bluuebunny/crossref_metadata_2025 huggingface dataset:
Chain-Type Wireless Sensor Network for Monitoring Long Range Infrastructures: Architecture and Protocols
Authors: Chen Chang Wen , Wang Yu
Published: October 2008

We present in this paper an investigation of a special class of wireless sensor networks for monitoring critical infrastructures that may extend for hundreds of miles in distances. Such networks are fundamentally different from traditional sensor networks in that the sensor nodes in this class of networks are deployed along narrowly elongated geographical areas and form a chain-type topology. Based on careful analysis of existing sensor network architectures, we first demonstrate the need to develop new architecture and networking protocols to match the unique topology of chain-type sensor networks. We then propose hierarchical network architecture that consists of clusters of sensor nodes to enable the chain-type sensor networks to be scalable to cover typically long range infrastructures with tolerable delay in network-wide data collection. To maintain energy efficient operations and maximize the lifetime for such a chain-type sensor network, we devise a smart strategy for the deployment of cluster heads. Protocols for network initialization and seamless operations of the chain-type sensor networks are also developed to match the proposed hierarchical architecture and cluster head deployment strategy. Simulations have been carried out to verify the performance of the hierarchical architecture, the smart node deployment strategy, and the corresponding network initialization and operation protocols.
The HECT E3 ligase Smurf2 is required for Mad2-dependent spindle assembly checkpoint
Authors: Osmundson Evan C. , Ray Dipankar , Moore Finola E. , Gao Qingshen , Thomsen Gerald H. , Kiyokawa Hiroaki
Published: October 2008

Activation of the anaphase-promoting complex/cyclosome (APC/C) by Cdc20 is critical for the metaphase–anaphase transition. APC/C-Cdc20 is required for polyubiquitination and degradation of securin and cyclin B at anaphase onset. The spindle assembly checkpoint delays APC/C-Cdc20 activation until all kinetochores attach to mitotic spindles. In this study, we demonstrate that a HECT (homologous to the E6-AP carboxyl terminus) ubiquitin ligase, Smurf2, is required for the spindle checkpoint. Smurf2 localizes to the centrosome, mitotic midbody, and centromeres. Smurf2 depletion or the expression of a catalytically inactive Smurf2 results in misaligned and lagging chromosomes, premature anaphase onset, and defective cytokinesis. Smurf2 inactivation prevents nocodazole-treated cells from accumulating cyclin B and securin and prometaphase arrest. The silencing of Cdc20 in Smurf2-depleted cells restores mitotic accumulation of cyclin B and securin. Smurf2 depletion results in enhanced polyubiquitination and degradation of Mad2, a critical checkpoint effector. Mad2 is mislocalized in Smurf2-depleted cells, suggesting that Smurf2 regulates the localization and stability of Mad2. These data indicate that Smurf2 is a novel mitotic regulator.
ODA16 aids axonemal outer row dynein assembly through an interaction with the intraflagellar transport machinery
Authors: Ahmed Noveera T. , Gao Chunlei , Lucker Ben F. , Cole Douglas G. , Mitchell David R.
Published: October 2008

Formation of flagellar outer dynein arms in Chlamydomonas reinhardtii requires the ODA16 protein at a previously uncharacterized assembly step. Here, we show that dynein extracted from wild-type axonemes can rebind to oda16 axonemes in vitro, and dynein in oda16 cytoplasmic extracts can bind to docking sites on pf28 (oda) axonemes, which is consistent with a role for ODA16 in dynein transport, rather than subunit preassembly or binding site formation. ODA16 localization resembles that seen for intraflagellar transport (IFT) proteins, and flagellar abundance of ODA16 depends on IFT. Yeast two-hybrid analysis with mammalian homologues identified an IFT complex B subunit, IFT46, as a directly interacting partner of ODA16. Interaction between Chlamydomonas ODA16 and IFT46 was confirmed through in vitro pull-down assays and coimmunoprecipitation from flagellar extracts. ODA16 appears to function as a cargo-specific adaptor between IFT particles and outer row dynein needed for efficient dynein transport into the flagellar compartment.
Uptake and recycling of pro-BDNF for transmitter-induced secretion by cortical astrocytes
Authors: Bergami Matteo , Santi Spartaco , Formaggio Elena , Cagnoli Cinzia , Verderio Claudia , Blum Robert , Berninger Benedikt , Matteoli Michela , Canossa Marco
Published: October 2008

Activity-dependent secretion of brain-derived neurotrophic factor (BDNF) is thought to enhance synaptic plasticity, but the mechanisms controlling extracellular availability and clearance of secreted BDNF are poorly understood. We show that BDNF is secreted in its precursor form (pro-BDNF) and is then cleared from the extracellular space through rapid uptake by nearby astrocytes after θ-burst stimulation in layer II/III of cortical slices, a paradigm resulting in long-term potentiation of synaptic transmission. Internalization of pro-BDNF occurs via the formation of a complex with the pan-neurotrophin receptor p75 and subsequent clathrin-dependent endocytosis. Fluorescence-tagged pro-BDNF and real-time total internal reflection fluorescence microscopy in cultured astrocytes is used to monitor single endocytic vesicles in response to the neurotransmitter glutamate. We find that endocytosed pro-BDNF is routed into a fast recycling pathway for subsequent soluble NSF attachment protein receptor–dependent secretion. Thus, astrocytes contain an endocytic compartment competent for pro-BDNF recycling, suggesting a specialized form of bidirectional communication between neurons and glia.
Stromal mesenteric lymph node cells are essential for the generation of gut-homing T cells in vivo
Authors: Hammerschmidt Swantje I. , Ahrendt Manuela , Bode Ulrike , Wahl Benjamin , Kremmer Elisabeth , Förster Reinhold , Pabst Oliver
Published: October 2008

T cells primed in the gut-draining mesenteric lymph nodes (mLN) are imprinted to express α4β7-integrin and chemokine receptor CCR9, thereby enabling lymphocytes to migrate to the small intestine. In vitro activation by intestinal dendritic cells (DC) or addition of retinoic acid (RA) is sufficient to instruct expression of these gut-homing molecules. We report that in vivo stroma cells, but not DC, allow the mLN to induce the generation of gut tropism. Peripheral LN (pLN) transplanted into the gut mesenteries fail to support the generation of gut-homing T cells, even though gut-derived DC enter the transplants and prime T cells. DC that fail to induce α4β7-integrin and CCR9 in vitro readily induce these factors in vivo upon injection into mLN afferent lymphatics. Moreover, uniquely mesenteric but not pLN stroma cells express high levels of RA-producing enzymes and support induction of CCR9 on activated T cells in vitro. These results demonstrate a hitherto unrecognized contribution of stromal cell delivered signals, including RA, on the imprinting of tissue tropism in vivo.
Regional CNS responses to IFN-γ determine lesion localization patterns during EAE pathogenesis
Authors: Lees Jason R. , Golumbek Paul T. , Sim Julia , Dorsey Denise , Russell John H.
Published: October 2008

The localization of inflammatory foci within the cerebellum is correlated to severe clinical outcomes in multiple sclerosis (MS). Previous studies of experimental autoimmune encephalomyelitis (EAE), a model of MS, revealed distinct clinical outcomes correlated with the capacity of the animal to produce IFN-γ. Outcomes were linked to localization of inflammatory cells in either the spinal cord (wild type [WT]) or the cerebellum and brain stem (IFN-γ deficient). We demonstrate, using an adoptive transfer system, that the ability of the central nervous system (CNS) to sense pathogenic T cell–produced IFN-γ during EAE initiation determines the sites of CNS pathogenesis. Transfer of WT Th1 cells into IFN-γ receptor–deficient mice results in pathogenic invasion of the brain stem and cerebellum with attendant clinical symptoms, which are identical to the disease observed after transfer of IFN-γ–deficient T cells to WT hosts. Inflammation of the spinal cord associated with classical EAE is abrogated in both IFN-γ–deficient systems. Cotransfer of CNS antigen-specific WT Th1 cells with IFN-γ–deficient T cells is sufficient to restore spinal cord invasion and block cerebellar and brain stem invasion. These data demonstrate that interaction between IFN-γ and host CNS cells during the initiation of EAE can selectively promote or suppress neuroinflammation and pathogenesis.
CXCL12 (SDF-1α) suppresses ongoing experimental autoimmune encephalomyelitis by selecting antigen-specific regulatory T cells
Authors: Meiron Moran , Zohar Yaniv , Anunu Rachel , Wildbaum Gizi , Karin Nathan
Published: October 2008

Experimental autoimmune encephalomyelitis (EAE) is a T cell–mediated autoimmune disease of the central nervous system induced by antigen-specific effector Th17 and Th1 cells. We show that a key chemokine, CXCL12 (stromal cell–derived factor 1α), redirects the polarization of effector Th1 cells into CD4+CD25−Foxp3−interleukin (IL) 10high antigen-specific regulatory T cells in a CXCR4-dependent manner, and by doing so acts as a regulatory mediator restraining the autoimmune inflammatory process. In an attempt to explore the therapeutic implication of these findings, we have generated a CXCL12-immunoglobulin (Ig) fusion protein that, when administered during ongoing EAE, rapidly suppresses the disease in wild-type but not IL-10–deficient mice. Anti–IL-10 neutralizing antibodies could reverse this suppression. The beneficial effect included selection of antigen-specific T cells that were CD4+CD25−Foxp3−IL-10high, which could adoptively transfer disease resistance, and suppression of Th17 selection. However, in vitro functional analysis of these cells suggested that, even though CXCL12-Ig–induced tolerance is IL-10 dependent, IL-10–independent mechanisms may also contribute to their regulatory function. Collectively, our results not only demonstrate, for the first time, that a chemokine functions as a regulatory mediator, but also suggest a novel way for treating multiple sclerosis and possibly other inflammatory autoimmune diseases.
The P2X7 Receptor Channel Pore Dilates under Physiological Ion Conditions
Authors: Yan Zonghe , Li Shuo , Liang Zhaodong , Tomić Melanija , Stojilkovic Stanko S.
Published: October 2008

Activation of the purinergic P2X7 receptor leads to the rapid opening of an integral ion channel that is permeable to small cations. This is followed by a gradual increase in permeability to fluorescent dyes by integrating the actions of the pannexin-1 channel. Here, we show that during the prolonged agonist application a rapid current that peaked within 200 ms was accompanied with a slower current that required tens of seconds to reach its peak. The secondary rise in current was observed under different ionic conditions and temporally coincided with the development of conductivity to larger organic cations. The biphasic response was also observed in cells with blocked pannexin channels and in cells not expressing these channels endogenously. The biphasic current was preserved in N-terminal T15A, T15S, and T15V mutants that have low or no permeability to organic cations, reflecting enhanced permeability to inorganic cations. In contrast, the T15E, T15K, and T15W mutants, and the Δ18 mutant with deleted P2X7 receptor–specific 18–amino acid C-terminal segment, were instantaneously permeable to organic cations and generated high amplitude monophasic currents. These results indicate that the P2X7 receptor channel dilates under physiological ion conditions, leading to generation of biphasic current, and that this process is controlled by residues near the intracellular side of the channel pore.
mspire: mass spectrometry proteomics in Ruby
Authors: Prince John T. , Marcotte Edward M.
Published: October 2008

Summary: Mass spectrometry-based proteomics stands to gain from additional analysis of its data, but its large, complex datasets make demands on speed and memory usage requiring special consideration from scripting languages. The software library ‘mspire’—developed in the Ruby programming language—offers quick and memory-efficient readers for standard xml proteomics formats, converters for intermediate file types in typical proteomics spectral-identification work flows (including the Bioworks .srf format), and modules for the calculation of peptide false identification rates.

Availability: Freely available at http://mspire.rubyforge.org. Additional data models, usage information, and methods available at http://bioinformatics.icmb.utexas.edu/mspire

Contact:  marcotte@icmb.utexas.edu
Rice Sheath Blight Disease Resistance Identified in Oryza spp. Accessions
Authors: Prasad B. , Eizenga G. C.
Published: October 2008

Oryza spp., wild relatives of cultivated rice (Oryza sativa), may contain novel resistance genes for sheath blight, caused by Rhizoctonia solani, that could be used to enhance resistance to this important disease in commercial rice. To identify resistant sources for sheath blight disease, 73 Oryza genotypes were evaluated with three different methods conducted in the greenhouse, growth chamber, or laboratory because there are significant limitations to screening wild Oryza spp. under field conditions. For the microchamber method, 4-week-old seedlings were inoculated with a potato dextrose agar plug containing mycelia, covered with a 2-liter soft drink bottle, and rated 1 week after inoculation. A detached-leaf method involved placing a potato dextrose agar plug containing mycelia on the abaxial surface of a leaf section that was cut from a 5-week-old plant and placed on moist filter paper in a petri dish under constant light, then evaluated after 72 h. For the toothpick inoculation method, toothpicks colonized with mycelia were placed in the leaf collar region of plants at the panicle initiation stage, plants were placed in a growth chamber, and disease symptoms were evaluated after 7 days. The microchamber method gave a more uniform, reproducible response, and was easier to use under greenhouse conditions. Seven Oryza spp. accessions were identified as moderately resistant with three accessions classified as O. nivara (IRGC104705, IRGC100898, and IRGC104443) and one each as O. barthii (IRGC100223), O. meridionalis (IRGC105306), O. nivara/O. sativa (IRGC100943), and O. officinalis (IRGC105979).
Effect of Transplant Age, Tobacco Cultivar, Acibenzolar-S-Methyl, and Imidacloprid on Tomato Spotted Wilt Infection in Flue-Cured Tobacco
Authors: Nischwitz C. , Csinos A. S. , Mullis S. W. , Hickman L. L. , Stevenson K. L. , Gitaitis R. D.
Published: October 2008

Tomato spotted wilt virus (TSWV) has become the most serious problem in flue-cured tobacco in Georgia and is a growing problem in other tobacco-growing areas in the United States. The effects of transplant age (6 to 10 weeks), tobacco cultivar (K-326 and NC-71), and preplant applications of acibenzolar-S-methyl (ASM) and the insecticide imidacloprid (IMD) were evaluated on levels of TSWV infection, number of symptomatic plants, and yield in field trials over 4 years. In all 4 years and in four of five trials, treatment of transplants with ASM and IMD resulted in fewer symptomatic plants, smaller areas under the disease progress curve (AUDPC), and higher yields compared with the nontreated controls. There were no consistent effects of transplant age or cultivar on number of symptomatic plants or systemic infections, AUDPC, or yield. Treatment of transplants with ASM and IMD can significantly reduce the number of symptomatic plants in the field and substantially increase yields and value per hectare.
Dose Response of Weed Seeds, Plant-Parasitic Nematodes, and Pathogens to Twelve Rates of Metam Sodium in a California Soil
Authors: Klose Susanne , Ajwa Husein A. , Browne Greg T. , Subbarao Krishna V. , Martin Frank N. , Fennimore Steve A. , Westerdahl Becky B.
Published: October 2008

Metam sodium (sodium N-methyl dithiocarbamate, metam-Na) is widely used in agricultural and floricultural production for controlling soilborne plant pathogens, parasitic nematodes, and weeds. It undergoes rapid decomposition to the biocide methyl isothiocyanate (MITC) in moist soils. In this study, the efficacy of 12 concentrations of metam-Na (10 to 2,650 μmol kg–1 soil) to control seeds or tubers of five major weed species, three soilborne pathogens, and one parasitic nematode was evaluated in a sandy loam soil under controlled conditions. Soils were exposed to the fumigant in microcosms for 24 h at 10 and 20°C. Generation and dissipation curves of MITC in soil under controlled conditions showed that MITC concentrations in soils were highest 2 h after metam-Na application and decreased steadily over the 24-h incubation period. After 24 h, remaining MITC concentrations in soil microcosms at 10 and 20°C were 53 and 38% of the original amount applied, respectively, indicating a 20% reduction in MITC dissipation at the lower soil temperature. Logistic dose-response models were used to estimate the effective concentration necessary to reduce soil pest viability by 50 (LC50) or 90 (LC90) percent under both temperatures. Seed of Portulaca oleracea, with LC90 values of ≤1,242 μmol kg–1 soil, was the most sensitive to soil fumigation with metam-Na, followed by Polygonum arenastrum with LC90 values of ≤1,922 μmol kg–1 soil. At 10°C fumigation temperature, metam-Na at the highest dose tested in this study, 2,650 μmol kg–1 soil, was not sufficient to achieve adequate control of Stellaria media and Malva parviflora seed and Cyperus esculentus tubers. Weed control efficacy (average reduction in LC90 values) of metam-Na was between 25 and 60% higher if soils were fumigated at 20°C compared with 10°C, with the exception of M. parviflora. Phytophthora cactorum and Pythium ultimum were more sensitive to soil fumigation with metam-Na (LC90 ≤ 165 μmol kg–1 soil) than Verticillium dahliae (LC90 ≤ 737 μmol kg–1 soil). The nematode Tylenchulus semipenetrans was highly sensitive to soil fumigation with metam-Na (LC90 ≤ 98 μmol kg–1 soil), and the efficacy of control increased by 30% if soil was fumigated at 20°C compared with 10°C. In this sandy loam soil, metam-Na at a concentration of 850 μmol kg–1 reduced the viability of Portulaca oleracea and Polygonum arenastrum seeds, C. esculentus tubers, and all soilborne pathogens and parasitic nematodes tested by 90% at 20°C after 24 h exposure. These results indicate that metam-Na can provide effective pest and disease control at maximum label rate for the commercial formulation, but there was a reduction in efficacy at low temperature.
Co-cultivation of ‘Candidatus Liberibacter asiaticus’ with Actinobacteria from Citrus with Huanglongbing
Authors: Davis Michael J. , Mondal Sachindra N. , Chen Huiqin , Rogers Michael E. , Brlansky Ronald H.
Published: October 2008

Huanglongbing (HLB), also known as citrus greening disease, is a devastating disease of citrus caused by phloem-limited bacteria that have not been grown in culture. Three species, ‘Candidatus Liberibacter asiaticus’, ‘Ca. L. africanus’, and ‘Ca. L. americanus’, are known. ‘Ca. L. asiaticus’ and its insect vector, the psyllid Diaphorina citri, have been recently introduced into Florida. We attempted to isolate ‘Ca. L. asiaticus’ using media formulations developed in response to the growth of another bacterium that appears to be related to the liberibacters based on 16S rRNA gene identities. Cultures were obtained that were polymerase chain reaction (PCR) positive for ‘Ca. L. asiaticus’. However, transmission electron microscope examination of the culture, PCR using generic primers, and sequencing of the PCR products revealed the presence of other bacteria in the cultures. These were actinobacteria related to Propionibacterium acnes based on 16S rRNA identities. The co-cultures remained after attempts to purify the cultures by single-colony isolation, suggesting that the bacteria might be mutually beneficial to each other in culture. The co-cultures have survived more than 10 weekly passages to fresh medium. PCR using P. acnes-specific primers indicated that actinobacteria are common inhabitants of citrus and psyllids, whether or not ‘Ca. L. asiaticus’ is present.
Select Calcium Compounds Reduce the Severity of Phytophthora Stem Rot of Soybean
Authors: Sugimoto T. , Watanabe K. , Yoshida S. , Aino M. , Irie K. , Matoh T. , Biggs A. R.
Published: October 2008

This study investigated the effects of several calcium compounds on Phytophthora stem rot of soybean (Glycine max) and fungal growth and zoospore release of a Phytophthora sojae isolate in vitro. All concentrations of five formulated calcium products [Ca(COOH)2-A, Ca(COOH)2-B, Ca(COOH)2-C, CaSO4-A, and CaCl2-A] and two chemical compounds [CaCl2 and Ca(NO3)2] applied prior to inoculation significantly suppressed disease incidence. Among all the products and chemicals, Ca(COOH)2-A was the most effective in suppressing the incidence of disease. In most cases, no significant relationship was observed between inhibition of growth rate in vitro and disease reduction in growth chamber tests. Therefore, disease suppression recorded in laboratory experiments using pathogen mycelium was likely due to the responses of plant tissues rather than the direct inhibition of pathogen fungal growth by the calcium compounds. The extent of disease reduction was related to increased calcium uptake by plants, suggesting that calcium was the effective element in reducing Phytophthora stem rot. Seedling tray experiments using zoospores indicated that the application of 10 mM Ca(COOH)2-A was more effective for reducing incidence of disease under growth chamber conditions, compared to other concentrations. The presence of 4 to 20 mM of all seven calcium solutions decreased the release of zoospores, although 0.4 mM of all compounds significantly increased zoospore release. Therefore, disease reduction in the growth-chamber experiments was due to the multiple effects of direct suppression on zoospore release and fungal growth in combination with the response of the host plant tissue to Ca(COOH)2-A.
Variation Within and BetweenVitisspp. for Foliar Resistance to the Downy Mildew PathogenPlasmopara viticola
Authors: Cadle-Davidson Lance
Published: October 2008

To complement existing control strategies, grape growers in humid climates desire cultivars with resistance to downy mildew caused by Plasmopara viticola. Numerous disease resistance screens of diverse Vitis germplasm have been conducted previously to identify downy mildew resistance; however, ratings of named cultivars were inconsistent and identities of resistant individuals in wild species were not typically provided. Inconsistencies among previous studies could be due to race-specific resistance. In the current study, controlled inoculations of two single isolates onto two leaf ages of 883 Vitis accessions were used and these results compared with natural infection in a fivefold replicated vineyard of 80 Vitis accessions in 2006 and 2007. Of the accessions rated in both assays, 16.2% were resistant to a single isolate but susceptible in the vineyard. Otherwise, there was good correlation of ratings between the field assay and the rating of older leaves (r = 0.62 to 0.71). Five accessions from Vitis cinerea, V. labrusca, and Vitis × champinii averaged zero severity in both vineyard years, yet some individuals of V. cinerea and V. labrusca were moderately or highly susceptible in the field. Similarly, although significant differences in mean severity separated V. vinifera, Vitis hybrid, V. riparia, and V. labrusca for single-isolate inoculations (from susceptible to resistant), notable intraspecies variation was identified for all well-represented species. Resistant individuals were identified in most species with the prominent exceptions of V. vinifera and V. acerifolia. Single-isolate, detached-leaf resistance ratings in 2006 corresponded well (94.6%) to 2007 ratings using a separate isolate collected from the same vineyard. Categorizing the ratings for this and previous studies, ratings infrequently corresponded among previous studies (31.9%) as well as between previous studies and the current single-isolate (34.9%) or vineyard (46.4%) ratings. These results highlight important factors for downy mildew resistance screens: leaf age, pathogen genotype, and host species and accession. The results further underscore the importance to breeders of uniform testing in multiple environments.
First Report of Brown Ring Patch Caused by Waitea circinata var. circinata on Poa trivialis in Florida
Authors: Flor N. , Harmon P. , Datnoff L. , Raid R. , Nagata R.
Published: October 2008

Brown ring patch is a newly described disease of cool-season turfgrass first reported in Japan on creeping bentgrass (Agrostis palustris) (2) and later reported in California on annual bluegrass (Poa annua) (1). The disease is characterized by either patches or rings of discolored to blighted turfgrass that can range from a few centimeters to a meter in diameter. Affected turfgrass plants turn chlorotic and can be blighted from the crown to the leaf tips. Blight symptoms have been associated with fluffy white-to-cream aerial mycelium after extended incubation of the sample. Symptoms including patches of blighted turfgrass approximately 10 cm in diameter were observed on roughstalk bluegrass (Poa trivialis) that had been overseeded onto a dormant ‘Tifdwarf’ bermudagrass (Cynodon dactylon) putting green in Palatka, FL. A sample was submitted by the superintendent in June 2005 because symptoms were confused with dollar spot and a fungicide resistance issue was suspected. The sample produced abundant aerial mycelium after incubation. The pathogen was isolated on potato dextrose agar amended with rifampicin (100 ppm) and streptomycin (100 ppm) from Poa plants surface disinfested with 70% ethanol for 30 s. Colony and sclerotia morphology were consistent with Waitea circinata var. circinata as previously described (1,2). The teleomorph W. circinata var. circinata was not observed on plant material or culture plates. Amplified fragments of rDNA including internal transcribed spacers from the isolate were sequenced bidirectionally from four bacterial clones. The consensus sequences (GenBank Accession Nos. FJ029103, FJ029104, FJ029105, and FJ029106) matched with 99% homology (99% sequence overlap) isolate TRGC1.1 of W. circinata var. circinata described by Wong, NCBI Accession No. DQ900586 (1). Pots of ‘Cypress’ roughstalk bluegrass that were 1 week postemergence were inoculated with the pathogen using 10 infested wheat grains. Plants were incubated at 25°C in a sealed plastic bag with a moist paper towel in the bottom. Hyphae grew from the grains and colonized the grass. Individual plants began to turn chlorotic within 3 days and greater than 90% of the turf in pots was dead after 1 week. The fungus was reisolated from affected plants. Control pots were inoculated with uninfested wheat grains and showed no disease symptoms after 1 week. Inoculations were repeated twice more with the same results. To our knowledge, this is the first report of brown ring patch on P. trivialis in Florida.

References: (1) K. A. de la Cerda et al. Plant Dis. 91:791, 2007. (2) T. Toda et al. Plant Dis. 89:536, 2005.
First Report of Leaf Blight of Chinese Ground Orchid (Phaius tankervilliae) Caused by Botrytis cinerea in India
Authors: Baiswar P. , Chandra S. , Kumar R. , Ngachan S. V. , Roy A. R. , Upadhayay D. N.
Published: October 2008

Chinese ground orchid (Phaius tankervilliae Banks:Blume) is a beautiful, terrestrial orchid, which belongs to the family Orchidaceae. It is used as a cut flower, which lasts for 4 to 5 weeks. This species is considered endangered and rare in nature. In June of 2007, potted plants of P. tankervilliae in Shillong, Meghalaya (northeast India; maximum temperature 24°C, minimum temperature 18°C, and 83.5% relative humidity) exhibited leaf blight. Symptoms included water-soaked lesions and dense, gray mold growing on infected tissues. Thirty-six percent of the plants surveyed were found to have this disease. For isolation, diseased tissue was surface disinfested by soaking it in 0.5% sodium hypochlorite for 1 min, air dried, plated on potato dextrose agar, and incubated at 20°C. Mycelia were initially white but later turned gray. Mature, unicellular, ellipsoid, hyaline conidia (6.3 to 8.2 × 9.6 to 11.4 μm) were formed in botryose heads. Hard, black, irregular-shaped sclerotia (average size 1.8 × 2.3 mm) were formed after 15 days. On the basis of these morphological characters, the pathogen was identified as Botrytis cinerea Pers.:Fr. (1). Pathogenicity was confirmed by spraying plants with a spore suspension (106 spores per ml), which were then maintained under high humidity for 48 h at 20 to 22°C by covering with cheesecloth. Five potted plants were inoculated and five were sprayed with sterile water. Lesions and spore masses that were identical to those observed appeared 5 to 6 days after inoculation. Water-treated control plants remained asymptomatic. B. cinerea was reisolated from inoculated plants. A literature search revealed no previous record of this disease in India. So, to our knowledge, this is the first record of B. cinerea on P. tankervilliae in India.

References: (1) M. B. Ellis. Dematiaceous Hyphomycetes. CMI, Kew, Surrey, England, 1971.
First Report of Fusarium Head Blight on Winter Wheat in the Grand Duchy of Luxembourg
Authors: Giraud F. , Vrancken C. , Delfosse P. , Bohn T. , Hoffmann L. , Munaut F. , El Jarroudi M.
Published: October 2008

Following a comparatively mild winter (1.9°C above average [2000–2007]), Fusarium head blight (FHB) on winter wheat was observed during the 2007 season in 17 sites representing all three districts of Diekirch, Grevenmacher, and Luxembourg. The cultivars encountered were diverse and included Achat, Akteur, Aron, Bussard, Cubus, Enorm, Exclusiv, Flair, Rosario, Tommi, and Urban. The preceding crops were maize (six sites), rapeseed (three sites), and one site each of pea, triticale, winter barley, and winter wheat. Rainfalls recorded during the flowering period (June 1–23, mean June 12 for GS 65) ranged from 13 to 62 (mean 38) mm. An overall prevalence of FHB (percentage of infected spikes) of 8.9 ± 15.5% (mean ± SD) and a severity (percentage of infected grains per spike) of 21.0 ± 17.8% were recorded. A significant difference in FHB severity was observed between the cantons north and south of Luxembourg City, 13.4 ± 13.1% (range 0.01 to 46.4) and 35.1 ± 18.1% (range 6.2 to 61.9), respectively (Man-Whitney, P = 0.027), indicating the importance to take regional specificities such as topoclimatological aspects into account. Maize as a preceding crop resulted in significant higher prevalence of FHB as opposed to the other crops (5.9 ± 1.6% versus 3.3 ± 2.2%, Man-Whitney, P = 0.022).
First Report of Soybean Rust Caused by Phakopsora pachyrhizi in Nebraska
Authors: Watson S. R. , Giesler L. J. , Ziems A. D. , Brovont T. E.
Published: October 2008

Soybean rust caused by Phakopsora pachyrhizi Sydow was first observed in the continental United States in Louisiana in November 2004 (2). As part of the national soybean rust monitoring effort, samples were collected on 3 October 2007 during the scouting of fields with green leaves in southeastern Nebraska. After incubation at room temperature for 24 h, uredinea and urediniospores were observed with microscopic examination. Urediniospores were obovoid, hyaline to pale brown, and measured 20 to 30 × 18 to 20 μm. The observed morphology was typical of P. pachyrhizi (1). In addition to microscopic observation, P. pachyrhizi was confirmed with real-time (q)-PCR with Taq DNA polymerase on 4 October 2007 with the q-PCR standard operating procedure version 1.9 outlined by the USDA-CSREES and utilized by the National Plant Diagnostic Network with appropriate positive and negative controls (1). Samples initially identified with soybean rust were from Richardson County near the town of Rulo and in Otoe County south of Nebraska City. On 12 October 2007, soybean rust was confirmed in adjacent Pawnee and Nemaha counties. Soybean rust was identified in six fields with an incidence and severity of less than 1%. In fields where the disease was identified, the disease was distributed in low-lying, shaded areas near wind breaks. Although soybean rust was detected in four southeastern Nebraska counties, soybean yields were not affected by the disease. At the time of first detection, more than 80% of the Nebraska soybean crop was harvested. To our knowledge, this is the first report of P. pachyrhizi on soybeans in Nebraska, and currently, the northwestern most find on any host in the continental United States.

References: (1) R. D. Frederick et al. Phytopathology 92:217, 2002. (2) R. W. Schneider et al. Plant Dis. 89:774, 2005.
First Report of Cherry virus A in Prunus mume in China
Authors: Marais A. , Faure C. , Svanella-Dumas L. , Candresse T.
Published: October 2008

Natural infections of Cherry virus A (CVA) have been reported in sweet (Prunus avium) and sour cherry (P. cerasus) from a number of European countries, North America, and Japan. CVA has been detected occasionally in other Prunus hosts such as peach, plum, and apricot (1). In the spring of 2007, samples from four Japanese apricot (Prunus mume) trees from the Jiangsu Province of China were analyzed by a polyvalent reverse transcriptase-PCR assay that amplifies a short region of the polymerase gene of viruses from several genera in the family Flexiviridae (2). Sequencing of the amplified products identified CVA in three samples. Two isolates (GenBank Accession Nos. EU730949 and EU730950) were closely related and highly homologous (97.5 to 99.3% identity) to noncherry isolates of CVA (GenBank Accession Nos AY792509 and DQ445275 to DQ445292). The third isolate (GenBank Accession No. EU730951) was approximately 90% identical to the other P. mume isolates and showed the highest identity (92.3%) to a cherry isolate (GenBank Accession No AF413923). CVA infection of the P. mume samples was confirmed by two CVA-specific primer pairs targeting genomic regions corresponding to the movement or coat protein genes. Since the samples showed mixed infections with Plum pox virus (PPV) or Asian Prunus virus 1 (APV1), potential CVA symptomatology could not be evaluated. To our knowledge, these results are the first identification of CVA in China and in P. mume, extending the geographical distribution and natural host range of this virus. Additional work is needed to evaluate whether CVA poses a threat to P. mume production or whether, as in other identified hosts, CVA is largely latent.

References: (1) M. Barone et al. Plant Dis. 90:1459, 2006. (2) X. Foissac et al. Phytopathology 95:617, 2005.
An Englishman abroad: Charles Blagden's visit to Paris in 1783
Authors: Fauque Danielle M.E
Published: October 2008

Once the preliminaries of peace had been signed in January 1783, after the war of American independence, exchanges between British and French men of science resumed their normal course. On a visit to Paris in 1783, the francophile Charles Blagden (with the encouragement of Joseph Banks) made a number of contacts that fostered relations between the Royal Society and the Académie royale des sciences. In the course of this and several subsequent visits to France, Blagden became especially intimate with the chemist Claude-Louis Berthollet. His correspondence, now in the Royal Society, is a rich source for our understanding of some of the leading scientific debates of the day, in particular concerning the nature of water, which forms the main subject of this article.
Surface temperatures of the Mid-Pliocene North Atlantic Ocean: implications for future climate
Authors: Dowsett Harry J , Chandler Mark A , Robinson Marci M
Published: October 2008

The Mid-Pliocene is the most recent interval in the Earth's history to have experienced warming of the magnitude predicted for the second half of the twenty-first century and is, therefore, a possible analogue for future climate conditions. With continents basically in their current positions and atmospheric CO2similar to early twenty-first century values, the cause of Mid-Pliocene warmth remains elusive. Understanding the behaviour of the North Atlantic Ocean during the Mid-Pliocene is integral to evaluating future climate scenarios owing to its role in deep water formation and its sensitivity to climate change. Under the framework of the Pliocene Research, Interpretation and Synoptic Mapping (PRISM) sea surface reconstruction, we synthesize Mid-Pliocene North Atlantic studies by PRISM members and others, describing each region of the North Atlantic in terms of palaeoceanography. We then relate Mid-Pliocene sea surface conditions to expectations of future warming. The results of the data and climate model comparisons suggest that the North Atlantic is more sensitive to climate change than is suggested by climate model simulations, raising the concern that estimates of future climate change are conservative.
The Arctic cryosphere in the Mid-Pliocene and the future
Authors: Lunt Daniel J , Haywood Alan M , Foster Gavin L , Stone Emma J
Published: October 2008

The Mid-Pliocene (
ca
3 Myr ago) was a relatively warm period, with increased atmospheric CO
2
relative to pre-industrial. It has therefore been highlighted as a possible palaeo-analogue for the future. However, changed vegetation patterns, orography and smaller ice sheets also influenced the Mid-Pliocene climate. Here, using a general circulation model and ice-sheet model, we determine the relative contribution of vegetation and soils, orography and ice, and CO
2
to the Mid-Pliocene Arctic climate and cryosphere. Compared with pre-industrial, we find that increased Mid-Pliocene CO
2
contributes 35 per cent, lower orography and ice-sheet feedbacks contribute 42 per cent, and vegetation changes contribute 23 per cent of Arctic temperature change. The simulated Mid-Pliocene Greenland ice sheet is substantially smaller than that of modern, mostly due to the higher CO
2
. However, our simulations of future climate change indicate that the same increase in CO
2
is not sufficient to melt the modern ice sheet substantially. We conclude that, although the Mid-Pliocene resembles the future in some respects, care must be taken when interpreting it as an exact analogue due to vegetation and ice-sheet feedbacks. These act to intensify Mid-Pliocene Arctic climate change, and act on a longer time scale than the century scale usually addressed in future climate prediction.
Constraints on the amplitude of Mid-Pliocene (3.6–2.4 Ma) eustatic sea-level fluctuations from the New Zealand shallow-marine sediment record
Authors: Naish Tim R , Wilson Gary S
Published: October 2008

Ice-volume calibrations of the deep-ocean foraminiferal δ
18
O record imply orbitally influenced sea-level fluctuations of up to 30 m amplitude during the Mid-Pliocene, and up to 30 per cent loss of the present-day mass of the East Antarctic Ice Sheet (EAIS) assuming complete deglaciation of the West Antarctic Ice Sheet (WAIS) and Greenland. These sea-level oscillations have driven recurrent transgressions and regressions across the world's continental shelves. Wanganui Basin, New Zealand, contains the most complete shallow-marine Late Neogene stratigraphic record in the form of a continuous cyclostratigraphy representing every 41 and 100 ka sea-level cycle since
ca
3.6 Ma. This paper presents a synthesis of faunally derived palaeobathymetric data for shallow-marine sedimentary cycles corresponding to marine isotope stages M2–100 (
ca
3.4–2.4 Ma). Our approach estimates the eustatic sea-level contribution to the palaeobathymetry curve by placing constraints on total subsidence and decompacted sediment accumulation. The sea-level estimates are consistent with those from δ
18
O curves and numerical ice sheet models, and imply a significant sensitivity of the WAIS and the coastal margins of the EAIS to orbital oscillations in insolation during the Mid-Pliocene period of relative global warmth. Sea-level oscillations of 10–30 m were paced by obliquity.
The origin of the prion agent of kuru: molecular and biological strain typing
Authors: Wadsworth Jonathan D.F , Joiner Susan , Linehan Jacqueline M , Asante Emmanuel A , Brandner Sebastian , Collinge John
Published: October 2008

Kuru is an acquired human prion disease that primarily affected the Fore linguistic group of the Eastern Highlands of Papua New Guinea. The central clinical feature of kuru is progressive cerebellar ataxia and, in sharp contrast to most cases of sporadic Creutzfeldt–Jakob disease (CJD), dementia is a less prominent and usually late clinical feature. In this regard, kuru is more similar to variant CJD, which also has similar prodromal symptoms of sensory disturbance and joint pains in the legs and psychiatric and behavioural changes. Since a significant part of the clinicopathological diversity seen in human prion disease is likely to relate to the propagation of distinct human prion strains, we have compared the transmission properties of kuru prions with those isolated from patients with sporadic, iatrogenic and variant CJD in both transgenic and wild-type mice. These data have established that kuru prions have prion strain properties equivalent to those of classical (sporadic and iatrogenic) CJD prions but distinct from variant CJD prions. Here, we review these findings and discuss how peripheral routes of infection and other factors may be critical modifiers of the kuru phenotype.
Lessons of kuru research: background to recent studies with some personal reflections
Authors: Collinge John
Published: October 2008

The widespread exposure of the UK population to bovine spongiform encephalopathy prions, and the potential consequences for public health, led to a renewed interest in kuru, the principal example of epidemic human prion disease. Kuru research in Papua New Guinea was expanded to study the range of incubation periods possible in human prion infection, to investigate maternal and other possible natural routes of transmission, to characterize genetic susceptibility and resistance factors and to gain insights into the peripheral pathogenesis of orally acquired prion disease in humans. Although now essentially over, the kuru epidemic continues to provide important lessons.
Dealing with incongruence in phylogenomic analyses
Authors: Galtier Nicolas , Daubin Vincent
Published: October 2008

Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent. We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.
Fast phylogenetic DNA barcoding
Authors: Munch Kasper , Boomsma Wouter , Willerslev Eske , Nielsen Rasmus
Published: October 2008

We present a heuristic approach to the DNA assignment problem based on phylogenetic inferences using constrained neighbour joining and non-parametric bootstrapping. We show that this method performs as well as the more computationally intensive full Bayesian approach in an analysis of 500 insect DNA sequences obtained from GenBank. We also analyse a previously published dataset of environmental DNA sequences from soil from New Zealand and Siberia, and use these data to illustrate the fact that statistical approaches to the DNA assignment problem allow for more appropriate criteria for determining the taxonomic level at which a particular DNA sequence can be assigned.
RhoC is essential for angiogenesis induced by hepatocellular carcinoma cells via regulation of endothelial cell organization
Authors: Wang Wei , Wu Fan , Fang Feng , Tao Yiming , Yang Lianyue
Published: October 2008

The angiogenesis induced by tumor cells is essential for metastasis of hepatocellular carcinoma. Available information suggests that RhoC participates in angiogenesis through regulation of vascular endothelial growth factor expression in tumor cells. For its broad functions in cell migration and cytoskeletal organization, we hypothesized that RhoC regulating angiogenesis does not exclusively depend on regulation of vascular endothelial growth factor expression. To address this question, in the present study, we used a retroviral small interfering RNA approach to selectively knockdown the expression of RhoC in a neovascularization model in vivo and in vitro. Our present results indicate that RhoC is the downstream regulator of vascular endothelial growth factor in endothelial cells and is essential for angiogenesis induced by vascular endothelial growth factor, notwithstanding that RhoC regulates the expression of vascular endothelial growth factor in tumor cells. Furthermore, we show that knockdown of RhoC is associated with the inhibition of invasion and migration but not apoptosis of endothelial cells. Knockdown of RhoC results in inhibition of endothelial cell organization through restraining the reorganization of F‐actin filaments, which represses endothelial cell network and sprout formation. In conclusion, our results demonstrate that knockdown of RhoC inhibits angiogenesis induced by tumor cells not only through effecting the release of vascular endothelial growth factor, but also through inhibiting endothelial cell migration and organization, which implies that it blocks tumor metastasis by specifically inhibiting RhoC in endothelial cells. (Cancer Sci 2008; 99: 2012–2018)
Antisense hypoxia‐inducible factor 1α gene therapy enhances the therapeutic efficacy of doxorubicin to combat hepatocellular carcinoma
Authors: Liu Fengjun , Wang Peijun , Jiang Xian , Tan Gang , Qiao Haiquan , Jiang Hongchi , Krissansen Geoffrey W. , Sun Xueying
Published: October 2008

Hepatocellular carcinoma (HCC), one of the most common cancers worldwide, is resistant to anticancer drugs. Hypoxia is a major cause of tumor resistance to chemotherapy, and hypoxia‐inducible factor (HIF)‐1 is a key transcription factor in hypoxic responses. We have previously demonstrated that gene transfer of an antisense HIF‐1α expression vector downregulates expression of HIF‐1α and vascular endothelial growth factor (VEGF), and synergizes with immunotherapy to eradicate lymphomas. The aim of the present study was to determine whether gene transfer of antisense HIF‐1α could enhance the therapeutic efficacy of doxorubicin to combat HCC. Both antisense HIF‐1α therapy and doxorubicin suppressed the growth of subcutaneous human HepG2 tumors established in BALB/c nude mice, tumor angiogenesis, and cell proliferation, and induced tumor cell apoptosis. The combination therapy with antisense HIF‐1α and doxorubicin was more effective in suppressing tumor growth, angiogenesis, and cell proliferation, and inducing cell apoptosis than the respective monotherapies. Gene transfer of antisense HIF‐1α downregulated the expression of both HIF‐1α and VEGF, whereas doxorubicin only downregulated VEGF expression. Antisense HIF‐1α and doxorubicin synergized to downregulate VEGF expression. Both antisense HIF‐1α and doxorubicin inhibited expression of proliferating cell nuclear antigen, and combined to exert even stronger inhibition of proliferating cell nuclear antigen expression. Antisense HIF‐1α therapy warrants investigation as a therapeutic strategy to enhance the efficacy of doxorubicin for treating HCC. (Cancer Sci 2008; 99: 2055–2061)