bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of a Field-Source Mixture of Citrus Viroids on the Performance of ‘Nules’ Clementine and ‘Navelina’ Sweet Orange Trees Grafted on Carrizo Citrange
Authors: Hashemian S. M. Bani , Serra P. , Barbosa C. J. , Juárez J. , Aleza P. , Corvera J. M. , Lluch A. , Pina J. A. , Duran-Vila N.
Published: June 2009

A field-source mixture of citrus viroids was characterized and shown to contain Citrus exocortis viroid (CEVd), Hop stunt viroid (HSVd), Citrus bent leaf viroid (CBLVd), and Citrus dwarfing viroid (CDVd). Sequencing results showed that: (i) CEVd contained the PL and PR characteristic of class A variants; (ii) HSVd was a noncachexia variant; (iii) CBLVd was related to CVd-Ia variants; (iv) CDVd was a mixture of two types (CVd-IIIa and CVd-IIIb) of variants. The presence of the same type of variants in inoculated clementine (Citrus clementina ‘Nules’) and sweet orange (C. sinensis ‘Navelina’) trees on Carrizo citrange (Poncirus trifoliata × C. sinensis) rootstocks was confirmed. The effect of infection was determined by assessing the performance of infected and noninfected trees growing in the field. Infection resulted in small trees with reduced canopy, yielding a reduced crop. Fruit characteristics were also affected: (i) clementine and sweet orange fruits from infected trees were larger than those from noninfected trees; (ii) clementine fruits from infected trees differed in shape from those of noninfected trees; (iii) sweet orange fruits from infected trees had maturity indexes and juice contents higher than those from noninfected trees; (iv) in both species, the density of the juice, the amount of soluble solids, and the acidity of the fruits from infected trees were lower than those of fruits from noninfected trees. Infected trees had a poorly developed root system with fibrous roots containing fewer amyloplasts than noninfected trees. The results of an in vitro assay on the induction and development of roots in cultured explants are discussed.
Distribution in Australia and Seed Transmission ofTobacco streak virusinParthenium hysterophorus
Authors: Sharman Murray , Persley Denis M. , Thomas John E.
Published: June 2009

Tobacco streak virus (TSV) was found to commonly occur in Parthenium hysterophorus, as symptomless infections, in central Queensland, Australia across a large area infested with this weed. Several isolates of TSV collected across the geographic range of P. hysterophorus were found to share identical coat protein sequence with each other and with TSV from crop plants in the same area. Seed transmission of TSV in P. hysterophorus was found to occur at rates of 6.8 to 48%. There was almost no change in the rate of TSV seed transmission when P. hysterophorus seed was stored for up to 24½ months. Implications of this relationship between TSV and P. hysterophorus for the development of virus disease epidemics in surrounding crops are discussed.
Molecular Detection and Discrimination of Blueberry red ringspot virus Strains Causing Disease in Cultivated Blueberry and Cranberry
Authors: Polashock James J. , Ehlenfeldt Mark K. , Crouch Jo Anne
Published: June 2009

Blueberry red ringspot virus (BRRV) causes red ringspots on the stems, leaves, and ripening fruit of infected highbush blueberry (Vaccinium corymbosum) plants. The disease was originally observed in New Jersey and has now been reported in other blueberry growing regions in the United States, as well as several locations in Europe. A disease with similar symptoms occurs in American cranberry (V. macrocarpon), but BRRV has never been confirmed as the causal agent. Serological detection of BRRV in infected plants has been unsatisfactory. Using a primer set designed for routine detection (RRSV3/RRSV4), we successfully amplified a fragment of the virus from all tissues of infected highbush blueberry plants. Using the same primer set, we confirmed natural infection of BRRV in rabbiteye (V. virgatum) blueberry cultivars and the rabbiteye × V. constablaei hybrid cultivar Little Giant. These species have not been previously reported as hosts for this virus. Viral fragments were cloned from representative blueberry and cranberry plants exhibiting ringspot symptoms. Phylogenetic analysis of sequence data showed that cranberry strains of BRRV are precursors to the more derived blueberry strains. The techniques reported in this paper are being used to evaluate strain variation in Vaccinium species and to identify the as yet unknown vector(s) of this virus.
Characterizing Reaction of Soybean to Phialophora gregata Using Pathogen Population Density and DNA Quantity in Stems
Authors: Impullitti A. E. , Malvick D. K. , Grau C. R.
Published: June 2009

Evaluation of soybean germplasm for resistance to brown stem rot (BSR) is typically based on symptom severity. However, this approach may not reflect the level of colonization of soybean by the casual agent, Phialophora gregata. A potentially more accurate method to characterize resistance to BSR is to estimate pathogen quantity. The primary goal of this study was to evaluate soybean accessions for resistance to BSR based on the quantity of pathogen in stems. Plants were collected from experiments in field and controlled environments, and CFU and pathogen DNA quantity were determined using dilution plating techniques and real-time quantitative PCR (qPCR), respectively. In the field, the BSR-susceptible cultivars Corsoy 79 and Century 84 expressed greater than 73% foliar and stem symptom severity and had the highest pathogen population density, with a range from log10 4.3 to 4.7 CFU per gram of stem tissue. The resistant cultivar Bell expressed less than 10% foliar symptom severity, but had a pathogen population density that was not statistically different from the susceptible accessions. CFU measured in Dwight and L84-5873 were consistently lower than CFU in susceptible accessions and several resistant accessions. The amount of pathogen DNA differed among accessions in controlled environments. For example, Corsoy 79 and Century 84 had the highest pathogen DNA quantity, ranging from log10 6.19 to 6.65 copies, whereas the resistant cultivars Bell, Dwight, and L84-5873 had significantly lower DNA quantities, ranging from log10 2.04 to 2.91 copies. PI 437833 and IA2008R expressed low symptom severity but contained high DNA quantities. Pella 86, a highly symptomatic cultivar, had fewer CFU and lower DNA quantity in comparison to two other highly symptomatic cultivars and some cultivars with low symptom severity. These results suggest that some accessions express resistance to both pathogen colonization and symptom development, while others are resistant to symptom development but not to pathogen colonization. Results also indicate that resistant and susceptible accessions can be distinguished based on DNA quantity in controlled environments. In the field, differences between the pathogen population in resistant and susceptible cultivars were less distinct, possibly due to when plants were assayed.
Effects of Mefenoxam, Phosphonate, and Paclobutrazol on In Vitro Characteristics ofPhytophthora cactorumandP. citricolaand on Canker Size of European Beech
Authors: Weiland Jerry E. , Nelson Angela H. , Hudler George W.
Published: June 2009

Phytophthora citricola and P. cactorum cause bleeding cankers that lead to the death of mature European beech (Fagus sylvatica) in the northeastern United States. The effects of two fungicides and a plant growth regulator on in vitro pathogen characteristics and on canker expansion were investigated. In the first experiment, 16 single-spore isolates (11 P. citricola and 5 P. cactorum) were grown on clarified V8 juice agar amended with (i) 0 to 20 μg a.i./ml of mefenoxam, (ii) 0 to 301,429 μg a.i./ml phosphonate either with or without a bark-penetrating surfactant at 0.5 mg a.i./ml, or (iii) 0 to 25 mg a.i./ml of the surfactant alone. Radial growth, oospore production, and zoospore germination were observed to be dependent on isolate and treatment. A species effect on growth was also observed, as P. cactorum isolates were 2.5- to sevenfold less sensitive to phosphonate, but 2- to 150-fold more sensitive to mefenoxam than P. citricola isolates (based on 50% inhibition of growth). In the second experiment, bark and soil drenches of mefenoxam (50 mg a.i./ml and 19 μg a.i./ml, respectively), phosphonate (301,429 and 101 μg a.i./ml, respectively), and a soil drench of paclobutrazol (21 mg a.i./ml) were evaluated for their efficacy as curative or preventive treatments against bleeding canker. None of the treatments (curative or preventive) were able to stop canker expansion or prevent infection. However, saplings inoculated with P. citricola and treated with the phosphonate bark drench as either a curative or preventive treatment had cankers that were 36 to 82% shorter than those of inoculated control stems treated with water. For saplings inoculated with P. cactorum, the phosphonate bark drench was only effective when applied as a preventive (38% shorter than inoculated control stems treated with water), and not as a curative treatment. No other treatment was effective at limiting canker expansion.
Russian Isolates of Potato spindle tuber viroid Exhibit Low Sequence Diversity
Authors: Owens Robert A. , Girsova Natalya V. , Kromina Ksenia A. , Lee Ing Ming , Mozhaeva Karina A. , Kastalyeva Tatyana B.
Published: June 2009

Potato spindle tuber viroid (PSTVd) is currently widespread in seed potatoes grown in Russia. Characterization of 39 PSTVd isolates collected over a 15-year period from widely separated areas in Russia revealed the presence of 17 different sequence variants, all but one of which were previously unknown. Most variants were recovered only once, but two were more widely distributed; one of these was a mild variant previously isolated in Germany, the second was a novel variant inducing symptoms similar to those of the type strain in tomato. Despite this apparent lack of population diversity, several informative PSTVd variants were recovered. Sequence changes in the pathogenicity and variable domains were particularly common, but previously unknown changes were also detected within the loop E motif in the central domain, a structural motif known to play a key role in PSTVd replication and host range determination.
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.
Risk-sensitive mating decisions in a visually compromised environment
Authors: Wong Bob B. M. , Järvenpää Marja , Lindström Kai
Published: June 2009

Reproductive activities are often conspicuous and can increase the risk of predation. Evidence suggests that individuals are capable of responding to predators in a risk-sensitive manner. However, most studies tend to consider only the predator-mediated responses of males and females in isolation and with little regard to differences in local environmental conditions. Here, we experimentally investigate the effects of environmental visibility (turbidity) and predation risk on reproductive decisions in the sand goby,
Pomatoschistus minutus
, when exposed to a visually oriented predator, the European perch,
Perca fluviatilis
. We found that gobies were more reluctant to spawn in the predator's presence, although larger males spawned sooner than smaller males. Interestingly, latency to spawning was unaffected by the visual environment, suggesting that gobies may be relying on non-visual cues under turbid conditions.
Life-history strategies affect aphid preference for yellowing leaves
Authors: Holopainen Jarmo K. , Semiz Gürkan , Blande James D.
Published: June 2009

According to the nutrient-translocation hypothesis, yellowing tree leaves are colonized by aphids at the end of the growing season owing to improved availability of nutrients in the phloem sap after chlorophyll degradation. We measured aphid densities on potted
Betula pendula
seedlings in a field site where a small proportion of foliage rapidly turned yellow before normal autumn coloration as a consequence of root anoxia. The number of adults and nymphs of the birch-feeding specialist aphids
Euceraphis betulae, Betulaphis brevipilosa
and
Callipterinella tuberculata
were counted from leaves on each of the 222 plants. Aphids were detected on 19 per cent of green leaves and on 41 per cent of yellow leaves. There was no indication of aphid avoidance of yellow leaves, and the number of winged (alate) viviparous
E. betulae
adults and their nymphs were significantly higher on yellow leaves than on green leaves, while the numbers of apterous
B. brevipilosa
and
C. tuberculata
did not differ between the leaf colour types. Our result suggests that only aphid species with alate generation during colour change can take advantage of yellowing leaves. This may explain the exceptional abundance of
E. betulae
compared with other aphid species on birches.
Why do shrews twitter? Communication or simple echo-based orientation
Authors: Siemers Björn M. , Schauermann Grit , Turni Hendrik , von Merten Sophie
Published: June 2009

Shrews are very vocal animals. We tested behaviourally whether the high-pitched laryngeal ‘twittering’ calls of as-yet unclear function serve for communication or echo-based orientation. We used a representative species from each of the two largest phylogenetic groups of shrews. In both species, experimental manipulation of substrate density, but not of the likelihood of conspecific presence, affected the shrews' call rate when exploring an unknown environment. This adaptation of call rate to the degree of habitat clutter parallels bat echolocation and suggests that shrews may use the echoes and reverberations of their calls for identifying routes through their habitat or for probing habitat type. To assess the acoustic feasibility of shrew echo orientation, we ensonified shrew habitats in the field with an ‘artificial shrew’ (small speaker mounted close to a sensitive microphone). The data showed that shrew-like calls can indeed yield echo scenes useful for habitat assessment at close range, but beyond the range of the shrews' vibrissae.
A programming language for composable DNA circuits
Authors: Phillips Andrew , Cardelli Luca
Published: June 2009

Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.
Plug-and-play inference for disease dynamics: measles in large and small populations as a case study
Authors: He Daihai , Ionides Edward L. , King Aaron A.
Published: June 2009

Statistical inference for mechanistic models of partially observed dynamic systems is an active area of research. Most existing inference methods place substantial restrictions upon the form of models that can be fitted and hence upon the nature of the scientific hypotheses that can be entertained and the data that can be used to evaluate them. In contrast, the so-calledplug-and-playmethods require only simulations from a model and are thus free of such restrictions. We show the utility of the plug-and-play approach in the context of an investigation of measles transmission dynamics. Our novel methodology enables us to ask and answer questions that previous analyses have been unable to address. Specifically, we demonstrate that plug-and-play methods permit the development of a modelling and inference framework applicable to data from both large and small populations. We thereby obtain novel insights into the nature of heterogeneity in mixing and comment on the importance of including extra-demographic stochasticity as a means of dealing with environmental stochasticity and model misspecification. Our approach is readily applicable to many other epidemiological and ecological systems.
Instability modelling of drumlin formation incorporating lee-side cavity growth
Authors: Fowler A. C.
Published: June 2009

It is proposed that the formation of the subglacial bedforms known as drumlins occurs through an instability associated with the flow of ice over a wet deformable till. We pose a mathematical model that describes this instability, and we solve a simplified version of the model numerically in order to establish the form of finite-amplitude two-dimensional waveforms. A feature of the solutions is that cavities frequently form downstream of the bedforms; we allow the model to cater for this possibility and we provide an efficient numerical method to solve the resulting free boundary problem.
Multiple convergent evolution of arboreal life in oribatid mites indicates the primacy of ecology
Authors: Maraun Mark , Erdmann Georgia , Schulz Garvin , Norton Roy A. , Scheu Stefan , Domes Katja
Published: June 2009

Frequent convergent evolution in phylogenetically unrelated taxa points to the importance of ecological factors during evolution, whereas convergent evolution in closely related taxa indicates the importance of favourable pre-existing characters (pre-adaptations). We investigated the transitions to arboreal life in oribatid mites (Oribatida, Acari), a group of mostly soil-living arthropods. We evaluated which general force—ecological factors, historical constraints or chance—was dominant in the evolution of arboreal life in oribatid mites. A phylogenetic study of 51 oribatid mite species and four outgroup taxa, using the ribosomal 18S rDNA region, indicates that arboreal life evolved at least 15 times independently. Arboreal oribatid mite species are not randomly distributed in the phylogenetic tree, but are concentrated among strongly sclerotized, sexual and evolutionary younger taxa. They convergently evolved a capitate sensillus, an anemoreceptor that either precludes overstimulation in the exposed bark habitat or functions as a gravity receptor. Sexual reproduction and strong sclerotization were important pre-adaptations for colonizing the bark of trees that facilitated the exploitation of living resources (e.g. lichens) and served as predator defence, respectively. Overall, our results indicate that ecological factors are most important for the observed pattern of convergent evolution of arboreal life in oribatid mites, supporting an adaptationist view of evolution.
Keystone effects of an alien top-predator stem extinctions of native mammals
Authors: Letnic Mike , Koch Freya , Gordon Chris , Crowther Mathew S. , Dickman Christopher R.
Published: June 2009

Alien predators can have catastrophic effects on ecosystems and are thought to be much more harmful to biodiversity than their native counterparts. However, trophic cascade theory and the mesopredator release hypothesis predict that the removal of top predators will result in the reorganization of trophic webs and loss of biodiversity. Using field data collected throughout arid Australia, we provide evidence that removal of an alien top-predator, the dingo, has cascading effects through lower trophic levels. Dingo removal was linked to increased activity of herbivores and an invasive mesopredator, the red fox (
Vulpes vulpes
), and to the loss of grass cover and native species of small mammals. Using species distribution data, we predict that reintroducing or maintaining dingo populations would produce a net benefit for the conservation of threatened native mammals across greater than 2.42 × 10
6
km
2
of Australia. Our study provides evidence that an alien top predator can assume a keystone role and be beneficial for biodiversity conservation, and also that mammalian carnivores more generally can generate strong trophic cascades in terrestrial ecosystems.
Acoustic mate copying: female cowbirds attend to other females' vocalizations to modify their song preferences
Authors: Freed-Brown Grace , White David J.
Published: June 2009

We conducted a tutoring experiment to determine whether female brown-headed cowbirds (
Molothrus ater
) would attend to vocalizations of other females and use those cues to influence their own preferences for male courtship songs. We collected recordings of male songs that were unfamiliar to the subject females and paired half of the songs with female chatter vocalizations—vocalizations that females give in response to songs sung by males that are courting the females effectively. Thus, chatter immediately following a song provided a cue indicating that the song was sung by a male who was of high-enough quality to court a female successfully. Using a cross-over design, we tutored two groups of females with song–chatter pairings prior to the breeding season. In the breeding season, we placed the tutored females into sound-attenuating chambers and played them the same songs without the chatter. Females produced significantly more copulation solicitation displays in response to the songs that they had heard paired with chatter than to songs that had not been paired with chatter. This experiment is the first demonstration that females can modify their song preferences by attending to the vocal behaviour of other females.
Components of change in the evolution of learning and unlearned preference
Authors: Dunlap Aimee S. , Stephens David W.
Published: June 2009

Several phenomena in animal learning seem to call for evolutionary explanations, such as patterns of what animals learn and do not learn. While several models consider how evolution should influence learning, we have very little data testing these models. Theorists agree that environmental change is a central factor in the evolution of learning. We describe a mathematical model and an experiment, testing two components of change: reliability of experience and predictability of the best action. Using replicate populations of
Drosophila
we varied statistical patterns of change across 30 generations. Our results provide the first experimental demonstration that some types of environmental change favour learning while others select against it, giving the first experimental support for a more nuanced interpretation of the selective factors influencing the evolution of learning.
Human ability to detect kinship in strangers' faces: effects of the degree of relatedness
Authors: Kaminski Gwenaël , Dridi Slimane , Graff Christian , Gentaz Edouard
Published: June 2009

The resemblance between human faces has been shown to be a possible cue in recognizing the relatedness between parents and children, and more recently, between siblings. However, the general inclusive fitness theory proposes that kin-selective behaviours are also relevant to more distant relatives, which requires the detection of larger kinship bonds. We conducted an experiment to explore the use of facial clues by ‘strangers’, i.e. evaluators from a different family, to associate humans of varying degrees of relatedness. We hypothesized that the visual capacity to detect relatedness should be weaker with lower degrees of relatedness. We showed that human adults are capable of (although not very efficient at) assessing the relatedness of unrelated individuals from photographs and that visible facial cues vary according to the degree of relatedness. This sensitivity exists even for kin pair members that are more than a generation apart and have never lived together. Collectively, our findings are in agreement with emerging knowledge on the role played by facial resemblance as a kinship cue. But we have progressed further to show how the capacity to distinguish between related and non-related pairs applies to situations relevant to indirect fitness.
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.
Variation in withholding of information in three monkey species
Authors: Amici Federica , Call Josep , Aureli Filippo
Published: June 2009

Studies on tactical deception have reported that informed subordinates can withhold information from naive dominants, but they have not directly compared species' performance. Here, we compared the performance in two withholding-of-information tasks of three monkey species differing in the strictness of their dominance hierarchy and degree of fission–fusion dynamics: spider monkeys, capuchin monkeys and long-tailed macaques. Food was hidden from the dominants' view either inside an opaque box or in a transparent box that could only be opened by knowledgeable subordinates. All species were capable of withholding information, with subjects refraining from interacting with the box when the dominant was nearby. Spider monkeys were the most efficient at retrieving food, by timing it when the dominant was far from the box. Capuchin monkeys were also quite efficient when alone at the box, but they lost much of the food when manipulating the box with the dominant nearby. The results supported our predictions based on interspecific differences in the strictness of the dominance hierarchy and the degree of fission–fusion dynamics, with the former constraining the subjects' tendency to approach the box and the latter affecting the subjects’ tendency to wait for the appropriate situation to retrieve the food.
Learning enhances female control over reproductive investment in the Japanese quail
Authors: Rutkowska Joanna , Adkins-Regan Elizabeth
Published: June 2009

The adaptive significance of learning is supported by studies showing its positive effects on mating behaviour, but they rarely go beyond fertilization success. Here we studied how learning contributes to qualitative reproductive investment, by testing the hypothesis that mating in the context that predicts male appearance has positive effects on female reproductive investment compared with unsignalled mating. Using Japanese quail (Coturnix japonica), we found that effects of mating in the context predicting mating opportunity depend on female body condition and receptivity, while the outcome of unexpected mating depends on male behaviour. In particular, among females mated with the familiar male in the context predicting that he will appear, female condition positively affected the number of fertilized eggs and egg mass and more receptive females tended to produce more sons. Additionally, conditioned females laid heavier eggs for daughters than for sons. In contrast, in females that were mated unexpectedly and with a novel male, the number of fertilized eggs was highly dependent on male behaviour and was negatively related to maternal body condition. Egg mass was not related to body condition, and there were no indications of sex allocation. This is, to our knowledge, the first study demonstrating how female body condition and behaviour interact with the context of mating in shaping maternal reproductive investment.
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

Plant 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

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.