bluuebunny/crossref_metadata_2025_split huggingface dataset:
GeBP and GeBP-Like Proteins Are Noncanonical Leucine-Zipper Transcription Factors That Regulate Cytokinin Response in Arabidopsis
Authors: Chevalier Florian , Perazza Daniel , Laporte Frédéric , Le Hénanff Gaëlle , Hornitschek Patricia , Bonneville Jean-Marc , Herzog Michel , Vachon Gilles 
Published: December 2007

AbstractUnderstanding the role of transcription factors (TFs) is essential in reconstructing developmental regulatory networks. The plant-specific GeBP TF family of Arabidopsis thaliana (Arabidopsis) comprises 21 members, all of unknown function. A subset of four members, the founding member GeBP and GeBP-like proteins (GPL) 1, 2, and 3, shares a conserved C-terminal domain. Here we report that GeBP/GPL genes represent a newly defined class of leucine-zipper (Leu-zipper) TFs and that they play a redundant role in cytokinin hormone pathway regulation. Specifically, we demonstrate using yeast, in vitro, and split-yellow fluorescent protein in planta assays that GeBP/GPL proteins form homo- and heterodimers through a noncanonical Leu-zipper motif located in the C-terminal domain. A triple loss-of-function mutant of the three most closely related genes gebp gpl1 gpl2 shows a reduced sensitivity to exogenous cytokinins in a subset of cytokinin responses such as senescence and growth, whereas root inhibition is not affected. We find that transcript levels of type-A cytokinin response genes, which are involved in the negative feedback regulation of cytokinin signaling, are higher in the triple mutant. Using a GPL version that acts as a constitutive transcriptional activator, we show that the regulation of Arabidopsis response regulators (ARRs) is mediated by at least one additional, as yet unknown, repressor acting genetically downstream in the GeBP/GPL pathway. Our results indicate that GeBP/GPL genes encode a new class of unconventional Leu-zipper TF proteins and suggest that their role in the cytokinin pathway is to antagonize the negative feedback regulation on ARR genes to trigger the cytokinin response.
PSY3, a New Member of the Phytoene Synthase Gene Family Conserved in the Poaceae and Regulator of Abiotic Stress-Induced Root Carotenogenesis
Authors: Li Faqiang , Vallabhaneni Ratnakar , Wurtzel Eleanore T. 
Published: December 2007

Abstract
Abscisic acid (ABA) plays a vital role in mediating abiotic stress responses in plants. De novo ABA biosynthesis involves cleavage of carotenoid precursors by 9-cis-epoxycarotenoid dioxygenase (NCED), which is rate controlling in leaves and roots; however, additional bottlenecks in roots must be overcome, such as biosynthesis of upstream carotenoid precursors. Phytoene synthase (PSY) mediates the first committed step in carotenoid biosynthesis; with PSY3 described here, maize (Zea mays) and other members of the Poaceae have three paralogous genes, in contrast to only one in Arabidopsis thaliana. PSY gene duplication has led to subfunctionalization, with each paralog exhibiting differential gene expression. We showed that PSY3 encodes a functional enzyme for which maize transcript levels are regulated in response to abiotic stresses, drought, salt, and ABA. Drought-stressed roots showed elevated PSY3 transcripts and ABA, responses reversed by rehydration. By blocking root carotenoid biosynthesis with the maize y9 mutation, we demonstrated that PSY3 mRNA elevation correlates with carotenoid accumulation and that blocking carotenoid biosynthesis interferes with stress-induced ABA accumulation. In parallel, we observed elevated NCED transcripts and showed that, in contrast to dicots, root zeaxanthin epoxidase transcripts were unchanged. PSY3 was the only paralog for which transcripts were induced in roots and abiotic stress also affected leaf PSY2 transcript levels; PSY1 mRNA was not elevated in any tissues tested. Our results suggest that PSY3 expression influences root carotenogenesis and defines a potential bottleneck upstream of NCED; further examination of PSY3 in the grasses is of value for better understanding root-specific stress responses that impact plant yield.
Quantitative Conversion of Phytate to Inorganic Phosphorus in Soybean Seeds Expressing a Bacterial Phytase
Authors: Bilyeu Kristin D. , Zeng Peiyu , Coello Patricia , Zhang Zhanyuan J. , Krishnan Hari B. , Bailey April , Beuselinck Paul R. , Polacco Joe C. 
Published: December 2007

Abstract
Phytic acid (PA) contains the major portion of the phosphorus in the soybean (Glycine max) seed and chelates divalent cations. During germination, both minerals and phosphate are released upon phytase-catalyzed degradation of PA. We generated a soybean line (CAPPA) in which an Escherichia coli periplasmic phytase, the product of the appA gene, was expressed in the cytoplasm of developing cotyledons. CAPPA exhibited high levels of phytase expression, ≥90% reduction in seed PA, and concomitant increases in total free phosphate. These traits were stable, and, although resulted in a trend for reduced emergence and a statistically significant reduction in germination rates, had no effect on the number of seeds per plant or seed weight. Because phytate is not digested by monogastric animals, untreated soymeal does not provide monogastrics with sufficient phosphorus and minerals, and PA in the waste stream leads to phosphorus runoff. The expression of a cytoplasmic phytase in the CAPPA line therefore improves phosphorus availability and surpasses gains achieved by other reported transgenic and mutational strategies by combining in seeds both high phytase expression and significant increases in available phosphorus. Thus, in addition to its value as a high-phosphate meal source, soymeal from CAPPA could be used to convert PA of admixed meals, such as cornmeal, directly to utilizable inorganic phosphorus.
Functional Coexpression of the Mitochondrial Alternative Oxidase and Uncoupling Protein Underlies Thermoregulation in the Thermogenic Florets of Skunk Cabbage
Authors: Onda Yoshihiko , Kato Yoshiaki , Abe Yukie , Ito Takanori , Morohashi Miyuki , Ito Yuka , Ichikawa Megumi , Matsukawa Kazushige , Kakizaki Yusuke , Koiwa Hiroyuki , Ito Kikukatsu 
Published: December 2007

AbstractTwo distinct mitochondrial energy dissipating systems, alternative oxidase (AOX) and uncoupling protein (UCP), have been implicated as crucial components of thermogenesis in plants and animals, respectively. To further clarify the physiological roles of AOX and UCP during homeothermic heat production in the thermogenic skunk cabbage (Symplocarpus renifolius), we identified the thermogenic cells and performed expression and functional analyses of these genes in this organism. Thermographic analysis combined with in situ hybridization revealed that the putative thermogenic cells surround the stamens in the florets of skunk cabbage and coexpress transcripts for SrAOX, encoding Symplocarpus AOX, and SrUCPb, encoding a novel UCP that lacks a fifth transmembrane segment. Mitochondria isolated from the thermogenic florets exhibited substantial linoleic acid (LA)-inducible uncoupling activities. Moreover, our results demonstrate that LA is capable of inhibiting the mitochondrial AOX pathway, whereas the proportion of pyruvate-stimulated AOX capacity was not significantly affected by LA. Intriguingly, the protein expression levels for SrAOX and SrUCPb were unaffected even when the ambient air temperatures increased from 10.3°C to 23.1°C or from 8.3°C to 24.9°C. Thus, our results suggest that functional coexpression of AOX and UCP underlies the molecular basis of heat production, and that posttranslational modifications of these proteins play a crucial role in regulating homeothermic heat production under conditions of natural ambient temperature fluctuations in skunk cabbage.
The NADPH-Dependent Thioredoxin Reductase/Thioredoxin System in Germinating Barley Seeds: Gene Expression, Protein Profiles, and Interactions between Isoforms of Thioredoxin h and Thioredoxin Reductase
Authors: Shahpiri Azar , Svensson Birte , Finnie Christine 
Published: December 2007

Abstract
The NADPH-dependent thioredoxin reductase (NTR)/thioredoxin (Trx) system catalyzes disulfide bond reduction in the cytoplasm and mitochondrion. Trx h is suggested to play an important role in seed development, germination, and seedling growth. Plants have multiple isoforms of Trx h and NTR; however, little is known about the roles of the individual isoforms. Trx h isoforms from barley (Hordeum vulgare) seeds (HvTrxh1 and HvTrxh2) were characterized previously. In this study, two NTR isoforms (HvNTR1 and HvNTR2) were identified, enabling comparison of gene expression, protein appearance, and interaction between individual NTR and Trx h isoforms in barley embryo and aleurone layers. Although mRNA encoding both Trx h isoforms is present in embryo and aleurone layers, the corresponding proteins differed in spatiotemporal appearance. HvNTR2, but not HvNTR1, gene expression seems to be regulated by gibberellic acid. Recombinant HvNTR1 and HvNTR2 exhibited virtually the same affinity toward HvTrxh1 and HvTrxh2, whereas HvNTR2 has slightly higher catalytic activity than HvNTR1 with both Trx h isoforms, and HvNTR1 has slightly higher catalytic activity toward HvTrxh1 than HvTrxh2. Notably, both NTRs reduced Trx h at the acidic conditions residing in the starchy endosperm during germination. Interspecies reactions between the barley proteins and Escherichia coli Trx or Arabidopsis thaliana NTR, respectively, occurred with 20- to 90-fold weaker affinity. This first investigation of regulation and interactions between members of the NTR/Trx system in barley seed tissues suggests that different isoforms are differentially regulated but may have overlapping roles, with HvNTR2 and HvTrxh1 being the predominant isoforms in the aleurone layer.
Functions of Chloroplastic Adenylate Kinases in Arabidopsis
Authors: Lange Peter Robert , Geserick Claudia , Tischendorf Gilbert , Zrenner Rita 
Published: December 2007

AbstractAdenosine monophosphate kinase (AMK; adenylate kinase) catalyses the reversible formation of ADP by the transfer of one phosphate group from ATP to AMP, thus equilibrating adenylates. The Arabidopsis (Arabidopsis thaliana) genome contains 10 genes with an adenylate/cytidylate kinase signature; seven of these are identified as putative adenylate kinases. Encoded proteins of at least two members of this Arabidopsis adenylate kinase gene family are targeted to plastids. However, when the individual genes are disrupted, the phenotypes of both mutants are strikingly different. Although absence of AMK2 causes only 30% reduction of total adenylate kinase activity in leaves, there is loss of chloroplast integrity leading to small, pale-looking plantlets from embryo to seedling development. In contrast, no phenotype for disruption of the second plastid adenylate kinase was found. From this analysis, we conclude that AMK2 is the major activity for equilibration of adenylates and de novo synthesis of ADP in the plastid stroma.
Landslide Erosion Rate in the Eastern Cordillera of Northern Bolivia
Authors: Blodgett Troy A. , Isacks Bryan L. 
Published: December 2007

AbstractThe northeastern edge of the Bolivian Eastern Cordillera is an example of a tectonically active plateau margin where orographically enhanced precipitation facilitates very high rates of erosion. The topography of the steepest part of the margin exhibits the classic signature of high erosion rates consisting of high-relief V-shaped valleys where landsliding is the dominant process of hillslope erosion and bedrock rivers are incising into the landscape. The authors mapped landslide scars on multitemporal aerial photographs to estimate hillslope erosion rates. Field surveys of landslide scars are used to calibrate a landslide volume versus area relationship. The mapped area of landsliding, in combination with an estimate of the time for landslide scars to revegetate, leads to an erosion rate estimate. The estimated revegetation time, 10–35 yr, is based on analysis of multitemporal aerial photographs and tree rings. About 4%–6% of two watersheds in the region considered were affected by landslides over the last 10–35 yr. This result implies an erosion rate of 9 ± 5 mm yr−1 assuming that 90% of a single landslide reaches the river on average. Classified Landsat Thematic Mapper images show that landslides are occurring at approximately the same rate all across an approximately 40-km-wide swath within the high-relief zones of the cordillera.
On the Interaction of Jupiter’s Great Red Spot and Zonal Jet Streams
Authors: Shetty Sushil , Asay-Davis Xylar S. , Marcus Philip S. 
Published: December 2007

Abstract
In this paper, Jupiter’s Great Red Spot (GRS) is used to determine properties of the Jovian atmosphere that cannot otherwise be found. These properties include the potential vorticity of the GRS and its neighboring jet streams, the shear imposed on the GRS by the jet streams, and the vertical entropy gradient (i.e., Rossby deformation radius). The cloud cover of the GRS, which is often used to define the GRS’s area and aspect ratio, is found to differ significantly from the region of the GRS’s potential vorticity anomaly. The westward-going jet stream to the north of the GRS and the eastward-going jet stream to its south are each found to have a large potential vorticity “jump.” The jumps have opposite signs, and as a consequence of their interaction with the GRS, the shear imposed on the GRS is reduced. The aspect ratio of the GRS’s potential vorticity anomaly depends on the ratio of the imposed shear to the strength of the anomaly. The east–west to north–south aspect ratio is found to be ∼2:1, but without the opposing jumps it would be much greater. The GRS’s high-speed collar and quiescent interior require that the potential vorticity in the interior be approximately half that in the collar. No other persistent geophysical vortex has a significant local minimum of potential vorticity in its interior, and laboratory vortices with such a minimum are unstable.
Seasonality and Regionality of the Madden–Julian Oscillation, Kelvin Wave, and Equatorial Rossby Wave
Authors: Masunaga Hirohiko 
Published: December 2007

Abstract
The Madden–Julian oscillation (MJO), Kelvin wave, and equatorial Rossby (ER) wave—collectively called intraseasonal oscillations (ISOs)—are investigated using a 25-yr record of outgoing longwave radiation (OLR) measurements as well as the associated dynamical fields. The ISO modes are detected by applying bandpass filters to the OLR data in the frequency–wavenumber space. An automated wave-tracking algorithm is applied to each ISO mode so that convection centers accompanied with the ISOs are traced in space and time in an objective fashion. The identified paths of the individual ISO modes are first examined and found strongly modulated regionally and seasonally. The dynamical structure is composited with respect to the convection centers of each ISO mode. A baroclinic mode of the combined Rossby and Kelvin structure is prominent for the MJO, consistent with existing work. The Kelvin wave exhibits a low-level wind field resembling the shallow-water solution, while a slight lead of low-level convergence over convection suggests the impact of frictional boundary layer convergence on Kelvin wave dynamics. A lagged composite analysis reveals that the MJO is accompanied with a Kelvin wave approaching from the west preceding the MJO convective maximum in austral summer. MJO activity then peaks as the Kelvin and ER waves constructively interfere to enhance off-equatorial boundary layer convergence. The MJO leaves a Kelvin wave emanating to the east once the peak phase is passed. The approaching Kelvin wave prior to the development of MJO convection is absent in boreal summer and fall. The composite ER wave, loosely concentrated around the MJO, is nearly stationary throughout. A possible scenario to physically translate the observed result is also discussed.
A Tropical and Subtropical Land–Sea–Atmosphere Drought Oscillation Mechanism
Authors: Abbot Dorian S. , Emanuel Kerry A. 
Published: December 2007

Abstract
A two-column atmospheric model on a land–sea interface is studied. The model has sophisticated convection, cloud, and radiation schemes, a mixed layer ocean, and a bucket model to simulate land hydrology. A self-sustained oscillation in soil moisture with a period on the order of months is found. This oscillation is strongest when the model is run with parameters chosen to correspond to the arid subtropics. The effect of changing model parameters on the oscillation is explored. The existence and qualitative behavior of the oscillation are relatively robust to changes in model parameters.
Rossby Waves and Jets in Two-Dimensional Decaying Turbulence on a Rotating Sphere
Authors: Hayashi Yoshi-Yuki , Nishizawa Seiya , Takehiro Shin-ichi , Yamada Michio , Ishioka Keiichi , Yoden Shigeo 
Published: December 2007

Abstract
Jet formation in decaying two-dimensional turbulence on a rotating sphere is reviewed from the viewpoint of Rossby waves. A series of calculations are performed to confirm the behavior of zonal mean flow generation on the parameter space of the rotation rate Ω and Froude number Fr. When the flow is nondivergent and Ω is large, intense easterly circumpolar jets tend to emerge in addition to the appearance of a banded structure of zonal mean flows with alternating flow directions. When the system allows surface elevation, circumpolar jets disappear and an equatorial easterly jet emerges with increasing Fr. The appearance of the intense easterly jets can be understood by the angular-momentum transport associated with the generation, propagation, and absorption of Rossby waves. When the flow is nondivergent, long Rossby waves tend to be absorbed near the poles. In contrast, when Fr is large, Rossby waves can hardly propagate poleward and tend to be absorbed near the equator.
Generalized Stability of Nongeostrophic Baroclinic Shear Flow. Part II: Intermediate Richardson Number Regime
Authors: Heifetz Eyal , Farrell Brian F. 
Published: December 2007

Abstract
This work continues the generalized stability theory (GST) analysis of baroclinic shear flow in the primitive equations (PE), focusing on the regime in which the mean baroclinic shear and the stratification are of the same order. The Eady model basic state is used and solutions obtained using the PE are compared to quasigeostrophic (QG) solutions.
Similar optimal growth is obtained in the PE and QG frameworks for eddies with horizontal scale equal to or larger than the Rossby radius, although PE growth rates always exceed QG growth rates. The primary energy growth mechanism is the conventional baroclinic conversion of mean available potential energy to perturbation energy mediated by the eddy meridional heat flux. However, for eddies substantially smaller than the Rossby radius, optimal growth rates in the PE greatly exceed those found in the QG. This enhanced growth rate in the PE is dominated by conversion of mean kinetic energy to perturbation kinetic energy mediated by the vertical component of zonal eddy momentum flux. This growth mechanism is filtered in QG. In the intermediate Richardson number regime mixed Rossby–gravity modes are nonorthogonal in energy, and these participate in the process of energy transfer from the barotropic source in the mean shear to predominantly baroclinic waves during the transient growth process.
The response of shear flow in the intermediate Richardson number regime to spatially and temporally uncorrelated stochastic forcing is also investigated. It is found that a comparable amount of shear turbulent variance is maintained in the rotational and mixed Rossby–gravity modes by such unbiased forcing suggesting that any observed dominance of rotational mode energy arises from restrictions on the effective forcing and damping.
Mean Climate and Variability of the Atmosphere and Ocean on an Aquaplanet
Authors: Marshall John , Ferreira David , Campin J-M. , Enderton Daniel 
Published: December 2007

Abstract
Numerical experiments are described that pertain to the climate of a coupled atmosphere–ocean–ice system in the absence of land, driven by modern-day orbital and CO2 forcing. Millennial time-scale simulations yield a mean state in which ice caps reach down to 55° of latitude and both the atmosphere and ocean comprise eastward- and westward-flowing zonal jets, whose structure is set by their respective baroclinic instabilities. Despite the zonality of the ocean, it is remarkably efficient at transporting heat meridionally through the agency of Ekman transport and eddy-driven subduction. Indeed the partition of heat transport between the atmosphere and ocean is much the same as the present climate, with the ocean dominating in the Tropics and the atmosphere in the mid–high latitudes. Variability of the system is dominated by the coupling of annular modes in the atmosphere and ocean. Stochastic variability inherent to the atmospheric jets drives variability in the ocean. Zonal flows in the ocean exhibit decadal variability, which, remarkably, feeds back to the atmosphere, coloring the spectrum of annular variability. A simple stochastic model can capture the essence of the process. Finally, it is briefly reviewed how the aquaplanet can provide information about the processes that set the partition of heat transport and the climate of Earth.
Large-Eddy Simulation of the Onset of the Sea Breeze
Authors: Antonelli M. , Rotunno R. 
Published: December 2007

Abstract
This paper describes results from a large-eddy simulation (LES) model used in an idealized setting to simulate the onset of the sea breeze. As the LES is capable of simulating boundary layer–scale, three-dimensional turbulence along with the mesoscale sea-breeze circulation, a parameterization of the planetary boundary layer was unnecessary. The basic experimental design considers a rotating, uniformly stratified, resting atmosphere that is suddenly heated at the surface over the “land” half of the domain. To focus on the simplest nontrivial problem, the diurnal cycle, effects of moisture, interactions with large-scale winds, and coastline curvature were all neglected in this study. The assumption of a straight coastline allows the use of a rectangular computational domain that extends to 50 km on either side of the coast, but only 5 km along the coast, with 100-m grid intervals so that the small-scale turbulent convective eddies together with the mesoscale sea breeze may be accurately computed. Through dimensional analysis of the simulation results, the length and velocity scales characterizing the simulated sea breeze as functions of the externally specified parameters are identified.
Numerical Simulation of Baroclinic Waves with a Parameterized Boundary Layer
Authors: Plant R. S. , Belcher S. E. 
Published: December 2007

Abstract
A dry three-dimensional baroclinic life cycle model is used to investigate the role of turbulent fluxes of heat and momentum within the boundary layer on midlatitude cyclones. Simulations are performed of life cycles for two basic states: with and without turbulent fluxes. The different basic states produce cyclones with contrasting frontal and mesoscale flow structures. The analysis focuses on the generation of potential vorticity (PV) in the boundary layer and its subsequent transport into the free troposphere. The dynamic mechanism through which friction mitigates a barotropic vortex is that of Ekman pumping. This has often been assumed to also be the dominant mechanism for baroclinic developments. The PV framework highlights an additional, baroclinic mechanism. Positive PV is generated baroclinically due to friction to the northeast of a surface low and is transported out of the boundary layer by a cyclonic conveyor belt flow. The result is an anomaly of increased static stability in the lower troposphere, which restricts the growth of the baroclinic wave. The reduced coupling between lower and upper levels can be sufficient to change the character of the upper-level evolution of the mature wave. The basic features of the baroclinic damping mechanism are robust for different frontal structures, with and without turbulent heat fluxes, and for the range of surface roughness found over the oceans.