bluuebunny/crossref_metadata_2025 huggingface dataset:
A melting model for variably depleted and enriched lherzolite in the plagioclase and spinel stability fields
Authors: Till Christy B. , Grove Timothy L. , Krawczynski Michael J.
Published: May 2012

Here we develop a lherzolite melting model and explore the effects of variations in mantle composition, pressure, temperature, and H2O content on melt composition. New experiments and a compilation of experimental liquids saturated with all of the mantle minerals (olivine, orthopyroxene, clinopyroxene, plagioclase and/or spinel) are used to calibrate a model that predicts the temperature and major element composition of a broad spectrum of primary basalt types produced under anhydrous to low H2O‐content conditions at upper mantle pressures. The model can also be used to calculate the temperature and pressure at which primary magmas were produced in the mantle, as well as to model both near‐fractional adiabatic decompression and batch melting. Our experimental compilation locates the pressure interval of the plagioclase to spinel transition on the solidus and shows that it is narrow (∼0.1 GPa) for melting of natural peridotite compositions. The multiple saturation boundaries determined by our model provide a method for assessing the appropriate mineral assemblage, as well as the extent of the fractional crystallization correction required to return a relatively primitive liquid to equilibrium with the mantle source. We demonstrate that an inaccurate fractionation correction can overestimate temperature and depths of melting by hundreds of degrees and tens of kilometers, respectively. This model is particularly well suited to examining the temperature and pressure of origin for intraplate basaltic volcanism and is used to examine the petrogenesis of a suite of Holocene basaltic lavas from Diamond Crater in Oregon's High Lava Plains (HLP).
Evapotranspiration: A process driving mass transport and energy exchange in the soil‐plant‐atmosphere‐climate system
Authors: Katul Gabriel G. , Oren Ram , Manzoni Stefano , Higgins Chad , Parlange Marc B.
Published: May 2012

The role of evapotranspiration (ET) in the global, continental, regional, and local water cycles is reviewed. Elevated atmospheric CO2, air temperature, vapor pressure deficit (D), turbulent transport, radiative transfer, and reduced soil moisture all impact biotic and abiotic processes controlling ET that must be extrapolated to large scales. Suggesting a blueprint to achieve this link is the main compass of this review. Leaf‐scale transpiration (fe) as governed by the plant biochemical demand for CO2 is first considered. When this biochemical demand is combined with mass transfer formulations, the problem remains mathematically intractable, requiring additional assumptions. A mathematical “closure” that assumes stomatal aperture is autonomously regulated so as to maximize the leaf carbon gain while minimizing water loss is proposed, which leads to analytical expressions for leaf‐scale transpiration. This formulation predicts well the effects of elevated atmospheric CO2 and increases in D on fe. The case of soil moisture stress is then considered using extensive gas exchange measurements collected in drought studies. Upscaling the fe to the canopy is then discussed at multiple time scales. The impact of limited soil water availability within the rooting zone on the upscaled ET as well as some plant strategies to cope with prolonged soil moisture stress are briefly presented. Moving further up in direction and scale, the soil‐plant system is then embedded within the atmospheric boundary layer, where the influence of soil moisture on rainfall is outlined. The review concludes by discussing outstanding challenges and how to tackle them by means of novel theoretical, numerical, and experimental approaches.
The formation of Valles Marineris: 3. Trough formation through super‐isostasy, stress, sedimentation, and subsidence
Authors: Andrews‐Hanna Jeffrey C.
Published: May 2012

Despite the enormous size of the Valles Marineris chasmata on Mars, the mechanism responsible for the formation of these unique troughs remains unknown. Previous studies proposed mechanisms of trough formation through extensional tectonism, vertical collapse into subsurface voids, or some combination of the two. Recent work in a pair of companion papers demonstrated that the troughs must have formed dominantly by vertical subsidence with little net horizontal extension, and that the modest extension required likely arose from the effect of the buried dichotomy boundary beneath Tharsis. This study now proposes a new mechanism of Valles Marineris formation, with a focus on the large‐scale geodynamic and tectonic processes. Prior to the formation of Valles Marineris, the lithosphere within Tharsis was maintained in a super‐isostatic state by the membrane‐flexural support of the rise. Local moderate extension at Valles Marineris controlled subsequent intrusive activity, resulting in the emplacement of long parallel dikes. This intrusive activity weakened the lithosphere, effectively removing the flexural support from long lithospheric blocks. Left unsupported, these blocks would have subsided approximately 0.49 ± 0.32 km to their isostatic level. The total subsidence would have been increased to 8.6 ± 5.6 km by the effects of contemporaneous sedimentary loading within the troughs and viscous deformation at the base of the crust. This mechanism successfully predicts the observed depths of the Valles Marineris chasmata, and is consistent with all geological and geophysical observations. The unique nature of Valles Marineris is explained as a result of the unique geodynamic and tectonic environment of Tharsis.
Biochemical and biosynthetic preparation of natural product-like cyclic peptide libraries
Authors: Bowers Albert A.
Published: May 2012

Natural product gene clusters are increasingly being used to compliment biochemical methods for production of cyclic peptide libraries.
The Effects of Distractors in Multiple Object Tracking are Modulated by the Similarity of Distractor and Target Features
Authors: Feria Cary S
Published: May 2012

Is the effect of distractors in multiple object tracking dependent on the distractors sharing the features of the targets? In experiment 1, observers tracked five targets among five distractors that were identical to the targets and a number of additional distractors that were either identical to or featurally distinct from the targets. Results showed that distractors that are distinct from the targets in shape or color, or are stationary, impair tracking less than distractors that are identical to the targets. However, tracking performance declined as the number of distractors increased, even for featurally distinct distractors. Experiment 2 showed that distractors that differ from the targets on two features impair tracking less than distractors that differ from the targets on only one feature, but only when target tracking load is low. These results indicate that shape, color, and motion information about distractors can be used to distinguish them from targets during tracking, although even distractors with a different feature from the targets produce some interference with tracking. These findings suggest that the effect of distractors on tracking is dependent on top–down settings for target features.
Cross-Modality Correspondence between Pitch and Spatial Location Modulates Attentional Orienting
Authors: Chiou Rocco , Rich Anina N
Published: May 2012

The brain constantly integrates incoming signals across the senses to form a cohesive view of the world. Most studies on multisensory integration concern the roles of spatial and temporal parameters. However, recent findings suggest cross-modal correspondences (eg high-pitched sounds associated with bright, small objects located high up) also affect multisensory integration. Here, we focus on the association between auditory pitch and spatial location. Surprisingly little is known about the cognitive and perceptual roots of this phenomenon, despite its long use in ergonomic design. In a series of experiments, we explore how this cross-modal mapping affects the allocation of attention with an attentional cuing paradigm. Our results demonstrate that high and low tones induce attention shifts to upper or lower locations, depending on pitch height. Furthermore, this pitch-induced cuing effect is susceptible to contextual manipulations and volitional control. These findings suggest the cross-modal interaction between pitch and location originates from an attentional level rather than from response mapping alone. The flexible contextual mapping between pitch and location, as well as its susceptibility to top–down control, suggests the pitch-induced cuing effect is primarily mediated by cognitive processes after initial sensory encoding and occurs at a relatively late stage of voluntary attention orienting.
Identification of Chinese plague foci from long-term epidemiological data
Authors: Ben-Ari Tamara , Neerinckx Simon , Agier Lydiane , Cazelles Bernard , Xu Lei , Zhang Zhibin , Fang Xiye , Wang Shuchun , Liu Qiyong , Stenseth Nils C.
Published: May 2012

Carrying out statistical analysis over an extensive dataset of human plague reports in Chinese villages from 1772 to 1964, we identified plague endemic territories in China (i.e., plague foci). Analyses rely on (
i
) a clustering method that groups time series based on their time-frequency resemblances and (
ii
) an ecological niche model that helps identify plague suitable territories characterized by value ranges for a set of predefined environmental variables. Results from both statistical tools indicate the existence of two disconnected plague territories corresponding to Northern and Southern China. Altogether, at least four well defined independent foci are identified. Their contours compare favorably with field observations. Potential and limitations of inferring plague foci and dynamics using epidemiological data is discussed.
RNA surveillance is required for endoplasmic reticulum homeostasis
Authors: Sakaki Kenjiro , Yoshina Sawako , Shen Xiaohua , Han Jaeseok , DeSantis Melinda R. , Xiong Mon , Mitani Shohei , Kaufman Randal J.
Published: May 2012

The unfolded protein response (UPR) is an intracellular stress-signaling pathway that counteracts the accumulation of misfolded proteins in the endoplasmic reticulum (ER). Because defects in ER protein folding are associated with many pathological states, including metabolic, neurologic, genetic, and inflammatory diseases, it is important to understand how the UPR maintains ER protein-folding homeostasis. All metazoans have conserved the fundamental UPR transducers IRE1, ATF6, and PERK. In
Caenorhabditis elegans
, the UPR is required to prevent larval lethality and intestinal degeneration. Although
ire-1
-null worms are viable, they are particularly sensitive to ER stress. To identify genes that are required for development of
ire-1
-null worms, we performed a comprehensive RNA interference screen to find 10 genes that exhibit synthetic growth and intestinal defects with the
ire-1(v33)
mutant but not with
atf-6(tm1153)
or
pek-1(ok275)
mutants. The expression of two of these genes,
exos-3
and
F48E8.6
, was induced by ER stress, and their knockdown in a wild-type strain caused ER stress. Because these genes encode subunits of the exosome complex that functions in mRNA surveillance, we analyzed other gene products required for nonsense-mediated mRNA decay (NMD). Our results demonstrate that defects in
smg-1
,
smg-4
, and
smg-6
in
C. elegans
and
SMG6
in mammalian cells cause ER stress and sensitize to the lethal effects of ER stress. Although ER stress did not activate mRNA surveillance complex assembly, ER stress did induce SMG6 expression, and NMD regulators were constitutively localized to the ER. Importantly, the findings demonstrate a unique and fundamental interaction where NMD-mediated mRNA quality control is required to prevent ER stress.
Allosteric inhibition of individual enzyme molecules trapped in lipid vesicles
Authors: Piwonski Hubert M. , Goomanovsky Mila , Bensimon David , Horovitz Amnon , Haran Gilad
Published: May 2012

Enzymatic inhibition by product molecules is an important and widespread phenomenon. We describe an approach to study product inhibition at the single-molecule level. Individual HRP molecules are trapped within surface-tethered lipid vesicles, and their reaction with a fluorogenic substrate is probed. While the substrate readily penetrates into the vesicles, the charged product (resorufin) gets trapped and accumulates inside the vesicles. Surprisingly, individual enzyme molecules are found to stall when a few tens of product molecules accumulate. Bulk enzymology experiments verify that the enzyme is noncompetitively inhibited by resorufin. The initial reaction velocity of individual enzyme molecules and the number of product molecules required for their complete inhibition are broadly distributed and dynamically disordered. The two seemingly unrelated parameters, however, are found to be substantially correlated with each other in each enzyme molecule and over long times. These results suggest that, as a way to counter disorder, enzymes have evolved the means to correlate fluctuations at structurally distinct functional sites.
Design principles of cell circuits with paradoxical components
Authors: Hart Yuval , Antebi Yaron E. , Mayo Avraham E. , Friedman Nir , Alon Uri
Published: May 2012

Biological systems display complex networks of interactions both at the level of molecules inside the cell and at the level of interactions between cells. Networks of interacting molecules, such as transcription networks, have been shown to be composed of recurring circuits called network motifs, each with specific dynamical functions. Much less is known about the possibility of such circuit analysis in networks made of communicating cells. Here, we study models of circuits in which a few cell types interact by means of signaling molecules. We consider circuits of cells with architectures that seem to recur in immunology. An intriguing feature of these circuits is their use of signaling molecules with a pleiotropic or paradoxical role, such as cytokines that increase both cell growth and cell death. We find that pleiotropic signaling molecules can provide cell circuits with systems-level functions. These functions include for different circuits maintenance of homeostatic cell concentrations, robust regulation of differentiation processes, and robust pulses of cells or cytokines.
Organization, dynamics, and segregation of Ras nanoclusters in membrane domains
Authors: Janosi Lorant , Li Zhenlong , Hancock John F. , Gorfe Alemayehu A.
Published: May 2012

Recent experiments have shown that membrane-bound Ras proteins form transient, nanoscale signaling platforms that play a crucial role in high-fidelity signal transmission. However, a detailed characterization of these dynamic proteolipid substructures by high-resolution experimental techniques remains elusive. Here we use extensive semiatomic simulations to reveal the molecular basis for the formation and domain-specific distribution of Ras nanoclusters. As model systems, we chose the triply lipidated membrane targeting motif of H-ras (tH) and a large bilayer made up of di16∶0-PC (DPPC), di18∶2-PC (DLiPC), and cholesterol. We found that 4–10 tH molecules assemble into clusters that undergo molecular exchange in the sub-μs to μs time scale, depending on the simulation temperature and hence the stability of lipid domains. Driven by the opposite preference of tH palmitoyls and farnesyl for ordered and disordered membrane domains, clustered tH molecules segregate to the boundary of lipid domains. Additionally, a systematic analysis of depalmitoylated and defarnesylated tH variants allowed us to decipher the role of individual lipid modifications in domain-specific nanocluster localization and thereby explain why homologous Ras isoforms form nonoverlapping nanoclusters. Moreover, the localization of tH nanoclusters at domain boundaries resulted in a significantly lower line tension and increased membrane curvature. Taken together, these results provide a unique mechanistic insight into how protein assembly promoted by lipid-modification modulates bilayer shape to generate functional signaling platforms.
W chromosome expression responds to female-specific selection
Authors: Moghadam Hooman K. , Pointer Marie A. , Wright Alison E. , Berlin Sofia , Mank Judith E.
Published: May 2012

The W chromosome is predicted to be subject to strong female-specific selection stemming from its female-limited inheritance and therefore should play an important role in female fitness traits. However, the overall importance of directional selection in shaping the W chromosome is unknown because of the powerful degradative forces that act to decay the nonrecombining sections of the genome. Here we greatly expand the number of known W-linked genes and assess the expression of the W chromosome after >100 generations of different female-specific selection regimens in different breeds of chicken and in the wild ancestor, the Red Jungle Fowl. Our results indicate that female-specific selection has a significant effect on W chromosome gene-expression patterns, with a strong convergent pattern of up-regulation associated with increased female-specific selection. Many of the transcriptional changes in the female-selected breeds are the product of positive selection, suggesting that selection is an important force in shaping the evolution of gene expression on the W chromosome, a finding consistent with both the importance of the W chromosome in female fertility and the haploid nature of the W. Taken together, these data provide evidence for the importance of the sex-limited chromosome in a female heterogametic species and show that sex-specific selection can act to preserve sex-limited chromosomes from degrading forces.
Wnt signaling induces proliferation of sensory precursors in the postnatal mouse cochlea
Authors: Chai Renjie , Kuo Bryan , Wang Tian , Liaw Eric J. , Xia Anping , Jan Taha A. , Liu Zhiyong , Taketo Makoto M. , Oghalai John S. , Nusse Roeland , Zuo Jian , Cheng Alan G.
Published: May 2012

Inner ear hair cells are specialized sensory cells essential for auditory function. Previous studies have shown that the sensory epithelium is postmitotic, but it harbors cells that can behave as progenitor cells in vitro, including the ability to form new hair cells.
Lgr5
, a Wnt target gene, marks distinct supporting cell types in the neonatal cochlea. Here, we tested the hypothesis that Lgr5
+
cells are Wnt-responsive sensory precursor cells. In contrast to their quiescent in vivo behavior, Lgr5
+
cells isolated by flow cytometry from neonatal

Lgr5
EGFP-CreERT2/+

mice proliferated and formed clonal colonies. After 10 d in culture, new sensory cells formed and displayed specific hair cell markers (myo7a, calretinin, parvalbumin, myo6) and stereocilia-like structures expressing F-actin and espin. In comparison with other supporting cells, Lgr5
+
cells were enriched precursors to myo7a
+
cells, most of which formed without mitotic division. Treatment with Wnt agonists increased proliferation and colony-formation capacity. Conversely, small-molecule inhibitors of Wnt signaling suppressed proliferation without compromising the myo7a
+
cells formed by direct differentiation. In vivo lineage tracing supported the idea that Lgr5
+
cells give rise to myo7a
+
hair cells in the neonatal

Lgr5
EGFP-CreERT2/+

cochlea. In addition, overexpression of β-catenin initiated proliferation and led to transient expansion of Lgr5
+
cells within the cochlear sensory epithelium. These results suggest that Lgr5 marks sensory precursors and that Wnt signaling can promote their proliferation and provide mechanistic insights into Wnt-responsive progenitor cells during sensory organ development.
Functional imaging reveals rapid reorganization of cortical activity after parietal inactivation in monkeys
Authors: Wilke Melanie , Kagan Igor , Andersen Richard A.
Published: May 2012

Impairments of spatial awareness and decision making occur frequently as a consequence of parietal lesions. Here we used event-related functional MRI (fMRI) in monkeys to investigate rapid reorganization of spatial networks during reversible pharmacological inactivation of the lateral intraparietal area (LIP), which plays a role in the selection of eye movement targets. We measured fMRI activity in control and inactivation sessions while monkeys performed memory saccades to either instructed or autonomously chosen spatial locations. Inactivation caused a reduction of contralesional choices. Inactivation effects on fMRI activity were anatomically and functionally specific and mainly consisted of: (i) activity reduction in the upper bank of the superior temporal sulcus (temporal parietal occipital area) for single contralesional targets, especially in the inactivated hemisphere; and (ii) activity increase accompanying contralesional choices between bilateral targets in several frontal and parieto-temporal areas in both hemispheres. There was no overactivation for ipsilesional targets or choices in the intact hemisphere. Task-specific effects of LIP inactivation on blood oxygen level-dependent activity in the temporal parietal occipital area underline the importance of the superior temporal sulcus for spatial processing. Furthermore, our results agree only partially with the influential interhemispheric competition model of spatial neglect and suggest an additional component of interhemispheric cooperation in the compensation of neglect deficits.
Discard Mortality Estimation of Yellowtail Flounder Using Reflex Action Mortality Predictors
Authors: Barkley Adam S. , Cadrin Steven X.
Published: May 2012

The southern New England mid‐Atlantic stock of yellowtail flounder Limanda ferruginea has a history of substantial discards, and the current stock assessment assumes 100% discard mortality. A controlled experimental trawl was used to test seven reflex actions, which in combination make up the reflex action mortality predictors (RAMPs), from stressed and unstressed yellowtail flounder. Tow time and air exposure were tested to identify their effects on mortality. Mortality was significantly related to reflex impairment. Exposure to air was the more influential stressor in the survivability of yellowtail flounder, suggesting that discard mortality in the fishery could be reduced by limiting the duration of on‐deck air exposure for the fish. An example application of RAMP monitoring demonstrates a 42–73% range of discard mortality estimates from the southern New England trawl fishery. The reflex impairment–mortality relationship enables the estimation of discard mortality aboard commercial fishing vessels, which will lead to more accurate estimates of yellowtail flounder discard mortality.
Universal asymptotical behaviour of poloidal spectra of resonant magnetic perturbations created by a set of saddle coils in tokamaks
Authors: Abdullaev S.S.
Published: May 2012

Universal asymptotical behaviour of poloidal spectra of resonant magnetic perturbations created by a set of saddle coils in tokamak plasmas is studied in a vacuum approximation. It is shown that the poloidal mode spectra for a given toroidal mode can be presented by a linear combination of three universal asymptotical formulae corresponding to horizontal and vertical segments of a set of saddle coils. Each of the asymptotical formulae depends only on the safety factor of the equilibrium plasma and the geometry of the perturbation coils. The validity of the universal formulae is confirmed by numerical computations of the poloidal mode spectra for typical plasmas with large and small inverse aspect ratios, DIII-D-like plasmas with internal (I-) coils (Jackson et al 2003 Proc. 30th EPS Conf. on Controlled Fusion and Plasma Physics (St Petersburg, Russia, 7–11 July 2003) vol 27A (ECA) P-4.47) and spherical NSTX-like plasmas with error field coils (Gates et al 2009 Nucl. Fusion
49 104016).
On the confinement of passing alpha particles in a tokamak-reactor with resonant magnetic field perturbations shielded by plasma currents
Authors: Heyn M.F. , Ivanov I.B. , Kasilov S.V. , Kernbichler W. , Loarte A. , Nemov V.V. , Runov A.M.
Published: May 2012

Alpha-particle losses due to the resonant magnetic field perturbations (RMPs) created by the coil system for edge-localized mode mitigation in ITER are studied numerically. If shielding of RMPs by the plasma is not taken into account, passing α-particles are the main loss channel which, together with the trapped particle contribution leads to a loss of more than 5% of fusion alpha particle power. Shielding of RMPs practically eliminates this channel so that the overall losses are reduced to about 1%.
Plasma response models for non-axisymmetric perturbations
Authors: Turnbull A.D.
Published: May 2012

The plasma response to non-axisymmetric perturbations arising from external coils or linear instabilities can be treated using various linear and nonlinear models, none of which are fully satisfactory. Linear models cannot provide the full response and the result can depend on the detailed physical model used. The nonlinear response can be treated as a dynamic stability problem or from a nearby perturbed equilibrium approach. The nearby equilibrium approach aims to bypass the detailed evolution and search for the appropriate final state. For these nonlinear models, there is no guarantee that the final state is the one chosen dynamically by the plasma among possible multiple states, or is even accessible. To assure accessibility of the final state, one needs to relate the two-dimensional and nearby three-dimensional system through some set of invariants. One implementation is to add a perturbation from an external field or obtained from a stability code to the equilibrium and solve for 3D force balance. In that case, the invariants are buried in the numerical details of the equilibrium code. An appropriate set of constraints is not presently known; they depend on whether the dynamic evolution should be considered adiabatic or not. It is proposed that a suitable set of invariants may be obtained from considering the magnetic helicity, which is conserved exactly in ideal magnetohydrodynamics (MHD) but is broken at rational surfaces by non-ideal effects. In general, constraints for the equilibrium approach, including magnetic helicity, can be validated using full nonlinear extended MHD calculations in the dynamic approach.
Dependence of a current driven ELM self-amplification process on the plasma shape
Authors: Wingen A. , Evans T.E. , Spatschek K.H.
Published: May 2012

The numerical model of the non-linear evolution of edge-localized modes (ELMs) in tokamaks being used in this paper assumes that thermoelectric currents flow in short connection length flux tubes, initially established by error fields or other non-axisymmetric magnetic perturbations. The additional magnetic perturbation of the current filaments changes the magnetic topology. In a self-amplification process, more flux tubes are created which eventually allow more thermoelectric current to flow through the plasma edge. The process of flux tube formation is highly sensitive to the position of the secondary X-point in typical single null discharges in DIII-D. A new scenario for cases with large distances Δs between the secondary X-point and the primary separatrix is presented. In the numerical simulations, as Δs is increased the current evolution through short connection length flux tubes changes significantly. Ultimately, a final state with large stripe structures is found that results in footprints on the vessel wall which are similar to those found when Δs is small (Wingen et al 2010 Phys. Rev. Lett.
104 175001).
Managing harvest risk with catch-pooling cooperatives
Authors: Sethi Suresh Andrew , Dalton Michael , Hilborn Ray
Published: May 2012

Sethi, S. A., Dalton, M., and Hilborn, R. 2012. Managing harvest risk with catch-pooling cooperatives – ICES Journal of Marine Science, 69: 1038–1044. Catch-pooling cooperatives are a strategy for fishers to manage variability which can be organized independently of a central management agency. We examined the statistical properties of equal-share catch-pooling cooperatives, and tested their potential to mitigate risk using data from two Bering Sea crab fisheries prior to rationalization. The results suggest that small cooperatives of crabbers could have reduced vessel-level catch risk by as much as 40% in the red king crab fishery, but would have been ineffective in the snow crab fishery. Analytical examination of catch variances under cooperatives explains the discrepancy between the two fisheries and demonstrates that variability reduction depends on the degree of correlation amongst participants' catches. In the best-case scenario, catch-pooling cooperatives can diversify away all season to season variation resulting from individuals' luck and skill, leaving only variation in fishery-wide harvest.
Persecution Perpetuated: The Medieval Origins of Anti-Semitic Violence in Nazi Germany*
Authors: Voigtländer Nico , Voth Hans-Joachim
Published: May 2012

How persistent are cultural traits? Using data on anti-Semitism in Germany, we find local continuity over 600 years. Jews were often blamed when the Black Death killed at least a third of Europe’s population during 1348–50. We use plague-era pogroms as an indicator for medieval anti-Semitism. They reliably predict violence against Jews in the 1920s, votes for the Nazi Party, deportations after 1933, attacks on synagogues, and letters to Der Stürmer . We also identify areas where persistence was lower: cities with high levels of trade or immigration. Finally, we show that our results are not driven by political extremism or by different attitudes toward violence.
XadM, a Novel Adhesin of Xanthomonas oryzae pv. oryzae, Exhibits Similarity to Rhs Family Proteins and Is Required for Optimum Attachment, Biofilm Formation, and Virulence
Authors: Pradhan Binod B. , Ranjan Manish , Chatterjee Subhadeep
Published: May 2012

By screening a transposon-induced mutant library of Xanthomonas oryzae pv. oryzae, the bacterial blight pathogen of rice, we have identified a novel 5.241-kb open reading frame (ORF) named xadM that is required for optimum virulence and colonization. This ORF encodes a protein, XadM, of 1,746 amino acids that exhibits significant similarity to Rhs family proteins. The XadM protein contains several repeat domains similar to a wall-associated surface protein of Bacillus subtilis, which has been proposed to be involved in carbohydrate binding. The role of XadM in X. oryzae pv. oryzae adhesion was demonstrated by the impaired ability of an xadM mutant strain to attach and form biofilms. Furthermore, we show that XadM is exposed on the cell surface and its expression is regulated by growth conditions and plays an important role in the early attachment and entry inside rice leaves. Interestingly, XadM homologs are present in several diverse bacteria, including many Xanthomonas spp. and animal-pathogenic bacteria belonging to Burkholderia spp. This is the first report of a role for XadM, an Rhs family protein, in adhesion and virulence of any pathogenic bacteria.
Response of Potato Cultivars to Five Isolates Belonging to Four Strains of Potato virus Y
Authors: Nie Bihua , Singh Mathuresh , Murphy Agnes , Sullivan Andrew , Xie Conghua , Nie Xianzhou
Published: May 2012

The responses of 14 potato cultivars to five Potato virus Y (PVY) isolates belonging to four strains (ordinary [PVYO], tobacco veinal necrosis [PVYN], N:O group [PVYN:O], and nonrecombinant potato tuber necrotic [PVYNTN]) were studied in primary and secondary infections. For the primary infection experiments, foliage symptoms were monitored daily after mechanical inoculation with a PVY isolate until harvest; and, for the secondary infection experiments, foliage symptoms were monitored regularly from plant emergence until harvest. Tuber symptoms (namely, tuber necrotic ringspots) were checked at harvest and monthly postharvest for up to 4 months. In both infections, symptoms varied significantly depending on potato cultivar and virus strain or isolate. In primary infections, local lesions occurred on inoculated leaves of ‘AC Chaleur’, ‘Eramosa’, ‘Goldrush’, ‘Jemseg’, ‘Katahdin’, ‘Ranger Russet’, and ‘Yukon Gold’ after inoculation with PVYO isolates, followed by systemic necrosis on latterly emerged uninoculated leaves. In contrast, plants of ‘CalWhite’, ‘La Rouge’, ‘Red LaSoda’, ‘Russet Burbank’, ‘Russet Norkotah’, and ‘Superior’ did not exhibit any visible symptoms on inoculated leaves but developed mild to severe mosaic on latterly emerged leaves after infection with PVYO isolates. In all cultivars, near-symptomless to mild mosaic was induced by PVYN and mild to severe mosaic by PVYN:O. PVYNTN induced mild to severe mosaic in plants of all cultivars except AC Chaleur, ‘Cherokee’, and Yukon Gold, which developed visible systemic necrosis. Necrotic ringspots were observed in tubers of PVYNTN-infected plants of AC Chaleur, Cherokee, and Yukon Gold. The tuber symptoms were also incited by PVYN-Jg on Cherokee. In secondary infections, the symptoms were generally more severe than primary infections even though the symptom types did not alter. As in the greenhouse, a clear symptom severity pattern (PVYO-FL > PVYO-RB > PVYNTN-Sl > PVYN:O-Mb58 > PVYN-Jg) was observed in AC Chaleur, Cherokee, Eramosa, Goldrush, Jemseg, Katahdin, Ranger Russet, and Yukon Gold in the field.
First Report of Dollar Spot Caused by Sclerotinia homoeocarpa on Agrostis stolonifera in North Dakota
Authors: LeBoldus J. M. , Zhang Q. , Kinzer K.
Published: May 2012

Dollar spot disease is a major concern for golf courses nationwide, resulting in poor turf quality and significant damage to playing surfaces. To manage this disease effectively, fungicides need to be applied regularly. This management strategy represents a significant cost to turfgrass managers and may impact the economics of the industry in North Dakota. In the summer of 2011, small, circular, sunken brown patches of dead turf approximately 5 cm in diameter and resembling dollar spot disease were observed on a creeping bentgrass (Agrostis stolonifera L.) variety trial at the North Dakota State University Agricultural Experiment Station in Fargo, ND. Fresh individual leaf specimens with distinct lesions having straw colored centers and reddish brown margins were collected. Leaves were surface disinfected in a 0.05% sodium chloride solution for 60 s, rinsed three times in sterile distilled water, then placed onto potato dextrose agar (PDA). Three isolates were obtained from the disease infested leaves with similar morphology to that described for Sclerotinia homoeocarpa F.T. Bennett (1). Fungal colonies were initially colorless followed by the development of sparse white columnar aerial mycelia with cinnamon colored bases. Hyphae were 5 to 8 μm wide and thin walled with dense granular contents and septations at irregular intervals. Fourteen days after culturing, dark brown to black mycelial stroma developed. A single representative isolate was selected to conduct inoculations. Inoculum was produced by placing six 5-mm-diameter plugs of PDA with actively growing mycelium into an Erlenmeyer flask with 40 g of sterile millet seed. The inoculum was incubated for 14 days at ambient temperature (20 to 25°C). Three creeping bentgrass cultivars, Crenshaw, Declaration, and L-93, were inoculated (two pots per cultivar). Following inoculation, the pots were misted with water, sealed in separate plastic bags, and placed in the dark for 48 h. For the next 5 days, plants were placed for 8 h outside of bags on a bench with full spectrum fluorescent bulbs, followed by 16 h in plastic bags in the dark. Finally, pots were placed on a bench for 48 h. Signs and symptoms of S. homoeocarpa developed on all pots, whereas the controls remained asymptomatic. The same fungus was reisolated from grass leaves, satisfying Koch's postulates. To confirm the identity of the fungus, the internal transcribed spacer was amplified using the ITS4 and ITS5 primers (2). The amplicon was sequenced, generating a 549-bp sequence (Accession No. JQ735942) with 100% similarity to sequences of S. homoeocarpa in GenBank (Accession Nos. GQ924924.1, GQ924923.1, and EU123801.1). To our knowledge, this is the first confirmed report of dollar spot in North Dakota.

References: (1) F. T. Bennett. Ann. Appl. Biol. 24:236, 1937. (2) T. J. White et al. PCR Protocols: A Guide to Methods and Applications. Academic Press Inc., New York, 1990.
Integration of Elicitors and Less-Susceptible Hybrids for the Control of Powdery Mildew in Organic Tomato Crops
Authors: Dafermos N. G. , Kasselaki A. M. , Goumas D. E. , Spantidakis K. , Eyre M. D. , Leifert C.
Published: May 2012

Powdery mildew is a serious economic problem in Mediterranean tomato production. The disease is currently controlled by fungicides (especially sulfur) in both conventional and organic production. Four factorial greenhouse experiments were conducted in successive cropping seasons (autumn 2005, autumn 2006, spring 2006, and spring 2007) to assess the main and combined effects of (i) a less-susceptible hybrid (‘Elpida’), (ii) chitin soil amendment, or (iii) Milsana or chitosan elicitor foliar treatments on the severity of powdery mildew and crop performance. Analysis of variance revealed significant effects of cropping season on disease severity and crop yield. All control practices reduced disease severity; reductions of approximately 40, 30, 15, and 15% were achieved by Milsana foliar treatment, the use of a less-susceptible hybrid, chitosan foliar treatment, and chitin soil amendment, respectively. In the season with the highest disease pressure, higher yields were obtained with the less-susceptible hybrid Elpida whereas, in the three seasons with no or low disease pressure, the use of the more susceptible hybrid ‘Bison’ produced higher yields. Milsana and sulfur treatments did not significantly affect yield (yields were slightly lower compared with untreated control plants) and, therefore, their use cannot be recommended based on the results obtained.
Outbreak of Blackleg in Canola in North Dakota is Caused by New Pathogenicity Groups
Authors: Mendoza Luis E. del Rio , Nepal Achala , Markell Samuel
Published: May 2012

In 2009, a blackleg outbreak was detected in canola fields of North Dakota. The disease, which is caused primarily by the fungus Leptosphaeria maculans, was observed in 88 of 99 fields scouted with 39 fields having incidences >30%. The mean blackleg incidence in these 39 fields was 61% (range 50 to 84%). Fifty nine L. maculans isolates were retrieved from 20 of these 39 fields and classified in five pathogenicity groups (PG) using a set of three differentials cultivars. PG-4 was the pathotype most commonly isolated from these fields with 51% of all isolates, followed by PG-3 with 25% and PG-T with 8% of isolates. Only 3% of the isolates belong to PG-2, a pathotype that was previously considered the most prevalent in the region. Increased prevalence of these new pathogenicity groups represents a threat to the canola industry in the state.

Accepted for publication 20 January 2012. Published 10 April 2012.
Identification of Three Distinct Classes of Satellite RNAs Associated With Two Cucumber mosaic virus Serotypes from the Ornamental Groundcover Vinca minor
Authors: Fisher John R.
Published: May 2012

Cucumber mosaic virus (CMV) is a cosmopolitan virus which may also have small satellite RNAs (satRNA) associated with it affecting symptom development. Vinca minor (periwinkle) plants exhibiting subtle mosaic symptoms tested positive for CMV by enzyme linked immunosorbent assay (ELISA). Double-stranded ribonucleic acid (dsRNA) analysis of CMV-Vinca field isolates in Nicotiana tabacum ‘Glurk’ suggested two sizes of putative satRNA associated with CMV. Immunocapture RT-PCR, cloning, and sequencing of the movement protein, coat protein, and satRNAs demonstrated serogroup 1A and serogroup 2 CMV helper strains and three distinct classes of satRNAs of four sizes. Further, two classes of satRNAs could be distinguished by their necrosis domains. Previously CMV was reported in V. minor in New Jersey. This is the first report of CMV in V. minor in Ohio and the first report of satRNA associated with CMV in V. minor in the United States.

Accepted for publication 1 February 2012. Published 12 April 2012.
Cultivar and Fungicide Effects on Pythium Leak of Snap Bean
Authors: Damicone John P. , Olson Jenifer D. , Kahn Brian A.
Published: May 2012

Pythium leak is a pod decay complex of several pathogens and is a problem in the processing industry where snap beans are harvested in bulk. In Oklahoma, Pythium leak of snap bean is caused primarily by Pythium aphanidermatum and P. ultimum. Fungicide programs alone have not provided adequate disease control. The objective of this study was to evaluate snap bean cultivars for their reaction to Pythium leak with and without fungicide (mefenoxam + copper hydroxide) treatment. Entries were compared to the regional standards of Roma II for flat pod types and Nelson for round pod types. Over two years, disease incidence (DI = plants with symptoms) in untreated plots averaged 22% for Roma II and 30% for Nelson. Among the flat-pod types, entries that had less (P = 0.05) disease and yielded similar to, or greater than, Roma II included Bogota (DI = 13%), Navarro (DI = 12%), Romano 942 (DI = 12%), Cerler (DI = 10%), Tapia (DI = 10%), Primo (DI = 10%), and Ebro (DI = 5%). Among the round pod types, PLS 75 (DI = 14%) and SB 4261 (11%) had less disease than Nelson. However, all of the entries with round pods yielded less than Nelson. Over entries, fungicide treatment reduced disease incidence by an average of 40%, but the effect of fungicide was not significant for entries with low disease incidence such as PLS 75, Cerler, and Ebro. Except for plant height and lodging which were weakly correlated with disease incidence, plant architectural characteristics did not explain observed differences in disease incidence. Results suggest that reaction to Pythium leak is an important characteristic in selecting processing snap bean cultivars.

Accepted for publication 30 January 2012. Published 18 April 2012.
Vegetable Seedling Diseases Associated with Earthworm Castings Contaminated with Phytophthora capsici and Pythium Attrantheridium
Authors: Liu Bo , Roos Debbie , Buttler Shawn , Richter Brantlee , Louws Frank J.
Published: May 2012

Earthworms and worm castings have been recommended for their beneficial effects in increasing yields and suppressing soilborne diseases. However, in a few cases, earthworm castings have been shown to harbor soilborne pathogens. The research documents that earthworm castings used as an amendment in soilless potting mixes at several organic farms in North Carolina were contaminated with Phytophthora capsici and several Pythium species. Phytophthora capsici and P. attrantheridium were subsequently isolated from rotted roots of vegetable seedlings grown in the potting mix. Commercial producers of earthworm castings should only use clean plant material to maintain earthworms and earthworm castings should be ascertained as pathogen-free before incorporation into plant growth media.

Accepted for publication 30 January 2012. Published 21 April 2012.
Multiple mating in the traumatically inseminating Warehouse pirate bug,Xylocoris flavipes: effects on fecundity and longevity
Authors: Backhouse Amy , Sait Steven M. , Cameron Tom C.
Published: May 2012

Optimal mating frequencies differ between sexes as a consequence of the sexual differentiation of reproductive costs per mating, where mating is normally more costly to females than males. In mating systems where sexual reproduction is costly to females, sexual conflict may cause both direct (i.e. by reducing female fecundity or causing mortality) and indirect (i.e. increased risk of mortality, reduced offspring viability) reductions in lifetime reproductive success of females, which have individual and population consequences. We investigated the direct and indirect costs of multiple mating in a traumatically inseminating (TI) predatory Warehouse pirate bug,Xylocoris flavipes(Reuter) (Hemiptera: Anthocoridae), where the male penetrates the female's abdomen during copulation. This study aimed to quantify the effects of TI on female fecundity, egg viability, the lifetime fecundity schedule, longevity and prey consumption in this cosmopolitan biocontrol agent. We found no difference in the total reproductive output between mating treatments in terms of total eggs laid or offspring viability, but there were significant differences found in daily fecundity schedules and adult longevity. In terms of lifetime reproduction, female Warehouse pirate bugs appear to be adapted to compensate for the costs of TI mating to their longevity.
The ontogenetic origins of mirror neurons: evidence from ‘tool-use’ and ‘audiovisual’ mirror neurons
Authors: Cook Richard
Published: May 2012

Since their discovery, mirror neurons—units in the macaque brain that discharge both during action observation and execution—have attracted considerable interest. Whether mirror neurons are an innate endowment or acquire their sensorimotor matching properties ontogenetically has been the subject of intense debate. It is widely believed that these units are an innate trait; that we are born with a set of mature mirror neurons because their matching properties conveyed upon our ancestors an evolutionary advantage. However, an alternative view is that mirror neurons acquire their matching properties during ontogeny, through correlated experience of observing and performing actions. The present article re-examines frequently overlooked neurophysiological reports of ‘tool-use’ and ‘audiovisual’ mirror neurons within the context of this debate. It is argued that these findings represent compelling evidence that mirror neurons are a product of sensorimotor experience, and not an innate endowment.
The impact of host immune status on the within-host and population dynamics of antigenic immune escape
Authors: Luo Shishi , Reed Michael , Mattingly Jonathan C. , Koelle Katia
Published: May 2012

Antigenically evolving pathogens such as influenza viruses are difficult to control owing to their ability to evade host immunity by producing immune escape variants. Experimental studies have repeatedly demonstrated that viral immune escape variants emerge more often from immunized hosts than from naive hosts. This empirical relationship between host immune status and within-host immune escape is not fully understood theoretically, nor has its impact on antigenic evolution at the population level been evaluated. Here, we show that this relationship can be understood as a trade-off between the probability that a new antigenic variant is produced and the level of viraemia it reaches within a host. Scaling up this intra-host level trade-off to a simple population level model, we obtain a distribution for variant persistence times that is consistent with influenza A/H3N2 antigenic variant data. At the within-host level, our results show that target cell limitation, or a functional equivalent, provides a parsimonious explanation for how host immune status drives the generation of immune escape mutants. At the population level, our analysis also offers an alternative explanation for the observed tempo of antigenic evolution, namely that the production rate of immune escape variants is driven by the accumulation of herd immunity. Overall, our results suggest that disease control strategies should be further assessed by considering the impact that increased immunity—through vaccination—has on the production of new antigenic variants.