bluuebunny/crossref_metadata_2025 huggingface dataset:
Wnt3a stimulates maturation of impaired neutrophils developed from severe congenital neutropenia patient-derived pluripotent stem cells
Authors: Hiramoto Takafumi , Ebihara Yasuhiro , Mizoguchi Yoko , Nakamura Kazuhiro , Yamaguchi Kiyoshi , Ueno Kazuko , Nariai Naoki , Mochizuki Shinji , Yamamoto Shohei , Nagasaki Masao , Furukawa Yoichi , Tani Kenzaburo , Nakauchi Hiromitsu , Kobayashi Masao , Tsuji Kohichiro
Published: February 2013

The derivation of induced pluripotent stem (iPS) cells from individuals of genetic disorders offers new opportunities for basic research into these diseases and the development of therapeutic compounds. Severe congenital neutropenia (SCN) is a serious disorder characterized by severe neutropenia at birth. SCN is associated with heterozygous mutations in the neutrophil elastase [elastase, neutrophil-expressed (ELANE)] gene, but the mechanisms that disrupt neutrophil development have not yet been clarified because of the current lack of an appropriate disease model. Here, we generated iPS cells from an individual with SCN (SCN-iPS cells). Granulopoiesis from SCN-iPS cells revealed neutrophil maturation arrest and little sensitivity to granulocyte-colony stimulating factor, reflecting a disease status of SCN. Molecular analysis of the granulopoiesis from the SCN-iPS cells vs. control iPS cells showed reduced expression of genes related to the wingless-type mmtv integration site family, member 3a (Wnt3a)/β-catenin pathway [e.g., lymphoid enhancer-binding factor 1], whereas Wnt3a administration induced elevation lymphoid enhancer-binding factor 1-expression and the maturation of SCN-iPS cell-derived neutrophils. These results indicate that SCN-iPS cells provide a useful disease model for SCN, and the activation of the Wnt3a/β-catenin pathway may offer a novel therapy for SCN with ELANE mutation.
Country-wide rainfall maps from cellular communication networks
Authors: Overeem Aart , Leijnse Hidde , Uijlenhoet Remko
Published: February 2013

Accurate and timely surface precipitation measurements are crucial for water resources management, agriculture, weather prediction, climate research, as well as ground validation of satellite-based precipitation estimates. However, the majority of the land surface of the earth lacks such data, and in many parts of the world the density of surface precipitation gauging networks is even rapidly declining. This development can potentially be counteracted by using received signal level data from the enormous number of microwave links used worldwide in commercial cellular communication networks. Along such links, radio signals propagate from a transmitting antenna at one base station to a receiving antenna at another base station. Rain-induced attenuation and, subsequently, path-averaged rainfall intensity can be retrieved from the signal’s attenuation between transmitter and receiver. Here, we show how one such a network can be used to retrieve the space–time dynamics of rainfall for an entire country (The Netherlands, ∼35,500 km
2
), based on an unprecedented number of links (∼2,400) and a rainfall retrieval algorithm that can be applied in real time. This demonstrates the potential of such networks for real-time rainfall monitoring, in particular in those parts of the world where networks of dedicated ground-based rainfall sensors are often virtually absent.
Quasiparticle dynamics in reshaped helical Dirac cone of topological insulators
Authors: Miao Lin , Wang Z. F. , Ming Wenmei , Yao Meng-Yu , Wang Meixiao , Yang Fang , Song Y. R. , Zhu Fengfeng , Fedorov Alexei V. , Sun Z. , Gao C. L. , Liu Canhua , Xue Qi-Kun , Liu Chao-Xing , Liu Feng , Qian Dong , Jia Jin-Feng
Published: February 2013

Topological insulators and graphene present two unique classes of materials, which are characterized by spin-polarized (helical) and nonpolarized Dirac cone band structures, respectively. The importance of many-body interactions that renormalize the linear bands near Dirac point in graphene has been well recognized and attracted much recent attention. However, renormalization of the helical Dirac point has not been observed in topological insulators. Here, we report the experimental observation of the renormalized quasiparticle spectrum with a skewed Dirac cone in a single Bi bilayer grown on Bi
2
Te
3
substrate from angle-resolved photoemission spectroscopy. First-principles band calculations indicate that the quasiparticle spectra are likely associated with the hybridization between the extrinsic substrate-induced Dirac states of Bi bilayer and the intrinsic surface Dirac states of Bi
2
Te
3
film at close energy proximity. Without such hybridization, only single-particle Dirac spectra are observed in a single Bi bilayer grown on Bi
2
Se
3
, where the extrinsic Dirac states Bi bilayer and the intrinsic Dirac states of Bi
2
Se
3
are well separated in energy. The possible origins of many-body interactions are discussed. Our findings provide a means to manipulate topological surface states.
How superhydrophobicity breaks down
Authors: Papadopoulos Periklis , Mammen Lena , Deng Xu , Vollmer Doris , Butt Hans-Jürgen
Published: February 2013

A droplet deposited or impacting on a superhydrophobic surface rolls off easily, leaving the surface dry and clean. This remarkable property is due to a surface structure that favors the entrainment of air cushions beneath the drop, leading to the so-called Cassie state. The Cassie state competes with the Wenzel (impaled) state, in which the liquid fully wets the substrate. To use superhydrophobicity, impalement of the drop into the surface structure needs to be prevented. To understand the underlying processes, we image the impalement dynamics in three dimensions by confocal microscopy. While the drop evaporates from a pillar array, its rim recedes via stepwise depinning from the edge of the pillars. Before depinning, finger-like necks form due to adhesion of the drop at the pillar’s circumference. Once the pressure becomes too high, or the drop too small, the drop slowly impales the texture. The thickness of the air cushion decreases gradually. As soon as the water–air interface touches the substrate, complete wetting proceeds within milliseconds. This visualization of the impalement dynamics will facilitate the development and characterization of superhydrophobic surfaces.
Resonance Raman and temperature-dependent electronic absorption spectra of cavity and noncavity models of the hydrated electron
Authors: Casey Jennifer R. , Larsen Ross E. , Schwartz Benjamin J.
Published: February 2013

Most of what is known about the structure of the hydrated electron comes from mixed quantum/classical simulations, which depend on the pseudopotential that couples the quantum electron to the classical water molecules. These potentials usually are highly repulsive, producing cavity-bound hydrated electrons that break the local water H-bonding structure. However, we recently developed a more attractive potential, which produces a hydrated electron that encompasses a region of enhanced water density. Both our noncavity and the various cavity models predict similar experimental observables. In this paper, we work to distinguish between these models by studying both the temperature dependence of the optical absorption spectrum, which provides insight into the balance of the attractive and repulsive terms in the potential, and the resonance Raman spectrum, which provides a direct measure of the local H-bonding environment near the electron. We find that only our noncavity model can capture the experimental red shift of the hydrated electron’s absorption spectrum with increasing temperature at constant density. Cavity models of the hydrated electron predict a solvation structure similar to that of the larger aqueous halides, leading to a Raman O–H stretching band that is blue-shifted and narrower than that of bulk water. In contrast, experiments show the hydrated electron has a broader and red-shifted O–H stretching band compared with bulk water, a feature recovered by our noncavity model. We conclude that although our noncavity model does not provide perfect quantitative agreement with experiment, the hydrated electron must have a significant degree of noncavity character.
Conditional inactivation of p53 in mature B cells promotes generation of nongerminal center-derived B-cell lymphomas
Authors: Gostissa Monica , Bianco Julia M. , Malkin Daniel J. , Kutok Jeffery L. , Rodig Scott J. , Morse Herbert C. , Bassing Craig H. , Alt Frederick W.
Published: February 2013

The p53 tumor suppressor exerts a central role in protecting cells from oncogenic transformation. Accordingly, the p53 gene is mutated in a large number of human cancers. In mice, germ-line inactivation of p53 confers strong predisposition to development of different types of malignancies, but the early onset of thymic lymphomas in the majority of the animals prevents detailed studies of tumorigenesis in other tissues. Here, we use the Cre/Lox approach to inactivate p53 in mature B cells in mice (referred to as “CP” B cells) and find that such p53 inactivation results in the routine development of IgM-positive CP peripheral B-cell lymphomas. The CP lymphomas generally appear to arise, even in mice subjected to immunization protocols to activate germinal center reaction, from naive B cells that had not undergone immunoglobulin (Ig) heavy chain gene class switching or somatic hypermutation. In contrast to thymic lymphomas that arise in p53-deficient mice, which generally lack clonal translocations, nearly all analyzed CP B-cell tumors carried clonal translocations. However, in contrast to spontaneous translocations in other mouse B-cell tumor models, CP B-cell tumor translocations were not recurrent and did not involve Ig loci. Therefore, CP tumors might provide models for human lymphomas lacking Ig translocations, such as splenic marginal zone B-cell lymphoma or Waldenstrom macroglobulinemia. Our studies indicate that deletion of p53 is sufficient to trigger transformation of mature B cells and support the notion that p53 deficiency may allow accumulation of oncogenic translocations in B cells.
Hierarchical model of natural images and the origin of scale invariance
Authors: Saremi Saeed , Sejnowski Terrence J.
Published: February 2013

The study of natural images and how our brain processes them has been an area of intense research in neuroscience, psychology, and computer science. We introduced a unique approach to studying natural images by decomposing images into a hierarchy of layers at different logarithmic intensity scales and mapping them to a quasi-2D magnet. The layers were in different phases: “cold” and ordered at large-intensity scales, “hot” and disordered at small-intensity scales, and going through a second-order phase transition at intermediate scales. There was a single “critical” layer in the hierarchy that exhibited long-range correlation similar to that found in the 2D Ising model of ferromagnetism at the critical temperature. We also determined the interactions between layers mapped from natural images and found mutual inhibition that generated locally “frustrated” antiferromagnetic states. Almost all information in natural images was concentrated in a few layers near the phase transition, which has biological implications and also points to the hierarchical origin of scale invariance in natural images.
CFTR-deficient pigs display peripheral nervous system defects at birth
Authors: Reznikov Leah R. , Dong Qian , Chen Jeng-Haur , Moninger Thomas O. , Park Jung Min , Zhang Yuzhou , Du Jianyang , Hildebrand Michael S. , Smith Richard J. H. , Randak Christoph O. , Stoltz David A. , Welsh Michael J.
Published: February 2013

Peripheral nervous system abnormalities, including neuropathy, have been reported in people with cystic fibrosis. These abnormalities have largely been attributed to secondary manifestations of the disease. We tested the hypothesis that disruption of the
cystic fibrosis transmembrane conductance regulator
(
CFTR
) gene directly influences nervous system function by studying newborn
CFTR

−/−

pigs. We discovered CFTR expression and activity in Schwann cells, and loss of CFTR caused ultrastructural myelin sheath abnormalities similar to those in known neuropathies. Consistent with neuropathic changes, we found increased transcripts for
myelin protein zero
, a gene that, when mutated, can cause axonal and/or demyelinating neuropathy. In addition, axon density was reduced and conduction velocities of the trigeminal and sciatic nerves were decreased. Moreover, in vivo auditory brainstem evoked potentials revealed delayed conduction of the vestibulocochlear nerve. Our data suggest that loss of
CFTR
directly alters Schwann cell function and that some nervous system defects in people with cystic fibrosis are likely primary.
8-CPT-cAMP/all-
trans
retinoic acid targets
t
(11;17) acute promyelocytic leukemia through enhanced cell differentiation and PLZF/RARα degradation
Authors: Jiao Bo , Ren Zhi-Hong , Liu Ping , Chen Li-Juan , Shi Jing-Yi , Dong Ying , Ablain Julien , Shi Lin , Gao Li , Hu Jun-Pei , Ren Rui-Bao , de Thé Hugues , Chen Zhu , Chen Sai-Juan
Published: February 2013

The refractoriness of acute promyelocytic leukemia (APL) with
t
(11;17)(q23;q21) to all-
trans
retinoic acid (ATRA)-based therapy concerns clinicians and intrigues basic researchers. By using a murine leukemic model carrying both
promyelocytic leukemia zinc finger/retinoic acid receptor-α
(
PLZF/RARα
) and
RARα/PLZF
fusion genes, we discovered that 8-chlorophenylthio adenosine-3′, 5′-cyclic monophosphate (8-CPT-cAMP) enhances cellular differentiation and improves gene
trans
-activation by ATRA in leukemic blasts. Mechanistically, in combination with ATRA, 8-CPT-cAMP activates PKA, causing phosphorylation of PLZF/RARα at Ser765 and resulting in increased dissociation of the silencing mediator for retinoic acid and thyroid hormone receptors/nuclear receptor corepressor from PLZF/RARα. This process results in changes of local chromatin and transcriptional reactivation of the retinoic acid pathway in leukemic cells. Meanwhile, 8-CPT-cAMP also potentiated ATRA-induced degradation of PLZF/RARα through its Ser765 phosphorylation. In vivo treatment of the
t
(11;17) APL mouse model demonstrated that 8-CPT-cAMP could significantly improve the therapeutic effect of ATRA by targeting a leukemia-initiating cell activity. This combined therapy, which induces enhanced differentiation and oncoprotein degradation, may benefit
t
(11;17) APL patients.
T cell activation induces proteasomal degradation of Argonaute and rapid remodeling of the microRNA repertoire
Authors: Bronevetsky Yelena , Villarino Alejandro V. , Eisley Christopher J. , Barbeau Rebecca , Barczak Andrea J. , Heinz Gitta A. , Kremmer Elisabeth , Heissmeyer Vigo , McManus Michael T. , Erle David J. , Rao Anjana , Ansel K. Mark
Published: February 2013

Activation induces extensive changes in the gene expression program of naive CD4+ T cells, promoting their differentiation into helper T cells that coordinate immune responses. MicroRNAs (miRNAs) play a critical role in this process, and miRNA expression also changes dramatically during T cell differentiation. Quantitative analyses revealed that T cell activation induces global posttranscriptional miRNA down-regulation in vitro and in vivo. Argonaute (Ago) proteins, the core effector proteins of the miRNA-induced silencing complex (miRISC), were also posttranscriptionally down-regulated during T cell activation. Ago2 was inducibly ubiquitinated in activated T cells and its down-regulation was inhibited by the proteasome inhibitor MG132. Therefore, activation-induced miRNA down-regulation likely occurs at the level of miRISC turnover. Measurements of miRNA-processing intermediates uncovered an additional layer of activation-induced, miRNA-specific transcriptional regulation. Thus, transcriptional and posttranscriptional mechanisms cooperate to rapidly reprogram the miRNA repertoire in differentiating T cells. Altering Ago2 expression in T cells revealed that Ago proteins are limiting factors that determine miRNA abundance. Naive T cells with reduced Ago2 and miRNA expression differentiated more readily into cytokine-producing helper T cells, suggesting that activation-induced miRNA down-regulation promotes acquisition of helper T cell effector functions by relaxing the repression of genes that direct T cell differentiation.
BION web server: predicting non-specifically bound surface ions
Authors: Petukh Marharyta , Kimmet Taylor , Alexov Emil
Published: February 2013

Motivation: Ions are essential component of the cell and frequently are found bound to various macromolecules, in particular to proteins. A binding of an ion to a protein greatly affects protein’s biophysical characteristics and needs to be taken into account in any modeling approach. However, ion’s bounded positions cannot be easily revealed experimentally, especially if they are loosely bound to macromolecular surface.

Results: Here, we report a web server, the BION web server, which addresses the demand for tools of predicting surface bound ions, for which specific interactions are not crucial; thus, they are difficult to predict. The BION is easy to use web server that requires only coordinate file to be inputted, and the user is provided with various, but easy to navigate, options. The coordinate file with predicted bound ions is displayed on the output and is available for download.

Availability:  http://compbio.clemson.edu/bion_server/

Supplementary information:  Supplementary data are available at Bioinformatics online.

Contact:  ealexov@clemson.edu
Cross-correlation of WMAP7 and the WISE full data release
Authors: Kovács András , Szapudi István , Granett Benjamin R. , Frei Zsolt
Published: February 2013

We measured the cross-correlation of the Wilkinson Microwave Anisotropy Probe (WMAP) 7-year temperature map and the full sky data release of the Wide-field Infrared Survey Explorer galaxy map. Using careful map-making and masking techniques we find a positive cross-correlation signal. The results are fully consistent with a ΛCDM universe, although not statistically significant. Our findings are robust against changing the Galactic latitude cut from |b| > 10° to |b| > 20° and no colour dependence was detected when we used WMAPQ, V or W maps. We confirm higher significance correlations found in the preliminary data release. The change in significance is consistent with cosmic variance.
Trans-Specific Gene Silencing of Acetyl-CoA Carboxylase in a Root-Parasitic Plant
Authors: Bandaranayake Pradeepa C. G. , Yoder John I.
Published: February 2013

Parasitic species of the family Orobanchaceae are devastating agricultural pests in many parts of the world. The control of weedy Orobanchaceae spp. is challenging, particularly due to the highly coordinated life cycles of the parasite and host plants. Although host genetic resistance often provides the foundation of plant pathogen management, few genes that confer resistance to root parasites have been identified and incorporated into crop species. Members of the family Orobanchaceae acquire water, nutrients, macromolecules, and oligonucleotides from host plants through haustoria that connect parasite and host plant roots. We are evaluating a resistance strategy based on using interfering RNA (RNAi) that is made in the host but inhibitory in the parasite as a parasite-derived oligonucleotide toxin. Sequences from the cytosolic acetyl-CoA carboxylase (ACCase) gene from Triphysaria versicolor were cloned in hairpin conformation and introduced into Medicago truncatula roots by Agrobacterium rhizogenes transformation. Transgenic roots were recovered for four of five ACCase constructions and infected with T. versicolor against parasitic weeds. In all cases, Triphysaria root viability was reduced up to 80% when parasitizing a host root bearing the hairpin ACCase. Triphysaria root growth was recovered by exogenous application of malonate. Reverse-transcriptase polymerase chain reaction (RT-PCR) showed that ACCase transcript levels were dramatically decreased in Triphysaria spp. parasitizing transgenic Medicago roots. Northern blot analysis identified a 21-nucleotide, ACCase-specific RNA in transgenic M. truncatula and in T. versicolor attached to them. One hairpin ACCase construction was lethal to Medicago spp. unless grown in media supplemented with malonate. Quantitative RT-PCR showed that the Medicago ACCase was inhibited by the Triphysaria ACCase RNAi. This work shows that ACCase is an effective target for inactivation in parasitic plants by trans-specific gene silencing.
Virulence Characterization of International Collections of the Wheat Stripe Rust Pathogen, Puccinia striiformis f. sp. tritici
Authors: Sharma-Poudyal D. , Chen X. M. , Wan A. M. , Zhan G. M. , Kang Z. S. , Cao S. Q. , Jin S. L. , Morgounov A. , Akin B. , Mert Z. , Shah S. J. A. , Bux H. , Ashraf M. , Sharma R. C. , Madariaga R. , Puri K. D. , Wellings C. , Xi K. Q. , Wanyera R. , Manninger K. , Ganzález M. I. , Koyda M. , Sanin S. , Patzek L. J.
Published: February 2013

Wheat stripe rust (yellow rust [Yr]), caused by Puccinia striiformis f. sp. tritici, is an economically important disease of wheat worldwide. Virulence information on P. striiformis f. sp. tritici populations is important to implement effective disease control with resistant cultivars. In total, 235 P. striiformis f. sp. tritici isolates from Algeria, Australia, Canada, Chile, China, Hungary, Kenya, Nepal, Pakistan, Russia, Spain, Turkey, and Uzbekistan were tested on 20 single Yr-gene lines and the 20 wheat genotypes that are used to differentiate P. striiformis f. sp. tritici races in the United States. The 235 isolates were identified as 129 virulence patterns on the single-gene lines and 169 virulence patterns on the U.S. differentials. Virulences to YrA, Yr2, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, YrUkn, Yr28, Yr31, YrExp2, Lemhi (Yr21), Paha (YrPa1, YrPa2, YrPa3), Druchamp (Yr3a, YrD, YrDru), Produra (YrPr1, YrPr2), Stephens (Yr3a, YrS, YrSte), Lee (Yr7, Yr22, Yr23), Fielder (Yr6, Yr20), Tyee (YrTye), Tres (YrTr1, YrTr2), Express (YrExp1, YrExp2), Clement (Yr9, YrCle), and Compair (Yr8, Yr19) were detected in all countries. At least 80% of the isolates were virulent on YrA, Yr2, Yr6, Yr7, Yr8, Yr17, YrUkn, Yr31, YrExp2, Yr21, Stephens (Yr3a, YrS, YrSte), Lee (Yr7, Yr22, Yr23), and Fielder (Yr6, Yr20). Virulences to Yr1, Yr9, Yr25, Yr27, Yr28, Heines VII (Yr2, YrHVII), Paha (YrPa1, YrPa2, YrPa3), Druchamp (Yr3a, YrD, YrDru), Produra (YrPr1, YrPr2), Yamhill (Yr2, Yr4a, YrYam), Tyee (YrTye), Tres (YrTr1, YrTr2), Hyak (Yr17, YrTye), Express (YrExp1, YrExp2), Clement (Yr9, YrCle), and Compair (Yr8, Yr19) were moderately frequent (>20 to <80%). Virulence to Yr10, Yr24, Yr32, YrSP, and Moro (Yr10, YrMor) was low (≤20%). Virulence to Moro was absent in Algeria, Australia, Canada, Kenya, Russia, Spain, Turkey, and China, but 5% of the Chinese isolates were virulent to Yr10. None of the isolates from Algeria, Canada, China, Kenya, Russia, and Spain was virulent to Yr24; none of the isolates from Algeria, Australia, Canada, Nepal, Russia, and Spain was virulent to Yr32; none of the isolates from Australia, Canada, Chile, Hungary, Kenya, Kenya, Nepal, Pakistan, Russia, and Spain was virulent to YrSP; and none of the isolates from any country was virulent to Yr5 and Yr15. Although the frequencies of virulence factors were different, most of the P. striiformis f. sp. tritici isolates from these countries shared common virulence factors. The virulences and their frequencies and distributions should be useful in breeding stripe-rust-resistant wheat cultivars and understanding the pathogen migration and evolution.
Age-Related Resistance to Phytophthora Fruit Rot in ‘Dickenson Field’ Processing Pumpkin and ‘Golden Delicious’ Winter Squash Fruit
Authors: Meyer M. D. , Hausbeck M. K.
Published: February 2013

Phytophthora fruit rot, caused by Phytophthora capsici, is a major constraint to cucurbit production for the processing industry in Michigan. Age-related resistance to Phytophthora fruit rot has been identified in pepper and some cucurbit fruit. In this study, ‘Dickenson Field’ processing pumpkin (Cucurbita moschata) and ‘Golden Delicious’ winter squash (C. maxima) were evaluated for age-related resistance to Phytophthora fruit rot. Hand-pollinated fruit were harvested 3, 7, 10, 14, 21, 28, 42, or 56 days post pollination (dpp), and inoculated with P. capsici isolate 12889. Susceptibility to Phytophthora fruit rot decreased with fruit age in Dickenson Field processing pumpkin, whereas Golden Delicious winter squash remained susceptible to fruit rot even as fruit reached full physiological maturity. Less than 15% of Dickenson Field fruit 21 dpp or older became diseased. Conversely, about 80% of Golden Delicious fruit 21 dpp or older became diseased. Lesion diameter and pathogen growth density ratings differed significantly (P < 0.0001) among fruit ages for both cultivars, and were negatively correlated (ρ = –0.37 to –0.87) with fruit age. Lesion diameter and pathogen growth were generally greater on younger fruit than older fruit. Lesion diameter was greatest on 7- and 10-dpp-old fruit of Dickenson Field and Golden Delicious, respectively. Pathogen growth density ratings were greatest on 3-dpp-old fruit of both cultivars. Several morphological and physiological changes were observed as fruit matured. Soluble solids content and exocarp firmness of both cultivars increased with fruit age. Lesion diameter and pathogen growth density ratings were negatively correlated (ρ = –0.29 to –0.73) with soluble solids content and exocarp firmness.
First Report of Southern tomato virus on Tomatoes in Southwest France
Authors: Candresse T. , Marais A. , Faure C.
Published: February 2013

Southern tomato virus (STV) is a recently described virus of tomato reported to be associated with a new disorder in this crop, the tomato yellow stunt disease (2). However, its detection in asymptomatic seedlings of some tomato varieties raises doubts about its pathogenicity (2). STV has a small 3.5-kb dsRNA genome with properties that place it in an intermediate position between the Totiviridae and Partitiviridae families. STV also has an unusual biology because, while being seed-transmitted at a high rate, it is neither mechanically nor graft-transmitted (2). It has so far only been reported from North America (Mississipi and California in the United States, as well as Mexico) (2). Agents with similar genomic organizations but apparently not associated with specific disease symptoms have recently been reported from faba bean, rhododendrons, and blueberry and proposed to represent a novel family of dsRNA viruses tentatively named Amalgamaviridae (1). In the course of plant virus metagenomics experiments, double stranded RNAs extracted from tomato samples from Southwest France collected in 2011 (variety unknown) were analyzed by 454 pyrosequencing. BLAST analysis of the contigs assembled from individual sequencing reads revealed a ca. 2.2 kb long contig with very high (99.7%) identity with the STV reference sequence deposited in GenBank (NC_011591). In order to confirm the presence of STV, an STV-specific primer pair (STV-fw 5′ CTGGAGATGAAGTGCTCGAAGA 3′ and STV-rev 5′ TGGCTCGTCTCGCATCCTTCG 3′) was designed and used to amplify by RT-PCR an 894-bp fragment from the relevant tomato sample. A PCR product of the expected size was obtained and the identity of the amplified agent verified by sequencing of the amplicon. The sequence obtained was identical to contig obtained through pyrosequencing of purified dsRNAs and has been deposited in GenBank (KC333078). This is, to our knowledge, the first report of STV infecting tomato crops outside of North America. The tomato sample from France from which STV was recovered showed distinct viral infection symptoms (e.g., mosaics, leaf deformation), that are clearly different from the symptoms reported for the tomato yellow stunt disease (2). However, the plants were found to be also infected with Tomato mosaic virus and Potato virus Y, so that it is not possible to draw firm conclusions about a potential contribution of STV to the symptoms observed. The high rate of STV seed transmission and its reported presence in commercial seed lots of several varieties (2) suggest that its distribution could be much broader than is currently known and further efforts are clearly needed to provide a final and conclusive answer as to the potential pathogenicity of this agent to tomato crops.

References: (1) R. R. Martin et al. Virus Res. 155:175, 2011. (2) S. Sabanadzovic et al. Virus Res. 140:130, 2009.
Revisiting the Specificity of PCR Primers for Diagnostics of Xanthomonas citri pv. citri by Experimental and In Silico Analyses
Authors: Delcourt Suzy , Vernière Christian , Boyer Claudine , Pruvost Olivier , Hostachy Bruno , Robène-Soustrade Isabelle
Published: February 2013

Asiatic citrus canker disease, caused by Xanthomonas citri pv. citri, seriously impacts citrus production worldwide. Two pathogenic variants, A and A*/Aw, have been described within this pathovar. Two additional pathovars of X. citri with a limited geographic distribution and reduced pathogenicity, namely X. citri pvs. aurantifolii and bilvae, are also pathogenic to citrus and some rutaceous species. Rapid and reliable identification is required for these citrus pathogens, which are classified as a quarantine organism in citrus-producing countries. The specificity of nine polymerase chain reaction primers previously designed for the identification of X. citri pv. citri or citrus bacterial canker strains (both pvs. citri and aurantifolii) was assayed on a large strain collection (n = 87), including the two pathotypes of X. citri pv. citri, other genetic related or unrelated pathogenic xanthomonads, and saprophytic xanthomonads. This study gave congruent results with the original articles when testing the same strains or pathovars but the use of a broad inclusivity and exclusivity panel of strains highlighted new findings. Particularly, primers 2/3, 4/7, and KingF/R failed to provide amplification for three strains from the pathotype A*/Aw. Moreover, all pairs of primers detected at least one non-target strain. These data were supported by in silico analysis of the DNA sequences available from National Center for Biotechnology Information databases.
Evaluation of Strategies for Fire Blight Control in Organic Pome Fruit Without Antibiotics
Authors: Johnson Kenneth B. , Temple Todd N.
Published: February 2013

Apple and pear produced organically under the U.S. National Organic Program (NOP) standard can be treated with antibiotics for suppression of fire blight caused by Erwinia amylovora. Recent regulatory actions by the NOP, however, have lessened the likelihood of antibiotic use after the 2014 season. In response, western U.S. organic apple and pear stakeholders identified two immediate-need research objectives related to fire blight control: development of effective non-antibiotic control programs based on combinations of registered biological products; and, in apple, integration of these products with lime sulfur, which is sprayed at early bloom to reduce fruit load. In orchard trials in Oregon, increasing the frequency of treatment with biological products improved suppression of floral infection. In apple, fruit load thinning with 2% lime sulfur plus 2% fish oil (LS+FO) at 30 and 70% bloom significantly (P ≤ 0.05) reduced the proportion of blighted flower clusters in four of five orchard trials. Moreover, lime sulfur significantly (P ≤ 0.05) suppressed epiphytic populations of E. amylovora after their establishment on apple flowers. Over four trials, treatment with Aureobasidium pullulans (Blossom Protect) after LS+FO reduced the incidence of fire blight by an average of 92% compared with water only; this level of control was similar to treatment with streptomycin. In three seasons, a spray of a Pantoea agglomerans product after the 70% bloom treatment of LS+FO established the antagonist on a significantly (P ≤ 0.05) higher proportion of flowers compared with a spray of this bacterium before the thinning treatment. Consequently, in apple, biological treatments for fire blight control are not advised until after lime sulfur treatments for fruit load thinning are completed.
Accounting for the Economic Risk Caused by Variation in Disease Severity in Fungicide Dose Decisions, Exemplified for Mycosphaerella graminicola on Winter Wheat
Authors: te Beest D. E. , Paveley N. D. , Shaw M. W. , van den Bosch F.
Published: February 2013

A method is presented to calculate economic optimum fungicide doses accounting for the risk aversion of growers responding to variability in disease severity between crops. Simple dose-response and disease-yield loss functions are used to estimate net disease-related costs (fungicide cost plus disease-induced yield loss) as a function of dose and untreated severity. With fairly general assumptions about the shapes of the probability distribution of disease severity and the other functions involved, we show that a choice of fungicide dose which minimizes net costs, on average, across seasons results in occasional large net costs caused by inadequate control in high disease seasons. This may be unacceptable to a grower with limited capital. A risk-averse grower can choose to reduce the size and frequency of such losses by applying a higher dose as insurance. For example, a grower may decide to accept “high-loss” years 1 year in 10 or 1 year in 20 (i.e., specifying a proportion of years in which disease severity and net costs will be above a specified level). Our analysis shows that taking into account disease severity variation and risk aversion will usually increase the dose applied by an economically rational grower. The analysis is illustrated with data on Septoria tritici leaf blotch of wheat caused by Mycosphaerella graminicola. Observations from untreated field plots at sites across England over 3 years were used to estimate the probability distribution of disease severities at mid-grain filling. In the absence of a fully reliable disease forecasting scheme, reducing the frequency of high-loss years requires substantially higher doses to be applied to all crops. Disease-resistant cultivars reduce both the optimal dose at all levels of risk and the disease-related costs at all doses.
Functional Analysis of Pid3-A4, an Ortholog of Rice Blast Resistance Gene Pid3 Revealed by Allele Mining in Common Wild Rice
Authors: Lv Qiming , Xu Xiao , Shang Junjun , Jiang Guanghuai , Pang Zhiqian , Zhou Zhuangzhi , Wang Jing , Liu Ya , Li Ting , Li Xiaobing , Xu Jichen , Cheng Zhukuan , Zhao Xianfeng , Li Shigui , Zhu Lihuang
Published: February 2013

The rice blast resistance gene Pid3 encodes a nucleotide-binding-site leucine-rich repeat (NBS-LRR) protein. This gene was cloned from the rice ‘Digu’ (indica) by performing a genome-wide comparison of the NBS-LRR gene family between two genome-sequenced varieties, ‘9311’ (indica) and ‘Nipponbare’ (japonica). In this study, we performed functional analysis of Pid3-A4, an ortholog of Pid3 revealed by allele mining in the common wild rice A4 (Oryza rufipogon). The predicted protein encoded by Pid3-A4 shares 99.03% sequence identity with Pid3, with only nine amino-acid substitutions. In wild rice plants, Pid3-A4 is constitutively expressed, and its expression is not induced by Magnaporthe oryzae isolate Zhong-10-8-14 infection. Importantly, in transgenic plants, Pid3-A4, as compared with Pid3, displays a distinct resistance spectrum to a set of M. oryzae isolates, including those that prevail in the rice fields of Sichuan Province. Therefore, Pid3-A4 should be quite useful for the breeding of rice blast resistance, especially in southwestern China.
Molecular evolutionary signatures reveal the role of host ecological dynamics in viral disease emergence and spread
Authors: Duke-Sylvester Scott M. , Biek Roman , Real Leslie A.
Published: February 2013

RNA viruses account for numerous emerging and perennial infectious diseases, and are characterized by rapid rates of molecular evolution. The ecological dynamics of most emerging RNA viruses are still poorly understood and difficult to ascertain. The availability of genome sequence data for many RNA viruses, in principle, could be used to infer ecological dynamics if changes in population numbers produced a lasting signature within the pattern of genome evolution. As a result, the rapidly emerging phylogeographic structure of a pathogen, shaped by the rise and fall in the number of infections and their spatial distribution, could be used as a surrogate for direct ecological assessments. Based on rabies virus as our example, we use a model combining ecological and evolutionary processes to test whether variation in the rate of host movement results in predictive diagnostic patterns of pathogen genetic structure. We identify several linearizable relationships between host dispersal rate and measures of phylogenetic structure suggesting genetic information can be used to directly infer ecological process. We also find phylogenetic structure may be more revealing than demography for certain ecological processes. Our approach extends the reach of current analytic frameworks for infectious disease dynamics by linking phylogeography back to underlying ecological processes.
Viral population analysis and minority-variant detection using short read next-generation sequencing
Authors: Watson Simon J. , Welkers Matthijs R. A. , Depledge Daniel P. , Coulter Eve , Breuer Judith M. , de Jong Menno D. , Kellam Paul
Published: February 2013

RNA viruses within infected individuals exist as a population of evolutionary-related variants. Owing to evolutionary change affecting the constitution of this population, the frequency and/or occurrence of individual viral variants can show marked or subtle fluctuations. Since the development of massively parallel sequencing platforms, such viral populations can now be investigated to unprecedented resolution. A critical problem with such analyses is the presence of sequencing-related errors that obscure the identification of true biological variants present at low frequency. Here, we report the development and assessment of the Quality Assessment of Short Read (QUASR) Pipeline (
http://sourceforge.net/projects/quasr
) specific for virus genome short read analysis that minimizes sequencing errors from multiple deep-sequencing platforms, and enables post-mapping analysis of the minority variants within the viral population. QUASR significantly reduces the error-related noise in deep-sequencing datasets, resulting in increased mapping accuracy and reduction of erroneous mutations. Using QUASR, we have determined influenza virus genome dynamics in sequential samples from an
in vitro
evolution of 2009 pandemic H1N1 (A/H1N1/09) influenza from samples sequenced on both the Roche 454 GSFLX and Illumina GAIIx platforms. Importantly, concordance between the 454 and Illumina sequencing allowed unambiguous minority-variant detection and accurate determination of virus population turnover
in vitro
.
Graph hierarchies for phylogeography
Authors: Cybis Gabriela B. , Sinsheimer Janet S. , Lemey Philippe , Suchard Marc A.
Published: February 2013

Bayesian phylogeographic methods simultaneously integrate geographical and evolutionary modelling, and have demonstrated value in assessing spatial spread patterns of measurably evolving organisms. We improve on existing phylogeographic methods by combining information from multiple phylogeographic datasets in a hierarchical setting. ConsiderNexchangeable datasets or strata consisting of viral sequences and locations, each evolving along its own phylogenetic tree and according to a conditionally independent geographical process. At the hierarchical level, a random graph summarizes the overall dispersion process by informing which migration rates between sampling locations are likely to be relevant in the strata. This approach provides an efficient and improved framework for analysing inherently hierarchical datasets. We first examine the evolutionary history of multiple serotypes of dengue virus in the Americas to showcase our method. Additionally, we explore an application to intrahost HIV evolution across multiple patients.
PRISM offers a comprehensive genomic approach to transcription factor function prediction
Authors: Wenger Aaron M. , Clarke Shoa L. , Guturu Harendra , Chen Jenny , Schaar Bruce T. , McLean Cory Y. , Bejerano Gill
Published: February 2013

The human genome encodes 1500–2000 different transcription factors (TFs). ChIP-seq is revealing the global binding profiles of a fraction of TFs in a fraction of their biological contexts. These data show that the majority of TFs bind directly next to a large number of context-relevant target genes, that most binding is distal, and that binding is context specific. Because of the effort and cost involved, ChIP-seq is seldom used in search of novel TF function. Such exploration is instead done using expression perturbation and genetic screens. Here we propose a comprehensive computational framework for transcription factor function prediction. We curate 332 high-quality nonredundant TF binding motifs that represent all major DNA binding domains, and improve cross-species conserved binding site prediction to obtain 3.3 million conserved, mostly distal, binding site predictions. We combine these with 2.4 million facts about all human and mouse gene functions, in a novel statistical framework, in search of enrichments of particular motifs next to groups of target genes of particular functions. Rigorous parameter tuning and a harsh null are used to minimize false positives. Our novel PRISM (predicting regulatory information from single motifs) approach obtains 2543 TF function predictions in a large variety of contexts, at a false discovery rate of 16%. The predictions are highly enriched for validated TF roles, and 45 of 67 (67%) tested binding site regions in five different contexts act as enhancers in functionally matched cells.
Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation
Authors: Hiatt Joseph B. , Pritchard Colin C. , Salipante Stephen J. , O'Roak Brian J. , Shendure Jay
Published: February 2013

The detection and quantification of genetic heterogeneity in populations of cells is fundamentally important to diverse fields, ranging from microbial evolution to human cancer genetics. However, despite the cost and throughput advances associated with massively parallel sequencing, it remains challenging to reliably detect mutations that are present at a low relative abundance in a given DNA sample. Here we describe smMIP, an assay that combines single molecule tagging with multiplex targeted capture to enable practical and highly sensitive detection of low-frequency or subclonal variation. To demonstrate the potential of the method, we simultaneously resequenced 33 clinically informative cancer genes in eight cell line and 45 clinical cancer samples. Single molecule tagging facilitated extremely accurate consensus calling, with an estimated per-base error rate of 8.4 × 10−6 in cell lines and 2.6 × 10−5 in clinical specimens. False-positive mutations in the single molecule consensus base-calls exhibited patterns predominantly consistent with DNA damage, including 8-oxo-guanine and spontaneous deamination of cytosine. Based on mixing experiments with cell line samples, sensitivity for mutations above 1% frequency was 83% with no false positives. At clinically informative sites, we identified seven low-frequency point mutations (0.2%–4.7%), including BRAF p.V600E (melanoma, 0.2% alternate allele frequency), KRAS p.G12V (lung, 0.6%), JAK2 p.V617F (melanoma, colon, two lung, 0.3%–1.4%), and NRAS p.Q61R (colon, 4.7%). We anticipate that smMIP will be broadly adoptable as a practical and effective method for accurately detecting low-frequency mutations in both research and clinical settings.
A new methanol solvate and Hirshfeld analysis of π-stacking in 2,3,6,7,10,11-hexahydroxytriphenylene solvates
Authors: Karmakar Anirban , Platero-Prats Ana E. , Öhrström Lars
Published: February 2013

The structure of 2,3,6,7,10,11-hexahydroxytriphenylene (hhtp) methanol monosolvate, C18H12O6·CH3OH, has triclinic symmetry (space groupP\overline{1}). The compound has a three-dimensional layered network structure formed by intermolecular hydrogen bonding. Structure analysis with Hirshfeld surfaces is shown to be a sensitive method for comparing π-stacking effects in the five known solvates of hhtp. The title structure shows slightly weaker π-stacking than the dihydrate, but stronger π-stacking than the other three solvates.
A polymeric cobalt(II) complex derived from citric acid (H4cit) and 2,6-diaminopurine (dap): {[Co4(cit)2(dap)4(H2O)4]·6.35H2O}n
Authors: Atria Ana María , Parada José , Garland Maria Teresa , Baggio Ricardo
Published: February 2013

Poly[[tetraaquadi-μ4-citrato-tetrakis(2,6-diaminopurine)tetracobalt(II)] 6.35-hydrate], {[Co4(C6H4O7)2(C5H6N6)4(H2O)4]·6.35H2O}n, presents three different types of CoIIcations in the asymmetric unit, two of them lying on symmetry elements (one on an inversion centre and the other on a twofold axis). The main fragment is further composed of one fully deprotonated citrate (cit) tetraanion, two 2,6-diaminopurine (dap) molecules and two aqua ligands. The structure is completed by a mixture of fully occupied and disordered solvent water molecules. The two independent dap ligands are neutral and the cit tetraanion provides for charge balance, compensating the 4+ cationic charge. There are two well defined coordination geometries in the structure. The simplest is mononuclear, with the CoIIcation arranged in a regular centrosymmetric octahedral array, coordinated by two aqua ligands, two dap ligands and two O atoms from the β-carboxylate groups of the bridging cit tetraanions. The second, more complex, group is trinuclear, bisected by a twofold axis, with the metal centres coordinated by two cit tetraanions through their α- and β-carboxylate and α-hydroxy groups, and by two dap ligands bridging through one of their pyridine and one of their imidazole N atoms. The resulting coordination geometry around each metal centre is distorted octahedral. Both groups are linked alternately to each other, defining parallel chains along [201], laterally interleaved and well connectedviahydrogen bonding to form a strongly coupled three-dimensional network. The compound presents a novel μ4-κ5O:O,O′:O′,O′′,O′′′:O′′′′ mode of coordination of the cit tetraanion.
An X-ray crystallographic and density functional theory study of (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one
Authors: Akerman Kate J. , Munro Orde Q.
Published: February 2013

The Schiff base enaminones (3Z)-4-(5-ethylsulfonyl-2-hydroxyanilino)pent-3-en-2-one, C13H17NO4S, (I), and (3Z)-4-(5-tert-butyl-2-hydroxyanilino)pent-3-en-2-one, C15H21NO2, (II), were studied by X-ray crystallography and density functional theory (DFT). Although the keto tautomer of these compounds is dominant, the O=C—C=C—N bond lengths are consistent with some electron delocalization and partial enol character. Both (I) and (II) are nonplanar, with the amino–phenol group canted relative to the rest of the molecule; the twist about the N(enamine)—C(aryl) bond leads to dihedral angles of 40.5 (2) and −116.7 (1)° for (I) and (II), respectively. Compound (I) has a bifurcated intramolecular hydrogen bond between the N—H group and the flanking carbonyl and hydroxy O atoms, as well as an intermolecular hydrogen bond, leading to an infinite one-dimensional hydrogen-bonded chain. Compound (II) has one intramolecular hydrogen bond and one intermolecular C=O...H—O hydrogen bond, and consequently also forms a one-dimensional hydrogen-bonded chain. The DFT-calculated structures [in vacuo, B3LYP/6-311G(d,p) level] for the keto tautomers compare favourably with the X-ray crystal structures of (I) and (II), confirming the dominance of the keto tautomer. The simulations indicate that the keto tautomers are 20.55 and 18.86 kJ mol−1lower in energy than the enol tautomers for (I) and (II), respectively.