bluuebunny/crossref_metadata_2025 huggingface dataset:
Convection in a horizontal fluid layer under an inclined temperature gradient
Authors: Ortiz-Pérez A. S. , Dávalos-Orozco L. A.
Published: August 2011

In this paper, we investigate the flow instability of a horizontal fluid layer under an inclined temperature gradient. The fluid layer is supposed to be of infinite extension, and the differentially heated lateral walls are very far away from the central region which is the subject of research. The layer is also inside two rigid, horizontal and parallel walls which are perpendicular to gravity and subjected to a vertical adverse temperature gradient. Calculations are done for Prandtl numbers Pr in the range from 0.026 to 1, which include materials from liquid metals to gases. By improving the Galerkin numerical method, new results and important extensions and corrections to the work of Nield [Int. J. Heat Fluid Flow 15, 157 (1994)] are obtained. It is found that inside the range 0.2 < Pr < 0.45, a new oblique oscillatory mode starts to appear and that it can be the first unstable one in a particular range of the horizontal Rayleigh number RH for all Prandtl numbers until Pr = 1. To the left, this mode separates from an oscillatory longitudinal even mode already found by Nield [Int. J. Heat Fluid Flow 15, 157 (1994)]. A new codimension two point is found when the Prandtl number is increased to Pr = 0.4886, where the curves of the oblique oscillatory mode and the even stationary longitudinal mode touch each other for the first time. Another new codimension two point starts to appear in the range 0.5 < Pr < 1.0 which corresponds to the crossing between the curves of the oblique oscillatory mode and the odd stationary longitudinal mode. As a consequence, another interesting result is that, to the right of this point, the odd stationary longitudinal mode is the first unstable one in a range of RH. The qualitative form of the curves of criticality changes notably between Pr = 0.026 and Pr = 1.0. Therefore, here we present a detailed description of this change by means of calculations for different Prandtl numbers inside that range.
Pair correlation function integrals: Computation and use
Authors: Wedberg Rasmus , O’Connell John P. , Peters Günther H. , Abildskov Jens
Published: August 2011

We describe a method for extending radial distribution functions obtained from molecular simulations of pure and mixed molecular fluids to arbitrary distances. The method allows total correlation function integrals to be reliably calculated from simulations of relatively small systems. The long-distance behavior of radial distribution functions is determined by requiring that the corresponding direct correlation functions follow certain approximations at long distances. We have briefly described the method and tested its performance in previous communications [R. Wedberg, J. P. O’Connell, G. H. Peters, and J. Abildskov, Mol. Simul. 36, 1243 (2010);10.1080/08927020903536366 Fluid Phase Equilib. 302, 32 (2011)]10.1016/j.fluid.2010.10.004, but describe here its theoretical basis more thoroughly and derive long-distance approximations for the direct correlation functions. We describe the numerical implementation of the method in detail, and report numerical tests complementing previous results. Pure molecular fluids are here studied in the isothermal-isobaric ensemble with isothermal compressibilities evaluated from the total correlation function integrals and compared with values derived from volume fluctuations. For systems where the radial distribution function has structure beyond the sampling limit imposed by the system size, the integration is more reliable, and usually more accurate, than simple integral truncation.
Van der Waals supercritical fluid: Exact formulas for special lines
Authors: Brazhkin V. V. , Ryzhov V. N.
Published: August 2011

In the framework of the van der Waals model, analytical expressions for the locus of extrema (ridges) for heat capacity, thermal expansion coefficient, compressibility, density fluctuation, and sound velocity in the supercritical region have been obtained. It was found that the ridges for different thermodynamic values virtually merge into single Widom line only at T < 1.07Tc, P < 1.25Pc and become smeared at T < 2Tc, P < 5Pc, where Tc and Pc are the critical temperature and pressure. The behavior of the Batschinski lines and the pseudo-Gruneisen parameter γ of a van der Waals fluid were analyzed. In the critical point, the van der Waals fluid has γ = 8/3, corresponding to a soft sphere particle system with exponent n = 14.
Mechanism of permanent image sticking induced by ion bombardment and reduction method for ac plasma display panels
Authors: Park Choon-Sang , Tae Heung-Sik , Chien Sung-Il
Published: August 2011

Ion bombardment of the phosphor layer during a sustain discharge was identified as the key factor inducing permanent image sticking and reducing the lifetime of alternating-current (ac) plasma display panels (PDPs). Secondary ion mass spectroscopy (SIMS) confirmed that ion bombardment of the phosphor layer facilitated the re-crystallization of the Mg particles sputtered from the MgO surface during a discharge, thereby degrading the visible conversion of the phosphor layer and eventually lowering the luminance and color temperature. Based on this mechanism, experimental results showed that the re-crystallization of the Mg particles was suppressed when using a positive-biased address electrode to diminish the ion bombardment of the phosphor layer. Consequently, minimizing the ion bombardment of the phosphor layer during a sustain discharge was shown to mitigate permanent image sticking in an ac PDP by suppressing the re-crystallization of the Mg particles.
Void formation in melt-grown silicon studied by molecular dynamics simulations: From grown-in faulted dislocation loops to vacancy clusters
Authors: Pohl Johan , Albe Karsten
Published: August 2011

Molecular dynamics simulations of a dislocation based mechanism for void formation in silicon are presented. By studying a moving solid-liquid interface in Si, we observe the formation of dislocation loops on (111) facets consisting of coherency and anticoherency dislocations, which disband within nanoseconds into vacancy clusters of 10 or more vacancies. These vacancy clusters can act as nucleation seeds for the experimentally observed octahedral single and double voids.
The million-year wait for macroevolutionary bursts
Authors: Uyeda Josef C. , Hansen Thomas F. , Arnold Stevan J. , Pienaar Jason
Published: August 2011

We lack a comprehensive understanding of evolutionary pattern and process because short-term and long-term data have rarely been combined into a single analytical framework. Here we test alternative models of phenotypic evolution using a dataset of unprecedented size and temporal span (over 8,000 data points). The data are body-size measurements taken from historical studies, the fossil record, and among-species comparative data representing mammals, squamates, and birds. By analyzing this large dataset, we identify stochastic models that can explain evolutionary patterns on both short and long timescales and reveal a remarkably consistent pattern in the timing of divergence across taxonomic groups. Even though rapid, short-term evolution often occurs in intervals shorter than 1 Myr, the changes are constrained and do not accumulate over time. Over longer intervals (1–360 Myr), this pattern of bounded evolution yields to a pattern of increasing divergence with time. The best-fitting model to explain this pattern is a model that combines rare but substantial bursts of phenotypic change with bounded fluctuations on shorter timescales. We suggest that these rare bursts reflect permanent changes in adaptive zones, whereas the short-term fluctuations represent local variations in niche optima due to restricted environmental variation within a stable adaptive zone.
Preclinical evaluation and validation of [
18
F]HX4, a promising hypoxia marker for PET imaging
Authors: Dubois Ludwig J. , Lieuwes Natasja G. , Janssen Marco H. M. , Peeters Wenny J. M. , Windhorst Albert D. , Walsh Joseph C. , Kolb Hartmuth C. , Öllers Michel C. , Bussink Johan , van Dongen Guus A. M. S. , van der Kogel Albert , Lambin Philippe
Published: August 2011

Hypoxia has been shown to be an important microenvironmental parameter influencing tumor progression and treatment efficacy. Patient guidance for hypoxia-targeted therapy requires evaluation of tumor oxygenation, preferably in a noninvasive manner. The aim of this study was to evaluate and validate the uptake of [
18
F]HX4, a novel developed hypoxia marker for PET imaging. A heterogeneous accumulation of [
18
F]HX4 was found within rat rhabdomyosarcoma tumors that was significantly (
P
< 0.0001) higher compared with the surrounding tissues, with temporal increasing tumor-to-blood ratios reaching a plateau of 7.638 ± 0.926 and optimal imaging properties 4 h after injection. [
18
F]HX4 retention in normal tissues was found to be short-lived, homogeneous and characterized by a fast progressive temporal clearance. Heterogeneity in [
18
F]HX4 tumor uptake was analyzed based on 16 regions within the tumor according to the different orthogonal planes at the largest diameter. Validation of heterogeneous [
18
F]HX4 tumor uptake was shown by a strong and significant relationship (
r
= 0.722;
P
< 0.0001) with the hypoxic fraction as calculated by the percentage pimonidazole-positive pixels. Furthermore, a causal relationship with tumor oxygenation was established, because combination treatment of nicotinamide and carbogen resulted in a 40% reduction (
P
< 0.001) in [
18
F]HX4 tumor accumulation whereas treatment with 7% oxygen breathing resulted in a 30% increased uptake (
P
< 0.05). [
18
F]HX4 is therefore a promising candidate for noninvasive detection and evaluation of tumor hypoxia at a macroscopic level.
Site-directed tryptophan fluorescence reveals two essential conformational changes in the Na
+
/H
+
antiporter NhaA
Authors: Kozachkov Lena , Padan Etana
Published: August 2011

NhaA, a Na
+
/H
+
antiporter critical for pH and Na
+
homeostasis in
Escherichia coli
, as well as other enterobacteria and possibly
Homo sapiens
, was modified for fluorescence spectroscopy by constructing a functional Trp-less NhaA mutant. Purified Trp-less NhaA lacks the Trp fluorescence emission characteristic of the wild type, thereby providing a background for studying structure–function relationships in NhaA by site-directed Trp fluorescence. Two single-Trp variants in the Trp-less background (F136W and F339W) were constructed. The mutants grow on selective media, have antiport activities that are similar to Trp-less NhaA, and exhibit Trp fluorescence with three different reversible responses to Li
+
, Na
+
, and/or pH. With single Trp/F136W, a pH shift from pH 6.0 to 8.5 induces a red shift and dramatically increases fluorescence in a reversible fashion; no effect is observed when either Na
+
or Li
+
is added. In marked contrast, with single Trp/F339W, changes in pH do not alter fluorescence, but addition of either Na
+
or Li
+
drastically quenches fluorescence at alkaline pH. Therefore, a Trp at position 136 specifically monitors a pH-induced conformational change that activates NhaA, whereas a Trp at position 339 senses a ligand-induced conformational change that does not occur until NhaA is activated at alkaline pH.
Time-resolved mass spectroscopic studies of an atmospheric-pressure helium microplasma jet
Authors: Oh Jun-Seok , Aranda-Gonzalvo Yolanda , Bradley James W
Published: August 2011

Using molecular beam mass spectroscopy, time-resolved measurements of the ionic species in the plasma plume of an atmospheric-pressure helium microplasma jet are made for a range of excitation frequencies (5, 10 and 25 kHz) and source–instrument orifice distances (1, 7 and 11 mm). Ionic species can only be observed in the visible plasma plume, with the main positive species being
(65.26%) and
(21.11%), and a few percentages of N+, O+, NO+and He+. For the negative ions, the majority species are
(22.68%),
(H2O) (10.49%) and a large range of minority species observed, namely
,
,
,
and clusters,
,
,
(CO3) and
. The flux of ions created from air species, such as NO+ and
, is seen to be maximized at a distance of several millimeters from the nozzle, whereas the He+ concentration continually decreases with distance from the exit orifice. The time-resolved measurements (time resolution down to 2 µs) show that positive ions appear twice in one full period of the voltage waveform, correlated directly with positive and negative current peaks. The rise and fall times of the positive ions are typically tens of μs. In contrast, the appearance of negative ions is correlated only with the negative part of discharge current, with one main peak in the detected ionic flux seen per cycle. The rise time of the negative ions is about 10 µs, independent of mass; however, we observed longer decay times, from 100 to 150 µs, increasing with mass. With increased driving frequency, the time modulation in the ionic fluxes is reduced, particularly for the negative species that show almost constant fluxes at 25 kHz throughout the cycle. The observations can be understood through a simple picture of the interaction of the He jet and the moist ambient air. The results indicate that the discrete plasma ‘bullets’ and their afterglow tail, that forms the jet, carry an associated positive or negative current depending on the time of their creation in the voltage cycle.
Structural characterization of ultrathin Cr-doped ITO layers deposited by double-target pulsed laser ablation
Authors: Cesaria Maura , Caricato Anna Paola , Leggieri Gilberto , Luches Armando , Martino Maurizio , Maruccio Giuseppe , Catalano Massimo , Manera Maria Grazia , Rella Roberto , Taurino Antonietta
Published: August 2011

In this paper we report on the growth and structural characterization of very thin (20 nm) Cr-doped ITO films, deposited at room temperature by double-target pulsed laser ablation on amorphous silica substrates. The role of Cr atoms in the ITO matrix is carefully investigated with increasing doping content by transmission electron microscopy (TEM). Selected-area electron diffraction, conventional bright field and dark field as well as high-resolution TEM analyses, and energy dispersive x-ray spectroscopy demonstrate that (i) crystallization features occur despite the low growth temperature and small thickness, (ii) no chromium or chromium oxide secondary phases are detectable, regardless of the film doping levels, (iii) the films crystallize as crystalline flakes forming large-angle grain boundaries; (iv) the observed flakes consist of crystalline planes with local bending of the crystal lattice. Thickness and compositional information about the films are obtained by Rutherford back-scattering spectrometry. Results are discussed by considering the combined effects of growth temperature, smaller ionic radius of the Cr cation compared with the trivalent In ion, doping level, film thickness, the double-target doping technique and peculiarities of the pulsed laser deposition method.
Rapid Variety Identification of Pure Rough Rice by Fourier‐Transform Near‐Infrared Spectroscopy
Authors: Attaviroj Namaporn , Kasemsumran Sumaporn , Noomhorm Athapol
Published: August 2011

Rice variety is considered as an important factor influencing cooking and processing quality because of variations in size, shape, and constitution. Difficulty in management of rough rice with lower varietal purity becomes a significant problem in rice production and can result in the reduction of rice quality. Fourier‐transform near‐infrared (FT‐NIR) spectroscopy was used to identify the variety of rough rice through whole‐grain techniques. Moist rough rice samples (n = 259) comprising five varieties (Khao Dawk Mali 105 [KDML105], Pathum Thani 1, Suphan Buri 60, Chainat 1, and Pitsanulok 2) were gathered from different locations around Thailand and scanned in the NIR region of 9088–4000 cm–1 in reflectance mode. Soft independent modeling of class analogies (SIMCA) and partial least squares discriminant analysis (PLSDA) methods were used for identification by utilizing preprocessed spectra. The highest identification accuracy achieved was 74.42% by the SIMCA model and 99.22% by the PLSDA model. The best PLSDA model demonstrated approximately 97% correct identification for KDML105 samples and 100% for the others. This study raises the possibility of applying FT‐NIR spectroscopy as a nondestructive technique for rapidly identifying moist rough rice varieties in routine quality assurance testing.
Phytoplasma-Induced Floral Abnormalities in Catharanthus roseus Are Associated with Phytoplasma Accumulation and Transcript Repression of Floral Organ Identity Genes
Authors: Su Yi-Ting , Chen Jen-Chih , Lin Chan-Pin
Published: August 2011

Floral symptoms caused by phytoplasma largely resemble floral reversion in other plants. Periwinkle leaf yellowing (PLY) phytoplasma and peanut witches'-broom (PnWB) phytoplasma caused different degrees of floral abnormalities on infected periwinkle plants. The PLY phytoplasma-infected plants exhibited floral discoloration, virescence, small flowers, and only occasionally full floral reversion. In contrast, PnWB phytoplasma frequently induced complete floral reversion and resulted in a witches'-broom symptom from the floral reversion. Although different degrees of floral symptoms were induced by these two phytoplasmas, the morphological disorders were similar to those of other plants carrying SEPALLATA mutations or gene silencing. Here, we compared expression levels of organ-identity-related genes and pigmentation genes during floral symptom development. Accumulation of phytoplasmas in malformed flowers and their closely surrounding leaves was also compared. In infected plants, transcript abundance of all examined organ identity genes and pigmentation genes was suppressed. Indeed, CrSEP3, a SEPALLALA3 ortholog, showed the greatest suppression among genes examined. Of the pigmentation genes, transcript reduction of chalcone synthase was most highly correlated with the loss in floral pigmentation. Floral symptom severities were associated with the accumulation of either phytoplasmas. Interestingly, both phytoplasmas accumulated to higher levels in malformed flowers than in their surrounding leaves. Many plant pathogens manipulate host plant development to their advantage. It is intriguing to see whether phytoplasmas alter floral development to increase their population.
Virulence, Frequency, and Distribution of Races of Puccinia striiformis f. sp. tritici and P. striiformis f. sp. hordei Identified in the United States in 2008 and 2009
Authors: Wan Anmin , Chen Xianming
Published: August 2011

Puccinia striiformis f. sp. tritici and P. striiformis f. sp. hordei, the causal agents of stripe rust on wheat and barley, respectively, can change rapidly in virulence, and such changes may overcome resistance in cultivars and result in severe epidemics. To monitor virulence changes in the pathogen populations, isolates obtained from stripe rust samples collected by the authors and collaborators from 17 U.S. states in 2008 and 13 states in 2009 were tested on 20 wheat and 12 barley differential lines to identify races of P. striiformis f. tritici and P. striiformis f. sp. hordei, respectively. In 2008, 33 P. striiformis f. tritici (PST) races were detected, including a new race, PST-138, which was similar to previously identified PST-127 (virulent on wheat differentials 1, 2, 3, 4, 6, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, and 20) but not virulent on differential 8. The five most frequent races were PST-114 (virulent on differentials 1, 3, 4, 8, 9, 10, 11, 12, 14, 16, 17, 18, 19, and 20), PST-100 (virulent on differentials 1, 3, 8, 9, 10, 11, 12, 16, 17, 18, 19, and 20), PST-116 (similar to PST-114 plus virulent on differential 5), PST-101 (similar to PST-100 plus virulent on differential 2), and PST-98 (similar to PST-100 but not virulent on differential 9). In 2009, 26 P. striiformis f. tritici races were identified, including two new races, PST-139 and PST-140. PST-139 was similar to PST-127 but not virulent on differentials 16 and 20. PST-140 was similar to PST-114 but not virulent on differential 9. The five most frequent races were PST-139 (19%), PST-140 (14%), PST-114 (11%), PST-116 (10%), and PST-127 (9%). However, the most widely distributed races were PST-98 (in 10 of the 14 states) and PST-102 (in 7 of the 14 states). Differential genotype AvSYr5NIL (Yr5) was the only one among the 20 differentials that remained resistant to all of the identified races. Virulence diversity of the P. striiformis f. tritici populations was higher west of the Rocky Mountains. For barley stripe rust, P. striiformis f. sp. hordei (PSH)-33 (virulent on barley differentials 1 and 7) was the most common (46%) of the 11 races detected in 2008, including a new race, PSH-82 (virulent only on barley differentials 1 and 11). In 2009, six previously identified races were detected, of which five (PSH-16, PSH-38, PSH-46, PSH-54, and PSH-71) were detected in Washington and two (PSH-54 and PSH-70) in Oregon. The information on P. striiformis f. sp. tritici and P. striiformis f. sp. hordei races should be useful in selecting genes for developing cultivars with effective stripe rust resistance.
First Report of Walnut Canker Caused by Fusarium incarnatum from India
Authors: Singh B. , Kalha C. S. , Razdan V. K. , Verma V. S.
Published: August 2011

While screening newly introduced cultivars of walnut (Juglans regia) at Bhaderwah (Mini Kashmir), Jammu and Kashmir, India in September 2008, 60% of grafted plants were found to be dying because of a cankerous growth observed on seedling stems. Later, these symptoms extended to lateral branches. In the surveyed nurseries, cvs. SKU 0002 and Opex Dachaubaria were severely affected by the disease. Cankers were also observed in all walnut nurseries in the area with several wild seedlings also being observed to be exhibiting similar cankerous symptoms on stem and branches. Necrotic lesions from cankerous tissues on seedling stems were surface disinfested with 0.4% NaOCl for 1 min and these disinfected cankerous tissues were grown on potato dextrose agar (potato-250 g, dextrose-15 g, agar-15 g, distilled water-1 liter). A Fusarium sp. was isolated consistently from these cankerous tissues, which was purified using single-spore culture. Carnation leaf agar was used for further culture identification (2,3). The fungal colony was floccose, powdery white to rosy in appearance when kept for 7 days at 25 ± 2°C. Macroconidia were straight to slightly curved, four to eight septate and 30 to 35 × 3.5 to 5.7 μm. These are characteristics consistent with Fusarium incarnatum (3). Pathogenicity was confirmed by spraying a conidial suspension (1 × 106 conidia/ml) onto bruised branches of 1-year-old walnut plants (cv. Opex Dachaubaria) while sterile distilled water sprays were used for the controls. Inoculated plants were incubated at 20 ± 2°C and 85% relative humidity for 48 h. Fifty days following inoculation, branch dieback followed by canker symptoms developed on inoculated plants. Control plants remained healthy with no symptoms of canker. F. incarnatum (Roberge) Sacc. was repeatedly isolated from inoculated walnut plants, thus satisfying Koch's postulates. Infected plant material has been deposited at Herbarium Crytogamae Indiae Orientalis (ITCC-6874-07), New Delhi. To our knowledge, this is the first report of walnut canker caused by F. incarnatum (Roberge) Sacc. from India. This fungus was previously reported to be affecting walnut in Italy (1) and Argentina (4).

References: (1) A. Belisario et al. Informatore Agrario 21:51, 1999. (2) J. C. Gilman. A Manual of Soil Fungi. The Iowa State University Press, Ames, 1959. (3) P. E. Nelson et al. Fusarium Species. An Illustrated Manual for Identification. The Pennsylvania State University Press, University Park, 1983. (4) S. Seta et al. Plant Pathol. 53:248, 2004.
Effect of Silicon Absorption on Soybean Resistance to Phakopsora pachyrhizi in Different Cultivars
Authors: Arsenault-Labrecque Geneviève , Menzies James G. , Bélanger Richard R.
Published: August 2011

Silicon (Si) is recognized for its prophylactic role in alleviating diseases when absorbed by plants and has been proposed as a possible solution against soybean rust, caused by Phakopsora pachyrhizi. However, little is known about its potential effects on soybean (Glycine max) because the plant's ability to absorb Si is poorly defined. In this work, our objectives were to evaluate and quantify the absorption of Si in leaves of different soybean cultivars and to determine if such absorption was able to enhance resistance to soybean rust. In a first set of experiments with cv. Williams 82, hydroponic plants were supplied or not with Si and inoculated with urediniospores of P. pachyrhizi. Chemical analyses revealed no significant differences in the plants' Si content regardless of the treatment, which translated into no effect on rust incidence. However, in a second set of experiments with different cultivars, plants of Korean cultivar Hikmok sorip absorbed nearly four times more Si than those of Williams 82. At the same time, plants from this cultivar exhibited a near absence of disease symptoms when supplied with Si. This resistance appeared to be the result of hypersensitive (HR) reactions that were triggered when plants were fed with Si. These results support the concept that a plant's innate ability to absorb Si will dictate the benefits conferred by a treatment with Si and provide evidence that Si can protect soybean plants against soybean rust through mediated resistance.
First Report of Tomato chlorosis virus Infecting Tomato in Sudan
Authors: Fiallo-Olivé E. , Hamed A. A. , Moriones E. , Navas-Castillo J.
Published: August 2011

In March 2011, interveinal yellowing and necrosis symptoms on middle and lower leaves were observed in tomato (Solanum lycopersicum L., cv. Castle Rock) plants grown in three adjacent greenhouses of the Agricultural Research Corporation at Wad Medani (Gezira State, Sudan). These symptoms resembled those caused by Tomato chlorosis virus (ToCV) and Tomato infectious chlorosis virus (TICV) (4) (genus Crinivirus, family Closteroviridae). Whitefly (Bemisia tabaci) infestation was also observed in these greenhouses. Total RNA was extracted by TRIzol Reagent (Invitrogen, Carlsbad, CA) from symptomatic leaves and analyzed by dot-blot hybridization with digoxigenin-labelled RNA probes to the coat protein (CP) gene of ToCV and to the minor coat protein (CPm) gene of TICV. Positive signal was obtained only with the ToCV probe. Reverse transcription (RT)-PCR reactions were performed with two pairs of primers specific for the detection of ToCV, MA380(+) (5′-GTGAGACCCCGATGACAGAT-3′) and MA381(-) (5′-TACAGTTCCTTGCCCTCGTT-3′), specific to the CP gene (ToCV RNA 2) (3), and MA396(+) (5′-TGGTCGAACAGTTTGAGAGC-3′) and MA397(-) (5′-TGAACTCGAATTGGGACAGA-3′), specific to the RNA-dependent RNA polymerase (RdRp) gene (ToCV RNA 1) (1). DNA fragments of the expected sizes (436 and 763 bp, respectively) were obtained, thus supporting the presence of ToCV in the symptomatic samples. Amplified DNA fragments were cloned in pGEM-T Easy vector (Promega, Madison, WI) and one clone per amplicon was sequenced (Macrogen Inc., Seoul, South Korea). The highest nucleotide sequence identity of the CP gene fragment obtained (GenBank Accession No. JN411685) was 99.2% related with North American ToCV isolates from Florida (DQ234674), Colorado (DQ234675), and Georgia (HQ879842), while the RdRp gene fragment (JN411686) was more closely related (99.0%) to the Spanish AT80/99 isolate (DQ983480). Although yellowing symptoms similar to those reported here have been observed sporadically during the last few years in open-field tomato crops in the state of Gezira, additional studies are needed to determine the prevalence and economic impact of ToCV infections in tomato cultivation in Sudan. To our knowledge, ToCV has been found in continental Africa only in Morocco and South Africa, in the Mediterranean climate areas in the northern and southern edges of the continent, respectively (2). The finding of ToCV infecting tomato in Sudan raises the question of whether this virus is emerging also in other tropical areas of the continent and illustrates the need to monitor whitefly-infested areas within Africa for the presence of ToCV.

References: (1) G. Lozano et al. J. Virol. 83:12973, 2009. (2) J. Navas-Castillo et al. Annu. Rev. Phytopathol. 49:219, 2011. (3) H. P. Trenado et al. Eur. J. Plant Pathol. 118:193, 2007. (4) G. C. Wisler et al. Plant Dis. 82:270, 1998.
Xylella fastidiosa Plasmid-Encoded PemK Toxin Is an Endoribonuclease
Authors: Lee Min Woo , Rogers Elizabeth E. , Stenger Drake C.
Published: August 2011

Stable inheritance of pXF-RIV11 in Xylella fastidiosa is conferred by the pemI/pemK toxin-antitoxin (TA) system. PemK toxin inhibits bacterial growth; PemI is the corresponding antitoxin that blocks activity of PemK by direct binding. PemK and PemI were overexpressed in Escherichia coli and activities of each were assessed. Purified PemK toxin specifically degraded single-stranded RNA but not double-stranded RNA, double-stranded DNA, or single-stranded DNA. Addition of PemI antitoxin inhibited nuclease activity of PemK toxin. Purified complexes of PemI bound to PemK exhibited minimal nuclease activity; removal of PemI antitoxin from the complex restored nuclease activity of PemK toxin. Sequencing of 5′ rapid amplification of cDNA ends products of RNA targets digested with PemK revealed a preference for cleavage between U and A residues of the sequence UACU and UACG. Nine single amino-acid substitution mutants of PemK toxin were constructed and evaluated for growth inhibition, ribonuclease activity, and PemI binding. Three PemK point-substitution mutants (R3A, G16E, and D79V) that lacked nuclease activity did not inhibit growth. All nine PemK mutants retained the ability to bind PemI. Collectively, the results indicate that the mechanism of stable inheritance conferred by pXF-RIV11 pemI/pemK is similar to that of the R100 pemI/pemK TA system of E. coli.
Exploring uncertainty in the calibration of the molecular clock
Authors: Warnock Rachel C. M. , Yang Ziheng , Donoghue Philip C. J.
Published: August 2011

Calibration is a critical step in every molecular clock analysis but it has been the least considered. Bayesian approaches to divergence time estimation make it possible to incorporate the uncertainty in the degree to which fossil evidence approximates the true time of divergence. We explored the impact of different approaches in expressing this relationship, using arthropod phylogeny as an example for which we established novel calibrations. We demonstrate that the parameters distinguishing calibration densities have a major impact upon the prior and posterior of the divergence times, and it is critically important that users evaluate the joint prior distribution of divergence times used by their dating programmes. We illustrate a procedure for deriving calibration densities in Bayesian divergence dating through the use of soft maximum constraints.
Incubation temperature affects multiple measures of immunocompetence in young wood ducks (Aix Sponsa)
Authors: DuRant Sarah E. , Hopkins William A. , Hawley Dana M. , Hepp Gary R.
Published: August 2011

Parental effects play a vital role in shaping offspring phenotype. In birds, incubation behaviour is a critical parental effect because it influences the early developmental environment and can therefore have lifelong consequences for offspring phenotype. Recent studies that manipulated incubation temperature found effects on hatchling body composition, condition and growth, suggesting that incubation temperature could also affect energetically costly physiological processes of young birds that are important to survival (e.g. immune responses). We artificially incubated wood duck (Aix sponsa) eggs at three biologically relevant temperatures. Following incubation, we used two immunoassays to measure acquired immune responses of ducklings. Ducklings incubated at the lowest temperature had reduced growth, body condition and responses to both of our immune challenges, compared with those from the higher temperatures. Our results show that incubation temperatures can be an important driver of phenotypic variation in avian populations.
Analysis and visualization of animal movement
Authors: Shamoun-Baranes Judy , van Loon E. Emiel , Purves Ross S. , Speckmann Bettina , Weiskopf Daniel , Camphuysen C. J.
Published: August 2011

The interdisciplinary workshop ‘
Analysis and Visualization of Moving Objects
’ was held at the Lorentz Centre in Leiden, The Netherlands, from 27 June to 1 July 2011. It brought together international specialists from ecology, computer science and geographical information science actively involved in the exploration, visualization and analysis of moving objects, such as marine reptiles, mammals, birds, storms, ships, cars and pedestrians. The aim was to share expertise, methodologies, data and common questions between different fields, and to work towards making significant advances in movement research. A data challenge based on GPS tracking of lesser black-backed gulls (
Larus fuscus
) was used to stimulate initial discussions, cross-fertilization between research groups and to serve as an initial focus for activities during the workshop.
Emergence, hierarchy and top-down causation in evolutionary biology
Authors: Okasha Samir
Published: August 2011

The concept of emergence and the related notion of ‘downward causation’ have arisen in numerous branches of science, and have also been extensively discussed in philosophy. Here, I examine emergence and downward causation in relation to evolutionary biology. I focus on the old, but ongoing discussion in evolutionary biology over the ‘levels of selection’ question: which level(s) of the biological hierarchy natural selection acts at, e.g. the gene, individual, group or species level? The concept of emergence has arisen in the levels-of-selection literature as a putative way of distinguishing between ‘true’ selection at a higher level from cases where selection acts solely at the lower level but has effects that percolate up the biological hierarchy, generating the
appearance
of higher level selection. At first blush, this problem seems to share a common structure with debates about emergence in other areas, but closer examination shows that it turns on issues that are sui generis to biology.
Emergence of coherent structures and large-scale flows in motile suspensions
Authors: Saintillan David , Shelley Michael J.
Published: August 2011

The emergence of coherent structures, large-scale flows and correlated dynamics in suspensions of motile particles such as swimming micro-organisms or artificial microswimmers is studied using direct particle simulations. A detailed model is proposed for a slender rod-like particle that propels itself in a viscous fluid by exerting a prescribed tangential stress on its surface, and a method is devised for the efficient calculation of hydrodynamic interactions in large-scale suspensions of such particles using slender-body theory and a smooth particle-mesh Ewald algorithm. Simulations are performed with periodic boundary conditions for various system sizes and suspension volume fractions, and demonstrate a transition to large-scale correlated motions in suspensions of rear-actuated swimmers, or Pushers, above a critical volume fraction or system size. This transition, which is not observed in suspensions of head-actuated swimmers, or Pullers, is seen most clearly in particle velocity and passive tracer statistics. These observations are consistent with predictions from our previous mean-field kinetic theory, one of which states that instabilities will arise in uniform isotropic suspensions of Pushers when the product of the linear system size with the suspension volume fraction exceeds a given threshold. We also find that the collective dynamics of Pushers result in giant number fluctuations, local alignment of swimmers and strongly mixing flows. Suspensions of Pullers, which evince no large-scale dynamics, nonetheless display interesting deviations from the random isotropic state.
Tilted cellulose arrangement as a novel mechanism for hygroscopic coiling in the stork's bill awn
Authors: Abraham Yael , Tamburu Carmen , Klein Eugenia , Dunlop John W. C. , Fratzl Peter , Raviv Uri , Elbaum Rivka
Published: August 2011

The sessile nature of plants demands the development of seed-dispersal mechanisms to establish new growing loci. Dispersal strategies of many species involve drying of the dispersal unit, which induces directed contraction and movement based on changing environmental humidity. The majority of researched hygroscopic dispersal mechanisms are based on a bilayered structure. Here, we investigate the motility of the stork's bill (
Erodium
) seeds that relies on the tightening and loosening of a helical awn to propel itself across the surface into a safe germination place. We show that this movement is based on a specialized single layer consisting of a mechanically uniform tissue. A cell wall structure with cellulose microfibrils arranged in an unusually tilted helix causes each cell to spiral. These cells generate a macroscopic coil by spiralling collectively. A simple model made from a thread embedded in an isotropic foam matrix shows that this cellulose arrangement is indeed sufficient to induce the spiralling of the cells.
Staining diatoms with rhodamine dyes: control of emission colour in photonic biocomposites
Authors: Kucki Melanie , Fuhrmann-Lieker Thomas
Published: August 2011

The incorporation of rhodamine dyes in the cell wall of diatomsCoscinodiscus graniiandCoscinodiscus wailesiifor the production of luminescent hybrid nanostructures is investigated. By systematic variation of the substitution pattern of the rhodamine core, we found that carbonic acids are considerably better suited than esters because of their physiological compatibility. The amino substitution pattern that controls the optical properties of the chromophore has no critical influence on dye uptake and incorporation, thus a variety of biocomposites with different emission maxima can be prepared. Applications in biomineralization studies as well as in materials science are envisioned.
Nanostructural self-assembly of iridescent feather barbules through depletion attraction of melanosomes during keratinization
Authors: Maia Rafael , Macedo Regina H. F. , Shawkey Matthew D.
Published: August 2011

Avian plumage colours are model traits in understanding the evolution of sexually selected ornamental traits. Paradoxically, iridescent structural colours, probably the most dazzling of these traits, remain the most poorly understood. Though some data suggest that expression of bright iridescent plumage colours produced by highly ordered arrays of melanosomes and keratin is condition-dependent, almost nothing is known of their ontogeny and thus of any developmental mechanisms that may be susceptible to perturbation. Here, we use light and electron microscopy to compare the ontogeny of iridescent male and non-iridescent female feathers in blue-black grassquits. Feather barbules of males contain a single layer of melanosomes bounded by a thin layer of keratin-producing blue iridescent colour, while those of females contain disorganized melanosomes and no outer layer. We found that nanostructural organization of male barbules occurs late in development, following death of the barbule cell, and is thus unlikely to be under direct cellular control, contrary to previous suggestions. Rather, organization appears to be caused by entropically driven self-assembly through depletion attraction forces that pin melanosomes to the edge of barbule cells and to one another. These forces are probably stronger in developing barbules of males than of females because their melanosomes are (i) larger, (ii) more densely packed, and (iii) more homogeneously distributed owing to the more consistent shape of barbules during keratinization. These data provide the first proposed developmental pathway for iridescent plumage colours, and suggest that any condition dependence of iridescent barbules is likely driven by factors other than direct metabolic cost.
The peopling of Europe and the cautionary tale of Y chromosome lineage R-M269
Authors: Busby George B. J. , Brisighelli Francesca , Sánchez-Diz Paula , Ramos-Luis Eva , Martinez-Cadenas Conrado , Thomas Mark G. , Bradley Daniel G. , Gusmão Leonor , Winney Bruce , Bodmer Walter , Vennemann Marielle , Coia Valentina , Scarnicci Francesca , Tofanelli Sergio , Vona Giuseppe , Ploski Rafal , Vecchiotti Carla , Zemunik Tatijana , Rudan Igor , Karachanak Sena , Toncheva Draga , Anagnostou Paolo , Ferri Gianmarco , Rapone Cesare , Hervig Tor , Moen Torolf , Wilson James F. , Capelli Cristian
Published: August 2011

Recently, the debate on the origins of the major European Y chromosome haplogroup R1b1b2-M269 has reignited, and opinion has moved away from Palaeolithic origins to the notion of a younger Neolithic spread of these chromosomes from the Near East. Here, we address this debate by investigating frequency patterns and diversity in the largest collection of R1b1b2-M269 chromosomes yet assembled. Our analysis reveals no geographical trends in diversity, in contradiction to expectation under the Neolithic hypothesis, and suggests an alternative explanation for the apparent cline in diversity recently described. We further investigate the young, STR-based time to the most recent common ancestor estimates proposed so far for R-M269-related lineages and find evidence for an appreciable effect of microsatellite choice on age estimates. As a consequence, the existing data and tools are insufficient to make credible estimates for the age of this haplogroup, and conclusions about the timing of its origin and dispersal should be viewed with a large degree of caution.
Manipulating individual state during migration provides evidence for carry-over effects modulated by environmental conditions
Authors: Legagneux Pierre , Fast Peter L. F. , Gauthier Gilles , Bêty Joël
Published: August 2011

Despite observational evidence of carry-over effects (COEs, events occurring in one season that produce residual effects on individuals the following seasons), to our knowledge no experimental studies have been carried out to explore how COEs might affect reproductive output. We simulated an environmental perturbation affecting spring-staging migrants to investigate COEs in greater snow geese (
Anser caerulescens atlanticus
). During three consecutive years, 2037 females captured during spring staging (approx. 3000 km south of their Arctic breeding grounds) were maintained in captivity (with or without access to food) for 0–4 days. Duration of captivity (but not food treatment) negatively affected reproductive success, probably through stress response. Reproductive success was reduced by 45–71% in 2 years, but not in a third year with unusually favourable breeding conditions. This unprecedented manipulation indicates that COEs can have a strong effect on individual reproductive success in long-distance migrants, but that this effect can be partly compensated for by good environmental conditions on the breeding ground.
Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
Authors: Schlattl Andreas , Anders Simon , Waszak Sebastian M. , Huber Wolfgang , Korbel Jan O.
Published: August 2011

Copy-number variants (CNVs) form an abundant class of genetic variation with a presumed widespread impact on individual traits. While recent advances, such as the population-scale sequencing of human genomes, facilitated the fine-scale mapping of CNVs, the phenotypic impact of most of these CNVs remains unclear. By relating copy-number genotypes to transcriptome sequencing data, we have evaluated the impact of CNVs, mapped at fine scale, on gene expression. Based on data from 129 individuals with ancestry from two populations, we identified CNVs associated with the expression of 110 genes, with 13% of the associations involving complex, multiallelic CNVs. Categorization of CNVs according to variant type, size, and gene overlap enabled us to examine the impact of different CNV classes on expression variation. While many small (<4 kb) CNVs were associated with expression variation, overall we observed an enrichment of large duplications and deletions, including large intergenic CNVs, relative to the entire set of expression-associated CNVs. Furthermore, the copy number of genes intersecting with CNVs typically correlated positively with the genes' expression, and also was more strongly correlated with expression than nearby single nucleotide polymorphisms, suggesting a frequent causal role of CNVs in expression quantitative trait loci (eQTLs). We also elucidated unexpected cases of negative correlations between copy number and expression by assessing the CNVs' effects on the structure and regulation of genes. Finally, we examined dosage compensation of transcript levels. Our results suggest that association studies can gain in resolution and power by including fine-scale CNV information, such as those obtained from population-scale sequencing.
Mutations in MYB3R1 and MYB3R4 Cause Pleiotropic Developmental Defects and Preferential Down-Regulation of Multiple G2/M-Specific Genes in Arabidopsis
Authors: Haga Nozomi , Kobayashi Kosuke , Suzuki Takamasa , Maeo Kenichiro , Kubo Minoru , Ohtani Misato , Mitsuda Nobutaka , Demura Taku , Nakamura Kenzo , Jürgens Gerd , Ito Masaki
Published: August 2011

R1R2R3-Myb proteins represent an evolutionarily conserved class of Myb family proteins important for cell cycle regulation and differentiation in eukaryotic cells. In plants, this class of Myb proteins are believed to regulate the transcription of G2/M phase-specific genes by binding to common cis-elements, called mitosis-specific activator (MSA) elements. In Arabidopsis (Arabidopsis thaliana), MYB3R1 and MYB3R4 act as transcriptional activators and positively regulate cytokinesis by activating the transcription of KNOLLE, which encodes a cytokinesis-specific syntaxin. Here, we show that the double mutation myb3r1 myb3r4 causes pleiotropic developmental defects, some of which are due to deficiency of KNOLLE whereas other are not, suggesting that multiple target genes are involved. Consistently, microarray analysis of the double mutant revealed altered expression of many genes, among which G2/M-specific genes showed significant overrepresentation of the MSA motif and a strong tendency to be down-regulated by the double mutation. Our results demonstrate, on a genome-wide level, the importance of the MYB3R-MSA pathway for regulating G2/M-specific transcription. In addition, MYB3R1 and MYB3R4 may have diverse roles during plant development by regulating G2/M-specific genes with various functions as well as genes possibly unrelated to the cell cycle.