bluuebunny/crossref_metadata_2025 huggingface dataset:
A cross-linguistic investigation of the combinational possibilities of the ‘for X time’ adverbial with different aspectual verb classes
Authors: Sioupi Athina
Published: October 2012

The paper observes that the Vendler classification is not sufficient as a classification of verbs, since it cannot explain why some telic verbs, such as change of state (COS) verbs and degree achievements (DAs) appear with the durational adverbial (d-adverbial) ‘for X time’ in Greek, in English and in German, while some atelics like semelfactives appear with the frame adverbial (f-adverbial) se X ora (‘in X time’) in Greek. In the spirit of Iatridou et al. (2003) it is proposed that the d-adverbial ‘for X time’ tests not only for (a)telicity but also for (im)perfectivity. It also argues that the two d-adverbials in Greek ja X ora and epi X ora (‘for X time’) are to be found with different grammatical (viewpoint) aspect: the former with perfective aspect and the latter with imperfective aspect. This is due to the fact that the ja X ora gives not only durative temporal information but also a lexical aspectual one, while the epi X ora gives only a durative temporal.
Genetic Pedigree Reconstruction Facilitates Lakewide Estimates of Age‐0 Largemouth Bass Dispersal
Authors: Hessenauer Jan‐Michael , Bremigan Mary Tate , Scribner Kim T.
Published: October 2012

Dispersal from natal areas is an important event for fishes, ultimately affecting individual adult reproductive success and population levels of recruitment and genetic diversity. However, quantification of dispersal rates and distance and the associated environmental covariates is difficult when individuals are too small to physically mark. Using genetic techniques, we studied the dispersal of largemouth bass Micropterus salmoides from their natal nests in two southern Michigan lakes. In Warner Lake, we sampled larvae from 33 nests during spring 2010 and collected 33 age‐0 fish during summer. In Lake Chemung, we collected 138 and 140 age‐0 fish during the summers of 2009 and 2010, respectively. Pedigree reconstruction techniques were used to determine (1) the dispersal distance of age‐0 largemouth bass from nests to late‐summer points of capture (Warner Lake) and (2) interindividual distances between age‐0 full‐sibling pairs (Lake Chemung). Age‐0 fish in Warner Lake dispersed an average of 301 ± 41 m (mean ± SE). In Lake Chemung, intersibling dispersion distances varied substantially among pairs, but the distribution of distances was not significantly different from that of randomly selected pairs of individuals. Together, the data showed that age‐0 largemouth bass dispersed considerable distances from their nests and that the distance and direction of dispersal by siblings appeared to be independent of nest site. Our methods can be widely used for detailed evaluation of fish dispersal and effects of physical and biotic lakescape features on dispersal and recruitment.
Language use depending on news frame and immigrant origin
Authors: Fernández Itziar , Igartua Juan‐José , Moral Félix , Palacios Elena , Acosta Tania , Muñoz Dolores
Published: October 2012

The purpose of this study was to analyze the effect of the media on individuals’ specific language use in relation to a news story on immigration: the influence of the news frame and group cue. Abstraction, complexity of language use, and negative affective language were evaluated. The 523 participants were randomly distributed to each of the four experimental conditions: news frame (crime versus economic contribution) by group cue (geographical origin of the immigrants involved: Moroccans versus Latin Americans). Through content analysis of the ideas and reflections that arose after the participants read the different news stories, using the Linguistic Category Model (LCM; Semin & Fiedler, 1991) to measure abstract language and the Linguistic Inquiry and Word Count (LIWC; Pennebaker, Booth, & Francis, 2007) to analyze complex language and negative affective language, it emerged that abstract language and negative affective language were more frequent in the participants assigned to the news frame on crime. Complex language was more commonly used when the news frame referred to the economic contribution of immigrants. Regression analyses showed the mediating role of attitude to immigration in the effects of news frame on negative affective language. The bootstrap method was used to assess the magnitude of the indirect effect. A significant mediator effect was also found through structural equation modeling. Analyses of covariance showed one interaction between news frame and group cue: Among those who read the news story in a frame linking immigration to crime and Moroccan origin, abstract language was more characteristic. The results are discussed from the theoretical perspective of framing.
Empirical Standard Weight Equation for the Aegean Chub Squalius fellowesii, an Endemic Freshwater Fish Species of Western Anatolia, Turkey
Authors: Giannetto Daniela , Pompei Laura , Lorenzoni Massimo , Tarkan Ali Serhan
Published: October 2012

Data on length and weight of Aegean chub Squalius fellowesii, an endemic species distributed in the Aegean drainages of Anatolia, Turkey, were used to calculate a standard weight (Ws) equation by means of the empirical percentile (EmP) method. The resulting Ws equation was log10  Ws = −3.801 + 1.783·log10TL + 0.329·(log10TL)2. Over the range of application (70–220 mm TL), the EmP Ws equation was not biased by length, and the use of this equation is suggested as a way to calculate the relative weight (Wr) of Aegean chub throughout the species’ distribution area.

Received June 12, 2012; accepted July 27, 2012
A systematic review of the literature on counselling and psychotherapy for the prevention of suicide: 2. Qualitative studies
Authors: Winter David , Bradshaw Siobhan , Bunn Frances , Wellsted David
Published: October 2012

Scope of review: The paper reports a meta‐synthesis of 13 qualitative studies of counselling and psychotherapy with people at risk of suicide. Publication time span: The studies considered were reported between 1997 and 2006. Publication origin: Seven studies were conducted in the UK, four in the USA, one in Canada, and one in Sweden. Findings: Themes in clients' and therapists' accounts of the process of counselling or psychotherapy were therapist qualities; therapy components; theoretical framework; and therapy techniques. Themes in their accounts of the effectiveness of counselling and psychotherapy were decrease in self‐destructive behaviour, and quality of life. Themes in clients' views of barriers to effective counselling or psychotherapy were therapist characteristics; therapy components; secrecy; and transferring to the real‐life situation. Secrecy was also identified as a barrier by therapists, as were responsibilities of the profession; training; and the nature of suicide and self‐harm. Facilitators of successful counselling and psychotherapy as identified by clients were responsibility; support; and teaching therapy skills to family members, the latter also being identified by therapists.
Discriminating Rainbow Trout Sources Using Freshwater and Marine Otolith Growth Chemistry
Authors: Veinott Geoff , Porter Rex
Published: October 2012

Rainbow Trout Oncorhynchus mykiss are nonindigenous to Newfoundland. Subsequent to the development of marine cage rearing of Rainbow Trout in the Atlantic provinces in the early 1970s, Rainbow Trout have been captured in 33 rivers on the west and south coast of Newfoundland. These escapees may have negative impacts on wild populations, particularly Atlantic Salmon Salmo salar and Brook Trout Salvelinus fontinalis. In this study, the chemical fingerprints in the freshwater and marine growth sections of otoliths were used to distinguish three groups of Rainbow Trout of known origins: two hatcheries and one wild population. The results were then used to assign fish of unknown origin to the three known-origin groups and thus estimate the proportion of escapees. The three known sources produced distinct chemical fingerprints in the freshwater growth of the otoliths (cross validation test, average accuracy of over 93%); whereas, the marine growth in the otoliths produced a single chemical fingerprint for the two hatchery-origin groups distinct from the wild population. Results indicated that at least 60% of the unknown-origin fish were aquaculture escapees. Vaterite was encountered in 70–80% of the known hatchery-origin fish, 0% in the wild population, and 50% in the escapees. It appears that escapees with vaterite had a lower survival rate. The presence–absence of vaterite did not appear to be useful in distinguishing escapees from a wild population.
Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants
Authors: Magana-Mora Arturo , Ashoor Haitham , Jankovic Boris R. , Kamau Allan , Awara Karim , Chowdhary Rajesh , Archer John A.C. , Bajic Vladimir B.
Published: October 2012

Summary: In higher eukaryotes, the identification of translation initiation sites (TISs) has been focused on finding these signals in cDNA or mRNA sequences. Using Arabidopsis thaliana (A.t.) information, we developed a prediction tool for signals within genomic sequences of plants that correspond to TISs. Our tool requires only genome sequence, not expressed sequences. Its sensitivity/specificity is for A.t. (90.75%/92.2%), for Vitis vinifera (66.8%/94.4%) and for Populus trichocarpa (81.6%/94.4%), which suggests that our tool can be used in annotation of different plant genomes. We provide a list of features used in our model. Further study of these features may improve our understanding of mechanisms of the translation initiation.

Availability and implementation: Our tool is implemented as an artificial neural network. It is available as a web-based tool and, together with the source code, the list of features, and data used for model development, is accessible at http://cbrc.kaust.edu.sa/dts.

Contact:  vladimir.bajic@kaust.edu.sa

Supplementary information: Supplementary data are available at Bioinformatics online.
MP-T: improving membrane protein alignment for structure prediction
Authors: Hill Jamie R. , Deane Charlotte M.
Published: October 2012

Motivation: Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying hydrophobicity, and membrane proteins have different amino-acid substitution preferences from their soluble counterparts. Here we include these factors into an alignment method to improve alignments and consequently improve membrane protein models.

Results: We developed Membrane Protein Threader (MP-T), a sequence-structure alignment tool for membrane proteins based on multiple sequence alignment. Alignment accuracy is tested against seven other alignment methods over 165 non-redundant alignments of membrane proteins. MP-T produces more accurate alignments than all other methods tested (δFM from +0.9 to +5.5%). Alignments generated by MP-T also lead to significantly better models than those of the best alternative alignment tool (one-fourth of models see an increase in GDT_TS of ≥4%).

Availability: All source code, alignments and models are available at http://www.stats.ox.ac.uk/proteins/resources

Contact:  deane@stats.ox.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Phenological and phenotypic changes in Atlantic salmon populations in response to a changing climate
Authors: Todd Christopher D. , Friedland Kevin D. , MacLean Julian C. , Whyte Bryce D. , Russell Ian C. , Lonergan Michael E. , Morrissey Michael B.
Published: October 2012

Todd, C. D., Friedland, K. D., MacLean, J. C., Whyte, B. D., Russell, I. C., Lonergan, M. E., and Morrissey, M. B. 2012. Phenological and phenotypic changes in Atlantic salmon populations in response to a changing climate. – ICES Journal of Marine Science, 69: 1686–1698. Atlantic salmon (Salmo salar) of southern European origin migrating to the Norwegian Sea currently encounter anomalously high sea-surface temperatures, and returning adults are of low mean condition factor. For the River North Esk (Scotland), time-series changes in river age-structure of emigrant smolts and returning one- and two-sea-winter (1SW and 2SW) adults are assessed. A comparison of the river age-structure of returning adults (1977–1999) with that of their respective annual emigrant smolt cohorts shows no evidence of river age-related bias in survivorship at sea. Evidence is presented of a possible transgenerational, or maternal, influence (poor somatic condition of spawners) driving reduced quality of emigrant S2 smolts in the North Esk. This effect is concurrent with an influence of freshwater climate as indicated by the North Atlantic Oscillation Index (NAOI). The maternal influence and NAOI variation in the winter immediately prior to smolt migration jointly explain approximately 29 (S2) and 17% (S3), respectively, of the variation in the mean size of smolts over the period 1975–2010. Run-timing of 1SW adult cohorts returning to Scotland shows recent delays. Variation in river flow did influence mean return date for the River Tweed, but adult condition factor, which itself shows temporal trends likely to be associated with ocean climate change, was the primary significant explanatory variable for run-timing in the rivers North Esk and Tweed. Overall, in years of poorer adult condition, 1SW salmon stay at sea longer.
Assessment of goose barnacle (Pollicipes pollicipes Gmelin, 1789) stocks in management plans: design of a sampling program based on the harvesters' experience
Authors: Parada J. M. , Outeiral R. , Iglesias E. , Molares J.
Published: October 2012

Parada, J. M., Outeiral, R., Iglesias, E., and Molares, J. 2012. Assessment of goose barnacle (Pollicipes pollicipes Gmelin, 1789) stocks in management plans: design of a sampling program based on the harvesters' experience. – ICES Journal of Marine Science, 69: 1840–1849. Management plans of coastal marine resources require a wealth of information on socioeconomic topics, harvesting activities, population dynamics, and stock status. Moreover, the information provided by technical experts must take into account the needs of the managers. It must also adapt to schedules to serve a useful purpose. In many cases, the methodologies used by research teams are not directly applicable as they may be too complicated, aimed at specific objectives related to basic scientific work, or too costly to apply to long-term monitoring of extensive shellfish beds. Also, rocky coastlines exposed to heavy wave action preclude the use of sampling techniques that involve time-consuming data collection. This paper proposes a quick and simple methodology for gathering data in the field, based on the knowledge of the harvesters, to obtain stock assessments in keeping with their information needs. This methodology uses coverage percentage as an abundance index and weighting factor for the biometric information gathered from 50 specimens in each sampling. The sampling design uses the knowledge of the harvesters to define homogeneous strata. The results are in agreement with both the scientific-technical knowledge and the harvesters' knowledge of the populations being analysed.
Cusk (Brosme brosme) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act
Authors: Hare Jonathan A. , Manderson John P. , Nye Janet A. , Alexander Michael A. , Auster Peter J. , Borggaard Diane L. , Capotondi Antonietta M. , Damon-Randall Kimberly B. , Heupel Eric , Mateo Ivan , O'Brien Loretta , Richardson David E. , Stock Charles A. , Biegel Sarah T.
Published: October 2012

Hare, J.A., Manderson, J.P., Nye, J.A., Alexander, M.A., Auster, P.J., Borggaard, D.L., Capotondi, A.M., Damon-Randall, K.B., Heupel, E., Mateo, I., O'Brien, L., Richardson, D.E., Stock, C.A., and Biege, S.T. 2012. Cusk (Brosme brosme) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act. – ICES Journal of Marine Science, 69: 1753–1768. In the Northwest Atlantic Ocean cusk (Brosme brosme) has declined dramatically, primarily as a result of fishing activities. These declines have led to concern about its status, which has prompted reviews under the US Endangered Species Act and the Canadian Species at Risk Act. Changes in distribution and abundance of a number of marine fish in the Northwest Atlantic have been linked to climate variability and change, suggesting that both fishing and climate may affect the status of cusk. Our goal was to evaluate potential effects of climate change on Northwest Atlantic cusk distribution. Coupling a species niche model with the output from an ensemble of climate models, we projected cusk distribution in the future. Our results indicate cusk habitat in the region will shrink and fragment, which is a result of a spatial mismatch between high complexity seafloor habitat and suitable temperature. The importance of habitat patch connectivity for cusk is poorly understood, so the population-level consequences of climate-related habitat fragmentation are uncertain. More broadly, climate change may reduce appropriate thermal habitat and increase habitat fragmentation for other cold-water species in the region; thereby, increasing the potential for regional overexploitation and extirpation.
A Metabolic Regulator Modulates Virulence and Quorum Sensing Signal Production in Pectobacterium atrosepticum
Authors: Cubitt Marion F. , Hedley Peter E. , Williamson Neil R. , Morris Jenny A. , Campbell Emma , Toth Ian K. , Salmond George P. C.
Published: October 2012

Plant cell wall–degrading enzymes (PCWDE) are key virulence determinants in the pathogenesis of the potato pathogen Pectobacterium atrosepticum. In this study, we report the impact on virulence of a transposon insertion mutation in the metJ gene that codes for the repressor of the methionine biosynthesis regulon. In a mutant strain defective for the small regulatory RNA rsmB, PCWDE are not produced and virulence in potato tubers is almost totally abolished. However, when the metJ gene is disrupted in this background, the rsmB– phenotype is suppressed and virulence and PCWDE production are restored. Additionally, when metJ is disrupted, production of the quorum-sensing signal, N-(3-oxohexanoyl)-homoserine lactone, is increased. The metJ mutant strains showed pleiotropic transcriptional impacts affecting approximately a quarter of the genome. Genes involved in methionine biosynthesis were most highly upregulated but many virulence-associated transcripts were also upregulated. This is the first report of the impact of the MetJ repressor on virulence in bacteria.
Genetic Determinants of Potato virus Y Required to Overcome or Trigger Hypersensitive Resistance to PVY Strain Group O Controlled by the Gene Ny in Potato
Authors: Tian Yan-Ping , Valkonen Jari P. T.
Published: October 2012

Potato virus Y (PVY) (genus Potyvirus) is the most economically damaging and widely distributed virus in potato. Spread of PVY in the field is controlled by growing resistant cultivars. The dominant potato gene Nytbr for hypersensitive resistance (HR) controls ordinary PVY strains (PVYO) but is overcome by PVYN strains. Studies with infectious PVY chimeras and mutants indicated that the viral determinants necessary and sufficient to overcome Nytbr reside within the helper component proteinase (HC-Pro) (residues 227 to 327). Specifically, eight residues and the modeled three-dimensional conformation of this HC-Pro region distinguish PVYN from PVYO strains. According to the model, the conserved IGN and CCCT motifs implicated in potyvirus replication and movement, respectively, are situated in a coiled structure and an α-helix, respectively, within this region in PVYO; however, their locations are reversed in PVYN. Two residues (R269 and K270) are crucial for the predicted PVYO-specific HC-Pro conformation. Two viral chimeras triggered Nytbr and induced veinal necrosis in tobacco, which is novel for PVY. One chimera belonged to strain group PVYE. Our results suggest a structure–function relationship in recognition of PVYO HC-Pro by Nytbr, reveal HC-Pro amino acid signatures specific to PVYO and PVYN, and facilitate identification of PVY strains overcoming Nytbr.
First Report of Laurel Oak as a Host for the Pecan Root-Knot Nematode, Meloidogyne partityla, in Florida
Authors: Brito J. A. , Han H. , Stanley J. D. , Hao M. , Dickson D. W.
Published: October 2012

Roots of laurel oak (Quercus laurifolia Michx.), member of the family Fagaceae, were found to be heavily galled by the pecan root-knot nematode, Meloidogyne partityla, in two separate home gardens between 2010 and 2012, in Alachua Co., FL. Distinct round galls were observed on secondary and tertiary roots. Internally, root-knot nematode females were clearly visible when the roots were thinly sliced and egg masses were seen protruding from the root surfaces. The nematode species identification was performed using morphology of the male stylet, selected characters of the second-stage juveniles (J2), female perineal patterns, and esterase (EST) and malate dehydrogenase (Mdh) isozyme phenotypes. Morphology of perineal patterns of females, body, stylet, and tail length of the J2 and males all matched those of the original description of M. partityla (2). A swollen deeply grooved rectum was observed in the J2. The male stylet had a blunt tip with a prominent thickening at the junction between the cone and shaft. The stylet knobs of males and females were bipartite, each incised by a deep medium longitudinal groove (2). The isozyme phenotypes (EST = Mp3; Mdh = N1a) were consistent with those previously reported for M. partityla from Florida (1). Mitochondrial DNA (mtDNA) (3) and ribosomal internal transcriber spacer (ITS) DNA (4) of females were amplified to further confirm the nematode species identification. The mtDNA amplification using the C2F3/1108 primer set (3) and the ITS amplification using a recently available M. partityla specific primer set (4) produced fragments of approximately 530 bp and 550 bp, respectively. These were consistent with those already reported for this nematode species. This first report of a plant host for the pecan root-knot nematode outside of the family Juglandaceae indicates that the nematode may have migrated from Quercus species to pecan trees during the period when orchards were being established in Florida. To our knowledge, this is the first report of the pecan root-knot nematode infecting laurel oak.

References: (1) J. A. Brito et al. Nematology 10:757, 2008. (2) Kleynhans, K. P. N. Phytophylatica 18:103, 1986. (3) T. O. Powers et al., J. Nematol. 37:226, 2005. (4) R. A. Stamler. M. S. thesis, New Mexico State University, Las Cruces, 2009.
Identification of Fusarium oxysporum f. sp. lycopersici Race 3 Infecting Tomatoes in Northeast Brazil
Authors: Barboza E. A. , Cabral C. S. , Gonçalves A. M. , Reis A. , Fonseca M. E. N. , Boiteux L. S.
Published: October 2012

The three races of Fusarium oxysporum f. sp. lycopersici (FOL) are important tomato pathogens throughout the world, causing severe economic losses (1). In Brazil, races 1 and 2 are widespread, but the current geographic distribution of race 3 is restricted to the mild climate areas of Espírito Santo and Rio de Janeiro States in the southeast region (2,3). Here we report the spread of FOL race 3 to the warm northeast region of Brazil. Plants in commercial fields of the hybrid ‘Alambra’ (resistant to FOL races 1 and 2) were found displaying chlorosis, vascular browning, and wilt symptoms in Jaguaquara County, Bahia State, Brazil. Disease incidence ranged from 10 to 50%. The virulence profile of six isolates obtained from three distinct tomato-producing fields was investigated by root-dipping inoculation (106 conidia/ml) of 21-day-old seedlings from a set of FOL race differential accessions: ‘Ponderosa’ (susceptible to all races), ‘IPA-5’ (FOL race 1 resistance; I-1 locus); ‘Alambra’ and ‘Floradade’ (FOL races 1 and 2 resistance; I-2 gene), and Solanum pennellii ‘LA 716’ (resistant to all three races; I-3 locus). All six isolates were able to induce severe wilt symptoms in 100% of the plants from all lines but S. pennellii ‘LA 716’. FOL race 3 identity was confirmed via PCR assays employing a specific set of primers that are able to discriminate all the three FOL races as well as F. oxysporum f. sp. radicis-lycopersici isolates (1). Total DNA was extracted from pure fungal colonies growing in agar medium. The typical FOL race 3 amplicon profiles (i.e. positive for the primers uni, sp13, and sp23 and negative for the primer sprl) were observed only in the six FOL 3 isolates from Bahia as well as in five reference isolates of race 3 (previously obtained from tomato in Espírito Santo and Rio de Janeiro States), thus confirming their race identities. This recent, fast, and wide geographic expansion of the FOL race 3 in Brazil suggests that the pathogen has been introduced into new tomato producing areas via either contaminated seeds or seedlings. Because of the complexity of establishing effective chemical and cultural control strategies, these epidemics caused by FOL race 3 in distinct areas of Brazil might cause the replacement of the currently grown susceptible hybrids by resistant ones.

References: (1) Y. Hirano and T. Arie. J. Gen. Plant Pathol. 72:273, 2006; (2) A. Reis et al. Fitopatol. Bras. 30:426, 2005; (3) A. Reis and L. S. Boiteux. Hort. Bras. 25:451, 2007.
First Report of Cherry necrotic rusty mottle virus on Stone Fruit Trees in China
Authors: Zhou J. F. , Wang G. P. , Qu L. N. , Deng C. L. , Wang Y. , Wang L. P. , Hong N.
Published: October 2012

During the growing seasons of 2010 through 2012, leaf tissues from 206 stone fruit trees, including one flowering cherry, three sour cherry, six nectarine (Prunus persica L. var. nucipersica Schneider), 14 apricot, 24 plum (P. domestica L.), 41 sweet cherry, and 117 peach [P. persica (L.) Batsch] trees, grown in six provinces of China, were randomly collected and tested for the CNRMV infection by RT-PCR. Out of those sampled trees, 37 showed shot holes and vein yellowing symptoms. Total RNA was extracted from leaves using the CTAB protocol reported by Li et al. (2). The primer pair CGRMV1/CGRMV2 (1) was used to amplify a fragment of 949 bp from CNRMV genome, which includes the CP gene (804 bp). PCR products with the expected size were detected in one sweet cherry, one apricot, one peach, one plum, and two sour cherry plants. However, no correlation between PCR data and symptom expression could be found. PCR products were cloned into the vector pMD18-T (TaKaRa, Dalian, China). Three independent clones from each isolate were sequenced by Genscript Corp., Nanjing, China, and sequences were deposited in the GenBank under accession nos. JX491635, JX491636, JX491637, JX648205, and JX648206. Results of sequence analysis showed that sequences of the five CNRMV isolates shared the highest nt (99.0 to 99.6%) and aa (98.9 to 100%) similarities with a cherry isolate from Germany (GenBank Accession No. AF237816). The sequence of one isolate from a peach tree (JX648205) was divergent and shared only 84.7 to 86.1% nt and 94.4 to 95.1% aa similarities with those cp sequences. Clones intra each isolate shared more than 99% nt similarities. To confirm CNRMV infection, seedlings of peach GF 305 were graft-inoculated with bud-woods from a peach and a sweet cherry tree, which was positive to CNRMV and also two other viruses: Cherry green ring mottle virus (CGRMV) and Plum bark necrosis stem pitting-associated virus (PBNSPaV), as tested by RT-PCR. Grafted seedlings were kept in an insectproof greenhouse and observed for symptom development. In May of the following year, some newly developed leaves of inoculated seedlings showed vein yellowing, ringspot, and shot hole symptoms. Results of Protein A sandwich (PAS)-ELISA using an antiserum raised against the recombinant CP of a CNRMV isolate (unpublished) and RT-PCR confirmed CNRMV infection in inoculated trees. In addition to CNRMV, tested seedlings were also found to be infected with CGRMV and PBNSPaV by RT-PCR. To our knowledge, this is the first report on the occurrence of CNRMV on stone fruit trees in China, and also the first record of the CNRMV infection in peach and plum plants. Given the economic importance of its hosts and the visible symptoms of the viral disease, it is important to prevent the virus spread by using virus-tested propagation materials.

References: (1) R. Li and R. Mock. J. Virol. Methods 129:162, 2005. (2) R. Li et al. J. Virol. Methods 154:48, 2008.
First Report of Root Rot on Pulsatilla koreana Caused by Fusarium oxysporum in China
Authors: Su D. , Fu J. F.
Published: October 2012

Windflowers (Pulsatilla spp.) are perennial medicinal plants in the family Ranunculaceae with high economic as well as medicinal value in China. It is commonly used as traditional Chinese medicine (1). In May 2012, a root rot disease was observed on windflower (Pulsatilla koreana Nakai) at flowering stages in fields of Liaoning Province, China. The diseased area was estimated to be over 500 ha in the province and the yield was reduced by 30% on average with up to 45% yield losses in some fields. As the disease progressed, brown lesion production extended onto lateral and main roots, and aboveground tissues shriveled and decayed; in severe cases, white mycelium was clearly visible on diseased root tissue. Isolations from symptomatic roots were made on potato dextrose agar (PDA) and single-spore cultures were obtained. Colonies were initially white, but became pale violet with age, and purple pigments were produced in the agar. Microconidia were abundant, unicellular, oval to reniform, and ranged from 5.6 to 13.1 (9.3) × 2.8 to 4.2 (3.2) μm. Macroconidia were sparse, three-septate, slightly curved, and ranged from 21.9 to 39.4 (31.2) × 3.4 to 4.5 (3.9) μm. The isolated fungus was morphologically similar to Fusarium oxysporum (2). Two isolates were selected for molecular identification, and the internal transcribed spacer (ITS) region of rDNA was amplified using the primers ITS1/ITS4 (3) and sequenced. The obtained sequences (GenBank Accession Nos. JX669525 and JX669526) showed 99% homology with the sequences of F. oxysporum in GenBank (GQ121303). For pathogenicity tests, the isolate was cultured on PDA for 10 days at 25°C. Inoculations were performed on 10 healthy P. koreana plants by spraying a conidial suspension (2.0 × 105 microconidia ml–1) on roots previously wounded with a metal needle. Ten non-treated plants used as controls were sprayed with distilled water. The inoculated plants were incubated at 25°C under conditions of 12/12 h (light and dark). After 2 weeks, root rot symptoms were similar to the original symptoms observed under field conditions. No disease was observed on water-inoculated control plants. The same fungus was reisolated from the roots of infected plants, satisfying Koch's postulates. To our knowledge, this is the first report of F. oxysporum on P. koreana in China. The disease was hitherto scarcely reported in any other countries, and may deserve more attention in the future.

References: (1) S. C. Bang et al. J. Nat. Prod. 68:268, 2005. (2) J. F. Leslie and B. A. Summerell. The Fusarium Laboratory Manual. Blackwell Professional, Ames, IA, 2006. (3) T. J. White et al. Page 315 in: PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990.
Evidence that the Biofungicide Serenade (Bacillus subtilis) Suppresses Clubroot on Canola via Antibiosis and Induced Host Resistance
Authors: Lahlali R. , Peng G. , Gossen B. D. , McGregor L. , Yu F. Q. , Hynes R. K. , Hwang S. F. , McDonald M. R. , Boyetchko S. M.
Published: October 2012

This study investigated how the timing of application of the biofungicide Serenade (Bacillus subtilis QST713) or it components (product filtrate and bacterial cell suspension) influenced infection of canola by Plasmodiophora brassicae under controlled conditions. The biofungicide and its components were applied as a soil drench at 5% concentration (vol/vol or equivalent CFU) to a planting mix infested with P. brassicae at seeding or at transplanting 7 or 14 days after seeding (DAS) to target primary and secondary zoospores of P. brassicae. Quantitative polymerase chain reaction (qPCR) was used to assess root colonization by B. subtilis as well as P. brassicae. The biofungicide was consistently more effective than the individual components in reducing infection by P. brassicae. Two applications were more effective than one, with the biofungicide suppressing infection completely and the individual components reducing clubroot severity by 62 to 83%. The biofungicide also reduced genomic DNA of P. brassicae in canola roots by 26 to 99% at 7 and 14 DAS, and the qPCR results were strongly correlated with root hair infection (%) assessed at the same time (r = 0.84 to 0.95). qPCR was also used to quantify the transcript activity of nine host-defense-related genes in inoculated plants treated with Serenade at 14 DAS for potential induced resistance. Genes encoding the jasmonic acid (BnOPR2), ethylene (BnACO), and phenylpropanoid (BnOPCL and BnCCR) pathways were upregulated by 2.2- to 23-fold in plants treated with the biofungicide relative to control plants. This induced defense response was translocated to the foliage (determined based on the inhibition of infection by Leptosphaeria maculans). It is possible that antibiosis and induced resistance are involved in clubroot suppression by Serenade. Activity against the infection from both primary and secondary zoospores of P. brassicae may be required for maximum efficacy against clubroot.
Verticillium dahliae Populations from Mint and Potato Are Genetically Divergent with Predominant Haplotypes
Authors: Dung Jeremiah K. S. , Peever Tobin L. , Johnson Dennis A.
Published: October 2012

In total, 286 Verticillium dahliae isolates from mint, potato, and other hosts and substrates were characterized for mating type, vegetative compatibility group (VCG), and multilocus microsatellite haplotype to determine population genetic structure among populations infecting mint and potato. Populations from mint and potato fit a clonal reproductive model, with all isolates a single mating type (MAT1-2) and multiple occurrences of the same haplotypes. Haplotype H02 represented 88% of mint isolates and was primarily VCG2B, while haplotype H04 represented 70% of potato isolates and was primarily VCG4A. Haplotypes H02 and H04 typically caused severe disease on mint and potato, respectively, in greenhouse assays regardless of host origin. Principal coordinate analysis and analysis of molecular variance indicated that mint and potato populations were significantly genetically diverged (P = 0.02), and identification of private alleles and estimation of migration rates suggested restricted gene flow. Migration was detected between infected potato plants and seed tubers, infested tare soil, and field soils. Genetic differentiation of V. dahliae from mint and potato may be due to the occurrence of a single mating type and differences in VCG. Populations of V. dahliae in potato and mint were characterized by the presence of aggressive, clonally reproducing haplotypes which are widely distributed in commercial mint and potato production.
SUBRETINAL DEPOSITS, PARAMACULAR ATROPHY AND PIGMENTARY RETINOPATHY IN MITOCHONDRIAL ENCEPHALOPATHY, LACTIC ACIDOSIS, AND STROKE-LIKE EPISODES
Authors: Fung Adrian T. , Engelbert Michael , Odel Jeffrey G. , Yannuzzi Lawrence A.
Published: October 2012

Purpose:

To report a case of subretinal deposits, paramacular atrophy, and pigmentary retinopathy associated with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes.

Methods:

Retrospective review of medical records.

Results:

A 45-year-old white woman presented with progressive deterioration of vision and dark adaptation over several years. She had a background of an undiagnosed neurodegenerative disorder, including sensorineural hearing loss, cognitive disturbance, and peripheral neuropathy. On examination, subretinal deposits were visible along the superotemporal arcades. A diagnosis of mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes was confirmed by genetic testing (A3243G gene mutation). Four years later, she had developed paramacular atrophy and pigmentary retinopathy.

Conclusion:

Mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes may be associated with paramacular atrophy and pigmentary retinopathy. Autofluorescent changes may precede these signs and can help distinguish this condition from Stargardt disease–fundus flavimaculatus. As far as we are aware, this is the first report of fundus autofluorescence imaging and optical coherence tomography in mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes–associated retinopathy. Subretinal deposit may be an early sign.
Monsters are people too
Authors: Levy J. , Foulsham T. , Kingstone A.
Published: October 2012

Animals, including dogs, dolphins, monkeys and man, follow gaze. What mediates this bias towards the eyes? One hypothesis is that primates possess a distinct neural module that is uniquely tuned for the eyes of others. An alternative explanation is that configural face processing drives fixations to the middle of peoples' faces, which is where the eyes happen to be located. We distinguish between these two accounts. Observers were presented with images of people, non-human creatures with eyes in the middle of their faces (`humanoids’) or creatures with eyes positioned elsewhere (`monsters’). There was a profound and significant bias towards looking early and often at the eyes of humans and humanoids and also, critically, at the eyes of monsters. These findings demonstrate that the eyes, and not the middle of the head, are being targeted by the oculomotor system.
As it happens: current directions in experimental evolution
Authors: Bataillon Thomas , Joyce Paul , Sniegowski Paul
Published: October 2012

Recent decades have seen a significant rise in studies in which evolution is observed and analysed directly—as it happens—under replicated, controlled conditions. Such ‘experimental evolution’ approaches offer a degree of resolution of evolutionary processes and their underlying genetics that is difficult or even impossible to achieve in more traditional comparative and retrospective analyses. In principle, experimental populations can be monitored for phenotypic and genetic changes with any desired level of replication and measurement precision, facilitating progress on fundamental and previously unresolved questions in evolutionary biology. Here, we summarize 10 invited papers in which experimental evolution is making significant progress on a variety of fundamental questions. We conclude by briefly considering future directions in this very active field of research, emphasizing the importance of quantitative tests of theories and the emerging role of genome-wide re-sequencing.
Increased conspicuousness can explain the match between visual sensitivities and blue plumage colours in fairy-wrens
Authors: Delhey Kaspar , Hall Michelle , Kingma Sjouke A. , Peters Anne
Published: October 2012

Colour signals are expected to match visual sensitivities of intended receivers. In birds, evolutionary shifts from violet-sensitive (V-type) to ultraviolet-sensitive (U-type) vision have been linked to increased prevalence of colours rich in shortwave reflectance (ultraviolet/blue), presumably due to better perception of such colours by U-type vision. Here we provide the first test of this widespread idea using fairy-wrens and allies (Family Maluridae) as a model, a family where shifts in visual sensitivities from V- to U-type eyes are associated with male nuptial plumage rich in ultraviolet/blue colours. Using psychophysical visual models, we compared the performance of both types of visual systems at two tasks: (i) detecting contrast between male plumage colours and natural backgrounds, and (ii) perceiving intraspecific chromatic variation in male plumage. While U-type outperforms V-type vision at both tasks, the crucial test here is whether U-type vision performs better at detecting and discriminating ultraviolet/blue colours when compared with other colours. This was true for detecting contrast between plumage colours and natural backgrounds (i), but not for discriminating intraspecific variability (ii). Our data indicate that selection to maximize conspicuousness to conspecifics may have led to the correlation between ultraviolet/blue colours and U-type vision in this clade of birds.
The paradox of extreme high-altitude migration in bar-headed geeseAnser indicus
Authors: Hawkes L. A. , Balachandran S. , Batbayar N. , Butler P. J. , Chua B. , Douglas D. C. , Frappell P. B. , Hou Y. , Milsom W. K. , Newman S. H. , Prosser D. J. , Sathiyaselvam P. , Scott G. R. , Takekawa J. Y. , Natsagdorj T. , Wikelski M. , Witt M. J. , Yan B. , Bishop C. M.
Published: October 2012

Bar-headed geese are renowned for migratory flights at extremely high altitudes over the world's tallest mountains, the Himalayas, where partial pressure of oxygen is dramatically reduced while flight costs, in terms of rate of oxygen consumption, are greatly increased. Such a mismatch is paradoxical, and it is not clear why geese might fly higher than is absolutely necessary. In addition, direct empirical measurements of high-altitude flight are lacking. We test whether migrating bar-headed geese actually minimize flight altitude and make use of favourable winds to reduce flight costs. By tracking 91 geese, we show that these birds typically travel through the valleys of the Himalayas and not over the summits. We report maximum flight altitudes of 7290 m and 6540 m for southbound and northbound geese, respectively, but with 95 per cent of locations received from less than 5489 m. Geese travelled along a route that was 112 km longer than the great circle (shortest distance) route, with transit ground speeds suggesting that they rarely profited from tailwinds. Bar-headed geese from these eastern populations generally travel only as high as the terrain beneath them dictates and rarely in profitable winds. Nevertheless, their migration represents an enormous challenge in conditions where humans and other mammals are only able to operate at levels well below their sea-level maxima.
A new stem-neopterygian fish from the Middle Triassic of China shows the earliest over-water gliding strategy of the vertebrates
Authors: Xu Guang-Hui , Zhao Li-Jun , Gao Ke-Qin , Wu Fei-Xiang
Published: October 2012

Flying fishes are extraordinary aquatic vertebrates capable of gliding great distances over water by exploiting their enlarged pectoral fins and asymmetrical caudal fin. Some 50 species of extant flying fishes are classified in the Exocoetidae (Neopterygii: Teleostei), which have a fossil record no older than the Eocene. The Thoracopteridae is the only pre-Cenozoic group of non-teleosts that shows an array of features associated with the capability of over-water gliding. Until recently, however, the fossil record of the Thoracopteridae has been limited to the Upper Triassic of Austria and Italy. Here, we report the discovery of exceptionally well-preserved fossils of a new thoracopterid flying fish from the Middle Triassic of China, which represents the earliest evidence of an over-water gliding strategy in vertebrates. The results of a phylogenetic analysis resolve the Thoracopteridae as a stem-group of the Neopterygii that is more crown-ward than the Peltopleuriformes, yet more basal than the Luganoiiformes. As the first record of the Thoracopteride in Asia, this new discovery extends the geographical distribution of this group from the western to eastern rim of the Palaeotethys Ocean, providing new evidence to support the Triassic biological exchanges between Europe and southern China. Additionally, the Middle Triassic date of the new thoracopterid supports the hypothesis that the re-establishment of marine ecosystems after end-Permian mass extinction is more rapid than previously thought.
SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
Authors: Ouyang Zhengqing , Snyder Michael P. , Chang Howard Y.
Published: October 2012

We present an integrative approach, SeqFold, that combines high-throughput RNA structure profiling data with computational prediction for genome-scale reconstruction of RNA secondary structures. SeqFold transforms experimental RNA structure information into a structure preference profile (SPP) and uses it to select stable RNA structure candidates representing the structure ensemble. Under a high-dimensional classification framework, SeqFold efficiently matches a given SPP to the most likely cluster of structures sampled from the Boltzmann-weighted ensemble. SeqFold is able to incorporate diverse types of RNA structure profiling data, including parallel analysis of RNA structure (PARS), selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), fragmentation sequencing (FragSeq) data generated by deep sequencing, and conventional SHAPE data. Using the known structures of a wide range of mRNAs and noncoding RNAs as benchmarks, we demonstrate that SeqFold outperforms or matches existing approaches in accuracy and is more robust to noise in experimental data. Application of SeqFold to reconstruct the secondary structures of the yeast transcriptome reveals the diverse impact of RNA secondary structure on gene regulation, including translation efficiency, transcription initiation, and protein-RNA interactions. SeqFold can be easily adapted to incorporate any new types of high-throughput RNA structure profiling data and is widely applicable to analyze RNA structures in any transcriptome.
Pluripotent stem cells escape from senescence-associated DNA methylation changes
Authors: Koch Carmen M. , Reck Kristina , Shao Kaifeng , Lin Qiong , Joussen Sylvia , Ziegler Patrick , Walenda Gudrun , Drescher Wolf , Opalka Bertram , May Tobias , Brümmendorf Tim , Zenke Martin , Šarić Tomo , Wagner Wolfgang
Published: October 2012

Pluripotent stem cells evade replicative senescence, whereas other primary cells lose their proliferation and differentiation potential after a limited number of cell divisions, and this is accompanied by specific senescence-associated DNA methylation (SA-DNAm) changes. Here, we investigate SA-DNAm changes in mesenchymal stromal cells (MSC) upon long-term culture, irradiation-induced senescence, immortalization, and reprogramming into induced pluripotent stem cells (iPSC) using high-density HumanMethylation450 BeadChips. SA-DNAm changes are highly reproducible and they are enriched in intergenic and nonpromoter regions of developmental genes. Furthermore, SA-hypomethylation in particular appears to be associated with H3K9me3, H3K27me3, and Polycomb-group 2 target genes. We demonstrate that ionizing irradiation, although associated with a senescence phenotype, does not affect SA-DNAm. Furthermore, overexpression of the catalytic subunit of the human telomerase (TERT) or conditional immortalization with a doxycycline-inducible system (TERT and SV40-TAg) result in telomere extension, but do not prevent SA-DNAm. In contrast, we demonstrate that reprogramming into iPSC prevents almost the entire set of SA-DNAm changes. Our results indicate that long-term culture is associated with an epigenetically controlled process that stalls cells in a particular functional state, whereas irradiation-induced senescence and immortalization are not causally related to this process. Absence of SA-DNAm in pluripotent cells may play a central role for their escape from cellular senescence.