bluuebunny/crossref_metadata_2025 huggingface dataset:
Model simulations of the adsorption of statherin to solid surfaces: Effects of surface charge and hydrophobicity
Authors: Skepö M.
Published: November 2008

The structural properties of the salivary protein statherin upon adsorption have been examined using a coarse-grained model and Monte Carlo simulation. A simple model system with focus on electrostatic interactions and short-ranged attractions among the uncharged amino acids has been used. To mimic hydrophobically modified surfaces, an extra short-ranged interaction was implemented between the amino acids and the surface. It has been shown that the adsorption and the thickness of the adsorbed layer are determined by (i) the affinity for the surface, i.e., denser layer with an extrashort-ranged potential, and (ii) the distribution of the charges along the chain. If all the amino acids have a high affinity for the surface, the protein adsorbs in a train conformation, if the surface is negatively charged the protein adsorbs in a tail-train conformation, whereas if the surface is positively charged the protein adsorbs in a loop conformation. The latter gives rise to a more confined adsorbed layer.
On the collective network of ionic liquid/water mixtures. II. Decomposition and interpretation of dielectric spectra
Authors: Schröder C. , Hunger J. , Stoppa A. , Buchner R. , Steinhauser O.
Published: November 2008

This study deals with the dielectric spectra of mixtures of the ionic liquid 1-butyl-3-methyl-imidazolium (BMIM+) tetrafluoroborate with water at three selected mole fractions 0.767≤xH2O≤0.967. The focus lies on the comparison of experimental and computational data. On the one hand, a computational analysis permits a complete decomposition of spectra, both with respect to dynamical behavior (translation and rotation) as well as to composition of the mixture (cation, anion, and water). Thereby, not only the peak assignment in experimental spectra is enabled but one can also learn more about solvation properties. Of particular importance is the interplay of the dielectric constant and the conductivity representing a measure of collective rotational and translational motion. On the other hand, the comparison with experimental spectra is essential for the validation of the force fields used in simulation. The satisfying agreement between corresponding peaks in the dielectric spectra confirms not only computed dielectric relaxation times but also other collective dynamical properties such as the viscosity. Nevertheless, the detailed fine structure of the conductivity regime reveals specific ion-pair effects not covered by the simulation. A possible confinement of dynamical heterogeneity as a consequence of a system size effect is also indicated.
Coarse-grained kinetic Monte Carlo models: Complex lattices, multicomponent systems, and homogenization at the stochastic level
Authors: Collins Stuart D. , Chatterjee Abhijit , Vlachos Dionisios G.
Published: November 2008

On-lattice kinetic Monte Carlo (KMC) simulations have extensively been applied to numerous systems. However, their applicability is severely limited to relatively short time and length scales. Recently, the coarse-grained MC (CGMC) method was introduced to greatly expand the reach of the lattice KMC technique. Herein, we extend the previous spatial CGMC methods to multicomponent species and/or site types. The underlying theory is derived and numerical examples are presented to demonstrate the method. Furthermore, we introduce the concept of homogenization at the stochastic level over all site types of a spatially coarse-grained cell. Homogenization provides a novel coarsening of the number of processes, an important aspect for complex problems plagued by the existence of numerous microscopic processes (combinatorial complexity). As expected, the homogenized CGMC method outperforms the traditional KMC method on computational cost while retaining good accuracy.
Power spectra for both interrupted and perennial aging processes
Authors: Lukovic Mirko , Grigolini Paolo
Published: November 2008

We study the power spectrum of a random telegraphic noise with the distribution density of waiting times τ given by ψ(τ)∝1∕τμ, with μ≈2. The condition μ<2 violates the ergodic hypothesis, and in this case the adoption of Wiener–Khintchine (WK) theorem for the spectrum evaluation requires some caution. We study this problem theoretically and numerically and we prove that the power spectrum obeys the prescription S(f)=K∕fη, with η=3−μ, namely, the 1∕f noise lives at border between the ergodic μ>2 and nonergodic μ<2 condition. We study sequences with the finite length L. In the case μ<2 the adoption of WK theorem is made legitimate by two different kinds of truncation effects: the physical and observation-induced effect. In the former case ψ(τ) is truncated at τ≈Tmax and L⪢Tmax ensures the condition of interrupted aging. In this case, we find that K is a number independent of L. The latter case, L⪡Tmax, is more challenging. It was already solved by Margolin and Barkai, who used time asymptotic arguments based on the ergodicity breakdown and obtained K∝1∕L2−μ, proving that the out-of-equilibrium nature of the condition μ<2 is signaled by the decrease of K with the increase of L. We use a generalized version of the Onsager principle that leads us to the same conclusion from a somewhat more extended view valid also for the transient out-of-equilibrium case of μ>2. We do not limit our treatment to the time asymptotic case, thereby producing a prediction that accounts for the transition from the 1∕fη to the 1∕f2 regime, recently observed in an experiment on blinking quantum dots. Our theoretical approach allows us to discuss some other recent experiments on molecular intermittent fluorescence and affords indications that should help to assess whether the spectrum is determined by the L⪡Tmax or by the L⪢Tmax condition.
Annealing-induced reduction in nanoscale heterogeneity of thermally evaporated amorphous As2S3 films
Authors: Liu A. C. Y. , Chen Xidong , Choi D.-Y. , Luther-Davies B.
Published: November 2008

The morphology and structural order of thermally deposited and annealed amorphous As2S3 films have been investigated using high resolution transmission electron microscopy. It was found that both the as-deposited and annealed films contained sparsely distributed nanocrystallites of the orpiment As2S3 crystalline phase. However, from selected area electron diffraction both films appeared amorphous. Fluctuation electron microscopy revealed that the as-deposited film contained greater nanoscale inhomogeneity. Low temperature annealing reduced the nanoscale inhomogeneity and resulted in a more homogeneous and energetically favorable network. The reduction in nanoscale inhomogeneity upon low temperature annealing was accompanied by the appearance of a first sharp diffraction peak in the diffraction pattern. This first-sharp diffraction peak has been attributed to chemical ordering of interstitial voids. Our measurements suggest that this chemical short-range ordering is associated with the dissolution of the energetically unfavorable larger correlated structures that contribute to the inhomogeneity of the as-deposited film.
Suppression of magnetic trench material in bit patterned media fabricated by blanket deposition onto prepatterned substrates
Authors: Hellwig O. , Moser A. , Dobisz E. , Bandic Z. Z. , Yang H. , Kercher D. S. , Risner-Jamtgaard J. D. , Yaney D. , Fullerton E. E.
Published: November 2008

An attractive approach for bit patterned media fabrication is the blanket deposition of magnetic material onto prepatterned substrates with elevated pillars and recessed trench areas. One issue with this method is the residual magnetic material in the trenches that causes disturbing stray fields during writing and readback. Here we present a technique to suppress the magnetic moment in the trenches with an additional annealing step by using prepatterned substrates consisting of SiN pillars on a Si wafer. The annealing triggers an interdiffusion process between the magnetic media and the Si in the trenches that results in the formation of a nonmagnetic silicide, while the magnetic moment on top of the SiN pillars remains substantially unaltered.
Resonant electron tunneling through defects in GaAs tunnel diodes
Authors: Jandieri K. , Baranovskii S. D. , Rubel O. , Stolz W. , Gebhard F. , Guter W. , Hermle M. , Bett A. W.
Published: November 2008

Current-voltage characteristics of GaAs tunnel diodes are studied experimentally and theoretically. In theoretical calculations contributions of three different transport mechanisms are considered: direct tunneling processes, nonresonant multiphonon tunneling processes via defects, and resonant tunneling processes through defects. The comparison between theoretical results and experimental data reveals resonant tunneling as the dominant transport mechanism at voltages corresponding to the peak current. At higher voltages this mechanism is replaced by nonresonant tunneling, which is in its turn replaced by over-barrier transport at even larger voltages.
Fountain-pen controlled dielectrophoresis for carbon nanotube-integration in device assembly
Authors: Schwamb Timo , Schirmer Niklas C. , Burg Brian R. , Poulikakos Dimos
Published: November 2008

A method to integrate functional nanoparticles, exemplified by carbon nanotubes (CNTs), in devices is presented. This method combines the dielectrophoretic deposition of nanoparticles with microscale liquid handling by the fountain-pen principle. This combination allows an automatable, precise, and point-wise deposition of nanoparticles. Furthermore, a method-intrinsic separation mechanism was observed, based on which, the unwanted deposition of spaghettilike CNT bundles could be controlled. The feasibility of the method was proven numerically and experimentally.
Histopathology comparison and phenylalanine ammonia lyase (PAL) gene expressions in Fusarium wilt infected watermelons
Authors: Chang P.-F. L. , Hsu C.-C. , Lin Y.-H. , Chen K.-S. , Huang J.-W. , Liou T.-D.
Published: November 2008

Fusarium wilt disease of watermelon (Citrullus lanatus (Thunb.) Matsum & Nakai), caused by Fusarium oxysporum f. sp. niveum (FON), is one of the limiting factors of worldwide watermelon production. In this study, a Fusarium wilt resistant watermelon JSB, which was derived from a spontaneous mutation of the susceptible Sugar Baby (SB), was used to investigate histopathology. The number and diameter of xylem vessels in the root (10 mm below the shoot base) of resistant JSB plants were significantly higher than those in susceptible SB plants. At 9 days post inoculation (dpi), using the plate assay on Nash-PCNB media, FON could be recovered from 86% of the roots in the symptomless plants of both watermelon lines, and from 55% and 64% of the stem segments (5 mm above the shoot base) in resistant and susceptible plants, respectively. In paraffin and free-hand tissue sections, at 8, 13, and 35 dpi, the xylem of roots and stems close to the soil surface in resistant watermelon JSB plants was also colonised by FON, but to a much lower percentage than the susceptible SB ones. No colonisation below the middle of stems was observed in the resistant JSB plants. The susceptible plants grown in infested soil were all dead by 35 dpi, while the resistant plants remained healthy. These observations suggest that reducing FON colonisation in the vascular systems of the host may contribute to the resistance in JSB. Furthermore, the higher expression of the phenylalanine ammonia lyase (PAL) gene in JSB induced by FON and the effects of PAL inhibitor on the resistance of JSB suggested that PAL is involved in resistance of watermelon to Fusarium wilt pathogen.
A method to differentiate summer-dormant from summer-active tall fescue and orchardgrass accessions at germination stage
Authors: Malinowski Dariusz P. , Belesky David P. , Kramp Betty A. , Ruckle Joyce , Kigel Jaime , Pinchak William E.
Published: November 2008

Summer-dormant, cool-season perennial grasses are being used in place of traditional, summer-active cultivars for high-quality winter forage. One reason for this change is the ability of cultivars with summer-dormant attributes to tolerate increasing annual temperature, decreasing precipitation, and repeated severe summer droughts. The mechanism of summer dormancy is still not understood in detail. Cultivar development for summer dormancy typically is conducted under field conditions in environments where summer-active types do not survive summer weather conditions. We developed a method based on germination responses to photoperiod to differentiate summer-dormant from summer-active types of tall fescue [Lolium arundinaceum (Schreb.) S. J. Darbyshire] and orchardgrass (Dactylis glomerata L.). Seed of cultivars with known summer dormancy characteristics was germinated at a constant temperature of 24°C under a range of photoperiods (0–24 h) for 14 days. Total germination, modelled cumulative germination, instantaneous rate of germination, and relative germination (to that in the dark) were analysed. Germination of summer-dormant orchardgrass was similar in the dark and short photoperiods (4–12 h), but it was inhibited by a photoperiod longer than 12 h. Germination of summer-active orchardgrass was promoted by any photoperiod compared with the control (0 h). Short photoperiods (4–12 h) promoted germination of summer-dormant tall fescue, while long photoperiods (>12 h) inhibited germination compared with germination in the dark. Summer-active types of tall fescue did not respond to photoperiod, regardless of length. A validation test using two Mediterranean origin cultivars of orchardgrass with contrasting summer dormancy characteristics and experimental lines of Mediterranean origin tall fescue with known expression of summer dormancy characteristics supported the use of seed germination analysis to differentiate among lines for this trait.
Identification of quantitative trait loci associated with salt tolerance during seedling growth in soybean (Glycine max L.)
Authors: Chen Huatao , Cui Shiyou , Fu Sanxiong , Gai Junyi , Yu Deyue
Published: November 2008

Salt stress is an important factor affecting the growth and development of soybean. The inheritance and expression of traits associated with salt tolerance during the seedling stage are complex. The present study was conducted to identify quantitative trait loci (QTLs) associated with salt tolerance during seedling growth in soybean. Field and greenhouse experiments were conducted to evaluate 184 recombinant inbred lines (RILs) derived from a cross between Kefeng No. 1 and Nannong1138-2 for salt tolerance and QTLs that are associated with salt tolerance. The molecular map of this RIL population, covering 2625.9 cM of the genome, converged into 24 linkage groups and consisted of 221 SSR markers and 1 disease-resistant gene (Rsc-7). QTL mapping was conducted using WinQTLCart. Eight putative QTLs significantly associated with salt tolerance were identified. One QTL was identified both in field and greenhouse experiments. In the field, salt tolerance was assessed (tolerance rating, TR) visually on a 0 (death) to 5 (unaffected by salt stress) scale. Three QTLs were detected on two linkage groups explaining 7.1–19.7% of the total phenotypic variance for salt tolerance. In the greenhouse, plant survival days (PSD) and percentage of plant survival (PPS) under salt stress were measured. Six QTLs were detected on six linkage groups, and explained 7.8–19.2% of total phenotypic variation for salt tolerance. A major QTL was identified between markers Sat_164 and Sat_358 on linkage group G in both the field and greenhouse. This QTL qppsN.1 was identified in the same location as a salt tolerance QTL previously reported in soybean. The detection of new QTLs will provide important information for marker-assisted selection (MAS) and further genetic studies on salt tolerance in soybean.
Modelling leaf phototropism in a cucumber canopy
Authors: Kahlen Katrin , Wiechers Dirk , Stützel Hartmut
Published: November 2008

Leaf phototropism might have significant effects on the light interception, dry matter production and yield of cucumber (Cucumis sativus L.). The objective of the present study was to model the phototropism of leaves in a greenhouse cucumber canopy. The dynamic structural model of cucumber using a parametric L-system was extended to mimic the leaf movement induced by gradients in the local light environment of each leaf. The red to far-red (R : FR) ratio is known to be a driving force in shade avoidance reactions of plants. In the model, R : FR ratios on the left and right leaf half of each individual leaf lamina were calculated and the change in tropism angle per phyllochron was based on the R : FR gradient across the leaf halves. The tropism angle of a leaf describes the deviation of the present leaf azimuth from the initial leaf orientation, which is predefined by the phyllotaxis of the plant. Even in its simple form, the model simulated photo-morphogenic canopy responses.
A stochastic 1D nearest-neighbour automaton models early development of the brown alga Ectocarpus siliculosus
Authors: Billoud Bernard , Le Bail Aude , Charrier Bénédicte
Published: November 2008

Early development of the filamentous brown alga Ectocarpus siliculosus (Dillwyn) Lyngbye involves two cell types that are arranged in a polymorphic, but constrained, pattern. The present study aimed to decipher the cellular processes responsible for the establishment of this pattern. Thorough observations characterised five different events of division and differentiation that occurred during the early development. The hypothesis that a local control is responsible for these processes was tested. To do so, Ectomat, a stochastic automaton in which each cell only interacts with its closest neighbour(s), was created. The probabilities for the five events were adjusted to fit to the observations. Simulations with Ectomat reconstructed most of the essential properties of the sporophyte development, in terms of cell-type proportion, relative position and growth dynamics. The whole organism properties emerged by applying local transition rules. In conclusion, no global position information system was required at this development stage. Randomly occurring cell events, driven by simple contact interactions, are sufficient to account for the early filament development and establishment of the cell-type pattern of E. siliculosus.
Comparison of architecture among different cultivars of hybrid rice using a spatial light model based on 3-D digitising
Authors: Zheng Bangyou , Shi Lijuan , Ma Yuntao , Deng Qiyun , Li Baoguo , Guo Yan
Published: November 2008

Modification of plant types (i.e. plant architecture) is an important strategy to enhance the yield potential of crops. The aims of this study were to specify rice plant types using 3-D modelling methodology. The architecture of three typical hybrid rice cultivars were measured in situ in a paddy field using a 3-D digitiser at four development stages from the panicle initiation to the filling stage. The structural parameters of the rice canopies were calculated and their light capture and potential carbon gain were simulated based on a 3-D light model. The results confirmed that a plant type with steeper leaf angles let light penetrate more deeply with relatively uniform light distribution in the canopy at higher sun elevation angles, although this result was related to leaf area index. The variations of plant types, however, did not convert into differences of light distribution across rice varieties at lower sun elevation angles. Light use efficiency at the higher leaf area index could be enhanced by reducing mutual-shading. These results indicate that a promising approach to quantify the rice architecture in situ is to combine 3-D digitising and a 3-D light model to evaluate light interception and photosynthesis of rice plant types.
Photosynthesis - stomatal conductance model LEAFC3-N: specification for barley, generalised nitrogen relations, and aspects of model application
Authors: Müller Johannes , Braune Henning , Diepenbrock Wulf
Published: November 2008

We discuss a generalised formulation of the nitrogen-sensitive photosynthesis−stomatal conductance model LEAFC3-N to be used as a submodel of functional–structural plant models (FSPMs) or traditional crop growth models for C3-crops. Based on a parameterisation study for barley, we demonstrate that the large variation of characteristics related to potential leaf photosynthesis and stomatal conductance, along with different factors, can be accounted for by introducing functions that relate parameter values to nitrogen contents. These relationships follow the same pattern for different C3 crops, and their parameters are in close range. The accuracy of the parameters and the minimum simulation time step required for reliable predictions of the integrated diurnal carbon gain (IDC) is assessed. For IDC predictions with an accuracy of about ±5%, the accuracy of the slope of the relationship between maximum carboxylation rate and leaf nitrogen content should be of similar order. For other key model parameters, an error of ±20% or even greater may be tolerated. A time step of 1–2 h will be sufficient to predict IDC with an accuracy of about ±5%.
The Role ofNDR1in Avirulence Gene-Directed Signaling and Control of Programmed Cell Death in Arabidopsis
Authors: Shapiro Allan D. , Zhang Chu
Published: November 2008

Arabidopsis plants containing the ndr1-1 mutation are incapable of mounting a hypersensitive response to bacteria carrying avrRpt2, but show an exaggerated cell death response to bacteria carrying avrB (Century et al., 1995). We show here that ndr1-1 plants are severely impaired in induction of systemic acquired resistance andPR1-driven transcription of a reporter gene in response to Pseudomonas syringae strains carryingavrRpt2 but not in response to P. syringae carrying avrB. Thendr1-1 mutation also impaired salicylic acid (SA) accumulation in response to treatments that produced reactive oxygen species (ROS) and impaired induction of systemic acquired resistance in response to in situ production of ROS. Hydrogen peroxide accumulated in wild-type Arabidopsis leaves beginning 4 to 7 h postinoculation with P. syringae carrying either avrRpt2or avrB. In ndr1-1 plants, P. syringae carrying avrRpt2 elicited no detectable hydrogen peroxide production. Hydrogen peroxide production in response to bacteria carrying avrB was similar to that of Columbia in kinetics but of lesser intensity at early time points. These data are interpreted to indicate that NDR1 links ROS generation to SA production and that the phenotypic consequences of the ndr1-1 mutation are caused by a reduced ability to accumulate SA upon pathogen infection.
Growth in Elevated CO2 Can Both Increase and Decrease Photochemistry and Photoinhibition of Photosynthesis in a Predictable Manner. Dactylis glomerata Grown in Two Levels of Nitrogen Nutrition
Authors: Hymus Graham J. , Baker Neil R. , Long Stephen P.
Published: November 2008

Biochemically based models of C3 photosynthesis can be used to predict that when photosynthesis is limited by the amount of Rubisco, increasing atmospheric CO2 partial pressure (pCO2) will increase light-saturated linear electron flow through photosystem II (J  t). This is because the stimulation of electron flow to the photosynthetic carbon reduction cycle (J  c) will be greater than the competitive suppression of electron flow to the photorespiratory carbon oxidation cycle (J  o). Where elevatedpCO2 increasesJ  t, then the ratio of absorbed energy dissipated photochemically to that dissipated non-photochemically will rise. These predictions were tested on Dactylis glomerata grown in fully controlled environments, at either ambient (35 Pa) or elevated (65 Pa) pCO2, and at two levels of nitrogen nutrition. As was predicted, forD. glomerata grown in high nitrogen,J  t was significantly higher in plants grown and measured at elevated pCO2 than for plants grown and measured at ambient pCO2. This was due to a significant increase inJ  c exceeding any suppression ofJ  o. This increase in photochemistry at elevated pCO2 protected against photoinhibition at high light. For plants grown at low nitrogen,J  t was significantly lower in plants grown and measured at elevated pCO2 than for plants grown and measured at ambient pCO2. Elevated pCO2 again suppressedJ  o; however growth in elevatedpCO2 resulted in an acclimatory decrease in leaf Rubisco content that removed any stimulation ofJ  c. Consistent with decreased photochemistry, for leaves grown at low nitrogen, the recovery from a 3-h photoinhibitory treatment was slower at elevatedpCO2.
Sulfur Economy and Cell Wall Biosynthesis during Sulfur Limitation of Chlamydomonas reinhardtii
Authors: Takahashi Hideki , Braby Caren E. , Grossman Arthur R.
Published: November 2008

We have identified two novel periplasmic/cell wall polypeptides that specifically accumulate during sulfur limitation ofChlamydomonas reinhardtii. These polypeptides, present at high levels in the extracellular polypeptide fraction from a sulfur-deprived, cell wall-minus C. reinhardtii strain, have apparent molecular masses of 76 and 88 kD and are designated Ecp76 and Ecp88. N-terminal sequences of these polypeptides facilitated the isolation of full-length Ecp76 and Ecp88cDNAs. Ecp76 and Ecp88 polypeptides are deduced to be 583 and 595 amino acids, respectively. Their amino acid sequences are similar to each other, with features characteristic of cell wall-localized hydroxyproline-rich glycoproteins; the N terminus of each polypeptide contains a predicted signal sequence, whereas the C terminus is rich in proline, alanine, and serine. Ecp76 and Ecp88 have either no (Ecp88) or one (Ecp76) sulfur-containing amino acid and transcripts encoding these polypeptides are not detected in cultures maintained on complete medium, but accumulate when cells are deprived of sulfur. This accumulation is temporally delayed relative to the accumulation of sulfur stress-induced arylsulfatase and ATP sulfurylase transcripts. The addition of sulfate back to sulfur-starved cultures caused a rapid decline in Ecp76 and Ecp88 mRNAs (half lives < 10 min). Furthermore, the C. reinhardtii sac1 mutant, which lacks a regulatory protein critical for acclimation to sulfur limitation, does not accumulate Ecp76 or Ecp88 transcripts. These results suggest that the Ecp76 and Ecp88 genes are underSacI control, and that restructuring of the C. reinhardtii cell wall during sulfur limitation may be important for redistribution of internal and efficient utilization of environmental sulfur-containing molecules.
Two Tomato Expansin Genes Show Divergent Expression and Localization in Embryos during Seed Development and Germination
Authors: Chen Feng , Dahal Peetambar , Bradford Kent J.
Published: November 2008

Expansins are plant proteins that can induce extension of isolated cell walls and are proposed to mediate cell expansion. Three expansin genes were expressed in germinating tomato (Lycopersicon esculentum Mill.) seeds, one of which (LeEXP4) was expressed specifically in the endosperm cap tissue enclosing the radicle tip. The other two genes (LeEXP8 andLeEXP10) were expressed in the embryo and are further characterized here. LeEXP8 mRNA was not detected in developing or mature seeds but accumulated specifically in the radicle cortex during and after germination. In contrast,LeEXP10 mRNA was abundant at an early stage of seed development corresponding to the period of rapid embryo expansion; it then decreased during seed maturation and increased again during germination. When gibberellin-deficient (gib-1) mutant seeds were imbibed in water, LeEXP8 mRNA was not detected, but a low level of LeEXP10 mRNA was present. Expression of both genes increased when gib-1 seeds were imbibed in gibberellin. Abscisic acid did not prevent the initial expression of LeEXP8 and LeEXP10, but mRNA abundance of both genes subsequently decreased during extended incubation. The initial increase in LeEXP8, but notLeEXP10, mRNA accumulation was blocked by low water potential, but LeEXP10 mRNA amounts fell after longer incubation. When seeds were transferred from abscisic acid or low water potential solutions to water, abundance of both LeEXP8and LeEXP10 mRNAs increased in association with germination. The tissue localization and expression patterns of bothLeEXP8 and LeEXP10 suggest developmentally specific roles during embryo and seedling growth.
High-Resolution Metabolic Phenotyping of Genetically and Environmentally Diverse Potato Tuber Systems. Identification of Phenocopies
Authors: Roessner Ute , Willmitzer Lothar , Fernie Alisdair R.
Published: November 2008

We conducted a comprehensive metabolic phenotyping of potato (Solanum tuberosum L. cv Desiree) tuber tissue that had been modified either by transgenesis or exposure to different environmental conditions using a recently developed gas chromatography-mass spectrometry profiling protocol. Applying this technique, we were able to identify and quantify the major constituent metabolites of the potato tuber within a single chromatographic run. The plant systems that we selected to profile were tuber discs incubated in varying concentrations of fructose, sucrose, and mannitol and transgenic plants impaired in their starch biosynthesis. The resultant profiles were then compared, first at the level of individual metabolites and then using the statistical tools hierarchical cluster analysis and principal component analysis. These tools allowed us to assign clusters to the individual plant systems and to determine relative distances between these clusters; furthermore, analyzing the loadings of these analyses enabled identification of the most important metabolites in the definition of these clusters. The metabolic profiles of the sugar-fed discs were dramatically different from the wild-type steady-state values. When these profiles were compared with one another and also with those we assessed in previous studies, however, we were able to evaluate potential phenocopies. These comparisons highlight the importance of such an approach in the functional and qualitative assessment of diverse systems to gain insights into important mediators of metabolism.
Characterization of Two cDNAs Encoding Mitochondrial Lipoamide Dehydrogenase from Arabidopsis
Authors: Lutziger Isabelle , Oliver David J.
Published: November 2008

In contrast to peas (Pisum sativum), where mitochondrial lipoamide dehydrogenase is encoded by a single gene and shared between the α-ketoacid dehydrogenase complexes and the Gly decarboxylase complex, Arabidopsis has two genes encoding for two mitochondrial lipoamide dehydrogenases. Northern-blot analysis revealed different levels of RNA expression for the two genes in different organs; mtLPD1 had higher RNA levels in green leaves compared with the much lower level in roots. The mRNA formtLPD2 shows the inverse pattern. The other organs examined showed nearly equal RNA expressions for both genes. Analysis of etiolated seedlings transferred to light showed a strong induction of RNA expression for mtLPD1 but only a moderate induction of mtLPD2. Based on the organ and light-dependent expression patterns, we hypothesize thatmtLPD1 encodes the protein most often associated with the Gly decarboxylase complex, and mtLPD2 encodes the protein incorporated into α-ketoacid dehydrogenase complexes. Due to the high level of sequence conservation between the two mtLPDs, we assume that the proteins, once in the mitochondrial matrix, are interchangeable among the different multienzyme complexes. If present at high levels, one mtLPD might substitute for the other. Supporting this hypothesis are results obtained with a T-DNA knockout mutant,mtlpd2, which shows no apparent phenotypic change under laboratory growth conditions. This indicates that mtLPD1 can substitute for mtLPD2 and associate with all these multienzyme complexes.
An Oligopeptide Transporter Gene Family in Arabidopsis
Authors: Koh Serry , Wiles Amy M. , Sharp Joshua S. , Naider Fred R. , Becker Jeffrey M. , Stacey Gary
Published: November 2008

We have identified nine oligopeptide transporter (OPT) orthologs (AtOPT1 to AtOPT9) in Arabidopsis. These proteins show significant sequence similarity to OPTs of Candida albicans (CaOpt1p),Schizosaccharomyces pombe (Isp4p), andSaccharomyces cerevisiae (Opt1p and Opt2p). Hydrophilicity plots of the OPTs suggest that they are integral membrane proteins with 12 to 14 transmembrane domains. Sequence comparisons showed that the AtOPTs form a distinct subfamily when compared with the fungal OPTs. Two highly conserved motifs (NPG and KIPPR) were found among all OPT members. The identification of multiple OPTs in Arabidopsis suggests that they may play different functional roles. This idea is supported by the fact that AtOPTs have a distinct, tissue-specific expression pattern. The cDNAs encoding seven of the AtOPTs were cloned into a yeast vector under the control of a constitutive promoter. AtOPT4 expressed in S. cerevisiae mediated the uptake of KLG-[3H]L. Similarly, expression of five of the seven AtOPT proteins expressed in yeast conferred the ability to uptake tetra- and pentapeptides as measured by growth. This study provides new evidence for multiple peptide transporter systems in Arabidopsis, suggesting an important physiological role for small peptides in plants.
Extracellular Protons Inhibit the Activity of Inward- Rectifying Potassium Channels in the Motor Cells ofSamanea samanPulvini
Authors: Yu Ling , Moshelion Menachem , Moran Nava
Published: November 2008

The intermittent influx of K+ into motor cells in motor organs (pulvini) is essential to the rhythmic movement of leaves and leaflets in various plants, but in contrast to the K+ influx channels in guard cells, those in pulvinar motor cells have not yet been characterized. We analyzed these channels in the plasma membrane of pulvinar cell protoplasts of the nyctinastic legume Samanea saman using the patch-clamp technique. Inward, hyperpolarization-activated currents were separated into two types: time dependent and instantaneous. These were attributed, respectively, to K+-selective and distinctly voltage-dependent KH channels and to cation-selective voltage-independent leak channels. The pulvinar KH channels were inhibited by external acidification (pH 7.8–5), in contrast to their acidification-promoted counterparts in guard cells. The inhibitory pH effect was resolved into a reversible decline of the maximum conductance and an irreversible shift of the voltage dependence of KH channel gating. The leak appeared acidification insensitive. External Cs (10 mm in 200 mmexternal K+) blocked both current types almost completely, but external tetraethylammonium (10 mm in 200 mm external K+) did not. Although these results do not link these two channel types unequivocally, both likely serve as K+ influx pathways into swelling pulvinar motor cells. Our results emphasize the importance of studying multiple model systems.
Long-Day Induction of Flowering in Lolium temulentumInvolves Sequential Increases in Specific Gibberellins at the Shoot Apex
Authors: King Rod W. , Moritz Thomas , Evans Lloyd T. , Junttila Olavi , Herlt Anthony J.
Published: November 2008

One challenge for plant biology has been to identify floral stimuli at the shoot apex. Using sensitive and specific gas chromatography-mass spectrometry techniques, we have followed changes in gibberellins (GAs) at the shoot apex during long day (LD)-regulated induction of flowering in the grass Lolium temulentum. Two separate roles of GAs in flowering are indicated. First, within 8 h of an inductive LD, i.e. at the time of floral evocation, the GA5 content of the shoot apex doubled to about 120 ng g−1 dry weight. The concentration of applied GA5 required for floral induction of excised apices (R.W. King, C. Blundell, L.T. Evans [1993] Aust J Plant Physiol 20: 337–348) was similar to that in the shoot apex. Leaf-applied [2H4] GA5 was transported intact from the leaf to the shoot apex, flowering being proportional to the amount of GA5 imported. Thus, GA5 could be part of the LD stimulus for floral evocation of L. temulentum or, alternatively, its increase at the shoot apex could follow import of a primary floral stimulus. Later, during inflorescence differentiation and especially after exposure to additional LD, a second GA action was apparent. The content of GA1 and GA4 in the apex increased greatly, whereas GA5 decreased by up to 75%. GA4 applied during inflorescence differentiation strongly promoted flowering and stem elongation, whereas it was ineffective for earlier floral evocation although it caused stem growth at all times of application. Thus, we conclude that GA1 and GA4are secondary, late-acting LD stimuli for inflorescence differentiation in L. temulentum.
Regulation of CAX1, an Arabidopsis Ca2+/H+ Antiporter. Identification of an N-Terminal Autoinhibitory Domain
Authors: Pittman Jon K. , Hirschi Kendal D.
Published: November 2008

Regulation of Ca2+ transport determines the duration of a Ca2+ signal, and hence, the nature of the biological response. Ca2+/H+ antiporters such as CAX1 (cation exchanger 1), play a key role in determining cytosolic Ca2+ levels. Analysis of a full-length CAX1 clone suggested that the CAX1 open reading frame contains an additional 36 amino acids at the N terminus that were not found in the original clone identified by suppression of yeast (Saccharomyces cerevisiae) vacuolar Ca2+ transport mutants. The long CAX1 (lCAX1) could not suppress the yeast Ca2+ transport defects despite localization to the yeast vacuole. Calmodulin could not stimulate lCAX1 Ca2+/H+ transport in yeast; however, minor alterations in the 36-amino acid region restored Ca2+/H+ transport. Sequence analysis suggests that a 36-amino acid N-terminal regulatory domain may be present in all Arabidopsis CAX-like genes. Together, these results suggest a structural feature involved in regulation of Ca2+/H+ antiport.
Sucrose Phosphate Synthase Activity Rises in Correlation with High-Rate Cellulose Synthesis in Three Heterotrophic Systems
Authors: Babb V. Michelle , Haigler Candace H.
Published: November 2008

Based on work with cotton fibers, a particulate form of sucrose (Suc) synthase was proposed to support secondary wall cellulose synthesis by degrading Suc to fructose and UDP-glucose. The model proposed that UDP-glucose was then channeled to cellulose synthase in the plasma membrane, and it implies that Suc availability in cellulose sink cells would affect the rate of cellulose synthesis. Therefore, if cellulose sink cells could synthesize Suc and/or had the capacity to recycle the fructose released by Suc synthase back to Suc, cellulose synthesis might be supported. The capacity of cellulose sink cells to synthesize Suc was tested by analyzing the Suc phosphate synthase (SPS) activity of three heterotrophic systems with cellulose-rich secondary walls. SPS is a primary regulator of the Suc synthesis rate in leaves and some Suc-storing, heterotrophic organs, but its activity has not been previously correlated with cellulose synthesis. Two systems analyzed, cultured mesophyll cells of Zinnia elegans L. var. Envy and etiolated hypocotyls of kidney beans (Phaseolus vulgaris), contained differentiating tracheary elements. Cotton (Gossypium hirsutum L. cv Acala SJ-1) fibers were also analyzed during primary and secondary wall synthesis. SPS activity rose in all three systems during periods of maximum cellulose deposition within secondary walls. The Z. elegans culture system was manipulated to establish a tight linkage between the timing of tracheary element differentiation and rising SPS activity and to show that SPS activity did not depend on the availability of starch for degradation. The significance of these findings in regard to directing metabolic flux toward cellulose will be discussed.
Arabidopsis RTM1 and RTM2 Genes Function in Phloem to Restrict Long-Distance Movement of Tobacco Etch Virus
Authors: Chisholm Stephen T. , Parra Michael A. , Anderberg Robert J. , Carrington James C.
Published: November 2008

Restriction of long-distance movement of tobacco etch virus (TEV) in Arabidopsis ecotype Col-0 plants requires the function of at least three genes: RTM1 (restricted TEV movement 1),RTM2, and RTM3. The mechanism of TEV movement restriction remains poorly understood, although it does not involve a hypersensitive response or systemic acquired resistance. A functional characterization of RTM1 andRTM2 was done. The RTM1 protein was found to be soluble with the potential to form self-interacting complexes. The regulatory regions of both the RTM1 and RTM2 genes were analyzed using reporter constructs. The regulatory sequences from both genes directed expression of β-glucuronidase exclusively in phloem-associated cells. Translational fusion proteins containing the green fluorescent protein and RTM1 or RTM2 localized to sieve elements when expressed from their native regulatory sequences. Thus, components of the RTM system may function within phloem, and sieve elements in particular, to restrict TEV long-distance movement.
Hydrogen Production. Green Algae as a Source of Energy
Authors: Melis Anastasios , Happe Thomas
Published: November 2008

Hydrogen gas is thought to be the ideal fuel for a world in which air pollution has been alleviated, global warming has been arrested, and the environment has been protected in an economically sustainable manner. Hydrogen and electricity could team to provide attractive options in transportation and power generation. Interconversion between these two forms of energy suggests on-site utilization of hydrogen to generate electricity, with the electrical power grid serving in energy transportation, distribution utilization, and hydrogen regeneration as needed. A challenging problem in establishing H2 as a source of energy for the future is the renewable and environmentally friendly generation of large quantities of H2 gas. Thus, processes that are presently conceptual in nature, or at a developmental stage in the laboratory, need to be encouraged, tested for feasibility, and otherwise applied toward commercialization.
AtFXG1, an Arabidopsis Gene Encoding α-l-Fucosidase Active against Fucosylated Xyloglucan Oligosaccharides
Authors: de la Torre Francisco , Sampedro Javier , Zarra Ignacio , Revilla Gloria
Published: November 2008

An α-l-fucosidase (EC 3.2.1.51) able to release the t-fucosyl residue from the side chain of xyloglucan oligosaccharides has been detected in the leaves of Arabidopsis plants. Moreover, an α-l-fucosidase with similar substrate specificity was purified from cabbage (Brassica oleracea) leaves to render a single band on SDS-PAGE. Two peptide sequences were obtained from this protein band, and they were used to identify an Arabidopsis gene coding for an α-fucosidase that we propose to call AtFXG1. In addition, an Arabidopsis gene with homology with known α-l-fucosidases has been also found, and we proposed to name it as AtFUC1. Both AtFXG1 andATFUC1 were heterologously expressed in Pichia pastoris cells and the α-l-fucosidase activities secreted to the culture medium. The α-l-fucosidase encoded by AtFXG1 was active against the oligosaccharides from xyloglucan XXFG as well as against 2′-fucosyl-lactitol but not againstp-nitrophenyl-α-l-fucopyranoside. However, the AtFUC1 heterologously expressed was active only against 2′-fucosyl-lactitol. Thus, the former must be related to xyloglucan metabolism.
Purification and Identification of a 42-Kilodalton Abscisic Acid-Specific-Binding Protein from Epidermis of Broad Bean Leaves
Authors: Zhang Da-Peng , Wu Zhong-Yi , Li Xi-Yan , Zhao Zhi-Xin
Published: November 2008

Purification of abscisic acid (ABA)-binding proteins is considered to constitute a major step toward isolating ABA receptors. We report here that an ABA-binding protein was for the first time, to our knowledge, purified from the epidermis of broad bean (Vicia faba) leaves via affinity chromatography. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis, isoelectric focusing electrophoresis, and isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis two-dimensional electrophoresis of the purified ABA-binding protein all identified a single protein band with a molecular mass of 42 kD and an isoelectric point 4.86. The Scatchard plot for the purified protein showed a linear function with a maximum binding activity of 0.87 mol mol−1protein and an equilibrium dissociation constant of 21 nm, indicating that the purified protein may be a monomeric one, possessing one binding site. The ABA-binding protein was enriched more than 300-fold with a yield of 14%. (−)ABA and trans-ABA were substantially incapable of displacing 3H-(±)ABA bound to the ABA-binding protein, and (±)ABA was less effective than (+)ABA in the competition. These findings allow establishment of the stereospecificity of the 42-kD protein and suggest its ABA receptor nature. Pretreatment of the guard cell protoplasts of broad bean leaves with the monoclonal antibody raised against the 42-kD protein significantly decreased the ABA specific-induced phospholipase D activity in a dose-dependent manner. This physiological significance provides more clear evidence for the potential ABA-receptor nature of the 42-kD protein.
Phytochrome E Controls Light-Induced Germination of Arabidopsis
Authors: Hennig Lars , Stoddart Wendy M. , Dieterle Monika , Whitelam Garry C. , Schäfer Eberhard
Published: November 2008

Germination of Arabidopsis seeds is light dependent and under phytochrome control. Previously, phytochromes A and B and at least one additional, unspecified phytochrome were shown to be involved in this process. Here, we used a set of photoreceptor mutants to test whether phytochrome D and/or phytochrome E can control germination of Arabidopsis. The results show that only phytochromes B and E, but not phytochrome D, participate directly in red/far-red light (FR)-reversible germination. Unlike phytochromes B and D, phytochrome E did not inhibit phytochrome A-mediated germination. Surprisingly, phytochrome E was required for germination of Arabidopsis seeds in continuous FR. However, inhibition of hypocotyl elongation by FR, induction of cotyledon unfolding, and induction of agravitropic growth were not affected by loss of phytochrome E. Therefore, phytochrome E is not required per se for phytochrome A-mediated very low fluence responses and the high irradiance response. Immunoblotting revealed that the need of phytochrome E for germination in FR was not caused by altered phytochrome A levels. These results uncover a novel role of phytochrome E in plant development and demonstrate the considerable functional diversification of the closely related phytochromes B, D, and E.
Differential Effect of Jasmonic Acid and Abscisic Acid on Cell Cycle Progression in Tobacco BY-2 Cells
Authors: Świa̧tek Agnieszka , Lenjou Marc , Van Bockstaele Dirk , Inzé Dirk , Van Onckelen Harry
Published: November 2008

Environmental stress affects plant growth and development. Several plant hormones, such as salicylic acid, abscisic acid (ABA), jasmonic acid (JA), and ethylene play a crucial role in altering plant morphology in response to stress. Developmental regulation often has the cell cycle machinery among its targets. We analyzed the effect of JA and ABA on cell cycle progression in synchronized tobacco (Nicotiana tabacum) BY-2 cells. Both compounds were found to prevent DNA replication, keeping the cells in the G1 stage, when applied just before the G1/S transition. However, ABA did not have any effect on subsequent phases of the cell cycle when applied at a later stage, whereas JA effectively prevented mitosis on application during DNA synthesis. This demonstrates that JA treatment can freeze synchronized BY-2 cells in both the G1 and G2 stages of the cell cycle. Jasmonate administered after the S-phase was less effective in decreasing the mitotic index, suggesting that cell sensitivity toward JA is dependent on the cell cycle phase. In cultures detained in the G2-phase, we observed a reduced histone H1 kinase activity of kinases associated with the p13sucl protein.