bluuebunny/crossref_metadata_2025 huggingface dataset:
Predation and Food Limitation Influence Fitness Traits of Growth‐Enhanced Transgenic and Wild‐Type Fish
Authors: Pennington Kelly M. , Kapuscinski Anne R.
Published: June 2011

Genetically engineered fish are nearing commercialization for aquaculture. If transgenic fish escape from farms, they could encounter and interbreed with natural populations. Relative advantages of transgenic fish for fitness‐related traits could drive population processes like gene flow, but fitness trait estimates will best inform risk assessments if measured under environmental conditions that are relevant to natural environments. Wild‐type and growth‐enhanced transgenic Japanese medakas Oryzias latipes of different genetic backgrounds were compared for the following fitness traits: fecundity, fertility, survival to sexual maturity, age at sexual maturity, and mating advantage. Because food availability and predation have been shown to alter the life histories of growth‐enhanced transgenic fish, we measured traits under four different environments: (1) high food availability and no predation, (2) high food availability with simulated predation, (3) low food availability and no predation, and (4) low food availability with simulated predation. We found that regardless of environment, there was no clear fitness trend by genotype: transgenic females were more fecund than wild‐type females, wild‐type males obtained more matings than transgenic males, and offspring of transgenic × wild‐type crosses had higher survival to sexual maturity than offspring of two wild‐type parents, possibly due to heterosis. Regardless of genotype, females produced more eggs in environments with high food availability and matured fastest under conditions of high food availability and no predation. Our results imply that population‐level processes like gene flow will be difficult to predict from measurements of one or two fitness traits taken on fish in a single environment. Therefore, gene flow risk assessments should be based on estimates of fitness traits that span the entire life cycle, incorporate relevant environmental variation, and compare the transgenic fish strain with a wild‐type strain of relevant genetic background.
Characterizing Uncertainty in Fish Stock Assessments: the Case of the Southern New England–Mid‐Atlantic Winter Flounder
Authors: Rothschild Brian J. , Jiao Yue
Published: June 2011

The reauthorization of the Magnuson–Stevens Act requires specification of scientific uncertainty associated with stock assessments. The scientific uncertainty associated with stock assessments of southern New England–mid‐Atlantic winter flounderPseudopleuronectes americanusis considered as a case study. Focus is placed upon the uncertainties associated with the assumptions, assertions, and choices (AACs) made in the stock assessment analysis. Two classes of AACs are discussed. The first class involves AACs that characterize the population dynamics of the stock; these AACs include the unit stock assumption, the problem of dealing with retrospective patterns, the method of averaging fishing mortality across cohorts to yield an annual value for fishing mortality, and the equilibrium structure of the stock. The second class of AACs is related to the choice of methods used to determine whether the stock is overfished; these AACs involve focusing on the maximum sustainable yield (MSY) proxy rather than MSY per se to determine overfishing levels. The MSY proxy approach is discussed and compared with heuristic calculations of the MSY approach. Arbitrary choices of instantaneous natural mortality and percent maximum spawning potential in the analysis can lead to an arbitrary decision on whether or not the stock is overfished. We conclude that there is considerable scientific uncertainty on the status of the southern New England–mid‐Atlantic winter flounder stock. The uncertainty identifies critical unknowns in winter flounder population dynamics.
Population Structure and Genetic Divergence of Coastal Rainbow and Redband Trout in the Upper Klamath Basin
Authors: Pearse Devon E. , Gunckel Stephanie L. , Jacobs Steven E.
Published: June 2011

Freshwater‐resident coastal rainbow trout Oncorhynchus mykiss irideus and the anadromous form of the subspecies, coastal steelhead (summer and winter runs), are present throughout the lower Klamath River–Trinity River system. Although coastal steelhead and other anadromous salmonids historically migrated into the Upper Klamath Basin (which encompasses the upper Klamath River and Upper Klamath Lake) and associated tributaries, the construction of Copco Dam in 1918 and Iron Gate Dam in 1962 stopped all upstream migration of fish past these barriers. In the Upper Klamath Lake basin, native Upper Klamath Lake redband trout O. mykiss newberrii are found along with coastal rainbow trout that were trapped above the dams or stocked from hatchery sources. However, relatively little is known about the genetic relationships among the O. mykiss populations within the Upper Klamath Basin. A population genetic analysis based on data from 17 variable microsatellite loci was conducted for samples collected in the Upper Klamath Basin, including rainbow trout and Upper Klamath Lake redband trout (presumably representative of the ancestral coastal and inland lineages) as well as samples of O. mykiss from neighboring inland lake basins. In addition, the Upper Klamath Basin samples were compared with data from O. mykiss populations below Iron Gate Dam. Results demonstrate the presence of distinct inland and coastal genetic lineages as well as divergent lineages represented by samples from the inland lake basins; these results have significant implications for future restoration of O. mykiss in the greater Klamath River–Trinity River system.
‘I never talked about, ever’: A comprehensive process analysis of a significant client disclosure event in therapy
Authors: Balmforth Jane , Elliott Robert
Published: May 2011

Aims: The present study was intended to examine how a particular client disclosure came about and what made it important to the client. Method: A client‐identified significant therapy event involving disclosure of childhood abuse was analysed using Comprehensive Process Analysis (CPA), a qualitative interpretive method for examining the process, effects and context of significant events in therapy. Results: The analysis identified therapist invitation and client universalisation as the key elements of the disclosure event. The context analysis showed how the event linked to the client's symbolisation of her fear earlier in the session and in the previous session. The client gained insight into how the earlier abuse had affected her life, linking it to the victimisation that was her primary reason for seeking therapy, and to her relationship with her mother. The therapist facilitated the event by following up the client's hints, trusting the strength of the alliance, and staying close to the client's frame of reference. Conclusion: The findings suggest that the initial significance of an invited disclosure event may diminish for a client over the course of therapy.
A thematic analysis of young people's experience of counselling in five secondary schools in the UK
Authors: Lynass Rosemarie , Pykhtina Olga , Cooper Mick
Published: May 2011

Aim: To investigate young people's views on the effects of school‐based counselling, and what they found helpful and unhelpful. Method: Eleven semi‐structured interviews were conducted and thematically analysed. Findings: Participants expressed predominantly positive views of school‐based counselling with changes in three main domains: emotional, interpersonal and behavioural. Participants viewed these changes as having had an important effect on their lives. The most commonly cited helpful aspects of counselling were related to talking or getting things out, and counsellor qualities. Conclusions: School‐based counselling is viewed positively by those who have experienced it, and appears to be an appropriate and valuable intervention for young people.
‘The third person in the room’: Recording the counselling interview for the purpose of counsellor training – barrier to relationship building or effective tool for professional development?
Authors: Gossman Marion , Miller Judi H.
Published: May 2011

Objective: Audio and videotape interview recording for training and supervision in counsellor education is commonplace within New Zealand, yet researchers have paid little attention to its value perceived by students. This study explores counselling students’ perceptions of the effects of recording counselling interviews on themselves, their clients and on the counselling process. Design: Counselling students from five tertiary educational settings in New Zealand participated in individual or focus group interviews to discuss their experiences of recording counselling interviews. Findings: All interviewees indicated that recording initially curtailed their ability to be completely present in the counselling interview. Some thought this may have negatively influenced their clients’ ability to use the counselling session effectively. Most noted their own increased confidence over time. Almost all considered recording to be extremely beneficial to the development of effective counselling skills. Conclusion: Most students considered the benefits of recording to outweigh the drawbacks. Implications for continuing the practice of recording and playing back interviews in counsellor‐education programmes are considered.
Agency Affects Adults', but not Children's, Guessing Preferences in a Game of Chance
Authors: Harris Adam J.L. , Rowley Martin G. , Beck Sarah R. , Robinson Elizabeth J. , McColgan Kerry L.
Published: May 2011

Adults and children have recently been shown to prefer guessing the outcome of a die roll after the die has been rolled (but remained out of sight) rather than before it has been rolled. This result is contrary to the predictions of the competence hypothesis (Heath & Tversky, 1991), which proposes that people are sensitive to the degree of their relative ignorance and therefore prefer to guess about an outcome it is impossible to know, rather than one that they could know, but do not. We investigated the potential role of agency in guessing preferences about a novel game of chance. When the experimenter controlled the outcome, we replicated the finding that adults and 5- to 6-year-old children preferred to make their guess after the outcome had been determined. For adults only, this preference reversed when they exerted control over the outcome about which they were guessing. The adult data appear best explained by a modified version of the competence hypothesis that highlights the notion of control or responsibility. It is proposed that potential attributions of blame are related to the guesser's role in determining the outcome. The child data were consistent with an imagination-based account of guessing preferences.
Stimulus/Response Learning in Masked Congruency Priming of Faces: Evidence for Covert Mental Classifications?
Authors: Eckstein Doris , Henson Richard N.
Published: May 2011

Reaction times for categorization of a probe face according to its sex or fame were contrasted as a function of whether the category of a preceding, sandwich-masked prime face was congruent or incongruent. Prime awareness was measured by the ability to later categorize the primes, and this was close to chance and typically uncorrelated with priming. When prime faces were never presented as visible probes within a test, priming was not reliable; when prime faces were also seen as probes, priming was only reliable if visible and masked presentation of faces were interleaved (not simply if primes had been visible in a previous session). In the latter case, priming was independent of experimentally induced face–response or face–category contingencies, ruling out any simple form of stimulus–response learning. We conclude that the reliable masked congruency priming reflects bindings between stimuli and multiple, abstract classifications that can be generated both overtly and covertly.
Face Processing as a Brain Adaptation at Multiple Timescales
Authors: Johnson Mark H.
Published: May 2011

I consider face processing as the brain's adaptive response to phylogenetic, ontogenetic, and task-specific factors. Focusing on wide-ranging evidence from both my own laboratory and others, evidence for a primitive “quick and dirty” route for face processing that exists prior to postnatal experience is reviewed. Next, I trace the emergence of cortical specialization for face processing influenced by individual developmental experience (ontogenetic adaptation) and suggest that this ontogenetic adaptation is also heavily constrained by the phylogenetic system. Finally, I turn to recent evidence on task-specific modulation of activity in the core face network that illustrates brain adaptation at a finer timescale than that for the other systems. Current evidence indicates that task-specific modulation of the cortical face network does not emerge until the teenage years. As previously proposed for other components of cognition, I propose that these systems are complementary to each other, each compensating for the others' weaknesses. Different face-related systems are adapted to respond to survival pressures at different timescales, from millennia, to months, to microseconds.
Fuel retention in impurity seeded discharges in JET after Be evaporation
Authors: Brezinsek S. , Loarer T. , Krieger K. , Jachmich S. , Tsalas M. , Coffey I. , Esser H.G. , Eich T. , Fundamenski W. , Giroud C. , Grünhagen S. , Huber A. , Kruezi U. , Knipe S. , Maddison G.P. , McCormick K. , Meigs A.G. , Morgan Ph. , Philipps V. , Sergienko G. , Stagg R. , Stamp M.F. , Tabares F.L.
Published: May 2011

Preparatory experiments for the ITER-Like Wall in JET were carried out to simulate the massive Be first wall by a thin Be layer, induced by evaporation of about 2.0 g Be, and to study its impact on fuel retention and divertor radiation with reduced C content and N seeding. Residual gas analysis reveals a reduction of hydrocarbons by one order of magnitude and of O by a factor of 5 in the partial pressure owing to the evaporation. The evolution of wall conditions, impurity fluxes and divertor radiation have been studied in ELMy H-mode plasmas (B
t = 2.7 T, I
p = 2.5 MA, P
aux = 16 MW) whereas a non-seeded reference discharge was executed prior to the evaporation.

The in situ measured Be flux at the midplane increased by about a factor of 40 whereas the C flux decreased by ∼50% in the limiter phase of the first discharge with respect to the reference, but erosion of the Be layer and partial coverage with C takes place quickly. To make best use of the protective Be layer, only the first four discharges were employed for a gas balance analysis providing a D retention rate of 1.94 × 1021 D s−1 which is comparable to rates with C walls. But the Be evaporation provides a non-saturated surface with respect to D and short term retention is not negligible in the balance; the measured retention is overestimated with respect to steady-state conditions like that of the ILW. Moreover, C was only moderately reduced and co-deposition of fuel with eroded Be and C occurs.

The lower C content leads to a minor reduction in divertor radiation as the reference phase prior to seeding indicates. N adds to the radiation of D and the remaining C, and the N content rises due to the legacy effect which has been quantified by gas balance to be 30% of the injected N. C radiation increases with exposure time, and both contributors cause an increase in the radiated fraction in the divertor from 50% to 70%. The radiation pattern suggests that N dominates the increase in the first discharges though C is still the dominating radiator. Therefore, the validity of a proxy of the Be first wall by a thin Be layer is limited and restricted to plasma operation directly after the Be evaporation.
ELM simulation experiments on Pilot-PSI using simultaneous high flux plasma and transient heat/particle source
Authors: De Temmerman G. , Zielinski J.J. , van Diepen S. , Marot L. , Price M.
Published: May 2011

A new experimental setup has been developed for edge localized mode (ELM) simulation experiments with relevant steady-state plasma conditions and transient heat/particle source. The setup is based on the Pilot-PSI linear plasma device and allows the superimposition of a transient heat/particle pulse to the steady-state heat flux plasma. Energy densities as high as 1 MJ m−2 have been reached for a pulse duration of about 1.5 ms, and for a variety of gases (H, He, Ar). In this contribution, we report on the first experiments investigating the effect of the combined steady-state/pulsed plasma on polycrystalline tungsten targets. Under such conditions the threshold for tungsten release and surface roughening is found to be much lower than in previously reported experiments. This suggests that the combination of the high flux plasma and transient heat/particle source leads to strong synergistic effects.
Turbulence propagation in heat flux-driven plasmas: implications for temperature profile structure
Authors: Wang Z.H. , Diamond P.H. , Gürcan Ö.D. , Garbet X. , Wang X.G.
Published: May 2011

Turbulence propagation and temperature profile evolution are studied in heat flux-driven plasmas. A simple model consisting of coupled non-linear reaction–diffusion equations for both turbulence and heat transport is proposed to elucidate several aspects of apparent non-local profile dynamics. Self-consistent E × B shear feedback on turbulence intensity growth and transport is also included in the model. Temperature profile evolution is studied in the presence of an intensity pulse propagating inwards but also interacting with an outward propagating heat pulse. It is found that as the heat flux Q increases, the intensity pulse speed first grows as
and then decays as 1/Q, while the heat pulse speed finally saturates at the level given by neoclassical transport. Intensity pulse propagation can be effectively saturated at or above a critical heat flux, so that the formation of an internal transport barrier (ITB) can be triggered. This suggests that the ITB location is ultimately determined by both heat flux and edge turbulence conditions, and thus the ITB inhibits both the inward turbulence propagation and the outward turbulent heat transport. As a test of turbulence spreading dynamics, the intensity pulse propagation through gaps in turbulence excitation and its implications for profile response to off-axis heat deposition are also investigated. It is shown that the profile resilience phenomena can be recovered by taking into account intensity pulse propagation.
Characterization of intrinsic rotation drive on DIII-D
Authors: Solomon W.M. , Burrell K.H. , deGrassie J.S. , Boedo J.A. , Garofalo A.M. , Moyer R.A. , Muller S.H. , Petty C.C. , Reimerdes H.
Published: May 2011

Recent experiments on DIII-D have focused on elucidating the drive mechanisms for intrinsic rotation in tokamak fusion plasmas. In H-mode plasmas, the effective torque at the edge (ρ > 0.8) associated with the intrinsic rotation shows a dependence on the pedestal pressure gradient ∇P
ped, which is qualitatively consistent with models describing E × B shear as a means of creating ‘residual stress’ and driving intrinsic rotation. However, direct measurement of the turbulent Reynolds stress using probes suggests that this is not the full picture. Specifically, there is a significant mismatch between the plasma spin up and the inferred torque from the Reynolds stress at the edge, indicating that additional mechanisms are necessary to completely understand edge intrinsic rotation generation. A narrow rotation layer is observed near the separatrix, which can qualitatively be explained using a model of thermal ion orbit loss. Parametrically, the torque from such a process is expected to vary with
. A good predictor of the edge intrinsic torque is obtained by including this dependence, together with the previously observed ∇P
ped dependence, in a regression fit of a wide range of H-mode conditions. The intrinsic torque in the core (ρ < 0.5) of H-mode plasmas tends to be much smaller than observed at the edge, although some examples have been found where it is large enough to modify the rotation profile. For instance, in certain plasmas with electron cyclotron heating, a significant counter-intrinsic torque has been observed in the inner region of the plasma.
Plasma regimes and research goals of JT-60SA towards ITER and DEMO
Authors: Kamada Y. , Barabaschi P. , Ishida S. , Ide S. , Lackner K. , Fujita T. , Bolzonella T. , Suzuki T. , Matsunaga G. , Yoshida M. , Shinohara K. , Urano H. , Nakano T. , Sakurai S. , Kawashima H.
Published: May 2011

The JT-60SA device has been designed as a highly shaped large superconducting tokamak with a variety of plasma actuators (heating, current drive, momentum input, stability control coils, resonant magnetic perturbation coils, W-shaped divertor, fuelling, pumping, etc) in order to satisfy the central research needs for ITER and DEMO. In the ITER- and DEMO-relevant plasma parameter regimes and with DEMO-equivalent plasma shapes, JT-60SA quantifies the operation limits, plasma responses and operational margins in terms of MHD stability, plasma transport and confinement, high-energy particle behaviour, pedestal structures, scrape-off layer and divertor characteristics. By integrating advanced studies in these research fields, the project proceeds ‘simultaneous and steady-state sustainment of the key performances required for DEMO’ with integrated control scenario development applicable to the highly self-regulating burning high-β high bootstrap current fraction plasmas.
Mechanisms of plasma rotation effects on the stability of type-I edge-localized mode in tokamaks
Authors: Aiba N. , Furukawa M. , Hirota M. , Oyama N. , Kojima A. , Tokuda S. , Yagi M.
Published: May 2011

Mechanisms of plasma rotation effects on edge magnetohydrodynamic (MHD) stability are investigated numerically by introducing energies that are distinguished by physics. By comparing them, it is found that an edge-localized MHD mode is destabilized by the difference between the eigenmode frequency and the equilibrium toroidal rotation frequency, which is induced by rotation shear. In addition, this destabilizing effect is found to be effective in the shorter wavelength region. The effect of poloidal rotation on the edge MHD stability is also investigated. Under the assumption that the change in equilibrium by poloidal rotation is negligible, it is identified numerically that poloidal rotation can have both stabilizing and destabilizing effects on the edge MHD stability, which depends on the direction of poloidal rotation. A numerical analysis demonstrates that these effects of plasma rotation in both the toroidal and poloidal directions can play important roles in type-I edge-localized mode phenomena in JT-60U H-mode plasmas.
The hull of Rudin’s Klein bottle
Authors: Anderson John
Published: June 2011

In 1981 Walter Rudin exhibited a totally real embedding of the Klein bottle into

C

2

\mathbb {C}^2

. We show that the polynomially convex hull of Rudin’s Klein bottle contains an open subset of

C

2

\mathbb {C}^2

. We also describe another totally real Klein bottle in

C

2

\mathbb {C}^2

whose hull has topological dimension equal to three.
RightField: embedding ontology annotation in spreadsheets
Authors: Wolstencroft Katy , Owen Stuart , Horridge Matthew , Krebs Olga , Mueller Wolfgang , Snoep Jacky L. , du Preez Franco , Goble Carole
Published: May 2011

Motivation: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, may have little experience in the use of such standards and require tools to support this form of data annotation.

Results: RightField is an open source application that provides a mechanism for embedding ontology annotation support for Life Science data in Excel spreadsheets. Individual cells, columns or rows can be restricted to particular ranges of allowed classes or instances from chosen ontologies. The RightField-enabled spreadsheet presents selected ontology terms to the users as a simple drop-down list, enabling scientists to consistently annotate their data. The result is ‘semantic annotation by stealth’, with an annotation process that is less error-prone, more efficient, and more consistent with community standards.

Availability and implementation: RightField is open source under a BSD license and freely available from http://www.rightfield.org.uk

Contact:  kwolstencroft@cs.man.ac.uk
Computational discovery of human coding and non-coding transcripts with conserved splice sites
Authors: Rose Dominic , Hiller Michael , Schutt Katharina , Hackermüller Jörg , Backofen Rolf , Stadler Peter F.
Published: May 2011

Motivation: Long non-coding RNAs (lncRNAs) resemble protein-coding mRNAs but do not encode proteins. Most lncRNAs are under lower sequence constraints than protein-coding genes and lack conserved secondary structures, making it hard to predict them computationally.

Results: We introduce an approach to predict spliced lncRNAs in vertebrate genomes combining comparative genomics and machine learning. It is based on detecting signatures of characteristic splice site evolution in vertebrate whole genome alignments. First, we predict individual splice sites, then assemble compatible sites into exon candidates, and finally predict multi-exon transcripts. Using a novel method to evaluate typical splice site substitution patterns that explicitly takes the species phylogeny into account, we show that individual splice sites can be accurately predicted. Since our approach relies only on predicted splice sites, it can uncover both coding and non-coding exons. We show that our predicted exons and partial transcripts are mostly non-coding and lack conserved secondary structures. These exons are of particular interest, since existing computational approaches cannot detect them. Transcriptome sequencing data indicate tissue-specific expression patterns of predicted exons and there is evidence that increasing sequencing depth and breadth will validate additional predictions. We also found a significant enrichment of predicted exons that form multi-exon transcript parts, and we experimentally validate such a novel multi-exon gene. Overall, we obtain 336 novel multi-exon transcript predictions from human intergenic regions. Our results indicate the existence of novel human transcripts that are conserved in evolution and our approach contributes to the completion of the human transcript catalog.

Availability and Implementation: Predicted human splice sites, exons and gene structures together with a Perl implementation of the tree-based log-odds scoring and a supplementary PDF file containing additional figures and tables are available at: http://www.bioinf.uni-leipzig.de/publications/supplements/10-010. The five experimentally confirmed partial transcript isoforms have been deposited in GenBank under accession numbers HM587422-HM587426.

Contact:  dominic@bioinf.uni-leipzig.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
TimeTree2: species divergence times on the iPhone
Authors: Kumar Sudhir , Hedges S. Blair
Published: May 2011

Summary: Scientists, educators and the general public often need to know times of divergence between species. But they rarely can locate that information because it is buried in the scientific literature, usually in a format that is inaccessible to text search engines. We have developed a public knowledgebase that enables data-driven access to the collection of peer-reviewed publications in molecular evolution and phylogenetics that have reported estimates of time of divergence between species. Users can query the TimeTree resource by providing two names of organisms (common or scientific) that can correspond to species or groups of species. The current TimeTree web resource (TimeTree2) contains timetrees reported from molecular clock analyses in 910 published studies and 17 341 species that span the diversity of life. TimeTree2 interprets complex and hierarchical data from these studies for each user query, which can be launched using an iPhone application, in addition to the website. Published time estimates are now readily accessible to the scientific community, K–12 and college educators, and the general public, without requiring knowledge of evolutionary nomenclature.

Availability: TimeTree2 is accessible from the URL http://www.timetree.org, with an iPhone app available from iTunes (http://itunes.apple.com/us/app/timetree/id372842500?mt=8) and a YouTube tutorial (http://www.youtube.com/watch?v=CxmshZQciwo).

Contact:  sbh1@psu.edu

Supplementary information:Supplementary data are available at Bioinformatics online.
Aligning short reads to reference alignments and trees
Authors: Berger Simon A. , Stamatakis Alexandros
Published: June 2011

Motivation: Likelihood-based methods for placing short read sequences from metagenomic samples into reference phylogenies have been recently introduced. At present, it is unclear how to align those reads with respect to the reference alignment that was deployed to infer the reference phylogeny. Moreover, the adaptability of such alignment methods with respect to the underlying reference alignment strategies/philosophies has not been explored. It has also not been assessed if the reference phylogeny can be deployed in conjunction with the reference alignment to improve alignment accuracy in this context.

Results: We assess different strategies for short read alignment and propose a novel phylogeny-aware alignment procedure. Our alignment method can improve the accuracy of subsequent phylogenetic placement of the reads into a reference phylogeny by up to 5.8 times compared with phylogeny-agnostic methods. It can be deployed to align reads to alignments generated by using fundamentally different alignment strategies (e.g. PRANK+F versus MUSCLE).

Availability:  http://www.exelixis-lab.org/software.html

Contact:  simon.berger@h-its.org; alexandros.stamatakis@h-its.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
First Report of Leaf Blight Caused by Nigrospora sphaerica on Curcuma in China
Authors: Zhang L. X. , Song J. H. , Tan G. J. , Li S. S.
Published: June 2011

Curcuma (family Zingiberaceae) is commonly cultivated for the use of rhizomes within traditional Chinese medicines. In October 2009 and 2010, severe leaf blight was observed on Curcuma wenyujin Y.H. Chen & C. Ling (4) in fields located in Ruian, China. The area of cultivation in Ruian encompasses 90% of the production in Zhejiang Province. Disease incidence was approximately 90% of plants observed in affected fields. Early symptoms were yellow-to-brown, irregular-shaped lesions on the leaf margin or tip. After several days, lesions expanded along the mid-vein until the entire leaf was destroyed. Blighted leaves turned grayish to dark brown and withered, and severely affected plants died. Eight fungal isolates were recovered from symptomatic C. wenyujin leaves, collected from eight different fields, on potato dextrose agar (PDA). These fungal colonies were initially white, becoming light to dark gray and produced black, spherical to subspherical, single-celled conidia (14 to 17 × 12 to 15 μm), which were borne on a hyaline vesicle at the tip of the conidiophores. On the basis of these morphological features, the isolates appeared to be similar to Nigrospora sphaerica (2). Strain ZJW-1 was selected as a representative for molecular identification. Genomic DNA was extracted from the isolate, and the internal transcribed spacer (ITS) region of the ribosomal DNA (ITS1-5.8S-ITS2) was amplified using ITS1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS4 (5′-TCCTCCGCTTATTGATATGC-3′) primers (3). The ITS region was further cloned and sequenced (GenBank Accession No. JF738028) and was 99% identical to N. sphaerica (GenBank Accession No. FJ478134.1). On the basis of morphological data and the ITS rDNA sequence, the isolate was determined to be N. sphaerica. Pathogenicity tests were conducted on four leaves of four C. wenyujin plants by placing agar pieces (5 mm in diameter) from 8-day-old cultures on pushpin-wounded leaves. An equal number of control plants were wounded and inoculated with noncolonized PDA agar pieces. Plants were placed in moist chambers at 25°C with a 12-h photoperiod. Brown-to-black lesions were observed on wounded leaves after 3 days and expanded to an average of 56 × 40 mm 15 days after inoculation. No symptoms developed on the control leaves. The pathogen was reisolated from the margins of necrotic tissues but not from the controls. The pathogen has been reported as a leaf pathogen on several hosts worldwide (1). To our knowledge, this is the first report of N. sphaerica as a leaf pathogen of C. wenyujin in China. Future research will focus primarily on management of this disease.

References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory, USDA-ARS, Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , March 31, 2011. (2) E. W. Mason. Trans. Brit. Mycol. Soc. 12:152, 1927. (3) T. J. White et al. PCR Protocols: A Guide to Methods and Applications. Academic Press, San Diego, 1990. (4) J. Zhao et al. Molecules 15:7547, 2010.
Aquimarina agarilytica sp. nov., an agarolytic species isolated from a red alga
Authors: Lin Bokun , Lu Guoyong , Zheng Yandan , Xie Wei , Li Shengkang , Hu Zhong
Published: May 2011

A novel yellow-pigmented, agarolytic bacterial strain, designated ZC1T, was isolated from the surface of the marine red algaPorphyra haitanensiscollected near Nan Ao Island, Guangdong province, China. The isolate was Gram-stain-negative, strictly aerobic and rod-shaped and displayed β-galactosidase, alkaline phosphatase, catalase and oxidase activities. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising C16 : 1ω7cand/or iso-C15 : 02-OH) and iso-C17 : 03-OH. The major menaquinone was menaquinone 6 (MK-6). The DNA G+C content was 32.8 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain ZC1Twas closely related to members of the genusAquimarinain the familyFlavobacteriaceae, phylumBacteroidetes. Based on phylogenetic and phenotypic evidence, strain ZC1T( = CCTCC AB 2010229T = NBRC 107695T) represents the type strain of a novel species in the genusAquimarina, for which the nameAquimarina agarilyticasp. nov. is proposed.
Streptomyces gramineus sp. nov., an antibiotic-producing actinobacterium isolated from bamboo (Sasa borealis) rhizosphere soil
Authors: Lee Hyo-Jin , Han Song-Ih , Whang Kyung-Sook
Published: May 2011

Two actinobacterial strains, JR-43T and JR-4, were isolated from bamboo (Sasa borealis) rhizosphere soil. The isolates produced grey aerial mycelium and a yellow soluble pigment on ISP 4. Microscopic observation revealed that strains JR-43T and JR-4 produced rectiflexibiles spore chains with spiny surfaces. Both isolates had antibacterial activity against plant-pathogenic bacteria, such as

Xanthomonas campestris

LMG 568T and

Xanthomonas axonopodis

pv. vesicatoria LMG 905. The isolates contained iso-C14 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C16 : 0 as the major fatty acids and MK-9(H6) and MK-9(H8) as the major isoprenoid quinones. Phylogenetic analysis of the 16S rRNA gene sequences of strains JR-43T and JR-4 showed that they grouped within

Streptomyces

cluster II and had highest sequence similarity to

Streptomyces seoulensis

NBRC 16668T and

Streptomyces recifensis

NBRC 12813T (both 98.2 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain JR-43T and

S. seoulensis

NBRC 16668T and

S. recifensis

NBRC 12813T ranged from 31.42 to 42.92 %. Based on DNA–DNA relatedness and morphological and phenotypic data, strains JR-43T and JR-4 could be distinguished from the type strains of phylogenetically related species. They are therefore considered to represent a novel species of the genus

Streptomyces

, for which the name Streptomyces gramineus sp. nov. is proposed. The type strain is JR-43T ( = KACC 15079T  = NBRC 107863T). Strain JR-43 ( = KACC 15078  = NBRC 107864) is a reference strain.
Lactobacillus

xiangfangensis sp. nov., isolated from Chinese pickle
Authors: Gu Chun Tao , Wang Fang , Li Chun Yan , Liu Fei , Huo Gui Cheng
Published: May 2011

A Gram-positive bacterial strain, 3.1.1T, was isolated from traditional pickle in Heilongjiang Province, China. The bacterium was characterized by a polyphasic approach, including 16S rRNA gene sequence analysis, pheS gene sequence analysis, rpoA gene sequence analysis, dnaK gene sequence analysis, fatty acid methyl ester analysis, determination of DNA G+C content, DNA–DNA hybridization and an analysis of phenotypic features. Based upon the data obtained in the present study, a novel species,

Lactobacillus

xiangfangensis sp. nov., is proposed with the type strain 3.1.1T ( = LMG 26013T  = NCIMB 14687T).
Streptomyces nanhaiensis sp. nov., a marine streptomycete isolated from a deep-sea sediment
Authors: Tian Xin-Peng , Long Li-Juan , Wang Fa-Zuo , Xu Ying , Li Jie , Zhang Jing , Zhang Chang-Sheng , Zhang Si , Li Wen-Jun
Published: May 2011

A novel aerobic streptomycete, strain SCSIO 01248T, was isolated from a sample of deep-sea sediment collected from the northern South China Sea, at a depth of 1632 m. This isolate formed yellow–white substrate mycelium and grey–white aerial hyphae. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain SCSIO 01248T was most closely related to

Streptomyces radiopugnans

R97T (98.8 % sequence similarity),

S. macrosporus

NBRC 14748T (97.5 %) and

S. megasporus

NBRC 14749T (97.3 %). The novel strain could, however, be readily differentiated from

S. radiopugnans

DSM 41901T on the basis of some physiological and cellular chemical characteristics; the level of DNA–DNA relatedness between these two strains was only 40 %. Based on phylogenetic and phenotypic evidence, strain SCSIO 01248T represents a novel species, for which the name Streptomyces nanhaiensis sp. nov. is proposed. The type strain is SCSIO 01248T ( = DSM 41926T  = KCTC 19401T  = CCTCC AA 208007T).
Brevibacillus aydinogluensis sp. nov., a moderately thermophilic bacterium isolated from Karakoc hot spring
Authors: Inan Kadriye , Canakci Sabriye , Belduz Ali Osman , Sahin Fikrettin
Published: May 2011

Two Gram-positive, moderately thermophilic, endospore-forming, rod-shaped, motile bacteria, designated PDF25T and PDF30, were isolated from Karakoc hot spring in the province of Izmir, Turkey, and were characterized in order to determine their phylogenetic positions. 16S rRNA gene sequence analysis revealed that the two strains belonged to the genus

Brevibacillus

; strain PDF25T showed highest sequence similarity to strain PDF30 (99.4 %) and

Brevibacillus thermoruber

DSM 7064T (98.5 %). The major fatty acids of strain PDF25T were iso-C15 : 0 (39.30 %), anteiso-C15 : 0 (26.10 %) and iso-C16 : 0 (14.75 %). Polar lipid analysis revealed diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine, and a variety of unidentified aminophospholipids, phospholipids and aminolipids. The major isoprenoid quinone was MK-7. The G+C content of the genomic DNA was 56.09 mol%. DNA–DNA hybridization experiments revealed 58 % relatedness between strain PDF25T and

B. thermoruber

DSM 7064T. Based on these data, the two strains are considered to represent a novel species of the genus

Brevibacillus

, for which the name Brevibacillus aydinogluensis sp. nov. is proposed. The type strain is PDF25T ( = DSM 24395T = LMG 26289T).
Differential Molecular Responses of Rice and Wheat Coleoptiles to Anoxia Reveal Novel Metabolic Adaptations in Amino Acid Metabolism for Tissue Tolerance
Authors: Shingaki-Wells Rachel N. , Huang Shaobai , Taylor Nicolas L. , Carroll Adam J. , Zhou Wenxu , Millar A. Harvey
Published: May 2011

Rice (Oryza sativa) and wheat (Triticum aestivum) are the most important starch crops in world agriculture. While both germinate with an anatomically similar coleoptile, this tissue defines the early anoxia tolerance of rice and the anoxia intolerance of wheat seedlings. We combined protein and metabolite profiling analysis to compare the differences in response to anoxia between the rice and wheat coleoptiles. Rice coleoptiles responded to anoxia dramatically, not only at the level of protein synthesis but also at the level of altered metabolite pools, while the wheat response to anoxia was slight in comparison. We found significant increases in the abundance of proteins in rice coleoptiles related to protein translation and antioxidant defense and an accumulation of a set of enzymes involved in serine, glycine, and alanine biosynthesis from glyceraldehyde-3-phosphate or pyruvate, which correlates with an observed accumulation of these amino acids in anoxic rice. We show a positive effect on wheat root anoxia tolerance by exogenous addition of these amino acids, indicating that their synthesis could be linked to rice anoxia tolerance. The potential role of amino acid biosynthesis contributing to anoxia tolerance in cells is discussed.
Virus-Induced Necrosis Is a Consequence of Direct Protein-Protein Interaction between a Viral RNA-Silencing Suppressor and a Host Catalase
Authors: Inaba Jun-ichi , Kim Bo Min , Shimura Hanako , Masuta Chikara
Published: May 2011

Many plant host factors are known to interact with viral proteins during pathogenesis, but how a plant virus induces a specific disease symptom still needs further research. A lily strain of Cucumber mosaic virus (CMV-HL) can induce discrete necrotic spots on infected Arabidopsis (Arabidopsis thaliana) plants; other CMV strains can induce similar spots, but they are not as distinct as those induced by CMV-HL. The CMV 2b protein (2b), a known RNA-silencing suppressor, is involved in viral movement and symptom induction. Using in situ proximity ligation assay immunostaining and the protoplast assays, we report here that CMV 2b interacts directly with Catalase3 (CAT3) in infected tissues, a key enzyme in the breakdown of toxic hydrogen peroxide. Interestingly, CAT3, normally localized in the cytoplasm (glyoxysome), was recruited to the nucleus by an interaction between 2b and CAT3. Although overexpression of CAT3 in transgenic plants decreased the accumulation of CMV and delayed viral symptom development to some extent, 2b seems to neutralize the cellular catalase contributing to the host defense response, thus favoring viral infection. Our results thus provide evidence that, in addition to altering the type of symptom by disturbing microRNA pathways, 2b can directly bind to a host factor that is important in scavenging cellular hydrogen peroxide and thus interfere specifically with that host factor, leading to the induction of a specific necrosis.
Frequent Gene Movement and Pseudogene Evolution Is Common to the Large and Complex Genomes of Wheat, Barley, and Their Relatives
Authors: Wicker Thomas , Mayer Klaus F.X. , Gundlach Heidrun , Martis Mihaela , Steuernagel Burkhard , Scholz Uwe , Šimková Hana , Kubaláková Marie , Choulet Frédéric , Taudien Stefan , Platzer Matthias , Feuillet Catherine , Fahima Tzion , Budak Hikmet , Doležel Jaroslav , Keller Beat , Stein Nils
Published: May 2011

All six arms of the group 1 chromosomes of hexaploid wheat (Triticum aestivum) were sequenced with Roche/454 to 1.3- to 2.2-fold coverage and compared with similar data sets from the homoeologous chromosome 1H of barley (Hordeum vulgare). Six to ten thousand gene sequences were sampled per chromosome. These were classified into genes that have their closest homologs in the Triticeae group 1 syntenic region in Brachypodium, rice (Oryza sativa), and/or sorghum (Sorghum bicolor) and genes that have their homologs elsewhere in these model grass genomes. Although the number of syntenic genes was similar between the homologous groups, the amount of nonsyntenic genes was found to be extremely diverse between wheat and barley and even between wheat subgenomes. Besides a small core group of genes that are nonsyntenic in other grasses but conserved among Triticeae, we found thousands of genic sequences that are specific to chromosomes of one single species or subgenome. By examining in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair. Thus, Triticeae seem to accumulate nonsyntenic genes frequently. Since many of them are likely to be pseudogenes, total gene numbers in Triticeae are prone to pronounced overestimates.
A cross sectional study of consumer awareness of functional foods in Thessaloniki, Greece
Authors: Christidis Nick , Tsoulfa Georgia , Varagunam Mira , Babatzimopoulou Maria
Published: May 2011

Purpose

Increasing awareness of functional foods would have many health benefits such as reducing the incidence of non communicable diseases. The aim of this study is to investigate consumer awareness and consumption of functional foods in the city of Thessaloniki, Greece.

Design/methodology/approach

A sample population of consumers was randomly selected outside popular supermarkets in the city of Thessaloniki (n=154). Trained interviewers conducted interviews and a questionnaire was completed by each participant. Socio‐demographic information and details of knowledge and consumption of functional foods were obtained. Data were analyzed using Stata.

Findings

The analysis of the data showed that only 33 per cent of the consumers were aware of the term “functional foods”. Interestingly, the proportion of the sample population that knew about foods with health promoting factors was over 95 per cent. The term “functional food” was unfamiliar to the sample population. Over 70 per cent of the consumers surveyed consumed such foods, unaware of the terminology.

Originality/value

This appears to be the first Greek study to examine consumer awareness and consumption of functional foods.
Consumption of Fairtrade products in a municipal catering organisation
Authors: Tikkanen Irma , Varkoi Tiina
Published: May 2011

Purpose

This paper seeks to explore the consumption of Fairtrade products in a municipal catering organisation from the viewpoint of corporate social responsibility (CSR).

Design/methodology/approach

In the paper, a theoretical foundation is established, concerning CSR, and a few studies related to CSR procurement are presented. Fairtrade Labelling Organisations International and its tasks are introduced. In addition, previous research related to the sustainable food procurement in the catering sector is introduced. Empirical data were collected from a municipal catering organisation by using a theme interview structure.

Findings

The findings indicate that the consumption of Fairtrade products encompasses eight Fairtrade products. Two products are consumed in each unit of the case organisation, whereas six products are consumed occasionally. The procurement of Fairtrade products were based on the values of the case organisation, the environmental programme and the laws and the European Union's communications.

Practical implications

The empirical results may be utilised when planning the consumption of Fairtrade products in the municipal catering organisation, and when preparing the competitive tendering of the catering services. The findings offer valuable information when transforming the catering operations into a more sustainable direction.

Originality/value

The extent of consumption concerning Fairtrade products by displaying an empirical case study is described.