bluuebunny/crossref_metadata_2025_split huggingface dataset:
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6
Authors: Bengtsson Henrik , Wirapati Pratyaksha , Speed Terence P. 
Published: June 2009

Abstract
Motivation: High-resolution copy-number (CN) analysis has in recent years gained much attention, not only for the purpose of identifying CN aberrations associated with a certain phenotype, but also for identifying CN polymorphisms. In order for such studies to be successful and cost effective, the statistical methods have to be optimized. We propose a single-array preprocessing method for estimating full-resolution total CNs. It is applicable to all Affymetrix genotyping arrays, including the recent ones that also contain non-polymorphic probes. A reference signal is only needed at the last step when calculating relative CNs.
Results: As with our method for earlier generations of arrays, this one controls for allelic crosstalk, probe affinities and PCR fragment-length effects. Additionally, it also corrects for probe sequence effects and co-hybridization of fragments digested by multiple enzymes that takes place on the latest chips. We compare our method with Affymetrix's CN5 method and the dChip method by assessing how well they differentiate between various CN states at the full resolution and various amounts of smoothing. Although CRMA v2 is a single-array method, we observe that it performs as well as or better than alternative methods that use data from all arrays for their preprocessing. This shows that it is possible to do online analysis in large-scale projects where additional arrays are introduced over time.
Availability: A bounded-memory implementation that can process any number of arrays is available in the open source R package aroma.affymetrix.
Contact: hb@stat.berkeley.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
A fast hybrid short read fragment assembly algorithm
Authors: Schmidt Bertil , Sinha Ranjan , Beresford-Smith Bryan , Puglisi Simon J. 
Published: June 2009

Abstract
Summary: The shorter and vastly more numerous reads produced by second-generation sequencing technologies require new tools that can assemble massive numbers of reads in reasonable time. Existing short-read assembly tools can be classified into two categories: greedy extension-based and graph-based. While the graph-based approaches are generally superior in terms of assembly quality, the computer resources required for building and storing a huge graph are very high. In this article, we present Taipan, an assembly algorithm which can be viewed as a hybrid of these two approaches. Taipan uses greedy extensions for contig construction but at each step realizes enough of the corresponding read graph to make better decisions as to how assembly should continue. We show that this approach can achieve an assembly quality at least as good as the graph-based approaches used in the popular Edena and Velvet assembly tools using a moderate amount of computing resources.
Availability and Implementation: Source code in C running on Linux is freely available at http://taipan.sourceforge.net
Contact: asbschmidt@ntu.edu.sg
First Report of a Fruit Rot Disease of Avocado Caused by Neofusicoccum mangiferae
Authors: Ni H. F. , Liou R. F. , Hung T. H. , Chen R. S. , Yang H. R. 
Published: June 2009

Production of avocado (Persea americana) has increased significantly during the last 10 years in Taiwan and the area of cultivation is approximately 500 ha. The most important postharvest disease of avocado is anthracnose caused by Colletotrichum gloeosporioides (Penz.) in Taiwan (1). In 2008, a new disease was found to be infecting avocado fruit at some orchards in Tainan County of southern Taiwan. Infected avocados developed smooth, brown, circular spots first on the surface of harvested fruits. A fungus was always isolated from the margin of lesions and could also be found from symptomless fruit pedicles and stems. Fungal colonies cultured on acidified potato dextrose agar (PDA with lactic acid; pH 3.8) were initially colorless, turned dark gradually, and ultimately became gray to dark gray. After 4 days under fluorescent light at 25°C, pycnidia formed on PDA. Conidia obtained from fruiting bodies were ovate, one celled, and hyaline, with an average length and width of 12.9 (9.9 to 15.6) × 6.4 (5.2 to 7.2) μm. The internal transcribed spacer (ITS) sequence of ribosomal DNA of this fungus was analyzed and submitted to GenBank (No. EU847427). It showed a sequence identity of 99% with Neofusicoccum mangiferae ((Syd. & P. Syd.) Crous, Slippers & A.J.L. Phillips) (GenBank No. AY615185). Thus, both morphological and molecular results confirmed the isolated fungus as N. mangiferae. Five avocado fruits were used to test the pathogenicity with three different treatment inoculation sites on each fruit. Wounded and unwounded sites on fruit were inoculated with mycelia agar plugs (0.5 mm in diameter) excised from a monoconidial culture and the fruit was kept in a plastic box with high humidity for 2 days at room temperature. Brown lesions appeared on all wounded sites 2 days postinoculation (dpi) and on unwounded sites at 4 dpi. The pathogen was reisolated from the lesions of inoculated fruits and found to be N. mangiferae, thus fulfilling Koch's postulates. In control experiments, sterile agar plugs were placed on the wounded avocado fruits. These fruits remained completely free from symptoms throughout the experiment. Several species of Botryosphaeria have been reported on avocado, including N. parvum (anamorph of B. parva), Fusicoccum aesculi (anamorph of B. dothidea), and Dothiorella aromatica (= F. luteum). To our knowledge, this is the first report of N. mangiferae causing fruit rot of avocado in Taiwan. Previously, N. mangiferae has been reported on mango trees worldwide, especially in Australia and Thailand (2). The presence of N. mangiferae in the subtropical area presents a serious disease problem not only to avocado but also to mango. References: (1) Y. P. Tsai, ed. List of Plant Diseases in Taiwan. 4th ed. Taiwan Phytopathological Society, 2002. (2) B. Slippers et al. Mycologia 97:99, 2005.
Identification and Incidence of Iris yellow spot virus, a New Pathogen in Onion and Leek in Greece
Authors: Chatzivassiliou E. K. , Giavachtsia V. , Mehraban A. H. , Hoedjes K. , Peters D. 
Published: June 2009

Iris yellow spot virus (IYSV; genus Tospovirus, family Bunyaviridae) is an emerging and serious pathogen affecting several Allium spp. worldwide (2). The virus causes straw-colored, chlorotic or necrotic lesions that coalesce, occasionally resulting in an extensive necrosis on onion (A. cepa L.) leaves. From February to June 2008, 530 onion and 439 leek (A. porum L.) leaf samples showing a variety of lesions were collected from different areas of Greece. All plants sampled were infested with Thrips tabaci Lindeman, the sole thrips species identified as the vector of this virus. Samples were analyzed by double-antibody sandwich (DAS)-ELISA using polyclonal antibodies against the N protein of IYSV (Laboratory of Virology, Wageningen Agricultural University). A higher percentage of onion samples than leek samples were infected, with IYSV detected in 36, 44, 23.7, 61.7, 10, 55, 15.3, and 9.4% of onion samples from the prefectures of Evros, Heraklion, Kavala, Magnissia, Pella, Rodopi, Thessaloniki, and Viotia, respectively, and in 5, 0, 0, 9.3, and 13% of leek samples from Evros, Heraklion, Magnissia, Pella, and Thessaloniki, respectively. No leek samples were tested from Kavala, Rodopi, and Viotia. Sap extracts from some positive samples were mechanically inoculated onto Nicotiana benthamiana leaves, and infected plants developed typical IYSV symptoms and were positive in DAS-ELISA, confirming transmission from the field samples. Viral RNA was extracted from ELISA-positive onion and leek samples and an ~800-bp amplicon was obtained from both hosts by reverse-transcription (RT)-PCR and N-gene primers derived from IYSV (IY1: 5′-CCCGAGGATCCATGGCTACCGTTAGGG-3′ and IY2: 5′-CCCGAGGATCCAAATTAATTATATCTATCTTTCTTGG-3′) (1). These amplicons were cloned and sequenced (GenBank Accession No. FJ785835) and nucleotide sequence comparisons showed a 98 to 99% identity with a Dutch isolate of IYSV (GenBank Accession No AF001387). The virus was transmitted among onion seedlings in the laboratory using a leek population of T. tabaci. Infected seedlings, as determined by DAS-ELISA, developed symptoms similar to those observed in the field samples. To our knowledge, this is the first report of IYSV in Greece; however, the virus seems already to be very well established. References: (1) I. Cortez et al. Phytopathology 88:1276, 1998. (2) D. Gent et al. Plant. Dis. 90:1468, 2006.
First Report of Tobacco mild green mosaic virus Infecting Capsicum annuum in Tunisia
Authors: Font M. I. , Córdoba-Sellés M. C. , Cebrián M. C. , Herrera-Vásquez J. A. , Alfaro-Fernández A. , Boubaker A. , Soltani I. , Jordá C. 
Published: June 2009

During the springs of 2007 and 2008, leaf deformations as well as symptoms of mild green and chlorotic mosaic were observed on pepper (Capsicum annuum) plants grown in Monastir (northwest Tunisia) and Kebili (southeast Tunisia). With the support of projects A/5269/06 and A/8584/07 from the Spanish Agency for International Cooperation (AECI), symptomatic leaf samples were analyzed by transmission electron microscopy (TEM) of leaf-dip preparations. Typical tobamovirus-like particles (rigid rods ≈300 nm long) were observed in crude plant extracts. According to literature, at least six tobamoviruses infect peppers: Paprika mild mottle virus (PaMMV); Pepper mild mottle virus (PMMoV); Ribgrass mosaic virus (RMV); Tobacco mild green mosaic virus (TMGMV); Tobacco mosaic virus (TMV); and Tomato mosaic virus (ToMV) (1). Extracts from six symptomatic plants from Monastir and four from Kebili fields tested negative for ToMV, TMV, and PMMoV and tested positive for TMGMV by double-antibody sandwich (DAS)-ELISA using polyclonal antibodies specific to each virus (Loewe Biochemica GMBH, Sauerlach, Germany). To confirm the positive TMGMV results, total RNAs from 10 symptomatic plants that tested positive by ELISA were extracted and analyzed by reverse transcription (RT)-PCR using primers designed to specifically amplify a region of the coat protein gene (CP) of TMGMV (2). The 524-bp TMGMV-CP specific DNA fragment was amplified from all samples, but was not amplified from healthy plants or the sterile water used with negative controls. RT-PCR products were purified and directly sequenced. BLAST analysis of the obtained sequence (GenBank No. EU770626) showed 99 to 98% nucleotide identity with TMGMV isolates PAN-1, DSMZ PV-0113, TMGMV-Pt, and VZ1 (GenBank Nos. EU934035, EF469769, AM262165, and DQ460731, respectively) and less than 69% with PaMMV and PMMoV isolates (GenBank Nos. X72586 and AF103777, respectively). Two TMGMV-positive, singly, infected symptomatic pepper plants collected from Monastir and Kebili were used in mechanical transmissions to new pepper and tomato plants. Inoculated pepper plants exhibited mild chlorosis symptoms and tested positive for TMGMV only; however, inoculated tomato plants cv. Marmande were asymptomatic and tested negative as expected for TMGMV infection (1). To our knowledge, although C. annuum has been shown as a natural host for TMGMV (2), this is the first report of TMGMV in Tunisia. Reference: (1) A. A. Brunt et al. Plant Viruses Online: Descriptions and Lists from the VIDE Database. Version: 20th August 1996. Online publication, 1996. (2) J. Cohen et al. Ann. Appl. Biol. 138:153, 2001.
First Report of Natural Infection of Penstemon acuminatus with Cucumber mosaic virus in the Treasure Valley Region of Idaho and Oregon
Authors: Sampangi R. K. , Almeyda C. , Druffel K. L. , Mohan S. Krishna , Shock C. C. , Pappu H. R. 
Published: June 2009

Penstemons are perennials that are grown for their attractive flowers in the United States. Penstemon species (P. acuminatus, P. deustus, and P. speciosus) are among the native forbs considered as a high priority for restoration of great basin rangelands. During the summer of 2008, symptoms of red spots and rings were observed on leaves of P. acuminatus (family Scrophulariaceae) in an experimental trial in Malheur County, Oregon where the seeds from several native forbs were multiplied for restoration of range plants in intermountain areas. These plants were cultivated as part of the Great Basin Native Plant Selection and Increase Project. Several native wildflower species are grown for seed production in these experimental plots. Plants showed red foliar ringspots and streaks late in the season. Fungal or bacterial infection was ruled out. Two tospoviruses, Impatiens necrotic spot virus and Tomato spotted wilt virus, and one nepovirus, Tomato ring spot virus, are known to infect penstemon (2,3). Recently, a strain of Turnip vein-clearing virus, referred to as Penstemon ringspot virus, was reported in penstemon from Minnesota (1). Symptomatic leaves from the penstemon plants were negative for these viruses when tested by ELISA or reverse transcription (RT)-PCR. However, samples were found to be positive for Cucumber mosaic virus (CMV) when tested by a commercially available kit (Agdia Inc., Elkhart, IN). To verify CMV infection, total nucleic acid extracts from the symptomatic areas of the leaves were prepared and used in RT-PCR. Primers specific to the RNA-3 of CMV were designed on the basis of CMV sequences available in GenBank. The primer pair consisted of CMV V166: 5′ CCA ACC TTT GTA GGG AGT GA 3′ and CMV C563: 5′ TAC ACG AGG ACG GCG TAC TT 3′. An amplicon of the expected size (400 bp) was obtained and cloned and sequenced. BLAST search of the GenBank for related sequences showed that the sequence obtained from penstemon was highly identical to several CMV sequences, with the highest identity (98%) with that of a sequence from Taiwan (GenBank No. D49496). CMV from infected penstemon was successfully transmitted by mechanical inoculation to cucumber seedlings. Infection of cucumber plants was confirmed by ELISA and RT-PCR. To our knowledge, this is the first report of CMV infection of P. acuminatus. With the ongoing efforts to revegetate the intermountain west with native forbs, there is a need for a comprehensive survey of pests and diseases affecting these plants. References: (1) B. E. Lockhart et al. Plant Dis. 92:725, 2008. (2) D. Louro. Acta Hortic. 431:99, 1996. (3) M. Navalinskiene et al. Trans. Estonian Agric. Univ. 209:140, 2000.
First Report of Brown Rot Caused by Monilinia fructicola in Peach Orchards in Ebro Valley, Spain
Authors: De Cal A. , Gell I. , Usall J. , Viñas I. , Melgarejo P. 
Published: June 2009

Monilinia fructicola causes brown rot of stone fruit in India, Japan, the Republic of Korea, Oceania, and North and South America and is in the A2 list of quarantine organisms for Europe. M. fructicola was found in peach orchards for the first time in Europe in 2001 in France (4) and later in the Czech Republic (2). M. fructicola was not detected among 428 isolates of Monilinia spp. collected from Spanish peach orchards from 1998 to 2005. In March of 2006, M. fructicola was detected to be overwintering in three mummified peach fruit (cv. Autumn Free) trees in an orchard located in Sudanell (Lleida, Spain). Morphological and molecular identification of isolates were performed according to protocols previously described (1,3). The characteristics of these isolates were: i) colonies were entire and showing concentric rings of spores when grown on potato dextrose agar (PDA); ii) sporogenous tissues were gray to buff; iii) single and nearly straight germ tubes were at least 220 μm long before branching; and iv) growth rates on PDA under long-wave UV/darkness were as much as 20 × 10 mm2. Isolates were further identified by a PCR test using primers developed with sequence-characterized amplification region markers obtained by random amplified polymorphic DNA for M. fructicola: IColaS (GAGACGCACACAGAGTCAG) and IColaAS (GAGACGCACATAGCATTGG) (3). The expected PCR product of 386 bp was produced only in M. fructicola isolates. Koch's postulates were fulfilled with the three isolates by inoculating five healthy fruit with a conidial suspension of each isolate (104 conidia ml–1). Symptoms similar to those observed in the field were small brown spots, which rapidly showed brown rot. Noninoculated control fruit did not show symptoms. The fungus was reisolated on PDA from inoculated fruit after 4 days of incubation at 22°C, 80 to 100% relative humidity, and 16 h under fluorescent lighting, 100 μE·m–2·s–1. To our knowledge, this is the first report of M. fructicola in peach orchards in Spain. References: (1) A. De Cal and P. Melgarejo. Plant Dis. 83:62, 1999. (2) J. Duchoslavová et al. Plant Dis. 91:907, 2007. (3) I. Gell et al. J. Appl. Microbiol. 103:2629, 2007. (4) J. Lichou et al. Phytoma 547:22, 2002.
First Report of the Occurrence of Sweet potato leaf curl virus in Tall Morningglory (Ipomoea purpurea) in China
Authors: Yang C. X. , Wu Z. J. , Xie L. H. 
Published: June 2009

Natural occurrence of Sweet potato leaf curl virus (SPLCV) has been reported in Ipomoea batatas (sweet potato, Convolvulaceae) or I. indica (Convolvulaceae) in several countries including the United States, Sicily, and China (1–3). In September of 2007, while collecting samples showing begomovirus-like symptoms in the Chinese province of Fujian, we observed tall morningglory (I. purpurea (L.) Roth, also known as Pharbitis purpurea (L.) Voigt), plants with slightly yellow mosaic and crinkled leaves. Total DNA was extracted from leaves of these plants and tested by rolling circle amplification (4). Amplification products were digested by the restriction enzyme BamHI for 30 min. Restriction products (2.8 kb) were then cloned into pMD18T vector (Takara Biotechnology, China) and sequenced. Comparison of complete DNA sequences by Clustal V analysis revealed that these samples were infected by the same virus, and an isolate denoted F-p1 was selected for further sequence analysis. F-p1 was 2,828 nucleotides, with the typical genomic organization of begomoviral DNA-A (GenBank Accession No. FJ515896). F-p1 was compared with the DNA sequences available in the NCBI database using BLAST. The whole DNA sequence showed the highest nucleotide sequence identity (92.1%) with an isolate of SPLCV (GenBank Accession No. FJ176701) from Jiangsu Province of China. The result confirmed that the samples from the symptomatic tall morningglory were infected by SPLCV. To our knowledge, this is the first report of the natural occurrence of SPLCV in I. purpurea, a common weed species in China. References: (1). P. Lotrakul et al. Plant Dis. 82:1253, 1998. (2). R. W. Briddon et al. Plant Pathol. 55:286, 2006. (3) Y. S. Luan et al. Virus Genes 35:379, 2007. (4) D. Haible et al. J. Virol. Methods 135:9, 2006.
A new psittacosaur from Inner Mongolia and the parrot-like structure and function of the psittacosaur skull
Authors: Sereno Paul C. , Xijin Zhao , Lin Tan 
Published: June 2009

We describe a new species of psittacosaur,Psittacosaurus gobiensis, from the Lower Cretaceous of Inner Mongolia and outline a hypothesis of chewing function in psittacosaurs that in many respects parallels that in psittaciform birds. Cranial features that accommodate increased bite force in psittacosaurs include an akinetic skull (both cranium and lower jaws) and differentiation of adductor muscle attachments comparable to that in psittaciform birds. These and other features, along with the presence of numerous large gastroliths, suggest that psittacosaurs may have had a high-fibre, nucivorous (nut-eating) diet.Psittacosaurs, alone among ornithischians, generate oblique wear facets from tooth-to-tooth occlusion without kinesis in either the upper or lower jaws. This is accomplished with a novel isognathous jaw mechanism that combines aspects of arcilineal (vertical) and propalinal (horizontal) jaw movement. Here termed clinolineal (inclined) jaw movement, the mechanism uses posteriorly divergent tooth rows, rather than kinesis, to gain the added width for oblique occlusion. As the lower tooth rows are drawn posterodorsally into occlusion, the increasing width between the upper tooth rows accommodates oblique shear. With this jaw mechanism, psittacosaurs were able to maintain oblique shearing occlusion in an akinetic skull designed to resist high bite forces.
HORMONOMETER: A Tool for Discerning Transcript Signatures of Hormone Action in the Arabidopsis Transcriptome
Authors: Volodarsky Dina , Leviatan Noam , Otcheretianski Andrei , Fluhr Robert 
Published: June 2009

AbstractPlant hormones regulate growth and responses to environmental change. Hormone action ultimately modifies cellular physiological processes and gene activity. To facilitate transcriptome evaluation of novel mutants and environmental responses, there is a need to rapidly assess the possible contribution of hormone action to changes in the levels of gene transcripts. We developed a vector-based algorithm that rapidly compares lists of transcripts yielding correlation values. The application as described here, called HORMONOMETER, was used to analyze hormone-related activity in a transcriptome of Arabidopsis (Arabidopsis thaliana). The veracity of the resultant analysis was established by comparison with cognate and noncognate hormone transcriptomes as well as with mutants and selected plant-environment interactions. The HORMONOMETER accurately predicted correlations between hormone action and biosynthetic mutants for which transcriptome data are available. A high degree of correlation was detected between many hormones, particularly at early time points of hormone action. Unforeseen complexity was detected in the analysis of mutants and in plant-herbivore interactions. The HORMONOMETER provides a diagnostic tool for evaluating the physiological state of being of the plant from the point of view of transcripts regulated by hormones and yields biological insight into the multiple response components that enable plant adaptation to the environment. A Web-based interface has been developed to facilitate external interfacing with this platform.
More Productive Than Maize in the Midwest: How Does Miscanthus Do It?
Authors: Dohleman Frank G. , Long Stephen P. 
Published: June 2009

Abstract
In the first side-by-side large-scale trials of these two C4 crops in the U.S. Corn Belt, Miscanthus (Miscanthus × giganteus) was 59% more productive than grain maize (Zea mays). Total productivity is the product of the total solar radiation incident per unit land area and the efficiencies of light interception (ϵ i) and its conversion into aboveground biomass (ϵ ca). Averaged over two growing seasons, ϵ ca did not differ, but ϵ i was 61% higher for Miscanthus, which developed a leaf canopy earlier and maintained it later. The diurnal course of photosynthesis was measured on sunlit and shaded leaves of each species on 26 dates. The daily integral of leaf-level photosynthetic CO2 uptake differed slightly when integrated across two growing seasons but was up to 60% higher in maize in mid-summer. The average leaf area of Miscanthus was double that of maize, with the result that calculated canopy photosynthesis was 44% higher in Miscanthus, corresponding closely to the biomass differences. To determine the basis of differences in mid-season leaf photosynthesis, light and CO2 responses were analyzed to determine in vivo biochemical limitations. Maize had a higher maximum velocity of phosphoenolpyruvate carboxylation, velocity of phosphoenolpyruvate regeneration, light saturated rate of photosynthesis, and higher maximum quantum efficiency of CO2 assimilation. These biochemical differences, however, were more than offset by the larger leaf area and its longer duration in Miscanthus. The results indicate that the full potential of C4 photosynthetic productivity is not achieved by modern temperate maize cultivars.