bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of high carrier densities on phonon and carrier lifetimes in Si by time-resolved anti-Stokes Raman scattering
Authors: Letcher Jeffrey J. , Kang Kwangu , Cahill David G. , Dlott Dana D.
Published: June 2007

The relaxation times T1 of nonequilibrium populations of elementary excitations in Si are studied by time-resolved Raman scattering using a subpicosecond pump-probe method. Incoherent anti-Stokes Raman scattering is used to monitor the decay of the nonequilibrium populations of holes and the generation and decay of zone-center longitudinal optical (LO) phonons. At lower levels of laser excitation, hole and LO phonon T1 lifetimes are less than 0.2ps and greater than 1.6ps, respectively. At higher laser intensities, the lifetime of holes increases and the lifetime of LO phonons decrease toward a common value of T1∼0.4ps.
Nanoimprinted large area heterojunction pentacene-C60 photovoltaic device
Authors: Dissanayake D. M. Nanditha M. , Adikaari A. A. D. T. , Curry Richard J. , Hatton Ross A. , Silva S. R. P.
Published: June 2007

A pentacene-C60 bilayer heterojunction organic photovoltaic device with interpenetrating donor-acceptor interface was fabricated by nanoimprinting the pentacene layer prior to C60 deposition. An amorphous silicon substrate nanostructured using an excimer laser was imprinted onto the pentacene layer at high temperature and pressure, using a nanoimprinting lithography system to form a textured pentacene surface. A fivefold improvement in power conversion efficiency was observed due to increased exciton dissociation at the large area heterojunction. Using the proposed technique, highly efficient bilayer large area heterojunction photovoltaics based on small molecule organic materials can be envisaged.
Optimal Reserve Site Selection with Multiple Levels of Protection
Authors: Williams Justin C , ReVelle Charles S , Song Wenjie
Published: June 2007

Most prior decision models for nature reserve-site selection have considered just two options for candidate sites: protected or not protected. In many reserve planning contexts this is an artificial and unrealistic limitation, as multiple categories of protection may be possible and desirable, especially if certain conservation elements such as rare species require special protection or management. In this paper we consider the implications of different levels of protection for species conservation and for the selection of reserve sites. New integer programming models are formulated for this problem of optimal site selection, and are presented in the context of a five-step procedure for identifying tradeoffs in the number of sites selected for each of multiple categories of protection. Results of a case study using data from Oregon are presented and compared to results from a previous study by Csuti et al.
The State and the Controversial Demands of Cultural Built Heritage: Modernism, Dirty Concrete, and Postwar Listing in England
Authors: While Aidan
Published: June 2007

Whilst it is generally accepted that architecturally or historically significant buildings should be protected in the common interest, conservation policy often raises a series of dilemmas for governments in terms of balancing demands for preservation and change. In 1987 statutory protection for historic buildings in England was extended to the post-Second World War (ie post-1945) era, taking conservation planning into new and sometimes controversial territory. This paper examines the origins and evolution of England's postwar listing programme, exploring the factors that prompted the state to extend protection into such a politically contentious area of conservation policy. Attention is drawn to the lobbying role of influential postwar conservation lobbyists located within and outside state structures in making the case for 1950s and 1960s architecture. However, the politics and practices of postwar listing are ultimately shown to be rooted in the underlying logic of built heritage regulation in England. The paper offers original insights into the state's role as conservation champion and its implications for what gets protected and why from the physical legacy of 1950s and 1960s design.
A GIS-Based Irregular Cellular Automata Model of Land-Use Change
Authors: Stevens Daniel , Dragićević Suzana
Published: June 2007

This study proposes an alternative cellular automata (CA) model, which relaxes the traditional CA regular square grid and synchronous growth, and is designed for representations of land-use change in rural-urban fringe settings. The model uses high-resolution spatial data in the form of irregularly sized and shaped land parcels, and incorporates synchronous and asynchronous development in order to model more realistically land-use change at the land parcel scale. The model allows urban planners and other stakeholders to evaluate how different subdivision designs will influence development under varying population growth rates and buyer preferences. A model prototype has been developed in a common desktop GIS and applied to a rapidly developing area of a midsized Canadian city.
Large Infrastructure Projects: A Review of the Quality of Demand Forecasts and Cost Estimations
Authors: van Wee Bert
Published: June 2007

Decision making with respect to large infrastructure projects is at least partly based on ex ante evaluations of costs and impacts. Impacts include economic, environmental, and social impacts, sometimes aggregated in a cost-benefit analysis (CBA). For such ex ante evaluations the quality of the related demand and costs forecasts is very important. This paper aims to answer four questions: (1) What is the quality of demand forecasts for large infrastructure projects? (2) What is the quality of cost forecasts for these projects? (3) How can current practices with respect to assessing the demand and cost forecasts be improved? (4) Which implications do the insights have for practice, and which challenges for future research can be derived from the findings? A literature review is used to answer the first three questions. It is concluded that the quality of transport demand and costs forecasts is often very poor, especially for rail projects. This is not so much a lack of adequate forecasting techniques or a matter of insight into the factors determining costs, but more the strategic behaviour of some actors. Improvements therefore should not only be looked for in the area of transport demand and cost-estimation methodologies, but should also focus on the question of how strategic behaviour can be avoided or at least limited. These conclusions are very important for CBA because cost underestimations and demand overestimations have a major impact on the cost-benefit ratio and decrease the potentially positive impact of CBA on the quality of decision making. The paper discusses several challenges for related future research.
Privatized Suburbia: The Planning Implications of Private Roads
Authors: Grant Jill , Curran Andrew
Published: June 2007

Over the last few decades new residential developments have increasingly featured private roads. Many planned unit developments and new-urbanism-style projects have turned to private roads. This paper considers some of the spatial, socioeconomic, and planning implications created by private roads in the Canadian context. While private streets provide a useful tool for achieving design and density objectives, and for transferring the burden of development costs to those who benefit from growth, they exacerbate social segregation and spatial fragmentation of the urban landscape.
The Rise of Azide–Alkyne 1,3-Dipolar 'Click' Cycloaddition and its Application to Polymer Science and Surface Modification
Authors: Evans Richard A.
Published: June 2007

New methods to synthesize and functionalize polymers are of constant interest to the polymer scientist. The 1,3-dipolar cycloaddition between an azide and terminal alkyne has received much attention since the reports that copper(i) provides high yields and regioselective synthesis of 1,4-substituted 1,2,3-triazoles. This coupling chemistry has been rapidly adopted by polymer scientists in the synthesis and post-polymerization modification of polymers. This Review will provide the historical context of the recent development of the copper-mediated azide–alkyne cycloaddition and its use in polymer science, particularly in dendrimer synthesis/functionalization, surface immobilization/modification, orthogonally functionalizing polymers, and its integration with ATRP (atom transfer radical polymerization).
'Click' Bioconjugation of a Well-Defined Synthetic Polymer and a Protein Transduction Domain
Authors: Lutz Jean-François , Börner Hans G. , Weichenhan Katja
Published: June 2007

The copper-catalyzed 1,3-dipolar ‘click’ cycloaddition of azides and alkynes was studied to link a model synthetic polymer to a sequence-defined protein transduction domain (PTD). The bromine chain-ends of a well-defined polystyrene (PS) sample synthesized by atom transfer radical polymerization (Mn 2200 g mol–1, Mw/Mn 1.21) were first transformed into azide functions by substitution with sodium azide, and subsequently reacted with an alkyne-functionalized PTD (i.e., the oligopeptide sequence GGYGRKKRRQRRRG, also known as the TAT peptide). The click bioconjugation proceeded successfully at room temperature, thus affording the targeted PS-b-GGYGRKKRRQRRRG bioconjugate in high yields. However, a slight molar excess of polystyrene was required for optimal coupling.
Hyperbranched Polymers via RAFT Copolymerization of an Acryloyl Trithiocarbonate
Authors: Vogt Andrew P. , Gondi Sudershan R. , Sumerlin Brent S.
Published: June 2007

Hyperbranched copolymers of N-isopropylacrylamide (NIPAM) and styrene were prepared by reversible addition-fragmentation chain transfer (RAFT) polymerization in the presence of a novel acryloyl trithiocarbonate, namely 1-[3-(2-methyl-2-dodecylsulfanylthiocarbonylsulfanylpropionyloxy)propyl]-1H-[1,2,3]triazol-4-ylmethyl acrylate. By employing an example of ‘click chemistry’, we were able to prepare the vinyl RAFT chain transfer agent (CTA) by copper-catalyzed 1,3-dipolar cycloaddition of an azido-functionalized trithiocarbonate and propargyl acrylate. The resulting CTA facilitated the preparation of highly branched poly(N-isopropylacrylamide) (PNIPAM) and polystyrene. Interestingly, the branched PNIPAM demonstrated a reduced lower critical solution temperature (LCST) of 25°C as opposed to the conventional value of 32°C expected for linear PNIPAM, an effect attributed to increased contribution of hydrophobic dodecyl trithiocarbonate end groups.
RAFT Chemistry and Huisgen 1,3-Dipolar Cycloaddition: A Route to Block Copolymers of Vinyl Acetate and 6-O-Methacryloyl Mannose?
Authors: Ting S. R. Simon , Granville Anthony M. , Quémener Damien , Davis Thomas P. , Stenzel Martina H. , Barner-Kowollik Christopher
Published: June 2007

The present communication explores a novel avenue to glycopolymer-block-poly(vinyl acetate) polymers by a combination of reversible addition fragmentation chain transfer (RAFT) chemistry and Huisgen 1,3-dipolar cycloaddition (i.e., so-called ‘click’ chemistry) under mild reaction conditions. Such block copolymers are—because of the strongly disparate reactivity of the two monomers—otherwise not obtainable. Poly(vinyl acetate) that has an azide end group (Mn 6800 g mol–1, PDI 1.15) was treated with poly(6-O-methacryloyl mannose) (Mn 7600 g mol–1, PDI 1.11) in the presence of 1,8-diaza[5,4,0]bicycloundec-7-ene and copper(i) iodide. The resulting poly(vinyl acetate)-block-poly(6-O-methacryloyl mannose) had a number-average molecular weight of 15400 g mol–1 and a PDI of 1.48, which indicates that while the cycloaddition had occurred the resulting polymer distribution featured a considerable width. The resulting slightly amphiphilic block copolymer was subsequently investigated with regard to its self-assembly in aqueous solution. Dynamic light scattering studies indicated a hydrodynamic diameter of close to 200 nm. Transmission electron microscopy studies indicate the formation of rods as well as spheres with transitions between these two phases. However, the segregation between core and shell in the spheres is not pronounced; such behaviour is expected for weakly amphiphilic block copolymers.
Exploring the Coordination Chemistry of Some Organometallic Mercury Derivatives of 4-Ethynylpyridine
Authors: Liu Li , Ho Cheuk-Lam , Wong Wai-Yeung
Published: June 2007

Two new heterotrinuclear organorhenium(i) mercury(ii) derivatives of 4-ethynylpyridine [Re(CO)3Cl(NC5H4C≡CHgMe)2] 1 and [Re(CO)3Cl(NC5H4C≡CHgC≡CC5H4N)2] 2 were prepared in good yields by the reaction of Re(CO)5Cl with a methylmercury(ii) derivative of 4-ethynylpyridine 1a and its inorganic mercury(ii) derivative, bis(4-pyridylethynyl)mercury 2a, respectively. The structures of these mixed-metal complexes were established by spectroscopic (FT-IR, NMR, and FABMS) techniques and their photophysical properties were examined in both fluid and solid phases.
Excluded volume, local structural cooperativity, and the polymer physics of protein folding rates
Authors: Qi Xianghong , Portman John J.
Published: June 2007

A coarse-grained variational model is used to investigate the polymer dynamics of barrier crossing for a diverse set of two-state folding proteins. The model gives reliable folding rate predictions provided excluded volume terms that induce minor structural cooperativity are included in the interaction potential. In general, the cooperative folding routes have sharper interfaces between folded and unfolded regions of the folding nucleus and higher free energy barriers. The calculated free energy barriers are strongly correlated with native topology as characterized by contact order. Increasing the rigidity of the folding nucleus changes the local structure of the transition state ensemble nonuniformly across the set of proteins studied. Nevertheless, the calculated prefactors
k
0
are found to be relatively uniform across the protein set, with variation in 1/
k
0
less than a factor of 5. This direct calculation justifies the common assumption that the prefactor is roughly the same for all small two-state folding proteins. Using the barrier heights obtained from the model and the best-fit monomer relaxation time 30 ns, we find that 1/
k
0
∼ 1–5 μs (with average 1/
k
0
∼ 4 μs). This model can be extended to study subtle aspects of folding such as the variation of the folding rate with stability or solvent viscosity and the onset of downhill folding.
Mapping of the preferred direction in the motor cortex
Authors: Georgopoulos Apostolos P. , Merchant Hugo , Naselaris Thomas , Amirikian Bagrat
Published: June 2007

Directional tuning is a basic functional property of cell activity in the motor cortex. Previous work has indicated that cells with similar preferred directions are organized in columns perpendicular to the cortical surface. Here we show that these columns are organized in an orderly fashion in the tangential dimension on the cortical surface. Based on a large number of microelectrode penetrations and systematic exploration of the proximal arm area of the motor cortex while monkeys made free reaching 3D movements, it was estimated that (
i
) directional minicolumns are ≈30 μm in width, (
ii
) minicolumns with similar preferred directions tend to occur in doublets or triplets, and (
iii
) such minicolumns tend to repeat every ≈240 μm (estimated width of a column), with intermediate preferred directions represented in a gradient. These findings provide evidence for an orderly mapping of the preferred direction in the motor cortex.
Canalization of segmentation and its evolution in
Drosophila
Authors: Lott Susan E. , Kreitman Martin , Palsson Arnar , Alekseeva Elena , Ludwig Michael Z.
Published: June 2007

Segmentation in
Drosophila
embryogenesis occurs through a hierarchical cascade of regulatory gene expression driven by the establishment of a diffusion-mediated morphogen gradient. Here, we investigate the response of this pattern formation process to genetic variation and evolution in egg size. Specifically, we ask whether spatial localization of gap genes
Kruppel
(
Kr
) and
giant
(
gt
) and the pair-rule gene
even-skipped
(
eve
) during cellularization is robust to genetic variation in embryo length in three
Drosophila melanogaster
isolines and two closely related species. We identified two wild-derived strains of
D. melanogaster
whose eggs differ by ≈25% in length when reared under identical conditions. These two lines, a
D. melanogaster
laboratory stock (
w1118
), and offspring from crosses between the lines all exhibit precise scaling in the placement of gap and pair-rule gene expression along the anterior–posterior axis in relation to embryo length. Genetic analysis indicates that this scaling is maternally controlled. Maternal regulation of scaling must be required for consistent localization of segmentation gene expression because embryo size, a genetically variable and adaptive trait, is maternally inherited. We also investigated spatial scaling between these
D. melanogaster
lines and single lines of
Drosophila sechellia
and
Drosophila simulans
, the latter two differing by ≈25% in egg length. In contrast to the robust scaling we observed within species, localization of gene expression relative to embryo length differs significantly between the three species. Thus, the developmental mechanism that assures robust scaling within a species does not prevent rapid evolution between species.
Detection of fractional steps in cargo movement by the collective operation of kinesin-1 motors
Authors: Leduc Cécile , Ruhnow Felix , Howard Jonathon , Diez Stefan
Published: June 2007

The stepping behavior of single kinesin-1 motor proteins has been studied in great detail. However, in cells, these motors often do not work alone but rather function in small groups when they transport cellular cargo. Until now, the cooperative interactions between motors in such groups were poorly understood. A fundamental question is whether two or more motors that move the same cargo step in synchrony, producing the same step size as a single motor, or whether the step size of the cargo movement varies. To answer this question, we performed
in vitro
gliding motility assays, where microtubules coated with quantum dots were driven over a glass surface by a known number of kinesin-1 motors. The motion of individual microtubules was then tracked with nanometer precision. In the case of transport by two kinesin-1 motors, we found successive 4-nm steps, corresponding to half the step size of a single motor. Dwell-time analysis did not reveal any coordination, in the sense of alternate stepping, between the motors. When three motors interacted in collective transport, we identified distinct forward and backward jumps on the order of 10 nm. The existence of the fractional steps as well as the distinct jumps illustrate a lack of synchronization and has implications for the analysis of motor-driven organelle movement investigated
in vivo
.
Regulation of synaptic growth and maturation by a synapse-associated E3 ubiquitin ligase at the neuromuscular junction
Authors: Lu Zhonghua , Je Hyun-Soo , Young Paul , Gross Jimmy , Lu Bai , Feng Guoping
Published: June 2007

The ubiquitin–proteasome pathway has been implicated in synaptic development and plasticity. However, mechanisms by which ubiquitination contributes to precise and dynamic control of synaptic development and plasticity are poorly understood. We have identified a PDZ domain containing RING finger 3 (PDZRN3) as a synapse-associated E3 ubiquitin ligase and have demonstrated that it regulates the surface expression of muscle-specific receptor tyrosine kinase (MuSK), the key organizer of postsynaptic development at the mammalian neuromuscular junction. PDZRN3 binds to MuSK and promotes its ubiquitination. Regulation of cell surface levels of MuSK by PDZRN3 requires the ubiquitin ligase domain and is mediated by accelerated endocytosis. Gain- and loss-of-function studies in cultured myotubes show that regulation of MuSK by PDZRN3 plays an important role in MuSK-mediated nicotinic acetylcholine receptor clustering. Furthermore, overexpression of PDZRN3 in skeletal muscle of transgenic mice perturbs the growth and maturation of the neuromuscular junction. These results identify a synapse-associated E3 ubiquitin ligase as an important regulator of MuSK signaling.
YGR198w (YPP1) targets A30P α-synuclein to the vacuole for degradation
Authors: Flower Todd R. , Clark-Dixon Cheryl , Metoyer Cheynita , Yang Hui , Shi Runhua , Zhang Zhaojie , Witt Stephan N.
Published: June 2007

Using a genetic screen we discovered that YGR198w (named YPP1), which is an essential Saccharomyces cerevisiae gene of unknown function, suppresses the toxicity of an α-synuclein (α-syn) mutant (A30P) that is associated with early onset Parkinson's disease. Here, we show that YPP1 suppresses lethality of A30P, but not of wild-type α-syn or the A53T mutant. The Ypp1 protein, when overexpressed, drives each of the three α-syns into vesicles that bud off the plasma membrane, but only A30P-containing vesicles traffick to and merge with the vacuole, where A30P is proteolytically degraded. We show that Ypp1p binds to A30P but not the other two α-syns; that YPP1 interacts with genes involved in endocytosis/actin dynamics (SLA1, SLA2, and END3), protein sorting (class E vps), and vesicle-vacuole fusion (MON1 and CCZ1) to dispose of A30P; and that YPP1 also participates in pheromone-triggered receptor-mediated endocytosis. Our data reveal that YPP1 mediates the trafficking of A30P to the vacuole via the endocytic pathway.
p75 neurotrophin receptor regulates tissue fibrosis through inhibition of plasminogen activation via a PDE4/cAMP/PKA pathway
Authors: Sachs Benjamin D. , Baillie George S. , McCall Julianne R. , Passino Melissa A. , Schachtrup Christian , Wallace Derek A. , Dunlop Allan J. , MacKenzie Kirsty F. , Klussmann Enno , Lynch Martin J. , Sikorski Shoana L. , Nuriel Tal , Tsigelny Igor , Zhang Jin , Houslay Miles D. , Chao Moses V. , Akassoglou Katerina
Published: June 2007

Clearance of fibrin through proteolytic degradation is a critical step of matrix remodeling that contributes to tissue repair in a variety of pathological conditions, such as stroke, atherosclerosis, and pulmonary disease. However, the molecular mechanisms that regulate fibrin deposition are not known. Here, we report that the p75 neurotrophin receptor (p75NTR), a TNF receptor superfamily member up-regulated after tissue injury, blocks fibrinolysis by down-regulating the serine protease, tissue plasminogen activator (tPA), and up-regulating plasminogen activator inhibitor-1 (PAI-1). We have discovered a new mechanism in which phosphodiesterase PDE4A4/5 interacts with p75NTR to enhance cAMP degradation. The p75NTR-dependent down-regulation of cAMP results in a decrease in extracellular proteolytic activity. This mechanism is supported in vivo in p75NTR-deficient mice, which show increased proteolysis after sciatic nerve injury and lung fibrosis. Our results reveal a novel pathogenic mechanism by which p75NTR regulates degradation of cAMP and perpetuates scar formation after injury.
Spindly, a novel protein essential for silencing the spindle assembly checkpoint, recruits dynein to the kinetochore
Authors: Griffis Eric R. , Stuurman Nico , Vale Ronald D.
Published: June 2007

The eukaryotic spindle assembly checkpoint (SAC) monitors microtubule attachment to kinetochores and prevents anaphase onset until all kinetochores are aligned on the metaphase plate. In higher eukaryotes, cytoplasmic dynein is involved in silencing the SAC by removing the checkpoint proteins Mad2 and the Rod–Zw10–Zwilch complex (RZZ) from aligned kinetochores (Howell, B.J., B.F. McEwen, J.C. Canman, D.B. Hoffman, E.M. Farrar, C.L. Rieder, and E.D. Salmon. 2001. J. Cell Biol. 155:1159–1172; Wojcik, E., R. Basto, M. Serr, F. Scaerou, R. Karess, and T. Hays. 2001. Nat. Cell Biol. 3:1001–1007). Using a high throughput RNA interference screen in Drosophila melanogaster S2 cells, we have identified a new protein (Spindly) that accumulates on unattached kinetochores and is required for silencing the SAC. After the depletion of Spindly, dynein cannot target to kinetochores, and, as a result, cells arrest in metaphase with high levels of kinetochore-bound Mad2 and RZZ. We also identified a human homologue of Spindly that serves a similar function. However, dynein's nonkinetochore functions are unaffected by Spindly depletion. Our findings indicate that Spindly is a novel regulator of mitotic dynein, functioning specifically to target dynein to kinetochores.
Association of ICAM3 Genetic Variant with Severe Acute Respiratory Syndrome
Authors: Chan Kelvin Y. K. , Ching Johannes C. Y. , Xu M. S. , Cheung Annie N. Y. , Yip Shea-Ping , Yam Loretta Y. C. , Lai Sik-To , Chu Chung-Ming , Wong Andrew T. Y. , Song You-Qiang , Huang Fang-Ping , Liu Wei , Chung P. H. , Leung G. M. , Chow Eudora Y. D. , Chan Eric Y. T. , Chan Jane C. K. , Ngan Hextan , Tam Paul , Chan Li-Chong , Sham Pak , Chan Vera S. F. , Peiris Malik , Lin Steve C. L. , Khoo Ui-Soon
Published: June 2007

Genetic polymorphisms have been demonstrated to be associated with vulnerability to human infection. ICAM3, an intercellular adhesion molecule important for T cell activation, and FCER2 (CD23), an immune response gene, both located on chromosome 19p13.3 were investigated for host genetic susceptibility and association with clinical outcome. A case-control study based on 817 patients with confirmed severe acute respiratory syndrome (SARS), 307 health care worker control subjects, 290 outpatient control subjects, and 309 household control subjects unaffected by SARS from Hong Kong was conducted to test for genetic association. No significant association to susceptibility to SARS-CoV infection was found for the FCER2 and the ICAM3 single nucleotide polymorphisms. However, patients with SARS homozygous for ICAM3 Gly143 showed significant association with higher lactate dehydrogenase levels (P=.0067; odds ratio [OR], 4.31 [95% confidence interval [CI], 1.37–13.56]) and lower total white blood cell counts (P=.022; OR, 0.30 [95% CI, 0.10–0.89]) on admission. These findings support the role of ICAM3 in the immunopathogenesis of SARS.
Recessive Resistance Genes and the Oryza sativa-Xanthomonas oryzae pv. oryzae Pathosystem
Authors: Iyer-Pascuzzi Anjali S. , McCouch Susan R.
Published: June 2007

Though recessive resistance is well-studied in viral systems, little is understood regarding the phenomenon in plant-bacterial interactions. The Oryza sativa-Xanthomonas oryzae pv. orzyae pathosystem provides an excellent opportunity to examine recessive resistance in plant-bacterial interactions, in which nine of 30 documented resistance (R) genes are recessively inherited. Infestations of X. oryzae pv. oryzae, the causal agent of bacterial blight, result in significant crop loss and damage throughout South and Southeast Asia. Two recently cloned novel recessive R genes, xa5 and xa13, have yielded insights to this system. Like their viral counterparts, these bacterial recessive R gene products do not conform to the five commonly described classes of R proteins. New findings suggest that such genes may more aptly be viewed as mutations in dominant susceptibility alleles and may also function in a gene-for-gene manner. In this review, we discuss recent accomplishments in the understanding of recessively inherited R genes in the rice-bacterial blight pathosystem and suggest a new model for the function of recessive resistance in plant-bacterial interactions.
pSITE Vectors for Stable Integration or Transient Expression of Autofluorescent Protein Fusions in Plants: Probing Nicotiana benthamiana-Virus Interactions
Authors: Chakrabarty Romit , Banerjee Rituparna , Chung Sang-Min , Farman Mark , Citovsky Vitaly , Hogenhout Saskia A. , Tzfira Tzvi , Goodin Michael
Published: June 2007

Plant functional proteomics research is increasingly dependent upon vectors that facilitate high-throughput gene cloning and expression of fusions to autofluorescent proteins. Here, we describe the pSITE family of plasmids, a new set of Agrobacterium binary vectors, suitable for the stable integration or transient expression of various autofluorescent protein fusions in plant cells. The pSITE vectors permit single-step Gateway-mediated recombination cloning for construction of binary vectors that can be used directly in transient expression studies or for the selection of transgenic plants on media containing kanamycin. These vectors can be used to express native proteins or fusions to monmeric red fluorescent protein or the enhanced green fluorescent protein and its cyan and yellow-shifted spectral variants. We have validated the vectors for use in transient expression assays and for the generation of transgenic plants. Additionally, we have generated markers for fluorescent highlighting of actin filaments, chromatin, endoplasmic reticulum, and nucleoli. Finally, we show that pSITE vectors can be used for targeted gene expression in virus-infected cells, which should facilitate high-throughput characterization of protein dynamics in host-virus interactions.
Streptomyces turgidiscabies Possesses a Functional Cytokinin Biosynthetic Pathway and Produces Leafy Galls
Authors: Joshi Madhumita V. , Loria Rosemary
Published: June 2007

Streptomyces turgidiscabies, a cause of potato scab, possesses a mobilizable pathogenicity island containing multiple virulence genes and a cytokinin biosynthetic pathway. These biosynthetic genes are homologous and collinear with the fas operon in Rhodococcus fascians. Reverse-transcriptase polymerase chain reaction of S. turgidiscabies demonstrated that all six genes were transcribed in oat bran broth with and without glucose, though transcription was partially repressed by glucose. The supernatant of S. turgidiscabies cultures had cytokinin activity in callus initiation and differentiation assays. Arabidopsis and tobacco plants inoculated with a thaxtomin-deficient mutant (Δnos) produced leafy galls, indistinguishable from those produced by R. fascians. Deletion of the ipt gene in the pathway eliminated gall phenotype. Other symptoms on tobacco included production of hairy roots and de novo meristems.
Expressed Sequence Tags fromPhytophthora sojaeReveal Genes Specific to Development and Infection
Authors: Torto-Alalibo Trudy A. , Tripathy Sucheta , Smith Brian M. , Arredondo Felipe D. , Zhou Lecong , Li Hua , Chibucos Marcus C. , Qutob Dinah , Gijzen Mark , Mao Chunhong , Sobral Bruno W. S. , Waugh Mark E. , Mitchell Thomas K. , Dean Ralph A. , Tyler Brett M.
Published: June 2007

Six unique expressed sequence tag (EST) libraries were generated from four developmental stages of Phytophthora sojae P6497. RNA was extracted from mycelia, swimming zoospores, germinating cysts, and soybean (Glycine max (L.) Merr.) cv. Harosoy tissues heavily infected with P. sojae. Three libraries were created from mycelia growing on defined medium, complex medium, and nutrient-limited medium. The 26,943 high-quality sequences obtained clustered into 7,863 unigenes composed of 2,845 contigs and 5,018 singletons. The total number of P. sojae unigenes matching sequences in the genome assembly was 7,412 (94%). Of these unigenes, 7,088 (90%) matched gene models predicted from the P. sojae sequence assembly, but only 2,047 (26%) matched P. ramorum gene models. Analysis of EST frequency from different growth conditions and morphological stages revealed genes that were specific to or highly represented in particular growth conditions and life stages. Additionally, our results indicate that, during infection, the pathogen derives most of its carbon and energy via glycolysis of sugars in the plant. Sequences identified with putative roles in pathogenesis included avirulence homologs possessing the RxLR motif, elicitins, and hydrolytic enzymes. This large collection of P. sojae ESTs will serve as a valuable public genomic resource.
Arabidopsis thaliana Expresses Multiple Lines of Defense to Counterattack Erwinia chrysanthemi
Authors: Fagard Mathilde , Dellagi Alia , Roux Camille , Périno Claude , Rigault Martine , Boucher Virginie , Shevchik Vladimir E. , Expert Dominique
Published: June 2007

Many taxonomically diverse plant species are attacked by Erwinia chrysanthemi, a member of the causal agents of soft-rotting diseases. Symptom development is due to the collective action of pectin-degrading enzymes secreted by the bacterium through a type II secretion system (T2SS). Using Arabidopsis thaliana as a susceptible host, we show that plants respond to E. chrysanthemi 3937 by expressing cell-wall reactions, production of an oxidative burst, and activation of salicylic acid (SA) and jasmonic acid (JA) or ethylene (ET) signaling pathways. We found that the oxidative burst is mainly generated via the expression of the AtrbohD gene, constitutes a barrier of resistance to bacterial attack, and acts independently of the SA-mediated response. To determine the importance of T2SS-secreted proteins in elicitation of these defenses, we used a T2SS deficient mutant and purified enzymatic preparations of representative members of strain 3937 pectate lyase activity. The T2SS-secreted proteins were responsible only partially for the activation of SA and JA or ET signaling pathways observed after infection with the wild-type bacterium and were not involved in the expression of other identified defense reactions. Our study shows the differential role played by pectate lyases isoenzymes in this process and highlights the complexity of the host immune network, which is finely controlled by the bacterium.
Pto- and Prf-Mediated Recognition of AvrPto and AvrPtoB Restricts the Ability of Diverse Pseudomonas syringae Pathovars to Infect Tomato
Authors: Lin Nai-Chun , Martin Gregory B.
Published: June 2007

The molecular basis underlying the ability of pathogens to infect certain plant species and not others is largely unknown. Pseudomonas syringae is a useful model species for investigating this phenomenon because it comprises more than 50 pathovars which have narrow host range specificities. Tomato (Solanum lycopersicum) is a host for P. syringae pv. tomato, the causative agent of bacterial speck disease, but is considered a nonhost for other P. syringae pathovars. Host resistance in tomato to bacterial speck disease is conferred by the Pto protein kinase which acts in concert with the Prf nucleotide-binding lucine-rich repeat protein to recognize P. syringae pv. tomato strains expressing the type III effectors AvrPto or AvrPtoB (HopAB2). The Pto and Prf genes were isolated from the wild tomato species S. pimpinellifolium and functional alleles of both of these genes now are known to exist in many species of tomato and in other Solanaceous species. Here, we extend earlier reports that avrPto and avrPtoB genes are widely distributed among pathovars of P. syringae which are considered nonhost pathogens of tomato. This observation prompted us to examine the possibility that recognition of these type III effectors by Pto or Prf might contribute to the inability of many P. syringae pathovars to infect tomato species. We show that 10 strains from presumed nonhost P. syringae pathovars are able to grow and cause pathovar-unique disease symptoms in tomato leaves lacking Pto or Prf, although they did not reach the population levels or cause symptoms as severe as a control P. syringae pv. tomato strain. Seven of these strains were found to express avrPto or avrPtoB. The AvrPto- and AvrPtoB-expressing strains elicited disease resistance on tomato leaves expressing Pto and Prf. Thus, a gene-for-gene recognition event may contribute to host range restriction of many P. syringae pathovars on tomato species. Furthermore, we conclude that the diverse disease symptoms caused by different Pseudomonas pathogens on their normal plant hosts are due largely to the array of virulence factors expressed by each pathovar and not to specific molecular or morphological attributes of the plant host.
Effects of AiiA-Mediated Quorum Quenching in Sinorhizobium meliloti on Quorum-Sensing Signals, Proteome Patterns, and Symbiotic Interactions
Authors: Gao Mengsheng , Chen Hancai , Eberhard Anatol , Gronquist Matthew R. , Robinson Jayne B. , Connolly Mary , Teplitski Max , Rolfe Barry G. , Bauer Wolfgang D.
Published: June 2007

Many behaviors in bacteria, including behaviors important to pathogenic and symbiotic interactions with eukaryotic hosts, are regulated by a mechanism called quorum sensing (QS). A “quorum-quenching” approach was used here to identify QS-regulated behaviors in the N-fixing bacterial symbiont Sinorhizobium meliloti. The AiiA lactonase from Bacillus produced in S. meliloti was shown to enzymatically inactivate S. meliloti's N-acyl homoserine lactone (AHL) QS signals, thereby disrupting normal QS regulation. Sixty proteins were differentially accumulated in the AiiA-producing strain versus the control in early log or early stationary phase cultures. Fifty-two of these QS-regulated proteins, with putative functions that include cell division, protein processing and translation, metabolite transport, oxidative stress, and amino acid metabolism, were identified by peptide mass fingerprinting. Transcription of representative genes was reduced significantly in the AiiA-producing strain, although the effects of AiiA on protein accumulation did not always correspond to effects on transcription. The QS signal-deficient strain was reduced significantly in nodule initiation during the first 12 h after inoculation onto Medicago truncatula host plants. The AiiA lactonase also was found to substantially inactivate two of the AHL mimic compounds secreted by M. truncatula. This suggests some structural similarity between bacterial AHLs and these mimic compounds. It also indicates that quorum quenching could be useful in identifying Sinorhizobium genes that are affected by such host QS mimics in planta.
Protein Accumulation in the Germinating Uromyces appendiculatus Uredospore
Authors: Cooper Bret , Neelam Anil , Campbell Kimberly B. , Lee Joohyun , Liu George , Garrett Wesley M. , Scheffler Brian , Tucker Mark L.
Published: June 2007

Uromyces appendiculatus is a rust fungus that causes disease on beans. To understand more about the biology of U. appendiculatus, we have used multidimensional protein identification technology to survey proteins in germinating asexual uredospores and have compared this data with proteins discovered in an inactive spore. The relative concentrations of proteins were estimated by counting the numbers of tandem mass spectra assigned to peptides for each detected protein. After germination, there were few changes in amounts of accumulated proteins involved in glycolysis, acetyl Co-A metabolism, citric acid cycle, ATP-coupled proton transport, or gluconeogenesis. Moreover, the total amount of translation elongation factors remained high, supporting a prior model that suggests that germlings acquire protein translation machinery from uredospores. However, germlings contained a higher amount of proteins involved in mitochondrial ADP:ATP translocation, which is indicative of increased energy production. Also, there were more accumulating histone proteins, pointing to the reorganization of the nuclei that occurs after germination prior to appressorium formation. Generally, these changes are indicative of metabolic transition from dormancy to germination and are supported by cytological and developmental models of germling growth.
Discovery and Characterization of Waitea circinata var. circinata Affecting Annual Bluegrass from the Western United States
Authors: de la Cerda Karla A. , Douhan Greg W. , Wong Francis P.
Published: June 2007

Waitea circinata var. circinata was identified as the causal agent of a new disease of annual bluegrass (Poa annua) in the United States. This pathogen is also known to cause brown ring patch on creeping bentgrass (Agrostis stolonifera) in Japan, but it had not been reported on any turf species outside of Japan. Symptoms on annual bluegrass caused by this fungus included regular to irregular yellow rings several centimeters to 1 m in diameter, typically at maximum daytime temperatures of 15 to 35°C. A total of 26 isolates were collected from diseased annual bluegrass. Twenty-two of these isolates were multinucleate, grew optimally at 25 to 30°C, and in culture formed irregular sclerotia approximately 2 to 5 mm in size that were white to orange and remained orange or turned brown to dark brown over a 28-day period. The remaining four isolates were characterized as being W. circinata var. zeae (Rhizoctonia zeae), which is a known pathogen of annual bluegrass in the United States. Sequence analysis of the internal transcribed spacer (ITS) regions of rDNA on a subset of isolates confirmed the identifications of W. circinata var. circinata (n = 8) and W. circinata var. zeae (n = 1) based on deposited sequences in GenBank. The identity of the remaining 14 isolates suspected to be W. circinata var. circinata was confirmed by HapII digestion of the amplified rDNA ITS region. Pathogenicity of four W. circinata var. circinata isolates was confirmed on both annual bluegrass and creeping bentgrass. This study is the first morphological and molecular confirmation of the presence of W. circinata var. circinata as a pathogen of turfgrass in the United States.
Integrating Disease Thresholds with TOM-CAST for Carrot Foliar Blight Management
Authors: Bounds R. S. , Podolsky R. H. , Hausbeck M. K.
Published: June 2007

Cercospora carotae and Alternaria dauci cause foliar blight on carrot (Daucus carota subsp. sativus) and are managed with fungicides to prevent yield loss. Sprays are initiated prior to disease symptoms and reapplied frequently, but some of these applications may not be necessary when the threat of disease is low. Delaying the initial fungicide spray until disease symptoms are observed and applying subsequent sprays according to the TOM-CAST disease forecaster may reduce fungicide inputs. The objective of this 2-year field study was to compare preventive, calendar-based application schedules with an integrated management approach that incorporates disease scouting to initiate fungicide application and the TOM-CAST system for timing subsequent fungicide sprays to manage foliar blight on processing, fresh market, and cut-and-peel carrot cultivars in Michigan. Applications of the fungicides chlorothalonil alternated with azoxystrobin were made prior to disease symptoms (0% blight) or when the foliage became blighted at a trace, 5%, or 10% severity level. Fungicides were reapplied every 7 or 10 days or according to TOM-CAST using disease severity value (DSV) thresholds of 15, 20, or 25. Initiating fungicide treatment at a trace level of disease and timing subsequent sprays according to the TOM-CAST 15-DSV forecaster was comparable to the preventive, calendar-based fungicide regime. One to five fewer applications were needed, while fungicide costs were reduced by $21 to $141 per hectare, when spraying at the trace disease threshold and reapplying according to the TOM-CAST 15-DSV program compared with the 7- or 10-day intervals initiated at 0% blight. Fungicide programs initiated at 5 or 10% leaf blight often provided less control than programs initiated at 0% and trace disease. This study highlights the importance of initiating a fungicide program prior to advanced foliar blight and validates the TOM-CAST 15-DSV forecaster for managing Cercospora leaf spot and Alternaria leaf blight in three carrot production systems.
Additional Vegetative Compatibility Groups in Colletotrichum coccodes Subpopulations from Europe and Israel
Authors: Shcolnick S. , Dinoor A. , Tsror (Lahkim) L.
Published: June 2007

Potato black dot, caused by Colletotrichum coccodes, damages tuber quality and may reduce yield. In previous work, four multimember vegetative compatibility groups (VCGs) have been reported. The objectives of the current study were to characterize a population of C. coccodes comprised of isolates from Israel and Northern Europe (EU/I) using VCG, and to assess the correlation between VCGs and aggressiveness of isolates on potato. A composite of 176 isolates was collected from symptomatic tissues of potato tubers or stems. A total of 6 (3.4%) isolates were characterized in VCG1; 29 (16.5%), 32 (18.2%), and 7 (4.0%) in VCG 2, 3, and 4, respectively; and 7 (4.0%), 9 (5.1%), 48 (27.3%), and 15 (8.5%) in the newly defined VCG 5, 6, 7, and 8, respectively. Twenty-three isolates (13%) were not assigned to any of the VCGs. Two of the VCGs had a specific geographical distribution: the 9 isolates assigned to VCG6 originated from The Netherlands, and 34 of 38 isolates assigned to VCG7 were from Scotland. Aggressiveness of isolates of a given VCG was examined on potato. VCGs 5 and 6 were comprised of the most aggressive isolates, and VCG1 of the least aggressive. These results could facilitate a more accurate evaluation of damage potential that may be caused by this pathogen.
Incidence and Ecology of Blackberry yellow vein associated virus
Authors: Susaimuthu James , Gergerich Rose C. , Bray Mark M. , Clay Kimberley A. , Clark John R. , Tzanetakis Ioannis E. , Martin Robert R.
Published: June 2007

Symptoms of leaf vein yellowing and bush decline in blackberry were attributed to infection by a novel crinivirus named Blackberry yellow vein associated virus (BYVaV). The disease is an emerging threat to blackberry production because it can cause substantial yield loss. The objective of this study was to identify the source and means of spread of BYVaV. A survey of blackberry plants for BYVaV from wild, cultivated, and nursery stocks was conducted. Insect traps and healthy blackberry sentinel plants were placed among symptomatic plants in a production field throughout two growing seasons to monitor the occurrence of potential vectors and virus spread. Virus indicator plants were grafted with BYVaV-infected blackberry because this virus was latent in some blackberry cultivars, but indicator plants failed to express symptoms when infected with BYVaV. Reverse-transcription polymerase chain reaction detection revealed the occurrence of BYVaV in blackberry nurseries in the United States, in production fields in Arkansas, South Carolina, and North Carolina, and in wild blackberry populations in Arkansas. Whiteflies (Trialeurodes packardii and T. ruborum), potential vectors of BYVaV, were observed on sticky traps placed in blackberry fields and were found colonizing blackberry plants; however, transmission studies failed to produce whitefly-mediated transmission of BYVaV. Further understanding of the disease etiology is needed to devise viable management strategies for this disease.
Virulence Diversity in the Population of Bipolaris sorokiniana
Authors: Ghazvini H. , Tekauz A.
Published: June 2007

Spot blotch, caused by Bipolaris sorokiniana, is a damaging disease of barley in Canada, especially in the prairie region (Manitoba, Saskatchewan, and Alberta) where most of Canadian crops are produced. Considerable interaction between isolates of the pathogen and barley genotypes necessitates the evaluation of the virulence diversity in the B. sorokiniana population in order to deploy effective resistance against the pathogen. The virulence diversity of 127 B. sorokiniana isolates from Canada and other countries was evaluated on 12 barley genotypes. Different virulence patterns were detected across B. sorokiniana isolates and eight virulence groups were identified using qualitative analysis of the virulence data. Results indicate broader virulence diversity in the pathogen population in the eastern prairie region of Canada, especially in Manitoba, compared with that previously reported. One group of isolates collected from Manitoba displayed a virulence pattern which had not been reported previously. This group was moderately virulent on most differential lines, including American six-rowed barley genotypes considered to possess durable resistance against B. sorokiniana. Although the classical method of pathotype identification can be exploited to analyze interactions in the barley-B. sorokiniana pathosystem, the continuous range of infection phenotypes found suggests that a quantitative analysis of the complex interactions occurring may be warranted.