the superconducting properties after long time storage, the benefit of using ultrathin PrBa2Cu3O7−δ buffer and overlayer in YBa2Cu3O7−δ constrictions is confirmed. Such YBa2Cu3O7−δ nanowires are shown well adapted to phase-slip based devices and expected to fulfill the performances required in high frequency applications.
Characterizing the nanoacoustic superlattice in a phonon cavity using a piezoelectric single quantum well
Authors: Lin Kung-Hsuan , Chang Chieh-Feng , Pan Chang-Chi , Chyi Jen-Inn , Keller Stacia , Mishra Umesh , DenBaars Steven P. , Sun Chi-Kuang
Published: October 2006

We have experimentally and theoretically investigated, both in the time domain and in the frequency domain, the characteristics of a nanoacoustic mirror, which is a 17-period 8nm∕8nm Al0.7Ga0.3N∕Al0.2Ga0.8N superlattice and its first phononic band gap frequency is centered at ∼280GHz. By using a femtosecond optical pulse to excite and detect the nanoacoustic strain pulses with an In0.2Ga0.8N single quantum well, we directly measured the transient dynamics of the acoustic nanowaves inside a phonon cavity composed of the studied nanoacoustic mirror. The phase-resolved reflection transfer function of the phononic band gap superlattice and the properties of the nanophononic cavity have been experimentally obtained and investigated.
Development, photosynthetic activity and habitat selection of the clonal plant Fragaria vesca growing in copper-polluted soil
Authors: Roiloa Sergio R. , Retuerto Rubén
Published: October 2006

The ability of clonal systems to spread by ramet production may expose the clone to spatial heterogeneity. This study explored the physiological and morphological responses in the clonal plant Fragaria vesca L. growing in homogeneous (Cu-contaminated or uncontaminated) or in heterogeneous environments with patches of contrasting quality (Cu-contaminated or uncontaminated). We also investigated the potential of this species to selectively establish ramets within a heterogeneous environment. In heterogeneous environments, plants expanded ramets randomly, but selectively established ramets in the favourable patches. We discuss whether the selective establishment of ramets is a consequence of direct suppression of plant growth due to copper toxicity. The assimilate demand from offspring ramets in unfavourable environments increased the chlorophyll content and photosynthetic efficiency of parents by a feedback regulation process. Integration ameliorated the effects of copper on the photochemical efficiency of the offspring ramets. We did not observe integration costs, in terms of total biomass, for parents supporting ramets in Cu-contaminated environments, although we did detect costs in terms of ramet production. Parents with offspring ramets in Cu-contaminated environments produced 25 times more reproductive biomass than parents with offspring ramets in uncontaminated environments. We interpret this as a strategy for escaping from stressful environments. In this study, we extend the concept of physiological integration in clonal plants to include photochemical responses.
Refilling of embolised conduits as a consequence of 'Münch water' circulation
Authors: Hölttä Teemu , Vesala Timo , Perämäki Martti , Nikinmaa Eero
Published: October 2006

‘Münch water’ is pushed from the phloem to the xylem at locations of phloem sugar unloading. Consequently, an internal radial water potential imbalance is developed in the plant at these sugar-unloading sites. The phloem is at a higher water potential than the xylem. The magnitude of this radial water potential imbalance is determined by the magnitude of the radial water flux and the hydraulic resistance along the phloem-to-xylem pathway. If, as a result, the water potential in the ray parenchyma cells adjacent to xylem conduits is higher than that in the embolised xylem conduits, then a proportion of the water flow from the phloem would be directed towards embolised xylem conduits, in addition to conduits under tension. In this theoretical paper we demonstrate how recycled ‘Münch water’ passing from the phloem to the xylem can induce xylem embolism refilling. We also calculate the conditions and the structural composition of the phloem-to-xylem pathway that are required for embolism refilling by ‘Münch water’ circulation, and the time that is required for the complete refilling of embolised conduits in varying conditions.
Physiological mechanisms of tolerance to high boron concentration in Brassica rapa
Authors: Kaur Sukhjiwan , Nicolas Marc E. , Ford Rebecca , Norton Robert M. , Taylor Paul W. J.
Published: October 2006

Tolerance to high boron concentration in Brassica rapa was primarily due to low net boron uptake by the roots. However, in the two tolerant genotypes, 39–43% of boron uptake was retained in the tap roots, which limited boron accumulation in the leaves, and also contributed to boron tolerance. In the sensitive genotype, 99% of the increase in boron uptake caused by high soil boron accumulated in the leaves, particularly in the leaf margins. Despite higher transpiration rates, lower net boron uptake occurred in the tolerant genotypes. This result cannot be explained by passive boron uptake alone. Active boron efflux was probably responsible for differences in net boron uptake among tolerant and sensitive genotypes. Boron concentration was much lower in the cell walls than in the cell sap of leaves, indicating that storage of boron in the cell walls was not a tolerance mechanism. Despite high boron concentrations in the leaf symplasm, rates of photosynthesis, transpiration and growth were almost unaffected in the tolerant genotypes. The results demonstrate that boron tolerance in Brassica rapa involves boron exclusion at the root level, boron partitioning away from leaves and, as boron accumulates in leaves despite the first two mechanisms, boron tolerance of the leaf tissue itself.
The history of early bee diversification based on five genes plus morphology
Authors: Danforth Bryan N. , Sipes Sedonia , Fang Jennifer , Brady Seán G.
Published: October 2006

Bees, the largest (>16,000 species) and most important radiation of pollinating insects, originated in early to mid-Cretaceous, roughly in synchrony with the angiosperms (flowering plants). Understanding the diversification of the bees and the coevolutionary history of bees and angiosperms requires a well supported phylogeny of bees (as well as angiosperms). We reconstructed a robust phylogeny of bees at the family and subfamily levels using a data set of five genes (4,299 nucleotide sites) plus morphology (109 characters). The molecular data set included protein coding (elongation factor-1α, RNA polymerase II, and LW rhodopsin), as well as ribosomal (28S and 18S) nuclear gene data. Analyses of both the DNA data set and the DNA+morphology data set by parsimony and Bayesian methods yielded a single well supported family-level tree topology that places Melittidae as a paraphyletic group at the base of the phylogeny of bees. This topology (“Melittidae-LT basal”) is significantly better than a previously proposed alternative topology (“Colletidae basal”) based both on likelihood and Bayesian methods. Our results have important implications for understanding the early diversification, historical biogeography, host–plant evolution, and fossil record of bees. The earliest branches of bee phylogeny include lineages that are predominantly host–plant specialists, suggesting that host–plant specificity is an ancestral trait in bees. Our results suggest an African origin for bees, because the earliest branches of the tree include predominantly African lineages. These results also help explain the predominance of Melittidae, Apidae, and Megachilidae among the earliest fossil bees.
Allosteric inhibition of
Staphylococcus aureus
d
-alanine:
d
-alanine ligase revealed by crystallographic studies
Authors: Liu Shenping , Chang Jeanne S. , Herberg John T. , Horng Miao-Miao , Tomich Paul K. , Lin Alice H. , Marotti Keith R.
Published: October 2006

d
-alanine:
d
-alanine ligase (DDl) is an essential enzyme in bacterial cell wall biosynthesis and an important target for developing new antibiotics. It catalyzes the formation of
d
-alanine:
d
-alanine dipeptide, sequentially by using one
d
-alanine and one ATP as substrates for the first-half reaction, and a second
d
-alanine substrate to complete the reaction. Some gain of function DDl mutants can use an alternate second substrate, causing resistance to vancomycin, one of the last lines of defense against life-threatening Gram-positive infections. Here, we report the crystal structure of
Staphylococcus aureus
DDl (StaDDl) and its cocrystal structures with 3-chloro-2,2-dimethyl-
N
-[4(trifluoromethyl)phenyl]propanamide (inhibitor 1) (
K
i
= 4 μM against StaDDl) and with ADP, one of the reaction products, at resolutions of 2.0, 2.2, and 2.6 Å, respectively. The overall structure of StaDDl can be divided into three distinct domains. The inhibitor binds to a hydrophobic pocket at the interface of the first and the third domain. This inhibitor-binding pocket is adjacent to the first
d
-alanine substrate site but does not overlap with any substrate sites. An allosteric inhibition mechanism of StaDDl by this compound was proposed. The mechanism provides the basis for developing new antibiotics targeting
d
-alanine:
d
-alanine ligase. Because this compound only interacts with residues from the first
d
-alanine site, inhibitors with this binding mode potentially could overcome vancomycin resistance.
Crystal structure of a substrate complex of
myo
-inositol oxygenase, a di-iron oxygenase with a key role in inositol metabolism
Authors: Brown Peter M. , Caradoc-Davies Tom T. , Dickson James M. J. , Cooper Garth J. S. , Loomes Kerry M. , Baker Edward N.
Published: September 2006

Altered metabolism of the inositol sugars
myo
-inositol (MI) and
d
-
chiro
-inositol is implicated in diabetic complications. In animals, catabolism of MI and
d
-
chiro
-inositol depends on the enzyme MI oxygenase (MIOX), which catalyzes the first committed step of the glucuronate–xylulose pathway, and is found almost exclusively in the kidneys. The crystal structure of MIOX, in complex with MI, has been determined by multiwavelength anomalous diffraction methods and refined at 2.0-Å resolution (
R
= 0.206,
R
free
= 0.253). The structure reveals a monomeric, single-domain protein with a mostly helical fold that is distantly related to the diverse HD domain superfamily. Five helices form the structural core and provide six ligands (four His and two Asp) for the di-iron center, in which the two iron atoms are bridged by a putative hydroxide ion and one of the Asp ligands, Asp-124. A key loop forms a lid over the MI substrate, which is coordinated in bidentate mode to one iron atom. It is proposed that this mode of iron coordination, and interaction with a key Lys residue, activate MI for bond cleavage. The structure also reveals the basis of substrate specificity and suggests routes for the development of specific MIOX inhibitors.
The HIV Env variant N283 enhances macrophage tropism and is associated with brain infection and dementia
Authors: Dunfee Rebecca L. , Thomas Elaine R. , Gorry Paul R. , Wang Jianbin , Taylor Joann , Kunstman Kevin , Wolinsky Steven M. , Gabuzda Dana
Published: October 2006

HIV infects tissue macrophages and brain microglia, which express lower levels of CD4 and CCR5 than CD4
+
T cells in peripheral blood. Mechanisms that enhance HIV tropism for macrophages in the CNS and other tissues are not well understood. Here, we identify an HIV envelope glycoprotein (Env) variant in the CD4-binding site of gp120, Asn 283 (N283), that is present at a high frequency in brain tissues from AIDS patients with HIV-associated dementia (HAD). N283 increases gp120 affinity for CD4 by decreasing the gp120-CD4 dissociation rate, enhancing the capacity of HIV Envs to use low levels of CD4 for virus entry and increasing viral replication in macrophages and microglia. Structural modeling suggests that the enhanced ability of Envs with N283 to use low levels of CD4 is due to a hydrogen bond formed with Gln 40 of CD4. N283 is significantly more frequent in brain-derived Envs from HAD patients (41%;
n
= 330) compared with non-HAD patients (8%;
n
= 151;
P
< 0.001). These findings suggest that the macrophage-tropic HIV Env variant N283 is associated with brain infection and dementia
in vivo
, representing an example of a HIV variant associated with a specific AIDS-related complication.
The structure of human ADP-ribosylhydrolase 3 (ARH3) provides insights into the reversibility of protein ADP-ribosylation
Authors: Mueller-Dieckmann Christoph , Kernstock Stefan , Lisurek Michael , von Kries Jens Peter , Haag Friedrich , Weiss Manfred S. , Koch-Nolte Friedrich
Published: October 2006

Posttranslational modifications are used by cells from all kingdoms of life to control enzymatic activity and to regulate protein function. For many cellular processes, including DNA repair, spindle function, and apoptosis, reversible mono- and polyADP-ribosylation constitutes a very important regulatory mechanism. Moreover, many pathogenic bacteria secrete toxins which ADP-ribosylate human proteins, causing diseases such as whooping cough, cholera, and diphtheria. Whereas the 3D structures of numerous ADP-ribosylating toxins and related mammalian enzymes have been elucidated, virtually nothing is known about the structure of protein de-ADP-ribosylating enzymes. Here, we report the 3Dstructure of human ADP-ribosylhydrolase 3 (hARH3). The molecular architecture of hARH3 constitutes the archetype of an all-α-helical protein fold and provides insights into the reversibility of protein ADP-ribosylation. Two magnesium ions flanked by highly conserved amino acids pinpoint the active-site crevice. Recombinant hARH3 binds free ADP-ribose with micromolar affinity and efficiently de-ADP-ribosylates poly- but not monoADP-ribosylated proteins. Docking experiments indicate a possible binding mode for ADP-ribose polymers and suggest a reaction mechanism. Our results underscore the importance of endogenous ADP-ribosylation cycles and provide a basis for structure-based design of ADP-ribosylhydrolase inhibitors.
The GLD-2 poly(A) polymerase activates
gld-1
mRNA in the
Caenorhabditis elegans
germ line
Authors: Suh Nayoung , Jedamzik Britta , Eckmann Christian R. , Wickens Marvin , Kimble Judith
Published: September 2006

mRNA regulation is crucial for many aspects of metazoan development and physiology, including regulation of stem cells and synaptic plasticity. In the nematode germ line, RNA regulators control stem cell maintenance, the sperm/oocyte decision, and progression through meiosis. Of particular importance to this work are three GLD (germ-line development) regulatory proteins, each of which promotes entry into the meiotic cell cycle: GLD-1 is a STAR/Quaking translational repressor, GLD-2 is a cytoplasmic poly(A) polymerase, and GLD-3 is a homolog of Bicaudal-C. Here we report that the
gld-1
mRNA is a direct target of the GLD-2 poly(A) polymerase: polyadenylation of
gld-1
mRNA depends on GLD-2, the abundance of GLD-1 protein is dependent on GLD-2, and the
gld-1
mRNA coimmunoprecipitates with both GLD-2 and GLD-3 proteins. We suggest that the GLD-2 poly(A) polymerase enhances entry into the meiotic cell cycle at least in part by activating GLD-1 expression. The importance of this conclusion is twofold. First, the activation of
gld-1
mRNA by GLD-2 identifies a positive regulatory step that reinforces the decision to enter the meiotic cell cycle. Second,
gld-1
mRNA is initially repressed by FBF (for
fem-3
binding factor) to maintain stem cells but then becomes activated by the GLD-2 poly(A) polymerase once stem cells begin to make the transition into the meiotic cell cycle. Therefore, a molecular switch regulates
gld-1
mRNA activity to accomplish the transition from mitosis to meiosis.
CCR5-dependent homing of naturally occurring CD4+ regulatory T cells to sites of Leishmania major infection favors pathogen persistence
Authors: Yurchenko Ekaterina , Tritt Michael , Hay Valerie , Shevach Ethan M. , Belkaid Yasmine , Piccirillo Ciriaco A.
Published: October 2006

Pathogen persistence after clinical cure is a hallmark of many chronic infections. Previously, we showed that naturally occurring CD4+CD25+ regulatory T (nTreg) cells rapidly accumulate within chronic dermal sites of Leishmania major infection where they suppress anti-pathogen CD4+ T cell responses, favor parasite persistence and dermal pathology, and consequently control concomitant immunity. Here, we postulated that chemokines might direct nTreg cell homing in sites of infection and show that CD4+CD25+ nTreg cells, compared with normal CD4+ T cells, preferentially express the CCR5 chemokine receptor, which enables them to migrate in response to CCR5 ligands in vitro. We show that in contrast to their wild-type (WT) counterparts, CCR5−/− CD4+CD25+ nTreg cells resulted in an increased magnitude of parasite-specific, interferon γ–producing CD4+ T cells within infection sites, dramatically reduced parasite numbers, and potent resistance to infection, a finding consistent with the clinical outcome of infected CCR5−/− mice. Interestingly, this resistance was related to an inefficient migration of CCR5−/− nTreg cells to infected dermal sites compared with WT nTreg cells. Thus, this study shows that CCR5 directs the homing of CD4+CD25+ nTreg cells to L. major–infected dermal sites where they promote the establishment of infection and long-term survival of the parasite in the immune host.
Characterization of a Two-Component High-Affinity Nitrate Uptake System in Arabidopsis. Physiology and Protein-Protein Interaction
Authors: Orsel Mathilde , Chopin Franck , Leleu Olivier , Smith Susan J. , Krapp Anne , Daniel-Vedele Françoise , Miller Anthony J.
Published: September 2006

The identification of a family of NAR2-type genes in higher plants showed that there was a homolog in Arabidopsis (Arabidopsis thaliana), AtNAR2.1. These genes encode part of a two-component nitrate high-affinity transport system (HATS). As the Arabidopsis NRT2 gene family of nitrate transporters has been characterized, we tested the idea that AtNAR2.1 and AtNRT2.1 are partners in a two-component HATS. Results using the yeast split-ubiquitin system and Xenopus oocyte expression showed that the two proteins interacted to give a functional HATS. The growth and nitrogen (N) physiology of two Arabidopsis gene knockout mutants, atnrt2.1-1 and atnar2.1-1, one for each partner protein, were compared. Both types of plants had lost HATS activity at 0.2 mm nitrate, but the effect was more severe in atnar2.1-1 plants. The relationship between plant N status and nitrate transporter expression revealed a pattern that was characteristic of N deficiency that was again stronger in atnar2.1-1. Plants resulting from a cross between both mutants (atnrt2.1-1 × atnar2.1-1) showed a phenotype like that of the atnar2.1-1 mutant when grown in 0.5 mm nitrate. Lateral root assays also revealed growth differences between the two mutants, confirming that atnar2.1-1 had a stronger phenotype. To show that the impaired HATS did not result from the decreased expression of AtNRT2.1, we tested if constitutive root expression of a tobacco (Nicotiana plumbaginifolia) gene, NpNRT2.1, previously been shown to complement atnrt2.1-1, can restore HATS to the atnar2.1-1 mutant. These plants did not recover wild-type nitrate HATS. Taken together, these results show that AtNAR2.1 is essential for HATS of nitrate in Arabidopsis.
Contribution of Ethylene Biosynthesis for Resistance to Blast Fungus Infection in Young Rice Plants
Authors: Iwai Takayoshi , Miyasaka Atsushi , Seo Shigemi , Ohashi Yuko
Published: September 2006

The role of ethylene (ET) in resistance to infection with blast fungus (Magnaporthe grisea) in rice (Oryza sativa) is poorly understood. To study it, we quantified ET levels after inoculation, using young rice plants at the four-leaf stage of rice cv Nipponbare (wild type) and its isogenic plant (IL7), which contains the Pi-i resistance gene to blast fungus race 003. Small necrotic lesions by hypersensitive reaction (HR) were formed at 42 to 72 h postinoculation (hpi) in resistant IL7 leaves, and whitish expanding lesions at 96 hpi in susceptible wild-type leaves. Notable was the enhanced ET emission at 48 hpi accompanied by increased 1-aminocyclopropane-1-carboxylic acid (ACC) levels and highly elevated ACC oxidase (ACO) activity in IL7 leaves, whereas only an enhanced ACC increase at 96 hpi in wild-type leaves. Among six ACC synthase (ACS) and seven ACO genes found in the rice genome, OsACS2 was transiently expressed at 48 hpi in IL7 and at 96 hpi in wild type, and OsACO7 was expressed at 48 hpi in IL7. Treatment with an inhibitor for ACS, aminooxyacetic acid, suppressed enhanced ET emission at 48 hpi in IL7, resulting in expanding lesions instead of HR lesions. Exogenously supplied ACC compromised the aminooxyacetic acid-induced breakdown of resistance in IL7, and treatment with 1-methylcyclopropene and silver thiosulfate, inhibitors of ET action, did not suppress resistance. These findings suggest the importance of ET biosynthesis and, consequently, the coproduct, cyanide, for HR-accompanied resistance to blast fungus in young rice plants and the contribution of induced OsACS2 and OsACO7 gene expression to it.
Developmental and Embryo Axis Regulation of Gibberellin Biosynthesis during Germination and Young Seedling Growth of Pea
Authors: Ayele Belay T. , Ozga Jocelyn A. , Kurepin Leonid V. , Reinecke Dennis M.
Published: September 2006

The expression patterns of five genes (PsGA20ox1, PsGA20ox2, PsGA3ox1, PsGA2ox1, and PsGA2ox2) encoding five regulatory gibberellin (GA) biosynthesis enzymes (two GA 20-oxidases, a GA 3β-hydroxylase, and two GA 2β-hydroxylases) were examined to gain insight into how these genes coordinate GA biosynthesis during germination and early postgermination stages of the large-seeded dicotyledonous plant pea (Pisum sativum). At the time the developing embryo fills the seed coat, high mRNA levels of PsGA20ox2 (primarily responsible for conversion of C20-GAs to GA20), PsGA2ox1 (primarily responsible for conversion of GA20 to GA29), and PsGA2ox2 (primarily responsible for conversion of GA1 to GA8) were detected in the seeds, along with high GA20 and GA29 levels, the enzymatic products of these genes. Embryo maturation was accompanied by a large reduction in PsGA20ox2 and PsGA2ox1 mRNA and lower GA20 and GA29 levels. However, PsGA2ox2 transcripts remained high. Following seed imbibition, GA20 levels in the cotyledons decreased, while PsGA3ox1 mRNA and GA1 levels increased, implying that GA20 was being used for de novo synthesis of GA1. The presence of the embryo axis was required for stimulation of cotyledonary GA1 synthesis at the mRNA and enzyme activity levels. As the embryo axis doubled in size, PsGA20ox1 and PsGA3ox1 transcripts increased, both GA1 and GA8 were detectable, PsGA2ox2 transcripts decreased, and PsGA2ox1 transcripts remained low. Cotyledonary-, root-, and shoot-specific expression of these GA biosynthesis genes and the resultant endogenous GA profiles support a key role for de novo GA biosynthesis in each organ during germination and early seedling growth of pea.
CO2 Sensing at Ocean Surface Mediated by cAMP in a Marine Diatom
Authors: Harada Hisashi , Nakajima Kensuke , Sakaue Kunihiro , Matsuda Yusuke
Published: September 2006

Marine diatoms are known to be responsible for about a quarter of global primary production and their photosynthesis is sustained by inorganic carbon-concentrating mechanisms and/or C4 metabolism. Activities of the inorganic carbon-concentrating mechanism are attenuated under enriched [CO2]; however, impacts of this factor on primary productivity and the molecular mechanisms of CO2 responses in marine diatoms are unknown. In this study, transgenic cells were generated of the marine diatom Phaeodactylum tricornutum by the introduction of a β-glucuronidase reporter gene under the control of an intrinsic CO2-responsive promoter, which is the sequence between −80 to +61 relative to the transcription start site of a chloroplastic-carbonic anhydrase gene, ptca1, obtained from P. tricornutum. The activity of the ptca1 promoter was effectively repressed in air-level CO2 by treating cells with a 1.0 mm cAMP analog, dibutyryl cAMP, or a cAMP phosphodiesterase inhibitor, 3-isobutyl-1-methylxanthine. Deletion of the intrinsic cAMP-response element from the ptca1 promoter caused a lack of repression of the reporter gene uidA, even under elevated [CO2] and a null phenotype to the strong repressive effects of dibutyryl cAMP and 3-isobutyl-1-methylxanthine on the ptca1 promoter. Deletion of the cAMP-response element was also shown to cause derepression of the uidA reporter gene in the dark. These results indicate that the cytosolic cAMP level increases under elevated [CO2] and represses the ptca1 promoter. This strongly suggests the participation of cAMP metabolism, presumably at the cytosolic level, in controlling CO2-acquisition systems under elevated [CO2] at the ocean surface in a marine diatom.
A Novel Function for the Cathepsin D Inhibitor in Tomato
Authors: Lisón Purificación , Rodrigo Ismael , Conejero Vicente
Published: September 2006

Proteinaceous aspartic proteinase inhibitors are rare in nature and are described in only a few plant species. One of them corresponds to a family of cathepsin D inhibitors (CDIs) described in potato (Solanum tuberosum), involving up to 15 isoforms with a high sequence similarity. In this work, we describe a tomato (Solanum lycopersicum) wound-inducible protein called jasmonic-induced protein 21 (JIP21). Sequence analysis of its cDNA predicted a putative function as a CDI. The JIP21 gene, whose protein has been demonstrated to be glycosylated, is constitutively expressed in flowers, stem, and fruit, and is inducible to high levels by wounding and methyl jasmonate in leaves of tomato plants. The genomic sequence of JIP21 shows that the gene is intronless and reveals the presence of both a methyl jasmonate box (TGACT) and a G-box (CACGT) in the promoter. In contrast to the presumed role of JIP21 based on sequence analysis, a detailed biochemical characterization of the purified protein uncovers a different function as a strong chymotrypsin inhibitor, which questions the previously predicted inhibitory activity against aspartic proteinases. Moreover, Egyptian cotton worm (Spodoptera littoralis) larvae fed on transgenic tomato plants overexpressing JIP21 present an increase in mortality and a delay in growth when compared with larvae fed on wild-type plants. These larvae belong to the Lepidoptera family whose main digestive enzymes have been described as being Ser proteases. All these results support the notion that tomato JIP21 should be considered as a chymotrypsin inhibitor belonging to the Ser proteinase inhibitors rather than a CDI. Therefore, we propose to name this protein tomato chymotrypsin inhibitor 21 (TCI21).
TheFLORAL ORGAN NUMBER4Gene Encoding a Putative Ortholog of Arabidopsis CLAVATA3 Regulates Apical Meristem Size in Rice
Authors: Chu Huangwei , Qian Qian , Liang Wanqi , Yin Changsong , Tan Hexin , Yao Xuan , Yuan Zheng , Yang Jun , Huang Hai , Luo Da , Ma Hong , Zhang Dabing
Published: September 2006

To understand the molecular mechanism regulating meristem development in the monocot rice (Oryza sativa), we describe here the isolation and characterization of three floral organ number4 (fon4) alleles and the cloning of the FON4 gene. The fon4 mutants showed abnormal enlargement of the embryonic and vegetative shoot apical meristems (SAMs) and the inflorescence and floral meristems. Likely due to enlarged SAMs, fon4 mutants produced thick culms (stems) and increased numbers of both primary rachis branches and floral organs. We identified FON4 using a map-based cloning approach and found it encodes a small putatively secreted protein, which is the putative ortholog of the Arabidopsis (Arabidopsis thaliana) CLAVATA3 (CLV3) gene. FON4 transcripts mainly accumulated in the small group of cells at the apex of the SAMs, whereas the rice ortholog of CLV1 (FON1) is expressed throughout the SAMs, suggesting that the putative FON4 ligand might be sequestered as a possible mechanism for rice meristem regulation. Exogenous application of the peptides FON4p and CLV3p corresponding to the CLV3/ESR-related (CLE) motifs of FON4 and CLV3, respectively, resulted in termination of SAMs in rice, and treatment with CLV3p caused consumption of both rice and Arabidopsis root meristems, suggesting that the CLV pathway in limiting meristem size is conserved in both rice and Arabidopsis. However, exogenous FON4p did not have an obvious effect on limiting both rice and Arabidopsis root meristems, suggesting that the CLE motifs of Arabidopsis CLV3 and FON4 are potentially functionally divergent.
The Cyclin-Dependent Kinase Inhibitor Orysa;KRP1 Plays an Important Role in Seed Development of Rice
Authors: Barrôco Rosa Maria , Peres Adrian , Droual Anne-Marie , De Veylder Lieven , Nguyen Le Son Long , De Wolf Joris , Mironov Vladimir , Peerbolte Rindert , Beemster Gerrit T.S. , Inzé Dirk , Broekaert Willem F. , Frankard Valerie
Published: September 2006

Kip-related proteins (KRPs) play a major role in the regulation of the plant cell cycle. We report the identification of five putative rice (Oryza sativa) proteins that share characteristic motifs with previously described plant KRPs. To investigate the function of KRPs in rice development, we generated transgenic plants overexpressing the Orysa;KRP1 gene. Phenotypic analysis revealed that overexpressed KRP1 reduced cell production during leaf development. The reduced cell production in the leaf meristem was partly compensated by an increased cell size, demonstrating the existence of a compensatory mechanism in monocot species by which growth rate is less reduced than cell production, through cell expansion. Furthermore, Orysa;KRP1 overexpression dramatically reduced seed filling. Sectioning through the overexpressed KRP1 seeds showed that KRP overproduction disturbed the production of endosperm cells. The decrease in the number of fully formed seeds was accompanied by a drop in the endoreduplication of endosperm cells, pointing toward a role of KRP1 in connecting endocycle with endosperm development. Also, spatial and temporal transcript detection in developing seeds suggests that Orysa;KRP1 plays an important role in the exit from the mitotic cell cycle during rice grain formation.
Regulation of Seed Size by Hypomethylation of Maternal and Paternal Genomes
Authors: Xiao Wenyan , Brown Roy C. , Lemmon Betty E. , Harada John J. , Goldberg Robert B. , Fischer Robert L.
Published: September 2006

DNA methylation is an epigenetic modification of cytosine that is important for silencing gene transcription and transposons, gene imprinting, development, and seed viability. DNA METHYLTRANSFERASE1 (MET1) is the primary maintenance DNA methyltransferase in Arabidopsis (Arabidopsis thaliana). Reciprocal crosses between antisense MET1 transgenic and wild-type plants show that DNA hypomethylation has a parent-of-origin effect on seed size. However, due to the dominant nature of the antisense MET1 transgene, the parent with a hypomethylated genome, its gametophyte, and both the maternal and paternal genomes of the F1 seed become hypomethylated. Thus, the distinct role played by hypomethylation at each generation is not known. To address this issue, we examined F1 seed from reciprocal crosses using a loss-of-function recessive null allele, met1-6. Crosses between wild-type and homozygous met1-6 parents show that hypomethylated maternal and paternal genomes result in significantly larger and smaller F1 seeds, respectively. Our analysis of crosses between wild-type and heterozygous MET1/met1-6 parents revealed that hypomethylation in the female or male gametophytic generation was sufficient to influence F1 seed size. A recessive mutation in another gene that dramatically reduces DNA methylation, DECREASE IN DNA METHYLATION1, also causes parent-of-origin effects on F1 seed size. By contrast, recessive mutations in genes that regulate a smaller subset of DNA methylation (CHROMOMETHYLASE3 and DOMAINS REARRANGED METHYLTRANSFERASES1 and 2) had little effect on seed size. Collectively, these results show that maternal and paternal genomes play distinct roles in the regulation of seed size in Arabidopsis.
Calcium Entry Mediated by GLR3.3, an Arabidopsis Glutamate Receptor with a Broad Agonist Profile
Authors: Qi Zhi , Stephens Nicholas R. , Spalding Edgar P.
Published: September 2006

The amino acids glutamate (Glu) and glycine (Gly) trigger large, rapid rises in cytosolic Ca2+ concentration and a concomitant rise in membrane potential (depolarization) in plants. The possibility that plant homologs of neuronal ionotropic glutamate receptors mediate these neuron-like ionic responses was tested in Arabidopsis (Arabidopsis thaliana) seedlings using a combination of Ca2+ measurements, electrophysiology, and reverse genetics. The membrane depolarization triggered by Glu was greatly reduced or completely blocked in some conditions by mutations in GLR3.3, one of the 20 GLR genes in Arabidopsis. The same mutations completely blocked the associated rise in cytosolic Ca2+. These results genetically demonstrate the participation of a glutamate receptor in the rapid ionic responses to an amino acid. The GLR3.3-independent component of the depolarization required Glu concentrations above 25 μ  m, did not display desensitization, and was strongly suppressed by increasing extracellular pH. It is suggested to result from H+-amino acid symport. Six amino acids commonly present in soils (Glu, Gly, alanine, serine, asparagine, and cysteine) as well as the tripeptide glutathione (γ-glutamyl-cysteinyl-Gly) were found to be strong agonists of the GLR3.3-mediated responses. All other amino acids induced a small depolarization similar to the non-GLR, putative symporter component and in most cases evoked little or no Ca2+ rise. From these results it may be concluded that sensing of six amino acids in the rhizosphere and perhaps extracellular peptides is coupled to Ca2+ signaling through a GLR-dependent mechanism homologous to a fundamental component of neuronal signaling.
Arabidopsis FHY3 Specifically Gates Phytochrome Signaling to the Circadian Clock
Authors: Allen Trudie , Koustenis Athanasios , Theodorou George , Somers David E. , Kay Steve A. , Whitelam Garry C. , Devlin Paul F.
Published: September 2006

Circadian gating of light signaling limits the timing of maximum responsiveness to light to specific times of day. The fhy3 (for far-red elongated hypocotyl3) mutant of Arabidopsis thaliana is involved in independently gating signaling from a group of photoreceptors to an individual response. fhy3 shows an enhanced response to red light during seedling deetiolation. Analysis of two independent fhy3 alleles links enhanced inhibition of hypocotyl elongation in response to red light with an arrhythmic pattern of hypocotyl elongation. Both alleles also show disrupted rhythmicity of central-clock and clock-output gene expression in constant red light. fhy3 exhibits aberrant phase advances under red light pulses during the subjective day. Release-from-light experiments demonstrate clock disruption in fhy3 during the early part of the subjective day in constant red light, suggesting that FHY3 is important in gating red light signaling for clock resetting. The FHY3 gating function appears crucial in the early part of the day for the maintenance of rhythmicity under these conditions. However, unlike previously described Arabidopsis gating mutants that gate all light signaling, gating of direct red light–induced gene expression in fhy3 is unaffected. FHY3 appears to be a novel gating factor, specifically in gating red light signaling to the clock during daytime.
Tocopherols Play a Crucial Role in Low-Temperature Adaptation and Phloem Loading in Arabidopsis
Authors: Maeda Hiroshi , Song Wan , Sage Tammy L. , DellaPenna Dean
Published: September 2006

To test whether tocopherols (vitamin E) are essential in the protection against oxidative stress in plants, a series of Arabidopsis thaliana  vitamin E (vte) biosynthetic mutants that accumulate different types and levels of tocopherols and pathway intermediates were analyzed under abiotic stress. Surprisingly subtle differences were observed between the tocopherol-deficient vte2 mutant and the wild type during high-light, salinity, and drought stresses. However, vte2, and to a lesser extent vte1, exhibited dramatic phenotypes under low temperature (i.e., increased anthocyanin levels and reduced growth and seed production). That these changes were independent of light level and occurred in the absence of photoinhibition or lipid peroxidation suggests that the mechanisms involved are independent of tocopherol functions in photoprotection. Compared with the wild type, vte1 and vte2 had reduced rates of photoassimilate export as early as 6 h into low-temperature treatment, increased soluble sugar levels by 60 h, and increased starch and reduced photosynthetic electron transport rate by 14 d. The rapid reduction in photoassimilate export in vte2 coincides with callose deposition exclusively in phloem parenchyma transfer cell walls adjacent to the companion cell/sieve element complex. Together, these results indicate that tocopherols have a more limited role in photoprotection than previously assumed but play crucial roles in low-temperature adaptation and phloem loading.
The Proteolytic Processing of Seed Storage Proteins inArabidopsisEmbryo Cells Starts in the Multivesicular Bodies
Authors: Otegui Marisa S. , Herder Rachel , Schulze Jan , Jung Rudolf , Staehelin L. Andrew
Published: September 2006

We have investigated the transport of storage proteins, their processing proteases, and the Vacuolar Sorting Receptor-1/Epidermal Growth Factor Receptor–Like Protein1 (VSR-1/ATELP1) receptor during the formation of protein storage vacuoles in Arabidopsis thaliana embryos by means of high-pressure freezing/freeze substitution, electron tomography, immunolabeling techniques, and subcellular fractionation. The storage proteins and their processing proteases are segregated from each other within the Golgi cisternae and packaged into separate vesicles. The storage protein–containing vesicles but not the processing enzyme–containing vesicles carry the VSR-1/ATELP1 receptor. Both types of secretory vesicles appear to fuse into a type of prevacuolar multivesicular body (MVB). We have also determined that the proteolytic processing of the 2S albumins starts in the MVBs. We hypothesize that the compartmentalized processing of storage proteins in the MVBs may allow for the sequential activation of processing proteases as the MVB lumen gradually acidifies.
INCREASED LEVEL OF POLYPLOIDY1, a Conserved Repressor of CYCLINA2 Transcription, Controls Endoreduplication in Arabidopsis
Authors: Yoshizumi Takeshi , Tsumoto Yuko , Takiguchi Tomoko , Nagata Noriko , Yamamoto Yoshiharu Y. , Kawashima Mika , Ichikawa Takanari , Nakazawa Miki , Yamamoto Naoki , Matsui Minami
Published: September 2006

Endoreduplication is a type of cell cycle in which DNA replication continues without cell division. We have isolated several dominant mutants from Arabidopsis thaliana activation tagging lines by flow cytometry. One of the mutants, increased level of polyploidy1-1D (ilp1-1D), showed increased polyploidy in both light- and dark-grown hypocotyls. The corresponding gene of ilp1-1D encodes a protein homologous to the C-terminal region of mammalian GC binding factor. We demonstrate that this protein functions as a transcriptional repressor in vivo. The expression of all members of the CYCLINA2 (CYCA2) family was reduced in an ILP1 overexpressing line, and the mouse (Mus musculus) homolog of ILP1 repressed cyclin A2 expression in mouse NIH3T3 cells. T-DNA insertion mutants of ILP1 showed reduced polyploidy and upregulated all CYCA2 expression. Furthermore, loss of CYCA2;1 expression induces an increase in polyploidy in Arabidopsis. We demonstrate that this protein regulates endoreduplication through control of CYCA2 expression in Arabidopsis.
LATTICE DIMENSIONS OF SOME SOLID SOLUTIONS IN THE SYSTEM MgO‐Al2O3*
Authors: CLARK G. L. , HOW E. E. , BADGER A. E.
Published: October 2006

The lattice dimension of magnesia spinel was determined to be a0= 8.064 0.002 A.U. The lattice dimension of solid solutions of this spinel with αAl2O3 decreases progressively with increase of Al2O3.
ON THE THERMAL. ENDURANCE OF GLASS*
Authors: TABATA KOZO , MORIYA TARO
Published: October 2006

The thermal endurance of borosilicate glasses in the form of perfectly annealed rods of five different diameters was studied. Temperature distribution in the rods, therma1 stress, relation between radius of rod and critical thermal shock are mathematically discussed from observed data. A new expression showing the relation between the radius of the rods and the minimum temperature difference to cause fracture in the rods is developed
THE CONSTITUTION OF GLASS*
Authors: MOREY GEORGE W.
Published: October 2006

Glass is to be regarded as a liquid which has a viscosity so great as to be practically rigid; and the glasses of commerce are all solutions undercooled far below their normal crystallizing temperatures. Nothing more is known regarding the constitution of these highly concentrated solutions than is known about the constitution of other concentrated solutions. The phase‐equilibrium diagram gives no information as to the compounds present in the liquid phase, for there is no known correlation between the properties of a homogeneous system and those of the heterogeneous system formed from it on crystallization. Evidence based on the rate of volatilization of alkali from alkali‐silicate glasses does not indicate compound formation. The discontinuous change of properties of a glass in the “annealing range” has been considered by some to be evidence that the glassy state is a fourth state of matter separated from the liquid state by this transition temperature; by others, as indicating that above this discontinuity the material is a liquid, below it, a brittle solid. These views are unsound, because they are based on measurements of physical properties made with changing temperature when those properties themselves not only change with temperature but also require at each temperature considerable time to reach their equilibrium value. When the measurements are made on glasses which have been held at constant temperature long enough for the equilibrium value of the property to be attained, no discontinuities are observed and there is no justification for calling glass a fourth state of matter or for separating a “brittle” from a “viscous” temperature range. Arguments, based on the variation of physical properties with composition in which it is considered that such variation is represented not by a continuous curve but by a series of straight lines determined by the composition of hypothetical compounds, are shown to be theoretically improbable and not in accord with the facts. Recent speculations on the constitution of glass based on X‐ray evidence and recent studies of glass by means of X‐rays indicate that the glassy state is distinguished by a random nonrepeating atomic network. This conclusion is in harmony with the view that glass is an undercooled liquid representing a solution in which definite compounds can not be identified.