bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure of the sliding clamp from the fungal pathogen Aspergillus fumigatus (AfumPCNA) and interactions with Human p21
Authors: Marshall Andrew C. , Kroker Alice J. , Murray Lauren A.M. , Gronthos Kahlia , Rajapaksha Harinda , Wegener Kate L. , Bruning John B. 
Published: February 2017

The fungal pathogen Aspergillus fumigatus has been implicated in a drastic increase in life‐threatening infections over the past decade. However, compared to other microbial pathogens, little is known about the essential molecular processes of this organism. One such fundamental process is DNA replication. The protein responsible for ensuring processive DNA replication is PCNA (proliferating cell nuclear antigen, also known as the sliding clamp), which clamps the replicative polymerase to DNA. Here we present the first crystal structure of a sliding clamp from a pathogenic fungus (A. fumigatus), at 2.6Å. Surprisingly, the structure bears more similarity to the human sliding clamp than other available fungal sliding clamps. Reflecting this, fluorescence polarization experiments demonstrated that AfumPCNA interacts with the PCNA‐interacting protein (PIP‐box) motif of human p21 with an affinity (Kd) of 3.1 μm. Molecular dynamics simulations were carried out to better understand how AfumPCNA interacts with human p21. These simulations revealed that the PIP‐box bound to AfuPCNA forms a secondary structure similar to that observed in the human complex, with a central 310 helix contacting the hydrophobic surface pocket of AfumPCNA as well as a β‐strand that forms an antiparallel sheet with the AfumPCNA surface. Differences in the 310 helix interaction with PCNA, attributed to residue Thr131 of AfumPCNA, and a less stable β‐strand formation, attributed to residues Gln123 and His125 of AfumPCNA, are likely causes of the over 10‐fold lower affinity of the p21 PIP‐box for AfumPCNA as compared to hPCNA.DatabaseThe atomic coordinates and structure factors for the Aspergillus fumigatus sliding clamp can be found in the RCSB Protein Data Bank (http://www.rcsb.org) under the accession code 5TUP.
The impacts of habitat disturbance on adult and larval dragonflies (Odonata) in rainforest streams in Sabah, Malaysian Borneo
Authors: Luke Sarah H. , Dow Rory A. , Butler Stephen , Vun Khen Chey , Aldridge David C. , Foster William A. , Turner Edgar C. 
Published: February 2017

Summary

Dragonfly assemblages (Odonata: comprising damselflies, Zygoptera; and dragonflies, Anisoptera) in Southeast Asian rainforests are extremely diverse but increasingly threatened by habitat disturbance, including logging and conversion of forest to oil palm plantations.

Land‐use change can affect dragonfly larval stages by altering within‐stream environmental conditions, and adults by loss of perches, shade and hunting habitat. However, the extent to which dragonflies are affected by land‐use change is not well known, and strategies for conservation are poorly developed.

We surveyed dragonfly adults and larvae, forest quality and stream environmental conditions across 16 streams in Sabah, Malaysia. Habitat surrounding the streams included pristine forest, selectively logged forest, oil palm with forested riparian buffer strips and oil palm without buffers.

Overall abundance and species richness of adult dragonflies stayed constant with habitat disturbance, but larval abundance and richness decreased with higher habitat disturbance, and larvae were largely absent from oil palm streams. There was also a clear shift in community composition of both adult and larval dragonflies. Anisoptera adults were more species rich and abundant, but Zygoptera adults were less species rich in more disturbed sites.

The presence of riparian buffers in oil palm plantations offered some protection for forest‐associated dragonfly species, and streams with wider riparian buffers supported adult assemblages more similar to those found in logged forest. However, oil palm streams with riparian buffers still contained a depauperate larval assemblage compared to logged forest areas, and dragonfly assemblages in narrow riparian buffer streams were similar to those found in streams surrounded by continuous oil palm.

Our results provide clear evidence of the effect of land‐use change on dragonflies. Conservation efforts to conserve forest communities should target the preservation of existing forest areas, but management within oil palm plantation landscapes to preserve riparian buffers can still have a marked beneficial effect on dragonfly communities.
Fine spatial grain, large spatial extent and biogeography of macrophyte‐associated cladoceran communities across Neotropical floodplains
Authors: Rocha Mariana P. , Heino Jani , Machado‐Velho Luiz F. , Lansac‐Tôha Fernando M. , Lansac‐Tôha Fábio A. 
Published: February 2017

SummaryMetacommunity structure may be strongly influenced by spatial dynamics and environmental factors, as well as biogeographic effects. Here, we examined variation in lake cladoceran communities associated with floating macrophytes in the four major Brazilian floodplain systems (Amazônia, Araguaia, Pantanal and Paraná) in relation to local environmental factors, spatial components, climate variables and basin identity.Moran's eigenvector maps were used as a proxy to examine spatial structures within each drainage basin. The final sets of local environmental, climate and spatial variables were selected for constrained ordination models, using a forward selection method. We used variation partitioning to decompose variation in cladoceran community composition in relation to the four sets of predictor variables. Beta‐diversity indices were calculated to quantify the contributions of turnover and nestedness components to total beta diversity of cladocerans within each basin and across the basins.Variation partitioning showed that the pure fractions were relatively small, ranging from around zero for spatial and basin identity variables to 2% for climate variables and 4% for local environmental variables. The shared effect of local environmental, climate and basin identity was considerable, accounting for 17% of the total variance. Furthermore, the shared effect of climate and basin identity was also considerable (6%). In total, 32% of variation in cladoceran community structure could be explained by our predictor variables. Cladoceran metacommunities showed high levels of beta diversity attributed to the turnover component, within each floodplain and across all four floodplains.Our finding showed that species sorting was likely to be the main agent structuring cladoceran communities. Spatial processes were not important at very large spatial scales, contrary to what has been found in previous studies. This finding was most likely due to the inclusion of climatic variables in our analysis, combined with the high dispersal ability of cladocerans.
Assessment of nutritional subsidies to freshwater mussels using a multiple natural abundance isotope approach
Authors: Weber Amy M. , Bauer James E. , Thomas Watters G. 
Published: February 2017

Summary

Freshwater mussels are a particularly imperilled group of aquatic organisms. To date, there is limited understanding of their dietary and nutritional subsidies, including those from both autochthonous (aquatic) and allochthonous (terrestrial) sources. The aim of this study was to evaluate the relative contributions of potential nutritional resources to mussel biomass using a Bayesian mixing model (MixSIAR) for (i) bulk suspended versus benthic organic matter (OM) pools, (ii) general autochthonous versus allochthonous OM sources and (iii) specific individual OM sources.

Nutritional subsidies of five species of freshwater mussels were assessed using natural abundance stable isotopes (δ13C, δ15N, δ2H) and natural radiocarbon (Δ14C). The ranges for each of the four isotopes were similar across all species and sampling dates, and mussel δ13C and δ15N values were similar to those measured in previous studies. Despite relatively low variability in this study, species and temporal differences in mussel δ15N, δ2H and Δ14C values were generally significant (P < 0.05).

Based on δ13C values alone, bulk suspended OM subsidised mussel biomass to a greater extent than bulk benthic OM (c. 60 and 40% respectively). Modelling of multiple isotopes indicated that while the collective allochthonous nutritional sources accounted for a significant part (c. 33%) of mussel biomass, autochthonous materials collectively subsidised mussel tissue at about twice this level (c. 67).

Significant amounts of 14C‐depleted aged carbon were incorporated into freshwater mussel tissue (mean equivalent 14C age = 1325 ± 68 years BP). Potential nutritional sources were also mostly aged, including benthic algae (1226 ± 556 years BP), zooplankton (1682 years BP), terrestrial soil (10 588 ± 4330 years BP) and suspended particulate OM (1443 ± 57 years BP).

No single potential individual nutritional OM source explained the multiple isotopic values of freshwater mussel tissue, indicating that these organisms have a multi‐source and potentially opportunistic diet. Benthic algae and phytoplankton were quantitatively the most important individual OM subsidies to freshwater mussel nutrition at our study site (27 and 19% respectively). Observed seasonal shifts in freshwater mussel isotopic values were minimal, suggesting (i) that mussels may not be seasonally limited by individual nutritional resources and/or (ii) the replacement times of C, N and H in freshwater mussel tissues make detection of temporal nutritional subsidy shifts – if they occur – difficult to discern.
Tree range expansion in eastern North America fails to keep pace with climate warming at northern range limits
Authors: Sittaro Fabian , Paquette Alain , Messier Christian , Nock Charles A. 
Published: February 2017

AbstractRising global temperatures are suggested to be drivers of shifts in tree species ranges. The resulting changes in community composition may negatively impact forest ecosystem function. However, long‐term shifts in tree species ranges remain poorly documented. We test for shifts in the northern range limits of 16 temperate tree species in Quebec, Canada, using forest inventory data spanning three decades, 15° of longitude and 7° of latitude. Range shifts were correlated with climate warming and dispersal traits to understand potential mechanisms underlying changes. Shifts were calculated as the change in the 95th percentile of latitudinal occurrence between two inventory periods (1970–1978, 2000–2012) and for two life stages: saplings and adults. We also examined sapling and adult range offsets within each inventory, and changes in the offset through time. Tree species ranges shifted predominantly northward, although species responses varied. As expected shifts were greater for tree saplings, 0.34 km yr−1, than for adults, 0.13 km yr−1. Range limits were generally further north for adults compared to saplings, but the difference diminished through time, consistent with patterns observed for range shifts within each life stage. This suggests caution should be exercised when interpreting geographic range offsets between life stages as evidence of range shifts in the absence of temporal data. Species latitudinal velocities were on average <50% of the velocity required to equal the spatial velocity of climate change and were mostly unrelated to dispersal traits. Finally, our results add to the body of evidence suggesting tree species are mostly limited in their capacity to track climate warming, supporting concerns that warming will negatively impact the functioning of forest ecosystems.
Multiple stressors threaten the imperiled coastal foundation species eelgrass (Zostera marina) in Chesapeake Bay,USA
Authors: Lefcheck Jonathan S. , Wilcox David J. , Murphy Rebecca R. , Marion Scott R. , Orth Robert J. 
Published: February 2017

AbstractInteractions among global change stressors and their effects at large scales are often proposed, but seldom evaluated. This situation is primarily due to lack of comprehensive, sufficiently long‐term, and spatially extensive datasets. Seagrasses, which provide nursery habitat, improve water quality, and constitute a globally important carbon sink, are among the most vulnerable habitats on the planet. Here, we unite 31 years of high‐resolution aerial monitoring and water quality data to elucidate the patterns and drivers of eelgrass (Zostera marina) abundance in Chesapeake Bay,USA, one of the largest and most valuable estuaries in the world, with an unparalleled history of regulatory efforts. We show that eelgrass area has declined 29% in total since 1991, with wide‐ranging and severe ecological and economic consequences. We go on to identify an interaction between decreasing water clarity and warming temperatures as the primary drivers of this trend. Declining clarity has gradually reduced eelgrass cover the past two decades, primarily in deeper beds where light is already limiting. In shallow beds, however, reduced visibility exacerbates the physiological stress of acute warming, leading to recent instances of decline approaching 80%. While degraded water quality has long been known to influence underwater grasses worldwide, we demonstrate a clear and rapidly emerging interaction with climate change. We highlight the urgent need to integrate a broader perspective into local water quality management, in the Chesapeake Bay and in the many other coastal systems facing similar stressors.
Evaluation of Lotus corniculatus L. accessions from different locations at different altitudes reveals phenotypic and genetic diversity
Authors: Merkouropoulos G. , Hilioti Z. , Abraham E. M. , Lazaridou M. 
Published: February 2017

AbstractThe phenotypic and genotypic diversity of natural populations of Lotus corniculatus from three locations in northern Greece was investigated. The collection locations were about 100–140 km apart at altitudes ranging from 50 to 900 m and therefore differed in bioclimatic conditions. The collected plants were transplanted and maintained under the same conditions before their phenotypic and genetic assessment. Plants from high altitudes differed from the low‐ or moderate‐altitude plants in terms of leaf characteristics (smaller leaf area: 1.1 cm2 compared to 1.5 cm2 from the low and moderate altitudes) and internode length (shorter internodes: 2.7 cm compared to 3.2 and 13.1 cm from the low and moderate altitudes respectively). At the genetic level, application of the Inter‐Specific Simple Sequence Repeats (ISSR) molecular markers led to distinct placement of the three populations into different clades of a dendrogram, thus revealing regional diversity. The phytogeographic distinction was also supported by principal components analysis. The results showed that even though phenotypic characters could be close, or even indistinguishable, as in the case of plants from the low and middle altitudes, the genetic background could be different. Therefore, assessment of the natural diversity of L. corniculatus requires a combined and integrative approach involving morphological description and molecular characterization. The natural populations of L. corniculatus constitute valuable germplasm for the development of improved and adapted cultivars.
Assessment of intradialysis calcium mass balance by a single pool variable‐volume calcium kinetic model
Authors: di Filippo Salvatore , Carfagna Fabio , la Milia Vincenzo , Bellasi Antonio , Casagrande Giustina , Bianchi Camilla , Vito Domenico , Costantino Maria Laura , Rombolà Giuseppe , Minoretti Claudio , Schönholzer Carlo , Pontoriero Giuseppe , Locatelli Francesco 
Published: February 2017

AbstractIntroduction: A reliable method of intradialysis calcium mass balance quantification is far from been established. We herein investigated the use of a single‐pool variable‐volume Calcium kinetic model to assess calcium mass balance in chronic and stable dialysis patients.Methods: Thirty‐four patients on thrice‐weekly HD were studied during 240 dialysis sessions. All patients were dialyzed with a nominal total calcium concentration of 1.50 mmol/L. The main assumption of the model is that the calcium distribution volume is equal to the extracellular volume during dialysis. This hypothesis is assumed valid if measured and predicted end dialysis plasma water ionized calcium concentrations are equal. A difference between predicted and measured end‐dialysis ionized plasma water calcium concentration is a deviation on our main hypothesis, meaning that a substantial amount of calcium is exchanged between the extracellular volume and a nonmodeled compartment.Findings: The difference between predicted and measured values was 0.02 mmol/L (range −0.08:0.16 mmol/L). With a mean ionized dialysate calcium concentration of 1.25 mmol/L, calcium mass balance was on average negative (mean ± SD −0.84 ± 1.33 mmol, range −5.42:2.75). Predialysis ionized plasma water concentration and total ultrafiltrate were the most important predictors of calcium mass balance. A significant mobilization of calcium from the extracellular pool to a nonmodeled pool was calculated in a group of patients.Discussion: The proposed single pool variable‐volume Calcium kinetic model is adequate for prediction and quantification of intradialysis calcium mass balance, it can evaluate the eventual calcium transfer outside the extracellular pool in clinical practice.
A distinctive, low‐grade oncocytic fumarate hydratase‐deficient renal cell carcinoma, morphologically reminiscent of succinate dehydrogenase‐deficient renal cell carcinoma
Authors: Smith Steven C , Sirohi Deepika , Ohe Chisato , McHugh Jonathan B , Hornick Jason L , Kalariya Jigna , Karia Sushil , Snape Katie , Hodgson Shirley V , Cani Andi K , Hovelson Daniel , Luthringer Daniel J , Martignoni Guido , Chen Ying‐Bei , Tomlins Scott A , Mehra Rohit , Amin Mahul B 
Published: February 2017

AimsFumarate hydratase (FH)‐deficient renal cell carcinoma (RCC) is a high‐grade, aggressive tubulopapillary carcinoma, arising predominantly in the setting of the hereditary leiomyomatosis–RCC syndrome of familial uterocutaneous leiomyomatosis and deficiency of FH. In contrast, succinate dehydrogenase (SDH)‐deficient RCC is a lower‐grade oncocytic carcinoma with cytoplasmic flocculence/vacuolation and inclusions, arising mostly in individuals harbouring germline mutations of subunit B of the SDH complex (SDHB). Herein we aim to report the clinicopathologic features of a novel form of FH‐deficient RCC showing a low grade oncocytic morphology, reminiscent of SDH‐deficient RCC.Methods and resultsThese distinctive, low‐grade oncocytic neoplasms, with solid, nested and focally tubular architecture (2–90 mm), arose in four males (aged 11–41 years). Uniform cytology of polygonal cells, with flocculent, vacuolated eosinophilic cytoplasm with scattered inclusions, fine chromatin, and inconspicuous nucleoli, was apparent. Despite these features suggestive of SDH‐deficient RCC, each tumour was confirmed as an FH‐deficient carcinoma with retained SDHB expression. One case showed a synchronous, anatomically separate, typical high‐grade FH‐deficient RCC; one other showed such a tumour at nephrectomy 4 years later. No progression has been noted at 3 and 7 years in the cases with only the SDH‐like lesions; the two cases with separate, typical FH‐deficient RCCs progressed.ConclusionsIn summary, we characterize a novel oncocytic type of FH‐deficient RCC with a striking resemblance to SDH‐deficient RCC, posing a diagnostic challenge and raising concerns about sampling and multifocality for syndrome‐associated cases under surveillance protocols.
Taxonomic revision of Cylindroporella ? lusitanica Ramalho, 1970: In search for the origins of the Family Dasycladaceae
Authors: Granier Bruno R. C. , Azerêdo Ana C. , Ramalho Miguel M. 
Published: February 2017

AbstractA study of new material of Cylindroporella ? lusitanica Ramalho, 1970, from the Upper Jurassic (Oxfordian) strata of Portugal identified features not observed previously. This includes the pattern of its laterals, including the gametophores. The algal body plan is unique and justifies the taxonomic reassessment of this species and the introduction of Barattoloporellopsis n. gen. Furthermore this species is most likely a primitive Dasycladaceae, a “missing link” between the modern ones (starting from the Cretaceous times) and their Jurassic ancestors.
Statistical analysis of the influence of microstructure on damage in fibrous ceramic matrix composites
Authors: Tracy Jared , Daly Samantha 
Published: February 2017

AbstractThe effect of microstructure on cracking was analyzed in a CMC using statistical methods. It was determined that the amounts of coating surrounding fibers and their dispersion within the matrix influenced where cracks evolved in transverse plies. Linear models predicted that maximum principal strains in transverse fiber coatings increased as (i) the fiber coating area increased and (ii) the length of matrix ligament between fibers decreased. Logistic models indicated that the likelihood of transverse fibers residing on a matrix crack increased as the (i) ratio of coating to filament decreased, (ii) distance between fibers decreased, or (iii) coating area increased.
The characteristics and antigenic properties of recently emerged subclade 3C.3a and 3C.2a human influenza A(H3N2) viruses passaged in MDCK cells
Authors: Lin Yipu , Wharton Stephen A. , Whittaker Lynne , Dai Mian , Ermetal Burcu , Lo Janice , Pontoriero Andrea , Baumeister Elsa , Daniels Rodney S. , McCauley John W. 
Published: February 2017

BackgroundTwo new subclades of influenza A(H3N2) viruses became prominent during the 2014‐2015 Northern Hemisphere influenza season. The HA glycoproteins of these viruses showed sequence changes previously associated with alterations in receptor‐binding properties. To address how these changes influence virus propagation, viruses were isolated and propagated in conventional MDCK cells and MDCK‐SIAT1 cells, cells with enhanced expression of the human receptor for the virus, and analysed at each passage.MethodsGene sequence analysis was undertaken as virus was passaged in conventional MDCK cells and MDCK‐SIAT1 cells. Alterations in receptor recognition associated with passage of virus were examined by haemagglutination assays using red blood cells from guinea pigs, turkeys and humans. Microneutralisation assays were performed to determine how passage‐acquired amino acid substitutions and polymorphisms affected virus antigenicity.ResultsViruses were able to infect MDCK‐SIAT1 cells more efficiently than conventional MDCK cells. Viruses of both the 3C.2a and 3C.3a subclades showed greater sequence change on passage in conventional MDCK cells than in MDCK‐SIAT1 cells, with amino acid substitutions being seen in both HA and NA glycoproteins. However, virus passage in MDCK‐SIAT1 cells at low inoculum dilutions showed reducing infectivity on continued passage.ConclusionsCurrent H3N2 viruses should be cultured in the MDCK‐SIAT1 cell line to maintain faithful replication of the virus, and at an appropriate multiplicity of infection to retain infectivity.