bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of Seed Size on Seedling Growth Response to Elevated CO2 in Picea abies and Picea rubens
Authors: Jones T. A. , Reekie E. G.
Published: November 2007

Abstract: Several previous studies have observed that species and individuals with large seeds respond more positively to elevated CO2 than those with small seeds. We explored the reasons for this pattern by examining the relationship between seed size and CO2 response in Picea abies and P. rubens using growth analysis. The large seeded species (P. abies) responded more positively to elevated CO2 than the small seeded species (P. rubens). At the intraspecific level, P. abies individuals from large seeds responded more positively to elevated CO2 than individuals from small seeds, however, there was no significant intraspecific variation in CO2 response in P. rubens. The greater CO2 response of plants from large seeds was not simply the result of a larger starting capital compounded at the same rate as in plants from small seeds. Elevated CO2 increased relative growth rate to a greater extent in individuals from large seeds. This effect appears to be related to differences in time of establishment, source to sink ratio and nutrient availability with seed size. These results are significant not only in understanding the potential effect of rising atmospheric CO2 concentrations on plant populations, but also in understanding the factors affecting plant success at current atmospheric CO2 levels due to the elevation of CO2 within the litter layer that occurs at many germination sites.
Structural, Biochemical, and Physiological Characterization of C4 Photosynthesis in Species Having Two Vastly Different Types of Kranz Anatomy in Genus Suaeda (Chenopodiaceae)
Authors: Voznesenskaya E. V. , Chuong S. D. X. , Koteyeva N. K. , Franceschi V. R. , Freitag H. , Edwards G. E.
Published: November 2007

Abstract: C4 species of family Chenopodiaceae, subfamily Suaedoideae have two types of Kranz anatomy in genus Suaeda, sections Salsina and Schoberia, both of which have an outer (palisade mesophyll) and an inner (Kranz) layer of chlorenchyma cells in usually semi‐terete leaves. Features of Salsina (S. aegyptiaca, S. arcuata, S. taxifolia) and Schoberia type (S. acuminata, S. eltonica, S. cochlearifolia) were compared to C3 type S. heterophylla. In Salsina type, two layers of chlorenchyma at the leaf periphery surround water‐storage tissue in which the vascular bundles are embedded. In leaves of the Schoberia type, enlarged water‐storage hypodermal cells surround two layers of chlorenchyma tissue, with the latter surrounding the vascular bundles. The chloroplasts in Kranz cells are located in the centripetal position in Salsina type and in the centrifugal position in the Schoberia type. Western blots on C4 acid decarboxylases show that both Kranz forms are NAD‐malic enzyme (NAD‐ME) type C4 species. Transmission electron microscopy shows that mesophyll cells have chloroplasts with reduced grana, while Kranz cells have chloroplasts with well‐developed grana and large, specialized mitochondria, characteristic of NAD‐ME type C4 chenopods. In both C4 types, phosphoenolpyruvate carboxylase is localized in the palisade mesophyll, and Rubisco and mitochondrial NAD‐ME are localized in Kranz cells, where starch is mainly stored. The C3 species S. heterophylla has Brezia type isolateral leaf structure, with several layers of Rubisco‐containing chlorenchyma. Photosynthetic response curves to varying CO2 and light in the Schoberia type and Salsina type species were similar, and typical of C4 plants. The results indicate that two structural forms of Kranz anatomy evolved in parallel in species of subfamily Suaedoideae having NAD‐ME type C4 photosynthesis.
Floral Scent in Food‐Deceptive Orchids: Species Specificity and Sources of Variability
Authors: Salzmann C. C. , Cozzolino S. , Schiestl F. P.
Published: November 2007

Abstract: One third of all orchid species are deceptive and do not reward their pollinators. Such deceptive orchids are often characterised by unusually high variation in floral signals such as colour and scent. In this study, we investigated the scent composition of two Mediterranean food‐deceptive orchids Orchis mascula, Orchis pauciflora, and their hybrid, O.×colemanii. Scent was collected in situ by headspace sorption and was subsequently analysed with gas chromatography and gas chromatography‐mass spectrometry. We compared variation of odour compounds within and between populations as well as species. We identified 35 floral scent compounds, mainly monoterpenes, which were shared by both species. Both quantitative and qualitative variability within and among populations was high. Many individuals within species could be classified to different “odour‐types”. In spite of high qualitative and quantitative intra‐ and inter‐population variability, the species were clearly differentiated in their scent bouquets, whereas most hybrid individuals emitted an intermediate scent.
Diffusion models for Knudsen compressors
Authors: Aoki Kazuo , Degond Pierre , Takata Shigeru , Yoshida Hiroaki
Published: November 2007

A rarefied gas in a long straight pipe with a periodic structure consisting of alternately arranged narrow and wide pipes and with periodic temperature distribution, which is known as the Knudsen compressor (or pump), is considered. Under the assumption that the pipe is much thinner than the period, a diffusion model that describes the pressure distribution and mass flux of the gas in each pipe element is derived, together with the connection conditions at the junctions of the narrow and wide pipes, from the kinetic system composed of the Boltzmann equation and its boundary condition on the pipe wall. Then, on the basis of the diffusion model and the connection conditions, a global diffusion model for the entire pipe is constructed by means of homogenization. The present work is a formal extension to the case of the Boltzmann equation of the previous work [K. Aoki and P. Degond, Multiscale Model. Simul. 1, 304 (2003)], where a simplified version of the Bhatnagar–Gross–Krook (BGK) collision model is used. Some numerical results based on the original BGK model are also presented both for the global diffusion model and for the local diffusion model with the connection conditions at the junctions.
Electronic transport in locally gated graphene nanoconstrictions
Authors: Özyilmaz Barbaros , Jarillo-Herrero Pablo , Efetov Dmitri , Kim Philip
Published: November 2007

We have developed the combination of an etching and deposition techniques that enables the fabrication of locally gated graphene nanostructures of arbitrary design. Employing this method, we have fabricated graphene nanoconstrictions with local tunable transmission and characterized their electronic properties. An order of magnitude enhanced gate efficiency is achieved adopting the local gate geometry with thin dielectric gate oxide. A complete turn off of the device is demonstrated as a function of the local gate voltage. Such strong suppression of device conductance was found to be due to both quantum confinement and Coulomb blockade effects in the constricted graphene nanostructures.
Beyond the bandwidth-length product: Graded index microstructured polymer optical fiber
Authors: Lwin R. , Barton G. , Harvey L. , Harvey J. , Hirst D. , Manos S. , Large M. C. J. , Poladian L. , Bachmann A. , Poisel H. , Klein K.-F.
Published: November 2007

Large core multimode polymer fibers for high data rate transmission are an important growth area. The conventional approach to reducing the intermodal dispersion in such fibers is to use a graded index (GI) profile. More recently, microstructures rather than differences in chemical composition have been used to produce the GI structure. We compare the bandwidth performance of two GI microstructured fibers to a conventional GI fiber made from the same material. The microstructured fibers not only show excellent bandwidth performance but also their bandwidth has an unconventional length dependence: no additional pulse broadening beyond a characteristic length.
Enhanced Seebeck coefficient of quantum-confined electrons in SrTiO3∕SrTi0.8Nb0.2O3 superlattices
Authors: Mune Yoriko , Ohta Hiromichi , Koumoto Kunihito , Mizoguchi Teruyasu , Ikuhara Yuichi
Published: November 2007

We report two-dimensional Seebeck coefficients (∣S∣2D) of [(SrTiO3)x∕(SrTi0.8Nb0.2O3)y]20 (x=1–60, y=1–20) superlattices, which were grown on the (100) face of insulating LaAlO3 substrates to clarify the origin of the giant ∣S∣2D values of the SrTiO3 superlattices [H. Ohta et al., Nat. Mater. 6, 129 (2007)]. The ∣S∣2D values of the [(SrTiO3)17∕(SrTi0.8Nb0.2O3)y]20 superlattices increased proportionally to y−0.5 and reached 320μVK−1 (y=1), which is approximately five times larger than that of the SrTi0.8Nb0.2O3 bulk (∣S∣3D=61μVK−1). The slope of the log∣S∣2D-logy plots was −0.5, proving that the density of states in the ground state for SrTiO3 increases inversely proportionally to y. The critical barrier thickness for quantum electron confinement was also clarified to be 6.25nm (16 unit cells of SrTiO3).
The fast release of sticky protons: Kinetics of substrate binding and proton release in a multidrug transporter
Authors: Adam Yoav , Tayer Naama , Rotem Dvir , Schreiber Gideon , Schuldiner Shimon
Published: November 2007

EmrE is an
Escherichia coli
H
+
-coupled multidrug transporter that provides a unique experimental paradigm because of its small size and stability, and because its activity can be studied in detergent solution. In this work, we report a study of the transient kinetics of substrate binding and substrate-induced proton release in EmrE. For this purpose, we measured transient changes in the tryptophan fluorescence upon substrate binding and the rates of substrate-induced proton release. The fluorescence of the essential and fully conserved Trp residue at position 63 is sensitive to the occupancy of the binding site with either protons or substrate. The maximal rate of binding to detergent-solubilized EmrE of TPP
+
, a high-affinity substrate, is 2 × 10
7
M
−1
·s
−1
, a rate typical of diffusion-limited reactions. Rate measurements with medium- and low-affinity substrates imply that the affinity is determined mainly by the
k
off
of the substrate. The rates of substrate binding and substrate-induced release of protons are faster at basic pHs and slower at lower pHs. These findings imply that the substrate-binding rates are determined by the generation of the species capable of binding; this is controlled by the high affinity to protons of the glutamate at position 14, because an Asp replacement with a lower pK is faster at the same pHs.
ATM regulates the length of individual telomere tracts in
Arabidopsis
Authors: Vespa Laurent , Warrington Ross T. , Mokros Petr , Siroky Jiri , Shippen Dorothy E.
Published: November 2007

Telomeres have the paradoxical ability of protecting linear chromosome ends from DNA damage sensors by using these same proteins as essential components of their maintenance machinery. We have previously shown that the absence of ataxia telangiectasia mutated (ATM), a central regulator of the DNA damage response, accelerates the onset of genome instability in telomerase-deficient
Arabidopsis
, without increasing the rate of bulk telomere shortening. Here, we examine individual telomere tracts through successive plant generations using both fluorescence
situ in
hybridization (FISH) and primer extension telomere repeat amplification (PETRA). Unexpectedly, we found that the onset of profound developmental defects and abundant end-to-end chromosome fusions in fifth generation (G
5
)
atm tert
mutants required the presence of only one critically shortened telomere. Parent progeny analysis revealed that the short telomere arose as a consequence of an unusually large telomere rapid deletion (TRD) event. The most dramatic TRD was detected in
atm tert
mutants that had undergone meiosis. Notably, in contrast to TRD, alternative lengthening of telomeres (ALT) was suppressed in the absence of ATM. Finally, we show that size differences between telomeres on homologous chromosome ends are greater for
atm tert
than
tert
plants. Altogether, these findings suggest a dual role for ATM in regulating telomere size by promoting elongation of short telomeres and by preventing the accumulation of cells that harbor large telomere deletions.
Overexpression of wild-type androgen receptor in muscle recapitulates polyglutamine disease
Authors: Monks Douglas Ashley , Johansen Jamie A. , Mo Kaiguo , Rao Pengcheng , Eagleson Bryn , Yu Zhigang , Lieberman Andrew P. , Breedlove S. Marc , Jordan Cynthia L.
Published: November 2007

We created transgenic mice that overexpress WT androgen receptor (AR) exclusively in their skeletal muscle fibers. Unexpectedly, these mice display androgen-dependent muscle weakness and early death, show changes in muscle morphology and gene expression consistent with neurogenic atrophy, and exhibit a loss of motor axons. These features reproduce those seen in models of Kennedy disease, a polyglutamine expansion disorder caused by a CAG repeat expansion in the AR gene. These findings demonstrate that toxicity in skeletal muscles is sufficient to cause motoneuron disease and indicate that overexpression of the WT AR can exert toxicity comparable with the polyglutamine expanded protein. This model has two clear implications for Kennedy disease: (
i
) mechanisms affecting AR gene expression may cause neuromuscular symptoms similar to those of Kennedy disease and (
ii
) therapeutic approaches targeting skeletal muscle may provide effective treatments for this disease.
Blood gene expression signatures predict exposure levels
Authors: Bushel P. R. , Heinloth A. N. , Li J. , Huang L. , Chou J. W. , Boorman G. A. , Malarkey D. E. , Houle C. D. , Ward S. M. , Wilson R. E. , Fannin R. D. , Russo M. W. , Watkins P. B. , Tennant R. W. , Paules R. S.
Published: November 2007

To respond to potential adverse exposures properly, health care providers need accurate indicators of exposure levels. The indicators are particularly important in the case of acetaminophen (APAP) intoxication, the leading cause of liver failure in the U.S. We hypothesized that gene expression patterns derived from blood cells would provide useful indicators of acute exposure levels. To test this hypothesis, we used a blood gene expression data set from rats exposed to APAP to train classifiers in two prediction algorithms and to extract patterns for prediction using a profiling algorithm. Prediction accuracy was tested on a blinded, independent rat blood test data set and ranged from 88.9% to 95.8%. Genomic markers outperformed predictions based on traditional clinical parameters. The expression profiles of the predictor genes from the patterns extracted from the blood exhibited remarkable (97% accuracy) transtissue APAP exposure prediction when liver gene expression data were used as a test set. Analysis of human samples revealed separation of APAP-intoxicated patients from control individuals based on blood expression levels of human orthologs of the rat discriminatory genes. The major biological signal in the discriminating genes was activation of an inflammatory response after exposure to toxic doses of APAP. These results support the hypothesis that gene expression data from peripheral blood cells can provide valuable information about exposure levels, well before liver damage is detected by classical parameters. It also supports the potential use of genomic markers in the blood as surrogates for clinical markers of potential acute liver damage.
Contrarian clade confirms the ubiquity of spatial origination patterns in the production of latitudinal diversity gradients
Authors: Krug Andrew Z. , Jablonski David , Valentine James W.
Published: November 2007

The latitudinal diversity gradient (LDG), wherein the number of species and higher taxa peaks in the tropics and decreases toward the poles, is the best-documented large-scale diversity pattern on Earth, but hypotheses explaining the standard LDG must also account for rare “contrarian” taxa that show diversity maxima outside of the tropics. For marine bivalves, one of the few groups that provide spatially explicit temporal data on a global scale, we show that a major contrarian group, the Anomalodesmata, unexpectedly exhibits the same large-scale dynamics as related clades having normal LDGs in two key respects. First, maxima in standing genus diversity and genus origination rates coincide spatially. Second, the strength of a clade's present-day LDG is significantly related to the proportion of its living genera that originated in the tropics during the late Cenozoic, with the contrarian gradient strength at both species and genus level predicted quantitatively by the values for the other clades. Geologic age distributions indicate that the anomalous LDG results from origination that is damped in the tropics rather than heightened in the temperate zones. The pervasive role of spatial origination patterns in shaping LDGs, regardless of the position of their diversity maxima, corroborates hypotheses based on clades showing standard gradients and underscores the insights that contrarian groups can provide into general principles of diversity dynamics.
A novel optical sensor for ammonia using a laser grade dye—Stilbene 3
Authors: Sahare P D , Pattanaik Amitansu
Published: November 2007

Fluorescence sensitization of a 2,2′-([1,1′-biphenyl]–4,4′-diyldi-2,1-ethenediyl)-bis-benzenesulfonic acid disodium salt (Stilbene 3) solution in ethanol (EtOH) due to the presence in aqueous solution of ammonia is reported here. In this study sensitization of the dye solution due to the presence of ammonia was observed. It was also found that the observed sensitization is dynamic in nature. Sensitization of the fluorescence of the indicator also has full reversibility. An optical sensor for the detection of ammonia could thus be constructed using these properties of the dye and the sensitizer.
Synthetic microarray data generation with RANGE and NEMO
Authors: Long James , Roth Mitchell
Published: November 2007

Motivation: For testing and sensitivity analysis purposes, it is beneficial to have known transcription networks of sufficient size and variability during development of microarray data and network deconvolution algorithms. Description of such networks in a simple language translatable to Systems Biology Markup Language would allow generation of model data for the networks.

Results: Described herein is software (RANGE: RAndom Network GEnerator) to generate large random transcription networks in the NEMO (NEtwork MOtif) language. NEMO is recognized by a grammar for transcription network motifs using lex and yacc to output Systems Biology Markup Language models for either specified or randomized gene input functions. These models of known networks may be input to a biochemical simulator, allowing the generation of synthetic microarray data.

Availability:  http://range.sourceforge.net

Contact:  jlong@alaska.edu
A Review of CAM for Procedural Pain in Infancy: Part I. Sucrose and Non‐Nutritive Sucking
Authors: Tsao Jennie C. I. , Evans Subhadra , Meldrum Marcia , Altman Tamara , Zeltzer Lonnie K.
Published: November 2007

There is increasing concern regarding the number of painful medical procedures that infants must undergo and the potential risks of alleviating infant pain with conventional pharmacologic agents. This article is Part I of a two‐part series that aims to provide an overview of the literature on complementary and alternative (CAM) approaches for pain and distress related to medical procedures among infants up to six weeks of age. The focus of this article is a review of the empirical literature on sucrose with or without non‐nutritive sucking (NNS) for procedural pain in infancy. Computerized databases were searched for relevant studies including prior reviews and primary trials. The most robust evidence was found for the analgesic effects of sucrose with or without NNS on minor procedural pain in healthy full‐term infants. Despite some methodological weaknesses, the literature to date supports the use of sucrose, NNS and other sweetened solutions for the management of procedural pain in infancy.
Regulation of Caspase‐3 and Bcl‐2 Expression in Dalton′s Lymphoma Ascites Cells by Abrin
Authors: Ramnath V. , Rekha P. S. , Kuttan G. , Kuttan R.
Published: November 2007

The role of abrin, a toxic lectin isolated from seeds of Abrus precatorius Linn in inducing apoptosis in murine Dalton′s Lymphoma Ascites (DLA) cells was evaluated. Abrin when incubated at the concentration of 10 ng per million DLA cells could bring about cell death as typical morphological changes with apoptosis. However, necrotic cell death dominated when a higher dose of abrin was used. DNA samples, isolated from DLA cells treated with abrin showed fragmentation. Abrin brought about induction of apoptosis by stimulating the expression of pro‐apoptotic Caspase‐3, at the same time blocking the expression of Bcl‐2, which is an anti apoptotic gene. However, the expression of tumor suppressor gene p53 has not been observed in control and abrin‐treated DLA cells. Results suggested that abrin effectively induced apoptotic changes in the tumor cells that led to cellular death.
Turo (Qi Dance) Training Attenuates Psychological Symptoms and Sympathetic Activation Induced by Mental Stress in Healthy Women
Authors: Lee Hwa-Jin , Chae Younbyoung , Park Hi-Joon , Hahm Dae-Hyun , An Kyungeh , Lee Hyejung
Published: November 2007

Vagal withdrawal and sympathetic overactivity accompany various types of stress. Qi training is reported to reduce sympathetic hyper‐reactivity in a stressful situation. Turo, which is a type of dance that uses the Meridian Qi System, may reduce the psychological symptoms induced by an imbalance of the autonomic nervous system (ANS). We observed whether Turo training alters psychopathological and psychological symptoms using the Symptom Checklist 90‐Revision (SCL‐90‐R) and examined whether it attenuates the stress response to mental stress in healthy adolescent females using the power spectrum analysis of heart rate variability (HRV). Twenty‐one subjects received Turo training and 27 subjects were trained with mimicking movements. The SCL‐90‐R was measured before and after the 2‐month training period. Heart rate (HR), total power (TP) and the LF/HF ratio of HRV were compared between the Turo and control groups during and after mental stress. The somatization and hostility subscales of the SCL‐90‐R of the Turo group were significantly lower than those of the control group after 2 months. The increases in HR and the LF/HF ratio of HRV induced by the stress test were significantly lower in the Turo group than in the control group. The TP of the Turo group was significantly higher than that of the control group. The psychological symptoms and sympathetic activation induced by the artificial stress were significantly reduced by the Turo training. These findings suggest that Turo training can play a critical role in attenuating psychological symptoms and stress‐induced sympathetic activation.
Growth variability in Atlantic mackerel (Scomber scombrus) and Spanish mackerel (Scomber japonicus) off Portugal
Authors: Martins Maria Manuel
Published: November 2007

Martins, M. M. 2007. Growth variability in Atlantic mackerel (Scomber scombrus) and Spanish mackerel (Scomber japonicus) off Portugal. – ICES Journal of Marine Science, 64. Year-class effects may be very important when analysing fish growth. This work aims to compare growth in weight and in length between year classes of Atlantic and Spanish mackerel found off the Portuguese coast. The analysis included Atlantic mackerel data from year classes 1986–1993 and Spanish mackerel data from year classes 1988–1995. The analyses indicated significant differences between year classes in terms of mean weight-at-length and mean length-at-age. Atlantic mackerel year classes also showed significant differences in mean weight-at-length between males and females, and Spanish mackerel year classes showed significant differences between sexes for mean length-at-age. No significant effects were found for the two-way interaction between year class and sex. Growth variability may be linked with variability in environmental factors as well as density-dependence.
Overexpression of the Apple MpNPR1 Gene Confers Increased Disease Resistance in Malus × domestica
Authors: Malnoy M. , Jin Q. , Borejsza-Wysocka E. E. , He S. Y. , Aldwinckle H. S.
Published: November 2007

The NPR1 gene plays a pivotal role in systemic acquired resistance in plants. Its overexpression in Arabidopsis and rice results in increased disease resistance and elevated expression of pathogenesis-related (PR) genes. An NPR1 homolog, MpNPR1-1, was cloned from apple (Malus × domestica) and overexpressed in two important apple cultivars, Galaxy and M26. Apple leaf pieces were transformed with the MpNPR1 cDNA under the control of the inducible Pin2 or constitutive Cauliflower mosaic virus (CaMV)35S promoter using Agrobacterium tumefaciens. Overexpression of MpNPR1 mRNA was shown by reverse transcriptase-polymerase chain reaction. Activation of some PR genes (PR2, PR5, and PR8) was observed. Resistance to fire blight was evaluated in a growth chamber by inoculation of the shoot tips of our own rooted 30-cm-tall plants with virulent strain Ea273 of Erwinia amylovora. Transformed Galaxy lines overexpressing MpNPR1 had 32 to 40% of shoot length infected, compared with 80% in control Galaxy plants. Transformed M26 lines overexpressing MpNPR1 under the control of the CaMV35S promoter also showed a significant reduction of disease compared with control M26 plants. Some MpNPR-overexpressing Galaxy lines also exhibited increased resistance to two important fungal pathogens of apple, Venturia inaequalis and Gymnosporangium juniperi-virginianae. Selected transformed lines have been propagated for field trials for disease resistance and fruit quality.
Sources of Resistance toTobacco streak virusin WildArachis(Fabaceae: Papilionoidae) Germplasm
Authors: Kalyani G. , Reddy A. S. , Kumar P. Lava , Rao R. D. V. J. Prasada , Aruna R. , Waliyar F. , Nigam S. N.
Published: November 2007

Stem necrosis disease caused by Tobacco streak virus (TSV), first recognized in 2000, has emerged as a potential threat to peanut (Arachis hypogaea) in southern states of India. The virus induces severe necrosis of shoots leading to death of the plant, and plants that survive are malformed, with severe reduction in pod yield. All the currently grown peanut cultivars in India are highly susceptible to the virus. Therefore, wild relatives of peanut were evaluated to identify potential sources of resistance to TSV infection. In all, 56 germplasm accessions from 20 wild Arachis spp. in four sections (Arachis, Erectoides, Procumbente, and Rhizomatosae), along with susceptible peanut cultivars (JL 24 and K 1375), were evaluated for resistance to TSV under greenhouse conditions using mechanical sap inoculations. Systemic virus infection, determined by enzyme-linked immunosorbent assay (ELISA), in the test accessions ranged between 0 and 100%. Twenty-four accessions in section Arachis that had 0 to 35% systemically infected plants were retested, and systemic infection was not detected in eight of these accessions in repeated trials in the greenhouse. These are International Crops Research Institute for the Semi-Arid Tropics groundnut (ICG) accession nos. 8139, 8195, 8200, 8203, 8205, and 11550 belonging to A. duranensis; ICG 8144 belonging to A. villosa; and ICG 13210 belonging to A. stenosperma. Even though the resistant accessions had 0 to 100% TSV infection in inoculated leaves, TSV was not detected in the subsequently emerged leaves. This is the first report of TSV resistance in Arachis spp. The eight TSV resistant accessions are cross compatible with A. hypogaea for utilization in breeding for stem necrosis disease resistance.
Baseline and Differential Sensitivity to Two QoI Fungicides Among Isolates of Phytophthora cactorum That Cause Leather Rot and Crown Rot on Strawberry
Authors: Rebollar-Alviter A. , Madden L. V. , Jeffers S. N. , Ellis M. A.
Published: November 2007

Sensitivities of 89 isolates of Phytophthora cactorum, the causal agent of crown rot and leather rot on strawberry plants, from seven states (Florida, Maine, North Carolina, Ohio, Oregon, South Carolina, and New York) to the QoI fungicide azoxystrobin were determined based on mycelium growth and zoospore germination. Radial growth of mycelia on lima bean agar amended with azoxystrobin at 0.001, 0.01, 0.1, 1.0, 10, and 30 μg/ml and salicylhydroxamic acid (SHAM) at 100 μg/ml was measured after 6 days. Effect on zoospore germination was evaluated in aqueous solutions of azoxystrobin at 0.005, 0.01, 0.05, 0.1, 0.5, and 1.0 μg/ml in 96-well microtiter plates by counting germinated and nongerminated zoospores after 4 h at room temperature. SHAM was not used to evaluate zoospore sensitivity. The effective dose to reduce mycelium growth by 50% (ED50) ranged from 0.16 to 12.52 μg/ml for leather rot isolates and 0.10 to 15 μg/ml for crown rot isolates. The Kolmogorov-Smirnov test showed significant differences (P < 0.001) between the two distributions. Zoospores were much more sensitive to azoxystrobin than were mycelia. Differences between sensitivity distributions for zoospores from leather rot and crown rot isolates were significant at P = 0.05. Estimated ED50 values ranged from 0.01 to 0.24 μg/ml with a median of 0.04 μg/ml. Experiments with pyraclostrobin, another QoI fungicide, demonstrated that both mycelia and zoospores of P. cactorum were more sensitive to pyraclostrobin than to azoxystrobin. Sensitivities to azoxystrobin and pyraclostrobin were moderately but significantly correlated (r = 0.60, P = 0.0001).
Management of Phytophthora Crown Rot in Pumpkin and Zucchini Seedlings with Phosphonates
Authors: Yandoc-Ables Camilla B. , Rosskopf Erin N. , Lamb Elizabeth M.
Published: November 2007

Experiments were conducted in the greenhouse to determine the efficacy of two phosphonate-containing fungicides (FNX-100 and FNX-2500) against Phytophthora crown rot of pumpkin. The experiments were designed to determine the effects of crop cultivar, application method (soil drench versus foliar spray), and phosphonate concentration on the level of effectiveness of a crown rot management strategy using phosphonates. Pumpkin cultivar, treatment (type of fungicide product), phosphonate concentration, and application method significantly influenced the level of Phytophthora crown rot control. Between the two fungicides, only FNX-100 suppressed Phytophthora crown rot in pumpkin. For cv. Phantom, the highest level of control was achieved with the drench application of 3.0% FNX-100 whereas, for cv. Spooktacular, all three concentrations of FNX-100 (1.0, 2.0, and 3.0%, vol/vol) applied as a soil drench suppressed or significantly reduced the severity of crown rot. Additional experiments using zucchini as test plants demonstrated that, at the concentrations tested, FNX-100 was more efficacious than FNX-2500 in controlling Phytophthora crown rot and that zucchini cultivar or FNX-100 concentration did not significantly influence crown rot control with phosphonates. In this study, FNX-100, which is not currently labeled for use in vegetables, provided satisfactory disease control in both pumpkin and zucchini whereas FNX-2500, a foliar fungicide comprised of the phosphate/phosphonates and copper, manganese, and zinc, did not significantly affect disease severity. This study, albeit limited in scope, showed that cultivar selection may play an important role in the successful management of Phytophthora crown rot on cucurbits with phosphonates, information which may be useful in designing additional tests and developing management strategies for pumpkin and zucchini that are grown in the field.
First Report of Soybean dwarf virus in Soybean in Northern Illinois
Authors: Thekkeveetil T. , Hobbs H. A. , Wang Y. , Kridelbaugh D. , Donnelly J. , Hartman G. L. , Domier L. L.
Published: November 2007

Soybean dwarf virus (SbDV), a member of the Luteoviridae, is transmitted persistently by colonizing aphids and causes significant yield losses in soybean (Glycine max L.) in Japan. In the United States, SbDV is endemic in red and white clover (Trifolium pratense L. and T. repens L.) (1,3). Even so, SbDV has been detected in soybean only in Virginia (2) and Wisconsin (4). A study conducted in Illinois during 2001 and 2002 detected SbDV in clover but not soybean (3). During August of 2006, two surveys for virus diseases in soybean were conducted in Illinois. In the first survey, 30 soybean leaf samples were collected without regard for symptoms from each of 10 fields in each of five northern Illinois counties (Carroll, Jo Daviess, Ogle, Stephenson, and Winnebago). In the second survey, 10 random soybean leaf samples and 10 samples with virus-like symptoms were collected from each of 30 soybean rust sentinel plots spread throughout Illinois. Total RNA was extracted from pools of 90 to 100 plants and analyzed by quantitative real-time reverse transcriptase (QRT)-PCR using a fluorescently labeled minor groove binding probe (VIC-5′-AGCATATCCAAAGACGC-3′-MGBNFQ, nt 2358-2374) and flanking primers (5′-TGGCTATTATAGAATGGTGCGTAAAC-3′, nt 2327-2351; and 5′-GCCATGGAAATGAGGGAATG-3′, nt 2395-2376). From the first survey, pools from Carroll, Jo Daviess, and Ogle were positive for SbDV. Analysis of individual leaf samples from positive pools by double-antibody sandwich-ELISA (Agdia, Elkhart, IN) showed that one sample in each county was positive for SbDV. On the basis of the number of randomly sampled plants, the incidence of SbDV infection in northern Illinois was approximately 0.3%. In the second survey, SbDV was detected in one pool containing symptomatic plants from five soybean rust sentinel plots. Further QRT-PCR analysis showed that the sentinel plot in Bureau County was positive for SbDV. Because of the sampling protocols used, it was not possible to determine symptom phenotypes of SbDV-positive samples. Sequence analysis of the combined coat protein (CP) and readthrough domain (RTD) encoding region (nt 3019-5094) of SbDV isolates from Bureau (GenBank Accession No. EU095847) and Carroll (GenBank Accession No. EU095846) counties showed that the predicted amino acid sequences were 96 and 95% identical to a Japanese dwarfing isolate of SbDV (GenBank Accession No. AB038150), respectively. The predicted CP amino acid sequences of the Illinois isolates were identical and RTD amino acid sequences differed at six positions. To our knowledge, this is the first report of infection of soybean plants in Illinois with SbDV.

References: (1) V. D. Damsteegt et al. Phytopathology 89:374, 1999. (2) A. Fayad et al. Phytopathology (Abstr.) 90(suppl.):S132, 2000. (3) B. Harrison et al. Plant Dis. 89:28, 2005. (4) A. Phibbs et al. Plant Dis. 88:1285, 2004.
First Report of Waitea circinata var. circinata Causing Brown Ring Patch on Poa trivialis in California
Authors: Chen C. M. , Douhan G. W. , Wong F. P.
Published: November 2007

Rough bluegrass (Poa trivialis L.) is a C3 (cool-season) turfgrass used on golf course putting greens. It is often used to overseed C4 (warm-season) turf for fall through early-summer use. In March 2007, at maximium daytime air temperatures of approximately 30 to 35°C, irregular, thin, yellow rings approximately 10 to 20 cm in diameter were reported on P. trivialis in putting greens from two golf courses in the Coachella Valley of southern California. Affected plants had a blight of the leaves and stems and a rot of the crown, with initial symptoms being a yellowing of the tissue followed by the development of a dark, water-soaked appearance of the whole plant. Plants turned reddish brown as the water-soaked tissue dessicated. A Rhizoctonia-like fungus was found to be colonizing the leaves, stems, and upper roots and thatch. Three isolates were obtained from the diseased turf samples. All were identified as Waitea circinata var. circinata based on colony morphology (2) and rDNA internal transcribed spacer (ITS) region sequences (1). The sequences of the three isolates were more than 99% similar to those of W. circinata var. circinata deposited in the NCBI database (1,2). To confirm pathogenicity, each isolate was inoculated onto 4-week-old P. trivialis (2 mg of seed per cm2) grown in 10-cm-diameter pots containing steam-sterilized UC-mix at 28°C. Five 8-mm-diameter plugs of each isolate were taken from 7-day-old cultures grown on potato dextrose agar (PDA) and placed in direct contact with the bases of the stems. The pots were then incubated in a moist chamber at 28°C. Five noncolonized PDA plugs were used as a negative control. Three pots were used for each of the three isolates and the check treatment. For all isolates, chlorosis of leaf and stems were observed 5 days after inoculation and the tissue appeared water soaked after 7 days with the production of abundant aerial mycelia being observed. All plants, except the negative controls, died after 10 days. W. circinata var. circinata was reisolated from symptomatic tissue from the inoculated plants. W. circinata var. circinata was previously reported as the causal agent of brown ring patch on creeping bentgrass (Agrostis palustris) in Japan (2) and as a pathogen of annual bluegrass (P. annua) in the United States (1). To our knowledge, this is the first report of W. circinata var. circinata infecting P. trivialis in California.

References: (1) K. de la Cerda et al. Plant Dis. 91:791, 2007. (2) T. Toda et al. Plant Dis. 89:536, 2005.
Gene-specific vulnerability to imprinting variability in human embryonic stem cell lines
Authors: Kim Kee-Pyo , Thurston Alexandra , Mummery Christine , Ward-van Oostwaard Dorien , Priddle Helen , Allegrucci Cinzia , Denning Chris , Young Lorraine
Published: November 2007

Disregulation of imprinted genes can be associated with tumorigenesis and altered cell differentiation capacity and so could provide adverse outcomes for stem cell applications. Although the maintenance of mouse and primate embryonic stem cells in a pluripotent state has been reported to disrupt the monoallelic expression of several imprinted genes, available data have suggested relatively higher imprint stability in the human equivalents. Identification of 202 heterozygous loci allowed us to examine the allelic expression of 22 imprinted genes in 22 human embryonic stem cell lines. Half of the genes examined (IPW, H19, MEG3, MEST isoforms 1 and 2, PEG10, MESTIT1, NESP55, ATP10A, PHLDA2, IGF2) showed variable allelic expression between lines, indicating vulnerability to disrupted imprinting. However, seven genes showed consistent monoallelic expression (NDN, MAGEL2, SNRPN, PEG3, KCNQ1, KCNQ1OT1, CDKN1C). Furthermore, four genes known to be monoallelic or to exhibit polymorphic imprinting in later-developing human tissues (TP73, IGF2R, WT1, SLC22A18) were always biallelic in hESCs. MEST isoform 1, PEG10, and NESP55 showed an association between the variability observed in interline allelic expression status and the DNA methylation of previously identified regulatory regions. Our results demonstrate gene-specific differences in the stability of imprinted loci in human embryonic stem cells and identify disrupted DNA methylation as one potential mechanism. We conclude the prudence of including comprehensive imprinting analysis in the continued characterization of human embryonic stem cell lines.
Identification and Characterization of Nucleotide-Binding Site-Leucine-Rich Repeat Genes in the Model Plant Medicago truncatula
Authors: Ameline-Torregrosa Carine , Wang Bing-Bing , O'Bleness Majesta S. , Deshpande Shweta , Zhu Hongyan , Roe Bruce , Young Nevin D. , Cannon Steven B.
Published: November 2007

The nucleotide-binding site (NBS)-Leucine-rich repeat (LRR) gene family accounts for the largest number of known disease resistance genes, and is one of the largest gene families in plant genomes. We have identified 333 nonredundant NBS-LRRs in the current Medicago truncatula draft genome (Mt1.0), likely representing 400 to 500 NBS-LRRs in the full genome, or roughly 3 times the number present in Arabidopsis (Arabidopsis thaliana). Although many characteristics of the gene family are similar to those described on other plant genomes, several evolutionary features are particularly pronounced in M. truncatula, including a high degree of clustering, evidence of significant numbers of ectopic translocations from clusters to other parts of the genome, a small number of more evolutionarily stable NBS-LRRs, and numerous truncations and fusions leading to novel domain compositions. The gene family clearly has had a large impact on the structure of the genome, both through ectopic translocations (potentially, a means of seeding new NBS-LRR clusters), and through two extraordinarily large superclusters. Chromosome 6 encodes approximately 34% of all TIR-NBS-LRRs, while chromosome 3 encodes approximately 40% of all coiled-coil-NBS-LRRs. Almost all atypical domain combinations are in the TIR-NBS-LRR subfamily, with many occurring within one genomic cluster. This analysis shows the gene family not only is important functionally and agronomically, but also plays a structural role in the genome.
Starch Serves as Carbohydrate Storage in Nematode-Induced Syncytia
Authors: Hofmann Julia , Szakasits Dagmar , Blöchl Andreas , Sobczak Miroslaw , Daxböck-Horvath Sabine , Golinowski Wladyslaw , Bohlmann Holger , Grundler Florian M.W.
Published: November 2007

The plant parasitic nematode Heterodera schachtii induces specific syncytial feeding sites in the roots of Arabidopsis thaliana from where it withdraws all required nutrients. Therefore, syncytia have to be well supplied with assimilates and generate strong sinks in the host plant's transport system. Import mechanisms and consequent accumulation of sucrose in syncytia were described recently. In this work, we studied the starch metabolism of syncytia. Using high-performance liquid chromatography and microscopic analyses, we demonstrated that syncytia store carbohydrates by starch accumulation. Further, we monitored the expression of genes involved in the starch metabolic pathway by gene chip analysis and quantitative reverse transcription-PCR. Finally, we provide functional proof of the importance of starch synthesis for nematode development using T-DNA insertion lines. We conclude that syncytia accumulate starch as a carbohydrate buffer to compensate for changing solute uptake by the nematode and as long-term storage during juvenile development.
Trehalose-6-Phosphate Synthase/Phosphatase Regulates Cell Shape and Plant Architecture in Arabidopsis
Authors: Chary S. Narasimha , Hicks Glenn R. , Choi Yoon Gi , Carter David , Raikhel Natasha V.
Published: November 2007

The vacuole occupies most of the volume of plant cells; thus, the tonoplast marker δ-tonoplast intrinsic protein-green fluorescent protein delineates cell shape, for example, in epidermis. This permits rapid identification of mutants. Using this strategy, we identified the cell shape phenotype-1 (csp-1) mutant in Arabidopsis thaliana. Beyond an absence of lobes in pavement cells, phenotypes included reduced trichome branching, altered leaf serration and stem branching, and increased stomatal density. This result from a point mutation in AtTPS6 encoding a conserved amino-terminal domain, thought to catalyze trehalose-6-phosphate synthesis and a carboxy-terminal phosphatase domain, is catalyzing a two-step conversion to trehalose. Expression of AtTPS6 in the Saccharomyces cerevisiae mutants tps1 (encoding a synthase domain) and tps2 (encoding synthase and phosphatase domains) indicates that AtTPS6 is an active trehalose synthase. AtTPS6 fully complemented defects in csp-1. Mutations in class I genes (AtTPS1–AtTPS4) indicate a role in regulating starch storage, resistance to drought, and inflorescence architecture. Class II genes (AtTPS5–AtTPS11) encode multifunctional enzymes having synthase and phosphatase activity. We show that class II AtTPS6 regulates plant architecture, shape of epidermal pavement cells, and branching of trichomes. Thus, beyond a role in development, we demonstrate that the class II gene AtTPS6 is important for controlling cellular morphogenesis.
A Set of Modular Binary Vectors for Transformation of Cereals
Authors: Himmelbach Axel , Zierold Uwe , Hensel Götz , Riechen Jan , Douchkov Dimitar , Schweizer Patrick , Kumlehn Jochen
Published: November 2007

Genetic transformation of crop plants offers the possibility of testing hypotheses about the function of individual genes as well as the exploitation of transgenes for targeted trait improvement. However, in most cereals, this option has long been compromised by tedious and low-efficiency transformation protocols, as well as by the lack of versatile vector systems. After having adopted and further improved the protocols for Agrobacterium-mediated stable transformation of barley (Hordeum vulgare) and wheat (Triticum aestivum), we now present a versatile set of binary vectors for transgene overexpression, as well as for gene silencing by double-stranded RNA interference. The vector set is offered with a series of functionally validated promoters and allows for rapid integration of the desired genes or gene fragments by GATEWAY-based recombination. Additional in-built flexibility lies in the choice of plant selectable markers, cassette orientation, and simple integration of further promoters to drive specific expression of genes of interest. Functionality of the cereal vector set has been demonstrated by transient as well as stable transformation experiments for transgene overexpression, as well as for targeted gene silencing in barley.
Distinct Light and Clock Modulation of Cytosolic Free Ca2+ Oscillations and RhythmicCHLOROPHYLL A/B BINDING PROTEIN2Promoter Activity inArabidopsis
Authors: Xu Xiaodong , Hotta Carlos T. , Dodd Antony N. , Love John , Sharrock Robert , Lee Young Wha , Xie Qiguang , Johnson Carl H. , Webb Alex A.R.
Published: November 2007

Plants have circadian oscillations in the concentration of cytosolic free calcium ([Ca2+]cyt). To dissect the circadian Ca2+-signaling network, we monitored circadian [Ca2+]cyt oscillations under various light/dark conditions (including different spectra) in Arabidopsis thaliana wild type and photoreceptor and circadian clock mutants. Both red and blue light regulate circadian oscillations of [Ca2+]cyt. Red light signaling is mediated by PHYTOCHROME B (PHYB). Blue light signaling occurs through the redundant action of CRYPTOCHROME1 (CRY1) and CRY2. Blue light also increases the basal level of [Ca2+]cyt, and this response requires PHYB, CRY1, and CRY2. Light input into the oscillator controlling [Ca2+]cyt rhythms is gated by EARLY FLOWERING3. Signals generated in the dark also regulate the circadian behavior of [Ca2+]cyt. Oscillations of [Ca2+]cyt and CHLOROPHYLL A/B BINDING PROTEIN2 (CAB2) promoter activity are dependent on the rhythmic expression of LATE ELONGATED HYPOCOTYL and CIRCADIAN CLOCK-ASSOCIATED1, but [Ca2+]cyt and CAB2 promoter activity are uncoupled in the timing of cab1 (toc1-1) mutant but not in toc1-2. We suggest that the circadian oscillations of [Ca2+]cyt and CAB2 promoter activity are regulated by distinct oscillators with similar components that are used in a different manner and that these oscillators may be located in different cell types in Arabidopsis.