bluuebunny/crossref_metadata_2025 huggingface dataset:
Pattern of retinoblastoma pathway inactivation dictates response to CDK4/6 inhibition in GBM
Authors: Wiedemeyer W. Ruprecht , Dunn Ian F. , Quayle Steven N. , Zhang Jianhua , Chheda Milan G. , Dunn Gavin P. , Zhuang Li , Rosenbluh Joseph , Chen Shujuan , Xiao Yonghong , Shapiro Geoffrey I. , Hahn William C. , Chin Lynda
Published: June 2010

Glioblastoma multiforme (GBM) is a fatal primary brain tumor harboring myriad genetic and epigenetic alterations. The recent multidimensional analysis of the GBM genome has provided a more complete view of the landscape of such alterations and their linked pathways. This effort has demonstrated that certain pathways are universally altered, but that the specific genetic events altered within each pathway can vary for each particular patient's tumor. With this atlas of genetic and epigenetic events, it now becomes feasible to assess how the patterns of mutations in a pathway influence response to drugs that are targeting such pathways. This issue is particularly important for GBM because, in contrast to other tumor types, molecularly targeted therapies have failed to alter overall survival substantially. Here, we combined functional genetic screens and comprehensive genomic analyses to identifyCDK6as a GBM oncogene that is required for proliferation and viability in a subset of GBM cell lines and tumors. Using an available small molecule targeting cyclin-dependent kinases (CDKs) 4 and 6, we sought to determine if the specific pattern of retinoblastoma pathway inactivation dictated the response to CDK4/6 inhibitor therapy. We showed that codeletion ofCDKN2AandCDKN2Cserves as a strong predictor of sensitivity to a selective inhibitor of CDK4/6. Thus, genome-informed drug sensitivity studies identify a subset of GBMs likely to respond to CDK4/6 inhibition. More generally, these observations demonstrate that the integration of genomic, functional and pharmacologic data can be exploited to inform the development of targeted therapy directed against specific cancer pathways.
Exploiting mosquito sugar feeding to detect mosquito-borne pathogens
Authors: Hall-Mendelin Sonja , Ritchie Scott A. , Johansen Cheryl A. , Zborowski Paul , Cortis Giles , Dandridge Scott , Hall Roy A. , van den Hurk Andrew F.
Published: June 2010

Arthropod-borne viruses (arboviruses) represent a global public health problem, with dengue viruses causing millions of infections annually, while emerging arboviruses, such as West Nile, Japanese encephalitis, and chikungunya viruses have dramatically expanded their geographical ranges. Surveillance of arboviruses provides vital data regarding their prevalence and distribution that may be utilized for biosecurity measures and the implementation of disease control strategies. However, current surveillance methods that involve detection of virus in mosquito populations or sero-conversion in vertebrate hosts are laborious, expensive, and logistically problematic. We report a unique arbovirus surveillance system to detect arboviruses that exploits the process whereby mosquitoes expectorate virus in their saliva during sugar feeding. In this system, infected mosquitoes captured by CO
2
-baited updraft box traps are allowed to feed on honey-soaked nucleic acid preservation cards within the trap. The cards are then analyzed for expectorated virus using real-time reverse transcription-PCR. In field trials, this system detected the presence of Ross River and Barmah Forest viruses in multiple traps deployed at two locations in Australia. Viral RNA was preserved for at least seven days on the cards, allowing for long-term placement of traps and continuous collection of data documenting virus presence in mosquito populations. Furthermore no mosquito handling or processing was required and cards were conveniently shipped to the laboratory overnight. The simplicity and efficacy of this approach has the potential to transform current approaches to vector-borne disease surveillance by streamlining the monitoring of pathogens in vector populations.
Disentangling the role of environmental and human pressures on biological invasions across Europe
Authors: Pyšek Petr , Jarošík Vojtěch , Hulme Philip E. , Kühn Ingolf , Wild Jan , Arianoutsou Margarita , Bacher Sven , Chiron Francois , Didžiulis Viktoras , Essl Franz , Genovesi Piero , Gherardi Francesca , Hejda Martin , Kark Salit , Lambdon Philip W. , Desprez-Loustau Marie-Laure , Nentwig Wolfgang , Pergl Jan , Poboljšaj Katja , Rabitsch Wolfgang , Roques Alain , Roy David B. , Shirley Susan , Solarz Wojciech , Vilà Montserrat , Winter Marten
Published: June 2010

The accelerating rates of international trade, travel, and transport in the latter half of the twentieth century have led to the progressive mixing of biota from across the world and the number of species introduced to new regions continues to increase. The importance of biogeographic, climatic, economic, and demographic factors as drivers of this trend is increasingly being realized but as yet there is no consensus regarding their relative importance. Whereas little may be done to mitigate the effects of geography and climate on invasions, a wider range of options may exist to moderate the impacts of economic and demographic drivers. Here we use the most recent data available from Europe to partition between macroecological, economic, and demographic variables the variation in alien species richness of bryophytes, fungi, vascular plants, terrestrial insects, aquatic invertebrates, fish, amphibians, reptiles, birds, and mammals. Only national wealth and human population density were statistically significant predictors in the majority of models when analyzed jointly with climate, geography, and land cover. The economic and demographic variables reflect the intensity of human activities and integrate the effect of factors that directly determine the outcome of invasion such as propagule pressure, pathways of introduction, eutrophication, and the intensity of anthropogenic disturbance. The strong influence of economic and demographic variables on the levels of invasion by alien species demonstrates that future solutions to the problem of biological invasions at a national scale lie in mitigating the negative environmental consequences of human activities that generate wealth and by promoting more sustainable population growth.
Natural selection on
EPAS1
(
HIF2α
) associated with low hemoglobin concentration in Tibetan highlanders
Authors: Beall Cynthia M. , Cavalleri Gianpiero L. , Deng Libin , Elston Robert C. , Gao Yang , Knight Jo , Li Chaohua , Li Jiang Chuan , Liang Yu , McCormack Mark , Montgomery Hugh E. , Pan Hao , Robbins Peter A. , Shianna Kevin V. , Tam Siu Cheung , Tsering Ngodrop , Veeramah Krishna R. , Wang Wei , Wangdui Puchung , Weale Michael E. , Xu Yaomin , Xu Zhe , Yang Ling , Zaman M. Justin , Zeng Changqing , Zhang Li , Zhang Xianglong , Zhaxi Pingcuo , Zheng Yong Tang
Published: June 2010

By impairing both function and survival, the severe reduction in oxygen availability associated with high-altitude environments is likely to act as an agent of natural selection. We used genomic and candidate gene approaches to search for evidence of such genetic selection. First, a genome-wide allelic differentiation scan (GWADS) comparing indigenous highlanders of the Tibetan Plateau (3,200–3,500 m) with closely related lowland Han revealed a genome-wide significant divergence across eight SNPs located near
EPAS1
. This gene encodes the transcription factor HIF2α, which stimulates production of red blood cells and thus increases the concentration of hemoglobin in blood. Second, in a separate cohort of Tibetans residing at 4,200 m, we identified 31
EPAS1
SNPs in high linkage disequilibrium that correlated significantly with hemoglobin concentration. The sex-adjusted hemoglobin concentration was, on average, 0.8 g/dL lower in the major allele homozygotes compared with the heterozygotes. These findings were replicated in a third cohort of Tibetans residing at 4,300 m. The alleles associating with lower hemoglobin concentrations were correlated with the signal from the GWADS study and were observed at greatly elevated frequencies in the Tibetan cohorts compared with the Han. High hemoglobin concentrations are a cardinal feature of chronic mountain sickness offering one plausible mechanism for selection. Alternatively, as
EPAS1
is pleiotropic in its effects, selection may have operated on some other aspect of the phenotype. Whichever of these explanations is correct, the evidence for genetic selection at the
EPAS1
locus from the GWADS study is supported by the replicated studies associating function with the allelic variants.
Identification of a protein required for recovery of full antenna capacity in OCP-related photoprotective mechanism in cyanobacteria
Authors: Boulay Clémence , Wilson Adjélé , D'Haene Sandrine , Kirilovsky Diana
Published: June 2010

High light can be lethal for photosynthetic organisms. Similar to plants, most cyanobacteria protect themselves from high irradiance by increasing thermal dissipation of excess absorbed energy. The photoactive soluble orange carotenoid protein (OCP) is essential for the triggering of this photoprotective mechanism. Light induces structural changes in the carotenoid and the protein, leading to the formation of a red active form. Through targeted gene interruption we have now identified a protein that mediates the recovery of the full antenna capacity when irradiance decreases. In
Synechocystis
PCC 6803, this protein, which we called the fluorescence recovery protein (FRP), is encoded by the
slr1964
gene. Homologues of this gene are present in all of the OCP-containing strains. The FRP is a 14-kDa protein, strongly attached to the membrane, which interacts with the active red form of the OCP. In vitro this interaction greatly accelerates the conversion of the red OCP form to the orange form. We propose that in vivo, FRP plays a key role in removing the red OCP from the phycobilisome and in the conversion of the free red OCP to the orange inactive form. The discovery of FRP and its characterization are essential elements in the understanding of the OCP-related photoprotective mechanism in cyanobacteria.
Reverse biological engineering of
hrdB
to enhance the production of avermectins in an industrial strain of
Streptomyces avermitilis
Authors: Zhuo Ying , Zhang Wenquan , Chen Difei , Gao Hong , Tao Jun , Liu Mei , Gou Zhongxuan , Zhou Xianlong , Ye Bang-Ce , Zhang Qing , Zhang Siliang , Zhang Li-Xin
Published: June 2010

Avermectin and its analogues are produced by the actinomycete
Streptomyces avermitilis
and are widely used in the field of animal health, agriculture, and human health. Here we have adopted a practical approach to successfully improve avermectin production in an industrial overproducer. Transcriptional levels of the wild-type strain and industrial overproducer in production cultures were monitored using microarray analysis. The avermectin biosynthetic genes, especially the pathway-specific regulatory gene,
aveR
, were up-regulated in the high-producing strain. The upstream promoter region of
aveR
was predicted and proved to be directly recognized by
σ

hrdB

in vitro. A mutant library of
hrdB
gene was constructed by error-prone PCR and selected by high-throughput screening. As a result of evolved
hrdB
expressed in the modified avermectin high-producing strain, 6.38 g/L of avermectin B1a was produced with over 50% yield improvement, in which the transcription level of
aveR
was significantly increased. The relevant residues were identified to center in the conserved regions. Engineering of the
hrdB
gene can not only elicit the overexpression of
aveR
but also allows for simultaneous transcription of many other genes. The results indicate that manipulating the key genes revealed by reverse engineering can effectively improve the yield of the target metabolites, providing a route to optimize production in these complex regulatory systems.
Space observations of cold-cloud phase change
Authors: Choi Yong-Sang , Lindzen Richard S. , Ho Chang-Hoi , Kim Jinwon
Published: June 2010

This study examines the vertically resolved cloud measurements from the cloud-aerosol lidar with orthogonal polarization instrument on Aqua satellite from June 2006 through May 2007 to estimate the extent to which the mixed cloud-phase composition can vary according to the ambient temperature, an important concern for the uncertainty in calculating cloud radiative effects. At -20 °C, the global average fraction of supercooled clouds in the total cloud population is found to be about 50% in the data period. Between -10 and -40 °C, the fraction is smaller at lower temperatures. However, there are appreciable regional and temporal deviations from the global mean (>  ± 20%) at the isotherm. In the analysis with coincident dust aerosol data from the same instrument, it appears that the variation in the supercooled cloud fraction is negatively correlated with the frequencies of dust aerosols at the -20 °C isotherm. This result suggests a possibility that dust particles lifted to the cold cloud layer effectively glaciate supercooled clouds. Observations of radiative flux from the clouds and earth’s radiant energy system instrument aboard Terra satellite, as well as radiative transfer model simulations, show that the 20% variation in the supercooled cloud fraction is quantitatively important in cloud radiative effects, especially in shortwave, which are 10 - 20 W m
-2
for regions of mixed-phase clouds affected by dust. In particular, our results demonstrate that dust, by glaciating supercooled water, can decrease albedo, thus compensating for the increase in albedo due to the dust aerosols themselves. This has important implications for the determination of climate sensitivity.
Alterations of cortical pyramidal neurons in mice lacking high-affinity nicotinic receptors
Authors: Ballesteros-Yáñez Inmaculada , Benavides-Piccione Ruth , Bourgeois Jean-Pierre , Changeux Jean-Pierre , DeFelipe Javier
Published: June 2010

The neuronal nicotinic acetylcholine receptors (nAChRs) are allosteric membrane proteins involved in multiple cognitive processes, including attention, learning, and memory. The most abundant form of heterooligomeric nAChRs in the brain contains the β2- and α4- subunits and binds nicotinic agonists with high affinity. In the present study, we investigated in the mouse the consequences of the deletion of one of the nAChR components: the β2-subunit (β2−/−) on the microanatomy of cortical pyramidal cells. Using an intracellular injection method, complete basal dendritic arbors of 650 layer III pyramidal neurons were sampled from seven cortical fields, including primary sensory, motor, and associational areas, in both β2−/−and WT animals. We observed that the pyramidal cell phenotype shows significant quantitative differences among different cortical areas in mutant and WT mice. In WT mice, the density of dendritic spines was rather similar in all cortical fields, except in the prelimbic/infralimbic cortex, where it was significantly higher. In the absence of the β2-subunit, the most significant reduction in the density of spines took place in this high-order associational field. Our data suggest that the β2-subunit is involved in the dendritic morphogenesis of pyramidal neurons and, in particular, in the circuits that contribute to the high-order functional connectivity of the cerebral cortex.
Simultaneous high-resolution analysis of vaccinia virus and host cell transcriptomes by deep RNA sequencing
Authors: Yang Zhilong , Bruno Daniel P. , Martens Craig A. , Porcella Stephen F. , Moss Bernard
Published: June 2010

Deep RNA sequencing was used to simultaneously analyze vaccinia virus (VACV) and HeLa cell transcriptomes at progressive times following infection. VACV, the prototypic member of the poxvirus family, replicates in the cytoplasm and contains a double-stranded DNA genome with ≈200 closely spaced open reading frames (ORFs). The acquisition of a total of nearly 500 million short cDNA sequences allowed construction of temporal strand-specific maps of the entire VACV transcriptome at single-base resolution and analysis of over 14,000 host mRNAs. Before viral DNA replication, transcripts from 118 VACV ORFs were detected; after replication, transcripts from 93 additional ORFs were characterized. The high resolution permitted determination of the precise boundaries of many mRNAs including read-through transcripts and location of mRNA start sites and adjacent promoters. Temporal analysis revealed two clusters of early mRNAs that were synthesized in the presence of inhibitors of protein as well as DNA synthesis, indicating that they do not correspond to separate immediate- and delayed-early classes as defined for other DNA viruses. The proportion of viral RNAs reached 25–55% of the total at 4 h. This rapid change, resulting in a relative decrease of the vast majority of host mRNAs, can contribute to the profound shutdown of host protein synthesis and blunting of antiviral responses. At 2 h, however, a minority of cellular mRNAs was increased. The overrepresented functional categories of the up-regulated RNAs were NF-κB cascade, apoptosis, signal transduction, and ligand-mediated signaling, which likely represent the host response to invasion.
The small GTPases ARL-13 and ARL-3 coordinate intraflagellar transport and ciliogenesis
Authors: Li Yujie , Wei Qing , Zhang Yuxia , Ling Kun , Hu Jinghua
Published: June 2010

Intraflagellar transport (IFT) machinery mediates the bidirectional movement of cargos that are required for the assembly and maintenance of cilia. However, little is known about how IFT is regulated in vivo. In this study, we show that the small guanosine triphosphatase (GTPase) adenosine diphosphate ribosylation factor–like protein 13 (ARL-13) encoded by the Caenorhabditis elegans homologue of the human Joubert syndrome causal gene ARL13B, localizes exclusively to the doublet segment of the cilium. arl-13 mutants have shortened cilia with various ultrastructural deformities and a disrupted association between IFT subcomplexes A and B. Intriguingly, depletion of ARL-3, another ciliary small GTPase, partially suppresses ciliogenesis defects in arl-13 mutants by indirectly restoring binding between IFT subcomplexes A and B. Rescue of arl-13 mutants by ARL-3 depletion is mediated by an HDAC6 deacetylase-dependent pathway. Thus, we propose that two conserved small GTPases, ARL-13 and ARL-3, coordinate to regulate IFT and that perturbing this balance results in cilia deformation.
Tubulin polyglutamylation stimulates spastin-mediated microtubule severing
Authors: Lacroix Benjamin , van Dijk Juliette , Gold Nicholas D. , Guizetti Julien , Aldrian-Herrada Gudrun , Rogowski Krzysztof , Gerlich Daniel W. , Janke Carsten
Published: June 2010

Posttranslational glutamylation of tubulin is present on selected subsets of microtubules in cells. Although the modification is expected to contribute to the spatial and temporal organization of the cytoskeleton, hardly anything is known about its functional relevance. Here we demonstrate that glutamylation, and in particular the generation of long glutamate side chains, promotes the severing of microtubules. In human cells, the generation of long side chains induces spastin-dependent microtubule disassembly and, consistently, only microtubules modified by long glutamate side chains are efficiently severed by spastin in vitro. Our study reveals a novel control mechanism for microtubule mass and stability, which is of fundamental importance to cellular physiology and might have implications for diseases related to microtubule severing.
Exocytosis of acid sphingomyelinase by wounded cells promotes endocytosis and plasma membrane repair
Authors: Tam Christina , Idone Vincent , Devlin Cecilia , Fernandes Maria Cecilia , Flannery Andrew , He Xingxuan , Schuchman Edward , Tabas Ira , Andrews Norma W.
Published: June 2010

Rapid plasma membrane resealing is essential for cellular survival. Earlier studies showed that plasma membrane repair requires Ca2+-dependent exocytosis of lysosomes and a rapid form of endocytosis that removes membrane lesions. However, the functional relationship between lysosomal exocytosis and the rapid endocytosis that follows membrane injury is unknown. In this study, we show that the lysosomal enzyme acid sphingomyelinase (ASM) is released extracellularly when cells are wounded in the presence of Ca2+. ASM-deficient cells, including human cells from Niemann-Pick type A (NPA) patients, undergo lysosomal exocytosis after wounding but are defective in injury-dependent endocytosis and plasma membrane repair. Exogenously added recombinant human ASM restores endocytosis and resealing in ASM-depleted cells, suggesting that conversion of plasma membrane sphingomyelin to ceramide by this lysosomal enzyme promotes lesion internalization. These findings reveal a molecular mechanism for restoration of plasma membrane integrity through exocytosis of lysosomes and identify defective plasma membrane repair as a possible component of the severe pathology observed in NPA patients.
Enterocyte-specific A20 deficiency sensitizes to tumor necrosis factor–induced toxicity and experimental colitis
Authors: Vereecke Lars , Sze Mozes , Guire Conor Mc , Rogiers Brecht , Chu Yuanyuan , Schmidt-Supprian Marc , Pasparakis Manolis , Beyaert Rudi , van Loo Geert
Published: June 2010

A20 is a nuclear factor κB (NF-κB) target gene that encodes a ubiquitin-editing enzyme that is essential for the termination of NF-κB activation after tumor necrosis factor (TNF) or microbial product stimulation and for the prevention of TNF-induced apoptosis. Mice lacking A20 succumb to inflammation in several organs, including the intestine, and A20 mutations have been associated with Crohn’s disease. However, ablation of NF-κB activity, specifically in intestinal epithelial cells (IECs), promotes intestinal inflammation. As A20 deficiency sensitizes cells to TNF-induced apoptosis yet also promotes NF-κB activity, it is not clear if A20 deficiency in IECs would exacerbate or ameliorate intestinal inflammation. We generated mice lacking A20 specifically in IECs. These mice did not show spontaneous intestinal inflammation but exhibited increased susceptibility to experimental colitis, and their IECs were hypersensitive to TNF-induced apoptosis. The resulting TNF-driven breakdown of the intestinal barrier permitted commensal bacterial infiltration and led to systemic inflammation. These studies define A20 as a major antiapoptotic protein in the intestinal epithelium and further indicate that defects in A20 might contribute to inflammatory bowel disease in humans.
MiRror: a combinatorial analysis web tool for ensembles of microRNAs and their targets
Authors: Friedman Yitzhak , Naamati Guy , Linial Michal
Published: June 2010

Summary: The miRror application provides insights on microRNA (miRNA) regulation. It is based on the notion of a combinatorial regulation by an ensemble of miRNAs or genes. miRror integrates predictions from a dozen of miRNA resources that are based on complementary algorithms into a unified statistical framework. For miRNAs set as input, the online tool provides a ranked list of targets, based on set of resources selected by the user, according to their significance of being coordinately regulated. Symmetrically, a set of genes can be used as input to suggest a set of miRNAs. The user can restrict the analysis for the preferred tissue or cell line. miRror is suitable for analyzing results from miRNAs profiling, proteomics and gene expression arrays.

Availability:  http://www.proto.cs.huji.ac.il/mirror

Contact:  michall@cc.huji.ac.il
Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes
Authors: Romiguier Jonathan , Ranwez Vincent , Douzery Emmanuel J.P. , Galtier Nicolas
Published: June 2010

The origin, evolution, and functional relevance of genomic variations in GC content are a long-debated topic, especially in mammals. Most of the existing literature, however, has focused on a small number of model species and/or limited sequence data sets. We analyzed more than 1000 orthologous genes in 33 fully sequenced mammalian genomes, reconstructed their ancestral isochore organization in the maximum likelihood framework, and explored the evolution of third-codon position GC content in representatives of 16 orders and 27 families. We showed that the previously reported erosion of GC-rich isochores is not a general trend. Several species (e.g., shrew, microbat, tenrec, rabbit) have independently undergone a marked increase in GC content, with a widening gap between the GC-poorest and GC-richest classes of genes. The intensively studied apes and (especially) murids do not reflect the general placental pattern. We correlated GC-content evolution with species life-history traits and cytology. Significant effects of body mass and genome size were detected, with each being consistent with the GC-biased gene conversion model.
Exoenzyme activities as indicators of dissolved organic matter composition in the hyporheic zone of a floodplain river
Authors: CLINTON SANDRA M. , EDWARDS RICK T. , FINDLAY STUART E. G.
Published: June 2010

1. We measured the hyporheic microbial exoenzyme activities in a floodplain river to determine whether dissolved organic matter (DOM) bioavailability varied with overlying riparian vegetation patch structure or position along flowpaths.

2. Particulate organic matter (POM), dissolved organic carbon (DOC), dissolved oxygen (DO), electrical conductivity and temperature were sampled from wells in a riparian terrace on the Queets River, Washington, U.S.A. on 25 March, 15 May, 20 July and 09 October 1999. Dissolved nitrate, ammonium and soluble reactive phosphorus were also collected on 20 July and 09 October 1999. Wells were characterised by their associated overlying vegetation: bare cobble/young alder, mid‐aged alder (8–20 years) and old alder/old‐growth conifer (25 to >100 years). POM was analysed for the ash‐free dry mass and the activities of eight exoenzymes (α‐glucosidase, β‐glucosidase, β ‐N‐acetylglucosaminidase, xylosidase, phosphatase, leucine aminopeptidase, esterase and endopeptidase) using fluorogenic substrates.

3. Exoenzyme activities in the Queets River hyporheic zone indicated the presence of an active microbial community metabolising a diverse array of organic molecules. Individual exoenzyme activity (mean ± standard error) ranged from 0.507 ± 0.1547 to 22.8 ± 5.69 μmol MUF (g AFDM)−1 h−1, was highly variable among wells and varied seasonally, with the lowest rates occurring in March. Exoenzyme activities were weakly correlated with DO, DOC and inorganic nutrient concentrations.

4. Ratios of leucine aminopeptidase : β‐glucosidase were low in March, May and October and high in July, potentially indicating a switch from polysaccharides to proteins as the dominant component of microbial metabolism.

5. Principal components analysis indicated that there were patch effects and that these effects were strongest in the summer.

6. DOM degradation patterns did not change systematically along hyporheic flowpaths but varied with overlying forest patch type in the Queets River hyporheic zone, suggesting that additional carbon inputs exist. We hypothesise that the most likely input is the downward movement of DOM from overlying riparian soils. Understanding this movement of DOM from soils to subsurface water is essential for understanding both the hyporheic metabolism and the carbon budget of streams and rivers.
Pressure‐response relationships in stream ecology: introduction and synthesis
Authors: FRIBERG NIKOLAI
Published: June 2010

1. The articles in this Special Issue on pressure‐response relationships in stream ecology cover a range of pressures including acidification, excess loading of metals, nutrients and organic matter to stream ecosystems and changes in riparian and catchment land use. Impacts on the biota (macroinvertebrates), ranging from single species to community responses, are addressed over a multitude of spatial scales using large data sets.

2. The majority of articles are based on monitoring data compiled as part of the EU‐funded project REBECCA, but the Special Issue also includes articles from outside Europe (US and New Zealand) as well of studies using other data sources.

3. Results from the six articles gave new insights of relevance to water managers and documented that large‐scale monitoring can be an asset to freshwater science. The large data sets enable a range of analytical approaches that single out important patterns in highly variable data.: importance of humic substances in reducing the negative impact of low pH; impact of very low levels of BOD (<2 mg L−1); higher sensitivity of trait‐based metrics compared with identity‐based metrics and importance of catchment and riparian vegetation for the ecological quality of streams.

3. We advocate an increased use of monitoring and survey data in addressing questions relevant to scientist and end‐users, but issues relating to especially data quality should be considered. In future, the use of these data could increase knowledge exchange between the scientific community and managers with the ultimate aim of improving our freshwater resources.
Cost effective prediction of the eutrophication status of lakes and reservoirs
Authors: CATHERINE A. , MOUILLOT D. , ESCOFFIER N. , BERNARD C. , TROUSSELLIER M.
Published: June 2010

1. Eutrophication is a serious threat in many parts of the world, and identifying the environmental factors that determine the spatial distribution of eutrophicated waterbodies as well as the development of management tools is a challenge.

2. In this study, data from the Ile‐de‐France region were analysed to determine if catchment scale environmental variables could predict concentrations of chlorophyll a (used as a proxy for eutrophication status) of artificial lakes and reservoirs.

3. General additive models (GAM) and random forest models (RF) displayed greater predictive power than generalised linear models, indicating the importance of non‐monotonic relationships. Using RF modelling, very high predictive accuracy was achieved for both continuous and binomial (eutrophic or not) response variables (continuous: R2 = 0.715; binomial: kappa = 0.764, 89% of waterbodies were accurately predicted). The better predictive power and robustness of RF versus GAM was attributed to the formers ability to better handle complex interactions between predictors and to account for threshold effects.

4. Our results confirmed the close link between the water quality of lakes and reservoirs and the characteristics of their catchments. Moreover, we also showed that (i) simple (e.g. linear and/or monotonic) relationships between catchment land use and water quality were only found for sub‐regional datasets, and (ii) land use needs to be considered in association with complementary environmental variables (hydromorphological variables) to best assess its impact on water quality.
Palatability of macrophytes to the invasive freshwater snail Pomacea canaliculata: differential effects of multiple plant traits
Authors: WONG PAK KI , LIANG YAN , LIU NGA YING , QIU JIAN‐WEN
Published: June 2010

1. By selective grazing, invasive grazers can alter macrophyte‐herbivore relationships in shallow freshwater bodies. Evaluating the palatability of macrophytes and understanding the determinants of plant palatability can help predict grazing impact. In no‐choice feeding assays, we tested the palatability of 21 species of freshwater macrophytes to the invasive freshwater apple snail Pomacea canaliculata.

2. Daily feeding rate varied greatly with plant species, ranging from 1.1 to 22% of snail body mass. We assessed six plant properties and examined their correlation with feeding rate. Total nitrogen content was positively related, and C:N ratio and dry matter content (DMC) negatively related, to snail feeding rate. There was no significant correlation between snail feeding rate and plant phenolic content, but the feeding rate on Myriophyllum aquaticum (the plant with the highest phenolic content) was very low.

3. We repeated the feeding assays for 15 species that were not palatable as fresh leaves with reconstituted plant tissues formed by mixing ground up dried leaves with agar. The feeding rate still differed greatly among macrophyte species. Phragmites australis and Vallisneria natans (two species with the highest DMC) were eaten much more as reconstituted plant than as fresh leaves, indicating that structure (i.e. DMC) may be important in their defence against snail herbivory. For two plants (M. aquaticum and Alternanthera philoxeroides) that had moderate amounts of nitrogen/phosphorus but were consumed very little as fresh and reconstituted tissues, we incorporated their extracts into a palatable agar‐based food. The extracts from both species greatly reduced snail feeding rate, indicating the presence of chemical defences in these two species.

4. These results indicated that feeding was affected by several plant traits. The snail favoured plants with a high nitrogen content and avoided plants with a high DMC. Only a few plants possessed chemical feeding deterrents that were effective against this snail. Given the invasive spread of P. canaliculata in Asia, ecologists and managers should consider plant palatability when selecting plants for use in wetland restoration and when predicting the impact of further invasion by this species.
A comparison of two techniques for the removal of calcium hydroxide from root canals
Authors: Balvedi R. P. A. , Versiani M. A. , Manna F. F. , Biffi J. C. G.
Published: June 2010

Balvedi RPA, Versiani MA, Manna FF, Biffi JCG. A comparison of two techniques for the removal of calcium hydroxide from root canals. International Endodontic Journal, 43, 763–768, 2010.

Aim  To compare the ability of two irrigant regimens to remove calcium hydroxide (CH) mixed with different vehicles from root canal walls.

Methodology  The root canals of 92 freshly extracted bovine incisor teeth were prepared with a step‐back technique and randomly assigned into two experimental groups (n = 40), whilst the remaining teeth (n = 12) served as positive and negative controls. In each experimental group, ten teeth were assigned to each CH preparation: G1 – CH powder; G2 – CH + saline solution; G3 – CH + polyethylene glycol (PEG); G4 – CH + PEG + camphorated paramonochlorophenol (CPMC). The negative control did not receive CH placement, and the positive control received the intracanal dressing, but no subsequent removal. After 7 days, the CH was retrieved using manual or passive ultrasonic irrigation (PUI). The roots were grooved longitudinally and split into halves. Images of each half of the canal were acquired by a digital camera, and the percentage of CH coated surface area in relation to the surface area of each third of the canal was calculated. The results were statistically analysed with anova with post hoc Tukey test with the null hypothesis set as 5%.

Results  Remnants of medicament were found in all experimental groups. The positive control group had complete coverage of the canal walls with CH in contrast to the negative control (P < 0.001). Considering the cervical and middle thirds, the percentage of CH retention in G1 was significantly lower using PUI (26.6% and 32.2%, respectively) than the manual (38.7% and 46.1%, respectively) technique (P < 0.05). No significant differences were observed between G2, G3 and G4 in all thirds and the experimental groups at the apical third (P > 0.05).

Conclusions  Neither syringe injection nor PUI methods were efficient in removing the inter‐appointment root canal medicaments. Remnants of medicament were found in all experimental groups regardless of the vehicle used.
Ex vivo cytotoxicity of a new calcium silicate–based canal filling material
Authors: Zhang W. , Li Z. , Peng B.
Published: June 2010

Zhang W, Li Z, Peng B.
Ex vivo cytotoxicity of a new calcium silicate–based canal filling material. International Endodontic Journal, 43, 769–774, 2010.

Aim  To evaluate the biocompatibility of iRoot SP root canal filling material to L929 mouse fibroblasts.

Methodology  Specimens of iRoot SP, AH Plus and ProRoot mineral trioxide aggregate (MTA) were prepared for direct contact using the Millipore filter diffusion test, as well as extracts in MTT assay. Mouse fibroblasts (L929) were used as toxicity targets. Differences in cytotoxicity between fresh and set specimens and between root canal material extracts were determined by t‐test. A P‐value <0.05 was considered statistically significant.

Results  In the filter diffusion test, iRoot SP was slightly cytotoxic when tested as a fresh mixture and not cytotoxic in a set condition tested after 24 h. AH Plus was rated moderately cytotoxic when tested as a fresh mixture and slightly cytotoxic in a set (24 h) condition. MTA was noncytotoxic in both a fresh or set state. AH Plus was significantly more toxic than iRoot SP and MTA (P < 0.05). In addition, iRoot SP was significantly more toxic than MTA (P < 0.05). In the MTT assay with set specimens, extracts of iRoot SP and MTA were noncytotoxic, whilst extracts of AH Plus were rated as slightly cytotoxic. AH Plus was significantly more toxic than iRoot SP and MTA (P < 0.05).

Conclusion  AH Plus root canal sealer was significantly more toxic to L‐929 cells than MTA and iRoot SP. iRoot SP had intermediate toxicity.
The impact of different viewing conditions on radiological file and working length measurement
Authors: Orafi I. , Worthington H. V. , Qualtrough A. J. E. , Rushton V. E.
Published: June 2010

Orafi I, Worthington HV, Qualtrough AJE, Rushton VE. The impact of different viewing conditions on radiological file and working length measurement. International Endodontic Journal, 43, 600–607, 2010.

Aim  To determine the effect of different viewing conditions and observer experience upon the accuracy of file and working length measurements using analogue intra‐oral radiographs.

Methodology  Twenty‐five observers from a range of clinical backgrounds examined working length analogue periapical radiographs of 30 extracted teeth. Each participant measured both file (FL) and working length (WL) on each of the radiographs using three different viewing conditions consisting of a viewing box, a viewing box with film masking and a viewing box with film masking and ×2 magnification. Statistical analysis was conducted to derive interobserver reliability by intraclass correlation coefficients, and multiple linear regression models were fitted to compare the mean differences between the joint consensus between specialists and estimated values for file length and working length for each of the three viewing conditions.

Results  Multiple regressions models were fitted and found significant differences between the use of the viewing box alone and a viewing box with masking (FL P = 0.001; WL P < 0.001) and the use of the viewing box alone and with a viewing box employing masking and magnification (FL P < 0.001; WL P = 0.002). Intraclass correlation coefficient showed a high level of agreement between all observers; however, no statistically significant differences were found between the five observers groups for either mean file length or working length values.

Conclusions  The results of this study are in agreement with National and European guidelines, which recommend the use of a viewing box, magnification and masking for radiographic interpretation.
Estuarine crocodiles ride surface currents to facilitate long‐distance travel
Authors: Campbell Hamish A. , Watts Matthew E. , Sullivan Scott , Read Mark A. , Choukroun Severine , Irwin Steve R. , Franklin Craig E.
Published: June 2010

1. The estuarine crocodile (Crocodylus porosus) is the world’s largest living reptile. It predominately inhabits freshwater and estuarine habitats, but widespread geographic distribution throughout oceanic islands of the South‐east Pacific suggests that individuals undertake sizeable ocean voyages.

2. Here we show that adult C. porosus adopt behavioural strategies to utilise surface water currents during long‐distance travel, enabling them to move quickly and efficiently over considerable distances.

3. We used acoustic telemetry to monitor crocodile movement throughout 63 km of river, and found that when individuals engaged in a long‐distance, constant direction journey (>10 km day−1), they would only travel when current flow direction was favourable. Depth and temperature measurements from implanted transmitters showed that they remained at the water surface during travel but would dive to the river substratum or climb out on the river bank if current flow direction became unfavourable.

4. Satellite positional fixes from tagged crocodiles engaged in ocean travel were overlaid with residual surface current (RSC) estimates. The data showed a strong correlation existed between the bearing of the RSC and that of the travelling crocodile (r2 = 0·92, P < 0·0001).

5. The study demonstrates that C. porosus dramatically increase their travel potential by riding surface currents, providing an effective dispersal strategy for this species.
Growth responses of neotropical trees to logging gaps
Authors: Herault Bruno , Ouallet Julia , Blanc Lilian , Wagner Fabien , Baraloto Christopher
Published: June 2010

1. Modelling growth strategies among tropical trees is an important objective in predicting the response of tree dynamics to selective logging and in gaining insights into the ecological processes that structure tree communities in managed tropical forests.

2. We developed a disturbance index to model the effects of distance to and area of logging gaps on stem radial growth rates. This index was tested using census data of 43 neotropical tree species, representing a variety of life‐history strategies and developmental stages, from a selectively logged forest at Paracou, French Guiana. Growth strategies were analyzed in light of two indicators: the inherent species growth rate (when disturbance index is null) and the species reaction (change in growth rate) to logging gaps.

3. Across species, the predicted inherent growth rates in unlogged forest ranged from 0·25 to 6·47 mm year−1, with an average growth of 2·29 mm year−1. Ontogenetic shifts in inherent growth rate were found in 26 of the 43 species.

4. Species growth response to logging gaps varied widely among species but was significantly positive for 27 species. The effect of ontogeny on growth response to logging was retained for 14 species, and species with inherent fast growth rate (5 mm year−1) responded less to logging gap disturbances than did species with slow inherent growth (1 mm year−1).

5. Functional traits explained 19–42% of the variation in the inherent growth rate and in species’ response across all developmental stages. Whereas maximum diameters and seed mass were strong predictors of inherent growth rate, maximum height, wood density, mode of germination and stem architecture were additionally involved in tree growth response.

6. Synthesis and applications: This study provides a necessary framework for developing predictive post‐logging growth models for the thousands of species comprising tropical forests and is sufficiently general to apply to a broad range of managed tropical forests.
Pollination services decline with distance from natural habitat even in biodiversity‐rich areas
Authors: Carvalheiro Luísa G. , Seymour Colleen L. , Veldtman Ruan , Nicolson Susan W.
Published: June 2010

1. There is considerable evidence for the negative impacts of habitat alteration on pollinators in highly disturbed regions of the world. However, it remains unclear whether these findings reflect a global crisis for crop pollination. Understanding the extent to which world agriculture is endangered by pollinator decline is essential if the economic valuation of nature is to be used to promote conservation.

2. We assess the susceptibility to pollinator limitation of one of the most important tropical and subtropical fruit crops, mango Mangifera indica L., commonly planted in a region of South Africa located between two large biodiversity‐rich protected natural areas. We conducted flower visitor surveys, exclusion experiments and spatial analysis of flower visitation and fruit production patterns.

3. Our results show that both ants and flower visitors were effective pollinators of mango, the latter significantly declining (in abundance and species richness) with distance to natural habitat while ants were not affected. Neither the absence of pesticides nor the supplementation of flower visitors by using managed honeybees served to offset these negative impacts. Food‐web data suggest that maintaining diversity of flower resources within farmland can help maintain pollinator communities.

4. Moreover, models based exclusively on pollinator abundance underestimated the negative effect of distance from natural habitat on production (42% less at 500 m from natural habitat). As soil nutrient levels and water content are regularly measured and corrected in all study sites, these results suggest that pollinator diversity may also be important.

5. Synthesis and applications. This study provides one of the first examples of marked pollination limitation in farms surrounded by well‐protected natural habitat. For mango farming to be sustainable, it is essential to limit contiguous growth of farmland and consider practices that restore the complexity of plant‐pollinator networks within farms, for example through the creation and maintenance of pollinator‐friendly areas. By highlighting the economic gains of adopting pollinator‐friendly practices in agriculture, this work contributes to a growing body of studies that reveal that making farmland more suitable for pollinators benefits both agriculture and nature conservation.
Assessing the impact of nurse and allied health professional consultants: developing an activity diary
Authors: Humphreys Ann , Richardson Janet , Stenhouse Elizabeth , Watkins Mary
Published: June 2010

Aims.  To construct and test an activity diary designed to measure the impact and explore the activities of nurse and allied health professional consultants in relation to each speciality and function of the role.

Background.  This was part of a funded feasibility study to assess the contribution of nurse and allied health professional consultants.

Design.  This was an exploratory study.

Method.  Thematic analysis of guided discussions with five nurse consultants and one physiotherapy consultant identified activities which were used to construct an activity diary. The activities were grouped under the four pillars or functions of the consultant role; expert practice, leadership, research and education. Participants recorded their activities in a diary over a one‐week period.

Conclusion.  Results suggest that with some modification, this activity diary could be used to capture the impact, complexity and diversity of activities of the consultant role.

Relevance to practice.  Advanced practice roles are essential to the healthcare workforce of the future. This tool provides a method for measuring the contribution and complexity of the consultant role.