bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning and characterization of small non‐coding RNAs from grape
Authors: Carra Andrea , Mica Erica , Gambino Giorgio , Pindo Massimo , Moser Claudio , Pè Mario Enrico , Schubert Andrea 
Published: May 2009

SummarySmall non‐coding RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are effectors of regulatory pathways underlying plant development, metabolism, and responses to biotic and abiotic stresses. To address the nature and functions of these regulators in grapevine (Vitis vinifera L.), we have produced a small RNA library from mixed‐stage grape berries. Thirteen conserved miRNAs belonging to nine miRNA families, a non‐conserved miRNA, and four putative non‐conserved miRNAs were isolated, and their expression and targets are described. Experimentally validated targets of non‐conserved miRNAs and putative miRNAs included three genes encoding NB‐LRR proteins and a gene encoding a heavy metal ion transport/detoxification protein. Of the endogenous and pathogen‐derived siRNAs that were also isolated, four endogenous siRNAs mapped to genes encoding RD22‐like proteins and two to a gene encoding a cytokinin synthase. The siRNA id65 targeted the cytokinin synthase gene transcript with antisense complementarity, and was specifically expressed in mature berries, in which, by contrast, expression of the cytokinin synthase gene was strongly repressed. 5′ RACE revealed that the transcript of this gene was processed in 21 nucleotide increments from the id65 cleavage site, and that further cleavage was mediated by secondary siRNAs in cis. These results indicate that grapevine miRNA‐ and siRNA‐mediated regulatory circuits have evolved to comprise processes associated with defence and fruit ripening, and broaden the range of small RNA‐mediated regulation, which was previously associated with auxin, ABA, gibberellins and jasmonate, to encompass cytokinin metabolism.
Chemoimmunotherapy: an emerging strategy for the treatment of malignant mesothelioma
Authors: McCoy M. J. , Nowak A. K. , Lake R. A. 
Published: May 2009

AbstractWhether the immune system can recognize malignant and premalignant cells and eliminate them to prevent the development of cancer is still a matter of open debate, but in our view, the balance of evidence favours this concept. Nonetheless, the International Agency for Research on Cancer has now predicted that cancer will overtake heart disease as the leading cause of death worldwide by 2010, showing that this protective mechanism often fails. Malignant mesothelioma has traditionally been considered a relatively non‐immunogenic cancer. However, mesothelioma cells do express a set of well‐defined tumour antigens that have been shown to engage with the host immune system. Mesothelioma should therefore be considered a target for immunotherapy. A variety of anticancer immunotherapies have been investigated in mesothelioma and in other malignancies, although these have been largely ineffective when used in isolation. Over recent years, there has been increasing interest in the possibility of combining immunotherapy with chemotherapy in the fight against cancer. Here, we discuss the rationale behind combining these two, long considered antagonistic, treatment options in the context of malignant mesothelioma.
A proficiency testing study to evaluate laboratory performance for the detection of different genotypes of parvovirus B19
Authors: Baylis S. A. , Buchheit K. H. 
Published: May 2009

Background and Objectives  In Europe, it is a regulatory requirement that parvovirus B19 (B19V) DNA nucleic acid amplification technique‐based testing is performed on plasma pools for certain classes of plasma‐derived medicinal products. This proficiency testing study set out to examine the ability of public quality control laboratories and plasma fractionation organizations to detect different genotypes of B19V using nucleic acid amplification technique‐based assays.Materials and Methods  Laboratories were supplied with cloned DNAs representing the main genotypes of B19V. All samples were adjusted to equivalent copy number and were distributed as part of a routine external quality assessment programme investigating the evaluation of B19V containing plasma samples by these laboratories. The plasmid clones were distributed to 25 laboratories, representing 13 quality control laboratories and 12 manufacturers of plasma derivatives. The criteria for acceptable detection of the different genotypes of B19V DNA was based upon the maximum theoretical efficiency for polymerase chain reaction amplification. Proficient laboratories were deemed to be those reporting results within 1 log10 dilution for each of the different virus genotypes.Results  Data were returned by 23 of the participating laboratories. Some laboratories returned data for more than one type of assay and in total 27 data sets were analysed. Nine of the participating laboratories were able to successfully detect all the virus genotypes according to the applied criteria, all except one used in‐house assays.Conclusions  The results of the study highlight that there are still discrepancies in the detection of a broad spectrum of B19V genotypes, with implications for batch release testing.
Nutritional niche separation in coexisting bog species demonstrated by 15N‐enriched simulated rainfall
Authors: CLARKSON BEVERLEY R. , SCHIPPER LOUIS A. , SILVESTER WARWICK B. 
Published: May 2009

Abstract Empodisma minus and Sporadanthus ferrugineus (both Restionaceae) coexist in New Zealand raised bogs, yet Sporadanthus have significantly more depleted 15N natural abundance signatures than coexisting Empodisma. Their root systems are spatially separated with Empodisma having a thick surface layer of about 50 mm of cluster roots overlying the deeper Sporadanthus roots. We hypothesized this root displacement allows Empodisma to preferentially access the primary N input from rainfall, thus establishing niche separation, and tested this using tracer stable isotopes. We aerially applied 1.6 mmol m−2 of 15N as (NH4)2SO4 chased by deionized water to simulate a rainfall event of 34 L m−2. Root/peat matrix cores were harvested after 5 h and analysed for 15N uptake. Approximately 80% of the tracer applied was recovered in the cores, with 90% of this recovered in the upper Empodisma cluster root layer. Seven weeks after application, young shoots of Empodisma were significantly enriched (mean δ15N = +7.21‰; reference = −0.42‰), whereas those of coexisting Sporadanthus were not (mean δ15N = −2.76‰; reference = −4.24‰). However, we were unable to quantify the 15N uptake because of the dilution effect of the large biomass. We calculated the contribution of biological nitrogen fixation as a possible alternative source of N in achieving niche separation. The acetylene reduction assay showed minor amounts of nitrogenase activity are associated with Empodisma and Sporadanthus roots (equivalent to 0.045 ± 0.019 and 0.104 ± 0.017 kg N ha−1 year−1 respectively). Our results suggest that the species acquire nutrients from different rooting zones, with Empodisma accessing nutrients at the surface from rainfall and Sporadanthus accessing nutrients from mineralization in deeper peat layers. Such niche differentiation probably facilitates species coexistence and may provide a mechanism for slowing the rate of competitive displacement during long‐term succession.
Predicting the unexpected: using a qualitative model of a New Zealand dryland ecosystem to anticipate pest management outcomes
Authors: RAMSEY DAVID S. L. , NORBURY GRANT L. 
Published: May 2009

AbstractPest management is expensive and there is often uncertainty about the benefits for the resources being protected. There can also be unintended consequences for other parts of the ecosystem, especially in complex food webs. In making decisions managers generally have to rely on qualitative information collected in a piecemeal fashion. A method to assist decision making is a qualitative modelling approach using fuzzy cognitive maps, a directed graphical model related to neural networks that can take account of interactions between pests and conservation assets in complex food webs. Using all available information on relationships between native and exotic resources and consumers, we generated hypotheses about potential consequences of single‐species and multi‐species pest control on the long‐term equilibrium abundances of other biotic components of an ecosystem. We applied the model to a dryland ecosystem in New Zealand because we had good information on its trophic structure, but the information on the strength of species interactions was imprecise. Our model suggested that pest control is unlikely to significantly boost native invertebrates and lizards in this ecosystem, suggesting that other forms of management may be required for these groups. Most of the pest control regimes tested resulted in greater abundances of at least one other pest species, which could potentially lead to other management problems. Some of the predictions were unexpected, such as more birds resulting from possum and mouse control. We also modelled the effects of an increase in invasive rabbits, which led to unexpected declines of stoats, weasels, mice and possums. These unexpected outcomes resulted from complex indirect pathways in the food web. Fuzzy cognitive maps allow rapid construction of prototype models of complex food webs using a wide range of data and expert opinion. Their utility lies in providing direction for future monitoring efforts and generating hypotheses that can be tested with field experiments.
Biodiversity recovery during rainforest reforestation as indicated by rapid assessment of epigaeic ants in tropical and subtropical Australia
Authors: PIPER SCOTT D. , CATTERALL CARLA P. , KANOWSKI JOHN J. , PROCTOR HEATHER C. 
Published: May 2009

AbstractThere is growing interest in the potential for reforestation to assist the recovery of rainforest biodiversity. There is also a need to identify taxonomically tractable groups for use as cost‐effective indicators when monitoring the status of biodiversity within reforested sites. Insects are an important component of terrestrial biodiversity but often require considerable resources to sample at species level. Ant genera and generic‐based functional groups have been suggested as possible indicators of environmental disturbance. Here we ask to what extent the development of biodiversity is indicated by epigaeic ant genera and functional groups, across different types of reforestation in tropical and subtropical Australia. In each region, we used pitfall traps to sample the ants in replicate sites of: unmanaged regrowth, monoculture and mixed species plantations and ‘ecological restoration’ plantings, together with reference sites in pasture and rainforest. We recorded 35 epigaeic ant genera (and 4623 individuals) from 50 tropical sites, and 39 genera (and 9904 individuals) from 54 subtropical sites, with 47 genera overall. Community composition of both genera and functional groups differed between pasture and rainforest, although many genera were widespread in both. Reforested sites were intermediate between pasture and rainforest in both regions, and showed a gradient associated with decreasing grass and increasing tree and litter cover. Older monoculture plantations and ecological restoration plantings had the most rainforest‐like ant assemblages, and mixed‐species cabinet timber plots the least, of the reforested sites. We conclude that ground‐active ant genera and functional groups sampled in rapid surveys by pitfall‐trapping showed only a modest ability to discriminate among different types of reforestation. Species‐level identification, perhaps together with expanded sampling effort, could be more informative, but would require resourcing beyond the scope of rapid assessments.
Gap‐crossing decisions of forest birds in a fragmented landscape
Authors: ROBERTSON OLIVER J. , RADFORD JAMES Q. 
Published: May 2009

AbstractHabitat loss and fragmentation are recognized as primary drivers of biodiversity loss worldwide. To understand the functional effects of habitat fragmentation on bird populations, data on movement across gaps in habitat cover are necessary, although rarely available. In this study, we used call playback to simulate a conspecific territorial intruder to entice birds to move through the landscape in a predictable and directional manner. We then quantified the probability of movement in continuous forest and across cleared gaps for two forest‐dependent species, the grey shrike‐thrush (Colluricincla harmonica) and the white‐throated treecreeper (Cormobates leucophaeus). Fifty‐four playback trials were conducted for each species across distances ranging from 25 to 480 m in continuous forest and 15–260 m across gaps in a forest‐agricultural landscape in southern Victoria, Australia. The probability of movement was significantly reduced by gaps in forest cover for both species. Shrike‐thrushes were six times more likely to move 170 m in continuous forest than to cross 170‐m gaps. The mean probability that treecreepers would cross any gap at all was less than 0.5, and they were three times less likely to move 50 m across a gap than through continuous forest. Both species displayed non‐linear responses to increasing gap distance: we identified a gap‐tolerance threshold of 85 m for the shrike‐thrush and 65 m for the treecreeper beyond which individuals were most unlikely to cross. The presence of scattered paddock trees increased functional connectivity for the shrike‐thrush, with individuals crossing up to 260 m when scattered trees were present. We conclude that gaps in habitat cover are barriers to movement, and that characteristics of the intervening matrix influence landscape permeability.
Misprescription and misuse of one‐tailed tests
Authors: LOMBARDI CELIA M. , HURLBERT STUART H. 
Published: May 2009

AbstractOne‐tailed statistical tests are often used in ecology, animal behaviour and in most other fields in the biological and social sciences. Here we review the frequency of their use in the 1989 and 2005 volumes of two journals (Animal BehaviourandOecologia), their advantages and disadvantages, the extensive erroneous advice on them in both older and modern statistics texts and their utility in certain narrow areas of applied research. Of those articles with data sets susceptible to one‐tailed tests, at least 24% inAnimal Behaviourand at least 13% inOecologiaused one‐tailed tests at least once. They were used 35% more frequently with nonparametric methods than with parametric ones and about twice as often in 1989 as in 2005. Debate in the psychological literature of the 1950s established the logical criterion that one‐tailed tests should be restricted to situations where there is interest only in results in one direction. ‘Interest’ should be defined; however, in terms of collective or societal interest and not by the individual investigator. By this ‘collective interest’ criterion, all uses of one‐tailed tests in the journals surveyed seem invalid. In his bookNonparametric Statistics,S. Siegel unrelentingly suggested the use of one‐tailed tests whenever the investigator predicts the direction of a result. That work has been a major proximate source of confusion on this issue, but so are most recent statistics textbooks. The utility of one‐tailed tests in research aimed at obtaining regulatory approval of new drugs and new pesticides is briefly described, to exemplify the narrow range of research situations where such tests can be appropriate. These situations are characterized by null hypotheses stating that the difference or effect size does not exceed, or is at least as great as, some ‘amount of practical interest’. One‐tailed tests rarely should be used for basic or applied research in ecology, animal behaviour or any other science.
Ecophysiology of Eucalyptus marginata and Corymbia calophylla in decline in an urban parkland
Authors: GRIGG ALASDAIR , CLOSE DUGALD C. , LAMBERS HANS , RUTHROF KATINKA X. , DIXON KINGSLEY W. 
Published: May 2009

AbstractEucalypt trees are in decline throughout urban landscapes of south western Australia. This study investigated the cause of decline in Eucalyptus marginata and Corymbia calophylla trees in parkland and compared water and nutrient relations with healthy trees in adjacent bushland in Perth, Western Australia. It was hypothesized that: (i) trees were drought stressed through competition for soil water by the vigorous turf; (ii) excessive uptake of nitrogen, because of fertilizer application to turf, caused toxicity; and/or (iii) micronutrient (Cu, Fe, Mn and/or Zn) deficit was induced by high‐pH irrigation water applied to turf around parkland trees. Leaf water potential showed aseasonal variation in the irrigated parkland trees and foliar δ13C indicated that parkland trees generally had low water‐use efficiency and were not drought stressed relative to bushland trees. Foliar N levels were not significantly different between parkland and bushland trees indicating that excess N uptake was not a factor in the decline. Foliar total Fe, ‘metabolically active’ Fe, Cu and Zn concentrations were not significantly different between parkland and bushland trees. Foliar manganese concentrations were indicative of deficiency and significantly lower in parkland trees (5–14 µg g−1) relative to bushland trees (22–35 µg g−1). It is concluded that application of alkaline irrigation water to the parkland site reduced the plant‐availability of Mn; however, our study of only one parkland site does not allow us to generalize the results across other parklands.
Do trails affect relative abundance estimates of rainforest frogs and lizards?
Authors: Von MAY RUDOLF , DONNELLY MAUREEN A. 
Published: May 2009

AbstractThe selection of a sampling protocol is critical to study amphibian and reptile communities and in many instances researchers have combined the use of visual encounter surveys (VES) conducted on trails and off trails. The effect of human‐made trails on relative abundance estimates of amphibians and reptiles has been assessed in a few temperate locations, but data are lacking for tropical sites. Our study was designed to address this issue by comparing abundance estimates of frogs and lizards on and off trails in a lowland rainforest in south‐eastern Perú. We used nocturnal VES to sample frogs and lizards along transects established on trails and off trails in two different forest types. We found that the observed relative abundance estimates of frogs and lizards were affected by the location of transects (on trail vs. off trail) and the type of forest (floodplain forest vs. terra firme forest). We also found an interaction between the two main effects, indicating that the effect of transect location with respect to trails varies as a function of habitat. Observed frog abundances were higher on trails than off trails, indicating that studies that include VES on trails will bias relative abundance estimates in contrast to studies that include only VES off trails. We suggest that transects should be established only off trails, especially for monitoring studies because trail use by humans can have a strong influence on observed animal abundance.
Do virus‐resistant plants pose a threat to non‐target ecosystems? II. Risk assessment of an Australian pathosystem using multi‐scale field experiments
Authors: GODFREE ROBERT C. , WOODS MATTHEW J. , YOUNG ANDREW G. 
Published: May 2009

AbstractIt has been widely argued that the acquisition of novel disease resistance genes by wild host populations following the release of novel pathogen‐resistant plants into agricultural systems could pose a significant threat to non‐target plant communities. However, predicting the magnitude of ecological release in wild plant populations following the removal of disease remains a major challenge. In this paper we report on the second phase of a tiered risk assessment designed to investigate the role of disease on host growth, survival, fecundity and fitness in a model pathosystem (the pasture species Trifolium repens infected with Clover yellow vein virus, ClYVV) and to assess the level of risk posed to at‐risk native plant communities in southeast Australia by newly developed genetically modified and conventionally bred virus‐resistant T. repens genotypes. Multi‐year field experiments conducted in woodland and grassland environments using host‐pathogen arrays derived from 14 ClYVV isolates and 21 T. repens genotypes indicate that viral infection reduces fecundity, growth and survival of wild T. repens plants but that the severity of these effects depends on host tolerance to infection, isolate aggressiveness and specific spatial and temporal environmental conditions. Demographic modelling showed that by reducing host survival and growth, ClYVV also limits the intrinsic population growth rate and niche size of wild T. repens populations. Given the significant fitness cost associated with viral infection we conclude that virus‐resistant T. repens genotypes may pose a threat to some high conservation‐value non‐target ecosystems in SE Australia. We also argue that long‐term, multi‐tiered experiments conducted in a range of controlled and non‐controlled environments are necessary to detect and accurately quantify risks associated with the release of disease‐resistant plants in general.
Prevalence and correlates of functional disability in Chinese older adults
Authors: Liu Jufen , Chi Iris , Chen Gong , Song Xinming , Zheng Xiaoying 
Published: May 2009

Aim:  This article examines the prevalence of functional disability as well as sociodemographic correlations among Chinese older adults based on the most recent China National Sample Survey on Disability in 2006.Methods:  Functional disability was defined as lost motor function or limited movements and activities according to the International Classification of Function, Disability and Health, and physicians made the diagnosis of disability. Utilizing stratified, multiphase and cluster probability sampling design, a nationally representative sample of the non‐institutionalized elderly Chinese population was studied. Factors associated with functional disability were determined using a logistic regression model.Results:  The prevalence of functional disability was 8.1%. Major causes were vascular disease, osteoarthritis and accidents. In the non‐institutionalized elders, increased age, rural residence, less education, lower income, unemployment, being unmarried, living in simple housing, and living with others or non‐homeowners emerged as factors associated with functional disability in men and women.Conclusion:  To face the challenge of the rising prevalence of functional disability, prevention strategies should focus on reducing the incidences of chronic disease and improving socioeconomic status of older adults.