bluuebunny/crossref_metadata_2025 huggingface dataset:
The Nature of Responsibility for Gain:Gain, Harm, and Keeping the Lid on Pandora's Box
Authors: Barker Kit
Published: May 2009

This chapter examines the nature and origins of legal responsibility for gain in private law. Contrary to recent suggestions, it argues that such responsibility is consistent with our traditional, liberal premises and stems from the relationship between a defendant's gain and some harm to the plaintiff (conceived of as a set-back of her entitlement, not just a factual loss). Legal responsibility for unjust enrichment arises where a defendant has caused harm; where such harm is in prospect and needs to be deterred; or where the plaintiff has suffered harm for which he was not morally responsible. These three different models of responsibility span the line regularly drawn between cases of unjust enrichment ‘by subtraction’ and ‘wrongdoing’, raising significant questions about its normative importance. The chapter explains why unjust enrichment law remains an important and necessary private law category, despite its seemingly paradoxical dependence on the concept of harm. It also criticizes the assumption that cases of un-induced mistaken payment are descriptively paradigmatic of unjust enrichment law. Most types of restitutionary liability, it argues, entail the defendant causing harm.
Philosophical Foundations of Proprietary Remedies
Authors: Smith Lionel
Published: May 2009

In the law of unjust enrichment, the question when a plaintiff should have access to proprietary remedies is one of the most controversial issues. This chapter attempts to expose the philosophical and historical foundations of the most important category of proprietary remedies; namely, trusts arising by operation of law, including trusts over traceable proceeds. In so doing, it also explores the historical and philosophical foundations of all trusts, and emphasises the conceptual unity between constructive trusts and express trusts.
Property, Unjust Enrichment, and Defective Transfers
Authors: Webb Charlie
Published: May 2009

It is widely accepted that a substantial chunk of restitutionary claims arise out of so-called defective transfers. An asset previously held by the claimant passes into the hands of the defendant, and the claimant's consent to its passing is either defective or wholly absent. But why exactly is a claim triggered on these facts? Unjust enrichment does a poor job of explaining why the law should require such gains to be given up. Appeals to corrective justice aren't much better. Instead, this chapter argues that these claims arise as a means of protecting and effectuating a claimant's interest in exclusively determining the disposition of his assets. In other words, it is because, at the outset — it was the claimant to whom the law had exclusively reserved the power to determine how and by whom that asset be used and enjoyed, and he did not (properly) consent to it being used and enjoyed by the defendant — that we recognise the defendant as liable to make restitution to the claimant. Such ‘proprietary’ theories have been given remarkably short shrift by a majority of restitution theorists. The chapter shows why their criticisms miss the mark, before concluding with an indication of how this understanding of defective transfer claims can offer principled solutions to perceived problem areas, such as indirect receipt, insolvency, and claims for services.
‘Mistakes of Law’ and Legal Reasoning: Interpreting Kleinwort Benson v Lincoln City Council
Authors: Nair Aruna
Published: May 2009

The chapter considers the implications of the decision of the House of Lords in Kleinwort Benson v Lincoln City Council for an understanding of the nature of legal reasoning. It also considers the implications of alternative models of legal reasoning for the substantive law relating to the recovery of benefits conferred under the influence of ‘mistakes of law’. In Kleinwort Benson, the House of Lords decided that a bank that had paid money to a local authority in reliance on a ‘settled interpretation of the law’, departed from by a later judicial decision, had made a mistake of law. They held that this mistake qualified as an ‘unjust factor’ entitling the bank to recover the money. It is argued, first, that Ronald Dworkin's explanation of the nature of legal reasoning cannot provide a plausible account of the facts of the case or of the response of the judges to those facts. It is claimed that this demonstrates the limitations of an analysis of legal reasoning that treats it as an individualistic process of moral reasoning; such an analysis cannot make sense of the way in which English law is experienced by those affected by it, as constrained, structured, and altered by a hierarchical system of authoritative decision-making. Secondly, it is argued that, if Dworkin's model of legal reasoning were applied in the context of the substantive law of unjust enrichment, unacceptable conclusions would follow. These can be avoided if a positivist account of law were accepted instead.
Apollo: a community resource for genome annotation editing
Authors: Lee Ed , Harris Nomi , Gibson Mark , Chetty Raymond , Lewis Suzanna
Published: May 2009

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students.

Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

Contact:  elee@berkeleybop.org
SOrt-ITEMS: Sequence orthology based approach for improved taxonomic estimation of metagenomic sequences
Authors: Monzoorul Haque M. , Ghosh Tarini Shankar , Komanduri Dinakar , Mande Sharmila S.
Published: May 2009

Motivation:One of the first steps in metagenomic analysis is the assignment of reads/contigs obtained from various sequencing technologies to their correct taxonomic bins. Similarity-based binning methods assign a read to a taxon/clade, based on the pattern of significant BLAST hits generated against sequence databases. Existing methods, which use bit-score as the sole parameter to ascertain the significance of BLAST hits, have limited specificity and accuracy of binning. A new binning algorithm, called SOrt-ITEMS is introduced, which addresses these limitations. The method uses alignment parameters besides the bit score to first identify an appropriate taxonomic level where the read can be assigned. An orthology-based approach is subsequently used by the method for the final assignment.

Results:The performance of SOrt-ITEMS has been validated with reads simulating sequences from 454 and Sanger sequencing technologies. In addition, the taxonomic composition of the Sargasso Sea data set has been analyzed using SOrt-ITEMS. SOrt-ITEMS shows improved specificity and accuracy of assignments especially in simulated scenarios, wherein sequences corresponding to the source organism of the reads are absent in the reference database.

Availability:SOrt-ITEMS software is available for download from: http://metagenomics.atc.tcs.com/binning/SOrt-ITEMS. No license is needed for academic and nonprofit use.

Contact:  sharmila@atc.tcs.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Comparative Susceptibility of Kudzu Accessions from the Southeastern United States to Infection by Phakopsora pachyrhizi
Authors: Bonde M. R. , Nester S. E. , Moore W. F. , Allen T. W.
Published: May 2009

Soybean rust, caused by Phakopsora pachyrhizi, was first discovered in the continental United States in the fall of 2004. The potential for economic loss in the United States hinges largely on whether or not the pathogen can survive winters in the absence of soybean. Kudzu (Pueraria lobata) is known to be a host for P. pachyrhizi in Asia and South America and is widely distributed in the southern United States. This study examined reactions of kudzu collected from several areas of the southeastern United States to three isolates of P. pachyrhizi, one each from Alabama, Louisiana, and Brazil. Susceptible tan (TAN) lesions, resistant reddish-brown (RB) lesions, and immune (IM) response, previously described on soybean, were produced on kudzu based on the evaluation of 125 plants. However, in contrast to soybean, the RB response on kudzu was common, with approximately 50% frequency. IM responses to at least one isolate were observed on five individual plants, and two plants were immune to all three pathogen isolates used in the test. TAN lesions averaged 3.2 uredinia per lesion with an average diameter per uredinium of 121 μm. In contrast, RB lesions had an average of 0.3 uredinia per lesion with an average uredinial diameter of 77 μm. In 25 of 39 (64%) instances in which multiple plants were tested from a site, each reacted the same to the individual pathogen isolates. This suggested a tendency for plants at specific sites to be genetically identical with respect to rust reaction. Only 19 of 125 (15%) individual plants produced a different reaction to one isolate than to the other two isolates. When four kudzu plants previously shown to produce only TAN lesions to P. pachyrhizi isolates Alabama 04-1, Brazil 01-1, and Louisiana 04-1 were inoculated with eight additional isolates from several areas of the world, all 11 isolates produced only TAN lesions. Likewise, when five other plants previously shown to produce only RB lesions when inoculated with the three isolates were inoculated with the 11 isolates, all produced only RB lesions. These results suggest that susceptibility or resistance to P. pachyrhizi in individual kudzu plants often is broad, extending over a wide range of P. pachyrhizi isolates.
Sugar Beet Cultivar Evaluation for Storability and Rhizomania Resistance
Authors: Strausbaugh Carl A. , Eujayl Imad , Rearick Eugene , Foote Paul , Elison Dave
Published: May 2009

To reduce storage losses and improve resistance to rhizomania caused by Beet necrotic yellow vein virus (BNYVV), studies were initiated to establish a storage cultivar selection program. In 2006 and 2007, 30 or more commercial sugar beet (Beta vulgaris) cultivars were grown in soil naturally infested with BNYVV. At harvest, two root samples from each plot were collected and used to establish percent sugar. Additional samples were placed on top of an indoor pile (set point 1.7°C) and inside an outdoor pile in a randomized complete block design with four replications. After 142 and 159 days in indoor storage, sucrose reduction ranged from 13 to 90% in 2007 and 57 to 100% in 2008. Outdoor storage sucrose reduction ranged from 13 to 32% in 2007 and 28 to 60% in 2008. An average of 31 and 45% of the root surface was covered with fungal growth in 2007 and 2008, respectively. Cultivars that retained the most sucrose had resistance to BNYVV and the least fungal growth and weight loss. Indoor storage with BNYVV-infested roots allowed for the most consistent cultivar separation and will potentially lead to selection of cultivars for improved storability and rhizomania resistance.
Determination of Resistance Spectra of the Pi-ta and Pi-k Genes to U.S. Races of Magnaporthe oryzae Causing Rice Blast in a Recombinant Inbred Line Population
Authors: Jia Yulin , Lee Fleet N. , McClung Anna
Published: May 2009

Molecular tagged resistance (R) genes are useful for developing improved cultivar resistance using marker-assisted breeding. In the present study, R genes to common races of Magnaporthe oryzae, the causal agent of blast disease of rice (Oryza sativa), were mapped using an F10 recombinant inbred line (RIL) population derived from a cross of tropical japonica cv. Katy with breeding line RU9101001. Katy was resistant to 10 common U.S. races: IA-45, IB-1, IB-45, IB-49, IB-54, IC-17, ID-1, IE-1, IG-1, and IH-1 of M. oryzae. RU9101001 was resistant to races IA-45, IB-45, IB-54, IG-1, and IH-1. Katy and RU9101001 were susceptible to race IE-1k. Twenty-three polymorphic simple sequence repeat (SSR) markers were used to map R genes. Segregation ratios of 1:1 (resistant/susceptible) to races IB-1, IB-49, IC-17, ID-1, and IE-1 indicated the presence of a single dominant R gene in Katy. Ratios of 3:1 (resistant/susceptible) to races IA-45, IB-45, IG-1, and IH-1 indicated that a single R gene was present in Katy and a different R gene was present in RU9101001. Resistance to the abovementioned races was correlated with the presences of the Pi-ta gene and 11 Katy SSR alleles, suggesting that Pi-ta confers resistance to IA-45, IB-1, IB-45, IB-49, IC-17, IG-1, ID-1, IE-1, and IH-1. Katy, RU9101001, and all RILs were resistant to race IB-54, which was consistent with the presence of Pi-ks in Katy and Pi-kh in RU9101001. Resistance to IA-45, IB-45, IG-1, and IH-1 correlated with the presence of Pi-kh, suggesting that Pi-kh confers resistance to IA-45, IB-45, IG-1, and IH-1. These data suggest that Pi-ta and Pi-kh are effective R genes with overlapped resistance to the 10 common races of M. oryzae.
Automated Image Analysis of the Severity of Foliar Citrus Canker Symptoms
Authors: Bock C. H. , Cook A. Z. , Parker P. E. , Gottwald T. R.
Published: May 2009

Citrus canker (caused by Xanthomonas citri subsp. citri) is a destructive disease, reducing yield and rendering fruit unfit for fresh sale. Accurate assessment of citrus canker severity and other diseases is needed for several purposes, including monitoring epidemics and evaluation of germplasm. We compared measurements of citrus canker severity (percent area infected) from automated image analysis to visual estimates by raters and true values using images from five leaf samples (65, 123, 50, 50, and 200 leaves; disease severity from 0 to 60%). Severity on leaves was measured by automated image analysis by (i) basing threshold values on a presample of leaves, or (ii) replacing healthy leaf color on a leaf-by-leaf basis before automating image analysis. Samples 1 to 4 were assessed by three trained plant pathologists, and sample 5 was assessed by an additional 25 raters. Healthy leaf area color replacement gave the most consistent agreement with the true severity data. Using color replacement, agreement with true values based on Lin's concordance correlation coefficient (ρc) was 0.93, 0.79, 0.71, 0.85, and 0.89 for each of the samples, respectively. The range and consistency of agreement was generally less good for automated thresholds based on a presample (ρc = 0.35–0.90) or visual raters (ρc = 0.30–0.94). The constituents of agreement (precision and accuracy) showed similar trends. No one rater or method was best for every leaf sample, but replacing healthy color in each leaf with a standard color before automation of image analysis improved agreement, and was relatively quick (20 s per image). The accuracy and precision of automated image analysis of citrus canker severity can be comparable to unaided, direct visual estimation by many raters.
First Report of Sooty Blotch and Flyspeck Caused by Species of Dissoconium, Mycosphaerella, and Peltaster on Hawthorn Fruit in China
Authors: Li H. Y. , Zhang R. , Sun G. Y. , Tang M. , Gleason M. L.
Published: May 2009

Sooty blotch and flyspeck (SBFS), a disease complex comprised of as many as 30 putative species of fungi, occurs on the cuticle of pome fruits in moist production regions worldwide, inciting cosmetic damage that causes significant economic losses (1). Chinese hawthorn (Crataegus pinnatifida Bge.) is an economically important tree species in China. Its fruit are sold fresh or dried and are used as a culinary spice as well as an ingredient in Chinese traditional medicine. In October of 2007, Chinese hawthorn fruit exhibiting SBFS signs were sampled from supermarkets in Yangling, Shaanxi Province and Luoyang, Henan Province, China. Thalli directly from the hawthorn fruit were transferred onto potato dextrose agar (PDA) slants under a dissecting microscope and cultured at 22 ± 1°C in darkness. DNA was extracted from pure isolates and the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA) was amplified and sequenced using primers ITS-1F and ITS4 (3). Phylogenetic analysis of the ITS sequences revealed that the 35 isolates generated in this study included five species in three genera: Dissoconium sp. (18 isolates), Mycosphaerella sp. (5 isolates), and Peltaster sp. 1 (4 isolates), Peltaster sp. 2 (4 isolates), and Peltaster sp. 3 (4 isolates). To fulfill Koch's postulates and verify that these fungi could also infest apple fruit, two representative isolates of each putative species were inoculated onto mature intact hawthorn and apple (cv. Fuji) fruit that had been surface disinfested with 75% ethanol and allowed to dry. Inoculum was prepared by comminuting 1-month-old cultures growing on PDA into a suspension of mycelial fragments and conidia (105 to ~106 CFU/ml) in a blender with sterile deionized water (SDW). Each isolate was inoculated on three hawthorn and three apple fruit by using cotton swabs. As controls, two surface-disinfested hawthorn and apple fruit were swabbed with SDW. After the inoculated hawthorn and apple fruit had been incubated in a moist chamber at 22 ± 1°C for 1 month, all inoculated hawthorn and apple fruit exhibited SBFS signs similar to those of the original colonies on hawthorn fruit, but the controls did not. Reservoir hosts have been inferred to play an important role in SBFS by providing the fungi with overwintering habitat and inoculum for infestations on apple. Many reservoir hosts have been reported in the United States and Japan (2). To our knowledge, this is the first report of fungi in the SBFS complex on hawthorn fruit and the first confirmation that fungi growing on hawthorn fruit can produce SBFS signs on apple fruit. These results identify hawthorn as a potential inoculum source for SBFS in apple orchards.

References: (1) J. C. Batzer et al. Mycologia 97:1283, 2005. (2) K. Hemnani et al. Phytopathology 98(suppl):S66, 2008. (3) T. J. White et al. PCR Protocols: A Guide to Methods and Applications. M. A. Innis et al., eds. Academic Press, San Diego, 1990.
First Report of Collar and Stem Rot Caused by Pythium aphanidermatum on Figmarigold (Lampranthus sp.) in Italy
Authors: Garibaldi A. , Bertetti D. , Pensa P. , Gullino M. L.
Published: May 2009

Lampranthus sp. N.B. Brown (figmarigold) of the Aizoaceae family is used as groundcover in gardens. In October of 2008, severe outbreaks of a previously unknown rot were observed in a nursery located in Liguria, near Savona (northern Italy), on 35-day-old rooted cuttings grown in a peat substrate. Approximately 50% of rooted cuttings of red-flowered cultivars were affected. Lesions on collars and young stems were brown, water soaked, and soft. Plants eventually collapsed as roots rotted. Thin, aerial hyphae were visible on the surface of the stems and substrate. Later, a thick, light yellow, mycelial mat surrounded infected plants. Tissue fragments were excised from the margins of the lesions, dipped in a solution containing 1% sodium hypochlorite, and plated on potato dextrose agar and a medium selective for Oomycetes (4). Plates were incubated under constant fluorescent light at 23 ± 1°C for 4 to 5 days. Hyphae of five isolates grown on V8 medium were aseptate and 4.2 to 7.9 (average 6.2) μm wide. Sporangia consisted of complexes of swollen hyphal branches. Oogonia were globose, smooth, and 23.5 to 28.0 (average 25.9) μm in diameter. Antheridia were barrel shaped, intercalary, and diclinous. Oospores were globose and 19.4 to 23.6 (average 21.4) μm in diameter. The internal transcribed spacer (ITS) region of rDNA of a single isolate (DB24112008) was amplified with primers ITS4/ITS6 and sequenced. A BLAST analysis (1) in GenBank of the 1,074-bp segment showed a 100% homology with the sequence of Pythium aphanidermatum (Accession No. EU245039). The nucleotide sequence has been assigned the GenBank Accession No. FJ492745. Pathogenicity tests were performed twice on a red-flower cultivar of a Lampranthus sp. grown in 1-liter pots containing a peat moss substrate infested with wheat and hemp kernels colonized with one isolate of P. aphanidermatum at a rate of 20 g/liter. Ten plants were grown in infested media and 10 plants were grown in noninfested media. Greenhouse temperatures were 18 to 24°C. The first symptoms of stem and root rot developed 15 days later, while control plants remained healthy. P. aphanidermatum was consistently reisolated from the lesions. To our knowledge, this is the first report of P. aphanidermatum on a Lampranthus sp. in Italy. The disease has been reported in Japan (3) in 2008, while in the United States, a Pythium sp. was reported on L. aureus and L. glomeratus (2). Currently, the economic importance of Pythium rot on figmarigold in Italy is still limited.

References: (1) S. F. Altschul et al. Nucleic Acids Res. 25:3389, 1997. (2) D. F. Farr et al. Fungi on Plants and Products in the United States. The American Phytopathological Society, St Paul, MN, 1989. (3) H. Kawarazachi et al. J. Gen. Plant Pathol. 74:94, 2008. (4) H. Masago et al. Phytopathology, 67, 425, 1977.
First Report of Onion yellow dwarf virus and Leek yellow stripe virus in Garlic in Turkey
Authors: Fidan H. , Baloglu S.
Published: May 2009

Garlic (Allium sativum L.) is one of the most important Allium spp. plants that are widely cultivated throughout the world. A significant reduction in yield and quality due to virus infection is now a serious economic problem (1). In many cases, garlic plants are infected with a variety of viruses, but elimination of these viruses is difficult because this crop is propagated through bulbs. Potyviruses, carlaviruses, and allexiviruses have been detected in diseased garlic. Onion yellow dwarf virus (OYDV) and Leek Yellow Stripe Virus (LYSV), genus Potyvirus, family Potyviridae, are two important viral pathogens of garlic. Virus diseases of garlic are widespread in the world, causing serious damage to yields and quality of the crop. The East Mediterranean Region produces 14% of the garlic production of Turkey (110,000 t). A survey was done in garlic fields in Adana, Mersin, Kahramanmaras, Hatay, and Gaziantep provinces of Turkey where virus-like symptoms were noted in samples collected during the 2007–2008 growing season. Leaf and bulb samples were taken from 202 plants with leaf yellow stripe, mosaic, enations, and deformation or dwarfism symptoms. ELISA was performed with antibodies from Agdia (Elkhart, IN). Results indicated that 57 samples (28.2%) were infected with OYDV and 43 samples (21.2%) were infected with LYSV. In addition, 23 samples were determined to be infected by both viruses. All ELISA-positive samples and 10 ELISA-negative samples were analyzed by reverse transcription-PCR with primers 1OYDV-G (5′ TTA CAT TCT AAT ACC AAG CA 3′) and 2OYDV-G (5′ GCA GGA GAT GGG GAG GAC GC 3′) for the detection of OYDV and primers 1LYSV (5′ TCA CTG CAT ATG CGC ACC AT 3′) and 2LYSV (5′ GCA CCA TAC AGT GAA TTG AG 3′) for the detection of LYSV. These primers were previously reported to be specific for the coat protein genes of OYDV and LYSV, respectively (2). Products of the expected size (774 bp for OYDV and 1,020 bp for LYSV) were amplified only from the ELISA-positive samples of the respective viruses, confirming infections by OYDV and LYSV. To our knowledge, this is the first report of OYDV and LYSV in garlic in Turkey.

References: (1) L. Bos et al. Neth. J. Plant Pathol. 84:185, 1978. (2) T. V. M. Fajardo et al. Fitopatol. Bras. 26:619, 2001.
First Report of Sclerotinia Stem Rot Caused by Sclerotinia sclerotiorum on Hibiscus trionum in New York
Authors: Strauss J. , Dillard H. R.
Published: May 2009

Hibiscus trionum L. (Venice mallow) is an annual weed widely distributed in the United States. In September of 2008, Venice mallow plants with bleached stems and necrotic tissues were observed in a commercial field of cabbage (Brassica oleracea L. cv. Moreton) in Geneva, NY. White, cottony mycelium and dark sclerotia were readily found on the stems and in the stem pith. Cabbage plants in direct contact with diseased Venice mallow also displayed signs and symptoms of infection by Sclerotinia sclerotiorum (Lib.) de Bary. Sclerotia from within diseased Venice mallow stems were placed in 9-cm-diameter petri plates on potato dextrose agar amended with 0.1 g/liter each of chloramphenicol and streptomycin (ABPDA) and incubated at room temperature. In addition, diseased stem tissue was surface disinfested for 3 min in 0.525% sodium hypochlorite solution, rinsed for 3 min in sterile distilled water, and placed on ABPDA. After 5 days, hyphae from the colony margin were excised and transferred to potato dextrose agar (PDA) plates. Fungal cultures consisting of white mycelia and medium-sized (~4 mm), black, irregular sclerotia were consistently recovered and identified as S. sclerotiorum based on morphological characteristics (1). Pathogenicity of two isolates (one from a sclerotium and one from stem tissue) was determined by inoculating seven 43-day-old Venice mallow plants growing in greenhouse pots (65 mm in diameter). Mycelia plugs (7 mm in diameter) were excised from 2-day-old PDA cultures of each isolate and placed on the stems at the soil line. Seven control plants were inoculated with noncolonized PDA plugs. All plants were enclosed in plastic bags for 72 h and placed under shade in the greenhouse with temperatures from 20 to 38°C (average 27°C). Symptoms similar to those observed in the affected fields were evident within 2 days after inoculation, while control plants remained symptomless. S. sclerotiorum was successfully recovered from infected plant tissue, fulfilling Koch's postulates. The experiment was repeated with similar results. To our knowledge, this is the first report of Sclerotinia stem rot of Hibiscus trionum caused by S. sclerotiorum (2,3).

References: (1) L. Buchwaldt. Sclerotinia White Mold. Page 43 in: Compendium of Brassica Diseases, 1st ed. S. R. Rimmer et al., eds. The American Phytopathological Society, St. Paul, MN, 2007. (2) D. F. Farr et al. Fungi on Plants and Plant Products in the United States. The American Phytopathological Society, MN, 1989. (3) C. Wehlburg et al. Index of Plant Diseases in Florida. Fla Dep. Agric. Consum. Serv. Bull. 11, 1975.
First Report of Plum pox virus Recombinant Strain on Prunus spp. in Canada
Authors: Thompson D. , Varga A. , De Costa H. , Birch C. , Glasa M. , James D.
Published: May 2009

In July of 2008, during the Canadian Plum pox virus (PPV) eradication survey, three Prunus spp. trees (B-5, B-6, and C-1) in a home owner's yard in Grimsby, ON, Canada were found to be infected with PPV by triple antibody sandwich (TAS)-ELISA using the 5B generic monoclonal detecting antibody (1) and reverse transcription (RT)-PCR using the well-validated universal primer set P1/P2. All three trees were grafted on an unknown plum rootstock cultivar. Tree B-5 contained grafts of unknown peach (P. persica) and plum (P. domestica) cultivars, tree B-6 contained the same peach graft as tree B-5 and an unknown apricot (P. armeniaca) cultivar, and tree C-1 was grafted with the same plum cultivar as tree B-5. Strain typing was done by TAS-ELISA using strain-specific monoclonal antibodies for D, M, C, and EA strains. Positive results were obtained with the M-specific test. Strain typing by RT-PCR also was done using primers specific for D, M, W, and recombinant (Rec) strains. Positive results were obtained with the M and Rec primers (4). The 605-bp fragment generated by the PPV Rec primers, which spans the recombination site, was cloned and sequenced. The nucleotide sequences obtained from B-5, B-6, and C-1 are 99% identical to each other and approximately 98 and 99% identical to the PPV Rec isolates BOR-3 and J4c, respectively. Correspondingly, percentage identities are approximately 90% for PPV M, 84% for PPV isolate D-Fan (a typical Canadian D isolate), and 69% for PPV W. The deduced amino acid sequence of B-5, B-6, and C-1 are 98 to 99% identical to each other, 99% identical to the PPV Rec isolates BOR-3 and J4c, 92% identical to isolates of PPV M, and only 84% identical to the typical Canadian D isolate PPV Fan. The P3-6K1 genomic region was amplified using primers that generate a 836-bp fragment (2). This region was 97 to 98% identical to the PPV Rec isolates BOR-3 and J4c, 96 to 97% identical to isolates of PPV D, but only 86% identical to isolates of PPV M. The data above confirm that the PPV isolates B-5, B-6, and C-1 belong to the strain PPV Rec (3). To our knowledge, this is the first report of PPV Rec in North America, and together with PPV D and W, it represents the third PPV strain found on this continent. An intensive survey of all Prunus spp. within a 1.5-km radius area surrounding the home owner's property failed to reveal any additional PPV-positive plants. The three positive plants were removed.

References: (1) M. Cambra et al. EPPO Bull. 24:569, 1994. (2) M. Glasa et al. Arch. Virol. 147:563, 2002. (3) M. Glasa et al. J. Gen. Virol. 85:2671, 2004. (4) A. Šubr et al. Acta Virol. 48:173, 2004.
First Report of Peronospora sparsa Causing Downy Mildew (Dryberry) of Rubus fruticosus in Mexico
Authors: Rebollar-Alviter A. , Silva-Rojas H. V. , Zelaya-Molina L. X. , Ellis M. A.
Published: May 2009

Michoacan State is the largest producer of blackberries (Rubus fruticosus) in Mexico with more than 4,000 ha in production. During the rainy season of 2007 (July to September), purple, angular, vein-delimited leaf spots along the midrib and major veins were observed. Affected young fruit lost their shine, became shriveled, and later dried. Some fruit split. Symptomatic leaflets from cv. Tupy were collected from the field in Tangancicuaro and Los Reyes counties. In the laboratory, 20 detached leaflets were washed with 10% bleach for 2 min, rinsed with sterile distilled water, and placed into sterile petri dishes containing 0.5% water agar. To promote sporulation of fungi, leaflets were incubated at 17°C with a 12-h photoperiod in a growth chamber. Sporangia and sporangiophores, which developed 20 days later on the underside of the leaves, were transferred to the underside of detached healthy leaves of the same cultivar with a sterile needle, and incubated as previously described. A set of noninoculated leaves were included as controls. Sporangiophores and sporangia developed on the underside of angular purple lesions on leaves 15 to 22 days after inoculation. Symptoms were identical to those observed on leaves in the field. The pathogenicity test was repeated twice with the same results. Sporangia were light brown, ovoid to elliptical, and measured 14 to 22 × 11 to 18 μm. Sporangiophores were dichotomously branched with slender curved ends. Symptoms on the leaves and fruit and oomycete morphology were similar to those described for downy mildew (2). To confirm pathogen identity, a product of ~500 bp of the nuclear ITS-rRNA was amplified from total DNA from symptomatic and asymptomatic leaves and fruit by nested PCR. The primers sets PS3/PS1 and PR3/PR4 were used for the first and second reaction, respectively (1,3). PCR products were sequenced in both directions and sequences were deposited in GenBank under Accession Nos. EU601168, EU601169, EU601170, and EU601171. Consensus sequences obtained in this study were compared with the same region of Peronospora sparsa (GenBank Accession Nos. EU391654 from Denmark and AF266783 from the UK). Similarity among these sequences varied between 99 and 100%. To our knowledge, this is the first report of downy mildew (dryberry) of blackberry caused by P. sparsa in Mexico.

References: (1) B. J. Aegerter et al. Plant Dis. 86:1363, 2002. (2) W. D. Gubler. Page 15 in: Compendium of Raspberry and Blackberry Diseases and Insects. M. A. Ellis et al., eds. The American Phytopathological Society, St Paul MN, 1998. (3) H. Lindqvist et al. Plant Dis. 82:1304, 1998.
Iris yellow spot virus in Onion in Nevada and Northern California
Authors: Bag S. , Singh J. , Davis R. M. , Chounet W. , Pappu H. R.
Published: May 2009

The disease caused by thrips-transmitted Iris yellow spot virus (IYSV; genus Tospovirus, family Bunyaviridae) has become a major constraint to bulb and seed onion crops in several parts of the country and the world (1,3). As part of an ongoing survey for IYSV incidence in onion in the western United States, commercial fields in Lyon County, Nevada and several commercial fields in the northern Californian counties of Colusa, San Benito, Sutter, and Yolo were surveyed during the summer of 2008. Symptomatic plants were found widespread in northern California, especially in seed-production fields. In Lyon County, NV, symptoms were observed only on volunteer onions in one commercial field. Symptoms on leaves and scapes included characteristic diamond-shaped lesions with or without green islands. Four samples from Nevada and fourteen from northern California were tested by double-antibody sandwich (DAS)-ELISA using a commercially available kit (Agdia Inc., Elkhart, IN). All tested samples were found positive in ELISA. IYSV infection was verified by reverse transcription (RT)-PCR. Total nucleic acids were prepared from symptomatic tissue, and primers specific to the small (S) RNA of IYSV were used to amplify an approximate 1.2-kb region of the S-RNA. This region included the complete nucleoprotein (N) gene (2). The amplicons from one sample each from Nevada and northern California were sequenced (GenBank Accession Nos. FJ713699 and FJ713700, respectively). Sequence analysis showed that the amplicons contained a single open reading frame of 822 bp, coding for a 273-amino acid N protein, and the gene shared 96 to 98% identity with known IYSV N gene sequences. To our knowledge, this is the first report of IYSV in onion in Nevada. In California, outbreaks of IYSV had been reported earlier in Imperial Valley and Antelope Valley in southern California (4), and the disease has been increasing in incidence in bulb and seed crops in northern California, as well. California and Nevada are major onion-producing states in the United States and regular surveys to determine the incidence and impact on yield are needed to develop an integrated disease management program.

References: (1) D. H. Gent et al. Plant Dis. 90:1468, 2006. (2) H. R. Pappu et al. Arch. Virol. 151:1015, 2006. (3) H. R. Pappu and M. E. Matheron. Online publication. doi:10.1094/PHP-2008-0711-01-BR. Plant Health Progress, 2008. (4) G. J. Poole et al. Online publication. doi:10.1094/PHP-2007-0508-01-BR. Plant Health Progress, 2007.
First Report of Root-Knot Nematode Meloidogyne enterolobii on Guava in Vietnam
Authors: Iwahori H. , Truc N. T. N. , Ban D. V. , Ichinose K.
Published: May 2009

In southern Vietnam, citrus is interplanted with guava (Psidium guajava L.) for the management of citrus greening disease. Guava seedlings exhibited decline symptoms including leaf browning, growth inhibition, leaf drop, and death. These symptomatic seedlings were accompanied by severely galled roots, possibly attributable to root-knot nematodes. We collected second-stage juveniles from the soil and picked adult females from roots to perform morphological observations. The perineal patterns of most specimens were similar to those in the original description of Meloidogyne enterolobii (3). However, some were similar to that of M. incognita. Such variability among perineal patterns precluded unequivocal identification. Therefore, DNA was extracted from these nematodes and their sequences were compared with those in the DNA sequence database. For the comparison, we employed the primer sets of Powers and Harris (1) to amplify a region between cytochrome oxidase II and the 16S ribosomal DNA gene of mitochondria by PCR. An approximate 700-bp fragment was obtained and analyzed, revealing more than 99.6% homology to M. mayaguensis, a synonym of M. enterolobii (2), when aligned with sequence data of isolates from France (GenBank Accession No. AJ421396), the United States (GenBank Accession No. AY446978), and China (GenBank Accession No. AY831967). These results indicate that the nematode species responsible for guava damage in southern Vietnam is M. enterolobii. To our knowledge, this is the first report of M. enterolobii in Vietnam.

References: (1) T. O. Powers and T. S. Harris. J. Nematol. 25:1, 1993. (2) J. Xu et al. Eur. J. Plant Pathol. 110:309, 2004. (3) B. Yang and J. D. Eisenback. J. Nematol. 15:381, 1983.
Conventions for writing the values of quantities in the SI
Authors: Mills Ian
Published: May 2009

Possible improvements to the conventional rules for using and writing the values of quantities in the International System of Units (SI) are discussed in the light of recent suggestions for improving the system with a view to making it more adaptable to use in computer codes.
Llandovery sporomorphs and graptolites from the Manbo Formation, the Mojiang County, Yunnan, China
Authors: Wang Yi , Zhang Yuandong
Published: May 2009

Llandovery sporomorphs and graptolites have been recovered from the Manbo Formation, Mojiang area, western Yunnan, China, which belonged to the Indo-China Palaeoplate in the Palaeozoic. The graptolite fauna, including 8 genera and 12 species, is considered Mid Telychian, Llandovery in geological age, confirming the existence of Llandovery rocks in this region. The Silurian stratigraphical sequence of this area is reconsidered as in the ascending order: Manbo Formation (Llandovery–early Wenlock), Shuiqing Formation (late Wenlock–Ludlow) and unnamed formation (Pridoli?). The sporomorph assemblage from the Manbo Formation includes seven species in five genera. The dominant members of this assemblage areTetrahedraletes medinensisandLaevolancis chibrikovae. Based on the low diversity and low abundance, the geological age of this assemblage is considered to be approximately the Telychian, Llandovery. The parent plants of sporomorphs probably inhabited the landmass near Mojiang area, these sporomorph-producing plants probably included bryophyte-like land plants and primitive vascular land plants. The sporomorph evidence shows that the South China and Indo-China palaeoplates may have been in close proximity (maybe with some continental bridges linking them) to each other at least in the Llandovery. They were also closely related with Gondwanaland in the Llandovery.
Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
Authors: Kassahn Karin S. , Dang Vinh T. , Wilkins Simon J. , Perkins Andrew C. , Ragan Mark A.
Published: May 2009

The significance of whole-genome duplications (WGD) for vertebrate evolution remains controversial, in part because the mechanisms by which WGD contributed to functional evolution or speciation are still incompletely characterized. Fish genomes provide an ideal context in which to examine the consequences of WGD, because the teleost lineage experienced an additional WGD soon after divergence from tetrapods and because five teleost genomes are available for comparative analysis. Here we present an integrated approach to characterize these post-duplication genomes based on genome-scale synteny, phylogenetic, temporal, and spatial gene expression and on protein sequence data. A minimum of 3%–4% of protein-coding loci have been retained in two copies in each of the five fish genomes, and many of these duplicates are key developmental genes that function as transcription factors or signaling molecules. Almost all duplicate gene pairs we examined have diverged in spatial and/or temporal expression during embryogenesis. A quarter of duplicate pairs have diverged in function via the acquisition of novel protein domains or via changes in the subcellular localization of their encoded proteins. We compared the spatial expression and protein domain architecture of zebrafish WGD-duplicates to those of their single mouse ortholog and found many examples supporting a model of neofunctionalization. WGD-duplicates have acquired novel protein domains more often than have single-copy genes. Post-WGD changes at the gene regulatory level were more common than changes at the protein level. We conclude that the most significant consequence of WGD for vertebrate evolution has been to enable more-specialized regulatory control of development via the acquisition of novel spatiotemporal expression domains. We find limited evidence that reciprocal gene loss led to reproductive isolation and speciation in this lineage.
Mobile elements create structural variation: Analysis of a complete human genome
Authors: Xing Jinchuan , Zhang Yuhua , Han Kyudong , Salem Abdel Halim , Sen Shurjo K. , Huff Chad D. , Zhou Qiong , Kirkness Ewen F. , Levy Samuel , Batzer Mark A. , Jorde Lynn B.
Published: May 2009

Structural variants (SVs) are common in the human genome. Because approximately half of the human genome consists of repetitive, transposable DNA sequences, it is plausible that these elements play an important role in generating SVs in humans. Sequencing of the diploid genome of one individual human (HuRef) affords us the opportunity to assess, for the first time, the impact of mobile elements on SVs in an individual in a thorough and unbiased fashion. In this study, we systematically evaluated more than 8000 SVs to identify mobile element-associated SVs as small as 100 bp and specific to the HuRef genome. Combining computational and experimental analyses, we identified and validated 706 mobile element insertion events (including Alu, L1, SVA elements, and nonclassical insertions), which added more than 305 kb of new DNA sequence to the HuRef genome compared with the Human Genome Project (HGP) reference sequence (hg18). We also identified 140 mobile element-associated deletions, which removed ∼126 kb of sequence from the HuRef genome. Overall, ∼10% of the HuRef-specific indels larger than 100 bp are caused by mobile element-associated events. More than one-third of the insertion/deletion events occurred in genic regions, and new Alu insertions occurred in exons of three human genes. Based on the number of insertions and the estimated time to the most recent common ancestor of HuRef and the HGP reference genome, we estimated the Alu, L1, and SVA retrotransposition rates to be one in 21 births, 212 births, and 916 births, respectively. This study presents the first comprehensive analysis of mobile element-related structural variants in the complete DNA sequence of an individual and demonstrates that mobile elements play an important role in generating inter-individual structural variation.
RNA Interference of LIN5 in Tomato Confirms Its Role in Controlling Brix Content, Uncovers the Influence of Sugars on the Levels of Fruit Hormones, and Demonstrates the Importance of Sucrose Cleavage for Normal Fruit Development and Fertility
Authors: Zanor María Inés , Osorio Sonia , Nunes-Nesi Adriano , Carrari Fernando , Lohse Marc , Usadel Björn , Kühn Christina , Bleiss Wilfrid , Giavalisco Patrick , Willmitzer Lothar , Sulpice Ronan , Zhou Yan-Hong , Fernie Alisdair R.
Published: May 2009

It has been previously demonstrated, utilizing intraspecific introgression lines, that Lycopersicum Invertase5 (LIN5), which encodes a cell wall invertase, controls total soluble solids content in tomato (Solanum lycopersicum). The physiological role of this protein, however, has not yet been directly studied, since evaluation of data obtained from the introgression lines is complicated by the fact that they additionally harbor many other wild species alleles. To allow a more precise comparison, we generated transgenic tomato in which we silenced the expression of LIN5 using the RNA interference approach. The transformants were characterized by an altered flower and fruit morphology, displaying increased numbers of petals and sepals per flower, an increased rate of fruit abortion, and a reduction in fruit size. Evaluation of the mature fruit revealed that the transformants were characterized by a reduction of seed number per plant. Furthermore, detailed physiological analysis revealed that the transformants displayed aberrant pollen morphology and a reduction in the rate of pollen tube elongation. Metabolite profiling of ovaries and green and red fruit revealed that metabolic changes in the transformants were largely confined to sugar metabolism, whereas transcript and hormone profiling revealed broad changes both in the hormones themselves and in transcripts encoding their biosynthetic enzymes and response elements. These results are discussed in the context of current understanding of the role of sugar during the development of tomato fruit, with particular focus given to its impact on hormone levels and organ morphology.
The K-Segment of Maize DHN1 Mediates Binding to Anionic Phospholipid Vesicles and Concomitant Structural Changes
Authors: Koag Myong-Chul , Wilkens Stephan , Fenton Raymond D. , Resnik Josh , Vo Evanly , Close Timothy J.
Published: May 2009

Dehydrins (DHNs; late embryogenesis abundant D11 family) are a family of intrinsically unstructured plant proteins that accumulate in the late stages of seed development and in vegetative tissues subjected to water deficit, salinity, low temperature, or abscisic acid treatment. We demonstrated previously that maize (Zea mays) DHNs bind preferentially to anionic phospholipid vesicles; this binding is accompanied by an increase in α-helicity of the protein, and adoption of α-helicity can be induced by sodium dodecyl sulfate. All DHNs contain at least one “K-segment,” a lysine-rich 15-amino acid consensus sequence. The K-segment is predicted to form a class A2 amphipathic α-helix, a structural element known to interact with membranes and proteins. Here, three K-segment deletion proteins of maize DHN1 were produced. Lipid vesicle-binding assays revealed that the K-segment is required for binding to anionic phospholipid vesicles, and adoption of α-helicity of the K-segment accounts for most of the conformational change of DHNs upon binding to anionic phospholipid vesicles or sodium dodecyl sulfate. The adoption of structure may help stabilize cellular components, including membranes, under stress conditions.
Influence of pH on copper, lead and cadmium binding by an ombrotrophic peat
Authors: Villaverde P. , Gondar D. , Antelo J. , López R. , Fiol S. , Arce F.
Published: May 2009

The effect of pH on the adsorption of copper (Cu), lead (Pb) and cadmium (Cd) by a peat soil was studied, and the results compared with those corresponding to cation binding by a dissolved peat humic acid (HA), and interpreted with a NICA–Donnan model. A potentiometric titration technique was used to determine the adsorption isotherms for H+, at different ionic strengths, and for Cu2+, Pb2+ and Cd2+ at different pH values, in a peat soil. The effect of the ionic strength on proton binding was similar for the soil (solid) organic matter and for dissolved HA. The adsorption isotherms for cation–peat and the binding curves cation–dissolved HA are almost parallel, although more cation was adsorbed per kg of C in the dissolved HA. The effect of pH on cation binding is similar for dissolved organic matter and for the organic soil. At low metal concentration the amount of adsorbed metal followed the order Cu2+ > Pb2+ > Cd2+. The cation‐binding parameters obtained with the NICA–Donnan model allow excellent simulation of the effect of pH on the adsorption of Cu, Pb and Cd ions in the studied peat soil. The binding constants for the peat suspension were greater than the corresponding generic parameters for dissolved HA. Speciation calculations showed that for Cu and Pb, the most abundant fraction was the metal adsorbed on peat, whereas for Cd the most abundant fraction was dissolved metal.